analysis of sequence from NP_061377.1.fa ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ >NP_061377.1 phosphatidylinositol glycan, class B; involved in GPI-anchor biosynthesis [Mus musculus]. MESQAADYNP ASRNLHGSSG EMKLRRRKSR QYVSAQEKRS PRRGLLGENT YLVLFTIALR ILNCFLVQTS FVPDEYWQSL EVAHRMVFSY GYLTWEWTER LRGYTYPLIF ASIYKVLHLL GKDSVQFLIW IPRLGQALLS AVADIRLYSL LKQLENQEVA QWVFLCQLCS WFTWYCCTRT LTNTMETSLT ALALFYYPLE GSRSVNSIKY SLLVALACVV RPTALIPWVP LLFRHFYQEQ RKLHLTLHHF LPVGFITFSL SLIIDRIFFG QWTLVQLNFL KFNVLQNLGT FYGSHPWHWY LSQGFPVVLG THLPFFIHGC FLAPRRLHIL LLTVLWTLLV YSMLGHKEFR FIYPVLPFCM VFCGYSLAHL KTWRKAALSF LLLSNVPLAF YTGLVHQRGT LDVMNHIQKV CPRGPDPASA SVFIMMPCHS TPYYSHVHCP LSMRFLQCPP DLTGKTQYLD EADMFYLNPL RWLQQEFHSN ASLPTHLVTF NVLEKEINTF LTSGNYERAA TFFHTHWPER RTGSHIHVYE RRLPGRVNTG GN ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ sec.str. with predator > NP_061377.1 . . . . . 1 MESQAADYNPASRNLHGSSGEMKLRRRKSRQYVSAQEKRSPRRGLLGENT 50 ____________________HHHHHHHHHHHHHHHHHH___________E . . . . . 51 YLVLFTIALRILNCFLVQTSFVPDEYWQSLEVAHRMVFSYGYLTWEWTER 100 EEEEHHHHHHHHHHH__________HHHHHHHHHHHHHH____HHHHHHH . . . . . 101 LRGYTYPLIFASIYKVLHLLGKDSVQFLIWIPRLGQALLSAVADIRLYSL 150 HHH___HHHHHHHHHHHHH____EEEEEEE_____HHHHHHHHHHHHHHH . . . . . 151 LKQLENQEVAQWVFLCQLCSWFTWYCCTRTLTNTMETSLTALALFYYPLE 200 HHHHHHHHHHHHHHEEE__EEEEEEEE_______HHHHHHHHHHH_____ . . . . . 201 GSRSVNSIKYSLLVALACVVRPTALIPWVPLLFRHFYQEQRKLHLTLHHF 250 ______HHHHHHHHHHHHH___________HHHHHHHHHHHHHHHHHHH_ . . . . . 251 LPVGFITFSLSLIIDRIFFGQWTLVQLNFLKFNVLQNLGTFYGSHPWHWY 300 ______HHHHHHHHHHHHHH_EEEEE_EEEEEEE_____________EEE . . . . . 301 LSQGFPVVLGTHLPFFIHGCFLAPRRLHILLLTVLWTLLVYSMLGHKEFR 350 EE____EEE____EEEEEE___HHHHHHHHHHHHHHHHH_________EE . . . . . 351 FIYPVLPFCMVFCGYSLAHLKTWRKAALSFLLLSNVPLAFYTGLVHQRGT 400 EEE____EEEEEE__HHHHHHHHHHHHHHHHHH_____HHHHHHHH____ . . . . . 401 LDVMNHIQKVCPRGPDPASASVFIMMPCHSTPYYSHVHCPLSMRFLQCPP 450 EEE___________________EEEE_________________EEEE___ . . . . . 451 DLTGKTQYLDEADMFYLNPLRWLQQEFHSNASLPTHLVTFNVLEKEINTF 500 ________HHHHHHH____HHHHHHH_________EEEEEEEHHHHHHH_ . . . . 501 LTSGNYERAATFFHTHWPERRTGSHIHVYERRLPGRVNTGGN 542 _______HHHHH____________EEEEEE____________ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ method : 1 alpha-contents : 24.3 % beta-contents : 53.1 % coil-contents : 22.5 % class : mixed method : 2 alpha-contents : 3.5 % beta-contents : 66.1 % coil-contents : 30.4 % class : beta ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ GPI: learning from metazoa -18.54 -0.49 -0.25 -1.24 -4.00 0.00 0.00 0.00 -1.89 -5.33 -1.86 -12.00 -12.00 0.00 -12.00 0.00 -69.60 -9.22 -0.10 -0.63 -0.98 0.00 0.00 0.00 0.00 -2.65 -4.28 -1.86 -12.00 -12.00 0.00 -12.00 0.00 -55.72 ID: NP_061377.1 AC: xxx Len: 542 1:I 523 Sc: -55.72 Pv: 3.011014e-01 NO_GPI_SITE GPI: learning from protozoa -26.98 -0.71 0.00 -0.03 -4.00 0.00 0.00 0.00 -1.70 -6.39 -7.24 -12.00 -12.00 0.00 -12.00 0.00 -83.06 -26.55 -0.06 0.00 0.00 -4.00 0.00 0.00 0.00 -1.24 -3.80 -7.24 -12.00 -12.00 0.00 -12.00 0.00 -78.90 ID: NP_061377.1 AC: xxx Len: 542 1:I 523 Sc: -78.90 Pv: 4.893359e-01 NO_GPI_SITE ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ # SignalP euk predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? NP_061377.1 0.624 343 Y 0.511 346 Y 0.968 336 Y 0.398 N # SignalP gram- predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? NP_061377.1 0.543 369 Y 0.448 390 Y 0.937 383 Y 0.279 N # SignalP gram+ predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? NP_061377.1 0.952 421 Y 0.455 392 Y 0.988 63 Y 0.403 N ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ low complexity regions: SEG 12 2.2 2.5 >NP_061377.1 phosphatidylinositol glycan, class B; involved in GPI-anchor biosynthesis [Mus musculus]. 1-329 MESQAADYNPASRNLHGSSGEMKLRRRKSR QYVSAQEKRSPRRGLLGENTYLVLFTIALR ILNCFLVQTSFVPDEYWQSLEVAHRMVFSY GYLTWEWTERLRGYTYPLIFASIYKVLHLL GKDSVQFLIWIPRLGQALLSAVADIRLYSL LKQLENQEVAQWVFLCQLCSWFTWYCCTRT LTNTMETSLTALALFYYPLEGSRSVNSIKY SLLVALACVVRPTALIPWVPLLFRHFYQEQ RKLHLTLHHFLPVGFITFSLSLIIDRIFFG QWTLVQLNFLKFNVLQNLGTFYGSHPWHWY LSQGFPVVLGTHLPFFIHGCFLAPRRLHI llltvlwtllv 330-340 341-542 YSMLGHKEFRFIYPVLPFCMVFCGYSLAHL KTWRKAALSFLLLSNVPLAFYTGLVHQRGT LDVMNHIQKVCPRGPDPASASVFIMMPCHS TPYYSHVHCPLSMRFLQCPPDLTGKTQYLD EADMFYLNPLRWLQQEFHSNASLPTHLVTF NVLEKEINTFLTSGNYERAATFFHTHWPER RTGSHIHVYERRLPGRVNTGGN low complexity regions: SEG 25 3.0 3.3 >NP_061377.1 phosphatidylinositol glycan, class B; involved in GPI-anchor biosynthesis [Mus musculus]. 1-542 MESQAADYNPASRNLHGSSGEMKLRRRKSR QYVSAQEKRSPRRGLLGENTYLVLFTIALR ILNCFLVQTSFVPDEYWQSLEVAHRMVFSY GYLTWEWTERLRGYTYPLIFASIYKVLHLL GKDSVQFLIWIPRLGQALLSAVADIRLYSL LKQLENQEVAQWVFLCQLCSWFTWYCCTRT LTNTMETSLTALALFYYPLEGSRSVNSIKY SLLVALACVVRPTALIPWVPLLFRHFYQEQ RKLHLTLHHFLPVGFITFSLSLIIDRIFFG QWTLVQLNFLKFNVLQNLGTFYGSHPWHWY LSQGFPVVLGTHLPFFIHGCFLAPRRLHIL LLTVLWTLLVYSMLGHKEFRFIYPVLPFCM VFCGYSLAHLKTWRKAALSFLLLSNVPLAF YTGLVHQRGTLDVMNHIQKVCPRGPDPASA SVFIMMPCHSTPYYSHVHCPLSMRFLQCPP DLTGKTQYLDEADMFYLNPLRWLQQEFHSN ASLPTHLVTFNVLEKEINTFLTSGNYERAA TFFHTHWPERRTGSHIHVYERRLPGRVNTG GN low complexity regions: SEG 45 3.4 3.75 >NP_061377.1 phosphatidylinositol glycan, class B; involved in GPI-anchor biosynthesis [Mus musculus]. 1-542 MESQAADYNPASRNLHGSSGEMKLRRRKSR QYVSAQEKRSPRRGLLGENTYLVLFTIALR ILNCFLVQTSFVPDEYWQSLEVAHRMVFSY GYLTWEWTERLRGYTYPLIFASIYKVLHLL GKDSVQFLIWIPRLGQALLSAVADIRLYSL LKQLENQEVAQWVFLCQLCSWFTWYCCTRT LTNTMETSLTALALFYYPLEGSRSVNSIKY SLLVALACVVRPTALIPWVPLLFRHFYQEQ RKLHLTLHHFLPVGFITFSLSLIIDRIFFG QWTLVQLNFLKFNVLQNLGTFYGSHPWHWY LSQGFPVVLGTHLPFFIHGCFLAPRRLHIL LLTVLWTLLVYSMLGHKEFRFIYPVLPFCM VFCGYSLAHLKTWRKAALSFLLLSNVPLAF YTGLVHQRGTLDVMNHIQKVCPRGPDPASA SVFIMMPCHSTPYYSHVHCPLSMRFLQCPP DLTGKTQYLDEADMFYLNPLRWLQQEFHSN ASLPTHLVTFNVLEKEINTFLTSGNYERAA TFFHTHWPERRTGSHIHVYERRLPGRVNTG GN low complexity regions: XNU # Score cutoff = 21, Search from offsets 1 to 4 # both members of each repeat flagged # lambda = 0.347, K = 0.200, H = 0.664 >NP_061377.1 phosphatidylinositol glycan, class B; involved in GPI-anchor biosynthesis [Mus musculus]. MESQAADYNPASRNLHGSSGEMKLRRRKSRQYVSAQEKRSPRRGLLGENTYLVLFTIALR ILNCFLVQTSFVPDEYWQSLEVAHRMVFSYGYLTWEWTERLRGYTYPLIFASIYKVLHLL GKDSVQFLIWIPRLGQALLSAVADIRLYSLLKQLENQEVAQWVFlcqlcswftwyCCTRT LTNTMETSLTALALFYYPLEGSRSVNSIKYSLLVALACVVRPTALIPWVPLLFRHFYQEQ RKLHLTLHHFLPVGFITFSLSLIIDRIFFGQWTLVQLNFLKFNVLQNLGTFYGSHPWHWY LSQGFPVVLGTHLPFFIHGCFLAPRRLHILLLTVLWTLLVYSMLGHKEFRFIYPVLPFCM VFCGYSLAHLKTWRKAALSFLLLSNVPLAFYTGLVHQRGTLDVMNHIQKVCPRGPDPASA SVFIMMPCHSTPYYSHVHCPLSMRFLQCPPDLTGKTQYLDEADMFYLNPLRWLQQEFHSN ASLPTHLVTFNVLEKEINTFLTSGNYERAATFFHTHWPERRTGSHIHVYERRLPGRVNTG GN 1 - 164 MESQAADYNP ASRNLHGSSG EMKLRRRKSR QYVSAQEKRS PRRGLLGENT YLVLFTIALR ILNCFLVQTS FVPDEYWQSL EVAHRMVFSY GYLTWEWTER LRGYTYPLIF ASIYKVLHLL GKDSVQFLIW IPRLGQALLS AVADIRLYSL LKQLENQEVA QWVF 165 - 175 lcqlcs wftwy 176 - 542 CCTRT LTNTMETSLT ALALFYYPLE GSRSVNSIKY SLLVALACVV RPTALIPWVP LLFRH FYQEQ RKLHLTLHHF LPVGFITFSL SLIIDRIFFG QWTLVQLNFL KFNVLQNLGT FYGSH PWHWY LSQGFPVVLG THLPFFIHGC FLAPRRLHIL LLTVLWTLLV YSMLGHKEFR FIYPV LPFCM VFCGYSLAHL KTWRKAALSF LLLSNVPLAF YTGLVHQRGT LDVMNHIQKV CPRGP DPASA SVFIMMPCHS TPYYSHVHCP LSMRFLQCPP DLTGKTQYLD EADMFYLNPL RWLQQ EFHSN ASLPTHLVTF NVLEKEINTF LTSGNYERAA TFFHTHWPER RTGSHIHVYE RRLPG RVNTG GN low complexity regions: DUST >NP_061377.1 phosphatidylinositol glycan, class B; involved in GPI-anchor biosynthesis [Mus musculus]. MESQAADYNPASRNLHGSSGEMKLRRRKSRQYVSAQEKRSPRRGLLGENTYLVLFTIALR ILNCFLVQTSFVPDEYWQSLEVAHRMVFSYGYLTWEWTERLRGYTYPLIFASIYKVLHLL GKDSVQFLIWIPRLGQALLSAVADIRLYSLLKQLENQEVAQWVFLCQLCSWFTWYCCTRT LTNTMETSLTALALFYYPLEGSRSVNSIKYSLLVALACVVRPTALIPWVPLLFRHFYQEQ RKLHLTLHHFLPVGFITFSLSLIIDRIFFGQWTLVQLNFLKFNVLQNLGTFYGSHPWHWY LSQGFPVVLGTHLPFFIHGCFLAPRRLHILLLTVLWTLLVYSMLGHKEFRFIYPVLPFCM VFCGYSLAHLKTWRKAALSFLLLSNVPLAFYTGLVHQRGTLDVMNHIQKVCPRGPDPASA SVFIMMPCHSTPYYSHVHCPLSMRFLQCPPDLTGKTQYLDEADMFYLNPLRWLQQEFHSN ASLPTHLVTFNVLEKEINTFLTSGNYERAATFFHTHWPERRTGSHIHVYERRLPGRVNTG GN ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ coiled coil prediction for NP_061377.1 sequence: 542 amino acids, 0 residue(s) in coiled coil state . | . | . | . | . | . 60 MESQAADYNP ASRNLHGSSG EMKLRRRKSR QYVSAQEKRS PRRGLLGENT YLVLFTIALR ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 120 ILNCFLVQTS FVPDEYWQSL EVAHRMVFSY GYLTWEWTER LRGYTYPLIF ASIYKVLHLL ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 180 GKDSVQFLIW IPRLGQALLS AVADIRLYSL LKQLENQEVA QWVFLCQLCS WFTWYCCTRT ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 240 LTNTMETSLT ALALFYYPLE GSRSVNSIKY SLLVALACVV RPTALIPWVP LLFRHFYQEQ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 300 RKLHLTLHHF LPVGFITFSL SLIIDRIFFG QWTLVQLNFL KFNVLQNLGT FYGSHPWHWY ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 360 LSQGFPVVLG THLPFFIHGC FLAPRRLHIL LLTVLWTLLV YSMLGHKEFR FIYPVLPFCM ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 420 VFCGYSLAHL KTWRKAALSF LLLSNVPLAF YTGLVHQRGT LDVMNHIQKV CPRGPDPASA ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 480 SVFIMMPCHS TPYYSHVHCP LSMRFLQCPP DLTGKTQYLD EADMFYLNPL RWLQQEFHSN ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 540 ASLPTHLVTF NVLEKEINTF LTSGNYERAA TFFHTHWPER RTGSHIHVYE RRLPGRVNTG ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local GN ~~ -- ~~ ~~ ~~ ~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ prediction of transmembrane regions with toppred2 *********************************** *TOPPREDM with eukaryotic function* *********************************** NP_061377.1.fa.___inter___ is a single sequence Using hydrophobicity file: /bio_software/2D/toppredm/lib/Engelman-Steitz.scale Using cyt/ext file: /bio_software/2D/toppredm/lib/Cyt-Ext.prok Using sequence file: NP_061377.1.fa.___inter___ (1 sequences) MESQAADYNPASRNLHGSSGEMKLRRRKSRQYVSAQEKRSPRRGLLGENT YLVLFTIALRILNCFLVQTSFVPDEYWQSLEVAHRMVFSYGYLTWEWTER LRGYTYPLIFASIYKVLHLLGKDSVQFLIWIPRLGQALLSAVADIRLYSL LKQLENQEVAQWVFLCQLCSWFTWYCCTRTLTNTMETSLTALALFYYPLE GSRSVNSIKYSLLVALACVVRPTALIPWVPLLFRHFYQEQRKLHLTLHHF LPVGFITFSLSLIIDRIFFGQWTLVQLNFLKFNVLQNLGTFYGSHPWHWY LSQGFPVVLGTHLPFFIHGCFLAPRRLHILLLTVLWTLLVYSMLGHKEFR FIYPVLPFCMVFCGYSLAHLKTWRKAALSFLLLSNVPLAFYTGLVHQRGT LDVMNHIQKVCPRGPDPASASVFIMMPCHSTPYYSHVHCPLSMRFLQCPP DLTGKTQYLDEADMFYLNPLRWLQQEFHSNASLPTHLVTFNVLEKEINTF LTSGNYERAATFFHTHWPERRTGSHIHVYERRLPGRVNTGGN (p)rokaryotic or (e)ukaryotic: e Charge-pair energy: 0 Length of full window (odd number!): 21 Length of core window (odd number!): 11 Number of residues to add to each end of helix: 1 Critical length: 60 Upper cutoff for candidates: 1 Lower cutoff for candidates: 0.6 Total of 8 structures are to be tested Candidate membrane-spanning segments: Helix Begin End Score Certainity 1 50 70 0.943 Putative 2 102 122 0.626 Putative 3 158 178 1.362 Certain 4 182 202 0.685 Putative 5 210 230 1.010 Certain 6 245 265 1.636 Certain 7 303 323 1.466 Certain 8 326 346 1.830 Certain 9 350 370 1.675 Certain 10 376 396 1.489 Certain 11 417 437 1.169 Certain ---------------------------------------------------------------------- Structure 1 Transmembrane segments included in this structure: Segment 1 3 5 6 7 8 9 10 11 Loop length 49 87 31 14 37 2 3 5 20 105 K+R profile 12.00 3.00 2.00 2.00 3.00 + 3.00 2.00 3.00 + CYT-EXT prof - - - - - 0.67 - - - 0.20 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 14.00 Tm probability: 0.86 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 5.00 (NEG-POS)/(NEG+POS): -0.3750 NEG: 5.0000 POS: 11.0000 -> Orientation: N-in CYT-EXT difference: -0.87 -> Orientation: N-in ---------------------------------------------------------------------- Structure 2 Transmembrane segments included in this structure: Segment 1 2 3 4 5 6 7 8 9 10 11 Loop length 49 31 35 3 7 14 37 2 3 5 20 105 K+R profile 12.00 4.00 2.00 2.00 2.00 3.00 3.00 1.00 3.00 2.00 3.00 + CYT-EXT prof - - - - - - - - - - - 0.20 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 13.00 Tm probability: 0.01 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 5.00 (NEG-POS)/(NEG+POS): -0.3750 NEG: 5.0000 POS: 11.0000 -> Orientation: N-in CYT-EXT difference: -0.20 -> Orientation: N-in ---------------------------------------------------------------------- Structure 3 Transmembrane segments included in this structure: Segment 1 3 4 5 6 7 8 9 10 11 Loop length 49 87 3 7 14 37 2 3 5 20 105 K+R profile 12.00 1.00 3.00 2.00 3.00 + + 2.00 2.00 2.00 3.00 CYT-EXT prof - - - - - 0.20 0.67 - - - - For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 12.00 Tm probability: 0.18 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 5.00 (NEG-POS)/(NEG+POS): -0.3750 NEG: 5.0000 POS: 11.0000 -> Orientation: N-in CYT-EXT difference: -0.47 -> Orientation: N-in ---------------------------------------------------------------------- Structure 4 Transmembrane segments included in this structure: Segment 1 2 3 5 6 7 8 9 10 11 Loop length 49 31 35 31 14 37 2 3 5 20 105 K+R profile 12.00 4.00 3.00 2.00 3.00 + 3.00 3.00 2.00 2.00 3.00 CYT-EXT prof - - - - - 0.20 - - - - - For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 11.00 Tm probability: 0.06 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 5.00 (NEG-POS)/(NEG+POS): -0.3750 NEG: 5.0000 POS: 11.0000 -> Orientation: N-in CYT-EXT difference: 0.20 -> Orientation: N-out ---------------------------------------------------------------------- Structure 5 Transmembrane segments included in this structure: Segment 2 3 4 5 6 7 8 9 10 11 Loop length 101 35 3 7 14 37 2 3 5 20 105 K+R profile + 1.00 3.00 2.00 3.00 + 4.00 2.00 2.00 2.00 3.00 CYT-EXT prof 0.49 - - - - 0.20 - - - - - For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: -4.00 Tm probability: 0.01 -> Orientation: N-out Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): -0.2000 NEG: 10.0000 POS: 15.0000 -> Orientation: undecided CYT-EXT difference: 0.68 -> Orientation: N-out ---------------------------------------------------------------------- Structure 6 Transmembrane segments included in this structure: Segment 2 3 5 6 7 8 9 10 11 Loop length 101 35 31 14 37 2 3 5 20 105 K+R profile + 3.00 2.00 2.00 3.00 4.00 3.00 2.00 3.00 + CYT-EXT prof 0.49 - - - - - - - - 0.20 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: -2.00 Tm probability: 0.07 -> Orientation: N-out Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): -0.2000 NEG: 10.0000 POS: 15.0000 -> Orientation: undecided CYT-EXT difference: 0.29 -> Orientation: N-out ---------------------------------------------------------------------- Structure 7 Transmembrane segments included in this structure: Segment 3 5 6 7 8 9 10 11 Loop length 157 31 14 37 2 3 5 20 105 K+R profile + 3.00 2.00 3.00 + 3.00 2.00 2.00 3.00 CYT-EXT prof 0.52 - - - 0.20 - - - - For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: -2.00 Tm probability: 1.00 -> Orientation: N-out Charge-difference over N-terminal Tm (+-15 residues): -1.00 (NEG-POS)/(NEG+POS): -0.1765 NEG: 14.0000 POS: 20.0000 -> Orientation: N-out CYT-EXT difference: 0.71 -> Orientation: N-out ---------------------------------------------------------------------- Structure 8 Transmembrane segments included in this structure: Segment 3 4 5 6 7 8 9 10 11 Loop length 157 3 7 14 37 2 3 5 20 105 K+R profile + 2.00 2.00 2.00 3.00 1.00 3.00 2.00 3.00 + CYT-EXT prof 0.52 - - - - - - - - 0.20 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 0.00 Tm probability: 0.21 -> Orientation: undecided Charge-difference over N-terminal Tm (+-15 residues): -1.00 (NEG-POS)/(NEG+POS): -0.1765 NEG: 14.0000 POS: 20.0000 -> Orientation: N-out CYT-EXT difference: 0.32 -> Orientation: N-out ---------------------------------------------------------------------- "NP_061377" 542 50 70 #f 0.942708 102 122 #f 0.626042 158 178 #t 1.3625 182 202 #f 0.685417 210 230 #t 1.01042 245 265 #t 1.63646 303 323 #t 1.46562 326 346 #t 1.83021 350 370 #t 1.675 376 396 #t 1.48854 417 437 #t 1.16875 ************************************ *TOPPREDM with prokaryotic function* ************************************ NP_061377.1.fa.___inter___ is a single sequence Using hydrophobicity file: /bio_software/2D/toppredm/lib/Engelman-Steitz.scale Using cyt/ext file: /bio_software/2D/toppredm/lib/Cyt-Ext.prok Using sequence file: NP_061377.1.fa.___inter___ (1 sequences) MESQAADYNPASRNLHGSSGEMKLRRRKSRQYVSAQEKRSPRRGLLGENT YLVLFTIALRILNCFLVQTSFVPDEYWQSLEVAHRMVFSYGYLTWEWTER LRGYTYPLIFASIYKVLHLLGKDSVQFLIWIPRLGQALLSAVADIRLYSL LKQLENQEVAQWVFLCQLCSWFTWYCCTRTLTNTMETSLTALALFYYPLE GSRSVNSIKYSLLVALACVVRPTALIPWVPLLFRHFYQEQRKLHLTLHHF LPVGFITFSLSLIIDRIFFGQWTLVQLNFLKFNVLQNLGTFYGSHPWHWY LSQGFPVVLGTHLPFFIHGCFLAPRRLHILLLTVLWTLLVYSMLGHKEFR FIYPVLPFCMVFCGYSLAHLKTWRKAALSFLLLSNVPLAFYTGLVHQRGT LDVMNHIQKVCPRGPDPASASVFIMMPCHSTPYYSHVHCPLSMRFLQCPP DLTGKTQYLDEADMFYLNPLRWLQQEFHSNASLPTHLVTFNVLEKEINTF LTSGNYERAATFFHTHWPERRTGSHIHVYERRLPGRVNTGGN (p)rokaryotic or (e)ukaryotic: p Charge-pair energy: 0 Length of full window (odd number!): 21 Length of core window (odd number!): 11 Number of residues to add to each end of helix: 1 Critical length: 60 Upper cutoff for candidates: 1 Lower cutoff for candidates: 0.6 Total of 8 structures are to be tested Candidate membrane-spanning segments: Helix Begin End Score Certainity 1 50 70 0.943 Putative 2 102 122 0.626 Putative 3 158 178 1.362 Certain 4 182 202 0.685 Putative 5 210 230 1.010 Certain 6 245 265 1.636 Certain 7 303 323 1.466 Certain 8 326 346 1.830 Certain 9 350 370 1.675 Certain 10 376 396 1.489 Certain 11 417 437 1.169 Certain ---------------------------------------------------------------------- Structure 1 Transmembrane segments included in this structure: Segment 1 3 5 6 7 8 9 10 11 Loop length 49 87 31 14 37 2 3 5 20 105 K+R profile 12.00 3.00 2.00 2.00 3.00 + 3.00 2.00 3.00 + CYT-EXT prof - - - - - 0.67 - - - 0.20 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 14.00 Tm probability: 0.86 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 5.00 (NEG-POS)/(NEG+POS): -0.3750 NEG: 5.0000 POS: 11.0000 -> Orientation: N-in CYT-EXT difference: -0.87 -> Orientation: N-in ---------------------------------------------------------------------- Structure 2 Transmembrane segments included in this structure: Segment 1 2 3 4 5 6 7 8 9 10 11 Loop length 49 31 35 3 7 14 37 2 3 5 20 105 K+R profile 12.00 4.00 2.00 2.00 2.00 3.00 3.00 1.00 3.00 2.00 3.00 + CYT-EXT prof - - - - - - - - - - - 0.20 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 13.00 Tm probability: 0.01 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 5.00 (NEG-POS)/(NEG+POS): -0.3750 NEG: 5.0000 POS: 11.0000 -> Orientation: N-in CYT-EXT difference: -0.20 -> Orientation: N-in ---------------------------------------------------------------------- Structure 3 Transmembrane segments included in this structure: Segment 1 3 4 5 6 7 8 9 10 11 Loop length 49 87 3 7 14 37 2 3 5 20 105 K+R profile 12.00 1.00 3.00 2.00 3.00 + + 2.00 2.00 2.00 3.00 CYT-EXT prof - - - - - 0.20 0.67 - - - - For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 12.00 Tm probability: 0.18 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 5.00 (NEG-POS)/(NEG+POS): -0.3750 NEG: 5.0000 POS: 11.0000 -> Orientation: N-in CYT-EXT difference: -0.47 -> Orientation: N-in ---------------------------------------------------------------------- Structure 4 Transmembrane segments included in this structure: Segment 1 2 3 5 6 7 8 9 10 11 Loop length 49 31 35 31 14 37 2 3 5 20 105 K+R profile 12.00 4.00 3.00 2.00 3.00 + 3.00 3.00 2.00 2.00 3.00 CYT-EXT prof - - - - - 0.20 - - - - - For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 11.00 Tm probability: 0.06 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 5.00 (NEG-POS)/(NEG+POS): -0.3750 NEG: 5.0000 POS: 11.0000 -> Orientation: N-in CYT-EXT difference: 0.20 -> Orientation: N-out ---------------------------------------------------------------------- Structure 5 Transmembrane segments included in this structure: Segment 2 3 4 5 6 7 8 9 10 11 Loop length 101 35 3 7 14 37 2 3 5 20 105 K+R profile + 1.00 3.00 2.00 3.00 + 4.00 2.00 2.00 2.00 3.00 CYT-EXT prof 0.49 - - - - 0.20 - - - - - For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: -4.00 Tm probability: 0.01 -> Orientation: N-out Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): -0.2000 NEG: 10.0000 POS: 15.0000 -> Orientation: undecided CYT-EXT difference: 0.68 -> Orientation: N-out ---------------------------------------------------------------------- Structure 6 Transmembrane segments included in this structure: Segment 2 3 5 6 7 8 9 10 11 Loop length 101 35 31 14 37 2 3 5 20 105 K+R profile + 3.00 2.00 2.00 3.00 4.00 3.00 2.00 3.00 + CYT-EXT prof 0.49 - - - - - - - - 0.20 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: -2.00 Tm probability: 0.07 -> Orientation: N-out Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): -0.2000 NEG: 10.0000 POS: 15.0000 -> Orientation: undecided CYT-EXT difference: 0.29 -> Orientation: N-out ---------------------------------------------------------------------- Structure 7 Transmembrane segments included in this structure: Segment 3 5 6 7 8 9 10 11 Loop length 157 31 14 37 2 3 5 20 105 K+R profile + 3.00 2.00 3.00 + 3.00 2.00 2.00 3.00 CYT-EXT prof 0.52 - - - 0.20 - - - - For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: -2.00 Tm probability: 1.00 -> Orientation: N-out Charge-difference over N-terminal Tm (+-15 residues): -1.00 (NEG-POS)/(NEG+POS): -0.1765 NEG: 14.0000 POS: 20.0000 -> Orientation: N-out CYT-EXT difference: 0.71 -> Orientation: N-out ---------------------------------------------------------------------- Structure 8 Transmembrane segments included in this structure: Segment 3 4 5 6 7 8 9 10 11 Loop length 157 3 7 14 37 2 3 5 20 105 K+R profile + 2.00 2.00 2.00 3.00 1.00 3.00 2.00 3.00 + CYT-EXT prof 0.52 - - - - - - - - 0.20 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 0.00 Tm probability: 0.21 -> Orientation: undecided Charge-difference over N-terminal Tm (+-15 residues): -1.00 (NEG-POS)/(NEG+POS): -0.1765 NEG: 14.0000 POS: 20.0000 -> Orientation: N-out CYT-EXT difference: 0.32 -> Orientation: N-out ---------------------------------------------------------------------- "NP_061377" 542 50 70 #f 0.942708 102 122 #f 0.626042 158 178 #t 1.3625 182 202 #f 0.685417 210 230 #t 1.01042 245 265 #t 1.63646 303 323 #t 1.46562 326 346 #t 1.83021 350 370 #t 1.675 376 396 #t 1.48854 417 437 #t 1.16875 ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ SAPS. Version of April 11, 1996. Date run: Wed Jan 30 14:33:13 2002 File: /people/b_eisen/NP_061377.1.fa.___saps___ ID NP_061377.1 DE phosphatidylinositol glycan, class B; involved in GPI-anchor biosynthesis [Mus musculus]. number of residues: 542; molecular weight: 63.1 kdal 1 MESQAADYNP ASRNLHGSSG EMKLRRRKSR QYVSAQEKRS PRRGLLGENT YLVLFTIALR 61 ILNCFLVQTS FVPDEYWQSL EVAHRMVFSY GYLTWEWTER LRGYTYPLIF ASIYKVLHLL 121 GKDSVQFLIW IPRLGQALLS AVADIRLYSL LKQLENQEVA QWVFLCQLCS WFTWYCCTRT 181 LTNTMETSLT ALALFYYPLE GSRSVNSIKY SLLVALACVV RPTALIPWVP LLFRHFYQEQ 241 RKLHLTLHHF LPVGFITFSL SLIIDRIFFG QWTLVQLNFL KFNVLQNLGT FYGSHPWHWY 301 LSQGFPVVLG THLPFFIHGC FLAPRRLHIL LLTVLWTLLV YSMLGHKEFR FIYPVLPFCM 361 VFCGYSLAHL KTWRKAALSF LLLSNVPLAF YTGLVHQRGT LDVMNHIQKV CPRGPDPASA 421 SVFIMMPCHS TPYYSHVHCP LSMRFLQCPP DLTGKTQYLD EADMFYLNPL RWLQQEFHSN 481 ASLPTHLVTF NVLEKEINTF LTSGNYERAA TFFHTHWPER RTGSHIHVYE RRLPGRVNTG 541 GN -------------------------------------------------------------------------------- COMPOSITIONAL ANALYSIS (extremes relative to: swp23s) A : 27( 5.0%); C : 13( 2.4%); D- : 10( 1.8%); E : 21( 3.9%); F : 37( 6.8%) G : 27( 5.0%); H+ : 25( 4.6%); I : 20( 3.7%); K : 15( 2.8%); L+ : 82(15.1%) M : 11( 2.0%); N : 19( 3.5%); P : 29( 5.4%); Q : 23( 4.2%); R : 34( 6.3%) S : 37( 6.8%); T : 35( 6.5%); V : 35( 6.5%); W : 15( 2.8%); Y : 27( 5.0%) KR : 49 ( 9.0%); ED : 31 ( 5.7%); AGP : 83 ( 15.3%); KRED : 80 ( 14.8%); KR-ED : 18 ( 3.3%); FIKMNY : 129 ( 23.8%); LVIFM : 185 ( 34.1%); ST : 72 ( 13.3%). -------------------------------------------------------------------------------- CHARGE DISTRIBUTIONAL ANALYSIS 1 0-0000-000 00+0000000 -0+0++++0+ 000000-++0 0++0000-00 000000000+ 61 0000000000 000--00000 -000+00000 00000-00-+ 0+00000000 0000+00000 121 0+-0000000 00+0000000 000-0+0000 0+00-00-00 0000000000 00000000+0 181 00000-0000 000000000- 00+00000+0 0000000000 +000000000 000+0000-0 241 ++00000000 0000000000 0000-+0000 0000000000 +000000000 0000000000 301 0000000000 0000000000 0000++0000 0000000000 000000+-0+ 0000000000 361 0000000000 +00++00000 0000000000 0000000+00 0-000000+0 00+00-0000 421 0000000000 0000000000 000+000000 -000+0000- -0-0000000 +0000-0000 481 0000000000 000-+-0000 000000-+00 00000000-+ +00000000- ++000+0000 541 00 A. CHARGE CLUSTERS. Positive charge clusters (cmin = 8/30 or 11/45 or 14/60): 1) From 23 to 43: KLRRRKSRQYVSAQEKRSPRR +0++++0+000000-++00++ quartile: 1; size: 21, +count: 10, -count: 1, 0count: 10; t-value: 5.40 * S: 3 (14.3%); K: 3 (14.3%); R: 7 (33.3%); Negative charge clusters (cmin = 6/30 or 8/45 or 10/60): none Mixed charge clusters (cmin = 12/30 or 16/45 or 19/60): none B. HIGH SCORING (UN)CHARGED SEGMENTS. There are no high scoring positive charge segments. There are no high scoring negative charge segments. There are no high scoring mixed charge segments. There are no high scoring uncharged segments. C. CHARGE RUNS AND PATTERNS. pattern (+)| (-)| (*)| (0)| (+0)| (-0)| (*0)|(+00)|(-00)|(*00)| (H.)|(H..)| lmin0 4 | 4 | 6 | 56 | 9 | 8 | 11 | 12 | 10 | 14 | 8 | 10 | lmin1 6 | 5 | 7 | 68 | 11 | 10 | 14 | 14 | 12 | 17 | 10 | 12 | lmin2 7 | 6 | 8 | 76 | 13 | 11 | 15 | 16 | 14 | 19 | 11 | 14 | (Significance level: 0.010000; Minimal displayed length: 6) There are no charge runs or patterns exceeding the given minimal lengths. Run count statistics: + runs >= 3: 1, at 25; - runs >= 3: 0 * runs >= 4: 1, at 25; 0 runs >= 37: 1, at 282; -------------------------------------------------------------------------------- DISTRIBUTION OF OTHER AMINO ACID TYPES 1. HIGH SCORING SEGMENTS. There are no high scoring hydrophobic segments. There are no high scoring transmembrane segments. 2. SPACINGS OF C. H2N-63-C-101-C-2-C-6-C-C-40-C-101-C-38-C-3-C-47-C-16-C-10-C-8-C-94-COOH 2*. SPACINGS OF C and H. (additional deluxe function for ALEX) H2N-15-H-47-C-19-H-33-H-47-C-2-C-6-C-C-40-C-16-H-8-H-3-H-H-45-H-2-H-13-H-5-H-1-C-7-H-17-H-12-C-3-C-5-H-26-H-9-H-4-C-16-C-H-6-H-1-H-C-8-C-29-H-7-H-27-H-1-H-8-H-1-H-15-COOH -------------------------------------------------------------------------------- REPETITIVE STRUCTURES. A. SEPARATED, TANDEM, AND PERIODIC REPEATS: amino acid alphabet. Repeat core block length: 5 B. SEPARATED AND TANDEM REPEATS: 11-letter reduced alphabet. (i= LVIF; += KR; -= ED; s= AG; o= ST; n= NQ; a= YW; p= P; h= H; m= M; c= C) Repeat core block length: 9 -------------------------------------------------------------------------------- MULTIPLETS. A. AMINO ACID ALPHABET. 1. Total number of amino acid multiplets: 32 (Expected range: 15-- 50) 2. Histogram of spacings between consecutive amino acid multiplets: (1-5) 7 (6-10) 9 (11-20) 10 (>=21) 7 3. Clusters of amino acid multiplets (cmin = 11/30 or 14/45 or 16/60): none B. CHARGE ALPHABET. 1. Total number of charge multiplets: 10 (Expected range: 0-- 13) 8 +plets (f+: 9.0%), 2 -plets (f-: 5.7%) Total number of charge altplets: 9 (Critical number: 15) 2. Histogram of spacings between consecutive charge multiplets: (1-5) 1 (6-10) 2 (11-20) 1 (>=21) 7 -------------------------------------------------------------------------------- PERIODICITY ANALYSIS. A. AMINO ACID ALPHABET (core: 4; !-core: 5) Location Period Element Copies Core Errors 45- 72 7 L...... 4 4 0 178- 185 2 T. 4 4 0 327- 342 4 L... 4 4 0 B. CHARGE ALPHABET ({+= KR; -= ED; 0}; core: 5; !-core: 6) and HYDROPHOBICITY ALPHABET ({*= KRED; i= LVIF; 0}; core: 6; !-core: 9) Location Period Element Copies Core Errors 250- 285 6 i..... 6 6 0 301- 324 4 i000 6 6 /0/1/2/2/ 313- 375 9 i0...00.. 7 7 /0/2/./././1/1/././ -------------------------------------------------------------------------------- SPACING ANALYSIS. Location (Quartile) Spacing Rank P-value Interpretation 178- 180 (2.) T( 2)T 36 of 36 0.0068 large minimal spacing 180- 182 (2.) T( 2)T 34 of 36 0.0068 matching minimum 182- 184 (2.) T( 2)T 35 of 36 0.0068 matching minimum ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ Start with Pfam (from /data/patterns/pfam) hmmpfam - search a single seq against HMM database HMMER 2.1.1 (Dec 1998) Copyright (C) 1992-1998 Washington University School of Medicine HMMER is freely distributed under the GNU General Public License (GPL). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HMM file: /data/patterns/pfam/Pfam Sequence file: NP_061377.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: NP_061377.1 phosphatidylinositol glycan, class B; involved in GPI-anchor biosynthesis [Mus musculus]. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- oxidored_q1_N NADH-Ubiquinone oxidoreductase (complex 2.2 69 1 TYA TYA transposon protein 0.0 31 1 Ribosomal_L2 Ribosomal Proteins L2 -0.1 59 1 fibrinogen_C Fibrinogen beta and gamma chains, C-ter -0.8 78 1 Abi CAAX amino terminal protease family -40.3 1e+02 1 PMT Dolichyl-phosphate-mannose-protein mann -63.2 9.4 1 CobS Cobalamin-5-phosphate synthase -135.9 83 1 STT3 Oligosaccharyl transferase STT3 subunit -303.9 88 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- TYA 1/1 1 18 [. 1 16 [. 0.0 31 fibrinogen_C 1/1 21 27 .. 266 272 .] -0.8 78 Ribosomal_L2 1/1 11 29 .. 232 250 .] -0.1 59 CobS 1/1 86 262 .. 1 250 [] -135.9 83 oxidored_q1_N 1/1 244 268 .. 1 25 [. 2.2 69 PMT 1/1 50 275 .. 1 267 [] -63.2 9.4 Abi 1/1 324 412 .. 1 119 [] -40.3 1e+02 STT3 1/1 55 541 .. 1 874 [] -303.9 88 Alignments of top-scoring domains: TYA: domain 1 of 1, from 1 to 18: score 0.0, E = 31 *->MESQQLsQns..rilHGS<-* MESQ n+ +r lHGS NP_061377. 1 MESQAADYNPasRNLHGS 18 fibrinogen_C: domain 1 of 1, from 21 to 27: score -0.8, E = 78 *->eMKiRPr<-* eMK+R+r NP_061377. 21 EMKLRRR 27 Ribosomal_L2: domain 1 of 1, from 11 to 29: score -0.1, E = 59 *->ktRrtkrlsdkfivrrRkk<-* ++R+ s+++++rrRk+ NP_061377. 11 ASRNLHGSSGEMKLRRRKS 29 CobS: domain 1 of 1, from 86 to 262: score -135.9, E = 83 *->lraalsFlTrLPvkgreSqsaDfEvirrnlwafPlvGallGalvali + + + lT ++ +E +r++++ ++ ++++ ++ NP_061377. 86 MVFSYGYLTW-----EW-----TERLRGYTYPLI-----FASIYKVL 117 lvlgsfvlGmdnpLaafLavllllaltGglHlDGLADtgDGlmapgdrkR + lg +v +l+++ ++ g +l ++ R NP_061377. 118 HLLGKD------------SVQFLIWIPRL---------GQALLSAVADIR 146 kLeaMkDsntGtgGvvavvvVlllkilaLaslsdrglflgillaevsAKv +++llk l ++++ ++ +l ++++ + NP_061377. 147 -------------------LYSLLKQLENQEVA-----QWVFLCQLCSWF 172 smlLllltsrPRyaleeGlGa.....yfmekldsRpdlliglilllllav + + +t+ e l+a y e ++s + + l+++l+ +v NP_061377. 173 TWYCCTRTLTN--TMETSLTAlalfyYPLEGSRSVNSIKYSLLVALACVV 220 plgYALpiErwlgviAvlvavliglalgkia.krnFGGvtGDVlGAanEl + AL+ +w +++l+ + +++++ ++F + NP_061377. 221 RPT-ALI--PW---VPLLFRHFYQEQRKLHLtLHHF-----------LPV 253 trvvsLLaL<-* ++ + L+L NP_061377. 254 GFITFSLSL 262 oxidored_q1_N: domain 1 of 1, from 244 to 268: score 2.2, E = 69 *->iitlwnWissgsfninwgFlfDsls<-* ++tl + +++g + +++++++D+++ NP_061377. 244 HLTLHHFLPVGFITFSLSLIIDRIF 268 PMT: domain 1 of 1, from 50 to 275: score -63.2, E = 9.4 *->kiltlllflirflllalpn.lvvfdevhfgkfasyYaeglffmdvhg l l+++++r+l+ +l+ ++ v de+++ + a ++ f +++ NP_061377. 50 TYLVLFTIALRILNCFLVQtSFVPDEYWQ-SL--EVAHRMVFSYGYL 93 lpplgkmlialggyylagypglflflsigsflkfgnvpyfsmRlfsallG ++ l +++++ ++ +++l l+ ++ f ++ Rl +all+ NP_061377. 94 TWEWTERLRGYTYPLIFASIYKVLHLLGKDSVQFL---IWIPRLGQALLS 140 altvplvyltlrklgfskeaAllaallvildnslvtlsryillDspLlFF a+ + +y +l+ l + +e+A + +l+ +++ + + + l+ + + NP_061377. 141 AVADIRLYSLLKQLEN-QEVAQWVFLCQLCSWFTWYCCTRTLTNTMETSL 189 ttLavylflkfeklrladlkapfsrgwllwllltgialglafltKgvglf t+La +++ + +sr+ +++ + +++al++++ ++++ NP_061377. 190 TALALFYYPLE-----------GSRSVNSIKYSLLVALACVV---RPTA- 224 tilpvgllfiwalwqllgqLawdkklpskrnqlwmsrvtivkhlfarlli + p ++l+++++ q + ++ l+++ ++ NP_061377. 225 -LIPWVPLLFRHFYQEQR----KLHLTLH---------------HFLPVG 254 LillPvllyllffyvhfflyf<-* +i + l ++ + + ++++ NP_061377. 255 FITFSLSLIIDRIFFGQWTLV 275 Abi: domain 1 of 1, from 324 to 412: score -40.3, E = 1e+02 *->llilllvllaplaEElfFRGilltalerrlkkry.tlfgpllaiiis ++ l ++ll+ l + +++ l+ +k ++ ++++l+ +++ NP_061377. 324 PRRLHILLLTVL-----WTLLVYSMLG---HKEFrFIYPVLPFCMVF 362 sliFallHlanalellqllgnvliqpvlinwlqllytfllGlvlgllylr + ++l+Hl ++++ + + ll ++l++++gl+ + NP_061377. 363 C-GYSLAHLKTWRK-------------AALSFLLLSNVPLAFYTGLVHQ- 397 rtgsLlapilvHalnNligfill<-* r L + +N i +++ NP_061377. 398 RGT-LDV-------MNHIQKVCP 412 STT3: domain 1 of 1, from 55 to 541: score -303.9, E = 88 *->llkvvifaliagvaifsralFtdtrglsyfhEfDpYYnyRltenlln + +++ ++++++v+++ + d++++s + ++ ++ NP_061377. 55 FTIALRILNCFLVQTSFV---PDEYWQSL----------EVAHRMVF 88 eGfpGDavypgkiwfdhsayYPpGsrvdyppllplLtlalygiiflflpg y+ ++w + r+ + + +pl+ + +y++++l + NP_061377. 89 S-------YGYLTWEWT-------ERLRGYT-YPLIFASIYKVLHLLGK- 122 lLrltvslrevcfwlp....PviggLlgIatylLvtLrelkndlaGliaA ++ + w+p+ ++++++ ++ I +y L + l n+ ++ NP_061377. 123 ------DSVQFLIWIPrlgqALLSAVADIRLYSLL--KQLENQEVA---- 160 fllaiaPgfyvsRTvaGfyRGDtdmlaiflpllvlfflllaiktgskrdL + ++++++l + f+++ ++t ++ NP_061377. 161 --------Q----------------WVFLCQLCSWFTWYCCTRTLTN--- 183 fkklkkkkiiyavlaaLllflmvlaWgGyqs.....fvfllilallfila + +l aL+lf++ l G+ s ++ ++ +l++la ++ NP_061377. 184 --------TMETSLTALALFYYPL--EGSRSvnsikYSLLVALACVVRPT 223 lLimgrlkkLkkfvkEfeskllilvilsyvltfpgivkilgfsvliativ +Li ++l++ + ++++ + NP_061377. 224 ALIP------------WVPLLFRHF--------------YQEQRKLHLTL 247 ggiiqllfvgfakvrkessehmgallifgllqllafgsvvkgvyPLFRLm ++++ f+ f+ +l+++ +f + v NP_061377. 248 HHFLPVGFITFS---------------LSLIIDRIFFGQWTLV------- 275 GaylsfyqfetdeeanlfypgildkvlglisegpvlfllgllGfialwee +l+f +f + + + fy+ l ++ pv+ l+ fi NP_061377. 276 --QLNFLKFNVLQNLGTFYGS-HPWHWYLSQGFPVVLGTHLPFFIH---- 318 iftnevvsdeieivgitGrfyslfdlkteyakidipiiilisewqptgla G f + ++ + i+ l + w+ + + NP_061377. 319 -----------------GCFLAPRR---------LHILLLTVLWT-LLVY 341 allaglrFlaiftaPlglllGiftgllledlavfsiiyssiliKvsqlrf + l F f++P++ f+ + ++ + ++ + NP_061377. 342 SMLGHKEFR--FIYPVLP----FCMVFCGYSLAHLKTWR----------- 374 lgvmvfvimlvlapvialiaaylasepifstyleeeaaklriiTlvlaag ++++ f l+ + +a+ + + + ++ ++ +++ + ++ NP_061377. 375 KAALSF--LLLSNVPLAFYTGLVHQ-----RGTLDVMNHIQK----VCPR 413 vasvlsaviekSlapeknegaerglewlkvntnrdtVvitwWdyghffay + + +++V+i + NP_061377. 414 GP----------------------------DPASASVFI--------MMP 427 fadrpkFNVtfdGgsa.psvvlgtprgywaltlmddsneageryyNPYay +++p + ++ p NP_061377. 428 CHSTP-----YYSHVHcP-------------------------------- 440 lsLginsmldtlkdeilsmLetsgvkswwdygNqilkvakRCDGPFPrav ls+++++ ++ d+ + + + + + NP_061377. 441 LSMRFLQCPP-------------------DLTGKTQYLDE------ADMF 465 ilnnilgvnaykYvrshaakvltaksgistkkYseeaekalnithprdpv +ln++ ++ ++ + n+ p++ NP_061377. 466 YLNPLRWLQ--------------QEFHS-------------NASLPTH-- 486 gyvlvtkegmigiakpwdinkgtwdevgklsyekdtlrlyiSyssrdnkN lvt++ + + +++++ t+ NP_061377. 487 ---LVTFNVLEK----EINTFLTS-------------------------- 503 aelyVlaldkteiimrirggaypyynsLeeykiivmkdveeinfytstgv g+y+ ++ t NP_061377. 504 -------------------GNYE---------------------RAATF- 512 qkgpvGeyrldtkeaskkngnsllvkifysgklevkv<-* + ++ ++ + ++ ++ + +g+++ NP_061377. 513 -------FHTHW-PERRTGSHIHVYERRLPGRVNTGG 541 // Start with PfamFrag (from /data/patterns/pfam) hmmpfam - search a single seq against HMM database HMMER 2.1.1 (Dec 1998) Copyright (C) 1992-1998 Washington University School of Medicine HMMER is freely distributed under the GNU General Public License (GPL). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HMM file: /data/patterns/pfam/PfamFrag Sequence file: NP_061377.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: NP_061377.1 phosphatidylinositol glycan, class B; involved in GPI-anchor biosynthesis [Mus musculus]. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- oxidored_q1_N NADH-Ubiquinone oxidoreductase (complex 2.2 69 1 Pterin_4a Pterin 4 alpha carbinolamine dehydratas 1.5 46 1 zf-BED BED zinc finger 1.5 57 1 MAPEG MAPEG family 0.9 73 1 TYA TYA transposon protein 0.0 31 1 Ribosomal_L2 Ribosomal Proteins L2 -0.1 59 1 GP3 Equine arteritis virus GP3 -0.6 84 1 fibrinogen_C Fibrinogen beta and gamma chains, C-ter -0.8 78 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- TYA 1/1 1 18 [. 1 16 [. 0.0 31 fibrinogen_C 1/1 21 27 .. 266 272 .] -0.8 78 Ribosomal_L2 1/1 11 29 .. 232 250 .] -0.1 59 MAPEG 1/1 34 68 .. 58 92 .] 0.9 73 Pterin_4a 1/1 136 162 .. 1 26 [. 1.5 46 GP3 1/1 220 242 .. 139 160 .] -0.6 84 oxidored_q1_N 1/1 244 268 .. 1 25 [. 2.2 69 zf-BED 1/1 404 412 .. 44 52 .] 1.5 57 Alignments of top-scoring domains: TYA: domain 1 of 1, from 1 to 18: score 0.0, E = 31 *->MESQQLsQns..rilHGS<-* MESQ n+ +r lHGS NP_061377. 1 MESQAADYNPasRNLHGS 18 fibrinogen_C: domain 1 of 1, from 21 to 27: score -0.8, E = 78 *->eMKiRPr<-* eMK+R+r NP_061377. 21 EMKLRRR 27 Ribosomal_L2: domain 1 of 1, from 11 to 29: score -0.1, E = 59 *->ktRrtkrlsdkfivrrRkk<-* ++R+ s+++++rrRk+ NP_061377. 11 ASRNLHGSSGEMKLRRRKS 29 MAPEG: domain 1 of 1, from 34 to 68: score 0.9, E = 73 *->aakkraaPlrasgfalgslltLllalgilnsaLqh<-* +a+ ++ P r + + +l++ al+iln +L + NP_061377. 34 SAQEKRSPRRGLLGENTYLVLFTIALRILNCFLVQ 68 Pterin_4a: domain 1 of 1, from 136 to 162: score 1.5, E = 46 *->rakasaLsdeelsekLgeLpdwEV.gW<-* +a +sa++d l +L++L EV +W NP_061377. 136 QALLSAVADIRLYSLLKQLENQEVaQW 162 GP3: domain 1 of 1, from 220 to 242: score -0.6, E = 84 *->iRPt.LiCWFaLLLvHFLPmPrc<-* +RPt Li W LL HF r NP_061377. 220 VRPTaLIPWVPLLFRHFYQEQRK 242 oxidored_q1_N: domain 1 of 1, from 244 to 268: score 2.2, E = 69 *->iitlwnWissgsfninwgFlfDsls<-* ++tl + +++g + +++++++D+++ NP_061377. 244 HLTLHHFLPVGFITFSLSLIIDRIF 268 zf-BED: domain 1 of 1, from 404 to 412: score 1.5, E = 57 *->rrHLrrkHp<-* ++H+++++p NP_061377. 404 MNHIQKVCP 412 // Start with Repeat Library (from /data/patterns/repeats-Miguel-Andrade/hmm) hmmpfam - search a single seq against HMM database HMMER 2.1.1 (Dec 1998) Copyright (C) 1992-1998 Washington University School of Medicine HMMER is freely distributed under the GNU General Public License (GPL). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HMM file: /data/patterns/repeats-Miguel-Andrade/hmm/repeats.hmm-lib Sequence file: NP_061377.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: NP_061377.1 phosphatidylinositol glycan, class B; involved in GPI-anchor biosynthesis [Mus musculus]. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- [no hits above thresholds] Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- [no hits above thresholds] Alignments of top-scoring domains: [no hits above thresholds] // ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ Start with Prosite --------------------------------------------------------- | ppsearch (c) 1994 EMBL Data Library | | based on MacPattern (c) 1990-1994 R. Fuchs | --------------------------------------------------------- PROSITE pattern search started: Wed Jan 30 14:35:19 2002 Sequence file: NP_061377.1.fa ---------------------------------------- Sequence NP_061377.1 (542 residues): Matching pattern PS00001 ASN_GLYCOSYLATION: 480: NASL Total matches: 1 Matching pattern PS00004 CAMP_PHOSPHO_SITE: 26: RRKS Total matches: 1 Matching pattern PS00005 PKC_PHOSPHO_SITE: 40: SPR 98: TER 207: SIK 372: TWR 442: SMR 453: TGK Total matches: 6 Matching pattern PS00006 CK2_PHOSPHO_SITE: 18: SSGE 34: SAQE Total matches: 2 Matching pattern PS00008 MYRISTYL: 289: GTFYGS Total matches: 1 Matching pattern PS00029 LEUCINE_ZIPPER: 45: LLGENTYLVLFTIALRILNCFL Total matches: 1 Total no of hits in this sequence: 12 ======================================== 1314 pattern(s) searched in 1 sequence(s), 542 residues. Total no of hits in all sequences: 12. Search time: 00:00 min ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ Start with Profile Search ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ Start with motif search against own library ***** bioMotif : Version V41a DB, 1999 Nov 11 ***** SeqTyp=2 : PROTEIN search; >APC D-Box is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >ER-GOLGI-traffic signal is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >INTRA-SIGNAL-M minimal SH3 binding is the MOTIF name >NP_061377.1 phosphatidylinositol glycan, class B; involved in GPI-anchor biosynthesis [Mus musculus]. ;LENGTH=542; DIRECT_SEQUENCE n 3 solutions m %_PXXP 227-230 f m %_PXXP 354-357 f m %_PXXP 412-415 f >STATISTICS Total : 3 solutions in 1 sequences, 542 units; out of 1 sequences, 542 units >INTRA-SIGNAL-M deubiquitinating enzyme SH3 domain binding motif (Kato, 2000) is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >INTRA-SIGNAL-M minimal class I consensus-SH3 binding motif is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >INTRA-SIGNAL-M minimal class II consensus-SH3 binding motif is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >INTRA-SIGNAL-M exact 14-3-3 binding consensus (Muslin 1996 Cell 84 889) is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >INTRA-SIGNAL-M 14-3-3 binding motif in RAF and others (Muslin 1996 Cell 84 889) is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >INTRA-SIGNAL-M WW domain binding motif in formins (Bedford 1997) is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >INTRA-SIGNAL-M PY motif for WW domain is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >TM-CYTOPLASMIC-M di-hydrophobic endocytosis motifs for internalized transmembrane proteins is the MOTIF name >NP_061377.1 phosphatidylinositol glycan, class B; involved in GPI-anchor biosynthesis [Mus musculus]. ;LENGTH=542; DIRECT_SEQUENCE n 1 solutions m %_E 48-48 %_XXXL 49-52 %_V 53-53 f >STATISTICS Total : 1 solutions in 1 sequences, 542 units; out of 1 sequences, 542 units >TM-CYTOPLASMIC-M tyrosine-based endocytosis motif for internalized transmembrane proteins is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >TM-EXTRACELL-M Endocytosis signal for internalized transmembrane proteins is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >EXTRACELL-M minimal furin protease cleavage site motif is the MOTIF name >NP_061377.1 phosphatidylinositol glycan, class B; involved in GPI-anchor biosynthesis [Mus musculus]. ;LENGTH=542; DIRECT_SEQUENCE n 2 solutions m %_RXXR 27-30 f m %_RXXR 39-42 f >STATISTICS Total : 2 solutions in 1 sequences, 542 units; out of 1 sequences, 542 units >EXTRACELL-M extended furin protease cleavage site motif is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >EXTRACELL-M zinc binding motif in MMPs is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >EXTRACELL-M g alpha binding go loco is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS PDX-1 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS QKI-5 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS HCDA experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS SV40 LrgT experimentally determined is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS H2B experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS v-Rel experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS Amida experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS Amida experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS RanBP3 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS Pho4p experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS DNAhelicaseQ1 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS LEF-1 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS TCF-1 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR p53-NLS1 NLS experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS hum-Ku70 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS GAL4 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS act/inh betaA experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS BDV-P experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS BDV-P experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS BDV-P experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS TR2 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS THOV NP experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS polyomaVP1 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS HIV-1 Tat experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS HIV-1 Rev experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS Rex experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS SRY experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS SRY experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS SOX9 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS SOX9 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS NS5A experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS DNAse EBV experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS DNAse EBV experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS adenovE1a experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS ystDNApolalpha experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS hVDR experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS CPV capsid experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS hGlu.cort.experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS cFOS experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS cJUN experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS hDNApolalpha experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS hDNAtopoII experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS hDNAtopoII experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS hBLM experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS hARNT experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS influenzaNP experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS influenzaNP experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS p54 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS hProTalpha experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS Tst1/Oct6 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS protHsc9 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS protHsci experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS protHsc3 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS Ta alpha experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS Pax-QNR experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS Hunt.Dis.pro experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS MyoD experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS MyoD experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS opaque2 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS CTP experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS HCV experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS HCV experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS p110RB1 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS VirD2-Nterm experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS VirD2-Cterm experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS Nucloplasmin experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS Nucleolin experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS ICP-8 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS Nab2 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS M9 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS lscMyc experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS humKprotein experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS FluA experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS Mat-alpha experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS polyoma Lrg-T experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS polyoma Lrg-T experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS SV40 VP1 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS SV40 VP2 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS polyoma VP2 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS c-myb experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS N-myc experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS p53 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS c-erb-A experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS yeast SKI3 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS L29 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS L29 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS Max experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS L3 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >NUCLEAR NLS dyskerin experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >PDZ domain binding motif science 278_2075_pawson is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units >WW domain binding motif science 278_2075_pawson is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 542 units ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~ ~~~ Start with HMM-search search against own library hmmpfam - search a single seq against HMM database HMMER 2.1.1 (Dec 1998) Copyright (C) 1992-1998 Washington University School of Medicine HMMER is freely distributed under the GNU General Public License (GPL). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HMM file: /data/patterns/own/own-hmm.lib Sequence file: NP_061377.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: NP_061377.1 phosphatidylinositol glycan, class B; involved in GPI-anchor biosynthesis [Mus musculus]. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- [no hits above thresholds] Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- [no hits above thresholds] Alignments of top-scoring domains: [no hits above thresholds] // hmmpfam - search a single seq against HMM database HMMER 2.1.1 (Dec 1998) Copyright (C) 1992-1998 Washington University School of Medicine HMMER is freely distributed under the GNU General Public License (GPL). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HMM file: /data/patterns/own/own-hmm-f.lib Sequence file: NP_061377.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: NP_061377.1 phosphatidylinositol glycan, class B; involved in GPI-anchor biosynthesis [Mus musculus]. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- [no hits above thresholds] Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- [no hits above thresholds] Alignments of top-scoring domains: [no hits above thresholds] // ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ L. Aravind's signalling DB+ PSSM from other authors IMPALA version 1.1 [20-December-1999] Reference: Alejandro A. Schaffer, Yuri I. Wolf, Chris P. Ponting, Eugene V. Koonin, L. Aravind, Stephen F. Altschul (1999), "IMPALA: Matching a Protein Sequence Against a Collection of "PSI-BLAST-Constructed Position-Specific Score Matrices", Bioinformatics 15:1000-1011. Query= NP_061377.1 phosphatidylinositol glycan, class B; involved in GPI-anchor biosynthesis [Mus musculus]. (542 letters) Searching..................................done Results from profile search Score E Sequences producing significant alignments: (bits) Value MYND MYND domain (A zinc coordinating Cysteine rich domain) 23 1.2 DHHC Novel zinc finger domain with DHHC signature 22 2.5 HECT A ubiquitin conjugating enzyme domain 21 4.7 CHROMO Chromodomain- A chromatin associated domain 21 5.8 BZIP Basic Zipper domain (A DNA binding domain) 20 7.4 PHD PHD zinc finger(A cysteine rich DNA binding domain) 20 7.6 >MYND MYND domain (A zinc coordinating Cysteine rich domain) Length = 107 Score = 22.8 bits (48), Expect = 1.2 Identities = 7/33 (21%), Positives = 7/33 (21%), Gaps = 7/33 (21%) Query: 153 QLENQEVAQWVFLC-----QLCS--WFTWYCCT 178 Sbjct: 42 HGNEIISAKKCANCNREALAECSLCRKTPYCSE 74 >DHHC Novel zinc finger domain with DHHC signature Length = 217 Score = 21.6 bits (45), Expect = 2.5 Identities = 15/84 (17%), Positives = 15/84 (17%), Gaps = 4/84 (4%) Query: 222 PTALIPWVPLLFRHFYQEQRKLHLTLHHFLPVGFITFSLSLIIDRIFFGQWTLVQLNFLK 281 Sbjct: 50 PLQIVAWLLYLFFAVIGFGILVPLLPHHWVPAGYACMGAIFAGHLVVHL--TAVSIDPAD 107 Query: 282 FNVLQNLGTFYGSHPWHWYLSQGF 305 Sbjct: 108 DNVRDK--SYAGPLPIFNRSQHAH 129 >HECT A ubiquitin conjugating enzyme domain Length = 255 Score = 20.9 bits (44), Expect = 4.7 Identities = 6/49 (12%), Positives = 6/49 (12%), Gaps = 1/49 (2%) Query: 459 LDEADMFYLNPLRWLQQEFHSNASLPTHLVTFNVLEKEINTFLTSGNYE 507 Sbjct: 120 LEEVDLLYVQTLNSI-LHIEDSGITEESFHEMIPLDSFVGQSADGKMVP 167 >CHROMO Chromodomain- A chromatin associated domain Length = 66 Score = 20.6 bits (43), Expect = 5.8 Identities = 6/14 (42%), Positives = 6/14 (42%) Query: 88 FSYGYLTWEWTERL 101 Sbjct: 26 FTDADNTWEPEENL 39 >BZIP Basic Zipper domain (A DNA binding domain) Length = 89 Score = 20.2 bits (41), Expect = 7.4 Identities = 5/11 (45%), Positives = 5/11 (45%) Query: 403 VMNHIQKVCPR 413 Sbjct: 70 VMNHVNSGCQL 80 >PHD PHD zinc finger(A cysteine rich DNA binding domain) Length = 54 Score = 20.0 bits (41), Expect = 7.6 Identities = 5/28 (17%), Positives = 5/28 (17%), Gaps = 1/28 (3%) Query: 162 WVFLCQLC-SWFTWYCCTRTLTNTMETS 188 Sbjct: 16 RIVFCDGCNTPFHQLCHEPYISDELLDS 43 Underlying Matrix: BLOSUM62 Number of sequences tested against query: 105 Number of sequences better than 10.0: 6 Number of calls to ALIGN: 6 Length of query: 542 Total length of test sequences: 20182 Effective length of test sequences: 16941.0 Effective search space size: 8661482.4 Initial X dropoff for ALIGN: 25.0 bits Y. Wolf's SCOP PSSM IMPALA version 1.1 [20-December-1999] Reference: Alejandro A. Schaffer, Yuri I. Wolf, Chris P. Ponting, Eugene V. Koonin, L. Aravind, Stephen F. Altschul (1999), "IMPALA: Matching a Protein Sequence Against a Collection of "PSI-BLAST-Constructed Position-Specific Score Matrices", Bioinformatics 15:1000-1011. Query= NP_061377.1 phosphatidylinositol glycan, class B; involved in GPI-anchor biosynthesis [Mus musculus]. (542 letters) Searching.................................................done Results from profile search Score E Sequences producing significant alignments: (bits) Value gi|267149 [417..1178] type II DNA topoisomerase 27 0.85 gi|2619052 [38..197] Flavodoxin-like 26 1.5 gi|1655857 [298..607] beta/alpha (TIM)-barrel 25 2.7 gi|1827606 [1..273] Flavodoxin-like 25 3.5 gi|1536958 [63..316] Periplasmic binding protein-like I 25 3.6 gi|1703166 [11..338] beta/alpha (TIM)-barrel 24 6.4 gi|485157 [209..476] Protein kinases (PK), catalytic core 24 6.7 gi|493806 [6..158] Apolipophorin-III 24 7.4 >gi|267149 [417..1178] type II DNA topoisomerase Length = 762 Score = 26.8 bits (59), Expect = 0.85 Identities = 5/23 (21%), Positives = 5/23 (21%) Query: 511 TFFHTHWPERRTGSHIHVYERRL 533 Sbjct: 138 AYFHLFWPQLIIHGFVKRLLTPL 160 >gi|2619052 [38..197] Flavodoxin-like Length = 160 Score = 26.1 bits (57), Expect = 1.5 Identities = 7/78 (8%), Positives = 7/78 (8%), Gaps = 14/78 (17%) Query: 254 GFITFSLSLIIDRIFFGQWTLVQLNFLKFNVLQNL--------GTFYGSHPWHW------ 299 Sbjct: 65 FTVPAVLHTYVDYLSRAGVTFKYTQEGPVGLMGGKKVALLNARGGVYSEGPMAALEMSLN 124 Query: 300 YLSQGFPVVLGTHLPFFI 317 Sbjct: 125 FMKTVLGFWGVQDLHTVV 142 >gi|1655857 [298..607] beta/alpha (TIM)-barrel Length = 310 Score = 25.2 bits (54), Expect = 2.7 Identities = 10/26 (38%), Positives = 10/26 (38%), Gaps = 3/26 (11%) Query: 74 DEYWQSLEVAHRMVFSYGYLTWEWTE 99 Sbjct: 242 EDYWQAF---HRHPQSCGGFVWEWCD 264 >gi|1827606 [1..273] Flavodoxin-like Length = 273 Score = 25.0 bits (54), Expect = 3.5 Identities = 17/93 (18%), Positives = 17/93 (18%), Gaps = 13/93 (13%) Query: 254 GFITFSLSLIIDRIFFGQWTLVQLNFLKFNVLQN-----LGTFYGSHPWHWYLSQGFPVV 308 Sbjct: 106 FGVPAILKGWFERVLVAGFAYTYATMYDKGPFQNKKTLLSITTGGSG--SMYSLQGVHGD 163 Query: 309 LGTHLPFFIHGCFLAPRRLHILLLTVLWTLLVY 341 Sbjct: 164 MNVILWPIQSGIL------RFCGFQVLEPQLVY 190 >gi|1536958 [63..316] Periplasmic binding protein-like I Length = 254 Score = 25.0 bits (54), Expect = 3.6 Identities = 4/70 (5%), Positives = 4/70 (5%), Gaps = 7/70 (10%) Query: 63 NCFLVQTSFVPDEYWQSLEVAHR-----MVFSYGYLTWEWTERLRGYTYPLIFASIYKVL 117 Sbjct: 33 QVMIGNSNYSQESEDRYIESMLLLGVDGFIIQPTSNFRKYSRIIDEKKKKMVFFD--SQL 90 Query: 118 HLLGKDSVQF 127 Sbjct: 91 YEHRTSWVKT 100 >gi|1703166 [11..338] beta/alpha (TIM)-barrel Length = 328 Score = 24.1 bits (52), Expect = 6.4 Identities = 8/37 (21%), Positives = 8/37 (21%) Query: 283 NVLQNLGTFYGSHPWHWYLSQGFPVVLGTHLPFFIHG 319 Sbjct: 246 NVKLQVVQSVSELPLQKFLDRDVPFSLNSDDPAYFGG 282 >gi|485157 [209..476] Protein kinases (PK), catalytic core Length = 268 Score = 23.9 bits (50), Expect = 6.7 Identities = 18/190 (9%), Positives = 18/190 (9%), Gaps = 17/190 (8%) Query: 276 QLNFLKFNVLQNLGTFYGSHPWHWYLSQGFPVVLGTHLPFFIHGCFLAPRRLHILLLTVL 335 Sbjct: 21 GESVPVAVKKLGLRESSKDERNPAFSEMEILEMVAHPNIVFYYGFSISGDEQALYLLFEL 80 Query: 336 WTLLVYSMLGHKEFRFIYPVLPFCMVFCGYSLAHLKTWRKAALSFLLLSNVPLAFYTGLV 395 Sbjct: 81 MDTSLDKFIDKSDAILSENERLDILAQICRGMSFLHTRTP-------------SIVHGDL 127 Query: 396 HQRGTLDVMNHIQKVCPRGPDPASASVFIMMPCHSTPYYSHVHCPLSMRFLQCPPDLTGK 455 Sbjct: 128 AARNVLLKKHPVYIKK----YICKITDLGLAKTCLDELYTSYDDPTKIPFKWLPPEVLGS 183 Query: 456 TQYLDEADMF 465 Sbjct: 184 RTLSLKTDIW 193 >gi|493806 [6..158] Apolipophorin-III Length = 153 Score = 23.9 bits (50), Expect = 7.4 Identities = 10/27 (37%), Positives = 10/27 (37%) Query: 476 EFHSNASLPTHLVTFNVLEKEINTFLT 502 Sbjct: 19 ELHETLGLPTPDEALNLLTEQANAFKT 45 Underlying Matrix: BLOSUM62 Number of sequences tested against query: 1187 Number of sequences better than 10.0: 8 Number of calls to ALIGN: 8 Length of query: 542 Total length of test sequences: 256703 Effective length of test sequences: 213024.0 Effective search space size: 107745280.8 Initial X dropoff for ALIGN: 25.0 bits ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ calculation of internal repeats with prospero ***** PROSPERO v1.3 Wed Jan 30 14:36:02 2002 ***** Copyright 2000, Richard Mott, Wellcome Trust Centre for Human Genetics, University of Oxford For help see http://www.well.ox.ac.uk/ariadne For usage use -help using gap penalty 11+1k using matrix BLOSUM62 printing all alignments with eval < 0.100000 using sequence1 NP_061377.1 using self-comparison ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ TIGRFAM hmmpfam - search a single seq against HMM database HMMER 2.1.1 (Dec 1998) Copyright (C) 1992-1998 Washington University School of Medicine HMMER is freely distributed under the GNU General Public License (GPL). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HMM file: /data/patterns/tigrfam/tigrfam.hmm Sequence file: NP_061377.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: NP_061377.1 phosphatidylinositol glycan, class B; involved in GPI-anchor biosynthesis [Mus musculus]. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- TIGR00494 crcB: crcB protein -60.3 43 1 TIGR00785 dass: anion transporter -328.2 87 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- TIGR00494 1/1 284 368 .. 1 119 [] -60.3 43 TIGR00785 1/1 41 395 .. 1 473 [] -328.2 87 Alignments of top-scoring domains: TIGR00494: domain 1 of 1, from 284 to 368: score -60.3, E = 43 *->LaiflGGglGAl.lRYllgkviPsallfgesLPlGTLtVNliGafil + lG + G+ + ++l+ + ++ g LP fi NP_061377. 284 VLQNLGTFYGSHpWHWYLSQGF--PVVLGTHLPF----------FIH 318 GivlayftvlavispdlklligTGFlGafTTFSTFslEtlkLLqegrlge G +++ l +l+ T +l l + + L + + NP_061377. 319 GC--------FLAPRRLHILLLT-VL--------WTLLVYSMLGHKEFR- 350 AvLYiLgtlvggligvalGwlLa<-* ++ v+ + +v +G+ La NP_061377. 351 -----FIYPVLPFCMVFCGYSLA 368 TIGR00785: domain 1 of 1, from 41 to 395: score -328.2, E = 87 *->PvPdglnkgAWlllAIfvaai....Vgwi.lEPlP.lpvtaLlalip P + l ++ +l++f+ a + +++++++ +P+++ +L ++ NP_061377. 41 PRRGLLGEN--TYLVLFTIALrilnCFLVqTSFVPdEYWQSLE--VA 83 iiavli.GvlsfdgkeLAdpafkfknaslsWgLsGFAdptiwLffgaFiL +v++ G+l+ ++ L G+ p+i+ + NP_061377. 84 HRMVFSyGYLT----------WEWTER-----LRGYTYPLIFASI----- 113 AtAlektgLgkRIAykLvkkmGsttLglGyflvfletlLapmwpSNTARa yk + ++G+ ++ ++ + L + S +A NP_061377. 114 --------------YKVLHLLGK----DSVQFLIWIPRLGQALLSAVA-- 143 ggilLPiiksllpllgskpgdksprkigkyLmLgiays.........asi i L sll +l ++ ++ ++ L + s + +++++ NP_061377. 144 -DIRL---YSLLKQLENQE-------VAQWVFLCQLCSwftwycctrTLT 182 gssgf.ltGsAPNaLAasllskilgieiswgdWflagfLPlgi...iLLL + ++lt++A + l ++ +++ i + +l++ L +++++++L++ NP_061377. 183 NTMETsLTALA--LFYYPLEGSRSVNSIKYS--LLVA-LACVVrptALIP 227 lvplLlYvlfpPelkskdevdlwAkeeLeemGplslrEkvliallgifll vplL + ++++l +l + + g + + NP_061377. 228 WVPLLFRHFYQ------EQRKLHL----------TLHHF---LPVGFITF 258 alllWiFggslginniAyFasvVALlavvlmlilgivtWkDiqknkvaWn +l+l i+ +++g W +q n +n NP_061377. 259 SLSL-------IID----------------RIFFG--QWTLVQLNFLKFN 283 tLvlfGGlitLaggLkksGfikW...lseklvgiLgfeGlsptiavlvlv +L ++G+ +G +W+ ls+ + +Lg +l+ +++ + ++ NP_061377. 284 VLQNLGTF---------YGSHPWhwyLSQGFPVVLG-THLP-FFIHGCFL 322 v...lfyillyfFaSntAhtaalvPiffsvAsialhGvPlellaLalalS ++++l ++ll+ + +lv +++ + +++ l ++ ++ NP_061377. 323 AprrLHILLLTV------LWTLLVYSMLGHKEFRF--IYPVLPFCMVFCG 364 aSlmGfltPyaTpPnaIvYGsGYvkikdmwrvGailgivglivlllvgtl Sl+ +k + ++ + + +++ + l+ + +l NP_061377. 365 YSLA--------------------HLKTWRKAALSFLLLSNVPLAFYTGL 394 ww<-* + NP_061377. 395 -V 395 // hmmpfam - search a single seq against HMM database HMMER 2.1.1 (Dec 1998) Copyright (C) 1992-1998 Washington University School of Medicine HMMER is freely distributed under the GNU General Public License (GPL). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HMM file: /data/patterns/tigrfam/tigrfam.hmm-f Sequence file: NP_061377.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: NP_061377.1 phosphatidylinositol glycan, class B; involved in GPI-anchor biosynthesis [Mus musculus]. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- TIGR00873 gnd: 6-phosphogluconate dehydrogenase, deca -1.2 42 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- TIGR00873 1/1 512 519 .. 473 480 .] -1.2 42 Alignments of top-scoring domains: TIGR00873: domain 1 of 1, from 512 to 519: score -1.2, E = 42 *->fFHTnWtg<-* fFHT W + NP_061377. 512 FFHTHWPE 519 // SMART hmmpfam - search a single seq against HMM database HMMER 2.1.1 (Dec 1998) Copyright (C) 1992-1998 Washington University School of Medicine HMMER is freely distributed under the GNU General Public License (GPL). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HMM file: /data/patterns/iprscan/data/smart.HMMs Sequence file: NP_061377.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: NP_061377.1 phosphatidylinositol glycan, class B; involved in GPI-anchor biosynthesis [Mus musculus]. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- [no hits above thresholds] Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- [no hits above thresholds] Alignments of top-scoring domains: [no hits above thresholds] // COG hmmpfam - search a single seq against HMM database HMMER 2.1.1 (Dec 1998) Copyright (C) 1992-1998 Washington University School of Medicine HMMER is freely distributed under the GNU General Public License (GPL). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HMM file: /data/patterns/cogs/cogs.hmm Sequence file: NP_061377.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: NP_061377.1 phosphatidylinositol glycan, class B; involved in GPI-anchor biosynthesis [Mus musculus]. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- COG2034 -44.0 84 1 COG0697 -95.9 22 1 COG1296 -153.2 56 1 COG0628 -187.7 77 1 COG1807 -191.8 22 1 COG2244 -214.3 69 1 COG2962 -225.5 35 1 COG1835 -268.1 97 1 COG1005 -309.4 90 1 COG1178 -338.0 87 1 COG1593 -394.0 87 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- COG1296 1/1 74 242 .. 1 257 [] -153.2 56 COG2962 1/1 53 266 .. 1 311 [] -225.5 35 COG1005 1/1 81 342 .. 1 380 [] -309.4 90 COG2034 1/1 264 347 .. 1 108 [] -44.0 84 COG0628 1/1 66 379 .. 1 381 [] -187.7 77 COG1178 1/1 11 401 .. 1 615 [] -338.0 87 COG0697 1/1 97 403 .. 1 321 [] -95.9 22 COG1593 1/1 21 411 .. 1 638 [] -394.0 87 COG2244 1/1 36 472 .. 1 510 [] -214.3 69 COG1835 1/1 33 492 .. 1 589 [] -268.1 97 COG1807 1/1 40 541 .. 1 627 [] -191.8 22 Alignments of top-scoring domains: COG1296: domain 1 of 1, from 74 to 242: score -153.2, E = 56 *->llknkedmnlssaminahespRqItaaFkqGfp.aslPiviGylPwg +++++ ++ m + t + + +++++ P NP_061377. 74 -DEYWQSLEVAHRMVFSYGY---LTWEWTERLRgYTYP--------- 107 lafGvlakqlGlSvlEallMSlliyAGAsQFvAigLlaagasllsiiltT l+f++ k l l ++++ + ++ i l+ + lls++ NP_061377. 108 LIFASIYKVLHLLGKDSVQF----------LIWIPRLG--QALLSAVA-- 143 llvNaRHlLYGlSlrsklsrltlkkrvylaFgLTDEvFAlavssavRrkr ++R LY Sl+ l + + + NP_061377. 144 ---DIR--LY--SLLKQL---------------------------E-NQE 158 vnkgwfmlGveLssylsWvlgtlvGalaGStLpadrPfnqqGLeFvmtAl v+ +++ L s+ +W t +++ +e ++tAl NP_061377. 159 VAQ--WVFLCQLCSWFTWYCCT-----------R---TLTNTMETSLTAL 192 FivLlipnvkkrlsvlvsaltGLvlavlfllLfgsevfilaallamllgl +L+ + + ++ s +L++a+++++ +++l+ ++ l NP_061377. 193 --ALFYYPLEGS-RSVNSIKYSLLVALACVVR--------PTALIPWVPL 231 tllrkkleapa<-* + + +++e + NP_061377. 232 LFRHFYQEQRK 242 COG2962: domain 1 of 1, from 53 to 266: score -225.5, E = 35 *->MfmkmkmkevkkGvllslsAyvlwGllPlYfkLLeplpAleIlaHRv + + ++ l + + ++ ++ Y+ Le +aHR+ NP_061377. 53 VLFTIALRI-----LNCFLVQTSFV-PDEYWQSLE-------VAHRM 86 vWSfvFmllLllflrqGqwsllrellrtlkkpwlalvLllaalL..igGs v+S + l + + lr+ + l a + ++ lL++++ NP_061377. 87 VFSYGY-----LTWE--WTERLRGYTYPLIF---ASIYKVLHLLgkDS-V 125 NWliFIWAvnnGhmLEaSLGYyinPLvnVlLGmvFLkERLsklQwiAVaL ++li I + G L+++++ + ++ L l+ NP_061377. 126 QFLIWI--PRLGQA-----------LLSAVADIRLY-SLLKQLENQE--- 158 AaaGVlhqlwltGSlPWVALvlAlsFgfYgLiRKkmkvdAlaGltlEtll V++ ++l + +W ++ + + ++ ++lt NP_061377. 159 ----VAQWVFLCQLCSWFTWYCCT---------RTLTNTMETSLT----- 190 llPlAliyLLfladtqptSqmalneprlwLLLvaaGlvTalPLlaFaaaA +++L++ +++ ++ + n+ + LL+ +a +v ++L+ + NP_061377. 191 -----ALALFYYPLE---GSRSVNSIKYSLLVALACVVRPTALIPWVP-- 230 krLplsllGfLqYiePtLmfLlAVfllGEqfdseqlvtFafIWlALiifg Ll +++Eq + l++ f+ ++ i f+ NP_061377. 231 --------------------LLFRHFYQEQ-RKLHLTLHHFLPVGFITFS 259 iDglrKHtqrrvrkeg<-* + + + NP_061377. 260 LSLII---------DR 266 COG1005: domain 1 of 1, from 81 to 342: score -309.4, E = 90 *->MnipldapivdllgmsdfglivvlalskllftalKiiiilivlll.i + ++ ++ +++ + + ++ +++++ i +l +l ++ NP_061377. 81 --EVAHRMVFSYGYLTWEWTERLRGYT-YPLIFASIYKVLHLLGKdS 124 vayltwaERKllAriQlRiGPnrVGPrlfG..LLQllADgiKL..lfKEd v +l+w+ R G+ LL ++AD i+L +l K+ NP_061377. 125 VQFLIWIPR-------------------LGqaLLSAVAD-IRLysLLKQ- 153 iiPrgaDkfiFtlAPIiafipallafavIPfgpefvlfdykikPiItdiN + +++ ++F + l+++ + + +l++ NP_061377. 154 LENQEVAQWVFL--------CQLCSW-FTWYCCTRTLTN----------- 183 vGlLlflAlsSLavYGiilAGWASNnKYalLGalRaaAqviSYEVpmgLs + +SL +++ Y+l G+ ++ +i Y L NP_061377. 184 ------TMETSLTALALFY--------YPLEGS--RSVNSIKY---SLLV 214 llgvvmlvGSls......lsdIVeaQsggglstiifvWfiflqPlaFivF +l+ v +l + + + + Q + l + ++P++Fi+F NP_061377. 215 ALACVVRPTALIpwvpllFRHFYQEQRKLHLT------LHHFLPVGFITF 258 lIAmlAEtnRtPFDlpEAEqElVaGYhtEYSGmkFgLFflGEwYiniilv + ++ Ff+ + ++ NP_061377. 259 SLSLIIDR----------------------------IFFGQW---TLVQL 277 Sal..istLFLGGWlGPfplewvapavSwLvvlgplp..GfiWfviKtaf +l+ ++ LG ++G +p + +++++Gf +++ + NP_061377. 278 NFLkfNVLQNLGTFYGSHP-------------WHWYLsqGFPVVL--GTH 312 lififiWlRAtlPRyRyDQlmrlGWKilLPLtLvNlvltAalvllviq<- l f++ + + R+ + l+lt +++llv + NP_061377. 313 LPFFIHGCFLAPRRLHI------------------LLLTVLWTLLVYS 342 * NP_061377. - - COG2034: domain 1 of 1, from 264 to 347: score -44.0, E = 84 *->rEdmmrgesgiLIllGiiLIiiGfflvFlGlllsAeeEdEREYERRR +g + L+ l++++ l lG++ + NP_061377. 264 IDRIFFGQW-TLVQLNFLKFNV---LQNLGTFYGS-------HPWHW 299 ifsqpksdepesnVEaGGVVmIGPIPIVFGssrgmailsvvLA......L +sq+ P V G+ +i + +LA+++ + L NP_061377. 300 YLSQGF-------------------PVVLGTHLPFFIHGCFLAprrlhiL 330 ILMllailLflllsrrv<-* +L +l+ lL++ + NP_061377. 331 LLTVLWTLLVYSMLGHK 347 COG0628: domain 1 of 1, from 66 to 379: score -187.7, E = 77 *->mlmspairrllkpv..vlrllvlllillllllflylfqplllplllA +++++ ++++++ +v + +v++ +l + ++ + +pl++A NP_061377. 66 LVQTSFVPDEYWQSleVAHRMVFSYGYLTWEW-TERLRGYTYPLIFA 111 lvlayllnPvvrwLerklgipRplavllvllllllllallllllvptlvg + ++ L+ lg ++ +l+++ l+ +ll +v + NP_061377. 112 SI--------YKVLHL-LGKD-----SVQFLIWIPRLGQALLSAVADI-- 145 idqlgqlirnnlPqlnnllqqllawlpnigllqlslyasldeliqqlisn + l++l+ ++l+++ ++ l ql + ++ +++l + NP_061377. 146 -R-LYSLL--------KQLENQEVAQWVF-LCQLCSWFTWYCCTRTLTNT 184 rlaailgsilssllnllgrqvknllglivslllvllllfffLldgeklke + +s++ +l++++ + ++ s+ ll++ ++ + l NP_061377. 185 ----METSLTALALFYYP---LEGSRSVNSIKYSLLVALACVVRPTALIP 227 gilsllPsrlyrprvkrilselnaslgnyirGqvlvaliiGvlsgiglll ++ l+ ++y+++ k l + + + + ++ ++lii +++ +l NP_061377. 228 WVPLLFR-HFYQEQRK--LHLTLHHFLPVGFITFSLSLIIDRIFFGQWTL 274 lgvpyalllallagllnlIPyiGaviiwiPaliyalltggglatwggllv ++++ +n++ ++G++ + P+ y+ + NP_061377. 275 VQLN--------FLKFNVLQNLGTFYGSHPWHWYLSQGFP---------- 306 livflviqqlednvLrPklmgkrlgLhPllillsllgGgslfGfvGlilg ++++ +l+ ++ +l +rl++ l++l ll+ s++G + + NP_061377. 307 ---VVLGTHLPFFIHGCFLAPRRLHILLLTVLWTLLV-YSMLGHKEFRFI 352 pPllavlkalldaylrgdiaelifkklaeqlgeees<-* P+l +++++ + l l++++++ s NP_061377. 353 YPVLPFCMVFCGYSL---------AHLKTWRKAALS 379 COG1178: domain 1 of 1, from 11 to 401: score -338.0, E = 87 *->vvaslyvmysaillvlavgalatlatvklvvmggdplriglwlligl ++ l+ +s+++++l +++ + + ++ + ++ ++++g ++ l NP_061377. 11 ASRNLH--GSSGEMKL-RRRKSRQYVSAQEKRSPRRGLLGENTYLVL 54 llaalllllpplvlavlalsafsgglaeflavlsdayllrllgnTLllal +a l +l ++ + +++ +++++ ++ +++ NP_061377. 55 FTIA---------LRILNCFLVQT-SFVPDEYWQSLEVAHRMVFS----- 89 lvTvlslilGlplAyllsrydfPGrrwlrwllaLPiLLviPalvvAfgfi NP_061377. - -------------------------------------------------- - slfGksGwLarllgelfGlssreywlpdiygPlgGiilalvlfnyPlvyl +G+L++ +w+ +++g ++yPl++ NP_061377. 90 -----YGYLTW------------EWTERLRG-----------YTYPLIF- 110 laaaalesidpsleEaArsLGasrwqvFrrVtLPllrPaiaagalLvFly +s + + +LG q++ ++ P l +a++++++ + ly NP_061377. 111 ----------ASIYKVLHLLGKDSVQFLIWI--PRLGQALLSAVADIRLY 148 cls......dFgavliLGGspqytTlttaIyqeilgsqldlatAalLall +l ++ ++++++ L + +++++ t +l + NP_061377. 149 SLLkqlenqEVAQWVFLC--------QLCSWFTWYC-----CTRTLTNTM 185 LLllsllllwvvvkllerfsrgrqkvyssgqswarpiprilllglaalva + l++l+l+ ++ + g +r++ +i +l al++ NP_061377. 186 ETSLTALALF--------YYPL------EG---SRSVNSIKYSLLVALAC 218 llfclllfsvlllgvilplsflllWtvlltsdewsdamlgplfstsfwha ++ ++l+ p++ +++++e+ ++ + NP_061377. 219 VVRPTALI---------PWV---PLLFRHFYQEQR----------KLHLT 246 linsLtlallAalialll..aLllaylvrrsrsrlsrfidrLsmLplAvP l + L ++++++ ++l +++ ++ ++ ++ ++ +++ L++ NP_061377. 247 LHHFLPVGFITFSLSLIIdrIFFGQWTLVQLNFLKFNVLQNLGT------ 290 GvVlalGllllfnnldnhwvdlaameGvkpllvlygtllllVlAyalral + ++ + hw +l++++++++ + l NP_061377. 291 ---------FYGSHPW-HW-------------YLSQGFPVVLGTH----L 313 PfalrsleaalrqidprLeeaArsLGasrwqifrrvtLPLllpgllaAaa Pf + + a r+++ ++++v + Ll NP_061377. 314 PFFIHGCFLAPRRLH---------------ILLLTVLWTLL--------- 339 lvFalsm...kElsATllLgppdftTLttaiynylsggdgryaaAavllv ++sm ++kE+ +++ p+ + + y +++ ++ Aa+ NP_061377. 340 ---VYSMlghKEFRFIYPVLPF---CMVFCGYSLAH--LKTWRKAALS-- 379 asaAlvLvlislllfvllikrygersqgt<-* ++l+s +++ + ++++++ + NP_061377. 380 ------FLLLSNVPL-AFYTGLVHQRGTL 401 COG0697: domain 1 of 1, from 97 to 403: score -95.9, E = 22 *->llgllllllaaliWGssfvliKlaledgnyrifvvppltivflRfli + l ++ li++s++ + l+ +d ++ +++++ l NP_061377. 97 WTERLRGYTYPLIFASIYKVLHLLGKD--------SVQFLIWIPRLG 135 aallLlpllllrrr.lprr.pgkllllglgsnvetlllllglllglflyf all ++ +++ l +++ + +++ ++l+ + + NP_061377. 136 QALLSAVADIRLYSlLKQLeNQEVAQW--------------VFLCQLCSW 171 llffyalqytsasvaalltslaPlftallaflllgerltrlqllglllaf + ++ ++ ++ + lt+la ++ +l +++ + l++l+ ++ NP_061377. 172 FTWYCCTRTLTNTMETSLTALALFYYPLEGSRSVNS-IKYSLLVALACVV 220 lGvvllll................lggllllGillaLlaalswAlytvlg ++l+ + + ++ +++++ +l+ +l+++++ ++ + + +g NP_061377. 221 RPTALIPWvpllfrhfyqeqrklhLTLHHFLPVGFITFSLSLIIDRIFFG 270 krlsarvprptplpltivflqlllgallllplalflggpplssptlpspf ++ + + + l +++lq l + p+++ l++ +++ + +pf NP_061377. 271 QWTLVQLN-----FLKFNVLQNLGTFYGSHPWHWYLSQGFPVVLGTHLPF 315 ielsfwlallylgvlatalgyllwnyalrrlg.askaallsylePvfall ++ +l+ l +l +lw+ ++ + + + + + P+ ++ NP_061377. 316 ---FIHGCFLAPRRLHILLLTVLWTLLVYSMLgHKEFRFIYPVLPFCMVF 362 lgwllLgErpltlaqllGaalilaGillvslrarkrarkaase<-* g+ l + + t++ + +l l+ + l+++ + +r + + NP_061377. 363 CGYSLAHLK--TWRKAALSFLLLSNVPLAFYTGLVHQRGTLDV 403 COG1593: domain 1 of 1, from 21 to 411: score -394.0, E = 87 *->seavlsqkakevleelekeararrllsgkvllvvsvv.alglslfhl + + k+ + + ek + +r ll +++ lv++ + +l f + NP_061377. 21 EMKLRRRKSRQYVSAQEKRSPRRGLLGENTYLVLFTIaLRILNCFLV 67 yt.tfag.vlstlilrsvhvAvflalafllypalrksklkgvplyDwLLa t++++++ ++ l +h +vf + ++ +++ +++ + y +++a NP_061377. 68 QTsFVPDeYWQ--SLEVAHRMVFSYGYLTW--EWTERLRG--YTYPLIFA 111 llalfsafYivlnyleLvlr.sggyttlDlvvmvvavllvleatrralGv + + +l L++ +s+ + + + r+ + NP_061377. 112 SI---------YKVLHLLGKdSVQF--------------LIWIPRLGQAL 138 Plaislglfilygllgadppgvqahhg.ysfr.v.gadrlvtllilaqeg a++ + +++ + + q+++ + +++ + ++ NP_061377. 139 LSAVADIRLYSLLKQLENQEVAQWVFLcQLCSwFtW--------YCCTRT 180 vfGtpdsvsllaIplFiLfGaflnkgGvgkrlidlAkalvGhrrGGlAka + + +sl+a lF NP_061377. 181 LTN-TMETSLTALALF---------------------------------- 195 aVvaSmLfgsiSGSsvAnvvatGsftIPlMkraGYppefAaAveaaAStg Yp +e + S + NP_061377. 196 ---------------------------------YYP------LEGSRSVN 206 GqLiPPsmgaiaFimaenvsIgYvdlfiAgiiPALLyflalmvmvyleAk sI Y+ l++ l+++v+ A NP_061377. 207 -------------------SIKYSLLVA------------LACVVRPTAL 225 knglpgrglkasq.lpllkgtlalkealwlLllpvilIgglfsGgftPte p l + + +++ k l+l l+ +l++ + +l + ++ NP_061377. 226 IPWVP--LLFRHFyQEQRK--LHLT--LHHFLPVGFITFSLSL----IID 265 AAavaaVAivlyalivalvsrrlillfiyrhtltglgklavalvlvkalg +++ +l+ f++ ++ NP_061377. 266 RIFFG-----QWTLVQLN--------FLK---FN---------------- 283 fivvilLlkGlrellkdlleaLeegarttapVaiavAaAgiisgvititg + + l+++ ++ NP_061377. 284 --------------VLQNLGTFYGSHP----------------------- 296 ipltladlllslsggnillllLllimlllLiLGmgmpttaayiIlspila ++ l++ + ++ g + l ++i G+++ + + i+l ++l NP_061377. 297 WHWYLSQGF-PVVLG---------THLPFFIHGCFLAPRRLHILLLTVLW 336 PvavqlllGidPihaalahlfvfyngiigdiTPPVGlalFvaagvAgaDP ++v +lG + + ++ ++ P+++ v +g + NP_061377. 337 TLLVYSMLGHKEFRF----IYPVL---------PFCM---VFCGYS---- 366 mktgieafkkaiapfivp..flfvlspvllfpeisllglvwlpllligta +++ka++ f++ +++ +++ ++l+ +++ + ++ i+ + NP_061377. 367 -LAHLKTWRKAALSFLLLsnVPLAFYTGLVHQRGT-----LDVMNHIQKV 410 i<-* NP_061377. 411 C 411 COG2244: domain 1 of 1, from 36 to 472: score -214.3, E = 69 *->slkrrllkg.sivlsiatliskllgfvvlvllaRllGpegfGlyafa ++kr+ +g + ++ l++ l ++ +l++ + p ++ + NP_061377. 36 QEKRSPRRGlLGENTYLVLFTIALRILNCFLVQTSFVPDEY-----W 77 laflgllviladlGlplalsryvaeyrekgdkerarrllstvlvltills +++ + +++++G +l+ + e r+r +++++++++ NP_061377. 78 QSLEVAHRMVFSYG---YLTWEWTE--------RLR-----GYTYPLIFA 111 vllflilllaapfiaefflnlkdpdlaalirllalalllisiisflrgif + ++ ll+ + f++ p+l ++ + + + l+s+ +l + + NP_061377. 112 SIYKVLHLLGKDSVQ-FLI--WIPRLGQALLSAVADIRLYSLLKQLENQE 158 qgfqrmkylalsqviesilrfllilslvflillvlsvlllgasGaAalaa +++ + + s++ + + ++l + l +l+++++ + G + NP_061377. 159 VAQWVFLCQLCSWFTWYCCTRTLTN-TMETSLTALALFYYPLEG---SRS 204 vigalvvgavlslligliklgrkflkpsr......kalfkrllrfgipll v + ++v++ ++ + +++ ++ +++ ++ + ++ l + +p++ NP_061377. 205 VNSIKYSLLVALACVVRPTALIPWVPLLFrhfyqeQRKLHLTLHHFLPVG 254 lsslagllygyiDrillgafLgAGvastlgdeavGiY..ngaaqplvtv. + +++ +l iDri++g + +++ ++ n + q l+t+ NP_061377. 255 FITFSLSLI--IDRIFFGQW---------TLVQLNFLkfN-VLQNLGTFy 292 ........llilasslstvlfPyisrayeegklkllslflksllrlllil ++++ + l+ +++ ++ +P++ + ++ +l+++++++l++ NP_061377. 293 gshpwhwyLSQGFPVVLGTHLPFFIHGCFLA--PRRLHILLLTVLWTLLV 340 aiPaalglllladplilllfgekylgseaapllillilvfllsilgvpga +++l + +++ ++ + +++ ++ ++ NP_061377. 341 ---------------YSMLGHKEFRF--------IYPVLPFCMVFCGYS- 366 slLqalgktklalyislfgallnlvLnf.llLiprfGieGAAlatvisya a+ kt+ + +++f +l n+ L f +L+++ G NP_061377. 367 ---LAHLKTWRKA-ALSFLLLSNVPLAFyTGLVHQRGT------------ 400 ivtilsiiysrklgglsaklkkilklliaallmalgivvlavllllllil + + +i ++ g+ +a ++++ ++ + +++ v++ l+ NP_061377. 401 LDVMNHIQKVCPRGPDPASASVF-----IMMPCHSTPYYSHVHCPLSMRF 445 laaaglvgalillgalvavglavrdylllrls<-* l+ l+g +++ a +yl + NP_061377. 446 LQCP-----PDLTGKTQYLDEADMFYLNPLRW 472 COG1835: domain 1 of 1, from 33 to 492: score -268.1, E = 97 *->MagvlerspPrPrmtlperrvlslnvavraelkyrpdldGLRAvAvL rsp +r +l e + l+l + + LR++ + NP_061377. 33 VSAQEKRSP--RRGLLGENTYLVLFTIA------------LRILNCF 65 lVVvyHlafawlpggpglgdalaellrfGfiGVDiFFVlSGFLitsillr lV ++ + + + + +++++ G+L t+ + + NP_061377. 66 LVQTSFVPDEYWQSLEVAH---RMVFSY------------GYL-TWEW-T 98 algrggsrfslreFwirRirRilPAlfvvlalvlavvlflfppgdfeslr +++rg + +P f+ + vl ++ ++ + +l NP_061377. 99 ERLRGYT---------------YPLIFASIYKVLHLL----GKDSVQFLI 129 ksllaslfftsNivlarlkgeYFdsasfgeesPYYLFllhlWSLsVEeqF + ++ ++ s ++++rl + + + ++ e++ ++Fl +l S NP_061377. 130 WIPRLGQALLSAVADIRLYS-LLKQLENQEVA-QWVFLCQLCS------- 170 YLafPLLllllarllrrRaRrevlarlalllvllaislapsvlslaidag + + ++++r l+ + l++++l+ + + s+++ + NP_061377. 171 WFTW----YCCTRTLT------NTMETSLTALALFYYPLEGSRSVNSIK- 209 alyqdtayfnlllrapeLlaGallaalvpggrdspnrFRgfflrlpawsr y +l + a+ + al +vp ++ ++ + ++ NP_061377. 210 -------YSLLVALACVVRPTALI-PWVPLLF--RH-------FYQEQRK 242 rlaallalLalailvsclylidgtvptaffpGlvallpvlavallivagl ++l +L++ ++ l li + + f G ++l+ + + ++++ NP_061377. 243 LHLTLHHFLPVGFITFSLSLIIDRI----FFGQWTLVQLNFLKFNVLQN- 287 aldd...dgllkrlLawrplVwlGaiSYsLYLWHwPvlafvrsyvglyel l+ ++++ + L+ +V lG+ H+P ++ ++g + + NP_061377. 288 -LGTfygSHPWHWYLSQGFPVVLGT--------HLP----FF-IHGCFLA 323 sgrdkrelvallavtlvLAalsysli...EkPfRewlrrlrsrlvwilsa ++ ++ l+ t++ + l+ys ++++E +f++ + +++ + NP_061377. 324 PR-----RLHILLLTVLWTLLVYSMLghkEFRFIYPV---LPFCMVFCGY 365 rvvsavvvgvisllgvaalakvpirlergas.aeAaeskhpnqesqckqg +++ ++++ ++l + +l vp+ + g+++++ + + ++ c +g NP_061377. 366 SLAHLKTWRKAALS-FLLLSNVPLAFYTGLVhQRGTLDVMNHIQKVCPRG 414 krAlvdesrcrkanarPtvlsvgkDShAatlkhfldevgteskinvtvls + ++a +v + h+ + ++ +++ + NP_061377. 415 P-----------DPASASVFIMM-PCHSTPYYSHVHCPLSMRFLQCPPDL 452 vsgcrpipgvdskdt..qlwaaaeClaeveavsdsvvndasihalliwsr ++ ++ +d + +++++w+ +e +as ++ l+ + NP_061377. 453 TGKTQYLDEADMFYLnpLRWLQQEFHS-----------NASLPTHLVTFN 491 a<-* + NP_061377. 492 V 492 COG1807: domain 1 of 1, from 40 to 541: score -191.8, E = 22 *->mkmkkkrlllvllllllyalllsinllwledttrarY...aevakeM + ++ + l+l+ al +++ +l + ++++ Y +++eva M NP_061377. 40 SPRRGLLGENTYLVLFTIALRILNCFLVQTSFVPDEYwqsLEVAHRM 86 lasgdakfwisPhylglvyfeGKPPllyWlqsisyllFG....Svnefgv + s w + +l ++++ l + ++ ++l+G+++ +++ NP_061377. 87 VFSYGYLTWEWTERLRGYTYP----LIFASIYKVLHLLGkdsvQFLIWIP 132 RlpsvLagvltalLvYlLakrlfgdkrkALlAslililfpiffansrlan Rl ++L+++ + + +Y+L k l + +++A +l +++ +++ ++ NP_061377. 133 RLGQALLSAVADIRLYSLLKQLEN-QEVAQWVFLCQLCSWFTWYCCTRTL 181 iDslLvFfltLalylfylalergkrarlrwfyLaflalGLafLtKGplaf + + + ++ al lfy l +g+ r++ + l+++La + + p a+ NP_061377. 182 TNTMET--SLTALALFYYPL-EGS--RSVNSIKYSLLVALACVVR-PTAL 225 i..lpvliPlllwlilqrrwkklkrisyilgvlLflLtslpWyvpVDiaS i+ +p+l+ +++ ++ + l +++ + + ++ +sl+ NP_061377. 226 IpwVPLLF-RHFYQEQRKLHLTLH--HFLPVGFITFSLSLIID------- 265 llylasSqtNSVLElhlkypgflrfFlieehfrrfatskaqheppsyfdi + + q l +fl+f + + ++ + p+ ++ NP_061377. 266 RIFFG--QW------TLVQLNFLKFNVLQNLGTFYGS------HPWHWYL 301 halpig...................Ng.qAaqPNglsalGGyllpwlglL + + +++ + ++ +++ + +l+ +l w++l+ NP_061377. 302 SQGFPVvlgthlpffihgcflaprrLHiL-----LLT-----VL-WTLLV 340 pgGnGGPGGGGKswvaafgtgrpgwlrrKrselsfllpWlllplllFsil + +++g ++++r ++ p l+F ++ NP_061377. 341 Y--------------SMLG------HKEFR---------FIYPVLPFCMV 361 ggkipvYIlpalllvalkearflvalLlpvagffalagfghllyllllgn + ++ ++a++++ + + a++f+l+ + l++++ l+ NP_061377. 362 FCGY---------SLAHLKTWR------KAALSFLLLSNVPLAFYTGLVH 396 llallvlfgwvalillltqeiewellLlpwavliTavFevvivsayallp +l + + ++ + + ++ + +++ + + + + NP_061377. 397 QRGTLDVMNHIQKVCPRGPDPASASVFIM-----------MPCHSTPYYS 435 glawsallkvwlvgllltlvlllfssrsmpyrndvveesgeallvepvle + + l +++l l++ +++ + ++++ l+ NP_061377. 436 HVHCP------LSMRFLQCPPDLTG-KTQYL-------DEADMFYLNPLR 471 prtpllyvnnnsLpEGPQLsSaGgMvaalydavLyRrdvglkekkgklyl ++++++ n sLp + + + + ++ NP_061377. 472 WLQQEFH-SNASLP-------------THLVTFNVLE--------KEINT 499 avvlkddprrpvrikekeayllekrfsgrdPilTivklkllikrgktlky +++ + ++ + ++ +++r+ g+ ++ +r ++++ NP_061377. 500 FLTSGNY--ER--AATFFHTHWPERRTGS-------HIHVYERRLPGRVN 538 fLassparg<-* + +g NP_061377. 539 T------GG 541 // hmmpfam - search a single seq against HMM database HMMER 2.1.1 (Dec 1998) Copyright (C) 1992-1998 Washington University School of Medicine HMMER is freely distributed under the GNU General Public License (GPL). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HMM file: /data/patterns/cogs/cogs.hmm-f Sequence file: NP_061377.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: NP_061377.1 phosphatidylinositol glycan, class B; involved in GPI-anchor biosynthesis [Mus musculus]. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- COG0362 -0.5 24 1 COG0087 -0.7 68 1 COG0004 -1.0 80 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- COG0087 1/1 35 47 .. 1 12 [. -0.7 68 COG0004 1/1 330 346 .. 161 177 .. -1.0 80 COG0362 1/1 506 526 .. 458 485 .] -0.5 24 Alignments of top-scoring domains: COG0087: domain 1 of 1, from 35 to 47: score -0.7, E = 68 *->arkhR.PRrGSla<-* a+ +R+PRrG l+ NP_061377. 35 AQEKRsPRRGLLG 47 COG0004: domain 1 of 1, from 330 to 346: score -1.0, E = 80 *->LlFsvLwttlvYpPvAH<-* Ll +vLwt lvY+ +H NP_061377. 330 LLLTVLWTLLVYSMLGH 346 COG0362: domain 1 of 1, from 506 to 526: score -0.5, E = 24 *->YERtDkeGsPRGEfFHTnWtgtggntas<-* YER fFHT W +++++ NP_061377. 506 YERAAT-------FFHTHWPERRTGSHI 526 //