analysis of sequence from tem17 ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ >gi|9857404|gb|AAG00869.1|AF279144_1 tumor endothelial marker 7 precursor [Homo sapiens] MRGELWLLVLVLREAARALSPQPGAGHDEGPGSGWAAKGTVRGWNRRARESPGHVSEPDRTQLSQDLGGG TLAMDTLPDNRTRVVEDNHSYYVSRLYGPSEPHSRELWVDVAEANRSQVKIHTILSNTHRQASRVVLSFD FPFYGHPLRQITIATGGFIFMGDVIHRMLTATQYVAPLMANFNPGYSDNSTVVYFDNGTVFVVQWDHVYL QGWEDKGSFTFQAALHHDGRIVFAYKEIPMSVPEISSSQHPVKTGLSDAFMILNPSPDVPESRRRSIFEY HRIELDPSKVTSMSAVEFTPLPTCLQHRSCDACMSSDLTFNCSWCHVLQRCSSGFDRYRQEWDGTMGCAQ EAEGQDVRGLPGMRTTTSASPDTSFSPYDGDLTTTSSSLFIDSLTTEDDTKLNPYAGGDGLQNNLSPKTK GTPVHLGTIVGIVLAVLLVAAIILAGIYINGHPTSNAALFFIERRPHHWPAMKFRSHPDHSTYAEVEPSG HEKEGFMEAEQC ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ sec.str. with predator > gi|9857404|gb|AAG00869.1|AF279144_1 . . . . . 1 MRGELWLLVLVLREAARALSPQPGAGHDEGPGSGWAAKGTVRGWNRRARE 50 ___HHHHHHHHHHHHHHH________________________________ . . . . . 51 SPGHVSEPDRTQLSQDLGGGTLAMDTLPDNRTRVVEDNHSYYVSRLYGPS 100 __________EEEEE______EEEE_____EEEEE_____EEEEE_____ . . . . . 101 EPHSRELWVDVAEANRSQVKIHTILSNTHRQASRVVLSFDFPFYGHPLRQ 150 ____HHHHHHHHHH______EEEEE_________EEEE_________EEE . . . . . 151 ITIATGGFIFMGDVIHRMLTATQYVAPLMANFNPGYSDNSTVVYFDNGTV 200 EEEE_________HHHHHHHHHHEEEE_____________EEEEE____E . . . . . 201 FVVQWDHVYLQGWEDKGSFTFQAALHHDGRIVFAYKEIPMSVPEISSSQH 250 EEEE____EEE_________EEEEE____EEEEEEE______________ . . . . . 251 PVKTGLSDAFMILNPSPDVPESRRRSIFEYHRIELDPSKVTSMSAVEFTP 300 ________EEEEE_________HHHHHHHHH________EEEEEEEEE__ . . . . . 301 LPTCLQHRSCDACMSSDLTFNCSWCHVLQRCSSGFDRYRQEWDGTMGCAQ 350 _______________________EEEEEE______HHHHHH______HHH . . . . . 351 EAEGQDVRGLPGMRTTTSASPDTSFSPYDGDLTTTSSSLFIDSLTTEDDT 400 HHH__________EEE_____________________EEEEE________ . . . . . 401 KLNPYAGGDGLQNNLSPKTKGTPVHLGTIVGIVLAVLLVAAIILAGIYIN 450 __________________________HHHHHHHHHHHHHHHHHHHHEEE_ . . . . . 451 GHPTSNAALFFIERRPHHWPAMKFRSHPDHSTYAEVEPSGHEKEGFMEAE 500 _____HHHHHHHH____________________EEE______________ 501 QC 502 __ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ method : 1 alpha-contents : 7.1 % beta-contents : 28.1 % coil-contents : 64.9 % class : beta method : 2 alpha-contents : 10.1 % beta-contents : 21.5 % coil-contents : 68.3 % class : beta ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ GPI: learning from metazoa -27.82 -2.64 -3.62 -1.48 -4.00 0.00 0.00 0.00 -0.59 -7.78 -2.08 -12.00 -12.00 0.00 -12.00 0.00 -86.00 -20.22 -7.71 -3.44 -0.55 -4.00 0.00 -4.00 0.00 0.00 -7.33 -2.08 -12.00 -12.00 0.00 -12.00 0.00 -85.33 ID: gi|9857404|gb|AAG00869.1|AF279144_1 AC: xxx Len: 490 1:I 474 Sc: -85.33 Pv: 8.734346e-01 NO_GPI_SITE GPI: learning from protozoa -16.33 -4.02 -0.64 -1.20 -4.00 0.00 -32.00 0.00 0.00 -6.32 -7.89 -12.00 -12.00 0.00 0.00 0.00 -96.41 -8.61 -0.99 -1.38 -1.32 -4.00 0.00 -24.00 0.00 0.00 -6.32 -7.89 -12.00 0.00 0.00 -12.00 0.00 -78.50 ID: gi|9857404|gb|AAG00869.1|AF279144_1 AC: xxx Len: 490 1:I 479 Sc: -78.50 Pv: 4.822081e-01 NO_GPI_SITE ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ # SignalP euk predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? gi|9857404| 0.663 442 Y 0.627 446 Y 0.977 435 Y 0.140 N # SignalP gram- predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? gi|9857404| 0.382 458 N 0.404 458 Y 0.982 437 Y 0.155 N # SignalP gram+ predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? gi|9857404| 0.804 28 Y 0.391 458 Y 0.982 436 Y 0.189 N ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ low complexity regions: SEG 12 2.2 2.5 >gi|9857404|gb|AAG00869.1|AF279144_1 tumor endothelial marker 7 precursor [Homo sapiens] 1-3 MRG elwllvlvlreaaral 4-19 20-428 SPQPGAGHDEGPGSGWAAKGTVRGWNRRAR ESPGHVSEPDRTQLSQDLGGGTLAMDTLPD NRTRVVEDNHSYYVSRLYGPSEPHSRELWV DVAEANRSQVKIHTILSNTHRQASRVVLSF DFPFYGHPLRQITIATGGFIFMGDVIHRML TATQYVAPLMANFNPGYSDNSTVVYFDNGT VFVVQWDHVYLQGWEDKGSFTFQAALHHDG RIVFAYKEIPMSVPEISSSQHPVKTGLSDA FMILNPSPDVPESRRRSIFEYHRIELDPSK VTSMSAVEFTPLPTCLQHRSCDACMSSDLT FNCSWCHVLQRCSSGFDRYRQEWDGTMGCA QEAEGQDVRGLPGMRTTTSASPDTSFSPYD GDLTTTSSSLFIDSLTTEDDTKLNPYAGGD GLQNNLSPKTKGTPVHLGT ivgivlavllvaaiilagi 429-447 448-502 YINGHPTSNAALFFIERRPHHWPAMKFRSH PDHSTYAEVEPSGHEKEGFMEAEQC low complexity regions: SEG 25 3.0 3.3 >gi|9857404|gb|AAG00869.1|AF279144_1 tumor endothelial marker 7 precursor [Homo sapiens] 1-364 MRGELWLLVLVLREAARALSPQPGAGHDEG PGSGWAAKGTVRGWNRRARESPGHVSEPDR TQLSQDLGGGTLAMDTLPDNRTRVVEDNHS YYVSRLYGPSEPHSRELWVDVAEANRSQVK IHTILSNTHRQASRVVLSFDFPFYGHPLRQ ITIATGGFIFMGDVIHRMLTATQYVAPLMA NFNPGYSDNSTVVYFDNGTVFVVQWDHVYL QGWEDKGSFTFQAALHHDGRIVFAYKEIPM SVPEISSSQHPVKTGLSDAFMILNPSPDVP ESRRRSIFEYHRIELDPSKVTSMSAVEFTP LPTCLQHRSCDACMSSDLTFNCSWCHVLQR CSSGFDRYRQEWDGTMGCAQEAEGQDVRGL PGMR tttsaspdtsfspydgdltttssslfidsl 365-400 tteddt 401-428 KLNPYAGGDGLQNNLSPKTKGTPVHLGT ivgivlavllvaaiilagi 429-447 448-502 YINGHPTSNAALFFIERRPHHWPAMKFRSH PDHSTYAEVEPSGHEKEGFMEAEQC low complexity regions: SEG 45 3.4 3.75 >gi|9857404|gb|AAG00869.1|AF279144_1 tumor endothelial marker 7 precursor [Homo sapiens] 1-358 MRGELWLLVLVLREAARALSPQPGAGHDEG PGSGWAAKGTVRGWNRRARESPGHVSEPDR TQLSQDLGGGTLAMDTLPDNRTRVVEDNHS YYVSRLYGPSEPHSRELWVDVAEANRSQVK IHTILSNTHRQASRVVLSFDFPFYGHPLRQ ITIATGGFIFMGDVIHRMLTATQYVAPLMA NFNPGYSDNSTVVYFDNGTVFVVQWDHVYL QGWEDKGSFTFQAALHHDGRIVFAYKEIPM SVPEISSSQHPVKTGLSDAFMILNPSPDVP ESRRRSIFEYHRIELDPSKVTSMSAVEFTP LPTCLQHRSCDACMSSDLTFNCSWCHVLQR CSSGFDRYRQEWDGTMGCAQEAEGQDVR glpgmrtttsaspdtsfspydgdltttsss 359-459 lfidsltteddtklnpyaggdglqnnlspk tkgtpvhlgtivgivlavllvaaiilagiy inghptsnaal 460-502 FFIERRPHHWPAMKFRSHPDHSTYAEVEPS GHEKEGFMEAEQC 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 >gi|9857404|gb|AAG00869.1|AF279144_1 tumor endothelial marker 7 precursor [Homo sapiens] MRGELWLLVLVLREAARALSPQPGAGHDEGPGSGWAAKGTVRGWNRRARESPGHVSEPDR TQLSQDLGGGTLAMDTLPDNRTRVVEDNHSYYVSRLYGPSEPHSRELWVDVAEANRSQVK IHTILSNTHRQASRVVLSFDFPFYGHPLRQITIATGGFIFMGDVIHRMLTATQYVAPLMA NFNPGYSDNSTVVYFDNGTVFVVQWDHVYLQGWEDKGSFTFQAALHHDGRIVFAYKEIPM SVPEISSSQHPVKTGLSDAFMILNPSPDVPESRRRSIFEYHRIELDPSKVTSMSAVEFTP LPTCLQHRSCDACMSSDLTFNCSWCHVLQRCSSGFDRYRQEWDGTMGCAQEAEGQDVRGL PGMRTTTSASPDTSFSPYDGDLTTTSSSLFIDSLTTEDDTKLNPYAGGDGLQNNLSPKTK GTPVHlgtivgivlavllvaaiilagiYINGHPTSNAALFFIERRPHHWPAMKFRSHPDH STYAEVEPSGHEKEGFMEAEQC 1 - 425 MRGELWLLVL VLREAARALS PQPGAGHDEG PGSGWAAKGT VRGWNRRARE SPGHVSEPDR TQLSQDLGGG TLAMDTLPDN RTRVVEDNHS YYVSRLYGPS EPHSRELWVD VAEANRSQVK IHTILSNTHR QASRVVLSFD FPFYGHPLRQ ITIATGGFIF MGDVIHRMLT ATQYVAPLMA NFNPGYSDNS TVVYFDNGTV FVVQWDHVYL QGWEDKGSFT FQAALHHDGR IVFAYKEIPM SVPEISSSQH PVKTGLSDAF MILNPSPDVP ESRRRSIFEY HRIELDPSKV TSMSAVEFTP LPTCLQHRSC DACMSSDLTF NCSWCHVLQR CSSGFDRYRQ EWDGTMGCAQ EAEGQDVRGL PGMRTTTSAS PDTSFSPYDG DLTTTSSSLF IDSLTTEDDT KLNPYAGGDG LQNNLSPKTK GTPVH 426 - 447 lgtiv givlavllva aiilagi 448 - 502 YIN GHPTSNAALF FIERRPHHWP AMKFRSHPDH STYAEVEPSG HEKEGFMEAE QC low complexity regions: DUST >gi|9857404|gb|AAG00869.1|AF279144_1 tumor endothelial marker 7 precursor [Homo sapiens] MRGELWLLVLVLREAARALSPQPGAGHDEGPGSGWAAKGTVRGWNRRARESPGHVSEPDR TQLSQDLGGGTLAMDTLPDNRTRVVEDNHSYYVSRLYGPSEPHSRELWVDVAEANRSQVK IHTILSNTHRQASRVVLSFDFPFYGHPLRQITIATGGFIFMGDVIHRMLTATQYVAPLMA NFNPGYSDNSTVVYFDNGTVFVVQWDHVYLQGWEDKGSFTFQAALHHDGRIVFAYKEIPM SVPEISSSQHPVKTGLSDAFMILNPSPDVPESRRRSIFEYHRIELDPSKVTSMSAVEFTP LPTCLQHRSCDACMSSDLTFNCSWCHVLQRCSSGFDRYRQEWDGTMGCAQEAEGQDVRGL PGMRTTTSASPDTSFSPYDGDLTTTSSSLFIDSLTTEDDTKLNPYAGGDGLQNNLSPKTK GTPVHLGTIVGIVLAVLLVAAIILAGIYINGHPTSNAALFFIERRPHHWPAMKFRSHPDH STYAEVEPSGHEKEGFMEAEQC ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ coiled coil prediction for gi|9857404|gb|AAG00869.1|AF279144_1 sequence: 490 amino acids, 0 residue(s) in coiled coil state . | . | . | . | . | . 60 MRGELWLLVL VLREAARALS PQPGAGHDEG PGSGWAAKGT VRGWNRRARE SPGHVSEPDR ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 TQLSQDLGGG TLAMDTLPDN RTRVVEDNHS YYVSRLYGPS EPHSRELWVD VAEANRSQVK ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 IHTILSNTHR QASRVVLSFD FPFYGHPLRQ ITIATGGFIF MGDVIHRMLT ATQYVAPLMA ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 NFNPGYSDNS TVVYFDNGTV FVVQWDHVYL QGWEDKGSFT FQAALHHDGR IVFAYKEIPM ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 SVPEISSSQH PVKTGLSDAF MILNPSPDVP ESRRRSIFEY HRIELDPSKV TSMSAVEFTP ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 LPTCLQHRSC DACMSSDLTF NCSWCHVLQR CSSGFDRYRQ EWDGTMGCAQ EAEGQDVRGL ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 PGMRTTTSAS PDTSFSPYDG DLTTTSSSLF IDSLTTEDDT KLNPYAGGDG LQNNLSPKTK ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 GTPVHLGTIV GIVLAVLLVA AIILAGIYIN GHPTSNAALF FIERRPHHWP AMKFRSHPDH ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 . | STYAEVEPSG ~~~~~~~~~~ ---------- ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ prediction of transmembrane regions with toppred2 *********************************** *TOPPREDM with eukaryotic function* *********************************** tem7.___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: tem7.___inter___ (1 sequences) MRGELWLLVLVLREAARALSPQPGAGHDEGPGSGWAAKGTVRGWNRRARE SPGHVSEPDRTQLSQDLGGGTLAMDTLPDNRTRVVEDNHSYYVSRLYGPS EPHSRELWVDVAEANRSQVKIHTILSNTHRQASRVVLSFDFPFYGHPLRQ ITIATGGFIFMGDVIHRMLTATQYVAPLMANFNPGYSDNSTVVYFDNGTV FVVQWDHVYLQGWEDKGSFTFQAALHHDGRIVFAYKEIPMSVPEISSSQH PVKTGLSDAFMILNPSPDVPESRRRSIFEYHRIELDPSKVTSMSAVEFTP LPTCLQHRSCDACMSSDLTFNCSWCHVLQRCSSGFDRYRQEWDGTMGCAQ EAEGQDVRGLPGMRTTTSASPDTSFSPYDGDLTTTSSSLFIDSLTTEDDT KLNPYAGGDGLQNNLSPKTKGTPVHLGTIVGIVLAVLLVAAIILAGIYIN GHPTSNAALFFIERRPHHWPAMKFRSHPDHSTYAEVEPSGHEKEGFMEAE QC (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 2 structures are to be tested Candidate membrane-spanning segments: Helix Begin End Score Certainity 1 146 166 0.741 Putative 2 427 447 2.374 Certain ---------------------------------------------------------------------- Structure 1 Transmembrane segments included in this structure: Segment 1 2 Loop length 145 260 55 K+R profile + 5.00 + CYT-EXT prof 0.95 - 0.73 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 5.00 Tm probability: 0.35 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 1.00 (NEG-POS)/(NEG+POS): -0.0286 NEG: 17.0000 POS: 18.0000 -> Orientation: N-in CYT-EXT difference: 0.22 -> Orientation: N-out ---------------------------------------------------------------------- Structure 2 Transmembrane segments included in this structure: Segment 2 Loop length 426 55 K+R profile + 5.00 CYT-EXT prof 0.93 - For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: -5.00 Tm probability: 1.00 -> Orientation: N-out Charge-difference over N-terminal Tm (+-15 residues): 2.00 (NEG-POS)/(NEG+POS): 0.1395 NEG: 49.0000 POS: 37.0000 -> Orientation: N-in CYT-EXT difference: 0.93 -> Orientation: N-out ---------------------------------------------------------------------- "tem7" 502 146 166 #f 0.740625 427 447 #t 2.37396 ************************************ *TOPPREDM with prokaryotic function* ************************************ tem7.___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: tem7.___inter___ (1 sequences) MRGELWLLVLVLREAARALSPQPGAGHDEGPGSGWAAKGTVRGWNRRARE SPGHVSEPDRTQLSQDLGGGTLAMDTLPDNRTRVVEDNHSYYVSRLYGPS EPHSRELWVDVAEANRSQVKIHTILSNTHRQASRVVLSFDFPFYGHPLRQ ITIATGGFIFMGDVIHRMLTATQYVAPLMANFNPGYSDNSTVVYFDNGTV FVVQWDHVYLQGWEDKGSFTFQAALHHDGRIVFAYKEIPMSVPEISSSQH PVKTGLSDAFMILNPSPDVPESRRRSIFEYHRIELDPSKVTSMSAVEFTP LPTCLQHRSCDACMSSDLTFNCSWCHVLQRCSSGFDRYRQEWDGTMGCAQ EAEGQDVRGLPGMRTTTSASPDTSFSPYDGDLTTTSSSLFIDSLTTEDDT KLNPYAGGDGLQNNLSPKTKGTPVHLGTIVGIVLAVLLVAAIILAGIYIN GHPTSNAALFFIERRPHHWPAMKFRSHPDHSTYAEVEPSGHEKEGFMEAE QC (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 2 structures are to be tested Candidate membrane-spanning segments: Helix Begin End Score Certainity 1 146 166 0.741 Putative 2 427 447 2.374 Certain ---------------------------------------------------------------------- Structure 1 Transmembrane segments included in this structure: Segment 1 2 Loop length 145 260 55 K+R profile + 5.00 + CYT-EXT prof 0.95 - 0.73 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 5.00 Tm probability: 0.35 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 1.00 (NEG-POS)/(NEG+POS): -0.0286 NEG: 17.0000 POS: 18.0000 -> Orientation: N-in CYT-EXT difference: 0.22 -> Orientation: N-out ---------------------------------------------------------------------- Structure 2 Transmembrane segments included in this structure: Segment 2 Loop length 426 55 K+R profile + 5.00 CYT-EXT prof 0.93 - For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: -5.00 Tm probability: 1.00 -> Orientation: N-out Charge-difference over N-terminal Tm (+-15 residues): 2.00 (NEG-POS)/(NEG+POS): 0.1395 NEG: 49.0000 POS: 37.0000 -> Orientation: N-in CYT-EXT difference: 0.93 -> Orientation: N-out ---------------------------------------------------------------------- "tem7" 502 146 166 #f 0.740625 427 447 #t 2.37396 ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ NOW EXECUTING: /bio_software/1D/stat/saps/saps-stroh/SAPS.SSPA/saps /people/maria/tem7.___saps___ SAPS. Version of April 11, 1996. Date run: Thu Oct 12 13:37:47 2000 File: /people/maria/tem7.___saps___ ID gi|9857404|gb|AAG00869.1|AF279144_1 DE tumor endothelial marker 7 precursor [Homo sapiens] number of residues: 502; molecular weight: 55.6 kdal 1 MRGELWLLVL VLREAARALS PQPGAGHDEG PGSGWAAKGT VRGWNRRARE SPGHVSEPDR 61 TQLSQDLGGG TLAMDTLPDN RTRVVEDNHS YYVSRLYGPS EPHSRELWVD VAEANRSQVK 121 IHTILSNTHR QASRVVLSFD FPFYGHPLRQ ITIATGGFIF MGDVIHRMLT ATQYVAPLMA 181 NFNPGYSDNS TVVYFDNGTV FVVQWDHVYL QGWEDKGSFT FQAALHHDGR IVFAYKEIPM 241 SVPEISSSQH PVKTGLSDAF MILNPSPDVP ESRRRSIFEY HRIELDPSKV TSMSAVEFTP 301 LPTCLQHRSC DACMSSDLTF NCSWCHVLQR CSSGFDRYRQ EWDGTMGCAQ EAEGQDVRGL 361 PGMRTTTSAS PDTSFSPYDG DLTTTSSSLF IDSLTTEDDT KLNPYAGGDG LQNNLSPKTK 421 GTPVHLGTIV GIVLAVLLVA AIILAGIYIN GHPTSNAALF FIERRPHHWP AMKFRSHPDH 481 STYAEVEPSG HEKEGFMEAE QC -------------------------------------------------------------------------------- COMPOSITIONAL ANALYSIS (extremes relative to: swp23s) A : 34( 6.8%); C : 8( 1.6%); D : 30( 6.0%); E : 27( 5.4%); F : 22( 4.4%) G : 40( 8.0%); H+ : 22( 4.4%); I : 20( 4.0%); K : 11( 2.2%); L : 39( 7.8%) M : 13( 2.6%); N : 16( 3.2%); P : 32( 6.4%); Q : 18( 3.6%); R : 31( 6.2%) S : 46( 9.2%); T : 35( 7.0%); V : 34( 6.8%); W : 9( 1.8%); Y : 15( 3.0%) KR : 42 ( 8.4%); ED : 57 ( 11.4%); AGP : 106 ( 21.1%); KRED : 99 ( 19.7%); KR-ED : -15 ( -3.0%); FIKMNY : 97 ( 19.3%); LVIFM : 128 ( 25.5%); ST : 81 ( 16.1%). -------------------------------------------------------------------------------- CHARGE DISTRIBUTIONAL ANALYSIS 1 0+0-000000 00+-00+000 0000000--0 0000000+00 0+000++0+- 000000-0-+ 61 00000-0000 0000-000-0 +0+00--000 0000+00000 -000+-000- 00-00+000+ 121 000000000+ 000+00000- 00000000+0 0000000000 00-000+000 0000000000 181 0000000-00 00000-0000 00000-0000 000--+0000 0000000-0+ 00000+-000 241 000-000000 00+0000-00 0000000-00 -0+++000-0 0+0-0-00+0 000000-000 301 0000000+00 -00000-000 000000000+ 00000-+0+0 -0-0000000 -0-00-0+00 361 000+000000 0-000000-0 -000000000 0-0000---0 +0000000-0 0000000+0+ 421 0000000000 0000000000 0000000000 0000000000 00-++00000 00+0+000-0 481 0000-0-000 0-+-000-0- 00 A. CHARGE CLUSTERS. Positive charge clusters (cmin = 8/30 or 11/45 or 13/60): none Negative charge clusters (cmin = 10/30 or 13/45 or 16/60): none Mixed charge clusters (cmin = 14/30 or 19/45 or 24/60): 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. ________________________________ High scoring uncharged segments: score= 1.00 frequency= 0.803 ( LAGSVTIPNFQYHMCW ) score= 0.00 frequency= 0.000 ( BZX ) score= -8.00 frequency= 0.197 ( KEDR ) Expected score/letter: -0.775 M_0.01= 50.04; M_0.05= 40.22 1) From 421 to 462: length= 42, score=42.00 * 421 GTPVHLGTIV GIVLAVLLVA AIILAGIYIN GHPTSNAALF FI L: 6(14.3%); A: 6(14.3%); G: 5(11.9%); V: 5(11.9%); I: 7(16.7%); C. CHARGE RUNS AND PATTERNS. pattern (+)| (-)| (*)| (0)| (+0)| (-0)| (*0)|(+00)|(-00)|(*00)| (H.)|(H..)| lmin0 4 | 5 | 7 | 42 | 9 | 10 | 12 | 11 | 12 | 15 | 8 | 10 | lmin1 6 | 6 | 8 | 51 | 11 | 12 | 15 | 13 | 14 | 18 | 9 | 12 | lmin2 7 | 7 | 9 | 56 | 12 | 13 | 17 | 15 | 16 | 20 | 11 | 14 | (Significance level: 0.010000; Minimal displayed length: 6) (0) 42(0,0,0); at 421- 462: GTPVHLGTIVGIVLAVLLVAAIILAGIYINGHPTSNAALFFI (4. quartile) 000000000000000000000000000000000000000000 L: 6 (14.3%); A: 6 (14.3%); G: 5 (11.9%); V: 5 (11.9%); I: 7 (16.7%); LVIFM: 20 (47.6%); Run count statistics: + runs >= 3: 1, at 273; - runs >= 3: 1, at 397; * runs >= 4: 0 0 runs >= 28: 1, at 421; ------------ -------------------------------------------------------------------- DISTRIBUTION OF OTHER AMINO ACID TYPES 1. HIGH SCORING SEGMENTS. __________________________________ High scoring hydrophobic segments: 2.00 (LVIFM) 1.00 (AGYCW) 0.00 (BZX) -2.00 (PH) -4.00 (STNQ) -8.00 (KEDR) Expected score/letter: -1.988 M_0.01= 23.24; M_0.05= 19.29 1) From 429 to 449: length= 21, score=35.00 ** 429 IVGIVLAVLL VAAIILAGIY I L: 4(19.0%); A: 4(19.0%); V: 4(19.0%); I: 6(28.6%); ____________________________________ High scoring transmembrane segments: 5.00 (LVIF) 2.00 (AGM) 0.00 (BZX) -1.00 (YCW) -2.00 (ST) -6.00 (P) -8.00 (H) -10.00 (NQ) -16.00 (KR) -17.00 (ED) Expected score/letter: -3.574 M_0.01= 55.42; M_0.05= 45.67; M_0.30= 34.07 1) From 426 to 449: length= 24, score=86.00 ** 426 LGTIVGIVLA VLLVAAIILA GIYI L: 5(20.8%); A: 4(16.7%); G: 3(12.5%); V: 4(16.7%); I: 6(25.0%); 2. SPACINGS OF C. H2N-303-C-5-C-2-C-8-C-2-C-5-C-16-C-153-C-0-COOH 2*. SPACINGS OF C and H. (additional deluxe function for ALEX) H2N-26-H-26-H-34-H-13-H-18-H-6-H-16-H-19-H-40-H-18-H-H-22-H-30-H-22-C-2-H-2-C-2-C-8-C-2-C-H-4-C-16-C-76-H-26-H-14-H-H-8-H-2-H-10-H-10-C-0-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: 31 (Expected range: 12-- 44) 2. Histogram of spacings between consecutive amino acid multiplets: (1-5) 9 (6-10) 7 (11-20) 8 (>=21) 8 3. Clusters of amino acid multiplets (cmin = 11/30 or 14/45 or 17/60): none B. CHARGE ALPHABET. 1. Total number of charge multiplets: 7 (Expected range: 0-- 18) 3 +plets (f+: 8.4%), 4 -plets (f-: 11.4%) Total number of charge altplets: 9 (Critical number: 21) 2. Histogram of spacings between consecutive charge multiplets: (1-5) 0 (6-10) 0 (11-20) 1 (>=21) 7 -------------------------------------------------------------------------------- PERIODICITY ANALYSIS. A. AMINO ACID ALPHABET (core: 4; !-core: 5) Location Period Element Copies Core Errors 304- 339 9 C........ 4 4 0 430- 441 3 V.. 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 7- 12 1 i 6 6 0 261- 308 8 i..0..0. 6 6 /0/././1/././2/./ 424- 453 5 i00.. 6 6 /0/1/2/././ -------------------------------------------------------------------------------- SPACING ANALYSIS. Location (Quartile) Spacing Rank P-value Interpretation 0- 304 (2.) C( 304)C 1 of 9 0.0048 large 1. maximal spacing 348- 502 (4.) C( 154)C 2 of 9 0.0164 large 2. maximal spacing 420- 463 (4.) *( 43)* 1 of 100 0.0049 large maximal spacing ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ 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: tem7 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: gi|9857404|gb|AAG00869.1|AF279144_1 tumor endothelial marker 7 precursor [Homo sapiens] Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- Plexin_repeat Plexin repeat 20.0 0.021 1 ART NAD:arginine ADP-ribosyltransferase 0.1 42 1 Peptidase_M45 D-ala-D-ala dipeptidase -0.6 1e+02 1 Syndecan Syndecan domain -2.0 51 1 Zn_clus Fungal Zn(2)-Cys(6) binuclear cluster d -16.6 90 1 Como_SCP Small coat protein -121.5 86 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- ART 1/1 1 20 [. 1 22 [. 0.1 42 Syndecan 1/1 2 23 .. 1 22 [. -2.0 51 Como_SCP 1/1 11 153 .. 1 178 [] -121.5 86 Zn_clus 1/1 308 339 .. 1 43 [] -16.6 90 Peptidase_M45 1/1 332 342 .. 183 193 .. -0.6 1e+02 Plexin_repeat 1/1 303 349 .. 1 67 [] 20.0 0.021 Alignments of top-scoring domains: ART: domain 1 of 1, from 1 to 20: score 0.1, E = 42 *->mpalhfvLllSVglllstqals<-* m +++L+l +l+++ +als gi|9857404 1 MRGELWLLVL--VLREAARALS 20 Syndecan: domain 1 of 1, from 2 to 23: score -2.0, E = 51 *->rkllllallllllslqaalaQr<-* r+ l+l++l l +++a+++Q+ gi|9857404 2 RGELWLLVLVLREAARALSPQP 23 Como_SCP: domain 1 of 1, from 11 to 153: score -121.5, E = 86 *->VyspiwrvrTPladtakqnfasFslDLlggtistDgsgsnWnfviin V + +r+ P + a + + g++ + g+ ++Wn + gi|9857404 11 VLREAARALSPQ-PGAGHDEGP------GSGWAAKGTVRGWNRRARE 50 SP..ivNLLrtAAWKrGTLhvklvm.rGkaaVKRsdWastvqldLrnsen SP++++ rt +l ++G ++ +d + ++ +n gi|9857404 51 SPghVSEPDRT----------QLSQdLG-GGTLAMDTLPDNRTRVVE-DN 88 tesydArtwvisePhsgeleFsiEicGPNnGFESMwnssWanQtsWyLev ++y r + sePhs el +++ E an +++ gi|9857404 89 HSYYVSRLYGPSEPHSRELW--VDVA------E-------ANRSQVKIHT 123 vigNpkQstiFevymrldenFevAGNtLmPPflL<-* +N + ++ +v l+ +F + G L + + gi|9857404 124 ILSNTHRQASRVV---LSFDFPFYGHPLRQ-ITI 153 Zn_clus: domain 1 of 1, from 308 to 339: score -16.6, E = 90 *->tACdrCRkrKvKCdgskkPapCsrCikngkleCtiysrksrks<-* ++Cd+C d + Cs C + C s + r++ gi|9857404 308 RSCDACMSS----DL-TFN--CSWCHVLQ--RCS--SGFDRYR 339 Peptidase_M45: domain 1 of 1, from 332 to 342: score -0.6, E = 1e+02 *->sgGFlrysgEW<-* s+GF ry+ EW gi|9857404 332 SSGFDRYRQEW 342 Plexin_repeat: domain 1 of 1, from 303 to 349: score 20.0, E = 0.021 *->nCsqhRqsCssClsapdpfgCgWCvsrkrCtrreaygpsfpygeCsr +C qh sC +C+s++ f+C WC+ ++rC++ + r gi|9857404 303 TCLQH-RSCDACMSSDLTFNCSWCHVLQRCSSGF---------DRYR 339 gekpedNswlgwsqsseqCp<-* +e + + C gi|9857404 340 QE----------WDGTMGCA 349 // 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: tem7 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: gi|9857404|gb|AAG00869.1|AF279144_1 tumor endothelial marker 7 precursor [Homo sapiens] Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- Plexin_repeat Plexin repeat 24.0 1.4e-06 1 RADICAL_ACTIVATING Radical activating enzymes 5.8 5.8 1 Herpes_glycop_D Herpesvirus glycoprotein D 3.3 6.7 1 ART NAD:arginine ADP-ribosyltransferas 0.1 42 1 Peptidase_M45 D-ala-D-ala dipeptidase -0.6 1e+02 1 Syndecan Syndecan domain -2.0 51 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- ART 1/1 1 20 [. 1 22 [. 0.1 42 Syndecan 1/1 2 23 .. 1 22 [. -2.0 51 RADICAL_ACTIVATING 1/1 319 326 .. 30 37 .] 5.8 5.8 Plexin_repeat 1/1 303 333 .. 1 32 [. 24.0 1.4e-06 Peptidase_M45 1/1 332 342 .. 183 193 .. -0.6 1e+02 Herpes_glycop_D 1/1 416 448 .. 353 390 .. 3.3 6.7 Alignments of top-scoring domains: ART: domain 1 of 1, from 1 to 20: score 0.1, E = 42 *->mpalhfvLllSVglllstqals<-* m +++L+l +l+++ +als gi|9857404 1 MRGELWLLVL--VLREAARALS 20 Syndecan: domain 1 of 1, from 2 to 23: score -2.0, E = 51 *->rkllllallllllslqaalaQr<-* r+ l+l++l l +++a+++Q+ gi|9857404 2 RGELWLLVLVLREAARALSPQP 23 RADICAL_ACTIVATING: domain 1 of 1, from 319 to 326: score 5.8, E = 5.8 *->nlrCpyCh<-* +++C++Ch gi|9857404 319 TFNCSWCH 326 Plexin_repeat: domain 1 of 1, from 303 to 333: score 24.0, E = 1.4e-06 *->nCsqhRqsCssClsapdpfgCgWCvsrkrCtr<-* +C qh sC +C+s++ f+C WC+ ++rC++ gi|9857404 303 TCLQH-RSCDACMSSDLTFNCSWCHVLQRCSS 333 Peptidase_M45: domain 1 of 1, from 332 to 342: score -0.6, E = 1e+02 *->sgGFlrysgEW<-* s+GF ry+ EW gi|9857404 332 SSGFDRYRQEW 342 Herpes_glycop_D: domain 1 of 1, from 416 to 448: score 3.3, E = 6.7 *->pspppatpaNpdakvtsviigivvlalligaiivgvvy<-* ++ ++ tp++ ++i+giv ++ll +aii++++y gi|9857404 416 SPKTKGTPVH-----LGTIVGIVLAVLLVAAIILAGIY 448 // 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: tem7 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: gi|9857404|gb|AAG00869.1|AF279144_1 tumor endothelial marker 7 precursor [Homo sapiens] 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: Thu Oct 12 13:39:53 2000 Sequence file: tem7 ---------------------------------------- Sequence gi|9857404|gb|AAG00869.1|AF279144_1 (502 residues): Matching pattern PS00001 ASN_GLYCOSYLATION: 80: NRTR 88: NHSY 115: NRSQ 189: NSTV 197: NGTV 321: NCSW Total matches: 6 Matching pattern PS00004 CAMP_PHOSPHO_SITE: 273: RRRS Total matches: 1 Matching pattern PS00005 PKC_PHOSPHO_SITE: 40: TVR 128: THR 272: SRR 416: SPK Total matches: 4 Matching pattern PS00006 CK2_PHOSPHO_SITE: 56: SEPD 76: TLPD 241: SVPE 276: SIFE 294: SAVE 333: SGFD 376: SPYD 395: TTED 396: TEDD 476: SHPD 482: TYAE 489: SGHE Total matches: 12 Matching pattern PS00007 TYR_PHOSPHO_SITE: 83: RVVEDNHSY 475: RSHPDHSTY Total matches: 2 Matching pattern PS00008 MYRISTYL: 32: GSGWAA 39: GTVRGW 69: GGTLAM 255: GLSDAF 344: GTMGCA 362: GMRTTT 410: GLQNNL 427: GTIVGI 431: GIVLAV 446: GIYING Total matches: 10 Total no of hits in this sequence: 35 ======================================== 1314 pattern(s) searched in 1 sequence(s), 502 residues. Total no of hits in all sequences: 35. Search time: 00:00 min ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ Start with Profile Search ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ Start with motif search against own library ***** bioMotif : Version V41a DB, 1999 Nov 11 ***** argv[1]=P argv[2]=-m /data/patterns/own/motif.fa argv[4]=-seq tem7 ***** 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, 502 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: tem7 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: gi|9857404|gb|AAG00869.1|AF279144_1 tumor endothelial marker 7 precursor [Homo sapiens] 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: tem7 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: gi|9857404|gb|AAG00869.1|AF279144_1 tumor endothelial marker 7 precursor [Homo sapiens] 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 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= gi|9857404|gb|AAG00869.1|AF279144_1 tumor endothelial marker 7 precursor [Homo sapiens] (502 letters) Searching..................................done Results from profile search Score E Sequences producing significant alignments: (bits) Value HOG HOG- intein(HINT) like domain 24 0.56 PAIRED Paired domain (A HTH domain) 22 1.5 MYND MYND domain (A zinc coordinating Cysteine rich domain) 22 1.8 ww 22 2.0 ACTIN Actin ATPase/ Cytoskeletal ATPase domain 22 2.4 RASGAP RAS-type GTPase GTP hydrolysis activating protein 21 2.8 LON The LON serine protease domain 21 4.3 HISDAC Histone deacetylase domain 20 5.6 ARR Arrestin domain 21 5.6 SET Su(var)3-9, Enhancer of Zeste, trithorax domain (A chrom... 20 6.0 AN1 AN1 like cysteine rich zinc coordinating domain 20 6.5 14-3-3 14-3-3 protein alpha Helical domain 20 6.7 PH Pleckstrin homology domain (lipid and protein interactio... 20 6.7 KIN Protein kinase domain 20 9.1 PUM Pumilio repeat RNA binding domain 20 9.5 >HOG HOG- intein(HINT) like domain Length = 389 Score = 23.8 bits (51), Expect = 0.56 Identities = 9/32 (28%), Positives = 17/32 (53%), Gaps = 4/32 (12%) Query: 204 QWDHVYL---QGWEDKGSFTFQAALHHDGRIV 232 +W + L + W++ Q +LH++GR V Sbjct: 94 EWPGIRLLVTESWDEDY-HHGQESLHYEGRAV 124 >PAIRED Paired domain (A HTH domain) Length = 127 Score = 22.4 bits (47), Expect = 1.5 Identities = 7/14 (50%), Positives = 10/14 (71%) Query: 444 LAGIYINGHPTSNA 457 L G+++NG P NA Sbjct: 8 LGGVFVNGRPLPNA 21 >MYND MYND domain (A zinc coordinating Cysteine rich domain) Length = 107 Score = 22.1 bits (46), Expect = 1.8 Identities = 8/26 (30%), Positives = 9/26 (33%), Gaps = 1/26 (3%) Query: 308 RSCDACMSSDLTFNCSWCHVLQRCSS 333 + C C L CS C CS Sbjct: 50 KKCANCNREAL-AECSLCRKTPYCSE 74 >ww Length = 38 Score = 22.1 bits (47), Expect = 2.0 Identities = 7/38 (18%), Positives = 14/38 (36%), Gaps = 1/38 (2%) Query: 177 PLMANFNPGYSDNSTVVYFDNGTVFVVQWDHVYLQGWE 214 P+ + Y + + D+ + WD L+ E Sbjct: 2 PMPQGWEMCYDSDGVRYFKDHNSK-TTTWDDPRLKQQE 38 >ACTIN Actin ATPase/ Cytoskeletal ATPase domain Length = 376 Score = 21.7 bits (46), Expect = 2.4 Identities = 8/30 (26%), Positives = 12/30 (39%) Query: 361 PGMRTTTSASPDTSFSPYDGDLTTTSSSLF 390 M+ A P+ +S + G S S F Sbjct: 324 SSMKIKVVAPPERKYSVWIGGSILASLSTF 353 >RASGAP RAS-type GTPase GTP hydrolysis activating protein Length = 292 Score = 21.3 bits (44), Expect = 2.8 Identities = 8/14 (57%), Positives = 11/14 (78%) Query: 284 ELDPSKVTSMSAVE 297 E+DPSK+ SAV+ Sbjct: 135 EIDPSKIKDRSAVD 148 >LON The LON serine protease domain Length = 132 Score = 20.9 bits (44), Expect = 4.3 Identities = 9/43 (20%), Positives = 16/43 (36%), Gaps = 8/43 (18%) Query: 235 YKEIPMSVP---EISSSQHPVKTGLSDAFMILNPSPDVPESRR 274 +EIP +V +I HPVK + + + + Sbjct: 92 LEEIPDNVIADLDI----HPVKR-IEEVLTLALQNEPSGMQVV 129 >HISDAC Histone deacetylase domain Length = 433 Score = 20.2 bits (42), Expect = 5.6 Identities = 10/55 (18%), Positives = 17/55 (30%), Gaps = 7/55 (12%) Query: 135 VVLSFDF-PFYGHPLRQITIATGGFIFMGDVIHRMLTATQYVAPLMANFNPGYSD 188 VVL G L ++ G + + + P+M GY+ Sbjct: 267 VVLQCGGDSLSGDRLGCFNLSMEGHANCVNYVK------SFGIPMMVVGGGGYTM 315 >ARR Arrestin domain Length = 454 Score = 20.6 bits (43), Expect = 5.6 Identities = 14/60 (23%), Positives = 16/60 (26%), Gaps = 10/60 (16%) Query: 361 PGMRTTTSASPDTSFSPYDGDLTTTSSSLFIDSLTTEDDTKLN----PYAGGDGLQNNLS 416 G R SP+ + Y G FID D N P G L Sbjct: 8 SGTRVFKKTSPNGKITTYLG------KRDFIDRGDYVDLIGENKGTEPQNVGFILTGLSH 61 >SET Su(var)3-9, Enhancer of Zeste, trithorax domain (A chromatin associated domain) Length = 219 Score = 20.3 bits (42), Expect = 6.0 Identities = 5/23 (21%), Positives = 7/23 (29%) Query: 362 GMRTTTSASPDTSFSPYDGDLTT 384 G+ S + Y G L Sbjct: 100 GVFARESIPAWSYIGEYTGILRR 122 >AN1 AN1 like cysteine rich zinc coordinating domain Length = 57 Score = 20.4 bits (42), Expect = 6.5 Identities = 5/19 (26%), Positives = 7/19 (36%), Gaps = 2/19 (10%) Query: 309 SCDACMS--SDLTFNCSWC 325 S C + + L C C Sbjct: 9 SFAKCTASTTTLGQFCMHC 27 >14-3-3 14-3-3 protein alpha Helical domain Length = 270 Score = 20.3 bits (42), Expect = 6.7 Identities = 19/62 (30%), Positives = 28/62 (44%), Gaps = 14/62 (22%) Query: 234 AYKEIPMSVPEISSSQ----HPVKTGLSDAFM-----ILNPSPDVPESRRRSIFEYHRIE 284 YK EI++++ HP++ GL+ F ILN SPD + F+ E Sbjct: 153 GYKA----ASEIATAELAPTHPIRLGLALNFSVFYYEILN-SPDRACYLAKQAFDEAISE 207 Query: 285 LD 286 LD Sbjct: 208 LD 209 >PH Pleckstrin homology domain (lipid and protein interaction domain) Length = 138 Score = 20.0 bits (41), Expect = 6.7 Identities = 15/64 (23%), Positives = 26/64 (40%), Gaps = 3/64 (4%) Query: 62 QLSQDLGGGTLAMDTLPDNRTRVVEDNHSYYVSRLYGPSEPHSRELWVDVAEANRSQVKI 121 +L G L + RVVE NH Y + P++ ++ W+ +A S Sbjct: 78 ELYIPNNKGQLIKACKTEADGRVVEGNHMVYR--ISAPTQ-EEKDEWIKSIQAAVSVDPF 134 Query: 122 HTIL 125 + +L Sbjct: 135 YEML 138 >KIN Protein kinase domain Length = 313 Score = 19.6 bits (40), Expect = 9.1 Identities = 15/68 (22%), Positives = 28/68 (41%), Gaps = 8/68 (11%) Query: 187 SDNSTVVYFDNGTVFVV--QWDHVYLQGWEDKGSF--TFQAALHHDGRIVFAYKEIPMSV 242 + N + YF G+ F V ++ V G G++ A + G V A K+I + Sbjct: 11 NFNDNISYFVYGSQFTVPRRYSIVKCIG---HGAYGVVCSAKDNLTGEKV-AIKKISKAF 66 Query: 243 PEISSSQH 250 + ++ Sbjct: 67 DNLKDTKR 74 >PUM Pumilio repeat RNA binding domain Length = 337 Score = 19.8 bits (41), Expect = 9.5 Identities = 12/51 (23%), Positives = 22/51 (42%), Gaps = 15/51 (29%) Query: 281 HRIELDPSKVTSMSAVEFTPLPTCLQHRSCDACMSSDLTFNCSWCHVLQRC 331 +I+L + + EFT + + + +DL N HV+Q+C Sbjct: 112 VQIDL----IIKGFSQEFTSIEQVVT-------LINDLNGN----HVIQKC 147 Underlying Matrix: BLOSUM62 Number of sequences tested against query: 105 Number of sequences better than 10.0: 15 Number of calls to ALIGN: 15 Length of query: 502 Total length of test sequences: 20182 Effective length of test sequences: 16637.0 Effective search space size: 7789758.6 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= gi|9857404|gb|AAG00869.1|AF279144_1 tumor endothelial marker 7 precursor [Homo sapiens] (502 letters) Searching.................................................done Results from profile search Score E Sequences producing significant alignments: (bits) Value gi|2392378 [1..380] Periplasmic binding protein-like II 28 0.32 gi|2209100 [9..467] PLP-dependent transferases 26 1.6 gi|1581788 [38..194] Hedgehog/DD-peptidase 25 4.2 gi|420193 [185..357] Integrin A (or I) domain 25 4.2 gi|629488 [18..291] Ribosome inactivating proteins (RIP) 24 5.8 gi|1421437 [1..65] A DNA topoisomerase I domain 24 7.2 gi|728990 [311..529] Periplasmic binding protein-like II 23 8.3 gi|1469051 [197..455] (Phosphotyrosine) protein phosphatases... 23 9.0 gi|2292739 [32..255] Zn metallo-beta-lactamase 23 9.2 gi|461959 [221..583] DNA/RNA polymerases 23 9.2 gi|1170097 [1..85] Thioredoxin-like 23 9.2 >gi|2392378 [1..380] Periplasmic binding protein-like II Length = 380 Score = 28.1 bits (62), Expect = 0.32 Identities = 18/179 (10%), Positives = 44/179 (24%), Gaps = 32/179 (17%) Query: 65 QDLGGGTLAMDTLPDNRTRVVEDNHSYYVSRLYG------------PSEPHSRELWVDVA 112 ++ D L V N + P+ P + E D Sbjct: 77 AEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPDPQ 136 Query: 113 EANRSQVKIHTILSNTHRQASRVVLSFDFPFYGHPLRQITIATGGFIFMGDV-------- 164 + + S ++ + P++ + A GG+ F + Sbjct: 137 DPRVRGLY--FPAGGLDPGKSALMFNLQEPYF---TWPLIAADGGYAFKYENGKYDIKDV 191 Query: 165 ---IHRMLTATQYVAPLMANFNPGYSDNSTVVY--FDNGTV-FVVQWDHVYLQGWEDKG 217 ++ L+ N + + ++ F+ G + + + Sbjct: 192 GVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAW-SNIDTSK 249 >gi|2209100 [9..467] PLP-dependent transferases Length = 459 Score = 26.0 bits (56), Expect = 1.6 Identities = 26/281 (9%), Positives = 50/281 (17%), Gaps = 40/281 (14%) Query: 12 LREAARALSPQPGAGHDEGPGSGWAA-----KGTVRGWNRRARESPGHV------SEPDR 60 A+A+ G + G A + R + Sbjct: 72 YYALAKAVKDIFGYEYTIPTHQGRGAEQIYIPVLIAKREREKGLDRSKMVVFSNYFFDTT 131 Query: 61 TQLSQDLGGGTLAMDTLPDNRTRVVEDNHSYYVSRLYGPSEPHSRELWVDVAEANRSQVK 120 SQ G + T + + N + Sbjct: 132 QGHSQINGATVRNVYIKEAFDTTAKHPFK-------GNFDLEKLEKGIQEAGAHNVPYIV 184 Query: 121 IHTILSNTHRQASRVVLSFDFPFYGHPLRQIT--IATGGFIFMGDVIHRMLTATQYVAPL 178 ++ A +S L+ + + D A Sbjct: 185 CTITCNS----AGGQPVSIAN------LKGMYEIARKYDIPVIMDSA--------RFAEN 226 Query: 179 MANFNPGYSDNSTVVYFDNGTVFVVQWDHVYLQGWEDKGSFTFQAALHHDGRIVFAYKEI 238 D + + +D D + Y E Sbjct: 227 AYFVQQREEAYKDWTIEQITYESYRYADGLAMSAKKDAMVPMGGILAFKDKSMEEVYHEC 286 Query: 239 --PMSVPEISSSQHPVKTGLSDAFMILNPSPDVPESRRRSI 277 V E + ++ G + + E I Sbjct: 287 RTLCVVQEGFPTYGGLEGGAMERLAVGLHDGMRQEWLAYRI 327 >gi|1581788 [38..194] Hedgehog/DD-peptidase Length = 157 Score = 24.5 bits (52), Expect = 4.2 Identities = 12/32 (37%), Positives = 19/32 (58%), Gaps = 4/32 (12%) Query: 204 QWDHVYL---QGWEDKGSFTFQAALHHDGRIV 232 QW V L +GW++ G + +LH++GR V Sbjct: 79 QWPGVKLRVTEGWDEDG-HHSEESLHYEGRAV 109 >gi|420193 [185..357] Integrin A (or I) domain Length = 173 Score = 24.6 bits (53), Expect = 4.2 Identities = 8/64 (12%), Positives = 22/64 (33%), Gaps = 1/64 (1%) Query: 98 GPSEPHSRELWVDVAEANRSQVKIHTILSN-THRQASRVVLSFDFPFYGHPLRQITIATG 156 G + H+ +V + + + + + + V++ L +I++ Sbjct: 102 GGARRHAELSFVFLTDGVTGNDSLEESVHSMRKQNVVPTVVAVGGDVDMDVLTKISLGDR 161 Query: 157 GFIF 160 IF Sbjct: 162 AAIF 165 >gi|629488 [18..291] Ribosome inactivating proteins (RIP) Length = 274 Score = 24.1 bits (52), Expect = 5.8 Identities = 20/97 (20%), Positives = 31/97 (31%), Gaps = 4/97 (4%) Query: 365 TTTSASPDTSFSPYDGDLTTTSSSLFIDSLTTEDDTKLNPYAGGDGLQNNLSPKTKGTPV 424 T AS + F + T + S F+ SL K G + L+ + K V Sbjct: 2 LTPPASSNIVFDV--ENATPETYSNFLTSLREAVKDKKLTCHGMI-MATTLTEQPKYVLV 58 Query: 425 HLGTIVGIVLAVLLVAAIILAGIYINGHPTSNAALFF 461 L G + + L G Y + + F Sbjct: 59 DLKFGSGTFTLAIRRGNLYLEG-YSDIYNGKCRYRIF 94 >gi|1421437 [1..65] A DNA topoisomerase I domain Length = 65 Score = 23.6 bits (50), Expect = 7.2 Identities = 14/51 (27%), Positives = 25/51 (48%), Gaps = 4/51 (7%) Query: 236 KEIPMSVPEI----SSSQHPVKTGLSDAFMILNPSPDVPESRRRSIFEYHR 282 KE P+ +PE+ S + ++ G + F+ N P E+R + E +R Sbjct: 9 KEDPVPLPELPCEKSDAYFVLRDGAAGVFLAANTFPKSRETRAPLVEELYR 59 >gi|728990 [311..529] Periplasmic binding protein-like II Length = 219 Score = 23.4 bits (50), Expect = 8.3 Identities = 14/79 (17%), Positives = 25/79 (30%), Gaps = 3/79 (3%) Query: 191 TVVYFDNGTVFVVQWDHVYLQGWEDKGSFTFQAALH--HDGRIVFAYKEIPMSVPE-ISS 247 + Y NG V V + D + T + + Y + + + S Sbjct: 77 SRPYVRNGMVIVTRQDPDAPVDADHLDGRTVALVRNSAAIPLLQRRYPQAKVVTADNPSE 136 Query: 248 SQHPVKTGLSDAFMILNPS 266 + V G +DA + S Sbjct: 137 AMLMVANGQADAVVQTQIS 155 >gi|1469051 [197..455] (Phosphotyrosine) protein phosphatases II Length = 259 Score = 23.5 bits (50), Expect = 9.0 Identities = 12/72 (16%), Positives = 22/72 (29%), Gaps = 13/72 (18%) Query: 228 DGRIVFA-YKEIPMSVPEISSSQHPVKTGLSDAFMILNPSPDVPESRRRSIFEYHRIELD 286 D I ++++ +P V M N DV ++ ++ L Sbjct: 2 DANIAANDFEQVVSYIP------PSVTKHQFVKNMHKNRFADVI------CLDHSKVHLS 49 Query: 287 PSKVTSMSAVEF 298 S S +E Sbjct: 50 DSSYIHASYLEL 61 >gi|2292739 [32..255] Zn metallo-beta-lactamase Length = 224 Score = 23.5 bits (50), Expect = 9.2 Identities = 18/158 (11%), Positives = 41/158 (25%), Gaps = 17/158 (10%) Query: 98 GPSEPHSRELWVDVAEANRSQVKIHTILSNTHR---QASRVVLSFDFPFYGHPLRQITIA 154 + +REL + +R V I +N H + S + + Sbjct: 37 TWTPDTARELHKLIKRVSRKPVL-EVINTNYHTDRAGGNAYWKSIGAKVISTRQTRDLMK 95 Query: 155 TGGFIFMGDVIHRMLTATQYVAPLMANFNPGYSDNSTVVYFDNGTVFVVQWDHVYLQG-- 212 + + + L + ++ N G + + Sbjct: 96 SDWAEIVAF-TRKGLPEYPDLPLVLPNVVHE-----GDFTLQEGKLRAFYLGPAHSPDGI 149 Query: 213 ---WEDKGS-FTFQAALHHDGRIVFAY-KEIPMSVPEI 245 + D+ + G + FA K P ++ + Sbjct: 150 FVYFPDQQVLYGNCILKEKLGNLSFADVKAYPQTLERL 187 >gi|461959 [221..583] DNA/RNA polymerases Length = 363 Score = 23.3 bits (50), Expect = 9.2 Identities = 9/47 (19%), Positives = 19/47 (40%), Gaps = 4/47 (8%) Query: 120 KIHTILSNTHRQASRVVLSF----DFPFYGHPLRQITIATGGFIFMG 162 + HT ++ + SR+ ++ P +R+ IA G + Sbjct: 123 RCHTFINPLQARTSRMSITGIPAQTLPSSDWIVRRCFIAEPGDVMAS 169 >gi|1170097 [1..85] Thioredoxin-like Length = 85 Score = 23.3 bits (50), Expect = 9.2 Identities = 10/60 (16%), Positives = 20/60 (32%), Gaps = 15/60 (25%) Query: 230 RIVFAYKEIPMSV--------PEISSSQHPVKTGLSDAFMILNPSPDVP--ESRRRSIFE 279 R++ Y + P+ SQ L++ F + P++P I + Sbjct: 18 RLLLEYTDSSYVEKKYTMGDAPDYDRSQW-----LNEKFKLGLDFPNLPYLIDGAHKITQ 72 Underlying Matrix: BLOSUM62 Number of sequences tested against query: 1187 Number of sequences better than 10.0: 11 Number of calls to ALIGN: 11 Length of query: 502 Total length of test sequences: 256703 Effective length of test sequences: 209547.0 Effective search space size: 96839557.8 Initial X dropoff for ALIGN: 25.0 bits