analysis of sequence from T18769.fa ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ >T18769 hypothetical protein B0491.1 - Caenorhabditis elegans. MQCVRSFVKN ETFNRNKILL VAFVARIILV FYAHIHDYLF KVNFTDIDYH VFSDAAKHVS NGGSPFDRAT YRYTPALAWI LLPVVHFPDF GKILFCIFDI LVAILYFKIM EKDLNETKSE TREEMKDDQT MNVVIYWLAN PLTAIISARG NAESIVAAVV LLNIVLLQKG YWKSAALVHG ALAIQLKIYP LIYLPSVFLS LSTIGEQSCV VNKFKSLVSN WKGFAYMLVT LTSFAAVVLF FFQIYGQLFL DEYLIYHVKR RDLAHNFSPY FYLLYLYEAN PTMSQIIGLG AFIPQIVLIV FFAFKHYDDL PFCWFITTFA FVTYNKVCTS QYFVWYIVLL PLLAHKIMMS RQLALSLMAA WFATQGIWLL AAYLFEFQGW NTFFLMFLAS CLFLIANSFI LKQIINHYVP IVKPKTD ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ sec.str. with predator > T18769 . . . . . 1 MQCVRSFVKNETFNRNKILLVAFVARIILVFYAHIHDYLFKVNFTDIDYH 50 ___EEEEE________HHHHHHHHHHHHHHHHHHHHHHHH_________E . . . . . 51 VFSDAAKHVSNGGSPFDRATYRYTPALAWILLPVVHFPDFGKILFCIFDI 100 EE_______________________HHHHHEEE________EEEHHHHHH . . . . . 101 LVAILYFKIMEKDLNETKSETREEMKDDQTMNVVIYWLANPLTAIISARG 150 HHHHHHHHHHHHH________HHHHHH______EEEE_____________ . . . . . 151 NAESIVAAVVLLNIVLLQKGYWKSAALVHGALAIQLKIYPLIYLPSVFLS 200 __HHHHHHHHHHHHHHHH____HHHHHHHHHHHHHHHEEEEEE__EEEEE . . . . . 201 LSTIGEQSCVVNKFKSLVSNWKGFAYMLVTLTSFAAVVLFFFQIYGQLFL 250 EEE___EEEEEEHHHHHH_____EEEEEEEHHHHHHHHHHHHHHHHHHHH . . . . . 251 DEYLIYHVKRRDLAHNFSPYFYLLYLYEANPTMSQIIGLGAFIPQIVLIV 300 HHHHHHHH____________HHHHHHHH_______________HHHHHHH . . . . . 301 FFAFKHYDDLPFCWFITTFAFVTYNKVCTSQYFVWYIVLLPLLAHKIMMS 350 HHHHH_______EEEEEEEEEEEE_______EEEEEEEE___HHHHHHHH . . . . . 351 RQLALSLMAAWFATQGIWLLAAYLFEFQGWNTFFLMFLASCLFLIANSFI 400 HHHHHHHHHHHHHH_HHHHHHHHHHHH____EEEEHHHHHHHEEE____E . 401 LKQIINHYVPIVKPKTD 417 EEHHHHHEEEEEE____ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ method : 1 alpha-contents : 34.2 % beta-contents : 65.8 % coil-contents : 0.0 % class : mixed method : 2 alpha-contents : 18.0 % beta-contents : 82.0 % coil-contents : 0.0 % class : mixed ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ GPI: learning from metazoa -29.01 -0.36 -0.60 -0.93 -4.00 0.00 0.00 -5.32 -0.91 -4.17 -2.37 -12.00 -12.00 -4.00 0.00 0.00 -75.67 -27.12 -0.36 -0.52 -0.34 -4.00 0.00 0.00 -0.97 -0.18 -4.12 -2.37 -12.00 -12.00 -4.00 0.00 0.00 -67.97 ID: T18769 AC: xxx Len: 417 1:I 390 Sc: -67.97 Pv: 5.229348e-01 NO_GPI_SITE GPI: learning from protozoa -32.75 -6.85 -3.73 -0.59 -4.00 0.00 0.00 0.00 -0.52 -5.25 -8.73 -12.00 -12.00 -4.00 0.00 0.00 -90.42 -43.54 -0.34 0.00 0.00 -4.00 0.00 0.00 -2.06 0.00 -3.67 -8.73 -12.00 -12.00 -4.00 0.00 0.00 -90.33 ID: T18769 AC: xxx Len: 417 1:I 390 Sc: -90.33 Pv: 7.019129e-01 NO_GPI_SITE ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ # SignalP euk predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? T18769 0.834 285 Y 0.689 399 Y 0.987 361 Y 0.441 N # SignalP gram- predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? T18769 0.582 236 Y 0.448 236 Y 0.987 236 Y 0.303 N # SignalP gram+ predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? T18769 0.439 236 Y 0.413 34 Y 0.998 233 Y 0.726 Y ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ low complexity regions: SEG 12 2.2 2.5 >T18769 hypothetical protein B0491.1 - Caenorhabditis elegans. 1-154 MQCVRSFVKNETFNRNKILLVAFVARIILV FYAHIHDYLFKVNFTDIDYHVFSDAAKHVS NGGSPFDRATYRYTPALAWILLPVVHFPDF GKILFCIFDILVAILYFKIMEKDLNETKSE TREEMKDDQTMNVVIYWLANPLTAIISARG NAES ivaavvllnivll 155-167 168-417 QKGYWKSAALVHGALAIQLKIYPLIYLPSV FLSLSTIGEQSCVVNKFKSLVSNWKGFAYM LVTLTSFAAVVLFFFQIYGQLFLDEYLIYH VKRRDLAHNFSPYFYLLYLYEANPTMSQII GLGAFIPQIVLIVFFAFKHYDDLPFCWFIT TFAFVTYNKVCTSQYFVWYIVLLPLLAHKI MMSRQLALSLMAAWFATQGIWLLAAYLFEF QGWNTFFLMFLASCLFLIANSFILKQIINH YVPIVKPKTD low complexity regions: SEG 25 3.0 3.3 >T18769 hypothetical protein B0491.1 - Caenorhabditis elegans. 1-417 MQCVRSFVKNETFNRNKILLVAFVARIILV FYAHIHDYLFKVNFTDIDYHVFSDAAKHVS NGGSPFDRATYRYTPALAWILLPVVHFPDF GKILFCIFDILVAILYFKIMEKDLNETKSE TREEMKDDQTMNVVIYWLANPLTAIISARG NAESIVAAVVLLNIVLLQKGYWKSAALVHG ALAIQLKIYPLIYLPSVFLSLSTIGEQSCV VNKFKSLVSNWKGFAYMLVTLTSFAAVVLF FFQIYGQLFLDEYLIYHVKRRDLAHNFSPY FYLLYLYEANPTMSQIIGLGAFIPQIVLIV FFAFKHYDDLPFCWFITTFAFVTYNKVCTS QYFVWYIVLLPLLAHKIMMSRQLALSLMAA WFATQGIWLLAAYLFEFQGWNTFFLMFLAS CLFLIANSFILKQIINHYVPIVKPKTD low complexity regions: SEG 45 3.4 3.75 >T18769 hypothetical protein B0491.1 - Caenorhabditis elegans. 1-332 MQCVRSFVKNETFNRNKILLVAFVARIILV FYAHIHDYLFKVNFTDIDYHVFSDAAKHVS NGGSPFDRATYRYTPALAWILLPVVHFPDF GKILFCIFDILVAILYFKIMEKDLNETKSE TREEMKDDQTMNVVIYWLANPLTAIISARG NAESIVAAVVLLNIVLLQKGYWKSAALVHG ALAIQLKIYPLIYLPSVFLSLSTIGEQSCV VNKFKSLVSNWKGFAYMLVTLTSFAAVVLF FFQIYGQLFLDEYLIYHVKRRDLAHNFSPY FYLLYLYEANPTMSQIIGLGAFIPQIVLIV FFAFKHYDDLPFCWFITTFAFVTYNKVCTS QY fvwyivllpllahkimmsrqlalslmaawf 333-405 atqgiwllaaylfefqgwntfflmflascl fliansfilkqii 406-417 NHYVPIVKPKTD 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 >T18769 hypothetical protein B0491.1 - Caenorhabditis elegans. MQCVRSFVKNETFNRNKILLVAFVARIILVFYAHIHDYLFKVNFTDIDYHVFSDAAKHVS NGGSPFDRATYRYTPALAWILLPVVHFPDFGKILFCIFDILVAILYFkimekdlnetkse treemkddQTMNVVIYWLANPLTAIISARGNAESIVAAVVLLNIVLLQKGYWKSAALVHG ALAIQLKIYPLIYLPSVFLSLSTIGEQSCVVNKFKSLVSNWKGFAYMLVTLTSFaavvlf ffQIYGQLFLDEYLIYHVKRRDLAHNFSPYFYLLYLYEANPTMSQIIGLGAFipqivliv ffafKHYDDLPFCWFITTFAFVTYNKVCTSQYFVWYIVLLPLLAHKIMMSRQLALSLMAA WFATQGIWLLAAYLFEFQGWNTFFLMFLASCLFLIANSFILKQIINHYVPIVKPKTD 1 - 107 MQCVRSFVKN ETFNRNKILL VAFVARIILV FYAHIHDYLF KVNFTDIDYH VFSDAAKHVS NGGSPFDRAT YRYTPALAWI LLPVVHFPDF GKILFCIFDI LVAILYF 108 - 128 kim ekdlnetkse treemkdd 129 - 234 QT MNVVIYWLAN PLTAIISARG NAESIVAAVV LLNIVLLQKG YWKSAALVHG ALAIQLKI YP LIYLPSVFLS LSTIGEQSCV VNKFKSLVSN WKGFAYMLVT LTSF 235 - 242 aavvlf ff 243 - 292 QIYGQLFL DEYLIYHVKR RDLAHNFSPY FYLLYLYEAN PTMSQIIGLG AF 293 - 304 ipqivliv ffaf 305 - 417 KHYDDL PFCWFITTFA FVTYNKVCTS QYFVWYIVLL PLLAHKIMMS RQLALSLMAA WFAT QGIWLL AAYLFEFQGW NTFFLMFLAS CLFLIANSFI LKQIINHYVP IVKPKTD low complexity regions: DUST >T18769 hypothetical protein B0491.1 - Caenorhabditis elegans. MQCVRSFVKNETFNRNKILLVAFVARIILVFYAHIHDYLFKVNFTDIDYHVFSDAAKHVS NGGSPFDRATYRYTPALAWILLPVVHFPDFGKILFCIFDILVAILYFKIMEKDLNETKSE TREEMKDDQTMNVVIYWLANPLTAIISARGNAESIVAAVVLLNIVLLQKGYWKSAALVHG ALAIQLKIYPLIYLPSVFLSLSTIGEQSCVVNKFKSLVSNWKGFAYMLVTLTSFAAVVLF FFQIYGQLFLDEYLIYHVKRRDLAHNFSPYFYLLYLYEANPTMSQIIGLGAFIPQIVLIV FFAFKHYDDLPFCWFITTFAFVTYNKVCTSQYFVWYIVLLPLLAHKIMMSRQLALSLMAA WFATQGIWLLAAYLFEFQGWNTFFLMFLASCLFLIANSFILKQIINHYVPIVKPKTD ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ coiled coil prediction for T18769 sequence: 417 amino acids, 21 residue(s) in coiled coil state Coil 1 * 111* 132* KDLNETKSETREEMKDDQTMNV . | . | . | . | . | . 60 MQCVRSFVKN ETFNRNKILL VAFVARIILV FYAHIHDYLF KVNFTDIDYH VFSDAAKHVS ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 NGGSPFDRAT YRYTPALAWI LLPVVHFPDF GKILFCIFDI LVAILYFKIM EKDLNETKSE ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~2222 2555555555 * 21 M'95 -w border ---------- ---------- ---------- ---------- ------defg abcdefgabc * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~2222 2555555555 * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~2225 5999999999 * 14 M'95 -w local . | . | . | . | . | . 180 TREEMKDDQT MNVVIYWLAN PLTAIISARG NAESIVAAVV LLNIVLLQKG YWKSAALVHG 5555555555 551~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border defgabcdef gab------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar 5555555555 551~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. 999999911~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 240 ALAIQLKIYP LIYLPSVFLS LSTIGEQSCV VNKFKSLVSN WKGFAYMLVT LTSFAAVVLF ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 FFQIYGQLFL DEYLIYHVKR RDLAHNFSPY FYLLYLYEAN PTMSQIIGLG AFIPQIVLIV ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 FFAFKHYDDL PFCWFITTFA FVTYNKVCTS QYFVWYIVLL PLLAHKIMMS RQLALSLMAA ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 . | . | . | . | . | . WFATQGIWLL AAYLFEFQGW NTFFLMFLAS CLFLIANSFI LKQIINHYVP IVKPKTD ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~ ---------- ---------- ---------- ---------- ---------- ------- ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ prediction of transmembrane regions with toppred2 *********************************** *TOPPREDM with eukaryotic function* *********************************** T18769.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: T18769.fa.___inter___ (1 sequences) MQCVRSFVKNETFNRNKILLVAFVARIILVFYAHIHDYLFKVNFTDIDYH VFSDAAKHVSNGGSPFDRATYRYTPALAWILLPVVHFPDFGKILFCIFDI LVAILYFKIMEKDLNETKSETREEMKDDQTMNVVIYWLANPLTAIISARG NAESIVAAVVLLNIVLLQKGYWKSAALVHGALAIQLKIYPLIYLPSVFLS LSTIGEQSCVVNKFKSLVSNWKGFAYMLVTLTSFAAVVLFFFQIYGQLFL DEYLIYHVKRRDLAHNFSPYFYLLYLYEANPTMSQIIGLGAFIPQIVLIV FFAFKHYDDLPFCWFITTFAFVTYNKVCTSQYFVWYIVLLPLLAHKIMMS RQLALSLMAAWFATQGIWLLAAYLFEFQGWNTFFLMFLASCLFLIANSFI LKQIINHYVPIVKPKTD (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 16 36 1.076 Certain 2 90 110 1.245 Certain 3 129 149 1.026 Certain 4 152 172 0.881 Putative 5 186 206 1.396 Certain 6 224 244 2.225 Certain 7 284 304 1.895 Certain 8 327 347 1.267 Certain 9 353 373 1.723 Certain 10 380 400 2.147 Certain ---------------------------------------------------------------------- Structure 1 Transmembrane segments included in this structure: Segment 1 2 3 4 5 6 7 8 9 10 Loop length 15 53 18 2 13 17 39 22 5 6 17 K+R profile 5.00 5.00 3.00 3.00 2.00 3.00 5.00 1.00 3.00 2.00 0.00 CYT-EXT prof - - - - - - - - - - - For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 10.00 Tm probability: 0.70 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 5.00 (NEG-POS)/(NEG+POS): -0.6000 NEG: 1.0000 POS: 4.0000 -> Orientation: N-in CYT-EXT difference: 0.00 -> Orientation: undecided ---------------------------------------------------------------------- Structure 2 Transmembrane segments included in this structure: Segment 1 2 3 5 6 7 8 9 10 Loop length 15 53 18 36 17 39 22 5 6 17 K+R profile 5.00 5.00 3.00 2.00 0.00 5.00 4.00 3.00 2.00 3.00 CYT-EXT prof - - - - - - - - - - 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): 5.00 (NEG-POS)/(NEG+POS): -0.6000 NEG: 1.0000 POS: 4.0000 -> Orientation: N-in CYT-EXT difference: 0.00 -> Orientation: undecided ---------------------------------------------------------------------- "T18769" 417 16 36 #t 1.07604 90 110 #t 1.24479 129 149 #t 1.02604 152 172 #f 0.88125 186 206 #t 1.39583 224 244 #t 2.225 284 304 #t 1.89479 327 347 #t 1.26667 353 373 #t 1.72292 380 400 #t 2.14688 ************************************ *TOPPREDM with prokaryotic function* ************************************ T18769.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: T18769.fa.___inter___ (1 sequences) MQCVRSFVKNETFNRNKILLVAFVARIILVFYAHIHDYLFKVNFTDIDYH VFSDAAKHVSNGGSPFDRATYRYTPALAWILLPVVHFPDFGKILFCIFDI LVAILYFKIMEKDLNETKSETREEMKDDQTMNVVIYWLANPLTAIISARG NAESIVAAVVLLNIVLLQKGYWKSAALVHGALAIQLKIYPLIYLPSVFLS LSTIGEQSCVVNKFKSLVSNWKGFAYMLVTLTSFAAVVLFFFQIYGQLFL DEYLIYHVKRRDLAHNFSPYFYLLYLYEANPTMSQIIGLGAFIPQIVLIV FFAFKHYDDLPFCWFITTFAFVTYNKVCTSQYFVWYIVLLPLLAHKIMMS RQLALSLMAAWFATQGIWLLAAYLFEFQGWNTFFLMFLASCLFLIANSFI LKQIINHYVPIVKPKTD (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 16 36 1.076 Certain 2 90 110 1.245 Certain 3 129 149 1.026 Certain 4 152 172 0.881 Putative 5 186 206 1.396 Certain 6 224 244 2.225 Certain 7 284 304 1.895 Certain 8 327 347 1.267 Certain 9 353 373 1.723 Certain 10 380 400 2.147 Certain ---------------------------------------------------------------------- Structure 1 Transmembrane segments included in this structure: Segment 1 2 3 4 5 6 7 8 9 10 Loop length 15 53 18 2 13 17 39 22 5 6 17 K+R profile 5.00 5.00 3.00 3.00 2.00 3.00 5.00 1.00 3.00 2.00 0.00 CYT-EXT prof - - - - - - - - - - - For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 10.00 Tm probability: 0.70 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 5.00 (NEG-POS)/(NEG+POS): -0.6000 NEG: 1.0000 POS: 4.0000 -> Orientation: N-in CYT-EXT difference: 0.00 -> Orientation: undecided ---------------------------------------------------------------------- Structure 2 Transmembrane segments included in this structure: Segment 1 2 3 5 6 7 8 9 10 Loop length 15 53 18 36 17 39 22 5 6 17 K+R profile 5.00 5.00 3.00 2.00 0.00 5.00 4.00 3.00 2.00 3.00 CYT-EXT prof - - - - - - - - - - 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): 5.00 (NEG-POS)/(NEG+POS): -0.6000 NEG: 1.0000 POS: 4.0000 -> Orientation: N-in CYT-EXT difference: 0.00 -> Orientation: undecided ---------------------------------------------------------------------- "T18769" 417 16 36 #t 1.07604 90 110 #t 1.24479 129 149 #t 1.02604 152 172 #f 0.88125 186 206 #t 1.39583 224 244 #t 2.225 284 304 #t 1.89479 327 347 #t 1.26667 353 373 #t 1.72292 380 400 #t 2.14688 ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ SAPS. Version of April 11, 1996. Date run: Thu Jan 24 14:26:27 2002 File: /people/b_eisen/T18769.fa.___saps___ ID T18769 DE hypothetical protein B0491.1 - Caenorhabditis elegans. number of residues: 417; molecular weight: 48.3 kdal 1 MQCVRSFVKN ETFNRNKILL VAFVARIILV FYAHIHDYLF KVNFTDIDYH VFSDAAKHVS 61 NGGSPFDRAT YRYTPALAWI LLPVVHFPDF GKILFCIFDI LVAILYFKIM EKDLNETKSE 121 TREEMKDDQT MNVVIYWLAN PLTAIISARG NAESIVAAVV LLNIVLLQKG YWKSAALVHG 181 ALAIQLKIYP LIYLPSVFLS LSTIGEQSCV VNKFKSLVSN WKGFAYMLVT LTSFAAVVLF 241 FFQIYGQLFL DEYLIYHVKR RDLAHNFSPY FYLLYLYEAN PTMSQIIGLG AFIPQIVLIV 301 FFAFKHYDDL PFCWFITTFA FVTYNKVCTS QYFVWYIVLL PLLAHKIMMS RQLALSLMAA 361 WFATQGIWLL AAYLFEFQGW NTFFLMFLAS CLFLIANSFI LKQIINHYVP IVKPKTD -------------------------------------------------------------------------------- COMPOSITIONAL ANALYSIS (extremes relative to: swp23s) A : 36( 8.6%); C : 6( 1.4%); D : 15( 3.6%); E : 11( 2.6%); F++: 40( 9.6%) G- : 13( 3.1%); H : 11( 2.6%); I : 36( 8.6%); K : 22( 5.3%); L : 53(12.7%) M : 10( 2.4%); N : 18( 4.3%); P : 14( 3.4%); Q : 14( 3.4%); R : 10( 2.4%) S : 22( 5.3%); T : 19( 4.6%); V : 34( 8.2%); W : 9( 2.2%); Y+ : 24( 5.8%) KR : 32 ( 7.7%); ED : 26 ( 6.2%); AGP : 63 ( 15.1%); KRED : 58 ( 13.9%); KR-ED : 6 ( 1.4%); FIKMNY+ : 150 ( 36.0%); LVIFM + : 173 ( 41.5%); ST : 41 ( 9.8%). -------------------------------------------------------------------------------- CHARGE DISTRIBUTIONAL ANALYSIS 1 0000+000+0 -000+0+000 00000+0000 000000-000 +0000-0-00 000-00+000 61 000000-+00 0+00000000 00000000-0 0+000000-0 0000000+00 -+-00-0+0- 121 0+--0+--00 0000000000 00000000+0 00-0000000 00000000+0 00+0000000 181 000000+000 0000000000 00000-0000 00+0+00000 0+00000000 0000000000 241 0000000000 --000000++ +-00000000 0000000-00 0000000000 0000000000 301 0000+00--0 0000000000 00000+0000 0000000000 00000+0000 +000000000 361 0000000000 00000-0000 0000000000 0000000000 0+00000000 00+0+0- A. CHARGE CLUSTERS. Positive charge clusters (cmin = 8/30 or 10/45 or 12/60): none Negative charge clusters (cmin = 7/30 or 9/45 or 11/60): none Mixed charge clusters (cmin = 11/30 or 15/45 or 19/60): 1) From 111 to 130: EKDLNETKSETREEMKDDQT -+-00-0+0-0+--0+--00 quartile: 2; size: 20, +count: 4, -count: 8, 0count: 8; t-value: 8.79 * K: 3 (15.0%); E: 5 (25.0%); T: 3 (15.0%); D: 3 (15.0%); ST: 4 (20.0%); 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 | 5 | 58 | 9 | 8 | 11 | 11 | 10 | 13 | 7 | 9 | lmin1 5 | 5 | 7 | 70 | 11 | 10 | 13 | 13 | 12 | 16 | 8 | 11 | lmin2 6 | 6 | 8 | 78 | 12 | 11 | 15 | 15 | 14 | 18 | 10 | 12 | (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 259; - runs >= 3: 0 * runs >= 4: 1, at 259; 0 runs >= 39: 0 -------------------------------------------------------------------------------- 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-2-C-92-C-112-C-103-C-14-C-62-C-26-COOH 2*. SPACINGS OF C and H. (additional deluxe function for ALEX) H2N-2-C-30-H-1-H-13-H-7-H-27-H-9-C-82-H-29-C-47-H-7-H-40-H-6-C-14-C-16-H-45-C-15-H-10-COOH -------------------------------------------------------------------------------- REPETITIVE STRUCTURES. A. SEPARATED, TANDEM, AND PERIODIC REPEATS: amino acid alphabet. Repeat core block length: 4 Aligned matching blocks: [ 157- 161] AAVVL [ 235- 239] AAVVL ______________________________ [ 164- 167] IVLL [ 337- 340] IVLL 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: 8 Aligned matching blocks: [ 198- 205]-( 4)-[ 210- 211] [ 228- 235]-( 4)-[ 240- 241] [ 198- 205] iioioois [ 228- 235] iioioois -------------------------------------------------------------------------------- MULTIPLETS. A. AMINO ACID ALPHABET. 1. Total number of amino acid multiplets: 33 (Expected range: 11-- 41) 2. Histogram of spacings between consecutive amino acid multiplets: (1-5) 11 (6-10) 7 (11-20) 11 (>=21) 5 3. Clusters of amino acid multiplets (cmin = 13/30 or 17/45 or 20/60): none B. CHARGE ALPHABET. 1. Total number of charge multiplets: 5 (Expected range: 0-- 10) 1 +plets (f+: 7.7%), 4 -plets (f-: 6.2%) Total number of charge altplets: 5 (Critical number: 12) 2. Histogram of spacings between consecutive charge multiplets: (1-5) 1 (6-10) 1 (11-20) 0 (>=21) 4 -------------------------------------------------------------------------------- PERIODICITY ANALYSIS. A. AMINO ACID ALPHABET (core: 4; !-core: 5) Location Period Element Copies Core Errors There are no periodicities of the prescribed length. B. CHARGE ALPHABET ({+= KR; -= ED; 0}; core: 5; !-core: 5) and HYDROPHOBICITY ALPHABET ({*= KRED; i= LVIF; 0}; core: 6; !-core: 9) Location Period Element Copies Core Errors 19- 54 4 i... 8 6 1 80- 114 5 i.... 7 7 0 95- 112 3 i.. 6 6 0 116- 129 2 *. 7 7 0 194- 258 5 i.... 11 7 2 231- 284 9 i....0..0 6 6 /0/././././2/././2/ 237- 242 1 i 6 6 0 274- 327 9 i0...0... 6 6 /0/2/./././2/./././ 286- 345 6 i.0... 9 7 /1/./3/./././ 296- 302 1 i 7 7 0 327- 396 10 i..00..... 7 7 /0/././2/1/./././././ 333- 362 5 i.00. 6 6 /0/./2/2/./ 369- 416 8 i...00.. 6 6 /0/./././2/1/././ 383- 388 1 i 6 6 0 -------------------------------------------------------------------------------- SPACING ANALYSIS. Location (Quartile) Spacing Rank P-value Interpretation 107- 198 (2.) F( 91)F 1 of 41 0.0012 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: T18769.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: T18769 hypothetical protein B0491.1 - Caenorhabditis elegans. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- ART NAD:arginine ADP-ribosyltransferase 0.1 44 1 Papilloma_E5 Papillomavirus E5 -38.1 13 1 PMT Dolichyl-phosphate-mannose-protein ma -51.0 2.2 1 CDP-OH_P_transf CDP-alcohol phosphatidyltransferase -56.9 29 1 DUF56 Integral membrane protein DUF56 -68.5 57 1 DUF216 Domain of unknown function DUF -71.3 91 1 UPF0056 Uncharacterised protein family UPF005 -123.7 9.9 1 60KD_IMP 60Kd inner membrane protein -141.0 29 1 UPF0118 Domain of unknown function DUF20 -163.1 85 1 7tm_2 7 transmembrane receptor (Secretin fa -174.2 70 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- CDP-OH_P_transf 1/1 44 193 .. 1 175 [] -56.9 29 UPF0056 1/1 29 214 .. 1 211 [] -123.7 9.9 DUF56 1/1 88 218 .. 1 182 [] -68.5 57 PMT 1/1 16 246 .. 1 267 [] -51.0 2.2 60KD_IMP 1/1 97 260 .. 1 240 [] -141.0 29 DUF216 1/1 137 300 .. 1 208 [] -71.3 91 ART 1/1 340 365 .. 1 26 [. 0.1 44 UPF0118 1/1 91 387 .. 1 340 [] -163.1 85 Papilloma_E5 1/1 337 403 .. 1 74 [] -38.1 13 7tm_2 1/1 186 409 .. 1 273 [] -174.2 70 Alignments of top-scoring domains: CDP-OH_P_transf: domain 1 of 1, from 44 to 193: score -56.9, E = 29 *->allfllasitDwlDGyiARklnqvtrFGafLDPvaDkllvvialiiL + + +++++D+ + v++ G +D + ++ + a i+L T18769 44 FTDIDYHVFSDA--------AKHVSNGGSPFDRATYRYTPALAWILL 82 aylglvpwwltipaalilgvaSHYmhrelllsglrevlaylglkepaiav + +++++ ++ ++ ++l++ l + + ++ l + T18769 83 PVVHFPDFGKIL----FCI-------FDILVAILYFKIMEKDL--NETKS 119 lyygkrktiftCAsaqivaiallLlgfslqsv....lvgseiysklagvi + + k ++ + L++++ +++ ++ s++++ +++ i T18769 120 ETREEMKDD-----QTMNVVIYWLANPLTAIIsargNAESIVAAVVLLNI 164 fwfilaaslcgyiaavltlitglqyvvaalay<-* + l+++ + + aa+++ + ++q+ ++ l y T18769 165 VL--LQKG-YWKSAALVHGALAIQLKIYPLIY 193 UPF0056: domain 1 of 1, from 29 to 214: score -123.7, E = 9.9 *->lkfiisafvsLfaiiNPiGnv..PvFisLtenyp...aeerkrIilr l f+ + Lf + ++ ++ vF+ +++++++++ +++ + T18769 29 LVFYAHIHDYLFKVN--FTDIdyHVFSDAAKHVSnggSPFDRATYRY 73 AsiiafliLllFlv..fGklIlklFGIsidAfriAGGILLFlIaldMlfg + +a ++L + +++fGk+++ +F+I L+++ +++++ T18769 74 TPALAWILLPVVHFpdFGKILFCIFDI-----------LVAILYFKIMEK 112 kqskvDPektsksEkeeseeideIavvPLAiPLiAGPGaITtvmvlmsea ++ + +k +++E+ ++ ++++ LA PL T++++++ a T18769 113 DLNE---TKSETREEMKDDQTMNVVIYWLANPL-------TAIISARGNA 152 sssTFADigeklavvlAilL......awlitflillsssfiiRlLGrtGi s i+ ++++ + lL+++ ++++++ + l + +i+ l+ + T18769 153 ES-----IVAAVVLLNIVLLqkgywkSAALVHGALAIQLKIYPLIYLPSV 197 naltRimGLlLvaiavQmivdGikgif<-* L+L i+ Q +v +++f T18769 198 F-------LSLSTIGEQSCV---VNKF 214 DUF56: domain 1 of 1, from 88 to 218: score -68.5, E = 57 *->mlillllalvfaiillflliRfnvlppfsklyerviellcRekeknr + ++ +l+ +f i+ ++l+ + ++ + ++ Re+ k+ T18769 88 PDFGKILFCIFDILVAILYFKIM-EKDLN-----ETKSETREEMKD- 127 dhglgaiifyilglvfvsllFpmevAiasilvLalGDglAaiIGrryGrr d + + +i++++ + +++ +++ + +Aa++ ++ T18769 128 DQTMNVVIYWLANPLTAIISARGNAESI----------VAAVVLLNIVL- 166 tpilgngKSlEGslAfFvasflillvfygyygGYYvnPaaiallSrlsav + +g KS +A + ++++i l +y ++ ++ T18769 167 -LQKGYWKS----AALVHGALAIQLKIYPLIY----------------LP 195 llalvlgliaalvEalelksRldDNLsiPllsAil<-* + l l++i++ + ++ ++ +++ T18769 196 SVFLSLSTIGEQSCVVNKFK------------SLV 218 PMT: domain 1 of 1, from 16 to 246: score -51.0, E = 2.2 *->kiltlllflirflllalpnlvvfdevhfgkfasyYaeglffmdvhgl +++ l +f++r+ l ++ ++ +++ +f + + + f + + T18769 16 NKILLVAFVARIILVFYA-HIHDYLFKV-NFT-DIDYHVFSDAAK-H 58 pplgkmlialggyylagypglflflsigsflkfgnvpyfsmRlfsallGa +g + + ++ ++ y +++ ++++ +++ + p f+ lf+++ T18769 59 VSNGGSPF---DRATYRYTPALAWILL--PVVHF--PDFGKILFCIFDI- 100 ltvplvyltlrklgfskeaA..........llaallvildn.slvtlsry l+++l + ++ k + +++ +++++ ++++ + +++ l n++ ++s+ T18769 101 LVAILYFKIMEKDLN-ETKSetreemkddqTMNVVIYWLANpLTAIISAR 149 illDspLlFFttLavylflkfeklrladlkapfsrgwllwllltgialgl + +s+ ++L++ l+ k++ w ++++ +l T18769 150 GNAESIVAAVVLLNIVLLQKGY-----------------WKSAALVHGAL 182 afltKgvglftilpvgllfiwalwqllgqLawdkklpskrnqlwmsrvti a+ K + l ++lp ++l + + + + k+ s+ v++ T18769 183 AIQLKIYPL-IYLPSVFLSLSTIGEQSC---VVNKFKSL--------VSN 220 vkhlfarlliLillPvllyllffyvhfflyf<-* +k ++ l +L++ + ++ ++ f+ y T18769 221 WKGFAYMLVTLTSFAAVVLFF-----FQIYG 246 60KD_IMP: domain 1 of 1, from 97 to 260: score -141.0, E = 29 *->gNWGlSIIllTiliRlllyPLtkkQyrSmrfQakMqeLQPkikaIqe ++ il+ +l ++ + k + + + +e T18769 97 --------IFDILVAILYFKIMEKDLNET---KS---------ETRE 123 KYkkakDpnDqqklqqEmmkLYkkegvNPLgGCLPiLiQiPIFiALYyvl k D q ++ + L NPL ++ T18769 124 EMK------DDQTMNVVIYWL-----ANPL-----------------TAI 145 riaGfipklntvElrsapffflWipDLsapDpvnafgapslftstppsfl + ++ E a +l i L ++ ++ + l++++ l T18769 146 I-----SARGNAESIVAAVVLLNI-VLLQKGY---WKSAALVHGA----L 182 ghpplgwdtviyyiLPilmgatmflqqkmsptsqtkeasqndpqQqqmKl +++ i P++++ ++fl + + +q T18769 183 --------AIQLKIYPLIYLPSVFLSLSTI-----------GEQSC---V 210 vmyvmPlm.....FtfFflnfPS..GLvLYWitnNlltiaQQyyinklle v ++ +l+++ ++F ++++++ S ++vL + ++ y+i+++ T18769 211 VNKFKSLVsnwkgFAYMLVTLTSfaAVVLFFFQIYGQLFLDEYLIYHVKR 260 <-* T18769 - - DUF216: domain 1 of 1, from 137 to 300: score -71.3, E = 91 *->qVFhlLlfLLAiqRFllYFfPsqRQtEksVkivQkfiqkriwylYlv + L+ + ++ +++ + V++ Qk k +++ + T18769 137 WLANPLTAIISARGNAESIVAA-VVLLNIVLL-QKGYWKSAALVHGA 181 FiiKdvisllviviliayrvlaFfllaslnnskkiefwltgfelleliyv ++i + i l ++l s + s + ++++ ++ + ++v T18769 182 LAIQLKIYPL-------------IYLPSVFLSLSTIGEQSCVVNKFKSLV 218 tvfivlnlLiflsaflYiPiiisirkdflshltSaqqhlllfnkpqkYil ++++ ++ +++ ++ ++ l+++ ++ q + Y + T18769 219 SNWKGFAYMLVTLTSF------AAVV--LFFFQIYGQ-----LFLDEYLI 255 WQtilVfifKlitspvgiififfyldsaafiiliIpitdmpSrkrivvtD + + ++ ++ ++f+ yl++a++++ I + T18769 256 YHVKRRDLAHNFS----PYFYLLYLYEANPTMSQII--G----------L 289 ivttPliIQiS<-* ++P i+ i T18769 290 GAFIPQIVLIV 300 ART: domain 1 of 1, from 340 to 365: score 0.1, E = 44 *->mpalhfvLllSVglllstqalssaiq<-* +p+l ++ S l ls++a++ a+q T18769 340 LPLLAHKIMMSRQLALSLMAAWFATQ 365 UPF0118: domain 1 of 1, from 91 to 387: score -163.1, E = 85 *->llliliflllilafipfinvietl..............lvplliAlv + +++ ++ +++a+++f + ++l++++++++++ +++ + ++ T18769 91 GKILFCIFDILVAILYFKIMEKDLnetksetreemkddQTMNVV--- 134 layllnPvvrfLqkkrgikrslaillvlllflval...vllgvlliplli ++ l+nP++ ++ + + + ++++v+ll +v+l+++++ + l+ T18769 135 IYWLANPLTAII--SARGNAESIVAAVVLLNIVLLqkgYWKSAALV---- 178 nqltqLikslPtgdyidslqnwlnelpeslpelealdasvviqqlnssls + L +l+ ++ ++ l s++ ++ s ++ T18769 179 --HGALAIQLK---IYPLIYLPSVFLSLSTIGEQ------------SCVV 211 dilsnilssilnsllsllasltglllqlilvLvllfffLldgeklrqgii + + +++s+ +++++ l+ ++ + v+lfff +g+ ++++ + T18769 212 NKFKSLVSNWKGFAYMLVTLTS-------FAAVVLFFFQIYGQLFLDEYL 254 sllPkryrervrailrelndtlggylrgqvivaliigvlvfigllilgvp + kr r+l+++++ y+ +l++ ++ T18769 255 IYHVKR---------RDLAHNFSPYF-----------------YLLYLYE 278 yAlllAllvglanlIPyiGpviiliPiaiialltggGiiwaalivlivvl + ++ ++gl ++IP i v+i+++ a+ + + + + +++ + T18769 279 ANPTMSQIIGLGAFIPQI--VLIVFF----AFKHYD--DLPFCWFITTFA 320 lv........qqiedniLrPklmgkrlglhPlvillsliaGgslfGlvGl +v+ ++ ++q ++ +i+ l+ +++ ++ + l ++ a+ G++ l T18769 321 FVtynkvctsQYFVWYIVLLPLLAHKIMMSRQLALSLMAAWFATQGIW-L 369 ilapPltavlkaildayr<-* + a + + ++ + T18769 370 LAAYLFEFQGWNTFFLMF 387 Papilloma_E5: domain 1 of 1, from 337 to 403: score -38.1, E = 13 *->illvFlLCFcVlLclClllRPLlLSvsvYAaLLlLVLClLWVfvt.. i+l+ lL+ + l l +L + +lL L+ f + + T18769 337 IVLLPLLAHKIMMSRQLAL-SLMAAWFATQGIWLLAA-YLFEFQGwn 381 SpLraFivYliFlYLPlflIHlHAqyLlq<-* + ++ F+++++Fl+ + ++ L q T18769 382 TFFLMFLASCLFLI-------ANSFILKQ 403 7tm_2: domain 1 of 1, from 186 to 409: score -174.2, E = 70 *->allLkviytVGyslSsLvcLllaiaifllfRkLrctRnyIHmNLfls + +iy+ + lS L + ++ f++L ++ + T18769 186 LKIYPLIYLPSVFLS-LSTIGEQSCVVNKFKSLVSNWKG------FA 225 fiLralsfLigdavllnsg................CkvvavflhYfflaN ++L l+ ++ ++ ++ ++ ++ ++ + ++ +++ f Yf+l T18769 226 YMLVTLTSFAAVVLFFFQIygqlfldeyliyhvkrRDLAHNFSPYFYL-- 273 FfWmLvEGlYLytLlvvtvevffserkrlwwYlliGWGvPavfvtiwaiv lYLy ++ ++ + + +G +P ++ ++ ++ T18769 274 --------LYLY----EA-------NPTMSQIIGLGAFIPQIVLIVFFAF 304 rpdkygpilaegpagygnegcCWlsndtnsgfwWiikGPilliilvNfif + +y++ +CW + t +++++ ++ f+ T18769 305 K-------------HYDDLPFCWFIT-T-----FAFVTYNKVCTSQYFVW 335 finilriLvqKlridslspqtgetdqyrkkrlvkstLlLlPLLGvtwilf i l L +K s+q + ++ +++ + + LL +++ T18769 336 YIVLLPLLAHKIM---MSRQLA---LSLM--AAWFATQGIWLLAA-YLFE 376 lfapedqsqGtlslvflylfliLnSfQGffVavlYCflNgEV<-* + ++ +l + lfli nSf +l N+ V T18769 377 FQGWNTF---FLMFLASCLFLIANSF------ILKQIINHYV 409 // 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: T18769.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: T18769 hypothetical protein B0491.1 - Caenorhabditis elegans. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- PSI_8 Photosystem I reaction centre subunit VIII 2.3 65 1 Cbl_N2 CBL proto-oncogene N-terminus, EF hand-like 1.3 69 1 YGGT YGGT family 1.0 82 1 PsbH Photosystem II 10 kDa phosphoprotein 0.6 82 1 DUF212 Uncharacterized BCR, COG1963 0.1 64 1 ART NAD:arginine ADP-ribosyltransferase 0.1 44 1 DDHD DDHD domain -0.9 87 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- PSI_8 1/1 77 85 .. 1 9 [. 2.3 65 Cbl_N2 1/1 214 225 .. 75 86 .] 1.3 69 YGGT 1/1 224 245 .. 1 22 [. 1.0 82 ART 1/1 340 365 .. 1 26 [. 0.1 44 DUF212 1/1 346 367 .. 1 22 [. 0.1 64 DDHD 1/1 398 406 .. 258 266 .] -0.9 87 PsbH 1/1 379 411 .. 21 52 .] 0.6 82 Alignments of top-scoring domains: PSI_8: domain 1 of 1, from 77 to 85: score 2.3, E = 65 *->LPSIfVPlV<-* L +I+ P+V T18769 77 LAWILLPVV 85 Cbl_N2: domain 1 of 1, from 214 to 225: score 1.3, E = 69 *->wktLlrNWqtLa<-* +k+L+ NW+ a T18769 214 FKSLVSNWKGFA 225 YGGT: domain 1 of 1, from 224 to 245: score 1.0, E = 82 *->lalllsillslliiysflLliy<-* +a++l +l s+ + +f++ iy T18769 224 FAYMLVTLTSFAAVVLFFFQIY 245 ART: domain 1 of 1, from 340 to 365: score 0.1, E = 44 *->mpalhfvLllSVglllstqalssaiq<-* +p+l ++ S l ls++a++ a+q T18769 340 LPLLAHKIMMSRQLALSLMAAWFATQ 365 DUF212: domain 1 of 1, from 346 to 367: score 0.1, E = 64 *->rAlltNevlLSsLasiilAQVI<-* + ++ ++ LS a++++ Q+I T18769 346 KIMMSRQLALSLMAAWFATQGI 367 DDHD: domain 1 of 1, from 398 to 406: score -0.9, E = 87 *->lFlLkeiyr<-* +F+Lk+i+ T18769 398 SFILKQIIN 406 PsbH: domain 1 of 1, from 379 to 411: score 0.6, E = 82 *->gWGttplmgvfmalfavFLliil.eiYnssvll<-* gW t lm ++ lf++ + il++i n v + T18769 379 GWNTFFLMFLASCLFLIANSFILkQIINHYVPI 411 // 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: T18769.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: T18769 hypothetical protein B0491.1 - Caenorhabditis elegans. 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 Jan 24 14:28:48 2002 Sequence file: T18769.fa ---------------------------------------- Sequence T18769 (417 residues): Matching pattern PS00001 ASN_GLYCOSYLATION: 10: NETF 43: NFTD 115: NETK Total matches: 3 Matching pattern PS00005 PKC_PHOSPHO_SITE: 70: TYR 147: SAR Total matches: 2 Matching pattern PS00006 CK2_PHOSPHO_SITE: 45: TDID 64: SPFD 117: TKSE 121: TREE 203: TIGE Total matches: 5 Matching pattern PS00008 MYRISTYL: 150: GNAESI Total matches: 1 Total no of hits in this sequence: 11 ======================================== 1314 pattern(s) searched in 1 sequence(s), 417 residues. Total no of hits in all sequences: 11. 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, 417 units >ER-GOLGI-traffic signal is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 units >INTRA-SIGNAL-M minimal SH3 binding is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 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, 417 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, 417 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, 417 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, 417 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, 417 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, 417 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, 417 units >TM-CYTOPLASMIC-M di-hydrophobic endocytosis motifs for internalized transmembrane proteins is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 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, 417 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, 417 units >EXTRACELL-M minimal furin protease cleavage site motif is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 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, 417 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, 417 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, 417 units >NUCLEAR NLS experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 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, 417 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, 417 units >NUCLEAR NLS HCDA experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 units >NUCLEAR NLS SV40 LrgT experimentally determined is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 units >NUCLEAR NLS H2B experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 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, 417 units >NUCLEAR NLS Amida experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 units >NUCLEAR NLS Amida experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 units >NUCLEAR NLS RanBP3 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 units >NUCLEAR NLS Pho4p experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 units >NUCLEAR NLS DNAhelicaseQ1 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 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, 417 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, 417 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, 417 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, 417 units >NUCLEAR NLS GAL4 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 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, 417 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, 417 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, 417 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, 417 units >NUCLEAR NLS TR2 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 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, 417 units >NUCLEAR NLS polyomaVP1 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 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, 417 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, 417 units >NUCLEAR NLS Rex experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 units >NUCLEAR NLS SRY experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 units >NUCLEAR NLS SRY experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 units >NUCLEAR NLS SOX9 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 units >NUCLEAR NLS SOX9 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 units >NUCLEAR NLS NS5A experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 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, 417 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, 417 units >NUCLEAR NLS adenovE1a experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 units >NUCLEAR NLS ystDNApolalpha experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 units >NUCLEAR NLS hVDR experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 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, 417 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, 417 units >NUCLEAR NLS cFOS experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 units >NUCLEAR NLS cJUN experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 units >NUCLEAR NLS hDNApolalpha experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 units >NUCLEAR NLS hDNAtopoII experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 units >NUCLEAR NLS hDNAtopoII experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 units >NUCLEAR NLS hBLM experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 units >NUCLEAR NLS hARNT experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 units >NUCLEAR NLS influenzaNP experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 units >NUCLEAR NLS influenzaNP experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 units >NUCLEAR NLS p54 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 units >NUCLEAR NLS hProTalpha experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 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, 417 units >NUCLEAR NLS protHsc9 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 units >NUCLEAR NLS protHsci experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 units >NUCLEAR NLS protHsc3 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 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, 417 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, 417 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, 417 units >NUCLEAR NLS MyoD experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 units >NUCLEAR NLS MyoD experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 units >NUCLEAR NLS opaque2 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 units >NUCLEAR NLS CTP experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 units >NUCLEAR NLS HCV experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 units >NUCLEAR NLS HCV experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 units >NUCLEAR NLS p110RB1 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 units >NUCLEAR NLS experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 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, 417 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, 417 units >NUCLEAR NLS Nucloplasmin experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 units >NUCLEAR NLS Nucleolin experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 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, 417 units >NUCLEAR NLS Nab2 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 units >NUCLEAR NLS M9 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 units >NUCLEAR NLS lscMyc experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 units >NUCLEAR NLS humKprotein experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 units >NUCLEAR NLS FluA experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 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, 417 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, 417 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, 417 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, 417 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, 417 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, 417 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, 417 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, 417 units >NUCLEAR NLS p53 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 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, 417 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, 417 units >NUCLEAR NLS L29 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 units >NUCLEAR NLS L29 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 units >NUCLEAR NLS Max experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 units >NUCLEAR NLS L3 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 units >NUCLEAR NLS dyskerin experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 417 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, 417 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, 417 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: T18769.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: T18769 hypothetical protein B0491.1 - Caenorhabditis elegans. 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: T18769.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: T18769 hypothetical protein B0491.1 - Caenorhabditis elegans. 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= T18769 hypothetical protein B0491.1 - Caenorhabditis elegans. (417 letters) Searching..................................done Results from profile search Score E Sequences producing significant alignments: (bits) Value HISDAC Histone deacetylase domain 21 2.2 POZ Pox virus Zinc finger domain (Also called BTB domain; a... 21 2.9 14-3-3 14-3-3 protein alpha Helical domain 21 3.2 DHHC Novel zinc finger domain with DHHC signature 21 3.5 UBHYD Ubiquitin C-terminal hydrolase domain 20 6.6 ARM Armadillo repeat 19 8.0 >HISDAC Histone deacetylase domain Length = 433 Score = 21.4 bits (45), Expect = 2.2 Identities = 5/15 (33%), Positives = 5/15 (33%), Gaps = 1/15 (6%) Query: 95 FCIF-DILVAILYFK 108 Sbjct: 160 FCYLNDIVLGIIELL 174 >POZ Pox virus Zinc finger domain (Also called BTB domain; a protein-protein interaction domain) Length = 229 Score = 21.3 bits (44), Expect = 2.9 Identities = 7/61 (11%), Positives = 7/61 (11%), Gaps = 2/61 (3%) Query: 4 VRSFVKNETFNRNKILLVAFVARIILVFYAHIHDYLFK--VNFTDIDYHVFSDAAKHVSN 61 Sbjct: 30 VQLNVGGSLYYTTVRALTRHDTMLKAMFSGRMEVLTDKEGWILIDRCGKHFGTILNYLRD 89 Query: 62 G 62 Sbjct: 90 D 90 >14-3-3 14-3-3 protein alpha Helical domain Length = 270 Score = 21.1 bits (44), Expect = 3.2 Identities = 8/16 (50%), Positives = 8/16 (50%) Query: 257 HVKRRDLAHNFSPYFY 272 Sbjct: 169 HPIRLGLALNFSVFYY 184 >DHHC Novel zinc finger domain with DHHC signature Length = 217 Score = 20.9 bits (43), Expect = 3.5 Identities = 10/39 (25%), Positives = 10/39 (25%) Query: 219 SNWKGFAYMLVTLTSFAAVVLFFFQIYGQLFLDEYLIYH 257 Sbjct: 39 SRRNGWSWPPHPLQIVAWLLYLFFAVIGFGILVPLLPHH 77 Score = 20.5 bits (42), Expect = 4.9 Identities = 8/46 (17%), Positives = 8/46 (17%), Gaps = 1/46 (2%) Query: 331 QYFVWYIVLLPLLAHKIMMSRQLALSLMAAWFATQG-IWLLAAYLF 375 Sbjct: 52 QIVAWLLYLFFAVIGFGILVPLLPHHWVPAGYACMGAIFAGHLVVH 97 Score = 19.7 bits (40), Expect = 8.6 Identities = 3/39 (7%), Positives = 3/39 (7%), Gaps = 1/39 (2%) Query: 286 IIGLGAFIPQIVLI-VFFAFKHYDDLPFCWFITTFAFVT 323 Sbjct: 54 VAWLLYLFFAVIGFGILVPLLPHHWVPAGYACMGAIFAG 92 >UBHYD Ubiquitin C-terminal hydrolase domain Length = 884 Score = 19.9 bits (41), Expect = 6.6 Identities = 3/11 (27%), Positives = 3/11 (27%) Query: 250 LDEYLIYHVKR 260 Sbjct: 180 LPPVLHLQLMR 190 >ARM Armadillo repeat Length = 532 Score = 19.5 bits (40), Expect = 8.0 Identities = 14/57 (24%), Positives = 14/57 (24%), Gaps = 5/57 (8%) Query: 271 FYLLYLYEANPTMSQIIGLGAFIPQIVLIVFFAFKHYDDLPF--CWFITTFAFVTYN 325 Sbjct: 96 FRKLLSIERSPPIEEVISAG-VVP--RFVEFLKKEDYPAIQFEAAWALTNIASGTSD 149 Underlying Matrix: BLOSUM62 Number of sequences tested against query: 105 Number of sequences better than 10.0: 6 Number of calls to ALIGN: 8 Length of query: 417 Total length of test sequences: 20182 Effective length of test sequences: 16839.0 Effective search space size: 6499042.3 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= T18769 hypothetical protein B0491.1 - Caenorhabditis elegans. (417 letters) Searching.................................................done Results from profile search Score E Sequences producing significant alignments: (bits) Value gi|2649774 [45..384] Periplasmic binding protein-like I 26 1.1 gi|1827635 [121..432] Metallo-dependent phosphatases 26 1.3 gi|951110 [5..279] ConA-like lectins/glucanases 25 2.2 gi|2144282 [125..305] S-adenosyl-L-methionine-dependent meth... 24 3.8 gi|2146173 [3..215] ADP-ribosylation 23 8.4 gi|1703166 [11..338] beta/alpha (TIM)-barrel 23 8.7 >gi|2649774 [45..384] Periplasmic binding protein-like I Length = 340 Score = 26.2 bits (57), Expect = 1.1 Identities = 6/81 (7%), Positives = 6/81 (7%), Gaps = 2/81 (2%) Query: 197 VFLSLSTIGEQSCVVNKFKSLVSNWKGFAYMLVTLTSFAAVVLFFFQIYGQLFLDEYLIY 256 Sbjct: 238 FLGIEYDFSTKTVTKGDLSLLEKTAGTSAPEALVQLPEVTSDYRNKVLTQDPLIEGYKVT 297 Query: 257 HVK--RRDLAHNFSPYFYLLY 275 Sbjct: 298 VSRIKERLGDYPVTWEHALEY 318 >gi|1827635 [121..432] Metallo-dependent phosphatases Length = 312 Score = 25.8 bits (56), Expect = 1.3 Identities = 9/42 (21%), Positives = 9/42 (21%) Query: 26 RIILVFYAHIHDYLFKVNFTDIDYHVFSDAAKHVSNGGSPFD 67 Sbjct: 195 KVDVVFAGHVHAYERSERVSNIAYKITDGLCTPVKDQSAPVY 236 >gi|951110 [5..279] ConA-like lectins/glucanases Length = 275 Score = 25.2 bits (55), Expect = 2.2 Identities = 18/63 (28%), Positives = 18/63 (28%), Gaps = 4/63 (6%) Query: 113 DLNETKSE--TREEMKDDQTMNVVIYWLA--NPLTAIISARGNAESIVAAVVLLNIVLLQ 168 Sbjct: 174 DVNSIKSAATTKWERRNGQTLNVLVSYDANSKNLQVTASYPDGQRYQVSYNVDLRDYLPE 233 Query: 169 KGY 171 Sbjct: 234 WGS 236 >gi|2144282 [125..305] S-adenosyl-L-methionine-dependent methyltransferases Length = 181 Score = 24.5 bits (52), Expect = 3.8 Identities = 13/117 (11%), Positives = 13/117 (11%), Gaps = 4/117 (3%) Query: 2 QCVRSFVKNETFNRNKILLVAFVARIILVFYAHIHDYLFKVNFTDIDYHVFSDAAKHVSN 61 Sbjct: 61 IGELNLGHFPGLTFNRALMDSLVEPGKRHSKPWCRYGYFDFILTNPPFGVTVEASGAAYS 120 Query: 62 GGSPFDRATYRYTPALAWILLPVVHFPDF----GKILFCIFDILVAILYFKIMEKDL 114 Sbjct: 121 GYDIAFTANGEPRARQSSEWLFVEQSLRWLKPGGTLAVVLPRSVLTNPSSAYERSLL 177 >gi|2146173 [3..215] ADP-ribosylation Length = 213 Score = 23.2 bits (49), Expect = 8.4 Identities = 19/62 (30%), Positives = 19/62 (30%), Gaps = 8/62 (12%) Query: 202 STIGEQSCVVNKFKSLVSNWKGFAYMLVTLTSFAAVVLFFFQIYGQLFLDEYLIYHVKRR 261 Sbjct: 23 STLGD---VRNFFEHILSTNFGRSYFISTSETPTAAIRFFGS-----WLREYVPEHPRRA 74 Query: 262 DL 263 Sbjct: 75 YL 76 >gi|1703166 [11..338] beta/alpha (TIM)-barrel Length = 328 Score = 23.3 bits (50), Expect = 8.7 Identities = 6/91 (6%), Positives = 6/91 (6%), Gaps = 18/91 (19%) Query: 221 WKGFAYMLVTLTSFAAVVLFFFQIYGQLFLDEYLIYHVKR---RDLAHNFSPYFYLLYLY 277 Sbjct: 44 YKKFRDLQDFLDYYYIGTNVLISE--------QDFFDLAWAYFKKVHKQGLVHAEVFY-- 93 Query: 278 EANPTMSQIIGLGAFIPQIVLI--VFFAFKH 306 Sbjct: 94 --DPQ-SHTSRGISIETVTKGFQRACDKAFS 121 Underlying Matrix: BLOSUM62 Number of sequences tested against query: 1187 Number of sequences better than 10.0: 6 Number of calls to ALIGN: 6 Length of query: 417 Total length of test sequences: 256703 Effective length of test sequences: 213024.0 Effective search space size: 81016068.5 Initial X dropoff for ALIGN: 25.0 bits ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ calculation of internal repeats with prospero ***** PROSPERO v1.3 Thu Jan 24 14:29:28 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 T18769 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: T18769.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: T18769 hypothetical protein B0491.1 - Caenorhabditis elegans. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- TIGR00427 TIGR00427: conserved hypothetical protein T -133.8 40 1 TIGR00861 MIP: MIP family channel proteins -143.5 76 1 TIGR00367 TIGR00367: K+-dependent Na+/Ca+ exchanger r -242.7 15 1 TIGR00784 citMHS: citrate transport -380.2 93 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- TIGR00427 1/1 47 191 .. 1 206 [] -133.8 40 TIGR00861 1/1 152 324 .. 1 258 [] -143.5 76 TIGR00784 1/1 70 350 .. 1 439 [] -380.2 93 TIGR00367 1/1 155 376 .. 1 523 [] -242.7 15 Alignments of top-scoring domains: TIGR00427: domain 1 of 1, from 47 to 191: score -133.8, E = 40 *->MdiafdLsFyikvFi.sLFaiinPiGnvPiFisLTesYtaeeRekia +d +vF++ ++n G P F T++Yt + T18769 47 ID--------YHVFSdAAKHVSN--GGSP-FDRATYRYTPA------ 76 kkAvIsafvILlifll..fGdlILkyFGIsIdAfriAGGILlflIAldml +a + L + +++fG + F+I + IL f+I m T18769 77 -----LAWILLPVVHFpdFGKILFCIFDILVA-------ILYFKI---ME 111 sGKesekkkhkhdEkeeskeidsIavvPLAlPLiAGPGAItatmvliaka + + e k+ +E ++ LA PL ta +++ a T18769 112 KD-LNETKSET-REEMKDDQTMNVVIYWLANPL-------TAIISARGNA 152 sdIgekflVvlaIalvllitfllflyaafiirrlgrtGinvitRiMGLlL +I+ ++Vvl + l+ + +aa + T18769 153 ESIV--AAVVL--LNIVLLQKGYWKSAALVHG------------------ 180 aAiAVefIvtGi<-* A+A+++ + T18769 181 -ALAIQLKIYPL 191 TIGR00861: domain 1 of 1, from 152 to 324: score -143.5, E = 76 *->AEflGTfllVffGvGsvlgvnvaskiiDkmksLssaygavGggasvp AE + V++ v + ++ ++ y+ + T18769 152 AESI-----VAAVVLLNIVLLQKG------------YWKSA------ 175 gqflgiaLAfG.LavatlvyavggkISGAHlNPAVTiAl.......llgr aL++G La+ + +y + P+V ++l++ +++++++ T18769 176 ------ALVHGaLAIQLKIYPLIY-------LPSVFLSLstigeqsCVVN 212 rf....plirvpvYiVAQliGAilGaallygltsgaitefegnlavagsv +f++ + ++ + Y+ ++ ++++++l+++ +g++ f ++++ T18769 213 KFkslvSNWKGFAYMLV-TLTSFAAVVLFFFQIYGQL--FLDEYLIYH-- 257 lsaGifatfPksyvsagqaffvEfIgTaiLvlvilattdpdrnrvprggi ++ ++ f + L + + a + p + + T18769 258 --------------VKRRDLAHNFSPYFYLLYLYEA-N-PTMSQ------ 285 laPLaIGllvalihlslgpyTGtgmNPARslGPalvagligwgnkaFtvg +IGl ++ ++l+ + +++ +++ T18769 286 ----IIGLGAFIPQIVLIVF--------------FAFK--HYDD------ 309 hwkYhWvywvGPivGailgalvY<-* ++ w+ + ++ + Y T18769 310 ----LPFCWFIT----TFAFVTY 324 TIGR00784: domain 1 of 1, from 70 to 350: score -380.2, E = 93 *->MLaILGFvMmlVFmiLIMtkrlSaLvALvvtPIVFALIaGFGFkdvG t r + A ++ P+V F d G T18769 70 ------------------TYRYTPALAWILLPVVH-------FPDFG 91 dMmieGiqdvAptAvmLLFAILYFGImIDaGLFDPLieKILSiVKGDPlK ++ i d +L AILYF Im eK L K T18769 92 K-ILFCIFD-------ILVAILYFKIM----------EKDLNETK----- 118 IaVGtAVLtMliALDGDGtTTYMITvsAMLPLYkrLGmnplVLAgiAmLg + T r m+ T18769 119 ------------------SET-------------REEMK----------D 127 lgimnGiiPWGgptaRaiSaLgLDpSelfvPLiPvmla.GilCviavAYv mn +i W l PL + a+G + i A v T18769 128 DQTMNVVIYW-----------------LANPLTAIISArGNAESIVAAVV 160 LGkkERkRLGVieLeqrHitKDAsasepaAalEdEqLKRPkLiwf.NLLL L L ++ L + K A a a+ qLK Li+++ +L T18769 161 L-------LNIVLLQK-GYWKSAALVHGALAI---QLKIYPLIYLpSVFL 199 tvSLma...aLVlgkvsLsVLFliAFvvALiVNYPNvkeQkkRIAaHSgN +S +++++++V +sL V +F+ L T18769 200 SLSTIGeqsCVVNKFKSL-VSNWKGFAYML-------------------- 228 aLaVvsmVFAAGV.FtGILsGTKMVDa..mAiSlvSlIPesMGGflPvIv V + FAA V F G D+ + + + +++ + T18769 229 ---VTLTSFAAVVlFFFQIYGQLFLDEylIYHVKRRDLAHNFSPYFYLL- 274 ALtSipFTFlmSNDAYYFGvlPIlAEAAsAYGidkvEIARASilGQPVHL Y + P ++ i+G T18769 275 ---------------YLYEANPTMSQ----------------IIG----- 288 LSPLVpSTyLLVgmvgvslgd..hQkFAvKWAVlt..........siVmT L +p +L V + +d ++ F A +t ++ +++ + + T18769 289 LGAFIPQIVLIVFFAFKHYDDlpFCWFITTFAFVTynkvctsqyfVWYIV 338 llALLiGaIsil<-* ll LL I ++ T18769 339 LLPLLAHKIMMS 350 TIGR00367: domain 1 of 1, from 155 to 376: score -242.7, E = 15 *->LillligllilGLiLliyg...adlfVkslvrIarkLGiSpliiGvT ++ + ++l + Ll +g ++ +V ++ +a L+i pli T18769 155 ---IVAAVVLLNIVLLQKGywkSAALVHGA--LAIQLKIYPLIY--- 193 vvAiGTSlPElftSLiAslagqpdigvGnviGSNIfNIlLiLGlsAiisr lP +f SL s +g S++ N +++s T18769 194 -------LPSVFLSL--STIGEQ---------SCVVNK-----FKSLVS- 219 piivdkdlPLrrdilflLlvsi.lLlffglDGqSYSFFvmwisrldgvvl ++ + + +L+++ ++++++++++q + g T18769 220 ------NW---KGFAYMLVTLTsFAAVVLFFFQ-----------IYGQLF 249 lilyvvYLlflvKeerwvekesnRNKVVKVTVSEAQAKASTAGDKEEPTL l y++Y + r T18769 250 LDEYLIY-----HVKR---------------------------------- 260 PNKPRLQRGGSSASLHNSLmRNSiFQLmiHTLDPLAEELGSYGKLKYYdt T18769 - -------------------------------------------------- - yteEGRFREKASiLHKiAKKKCqldenerqvGAANHVDYAAEKiELPNST + + ++ + T18769 261 --RD------------------LAHNFS-PY------------------- 270 STEVEmTPSSEASEPVQNGNLSHSiEAADAPQATETAEEDDDQPLSLSWP T18769 - -------------------------------------------------- - skTekqiffklvlliigPLWiTLPDVRKPASKKFFPiTFFGSliglvVgs +++l++ T18769 271 ------------------------------------------FYLLYL-- 276 rLLVdsAvkiAeNilgISEkiiGLtllAiGTSlPELvvSvaaarkglgDi + A iiGL G +P v v+ a k D T18769 277 ----YEANPTMS-------QIIGL-----GAFIPQIVLIVFFAFKHYDD- 309 AvGnviGSNIFNIlvgLgvpaLfvpiiipveplalslDapVmviVtLvlm L++ +++++ + ++++ V iV+L l+ T18769 310 ----------------LPFCWFITTFAFVTYNKVCTSQYFVWYIVLLPLL 343 LlfktlsmklgRwRmN...KieGvlllalYiaY<-* + s++l m +G+ lla Y+ T18769 344 AHKIMMSRQLALSLMAawfATQGIWLLAAYLFE 376 // 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: T18769.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: T18769 hypothetical protein B0491.1 - Caenorhabditis elegans. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- TIGR00360 ComEC_N-term: ComEC/Rec2-related N-terminal 4.6 5.2 1 TIGR00748 fabH_rel: condensing enzyme, putative, FabH -0.3 37 1 TIGR00386 fucP: sugar transporter, fucose permease fa -1.0 52 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- TIGR00748 1/1 283 295 .. 1 13 [. -0.3 37 TIGR00386 1/1 297 308 .. 407 418 .] -1.0 52 TIGR00360 1/1 371 412 .. 1 42 [. 4.6 5.2 Alignments of top-scoring domains: TIGR00748: domain 1 of 1, from 283 to 295: score -0.3, E = 37 *->maGivGYGaYiPk<-* m i+G Ga+iP+ T18769 283 MSQIIGLGAFIPQ 295 TIGR00386: domain 1 of 1, from 297 to 308: score -1.0, E = 52 *->vvIliFAlkayk<-* v I +FA+k y T18769 297 VLIVFFAFKHYD 308 TIGR00360: domain 1 of 1, from 371 to 412: score 4.6, E = 5.2 *->iahllaisGlhlgllfglgfglarsleyflpkrgihwylpll<-* a+l+ G + +l+ l+ +l + f++k i+ y+p++ T18769 371 AAYLFEFQGWNTFFLMFLASCLFLIANSFILKQIINHYVPIV 412 // 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: T18769.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: T18769 hypothetical protein B0491.1 - Caenorhabditis elegans. 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: T18769.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: T18769 hypothetical protein B0491.1 - Caenorhabditis elegans. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- COG2246 -69.0 74 1 COG2891 -81.3 20 1 COG0096 -92.8 62 1 COG2095 -133.7 83 1 COG0382 -149.8 47 1 COG0682 -160.6 4 1 COG1275 -177.5 26 1 COG1175 -189.0 17 1 COG0628 -190.0 94 1 COG1906 -223.7 1.9 1 COG0475 -224.2 69 1 COG0109 -247.7 84 1 COG2807 -320.9 87 1 COG2271 -328.5 66 1 COG1178 -334.4 68 1 COG1113 -419.6 28 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- COG2095 1/1 16 194 .. 1 218 [] -133.7 83 COG0096 1/1 132 212 .. 1 145 [] -92.8 62 COG1113 1/1 1 269 [. 1 481 [] -419.6 28 COG2891 1/1 124 285 .. 1 173 [] -81.3 20 COG2246 1/1 181 309 .. 1 166 [] -69.0 74 COG0682 1/1 80 312 .. 1 365 [] -160.6 4 COG0109 1/1 138 359 .. 1 331 [] -247.7 84 COG0382 1/1 148 402 .. 1 289 [] -149.8 47 COG1175 1/1 172 404 .. 1 314 [] -189.0 17 COG1906 1/1 1 406 [. 1 419 [] -223.7 1.9 COG0628 1/1 80 406 .. 1 381 [] -190.0 94 COG2807 1/1 105 408 .. 1 426 [] -320.9 87 COG1275 1/1 122 410 .. 1 348 [] -177.5 26 COG1178 1/1 1 416 [. 1 615 [] -334.4 68 COG2271 1/1 69 416 .. 1 472 [] -328.5 66 COG0475 1/1 69 417 .] 1 427 [] -224.2 69 Alignments of top-scoring domains: COG2095: domain 1 of 1, from 16 to 194: score -133.7, E = 83 *->mdmmemlsfilsafllLfa.iidPfGnl.......PvFlsLtenl.. +++ + f+ + +l ++a+i d + ++ ++ + vF+ ++++++ T18769 16 NKI-LLVAFVARIILVFYAhIHDYLFKVnftdidyHVFSDAAKHVsn 61 ..saeeRkrvalrAsliAlliLlvFll..fGeliLkdlFGIsidafriAG ++s+ +R + ++ A ++L v +++fG+ ++ +F+I T18769 62 ggSPFDR-ATYRYTPALAWILLPVVHFpdFGKILFC-IFDI--------- 100 GilLfliAidMlfgktsatksdpaeiqeeEaieresiapfvvPLAiPLiA l+ + ++ + ++tks+ + eE+++ + ++ LA PL T18769 101 --LVAILYFKIMEKDLNETKSETR----EEMKDDQTMNVVIYWLANPL-- 142 GPGaIttvivlmseygsigklavvlaillawaityliLlsSsfivrlLGk t++i+ ++ + si ++ +++l + ++ + s++ + T18769 143 -----TAIISARGNAESI---VAAVVLLNIVLLQKGYWKSAALVH----- 179 tGinaitRimGLlLvalavQmivdGlkgifkglas<-* ala+Q+ i+++++ T18769 180 --------------GALAIQL------KIYPLIYL 194 COG0096: domain 1 of 1, from 132 to 212: score -92.8, E = 62 *->MmmtDpIADmLTrIRNAemaGkketvslPsSKLkgaIlkvLkkEGYI ++ + +A+ LT+I a + + s+ ++ + ++I vL ++GY T18769 132 NVVIYWLANPLTAI---ISA-RGNAESIVAAVVLLNI--VLLQKGYW 172 kdFevieedkkddfvvpnkdgrkgklrVqLKYrenrkpVInpikrVSkpG k+ + g l +qLK T18769 173 KSAALVH----------------GALAIQLKIYPL--------------- 191 lRvYkskeklprvlnGlGIaIvSTSkGVMtdreARkkgvGGEvLcyVw<- +Y lp v+ l ++ GE c V T18769 192 --IY-----LPSVFLSLSTI--------------------GEQSCVVN 212 * T18769 - - COG1113: domain 1 of 1, from 1 to 269: score -419.6, E = 28 *->M.dpslvmaddnqdaeqeLkRgLknRHIqlIAlGGAIGTGLFlGSgs M+ + ++ ++ +++ T18769 1 MqCVRSFVKNETFNRNK------------------------------ 17 aIqmAGPsvlLaYaIaGlivfl...IMRaLGEMavanPvaGSFsdYArky +lL+ +a +i+++ +I + L + +++ Fsd A+++ T18769 18 --------ILLVAFVARIILVFyahIHDYLFKVNFTDIDYHVFSDAAKHV 59 lGpwAGF...ltGWlYWflWvlvgmaElTAvgiYmqyWfpaFPdvPqWiw + F++ + +++ +W+l ++ FPd T18769 60 SNGGSPFdraTYRYTPALAWILLPV-------------VH-FPD------ 89 ALialvlllavNLisVKlFGElEFWFAlIKVaAIvafIvlGlvllfggfg FG+ + f ++ ++ + f T18769 90 ------------------FGK-------------ILFCIFDILVAILYFK 108 ggg...tGfsNLwahtGGFFPnGllGlllalqvvvFAFgGiElvGitAgE +++ + ++ E T18769 109 IMEkdlNETKSETRE----------------------------------E 124 akdPeksipkAinsViwRIliFYvGslfvilslyPWnqvgsggsgSPFVt kd ++ +n Vi+ ++ P++++ s g T18769 125 MKDDQT-----MNVVIYWLA-------------NPLTAIISAR-G----- 150 vFskiGipaAasImNfVVLTAAlSslNSGlYstsRMLysLAeqGdAPkff + i aA ++N+V L k++ T18769 151 --NAESIVAAVVLLNIVLLQ---------------------------KGY 171 aklsrrGVPvnAillsavvlllgVlLNYvaPsvekvFelltsssglgalf k +A++ a+++ l ++ ++Psv ++s+s++g T18769 172 WK-------SAALVHGALAIQLKIYPLIYLPSV------FLSLSTIG--- 205 vWlmIllsqLkfRkarkpaqgaalkFkmpLyPfttyltlaFllfvLvlMa ++++ +kFk + + ++ + + Lv+++ T18769 206 -----------------EQSCVVNKFKSLVSNWKGFAYM------LVTLT 232 fdpdtRislfvtpiwlvlLvigYlvfgkrrkaeahgarpvkaee<-* + ++ lf++ i l + Yl++ +r + ah + + T18769 233 SF--AAVVLFFFQIYGQLFLDEYLIYHVKRRDLAHNF-----SP 269 COG2891: domain 1 of 1, from 124 to 285: score -81.3, E = 20 *->mmtRfilnrwvilvsfllalvLqlvpwPyfvsyqvlrPdwLlL..vL m+ +++ + ++ l +++++ ++ ++++ + +lL+ vL T18769 124 EMKD--DQTMNVVIYWLANPLTAIISAR--GNAESIVAAVVLLniVL 166 l...yw.vlalphrVGigtgfimGllfD...llyGslLGvhalglsiigY l+++yw+++al h + ++ i+ l++ ++ +l+ s++G+++ + T18769 167 LqkgYWkSAALVHGALAIQLKIYPLIYLpsvFLSLSTIGEQSCVVNKFKS 216 lvaknylrLrnnvllplwqqaLvvillvflvlvLiflvellimnysgFvl lv+ +++ + l+++ + +v+l+ f +++ +fl e+li + T18769 217 LVSNWKGFAYM---LVTLTSFAAVVLFFFQIYGQLFLDEYLIYHVK---- 259 drFsptlllnillailLwPwvflLLrkvrkelrvr<-* +++l+ n + P ++lL + ++ T18769 260 ---RRDLAHN------FSPYFYLLYLYEANPTMSQ 285 COG2246: domain 1 of 1, from 181 to 309: score -69.0, E = 74 *->idertarrikallrrvtlklkrsrLl.kFiiVGvvGalV.nleafLl i l + + l++s+++++ + V + +lV+n +f + T18769 181 -ALAIQLKIYPLIYLPSVFLSLSTIGeQSCVVNKFKSLVsNWKGFAY 226 ilveaveGDVayiaasiaaieasIlnnFilNdrWTFqnRdkrkgsvsPef +lv + +a++ + I + +l ++ +kr + + T18769 227 MLVTLTS------FAAVVLFFFQIYGQLFLDEYLIYH--VKRRDLAH--- 265 lrRLlkfnlvrvaGlgiqLglltiLvelgkvDAtvFGvDlhyllanalGI +++ ++ L++l+ +++ ++++G T18769 266 -----------------NFSPYFYLLYLYE---------ANPTMSQIIGL 289 avafivNYifnsrltWrvtke<-* + afi ++ + ++ ++ T18769 290 G-AFIPQIVLIVFFAFKHYDD 309 COG0682: domain 1 of 1, from 80 to 312: score -160.6, E = 4 *->mmnemiisyyppldPvaFsiGPglairWYGllyvlGiliayllarrr + ++ ++ +p++ +++F i+ il+a+l++ + T18769 80 ILLPVVH--FPDFGKILFCIFD--------------ILVAILYF-KI 109 akrde.kdre.fsrginkdsfedfifwav...lgviiGAR..LgYvLfyw +++d ++ +++ ++ +++d++++ +++ + ++l++ii AR++ ++ T18769 110 MEKDLnETKSeTREEMKDDQTMNVVIYWLanpLTAIISARgnAESIVAA- 158 infsdYlahpldiFki....WeGhgFvGiRGmSiHGGlIGgiiaalifsr +l+i ++++ W+ +++ +++ + T18769 159 -------VVLLNIVLLqkgyWKS----------------AALVHGALAI- 184 khkkmktktktiallNykirqlsFlqlaDliAPlvplGqaiGRlGNFiNq ++k ++ l+++ P+v l + + T18769 185 -QLK-----------------IYPLIYL----PSVFLSLSTI-------- 204 ElyGrvtpgaigeelnlpnlwgmifPnmniggsegaqenevrfaqlqqlg G + + n ++ + n + + T18769 205 ---GEQS--------CVVNKFKSLVSNWKGFAY----------------- 226 dllgflprHPsQLYEaflegvvlFillylfrrkirplkrGfvfglYligY ++++ + +F+ + lf++ i + G++f + Y T18769 227 --MLVT--------------LTSFAAVVLFFFQI--Y--GQLFLDEYLIY 256 gifRFfiEffRepdaqlgglilikafsfsiltmgQiLslplilaglcqfi + R + + p ++l +l+ + tm Qi+ l+ ++ + T18769 257 HVKRRDLAHNFSPYFYLLYLY------EANPTMSQIIGLGAFIPQI---- 296 avkLRkyFwtefilvwaykkkkkvtkvav<-* +++ k++ ++ T18769 297 -------------VLIVFFAFKHYDDLPF 312 COG0109: domain 1 of 1, from 138 to 359: score -247.7, E = 84 *->lvdplvrk.....sarssiaisesarvkasqqstlKdYlqLTKPrii l pl+++ + +++a s +a++ ++ q+ +K T18769 138 LANPLTAIisargNAESIVAAVVLLNIVLLQKGYWKS---------- 174 sLlliTtlgGmfLAsrglgltgsvdplllv.ltliGgsLaaAsacalNny ++l+ +LA+ ++pl+ ++ ++ s +c++N T18769 175 -----AALVHGALAIQ-----LKIYPLIYLpSVFLSLSTIGEQSCVVNKF 214 iDRDIDakMaRTrkRPlVtGkisPrnALaFGlvLgvlGlaiLaafvNpla + ++s + +a+ +L +++ + a T18769 215 ------------------KSLVSNWKGFAY----------MLVTLTSFAA 236 AvLglaGlffYvvl..YTlw.lKRrtpqNiviGGlaGAmPPLiGWaAVtG vL ++ +++ +l++Y ++++KRr T18769 237 VVLFFFQIYGQLFLdeYLIYhVKRRDL---------------------AH 265 sisigawllLfaIiFlWqPPHFWaLAifrkdDYrrAgIPmLPVvkGeevT ++s+++ lL++ Y++ ++ + T18769 266 NFSPYFY-LLYL--------------------YEA----------NPTMS 284 krqIllYtialfavslllpyllGlggyilYlvvAlvlgawfLflAiklyr + l + i +++ +++ + +++ +++f +++ +++ T18769 285 QIIGLGAFIPQIVLI-VFFAFKHYD------------DLPFCWFITTFAF 321 qqrindaddrkwArklFkySiiYLallfvalvidsflvlllll<-* + ++ + F+ i+ L ll ++++ + l+l+l T18769 322 -----VTYNKVCTSQYFVWYIVLLPLLAHKIMMSRQLALSLMA 359 COG0382: domain 1 of 1, from 148 to 402: score -149.8, E = 47 *->mmnklkayleLirlerpifallfllpgllgallaagg.lpslkalll + + +++ ++l+ + +++ + a l g + lk+++l T18769 148 ARGNAESIVAAVVLLNIVLLQKGYWKS---AALVHGAlAIQLKIYPL 191 fllavflaraagmviNDlfDreiDriNpRtknRPLpsGavSrreAlalsi ++l ++++ ++ + ++ N + +vS + a+ + T18769 192 IYLPSVFLSLSTIGEQSCV------VN--K-----FKSLVSNWKGFAYML 228 allalglalalGllnplafllalpalllllltYpllKRftplphlvlGll + l ++a++l + + l ++ +l++ + + + + p ++l +l T18769 229 VTLTSFAAVVL-FFFQIYGQL-FLDEYLIYHVKRRDLAHNFSPYFYLLYL 276 yglailagfaAvsgtlpptawlLflavfLwtagfdiiyaveDvEgDrkaG y + + + ++++g + p+++l+++++f + + D + + T18769 277 YEANPTMSQIIGLGAFIPQIVLIVFFAF---------KHYDDLPFCWFI- 316 lkSlPvlfGkkralaiaslfhllaallsllglllgllliyligllvaaal + f ++++ ++ f++ ++ll ll +++ ++ l ++aa T18769 317 ---TTFAFVTYNKVCTSQYFVWYIVLLPLLAHKIMMSRQLA--LSLMAAW 361 lvyehaivlkrpdeekacfafflantlvgivlflglaldvalr<-* + + + +l+++ e ++ +f + l + +++ +a +++l+ T18769 362 FATQGIWLLAAYLFEFQGWNTFFLMFLASCLFL--IANSFILK 402 COG1175: domain 1 of 1, from 172 to 404: score -189.0, E = 17 *->wlayllllPalllfllFiyyPlietlaiylSFtdwdgfppaaaqitp w +l+ al+ + + +yPli+ +++lS+ + T18769 172 WKSAALVHGALA--IQLKIYPLIYLPSVFLSLST------------I 204 gesefVGlkNfvrlftlfsDptFwqalknTll.ytllsvplqlvlgLllA ge++ V k f+ l++ ++ + +Tl +++++++++ + g l+ T18769 205 GEQSCVVNK-FKSLVS---NWKGFAYMLVTLTsFAAVVLFFFQIYGQLFL 250 ..lLLnqkrlkGrglfRtllflPyaiSpVvaaliWkflFnprdsfGliNq ++ L++ +k r l f Py ++ l+ + + + q T18769 251 deYLIYH--VKRRDLAHN--FSPY----------FYLLYLY-EANPTMSQ 285 lLnllGidpppv.iaipWlndpfwAllaiilvnvWkgtgfnmlifLAgLQ +++l ++p++v i+++ + ++ ++ ++ + ++ +n + T18769 286 IIGLGAFIPQIVlIVFFAFKHYDDLPFCWFIT-TFAFVTYNKVC------ 328 sIPqeLYEAAriDGAsrwqrFrhITLPlLrPtilfvlilstigafqvFde ++ ++I+L P ++ +++s a+ + T18769 329 ---------------TSQYFVWYIVL---LPLLAHKIMMSRQLALSL-MA 359 iyllTgGGPagGPpvgnaTdtlalyiYreaFeggpQdfGyAsAiavilfl ++ T+G ++la y+++ F+g++ f+ T18769 360 AWFATQG-----------IWLLAAYLFE--FQGWN------------TFF 384 ivliltliqfklfkrkveegs<-* + + + +++ +++++++++ T18769 385 LMFLASCLFLI-ANSFILKQI 404 COG1906: domain 1 of 1, from 1 to 406: score -223.7, E = 1.9 *->mmkvLnsGeqnFvPMvaislLlllFsVvvVli........llRKvn. m+ + s +n + +Ll+ F ++l + ++ l+ Kvn T18769 1 -MQCVRSFVKNET-FNRNKILLVAFVARIILVfyahihdyLF-KVNf 44 ..iGiSifvGaliLaiLSG.......LgidGiLe.vlyktvaswstlrLI ++i +f+ a+ G++ ++ + +L +l+ v +++ ++ T18769 45 tdIDYHVFSDAAKHVSNGGspfdratYRYTPALAwILLPVVHFPDFGKIL 94 vivi...LimgltgvmeqiGyLkkmeegllelFpKAkhsllllPaLIGLm +++ + + +me+ +L +++e + ++ I + T18769 95 FCIFdilVAILYFKIMEK--DLNETKSETREEMK----DDQTMNVVIYWL 138 PMPgGALvSA.pmiepvakkfrlnpekktliNYWFRHvwelfWPlYpAvV P A +SA+ e + l ++ + YW T18769 139 ANPLTAIISArGNAESIVAAVVLLNIVLLQKGYW---------------- 172 lvSavvGisireiSvklFPltil.altiGylffvrklkerlrksRnKvkG Sa + i +k++Pl l+ ++ l ++ + k ++ T18769 173 -KSAALVHGALAIQLKIYPLIYLpSVFLS-LSTIGEQSCVVNKFKS---- 216 LkmlLinlYPiiiilvl.....SVllgLdlLyGsfvgllSisipnvarie L + n + lv+ ++ V+l + +yG + l +i+ v+r+ T18769 217 L---VSNWKGFAYMLVTltsfaAVVLFFFQIYGQLF-LDEYLIYHVKRRD 262 dLkevLkrafqkrDIvLLLfaVmvYKsVIenSGlvesilpeivl.sFhv. L f + + LL + Gl+ +p+ivl F + T18769 263 -----LAHNFSPY--FYLLYLYEANPTMSQIIGLGA-FIPQIVLiVFFAf 304 ......PvillLlltPLiiG..lmTGIsfAyvaivLPLL.tefftsGivv ++ ++ P ++++ ++ ++ T f + LPLL + s T18769 305 khyddlPFCWFITTFAFVTYnkVCTSQYFVWYIVLLPLLaHKIMMS---- 350 fkklvLaylgGym...GvlLSPvHLClVLSAeYfgaElgkvYrklLlpsv +l+L +++ ++G+ L L A f+ ++ ++l s T18769 351 -RQLALSLMAAWFatqGIWL--------LAAYLFEFQGWNTFFLMFLASC 391 LTlilvgLvYiViiL<-* L li ++ ii T18769 392 LFLIANSFILKQIIN 406 COG0628: domain 1 of 1, from 80 to 406: score -190.0, E = 94 *->mlmspairrllkpvvlrllvlllillllll............flylf l + + ++ ++l++++ +l ++l + +++ +++ T18769 80 ILLPVVHFPDFG----KILFCIFDILVAILyfkimekdlnetKSETR 122 qplllplllAlvlayllnPvvrwLerklgipRplavllvllllllllall +++ + + +v+++l+nP++ + +++ + ++++ T18769 123 EEMKDDQTMNVVIYWLANPLTAIISA--RGN------------AESIVAA 158 llllvptlvgidqlgqlirnnlPqlnnllqqllawlpnig..llqlslya ++ll ++l ++ ++ ++l+ + la + +i + +s ++ T18769 159 VVLLNIVL--LQKGYWKS-------AALVHGALAIQLKIYplIYLPSVFL 199 sldeliqqlisnrlaailgsilssllnllgrqvknllglivslllvllll sl+ + +q ++++ s ++n+ g + l++ + ++l T18769 200 SLSTIGEQSC------VVNKFKSLVSNWKG----FAYMLVTLTSFAAVVL 239 fffLldgeklk.egilsllPsrlyrprvkrilselnaslgnyirGqvlva fff +g+ + +e++++ + +++l++ ++ y+ T18769 240 FFFQIYGQLFLdEYLIYHVK-----------RRDLAHNFSPYF------- 271 liiGvlsgigllllgvpyalllallagllnlIPyiGaviiwiPaliyall +ll ++ + ++gl ++IP i ++++ +a++ T18769 272 ----------YLLYLYEANPTMSQIIGLGAFIPQI------VLIVFFAFK 305 tggglatwggllvlivflv.......iqqlednvLrPklmgkrlgLhPll + + ++ ++++ +++v+ ++ + q +++++ l+ +++ ++ l T18769 306 HYD--DLPFCWFITTFAFVtynkvctSQYFVWYIVLLPLLAHKIMMSRQL 353 illsllgGgslfGfvGlilgpPl.....lavlkalldaylrgdiaelifk l + ++ + G++ l+ + +++ ++ ++++ +l l + + T18769 354 ALSLMAAWFATQGIW-LLAAYLFefqgwNTFFLMFLASCLFL-------I 395 klaeqlgeees<-* + +l++ T18769 396 ANSFILKQIIN 406 COG2807: domain 1 of 1, from 105 to 408: score -320.9, E = 87 *->lsARiGAHPGHPPEELLiDaevddmptmnsakkqlwvlllgIvlvAl l i ++ n k T18769 105 LYFKI------------------MEKDLNETKSETR----------- 122 NLRpalTsvGPLLdqiRaelgLSfaaagLLTaLPlLcfGliallaprLaR ++++++ ++ ++ L+ l a + + T18769 123 -------------EEMKDDQTMNV-------VIYWLANPLTAIISA---- 148 rlgeeRsivlgLlLIaaGillRsllpvpalLlGStaLaGvGIAIinVLLP +g+ siv++ +L+ + l + ++al G ++++ T18769 149 -RGNAESIVAAVVLLNIVLLQKGYWKSAALVHG-ALAI------------ 184 slIKrdFPrrvglmmGLYSlalmaGAA.LaaalavpLaehfggWrg.aLg + + ++ L S l+++ ++ + ++ ++ ++W+g a T18769 185 -------QLKIYPLIYLPSVFLSLSTIgEQSCVVNKFKSLVSNWKGfAYM 227 fWAllAlLALlaWlPQaksRerasahktkalpvrslwrnplaWqvTLfmG + l +++A ++ +Q ++ + ++ r l n T18769 228 LVTLTSFAAVVLFFFQIYGQLFLDEYLIYHVKRRDLAHNF---------- 267 LqSllyysliaWLPailierGwSaqeaGsLlslmqlvqlpsaLLvPlLas S +y l +l e + + +l+ + ++ L+ +a T18769 268 --SPYFYLL------YLYEANPTMSQ---IIGLGAFIPQIV--LIVFFAF 304 RLvkDrRplvvallavmLvGllGLlfaPd.lqlpilWalllGlGlGgaFp + + D p+ + + v ++ ++ W ++l T18769 305 K-HYDDLPFCWFITTFAFV-----TYNKVcTSQYFVWYIVL--------- 339 LaLtLIllrssnAqqAarLSAma.....QGfGYLlAAvGPwlvGvLhDat L L + + +q a LS ma +QG+ LlAA +L+ T18769 340 --LPLLAHKIMMSRQLA-LSLMAawfatQGI-WLLAA-------YLFEFQ 378 GnwsaawllLaavailmlifGLragrsryirlseeer<-* G ++ +++La ++ l + s + ++ + T18769 379 GWNTFFLMFLASCLFLI-------ANSFILKQIINHY 408 COG1275: domain 1 of 1, from 122 to 410: score -177.5, E = 26 *->vntMrmskiknfppswFAivLGtggLAlawlsySsvlpalkaasivL + M ++ n+ + w A +L ++ A + ++s + a+ + ivL T18769 122 REEMKDDQTMNVVIYWLANPLTAIISARGN--AESIVAAVVLLNIVL 166 ty.....lataifflLLipw.llkwilypnevla....DLrHPVlgSFyp + ++ + a+++ ++L i ++++ +i+ p+++l+ ++ + V+ F + T18769 167 LQkgywkSAALVHGALAIQLkIYPLIYLPSVFLSlstiGEQSCVVNKFKS 216 ti....piaamvvgaalihiypfaaapkvLwaiGvilqLlfSlllpyllf ++++ ++ a m+v + faa++ L+++ +qL++ +l y+ T18769 217 LVsnwkGFAYMLVTLT-----SFAAVV--LFFFQIYGQLFLDEYLIYHVK 259 rgesfelkhitPgWfiPPVglivisalslsllpHlsgvtqElhdlinlfg r ++ ++++ l +l E++ + + T18769 260 RR---------------DLAHNFSPYFYLLYLY-------EANPTMSQI- 286 fGaGmflyLaLlpGvvlyRLilhepLPtaarPtlgInLAPigvgvvayla +G G f++ + l+ v++++ + LP+ +t + + v+y T18769 287 IGLGAFIPQIVLI--VFFAFKHYDDLPFCWFITTF--------AFVTYNK 326 iakhesaiqiaNikepalilafiLwGfGlwqllfailltlrylrkLklPf + + ++ w + l+ ll+ +++ r l l + T18769 327 VCTSQYFV----------------WYIVLLPLLAHKIMMSRQLA---LSL 357 slswWAFtFPlaayavstlhlassfgigvlstagfaLywflilawaillv ++w A ++ +++ + ++ g + + +la + l+ T18769 358 MAAWFA---TQGIWLLAA---------YLFEFQGWNTFFLMFLASCLFLI 395 kTlyvvisgaaflsp<-* + + ++ + + + p T18769 396 ANSFILKQIINHYVP 410 COG1178: domain 1 of 1, from 1 to 416: score -334.4, E = 68 *->vvasly.v.m.ysaillvlavgalatlatvklvvmggdplriglwll + ++ v+ + + + l v++ a++ +v+++ + +++++ + T18769 1 MQCVRSfVkNeTFNRNKILLVAFVARIILVFYAHIHDYLFKVNFTDI 47 iglllaalllllpplvlavlalsafsg..glaeflavlsdayllrllgnT +++ +a+ + +g+++++++ + a+ + ll T18769 48 DYHVFSD------------AAKHVSNGgsPFDRATYRYTPALAWILLP-- 83 LllallvTvlslilGlplAyllsrydfPGrrwlrwllaLPiLLviPalvv ++++ +G+ iL++i v T18769 84 ---------------------VVHFPDFGK----------ILFCIFDILV 102 AfgfislfGksGwLarllgelfGlssreywlpdiygPlgGiilalvlfny A+ + ++ + l+ + ++re+ d T18769 103 AILYFKIM------EKDLN-ETKSETREEMKDDQT--------------- 130 PlvyllaaaalesidpsleEaArsLGasrwqvFrrVtLPllrPaiaagal + + + +++ +++++ +Ar G + +i a++ T18769 131 ----MNVVIYWLANPLTAIISAR--GNAE--------------SIVAAVV 160 LvFlyclsdFgavliLGGspqytTlttaIyqeilgsqldlatAalLallL L + +vl+ G+ +++++ +La+ L T18769 161 L--------LNIVLLQKGY----------WKSAAL------VHGALAIQL 186 Lllsllllwvvvkllerfsrgrqkvyssgqswarpiprilllglaalval ++ l+ l v l++ ++g ++++ ++++++++ T18769 187 KIYPLIYLPSVF--LSLSTIG------EQSCVVNKFKSLVSNWK------ 222 lfclllfsvlllgvilplsflllWtvlltsdewsdamlgplfstsfwhal f +l+ l ++ ++ f+ + +++l++de+ T18769 223 GFAYMLV--TLTSFAAVVLFFFQIYGQLFLDEYL---------------- 254 insLtlallAalialllaLllaylvrrsrsrlsrfidrLsmLplAvPGvV i+ ++ lA ++ + Ll+ y + + ++ L+ +P+ V T18769 255 IYHVKRRDLAHNFSPYFYLLYLYEANPT-------MSQIIGLGAFIPQIV 297 lalGllllfnnldnhwvdlaameGvkpllvlygtllllVlAyalralPfa l + +++f+++d lPf T18769 298 LIV--FFAFKHYD--------------------------------DLPFC 313 lrsleaalrqidprLeeaArsLGasrwqifrrvtLPLllpgllaAaalvF +++ a+ +++ s++ +++ v LPLl + + l++ T18769 314 WFITTFAFVTYNK--------VCTSQYFVWYIVLLPLLAHKIMMSRQLAL 355 alsmkElsATllLgppdftTLttaiynylsggdgryaaAavllvasaAlv l ++ ++++++ L+ +++++ + ++ +++ +l+ T18769 356 SLMAA------WFATQGIWLLAAYLFEFQG--WNTFFLMFLA----SCLF 393 Lvlislllfvllikrygersqgt<-* L++ s++l + +++ ++ +t T18769 394 LIANSFILKQIINHYVPIVKPKT 416 COG2271: domain 1 of 1, from 69 to 416: score -328.5, E = 66 *->mlnifkpaphiprlpdeevrdkkYkrwRiQiFigifiGYAaFYftRK + pa+ +lp v + + iF +++ A Y T18769 69 ATYRYTPALAWILLP--VVHFPDFGKILFCIFDILV---AILY---- 106 nFnvAmpgliedggFelsktqLGiigsafsiaYGvSKFvmGvvSDrsNpR F + ++l e+ + +++++ + + Y + + +++S r N+ T18769 107 -FKIMEKDLNETKS--ETREEMKDDQTMNVVIYWLANPLTAIISARGNAE 153 yFmafGLllsaivnilfGfspWaTsslflfvllwflnGwFQGmGWPPcar +a+ ll iv + G s++l + ++++ T18769 154 SIVAAVVLLN-IVLLQKGYW----KSAALVHGALAIQ------------- 185 tlthWfSkkERGtvwsiWNtsHNiGGalipilvglgaayfgd........ + ++ ++ ++v l++++ g+++ ++ T18769 186 --LKIYP-------------------LIYLPSVFLSLSTIGEqscvvnkf 214 .....dWraaFyfPgivAiivalflllllRDtPqsvGLPpiEeykedepe ++ + W++ y+ ++a++l++ q +G ++ de T18769 215 kslvsNWKGFAYMLVTLTSFAAVVLFFF-----QIYG-----QLFLDEYL 254 dydeekapeeeereLttkeiflkYVLkNKllWylalAnvFVYvvRyGvld +y+ r+L+ f Y yl T18769 255 IYHV------KRRDLA--HNFSPY-------FYL---------------- 273 WapvYLkEtkgfsGkvkAgiavtlFEvAGlpGtLLaGWlSDKlFkGrRgP +YL+E+ + + +i+ ++F +p L+ + Fk + + T18769 274 ---LYLYEANPTM---SQIIGLGAF----IPQIVLIVFF---AFKHYDDL 310 anvifmllitlavllywlnpaGnpsllvdaalLfmIGFlvyGPdqMLiGl + + f + + + + +++ + +++++++ L + M+ T18769 311 PFCWFITTFAFVTYNKVCTSQ-YFVWYIVLLPLLAH-------KIMMSRQ 352 aAaelapKkAAGTAaGftGlFgYlGGaafAgaplGliadtevhfGlkGWd A+ l+ + +F+ G ++l+ +f +GW+ T18769 353 LALSLMAA-----------WFATQG-----IWLLAAYLF---EF--QGWN 381 GgFivliiaAlGvlavllLlpvwnarkgaeedklqqlt<-* ++F ++++++l +a ++l + + + + + +t T18769 382 TFFLMFLASCLFLIANSFILKQII-NHYVPI--VKPKT 416 COG0475: domain 1 of 1, from 69 to 417: score -224.2, E = 69 *->atsfllelaiiLlvafllgiillakrlrlPpvlGyliaGiilGpsgl at + +l+ ++ ++ ++ +l +++ i+++ + T18769 69 ATYRYTPALAWILLPVVHFP-------DFGKILFCIFD-ILVAILYF 107 g...............k.lliiessetiklLaelGvilLlFliGLEfdle + +++ +++++++++ + + +i La+ l T18769 108 KimekdlnetksetreEmKDDQTMNVVIYWLAN--------------PLT 143 kLkkvgkrafglgllqgvltplllglllllyvlGlsfiaalflGg..... ++++ + + + ++v++ ll ++ll G+ aal+ G+ + T18769 144 AIISAR-----GNAESIVAAVVLLNIVLLQ--KGYWKSAALVHGAlaiql 186 ....iLslsStaivvkiLedlgllktreGqlalgalifeDiaaillLalv + ++++l+S+ + ++ + + ++ + T18769 187 kiypLIYLPSVFLSLSTIGEQS----------------------CVVNKF 214 palasggsgsdpGldeanelgglvvlllkiaaffalllll.grylvprll +l s+++g ++ ++v+l ++aa +++++ + g ++++ +l T18769 215 KSLVSNWKG----------FAYMLVTLTSFAAVVLFFFQIyGQLFLDEYL 254 rlvakdtgsrelflltvLllvlglAyglaellGlsmiLGAFlAGlllset ++ k ++ + + l+ + + +s i+G +G ++ T18769 255 IYHVK-RRDLAHNFSPYFYLLYLYEA----NPTMSQIIG---LGAFIPQ- 295 eyrkkhleLaeklispfrgfFiPlFFisvGmslDlgvlleailllLavil ++ + + + +pf +f F +v + + ++ + +l T18769 296 IVLIVFFAFKHYDDLPFCWFITT--FAFVTYNKVCTSQYFVWYI----VL 339 alllivvailgKilavyllarllgfskregdfrealkiGlllaprGEfsl ++ll+ +++++ la +l a ++ +G l T18769 340 LPLLAHKIMMSRQLALSLMAAWFAT-------------------QGIWLL 370 iiaslGlalglisevpetlfaalilvvlismiitPlllkllykrklgaar ++ + +++ + +f ++++ l+ i+++++lk + + + T18769 371 AAYLFEFQGWNT------FFLMFLASCLF-LIANSFILKQIINHY--VPI 411 vekaae<-* v++++ T18769 412 VKPKTD 417 // 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: T18769.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: T18769 hypothetical protein B0491.1 - Caenorhabditis elegans. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- COG0233 2.4 22 1 COG0010 1.7 16 1 COG2271 0.7 20 1 COG2314 0.4 47 1 COG2171 -0.7 66 1 COG1880 -1.1 58 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- COG1880 1/1 105 117 .. 218 230 .] -1.1 58 COG2314 1/1 77 123 .. 111 162 .] 0.4 47 COG0233 1/1 111 126 .. 1 16 [. 2.4 22 COG0010 1/1 150 174 .. 323 347 .] 1.7 16 COG2171 1/1 210 220 .. 1 11 [. -0.7 66 COG2271 1/1 376 392 .. 427 445 .. 0.7 20 Alignments of top-scoring domains: COG1880: domain 1 of 1, from 105 to 117: score -1.1, E = 58 *->lYlkyLekllael<-* lY+k+ ek+l e T18769 105 LYFKIMEKDLNET 117 COG2314: domain 1 of 1, from 77 to 123: score 0.4, E = 47 *->fcwlllpllaiiLvlgvhrtviiawIigiIdgflsatkfdarlnrky ++w+llp +v+ + i++ I++i++++l+ + + +ln + T18769 77 LAWILLP-----VVHFPDFGKILFCIFDILVAILYFKIMEKDLNETK 118 lqkgs<-* + T18769 119 SETRE 123 COG0233: domain 1 of 1, from 111 to 126: score 2.4, E = 22 *->mmmlneilkdaeekMe<-* +++lne + +++e+M+ T18769 111 EKDLNETKSETREEMK 126 COG0010: domain 1 of 1, from 150 to 174: score 1.7, E = 16 *->ggnTsllaAklilelLlgevllvkk<-* g+++s+ aA+++l + l ++ ++k T18769 150 GNAESIVAAVVLLNIVLLQKGYWKS 174 COG2171: domain 1 of 1, from 210 to 220: score -0.7, E = 66 *->MiNkFkllvkn<-* +NkFk lv+n T18769 210 VVNKFKSLVSN 220 COG2271: domain 1 of 1, from 376 to 392: score 0.7, E = 20 *->hfGlkGWdGgFivliiaAl<-* +f +GW+++F ++++++l T18769 376 EF--QGWNTFFLMFLASCL 392 //