analysis of sequence from pig-s.AAL27645.fa ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ >AAL27645.1 SD10476p [Drosophila melanogaster]. metsssspvk prrkdkdedk frigatlafi vviigigvpm wwrtttvyrv nlpsteilsl skipiktavq vaiytqqtsr gqlliaelqn afsdneiwsv efkqlsptpm tqeahtpaal eklllenhvq svgdfmfiew pklqeelllt tersalmrsd tpsnkiaqll hakilqtyri nqilstderm gakseapqpa ydvivsvlnp kprlthakwn iamavktyie pwlakvsgvs nytvrsqwky rvaieadlkq vrdqsklgrh yalqetalph lltsiaqnls asttdkpain lvvyippchi aplhiynskd qrltrndvda fisppwggfi ianppehvcl aamsdqeavp yhvsttdnmq vmldqlhkll disselqmeg vkvvdieqle prrweyeayl rrsairhist asstlqslik lldqisyivi ddevgaaitn syadilaaka allehrlada svlakrafva sergffdasl laqlyfpdeq kyaiyiplfl pimvpvlssf nmlrgvlqar rkekqs ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ sec.str. with predator > AAL27645.1 . . . . . 1 METSSSSPVKPRRKDKDEDKFRIGATLAFIVVIIGIGVPMWWRTTTVYRV 50 ___________________HHHHHHHHHHHEEEEE__________EEEEE . . . . . 51 NLPSTEILSLSKIPIKTAVQVAIYTQQTSRGQLLIAELQNAFSDNEIWSV 100 _____EEEEE_____HHHHHHHHHHH____HHHHHHHHHHH_____EEEE . . . . . 101 EFKQLSPTPMTQEAHTPAALEKLLLENHVQSVGDFMFIEWPKLQEELLLT 150 EE____________HHHHHHHHHHHH________EEEEE___HHHHHHHH . . . . . 151 TERSALMRSDTPSNKIAQLLHAKILQTYRINQILSTDERMGAKSEAPQPA 200 HHHHHHH_______HHHHHHHHHHHHHHHHHHHH________________ . . . . . 201 YDVIVSVLNPKPRLTHAKWNIAMAVKTYIEPWLAKVSGVSNYTVRSQWKY 250 __EEEEE_______HHHHHHHHHHHHHH_HHHHHHHH_______HHHHHH . . . . . 251 RVAIEADLKQVRDQSKLGRHYALQETALPHLLTSIAQNLSASTTDKPAIN 300 HHHHHHHHHHHH______HHHHHHHHH_HHHHHHHHHH__________EE . . . . . 301 LVVYIPPCHIAPLHIYNSKDQRLTRNDVDAFISPPWGGFIIANPPEHVCL 350 EEEEE_____EEEEE_____________EEEE______EEE______HHH . . . . . 351 AAMSDQEAVPYHVSTTDNMQVMLDQLHKLLDISSELQMEGVKVVDIEQLE 400 HHHH_______EEEEHHHHHHHHHHHHHHHHHHHHHHHH__EEEE_____ . . . . . 401 PRRWEYEAYLRRSAIRHISTASSTLQSLIKLLDQISYIVIDDEVGAAITN 450 ___HHHHHHHHHHHHEEEEEHHHHHHHHHHHHHHHHHH____________ . . . . . 451 SYADILAAKAALLEHRLADASVLAKRAFVASERGFFDASLLAQLYFPDEQ 500 _HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH____HHHHHHH_____H . . . 501 KYAIYIPLFLPIMVPVLSSFNMLRGVLQARRKEKQS 536 HHHHEEEEEEEEEE_____HHHHHHHHHHHHHH___ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ Warning no amino acid in given sequence!!! method : 1 alpha-contents : 18.3 % beta-contents : 30.7 % coil-contents : 51.0 % class : mixed method : 2 alpha-contents : 28.3 % beta-contents : 34.3 % coil-contents : 37.4 % class : mixed ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ GPI: learning from metazoa -9.77 -3.01 -5.56 -5.14 -4.00 0.00 -24.00 0.00 -1.41 -16.05 -5.15 -12.00 -12.00 0.00 -12.00 0.00 -110.08 -14.35 -2.36 -0.73 -0.03 -4.00 0.00 -32.00 0.00 -3.22 -16.05 -5.15 -12.00 -12.00 0.00 0.00 0.00 -101.89 ID: AAL27645.1 AC: xxx Len: 536 1:I 527 Sc: -101.89 Pv: 9.959492e-01 NO_GPI_SITE GPI: learning from protozoa -16.59 -3.50 -1.25 -3.81 -4.00 0.00 -24.00 0.00 -0.52 -13.40 -16.39 -12.00 -12.00 0.00 -12.00 0.00 -119.47 -26.62 -1.69 -0.51 -0.07 -4.00 0.00 -28.00 0.00 -0.74 -13.40 -16.39 -12.00 0.00 0.00 -12.00 0.00 -115.43 ID: AAL27645.1 AC: xxx Len: 536 1:I 526 Sc: -115.43 Pv: 9.878547e-01 NO_GPI_SITE ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ # SignalP euk predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? AAL27645.1 0.596 94 Y 0.306 520 N 0.936 33 Y 0.120 N # SignalP gram- predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? AAL27645.1 0.455 311 N 0.243 530 N 0.888 419 Y 0.150 N # SignalP gram+ predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? AAL27645.1 0.554 471 Y 0.373 292 Y 0.949 29 N 0.219 N ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ low complexity regions: SEG 12 2.2 2.5 >AAL27645.1 SD10476p [Drosophila melanogaster]. 1-536 METSSSSPVKPRRKDKDEDKFRIGATLAFI VVIIGIGVPMWWRTTTVYRVNLPSTEILSL SKIPIKTAVQVAIYTQQTSRGQLLIAELQN AFSDNEIWSVEFKQLSPTPMTQEAHTPAAL EKLLLENHVQSVGDFMFIEWPKLQEELLLT TERSALMRSDTPSNKIAQLLHAKILQTYRI NQILSTDERMGAKSEAPQPAYDVIVSVLNP KPRLTHAKWNIAMAVKTYIEPWLAKVSGVS NYTVRSQWKYRVAIEADLKQVRDQSKLGRH YALQETALPHLLTSIAQNLSASTTDKPAIN LVVYIPPCHIAPLHIYNSKDQRLTRNDVDA FISPPWGGFIIANPPEHVCLAAMSDQEAVP YHVSTTDNMQVMLDQLHKLLDISSELQMEG VKVVDIEQLEPRRWEYEAYLRRSAIRHIST ASSTLQSLIKLLDQISYIVIDDEVGAAITN SYADILAAKAALLEHRLADASVLAKRAFVA SERGFFDASLLAQLYFPDEQKYAIYIPLFL PIMVPVLSSFNMLRGVLQARRKEKQS low complexity regions: SEG 25 3.0 3.3 >AAL27645.1 SD10476p [Drosophila melanogaster]. 1-452 METSSSSPVKPRRKDKDEDKFRIGATLAFI VVIIGIGVPMWWRTTTVYRVNLPSTEILSL SKIPIKTAVQVAIYTQQTSRGQLLIAELQN AFSDNEIWSVEFKQLSPTPMTQEAHTPAAL EKLLLENHVQSVGDFMFIEWPKLQEELLLT TERSALMRSDTPSNKIAQLLHAKILQTYRI NQILSTDERMGAKSEAPQPAYDVIVSVLNP KPRLTHAKWNIAMAVKTYIEPWLAKVSGVS NYTVRSQWKYRVAIEADLKQVRDQSKLGRH YALQETALPHLLTSIAQNLSASTTDKPAIN LVVYIPPCHIAPLHIYNSKDQRLTRNDVDA FISPPWGGFIIANPPEHVCLAAMSDQEAVP YHVSTTDNMQVMLDQLHKLLDISSELQMEG VKVVDIEQLEPRRWEYEAYLRRSAIRHIST ASSTLQSLIKLLDQISYIVIDDEVGAAITN SY adilaakaallehrladasvlakrafvase 453-492 rgffdaslla 493-536 QLYFPDEQKYAIYIPLFLPIMVPVLSSFNM LRGVLQARRKEKQS low complexity regions: SEG 45 3.4 3.75 >AAL27645.1 SD10476p [Drosophila melanogaster]. 1-391 METSSSSPVKPRRKDKDEDKFRIGATLAFI VVIIGIGVPMWWRTTTVYRVNLPSTEILSL SKIPIKTAVQVAIYTQQTSRGQLLIAELQN AFSDNEIWSVEFKQLSPTPMTQEAHTPAAL EKLLLENHVQSVGDFMFIEWPKLQEELLLT TERSALMRSDTPSNKIAQLLHAKILQTYRI NQILSTDERMGAKSEAPQPAYDVIVSVLNP KPRLTHAKWNIAMAVKTYIEPWLAKVSGVS NYTVRSQWKYRVAIEADLKQVRDQSKLGRH YALQETALPHLLTSIAQNLSASTTDKPAIN LVVYIPPCHIAPLHIYNSKDQRLTRNDVDA FISPPWGGFIIANPPEHVCLAAMSDQEAVP YHVSTTDNMQVMLDQLHKLLDISSELQMEG V kvvdieqleprrweyeaylrrsairhista 392-519 sstlqsliklldqisyividdevgaaitns yadilaakaallehrladasvlakrafvas ergffdasllaqlyfpdeqkyaiyiplflp imvpvlss 520-536 FNMLRGVLQARRKEKQS 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 >AAL27645.1 SD10476p [Drosophila melanogaster]. METSSSSPVKPRRKDKDEDKFRIGATLAFIVVIIGIGVPMWWRTTTVYRVNLPSTEILSL SKIPIKTAVQVAIYTQQTSRGQLLIAELQNAFSDNEIWSVEFKQLSPTPMTQEAHTPAAL EKLLLENHVQSVGDFMFIEWPKLQEELLLTTERSALMRSDTPSNKIAQLLHAKILQTYRI NQILSTDERMGAKSEAPQPAYDVIVSVLNPKPRLTHAKWNIAMAVKTYIEPWLAKVSGVS NYTVRSQWKYRVAIEADLKQVRDQSKLGRHYALQETALPHLLTSIAQNLSASTTDKPAIN LVVYIPPCHIAPLHIYNSKDQRLTRNDVDAFISPPWGGFIIANPPEHVCLAAMSDQEAVP YHVSTTDNMQVMLDQLHKLLDISSELQMEGVKVVDIEQLEPRRWEYEAYLRRSAIRHIST ASSTLQSLIKLLDQISYIVIDDEVGAAITNSYADILAAKAALLEHRLADASVLAKRAFVA SERGFFDASLLAQLYFPDEQKYaiyiplflpimvpvlSSFNMLRGVLQARRKEKQS 1 - 502 METSSSSPVK PRRKDKDEDK FRIGATLAFI VVIIGIGVPM WWRTTTVYRV NLPSTEILSL SKIPIKTAVQ VAIYTQQTSR GQLLIAELQN AFSDNEIWSV EFKQLSPTPM TQEAHTPAAL EKLLLENHVQ SVGDFMFIEW PKLQEELLLT TERSALMRSD TPSNKIAQLL HAKILQTYRI NQILSTDERM GAKSEAPQPA YDVIVSVLNP KPRLTHAKWN IAMAVKTYIE PWLAKVSGVS NYTVRSQWKY RVAIEADLKQ VRDQSKLGRH YALQETALPH LLTSIAQNLS ASTTDKPAIN LVVYIPPCHI APLHIYNSKD QRLTRNDVDA FISPPWGGFI IANPPEHVCL AAMSDQEAVP YHVSTTDNMQ VMLDQLHKLL DISSELQMEG VKVVDIEQLE PRRWEYEAYL RRSAIRHIST ASSTLQSLIK LLDQISYIVI DDEVGAAITN SYADILAAKA ALLEHRLADA SVLAKRAFVA SERGFFDASL LAQLYFPDEQ KY 503 - 517 aiyiplfl pimvpvl 518 - 536 SSF NMLRGVLQAR RKEKQS low complexity regions: DUST >AAL27645.1 SD10476p [Drosophila melanogaster]. metsssspvkprrkdkdedkfrigatlafivviigigvpmwwrtttvyrvnlpsteilsl skipiktavqvaiytqqtsrgqlliaelqnafsdneiwsvefkqlsptpmtqeahtpaal eklllenhvqsvgdfmfiewpklqeelllttersalmrsdtpsnkiaqllhakilqtyri nqilstdermgakseapqpaydvivsvlnpkprlthakwniamavktyiepwlakvsgvs nytvrsqwkyrvaieadlkqvrdqsklgrhyalqetalphlltsiaqnlsasttdkpain lvvyippchiaplhiynskdqrltrndvdafisppwggfiianppehvclaamsdqeavp yhvsttdnmqvmldqlhklldisselqmegvkvvdieqleprrweyeaylrrsairhist asstlqsliklldqisyividdevgaaitnsyadilaakaallehrladasvlakrafva sergffdasllaqlyfpdeqkyaiyiplflpimvpvlssfnmlrgvlqarrkekqs ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ coiled coil prediction for AAL27645.1 sequence: 536 amino acids, 0 residue(s) in coiled coil state . | . | . | . | . | . 60 metsssspvk prrkdkdedk frigatlafi vviigigvpm wwrtttvyrv nlpsteilsl ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 skipiktavq vaiytqqtsr gqlliaelqn afsdneiwsv efkqlsptpm tqeahtpaal ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 180 eklllenhvq svgdfmfiew pklqeelllt tersalmrsd tpsnkiaqll hakilqtyri ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 240 nqilstderm gakseapqpa ydvivsvlnp kprlthakwn iamavktyie pwlakvsgvs ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 nytvrsqwky rvaieadlkq vrdqsklgrh yalqetalph lltsiaqnls asttdkpain ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 lvvyippchi aplhiynskd qrltrndvda fisppwggfi ianppehvcl aamsdqeavp ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 420 yhvsttdnmq vmldqlhkll disselqmeg vkvvdieqle prrweyeayl rrsairhist ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 480 asstlqslik lldqisyivi ddevgaaitn syadilaaka allehrlada svlakrafva ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 . | . | . | . | . | . sergffdasl laqlyfpdeq kyaiyiplfl pimvpvlssf nmlrgvlqar rkekqs ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~ ---------- ---------- ---------- ---------- ---------- ------ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ prediction of transmembrane regions with toppred2 *********************************** *TOPPREDM with eukaryotic function* *********************************** pig-s.AAL27645.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: pig-s.AAL27645.fa.___inter___ (1 sequences) METSSSSPVKPRRKDKDEDKFRIGATLAFIVVIIGIGVPMWWRTTTVYRV NLPSTEILSLSKIPIKTAVQVAIYTQQTSRGQLLIAELQNAFSDNEIWSV EFKQLSPTPMTQEAHTPAALEKLLLENHVQSVGDFMFIEWPKLQEELLLT TERSALMRSDTPSNKIAQLLHAKILQTYRINQILSTDERMGAKSEAPQPA YDVIVSVLNPKPRLTHAKWNIAMAVKTYIEPWLAKVSGVSNYTVRSQWKY RVAIEADLKQVRDQSKLGRHYALQETALPHLLTSIAQNLSASTTDKPAIN LVVYIPPCHIAPLHIYNSKDQRLTRNDVDAFISPPWGGFIIANPPEHVCL AAMSDQEAVPYHVSTTDNMQVMLDQLHKLLDISSELQMEGVKVVDIEQLE PRRWEYEAYLRRSAIRHISTASSTLQSLIKLLDQISYIVIDDEVGAAITN SYADILAAKAALLEHRLADASVLAKRAFVASERGFFDASLLAQLYFPDEQ KYAIYIPLFLPIMVPVLSSFNMLRGVLQARRKEKQS (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 4 structures are to be tested Candidate membrane-spanning segments: Helix Begin End Score Certainity 1 22 42 2.121 Certain 2 297 317 0.854 Putative 3 327 347 0.632 Putative 4 502 522 1.849 Certain ---------------------------------------------------------------------- Structure 1 Transmembrane segments included in this structure: Segment 1 2 3 4 Loop length 21 254 9 154 14 K+R profile 8.00 3.00 5.00 + + CYT-EXT prof - - - 0.45 -0.01 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 16.00 Tm probability: 0.05 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 2.00 (NEG-POS)/(NEG+POS): -0.1667 NEG: 5.0000 POS: 7.0000 -> Orientation: N-in CYT-EXT difference: -0.44 -> Orientation: N-in ---------------------------------------------------------------------- Structure 2 Transmembrane segments included in this structure: Segment 1 4 Loop length 21 459 14 K+R profile 8.00 5.00 + CYT-EXT prof - - 0.46 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 13.00 Tm probability: 1.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 2.00 (NEG-POS)/(NEG+POS): -0.1667 NEG: 5.0000 POS: 7.0000 -> Orientation: N-in CYT-EXT difference: -0.46 -> Orientation: N-in ---------------------------------------------------------------------- Structure 3 Transmembrane segments included in this structure: Segment 1 3 4 Loop length 21 284 154 14 K+R profile 8.00 + + 5.00 CYT-EXT prof - -0.01 0.51 - For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 3.00 Tm probability: 0.08 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 2.00 (NEG-POS)/(NEG+POS): -0.1667 NEG: 5.0000 POS: 7.0000 -> Orientation: N-in CYT-EXT difference: -0.52 -> Orientation: N-in ---------------------------------------------------------------------- Structure 4 Transmembrane segments included in this structure: Segment 1 2 4 Loop length 21 254 184 14 K+R profile 8.00 + + 5.00 CYT-EXT prof - 0.11 0.45 - For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 3.00 Tm probability: 0.64 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 2.00 (NEG-POS)/(NEG+POS): -0.1667 NEG: 5.0000 POS: 7.0000 -> Orientation: N-in CYT-EXT difference: -0.34 -> Orientation: N-in ---------------------------------------------------------------------- "pig-s" 536 22 42 #t 2.12083 297 317 #f 0.854167 327 347 #f 0.632292 502 522 #t 1.84896 ************************************ *TOPPREDM with prokaryotic function* ************************************ pig-s.AAL27645.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: pig-s.AAL27645.fa.___inter___ (1 sequences) METSSSSPVKPRRKDKDEDKFRIGATLAFIVVIIGIGVPMWWRTTTVYRV NLPSTEILSLSKIPIKTAVQVAIYTQQTSRGQLLIAELQNAFSDNEIWSV EFKQLSPTPMTQEAHTPAALEKLLLENHVQSVGDFMFIEWPKLQEELLLT TERSALMRSDTPSNKIAQLLHAKILQTYRINQILSTDERMGAKSEAPQPA YDVIVSVLNPKPRLTHAKWNIAMAVKTYIEPWLAKVSGVSNYTVRSQWKY RVAIEADLKQVRDQSKLGRHYALQETALPHLLTSIAQNLSASTTDKPAIN LVVYIPPCHIAPLHIYNSKDQRLTRNDVDAFISPPWGGFIIANPPEHVCL AAMSDQEAVPYHVSTTDNMQVMLDQLHKLLDISSELQMEGVKVVDIEQLE PRRWEYEAYLRRSAIRHISTASSTLQSLIKLLDQISYIVIDDEVGAAITN SYADILAAKAALLEHRLADASVLAKRAFVASERGFFDASLLAQLYFPDEQ KYAIYIPLFLPIMVPVLSSFNMLRGVLQARRKEKQS (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 4 structures are to be tested Candidate membrane-spanning segments: Helix Begin End Score Certainity 1 22 42 2.121 Certain 2 297 317 0.854 Putative 3 327 347 0.632 Putative 4 502 522 1.849 Certain ---------------------------------------------------------------------- Structure 1 Transmembrane segments included in this structure: Segment 1 2 3 4 Loop length 21 254 9 154 14 K+R profile 8.00 3.00 5.00 + + CYT-EXT prof - - - 0.45 -0.01 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 16.00 Tm probability: 0.05 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 2.00 (NEG-POS)/(NEG+POS): -0.1667 NEG: 5.0000 POS: 7.0000 -> Orientation: N-in CYT-EXT difference: -0.44 -> Orientation: N-in ---------------------------------------------------------------------- Structure 2 Transmembrane segments included in this structure: Segment 1 4 Loop length 21 459 14 K+R profile 8.00 5.00 + CYT-EXT prof - - 0.46 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 13.00 Tm probability: 1.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 2.00 (NEG-POS)/(NEG+POS): -0.1667 NEG: 5.0000 POS: 7.0000 -> Orientation: N-in CYT-EXT difference: -0.46 -> Orientation: N-in ---------------------------------------------------------------------- Structure 3 Transmembrane segments included in this structure: Segment 1 3 4 Loop length 21 284 154 14 K+R profile 8.00 + + 5.00 CYT-EXT prof - -0.01 0.51 - For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 3.00 Tm probability: 0.08 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 2.00 (NEG-POS)/(NEG+POS): -0.1667 NEG: 5.0000 POS: 7.0000 -> Orientation: N-in CYT-EXT difference: -0.52 -> Orientation: N-in ---------------------------------------------------------------------- Structure 4 Transmembrane segments included in this structure: Segment 1 2 4 Loop length 21 254 184 14 K+R profile 8.00 + + 5.00 CYT-EXT prof - 0.11 0.45 - For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 3.00 Tm probability: 0.64 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 2.00 (NEG-POS)/(NEG+POS): -0.1667 NEG: 5.0000 POS: 7.0000 -> Orientation: N-in CYT-EXT difference: -0.34 -> Orientation: N-in ---------------------------------------------------------------------- "pig-s" 536 22 42 #t 2.12083 297 317 #f 0.854167 327 347 #f 0.632292 502 522 #t 1.84896 ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ SAPS. Version of April 11, 1996. Date run: Wed Feb 20 11:40:40 2002 File: /people/b_eisen/pig-s.AAL27645.fa.___saps___ ID AAL27645.1 DE SD10476p [Drosophila melanogaster]. number of residues: 536; molecular weight: 60.4 kdal 1 METSSSSPVK PRRKDKDEDK FRIGATLAFI VVIIGIGVPM WWRTTTVYRV NLPSTEILSL 61 SKIPIKTAVQ VAIYTQQTSR GQLLIAELQN AFSDNEIWSV EFKQLSPTPM TQEAHTPAAL 121 EKLLLENHVQ SVGDFMFIEW PKLQEELLLT TERSALMRSD TPSNKIAQLL HAKILQTYRI 181 NQILSTDERM GAKSEAPQPA YDVIVSVLNP KPRLTHAKWN IAMAVKTYIE PWLAKVSGVS 241 NYTVRSQWKY RVAIEADLKQ VRDQSKLGRH YALQETALPH LLTSIAQNLS ASTTDKPAIN 301 LVVYIPPCHI APLHIYNSKD QRLTRNDVDA FISPPWGGFI IANPPEHVCL AAMSDQEAVP 361 YHVSTTDNMQ VMLDQLHKLL DISSELQMEG VKVVDIEQLE PRRWEYEAYL RRSAIRHIST 421 ASSTLQSLIK LLDQISYIVI DDEVGAAITN SYADILAAKA ALLEHRLADA SVLAKRAFVA 481 SERGFFDASL LAQLYFPDEQ KYAIYIPLFL PIMVPVLSSF NMLRGVLQAR RKEKQS -------------------------------------------------------------------------------- COMPOSITIONAL ANALYSIS (extremes relative to: swp23s) A : 51( 9.5%); C : 2( 0.4%); D : 26( 4.9%); E : 31( 5.8%); F : 14( 2.6%) G- : 14( 2.6%); H : 13( 2.4%); I : 41( 7.6%); K : 29( 5.4%); L : 59(11.0%) M : 13( 2.4%); N : 17( 3.2%); P : 30( 5.6%); Q : 30( 5.6%); R : 28( 5.2%) S : 44( 8.2%); T : 30( 5.6%); V : 37( 6.9%); W : 9( 1.7%); Y : 18( 3.4%) KR : 57 ( 10.6%); ED : 57 ( 10.6%); AGP : 95 ( 17.7%); KRED : 114 ( 21.3%); KR-ED : 0 ( 0.0%); FIKMNY : 132 ( 24.6%); LVIFM : 164 ( 30.6%); ST : 74 ( 13.8%). -------------------------------------------------------------------------------- CHARGE DISTRIBUTIONAL ANALYSIS 1 0-0000000+ 0+++-+---+ 0+00000000 0000000000 00+00000+0 00000-0000 61 0+000+0000 000000000+ 000000-000 000-0-0000 -0+0000000 00-0000000 121 -+000-0000 000-0000-0 0+00--0000 0-+0000+0- 0000+00000 00+00000+0 181 000000--+0 00+0-00000 0-00000000 +0+0000+00 00000+000- 0000+00000 241 0000+000+0 +000-0-0+0 0+-00+00+0 0000-00000 0000000000 0000-+0000 301 0000000000 00000000+- 0+00+0-0-0 0000000000 00000-0000 0000-0-000 361 000000-000 000-000+00 -000-000-0 0+00-0-00- 0++0-0-000 ++000+0000 421 000000000+ 00-0000000 ---0000000 000-0000+0 000-0+00-0 0000++0000 481 0-+000-000 0000000--0 +000000000 0000000000 000+00000+ ++-+00 A. CHARGE CLUSTERS. Positive charge clusters (cmin = 9/30 or 13/45 or 15/60): none Negative charge clusters (cmin = 9/30 or 13/45 or 15/60): none Mixed charge clusters (cmin = 15/30 or 20/45 or 25/60): none B. HIGH SCORING (UN)CHARGED SEGMENTS. There are no high scoring positive charge segments. There are no high scoring negative charge segments. There are no high scoring mixed charge segments. There are no high scoring uncharged segments. C. CHARGE RUNS AND PATTERNS. pattern (+)| (-)| (*)| (0)| (+0)| (-0)| (*0)|(+00)|(-00)|(*00)| (H.)|(H..)| lmin0 5 | 5 | 7 | 39 | 10 | 10 | 13 | 11 | 11 | 15 | 7 | 9 | lmin1 6 | 6 | 9 | 47 | 12 | 12 | 15 | 14 | 14 | 18 | 8 | 11 | lmin2 7 | 7 | 10 | 53 | 13 | 13 | 17 | 16 | 16 | 21 | 10 | 12 | (Significance level: 0.010000; Minimal displayed length: 6) (*) 9(0,0,0); at 12- 20: RRKDKDEDK (1. quartile) +++-+---+ Run count statistics: + runs >= 3: 2, at 12; 530; - runs >= 3: 2, at 17; 441; * runs >= 5: 2, at 12; 530; 0 runs >= 26: 0 -------------------------------------------------------------------------------- DISTRIBUTION OF OTHER AMINO ACID TYPES 1. HIGH SCORING SEGMENTS. __________________________________ High scoring hydrophobic segments: 2.00 (LVIFM) 1.00 (AGYCW) 0.00 (BZX) -2.00 (PH) -4.00 (STNQ) -8.00 (KEDR) Expected score/letter: -1.978 M_0.01= 25.73; M_0.05= 21.37 1) From 27 to 42: length= 16, score=23.00 * 27 LAFIVVIIGI GVPMWW G: 2(12.5%); V: 3(18.8%); I: 4(25.0%); W: 2(12.5%); ____________________________________ High scoring transmembrane segments: 5.00 (LVIF) 2.00 (AGM) 0.00 (BZX) -1.00 (YCW) -2.00 (ST) -6.00 (P) -8.00 (H) -10.00 (NQ) -16.00 (KR) -17.00 (ED) Expected score/letter: -3.547 M_0.01= 63.48; M_0.05= 52.33; M_0.30= 39.06 1) From 23 to 38: length= 16, score=58.00 * 23 IGATLAFIVV IIGIGV A: 2(12.5%); G: 3(18.8%); V: 3(18.8%); I: 5(31.2%); 2. SPACINGS OF C. H2N-307-C-40-C-187-COOH 2*. SPACINGS OF C and H. (additional deluxe function for ALEX) H2N-114-H-12-H-42-H-44-H-53-H-9-H-27-C-H-4-H-32-H-1-C-12-H-14-H-39-H-47-H-71-COOH -------------------------------------------------------------------------------- REPETITIVE STRUCTURES. A. SEPARATED, TANDEM, AND PERIODIC REPEATS: amino acid alphabet. Repeat core block length: 5 B. SEPARATED AND TANDEM REPEATS: 11-letter reduced alphabet. (i= LVIF; += KR; -= ED; s= AG; o= ST; n= NQ; a= YW; p= P; h= H; m= M; c= C) Repeat core block length: 9 -------------------------------------------------------------------------------- MULTIPLETS. A. AMINO ACID ALPHABET. 1. Total number of amino acid multiplets: 40 (Expected range: 15-- 49) 2. Histogram of spacings between consecutive amino acid multiplets: (1-5) 16 (6-10) 12 (11-20) 7 (>=21) 6 3. Clusters of amino acid multiplets (cmin = 12/30 or 16/45 or 19/60): none B. CHARGE ALPHABET. 1. Total number of charge multiplets: 10 (Expected range: 1-- 21) 5 +plets (f+: 10.6%), 5 -plets (f-: 10.6%) Total number of charge altplets: 10 (Critical number: 24) 2. Histogram of spacings between consecutive charge multiplets: (1-5) 2 (6-10) 1 (11-20) 1 (>=21) 7 -------------------------------------------------------------------------------- PERIODICITY ANALYSIS. A. AMINO ACID ALPHABET (core: 4; !-core: 5) Location Period Element Copies Core Errors 4- 7 1 S 4 4 0 B. CHARGE ALPHABET ({+= KR; -= ED; 0}; core: 5; !-core: 6) and HYDROPHOBICITY ALPHABET ({*= KRED; i= LVIF; 0}; core: 6; !-core: 9) Location Period Element Copies Core Errors 12- 20 1 * 9 9 ! 0 29- 34 1 i 6 6 0 30- 41 2 i0 6 6 /0/2/ 245- 280 6 *00..0 6 6 /0/2/1/././1/ 504- 523 2 i. 9 7 1 -------------------------------------------------------------------------------- SPACING ANALYSIS. There are no unusual spacings. ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ 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: pig-s.AAL27645.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: AAL27645.1 SD10476p [Drosophila melanogaster]. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- gntR Bacterial regulatory proteins, gntR f 4.6 7.5 1 IGPS Indole-3-glycerol phosphate synthase 3.6 4.9 1 Na_sulph_symp Sodium:sulfate symporter transmembran -1.9 81 1 Clathrin_repeat 7-fold repeat in Clathrin and VPS -37.0 71 1 Adenine_deam Adenine deaminase -388.1 23 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- Na_sulph_symp 1/1 22 49 .. 558 585 .] -1.9 81 IGPS 1/1 154 169 .. 258 273 .] 3.6 4.9 gntR 1/1 166 186 .. 1 22 [. 4.6 7.5 Adenine_deam 1/1 65 395 .. 1 577 [] -388.1 23 Clathrin_repeat 1/1 373 535 .. 1 158 [] -37.0 71 Alignments of top-scoring domains: Na_sulph_symp: domain 1 of 1, from 22 to 49: score -1.9, E = 81 *->rlGfilsIigliiwllvGalWWkaLglw<-* r+G+ l++i +ii ++v ++W +++ AAL27645.1 22 RIGATLAFIVVIIGIGVPMWWRTTTVYR 49 IGPS: domain 1 of 1, from 154 to 169: score 3.6, E = 4.9 *->EsLMraeDvraaireL<-* ++LMr++ + ++i++L AAL27645.1 154 SALMRSDTPSNKIAQL 169 gntR: domain 1 of 1, from 166 to 186: score 4.6, E = 7.5 *->vaerLrqlIrsGelrpGdkLPs<-* +a+ L ++I + ++r +++L++ AAL27645.1 166 IAQLLHAKILQ-TYRINQILST 186 Adenine_deam: domain 1 of 1, from 65 to 395: score -388.1, E = 23 *->ikNakIlDvyngeiikgnIaIaggrIagVglndeisgrieKiaEeik ik a + +y+++ g Ia+ a+ + ei + AAL27645.1 65 IKTAVQVAIYTQQTSRGQLLIAELQNAFSD--NEIWSV--------- 100 tIDaegkyivPGFIDaHiHIESSmltPseFAkaVlphGtttvVsDPHEIA e k ++P+ +H tP ++k+ l + +v AAL27645.1 101 ----EFKQLSPTPMTQEAH------TPAALEKLLLENHVQSV-------- 132 NVsGkdGilfMLneAkktplkfYfmvPSCVPAtsepfEtsGAvltaedik G +++ k ++ + l ++ AAL27645.1 133 ------GDFMFIEWPK-------------LQEE---------LLLTTERS 154 ellelddVlgLAEmMdyPgVisgDdemLkKieaArkqnKriDGHaPGLsg +l++ d P+ +Ki + Ha L + AAL27645.1 155 ALMRSDT----------PS---------NKIAQLL--------HAKILQT 177 keLnkYisaGissDHEsvslEEaleKLrLGMkvMiREGSaAkNlraLlpl +n +s +E + ++ AAL27645.1 178 YRINQ-----------ILSTDERM------------------------GA 192 inEkgkkncdslmlctDDahpndllsEGhinhiiRrAieeGvdpidvAyq ++E +d +++ +p+ l h i++A++ + p AAL27645.1 193 KSEAPQPAYDVIVS---VLNPKPRL--THAKWNIAMAVKTYIEPWL---- 233 masiNpAeyYGldtyLGliaPGrdADlvileDlrnfkVkkVlvkGrpvre A+ G + y ++ + i Dl+ + vr+ AAL27645.1 234 ------AKVSGVSNY--TVRSQWKYRVAIEADLK-----------Q-VRD 263 dglallkrfnktqkaPwkklnvskkpvsalnKqDfkmqGiDldegqfrir + + l r+ + + +l + +++ q+ +++ ++++ i+ AAL27645.1 264 Q--SKLGRHY---ALQETALPHLLTSIA----QNLSAS---TTDKP-AIN 300 VIkvidnqlITeeliisaeveesefqldteeDi.lkiaVleRHkrsgkig + i+ I ++i + + q +t++D++ +i+ +g AAL27645.1 301 LVVYIPPCHIAPLHIY--NSKD---QRLTRNDVdAFIS-----PPWG--- 337 kGlikGFGlkeGAiAstvaHDSHNIiavGvndedmalAVNrlkeiGGGLv GF Iia + +e +lA AAL27645.1 338 -----GF-----------------IIA--NPPEHVCLA------------ 351 aaknGevlheLPLPiAGlMSdesaerVaeklekLndkleevlGsrlddPf a +++ +P ++ ++ + +++l kL d +e AAL27645.1 352 AM---SDQEAVPYHVS---TTDNMQVMLDQLHKLLDISSE---------- 385 lTLSFLsLpVIPeLKiTdrGLFDVekFqvvd<-* l++ G vvd AAL27645.1 386 LQM---------------EGV------KVVD 395 Clathrin_repeat: domain 1 of 1, from 373 to 535: score -37.0, E = 71 *->lielsdridiselVeife......e.lkrglleeLipyLesalkenn l +l+ +dis ++ + + e+l+ ++e+ ++ +sa+ + AAL27645.1 373 LDQLHKLLDISSELQMEGvkvvdiEqLEPRRWEYEAYLRRSAIRHI- 418 fseepalqnlLielyikydpqkemellealfinlknnnyDvekvadlcek s+ + + +Li+l ++ +++ +++ + n+++D+ ++++ + AAL27645.1 419 -STASSTLQSLIKLLDQISYIVIDDEVG---AAITNSYADILAAKAALLE 464 aglyFwe......eAfllykkdlqdfkdaivtlielieannyqkavdyav + l + + ++Af++ ++++ d + +++++ + +y ++ + AAL27645.1 465 HRLA--DasvlakRAFVASERGFFDASLLAQLYFPDE--QKYAIYIPLFL 510 krnnpelwae.vlkacldkkrflla<-* + p l + ++l l+++r + + AAL27645.1 511 PIMVPVLSSFnMLRGVLQARRKEKQ 535 // 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: pig-s.AAL27645.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: AAL27645.1 SD10476p [Drosophila melanogaster]. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- gntR Bacterial regulatory proteins, gntR fam 4.6 7.5 1 e3_binding e3 binding domain 4.0 33 1 IGPS Indole-3-glycerol phosphate synthase 3.6 4.9 1 HEAT_PBS PBS lyase HEAT-like repeat 3.6 54 1 DUF144 Domain of unknown function DUF144 2.5 12 1 DPS Dps protein family 2.2 13 1 CinA Competence-damaged protein 2.2 20 1 W2 eIF4-gamma/eIF5/eIF2-epsilon 1.4 35 1 HEV_ORF2 Hepatitis E virus ORF-2 (Putative capsi 1.2 33 1 Omptin Omptin family 0.8 14 1 aa_permeases Amino acid permease -0.5 52 1 Fragilysin Fragilysin metallopeptidase (M10C) ente -0.9 61 1 Fimbrial_K88 Fimbrial, major and minor subunit -1.7 97 1 Na_sulph_symp Sodium:sulfate symporter transmembrane -1.9 81 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- Omptin 1/1 1 33 [. 1 33 [. 0.8 14 aa_permeases 1/1 26 43 .. 481 498 .] -0.5 52 Na_sulph_symp 1/1 22 49 .. 558 585 .] -1.9 81 Fimbrial_K88 1/1 69 100 .. 251 284 .. -1.7 97 DUF144 1/1 138 145 .. 138 145 .] 2.5 12 IGPS 1/1 154 169 .. 258 273 .] 3.6 4.9 W2 1/1 141 172 .. 1 33 [. 1.4 35 gntR 1/1 166 186 .. 1 22 [. 4.6 7.5 e3_binding 1/1 319 332 .. 29 42 .] 4.0 33 Fragilysin 1/1 360 378 .. 365 382 .] -0.9 61 HEV_ORF2 1/1 392 403 .. 112 123 .] 1.2 33 CinA 1/1 412 432 .. 138 157 .] 2.2 20 HEAT_PBS 1/1 410 434 .. 1 27 [] 3.6 54 DPS 1/1 463 474 .. 1 12 [. 2.2 13 Alignments of top-scoring domains: Omptin: domain 1 of 1, from 1 to 33: score 0.8, E = 14 *->Mktklplqitseyedkrnektclaimliavlsi<-* M t++ + +dk ++k ++++l+ +++i AAL27645.1 1 METSSSSPVKPRRKDKDEDKFRIGATLAFIVVI 33 aa_permeases: domain 1 of 1, from 26 to 43: score -0.5, E = 52 *->laiplfiilwigykfikr<-* ++ ++++i++ig ++r AAL27645.1 26 TLAFIVVIIGIGVPMWWR 43 Na_sulph_symp: domain 1 of 1, from 22 to 49: score -1.9, E = 81 *->rlGfilsIigliiwllvGalWWkaLglw<-* r+G+ l++i +ii ++v ++W +++ AAL27645.1 22 RIGATLAFIVVIIGIGVPMWWRTTTVYR 49 Fimbrial_K88: domain 1 of 1, from 69 to 100: score -1.7, E = 97 *->vqvegvYalgIaaGqtieltfngpvtttRtkWsA<-* vqv+ +Y +++ Gq + +++ +++ + ++Ws+ AAL27645.1 69 VQVA-IYTQQTSRGQLLIAELQNAFS-DNEIWSV 100 DUF144: domain 1 of 1, from 138 to 145: score 2.5, E = 12 *->IeWPekPe<-* IeWP+++e AAL27645.1 138 IEWPKLQE 145 IGPS: domain 1 of 1, from 154 to 169: score 3.6, E = 4.9 *->EsLMraeDvraaireL<-* ++LMr++ + ++i++L AAL27645.1 154 SALMRSDTPSNKIAQL 169 W2: domain 1 of 1, from 141 to 172: score 1.4, E = 35 *->eeeqidlLlaiEefcvkleeelvikllakiLks<-* ++ q +lLl+ E++ + ++++ +++a++L++ AAL27645.1 141 PKLQEELLLTTERSALMRSDTP-SNKIAQLLHA 172 gntR: domain 1 of 1, from 166 to 186: score 4.6, E = 7.5 *->vaerLrqlIrsGelrpGdkLPs<-* +a+ L ++I + ++r +++L++ AAL27645.1 166 IAQLLHAKILQ-TYRINQILST 186 e3_binding: domain 1 of 1, from 319 to 332: score 4.0, E = 33 *->pgGRItKeDVeaal<-* ++ R t+ DV+a++ AAL27645.1 319 KDQRLTRNDVDAFI 332 Fragilysin: domain 1 of 1, from 360 to 378: score -0.9, E = 61 *->PnHLS.edNmvrilknlgk<-* P H S+ dNm +l l k AAL27645.1 360 PYHVStTDNMQVMLDQLHK 378 HEV_ORF2: domain 1 of 1, from 392 to 403: score 1.2, E = 33 *->pvvDLPqlGlRR<-* +vvD+ ql +RR AAL27645.1 392 KVVDIEQLEPRR 403 CinA: domain 1 of 1, from 412 to 432: score 2.2, E = 20 *->ReaiRrrsvqhA.LalLlrlL<-* R+aiR++s+ +++L+ L +lL AAL27645.1 412 RSAIRHISTASStLQSLIKLL 432 HEAT_PBS: domain 1 of 1, from 410 to 434: score 3.6, E = 54 *->vRraAaraLgalgdpeAipaLleaLed<-* +Rr+A+r + + ++ L+++L++ AAL27645.1 410 LRRSAIRHISTASS--TLQSLIKLLDQ 434 DPS: domain 1 of 1, from 463 to 474: score 2.2, E = 13 *->LnrlLAdlyvLy<-* L+++LAd+ vL+ AAL27645.1 463 LEHRLADASVLA 474 // 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: pig-s.AAL27645.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: AAL27645.1 SD10476p [Drosophila melanogaster]. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- [no hits above thresholds] Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- [no hits above thresholds] Alignments of top-scoring domains: [no hits above thresholds] // ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ Start with Prosite --------------------------------------------------------- | ppsearch (c) 1994 EMBL Data Library | | based on MacPattern (c) 1990-1994 R. Fuchs | --------------------------------------------------------- PROSITE pattern search started: Wed Feb 20 11:42:47 2002 Sequence file: pig-s.AAL27645.fa ---------------------------------------- Sequence AAL27645.1 (536 residues): Matching pattern PS00001 ASN_GLYCOSYLATION: 241: NYTV 288: NLSA Total matches: 2 Matching pattern PS00005 PKC_PHOSPHO_SITE: 78: TSR 151: TER 163: SNK 177: TYR 243: TVR 294: TDK 481: SER Total matches: 7 Matching pattern PS00006 CK2_PHOSPHO_SITE: 93: SDNE 131: SVGD 185: STDE 227: TYIE 292: STTD 324: TRND 354: SDQE 364: STTD 451: SYAD Total matches: 9 Matching pattern PS00008 MYRISTYL: 24: GATLAF 445: GAAITN 525: GVLQAR Total matches: 3 Total no of hits in this sequence: 21 ======================================== 1314 pattern(s) searched in 1 sequence(s), 536 residues. Total no of hits in all sequences: 21. 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, 0 units >ER-GOLGI-traffic signal is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >INTRA-SIGNAL-M minimal SH3 binding is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 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, 0 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, 0 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, 0 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, 0 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, 0 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, 0 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, 0 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, 0 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, 0 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, 0 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, 0 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, 0 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, 0 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, 0 units >NUCLEAR NLS experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 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, 0 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, 0 units >NUCLEAR NLS HCDA experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS SV40 LrgT experimentally determined is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS H2B experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 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, 0 units >NUCLEAR NLS Amida experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS Amida experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS RanBP3 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS Pho4p experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS DNAhelicaseQ1 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 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, 0 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, 0 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, 0 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, 0 units >NUCLEAR NLS GAL4 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 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, 0 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, 0 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, 0 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, 0 units >NUCLEAR NLS TR2 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 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, 0 units >NUCLEAR NLS polyomaVP1 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 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, 0 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, 0 units >NUCLEAR NLS Rex experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS SRY experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS SRY experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS SOX9 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS SOX9 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS NS5A experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 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, 0 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, 0 units >NUCLEAR NLS adenovE1a experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS ystDNApolalpha experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS hVDR experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 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, 0 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, 0 units >NUCLEAR NLS cFOS experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS cJUN experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS hDNApolalpha experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS hDNAtopoII experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS hDNAtopoII experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS hBLM experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS hARNT experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS influenzaNP experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS influenzaNP experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS p54 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS hProTalpha experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 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, 0 units >NUCLEAR NLS protHsc9 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS protHsci experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS protHsc3 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 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, 0 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, 0 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, 0 units >NUCLEAR NLS MyoD experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS MyoD experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS opaque2 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS CTP experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS HCV experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS HCV experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS p110RB1 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 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, 0 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, 0 units >NUCLEAR NLS Nucloplasmin experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS Nucleolin experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 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, 0 units >NUCLEAR NLS Nab2 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS M9 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS lscMyc experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS humKprotein experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS FluA experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 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, 0 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, 0 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, 0 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, 0 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, 0 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, 0 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, 0 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, 0 units >NUCLEAR NLS p53 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 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, 0 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, 0 units >NUCLEAR NLS L29 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS L29 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS Max experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS L3 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS dyskerin experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 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, 0 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, 0 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: pig-s.AAL27645.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: AAL27645.1 SD10476p [Drosophila melanogaster]. 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: pig-s.AAL27645.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: AAL27645.1 SD10476p [Drosophila melanogaster]. 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= AAL27645.1 SD10476p [Drosophila melanogaster]. (536 letters) Searching..................................done Results from profile search Score E Sequences producing significant alignments: (bits) Value TBC Probable RAB-type GTPase GTP hydrolysis activating prote... 23 0.93 S1 S1 RNA binding domain 22 1.7 ACTIN Actin ATPase/ Cytoskeletal ATPase domain 22 1.8 FKBP FK506 binding protein (Peptidyl prolyl isomerase) 21 3.0 HISDAC Histone deacetylase domain 21 5.3 MBL Metallo-betalactamase domain 20 5.7 RHOGAP RHO-type GTPase GTP hydrolysis activating protein 20 6.0 ARR Arrestin domain 20 6.2 INSL Insulinase like Metallo protease domain 20 7.2 >TBC Probable RAB-type GTPase GTP hydrolysis activating protein Length = 225 Score = 22.9 bits (49), Expect = 0.93 Identities = 8/61 (13%), Positives = 8/61 (13%), Gaps = 8/61 (13%) Query: 339 FIIANPPEH---VCLAAMSDQEAVPYHVSTTDNMQVMLDQLHKLL-----DISSELQMEG 390 Sbjct: 108 LLYSCPSEPMAYQLFTKLCYEMIPTYLTKNLNGAQNGAKLLDISLRIIDPKLSKFLSDNL 167 Query: 391 V 391 Sbjct: 168 L 168 >S1 S1 RNA binding domain Length = 305 Score = 22.2 bits (47), Expect = 1.7 Identities = 4/30 (13%), Positives = 4/30 (13%), Gaps = 2/30 (6%) Query: 7 SPVKPRRKDKDEDKFRIGATLAFIVVIIGI 36 Sbjct: 59 QELGLRPHAEIEDSFPLDSAW--DFLVTSE 86 Score = 22.2 bits (47), Expect = 1.8 Identities = 13/38 (34%), Positives = 13/38 (34%) Query: 152 ERSALMRSDTPSNKIAQLLHAKILQTYRINQILSTDER 189 Sbjct: 143 PRSHLMHKDNMDALVGQVLKAHILEANQDNNKLVLTQR 180 Score = 20.6 bits (43), Expect = 4.9 Identities = 8/33 (24%), Positives = 8/33 (24%), Gaps = 2/33 (6%) Query: 7 SPVKPRRKDKDEDKFRIGATLAFIVVIIGIGVP 39 Sbjct: 223 SQVSGTRVDSLNTLFAFGQAI--SVYVQEIDEY 253 >ACTIN Actin ATPase/ Cytoskeletal ATPase domain Length = 376 Score = 22.1 bits (47), Expect = 1.8 Identities = 8/23 (34%), Positives = 8/23 (34%) Query: 115 HTPAALEKLLLENHVQSVGDFMF 137 Sbjct: 285 KCDVDIRKDLYGNIVLSGGSTMF 307 Score = 19.8 bits (41), Expect = 9.9 Identities = 10/34 (29%), Positives = 10/34 (29%), Gaps = 1/34 (2%) Query: 406 YEAYLRRSAIRHISTASSTL-QSLIKLLDQISYI 438 Sbjct: 167 YEGDALPHAILRLDLAGRDLTDHLMKILTERGYM 200 >FKBP FK506 binding protein (Peptidyl prolyl isomerase) Length = 149 Score = 21.4 bits (45), Expect = 3.0 Identities = 7/49 (14%), Positives = 7/49 (14%) Query: 350 LAAMSDQEAVPYHVSTTDNMQVMLDQLHKLLDISSELQMEGVKVVDIEQ 398 Sbjct: 100 LFTAMDGSEMPGVIREINGDSITVDFNHPLAGQTVHFDIEVLEIDPALE 148 >HISDAC Histone deacetylase domain Length = 433 Score = 20.6 bits (43), Expect = 5.3 Identities = 3/17 (17%), Positives = 3/17 (17%) Query: 505 YIPLFLPIMVPVLSSFN 521 Sbjct: 247 YRSVFEPVIKKIMEWYQ 263 >MBL Metallo-betalactamase domain Length = 256 Score = 20.5 bits (42), Expect = 5.7 Identities = 2/24 (8%), Positives = 2/24 (8%) Query: 35 GIGVPMWWRTTTVYRVNLPSTEIL 58 Sbjct: 13 AFTVGADNFQSNAILTLDNGKKFL 36 >RHOGAP RHO-type GTPase GTP hydrolysis activating protein Length = 194 Score = 20.2 bits (42), Expect = 6.0 Identities = 4/48 (8%), Positives = 4/48 (8%), Gaps = 2/48 (4%) Query: 391 VKVVDIEQLEPRRWEYEAYLRR--SAIRHISTASSTLQSLIKLLDQIS 436 Sbjct: 86 ISQFSGGSAEQMCKTYSEFCSRHSKALKFYKELYARDKRFQQFIRKVT 133 >ARR Arrestin domain Length = 454 Score = 20.2 bits (42), Expect = 6.2 Identities = 17/89 (19%), Positives = 17/89 (19%), Gaps = 13/89 (14%) Query: 48 YRVNLPSTEILSLSKIPI---------KTAVQVAIYTQQTSRGQLLIAELQNAFSDNEIW 98 Sbjct: 230 MEVSLDKEMYYHGESISVNVHIQNNSNKTVKKLKIYIIQVAD----ICLFTTASYSCEVA 285 Query: 99 SVEFKQLSPTPMTQEAHTPAALEKLLLEN 127 Sbjct: 286 RIESNEGFPVGPGGTLSKVFAVCPLLSNN 314 >INSL Insulinase like Metallo protease domain Length = 433 Score = 20.3 bits (42), Expect = 7.2 Identities = 5/42 (11%), Positives = 5/42 (11%), Gaps = 1/42 (2%) Query: 151 TERSALMRSDTPSNKIAQLLHAKILQTYRINQILSTDERMGA 192 Sbjct: 360 IINSRLFEEERVEN-DAFDIGYSYTVVRDLDFYRFFDKNLSR 400 Underlying Matrix: BLOSUM62 Number of sequences tested against query: 105 Number of sequences better than 10.0: 9 Number of calls to ALIGN: 12 Length of query: 536 Total length of test sequences: 20182 Effective length of test sequences: 16235.0 Effective search space size: 8094459.0 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= AAL27645.1 SD10476p [Drosophila melanogaster]. (536 letters) Searching.................................................done Results from profile search Score E Sequences producing significant alignments: (bits) Value gi|1787795 [28..297] Periplasmic binding protein-like I 26 0.97 gi|2338023 [8..273] Ferritin-like 26 1.1 gi|1352423 [103..429] Isocitrate & isopropylmalate dehydroge... 26 1.5 gi|2496715 [53..359] NAD(P)-binding Rossmann-fold domains 25 2.5 gi|120586 [1..210] Class II aldolase 25 3.5 gi|2129405 [8..201] S-adenosyl-L-methionine-dependent methyl... 24 6.0 gi|666883 [313..633] beta/alpha (TIM)-barrel 24 7.9 gi|2144282 [125..305] S-adenosyl-L-methionine-dependent meth... 24 8.1 gi|1001472 [191..704] N-terminal nucleophile aminohydrolases... 23 8.7 >gi|1787795 [28..297] Periplasmic binding protein-like I Length = 270 Score = 26.5 bits (58), Expect = 0.97 Identities = 12/193 (6%), Positives = 12/193 (6%), Gaps = 32/193 (16%) Query: 323 LTRNDVDAFISPPWGGFIIANPPEH--------VCLAAMSDQEAVPYHVSTTDNMQVMLD 374 Sbjct: 53 FVNQGYNAIIVSAVSPDGLCPALKRAMQRGVRVLTWDSDTKPECRSYYINQGTPAQLGGM 112 Query: 375 QLHKLLDIS--SELQMEGVKVVDIEQLEPRRWEYEAYLRRSAIR-----HISTASSTLQS 427 Sbjct: 113 LVDMAARQVNKDKAKVAFFYSSPTVTDQNQWVKEAKAKIAKEHPGWEIVTTQFGYNDATK 172 Query: 428 LIKLLDQISYIVIDDEVGAAITNSYADILAAKA--ALLEHRLADASVLAKRAFVASERGF 485 Sbjct: 173 SLQTAEGI--LKAYSDLDAIIAPD--ANALPAAAQAAENLKNDKVAIVG----------- 217 Query: 486 FDASLLAQLYFPD 498 Sbjct: 218 FSTPNVMRPYVER 230 >gi|2338023 [8..273] Ferritin-like Length = 266 Score = 26.4 bits (58), Expect = 1.1 Identities = 20/133 (15%), Positives = 20/133 (15%), Gaps = 9/133 (6%) Query: 366 TDNMQVMLDQLHKLLDISSELQMEGVKVVDIEQLEPRRWEYEAYLRRSAIRHISTASSTL 425 Sbjct: 39 SEADVNFYKYLFTFLGMAETLVNFNIDELLVDFECHDIKHYYCEQMAMECVHGKVYFNIL 98 Query: 426 QSLIKLLDQISYIVIDDEVGAAITNSYADILAAKAALLEHRLADASVLAKR--AFVASER 483 Sbjct: 99 NMLFKNNLAATWEFAE----AVLKDEA---LQKKLEWLESKIKMAKTKAEKVLIFYLIEG 151 Query: 484 GFFDASLLAQLYF 496 Sbjct: 152 VFFISSFYCIGLL 164 >gi|1352423 [103..429] Isocitrate & isopropylmalate dehydrogenases Length = 327 Score = 26.0 bits (57), Expect = 1.5 Identities = 9/26 (34%), Positives = 9/26 (34%), Gaps = 1/26 (3%) Query: 441 DDEVGAAITNSYADILAAKAALLEHR 466 Sbjct: 256 HQKGRPTSTNPIASIFAW-TRGLEHR 280 >gi|2496715 [53..359] NAD(P)-binding Rossmann-fold domains Length = 307 Score = 25.4 bits (54), Expect = 2.5 Identities = 13/141 (9%), Positives = 13/141 (9%), Gaps = 12/141 (8%) Query: 305 IPPCHIAPLHIYNSKDQRLTRNDVDAFISP----------PWGGFIIANPPEHVCLAAMS 354 Sbjct: 150 LDVAIVRPRTVLGYGRQGVVQILFDWVERGLDIPVLGGGNNKYQFVHSDDLASACIAASN 209 Query: 355 DQEAVPYHVSTTDNMQV--MLDQLHKLLDISSELQMEGVKVVDIEQLEPRRWEYEAYLRR 412 Sbjct: 210 VKGFATYNIGAAEFGTMRELLQVVIKHAETGSRIKSIPMGPTALAANLASALGLSPLGPY 269 Query: 413 SAIRHISTASSTLQSLIKLLD 433 Sbjct: 270 HSLMYGRAMYFDISKAQKELG 290 >gi|120586 [1..210] Class II aldolase Length = 210 Score = 24.8 bits (54), Expect = 3.5 Identities = 23/123 (18%), Positives = 23/123 (18%), Gaps = 6/123 (4%) Query: 406 YEAYLRRSAIRHI----STASSTLQSLIKLLDQISYIVIDDEVGAAITNSYADILAAKAA 461 Sbjct: 81 YQSRPDANAVVHNHAVHCTAVSILNRSIPAIHYMIAAAGGNSIPCAPYATFGTRELSEHV 140 Query: 462 LLEHRLADASVLAKRAFVASERGFFDASLLAQLYFPDEQKYAIYIPLFLPIMVPVLSSFN 521 Sbjct: 141 ALALKNRKATLLQHHGLIACEVNLEKALWLAHEV--EVLAQLYLTTLAITDPVPVLSDEE 198 Query: 522 MLR 524 Sbjct: 199 IAV 201 >gi|2129405 [8..201] S-adenosyl-L-methionine-dependent methyltransferases Length = 194 Score = 24.0 bits (52), Expect = 6.0 Identities = 12/80 (15%), Positives = 12/80 (15%), Gaps = 4/80 (5%) Query: 268 GRHYALQETALPHLL-TSIAQNLSASTTDKPAINLVVYIPPCHIAPLHIYNSKDQR--LT 324 Sbjct: 10 GLSTGVAKACEDLNLEPGEDLELHAVNHWKPAIRTHEENHGWANHYHARIEELYPPNVVD 69 Query: 325 RNDVDAFI-SPPWGGFIIAN 343 Sbjct: 70 PGSVTLLTGGPECTHFSNAR 89 >gi|666883 [313..633] beta/alpha (TIM)-barrel Length = 321 Score = 23.8 bits (50), Expect = 7.9 Identities = 5/99 (5%), Positives = 5/99 (5%), Gaps = 16/99 (16%) Query: 313 LHIYNSKDQRLTRNDVDAF-ISPPWGGFIIANPPEHVCLAAMSDQEAVPYHVSTTDNMQV 371 Sbjct: 18 FELGEKDVQILAENGFKSLRLPIDLDLYATNR--------DAFVKGTDTELK---FDDDT 66 Query: 372 MLDQLHKLLDISSELQMEGVKV-VDIEQLEPRRWEYEAY 409 Sbjct: 67 LFLVLDSFVE---WTGKYNMSLVIDYHEYDNSYNTTSVK 102 >gi|2144282 [125..305] S-adenosyl-L-methionine-dependent methyltransferases Length = 181 Score = 23.7 bits (50), Expect = 8.1 Identities = 18/130 (13%), Positives = 18/130 (13%), Gaps = 11/130 (8%) Query: 295 DKPAINLVVYIPPCHIAPLHIYNSKDQRLTRNDVDAFISPPWGGF--IIANPPEHVCLAA 352 Sbjct: 55 NPRMLLIGELNLGHFPGLTFNRALMDSLVEPGKRHSKPWCRYGYFDFILTNPPFGVTVEA 114 Query: 353 MSDQEAVPYHVST--TDNMQVMLDQLHKLLDISSELQMEGVKVVDIEQLEPRRW---EYE 407 Sbjct: 115 SGAAYSGYDIAFTANGEPRARQSSEWLFVEQSLRWLKPGGTLAV----VLPRSVLTNPSS 170 Query: 408 AYLRRSAIRH 417 Sbjct: 171 AYERSLLAKL 180 >gi|1001472 [191..704] N-terminal nucleophile aminohydrolases (Ntn hydrolases) Length = 514 Score = 23.4 bits (50), Expect = 8.7 Identities = 9/68 (13%), Positives = 9/68 (13%), Gaps = 3/68 (4%) Query: 37 GVPMWWRTTTVYRVNLPSTEILSLSKIPIKTAVQVAIYTQQTSRGQ---LLIAELQNAFS 93 Sbjct: 264 AAPDLSFAPSLLRTQRSIKLLKNNSSLTFEQFKQKVFDSQMELGDRIVPLLVSAAKVLAN 323 Query: 94 DNEIWSVE 101 Sbjct: 324 PIGIEAAE 331 Underlying Matrix: BLOSUM62 Number of sequences tested against query: 1187 Number of sequences better than 10.0: 9 Number of calls to ALIGN: 9 Length of query: 536 Total length of test sequences: 256703 Effective length of test sequences: 203778.0 Effective search space size: 100231666.6 Initial X dropoff for ALIGN: 25.0 bits ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ calculation of internal repeats with prospero ***** PROSPERO v1.3 Wed Feb 20 11:43:30 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 AAL27645.1 using self-comparison ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ TIGRFAM hmmpfam - search a single seq against HMM database HMMER 2.1.1 (Dec 1998) Copyright (C) 1992-1998 Washington University School of Medicine HMMER is freely distributed under the GNU General Public License (GPL). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HMM file: /data/patterns/tigrfam/tigrfam.hmm Sequence file: pig-s.AAL27645.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: AAL27645.1 SD10476p [Drosophila melanogaster]. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- TIGR00054 TIGR00054: membrane-associated zinc metallo -247.6 68 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- TIGR00054 1/1 21 325 .. 1 463 [] -247.6 68 Alignments of top-scoring domains: TIGR00054: domain 1 of 1, from 21 to 325: score -247.6, E = 68 *->msflwiLasFIiaLavLIfVHELGHFlaARlcGvkVerFSIGFGpkl + ++La FI+++ IG+G + AAL27645.1 21 FRIGATLA-FIVVI--------------------------IGIGVPM 40 WlkfkkngTeYaisl....IPLGGYVKmkGFDglDkeeeevkppetdkdl W ++ T+Y++ l++++I + l k ++ k + ++ AAL27645.1 41 WWRTT---TVYRVNLpsteI-------LS----LSKIPI--KTAVQVAIY 74 fnnkSvlqkaiIifAGplaNfiFAifvyidlvsliGvpgyevgpvieeld + S +q +i ++ + +++ ++s ++ + + AAL27645.1 75 TQQTSRGQLLIAELQNAFSDNEIWSVEFK-QLSPTPMT---------QEA 114 knSialeagiepGdeilsvngkkipgfkdvr..kqiadivaGepmveIla + +ale ++ + ++sv + ++ + +++++ +++ + +m + AAL27645.1 115 HTPAALEKLLLEN-HVQSVGDFMFIEWPKLQeeLLLTTER-SALMRSDTP 162 aPFnSdiErevkLdLrnwtfevekedaveqlglkprgPkiEpvlsdvtpN S+ + L + ++ + + ++ E + +++ AAL27645.1 163 ----SNKIAQ----LLHAKILQTYR-------INQILSTDERMGAKSEAP 197 spAekAGLkeGDkIisidgeklksWrDfvslvkenpgksleikveRnGet pA D I+s+ AAL27645.1 198 QPAY-------DVIVSVL-------------------------------- 208 lsisLtPeakkdkgKaIgfiGisPslkkledeykvvvsygileAlakaae + K P l+ + ++ +++ ++ + AAL27645.1 209 ------------NPK--------PRLTHAK--WN--IAMAVKTYIEPWLA 234 atkdivkLilklLgkL.itGslklknLSGPVgIvkgagssAnlGivyllq + ++ ++ + +k ++ ++lk++ +lG y lq AAL27645.1 235 KVSGVSNYTVRSQWKYrVAIEADLKQV----------RDQSKLGRHYALQ 274 FgAllSiNLGIiNLlPiViPaLDGGqLlfLfIEairGKPlpekvqafvyr A lP +Ll + ++ + + ++ v+ AAL27645.1 275 ETA-----------LP---------HLLTSIAQNLSASTTDKPAINLVVY 304 iGvalLllLmvlgLFN..DllRLll<-* i + l ++N++D +RL+ AAL27645.1 305 IPPC---HIAPLHIYNskD-QRLTR 325 // 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: pig-s.AAL27645.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: AAL27645.1 SD10476p [Drosophila melanogaster]. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- TIGR00554 panK_bact: pantothenate kinase, bacterial 3.2 4.2 1 TIGR01085 murE: UDP-N-acetylmuramyl-tripeptide synthe -1.2 72 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- TIGR01085 1/1 114 124 .. 354 364 .. -1.2 72 TIGR00554 1/1 138 173 .. 274 309 .] 3.2 4.2 Alignments of top-scoring domains: TIGR01085: domain 1 of 1, from 114 to 124: score -1.2, E = 72 *->AHTPDALEkvL<-* AHTP ALEk+L AAL27645.1 114 AHTPAALEKLL 124 TIGR00554: domain 1 of 1, from 138 to 173: score 3.2, E = 4.2 *->inglnlyenilPtreradlilrkgdnhkveevllrk<-* i ++ l e +l t er+ l+ ++k+ ++l k AAL27645.1 138 IEWPKLQEELLLTTERSALMRSDTPSNKIAQLLHAK 173 // 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: pig-s.AAL27645.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: AAL27645.1 SD10476p [Drosophila melanogaster]. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- TGFB Transforming growth factor-beta (TGF-beta) -64.7 42 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- TGFB 1/1 394 463 .. 1 102 [] -64.7 42 Alignments of top-scoring domains: TGFB: domain 1 of 1, from 394 to 463: score -64.7, E = 42 *->CrRhdLyVDFkdlGWddWIIaPkgYnAyyCeGeCpfPlsehlnatva VD ++l +W +Y+Ay + +++ a+ AAL27645.1 394 -------VDIEQLEPRRW-----EYEAY----LRRSAIRHISTAS-- 422 NHAivqsLvhaldPvpkPCCVPtklsplsmLYydddgnvvlrk.YedMvV +++qsL+++ld +s + +dd+ ++++Y d ++ AAL27645.1 423 --STLQSLIKLLDQ-------------ISYIVIDDEVGAAITNsYADILA 457 eeCGCr<-* + AAL27645.1 458 AKAALL 463 // 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: pig-s.AAL27645.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: AAL27645.1 SD10476p [Drosophila melanogaster]. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- COG0350 -68.7 26 1 COG0783 -105.4 51 1 COG3265 -129.0 91 1 COG2003 -168.8 20 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- COG0783 1/1 242 469 .. 1 205 [] -105.4 51 COG0350 1/1 327 472 .. 1 172 [] -68.7 26 COG2003 1/1 341 486 .. 1 228 [] -168.8 20 COG3265 1/1 407 533 .. 1 196 [] -129.0 91 Alignments of top-scoring domains: COG0783: domain 1 of 1, from 242 to 469: score -105.4, E = 51 *->mtvvv.vksela.kalasGageqsadgmstsknvnatAanvgtsnig tv ++ k + a +a + qs g ++ + + ++++ts ++ AAL27645.1 242 YTVRSqWKYRVAiEADLKQVRDQSKLGRHYA-LQETALPHLLTSIAQ 287 lddadrllek........................................ + a+ +k+ + ++ + + + ++++++ ++++ + +++ AAL27645.1 288 NLSAST-TDKpainlvvyippchiaplhiynskdqrltrndvdafisppw 336 ..............dlkkiaeaLnqlLAdlivLYlKthnyHWNVkGpeFf ++ +++++ ++ +ea ++ ++ +++ + AAL27645.1 337 ggfiianppehvclAAMSDQEAVPYHVSTTDNMQVML------------D 374 tLHekfE...ElYeelaeaiDeiAERilaLGgkppatyseylklssikEe +LH++++ ++El e ++++D i +L + y+ yl+ s i AAL27645.1 375 QLHKLLDissELQMEGVKVVD-----IEQLEPRRW-EYEAYLRRSAI--- 415 tgdsttptdaremlaelvqdyetilkefrevlklAeeagDetTAdlltdi + st a + l++l++ +++i+ + +De+ A++ + + AAL27645.1 416 RHIST----ASSTLQSLIKLLDQISYIVI---------DDEVGAAITNSY 452 irelEKhlWMLrAlLqn<-* +l + L++ L++ AAL27645.1 453 ADILAAKAALLEHRLAD 469 COG0350: domain 1 of 1, from 327 to 472: score -68.7, E = 26 *->lyyteiesplgelllvasesglc.ivfldqnsrletlklsplqkkkl + ++i+ p+g+++++ ++++c ++dq+ + AAL27645.1 327 DVDAFISPPWGGFIIANPPEHVClAAMSDQEAV-------------- 359 slgppedealeelvrqleeYfag....elkefslpldlrgtpFqqrV... ++ + + +++ ++ql++ ++ +++ +++ + + + p++ +++ AAL27645.1 360 PYHVSTTDNMQVMLDQLHKLLDIsselQMEGVKVVDIEQLEPRRWEYeay 409 ..WqaLreIPyGetrTYgeiAkliGtPpAvRAVGaAlgrNPlpiiiPCHR + +a+r+I+ +T + + kl++ + +++ + AAL27645.1 410 lrRSAIRHIST-ASSTLQSLIKLLDQIS------YIVIDDEVG------- 445 VigknGsltGyagGllerKkfLLrlEgvslsdsgr<-* ++t + l K++LL++ +l+d+ + AAL27645.1 446 -----AAITNSYADILAAKAALLEH---RLADASV 472 COG2003: domain 1 of 1, from 341 to 486: score -168.8, E = 20 *->lslsmklkdwPeeerPREKLLkrGAeaLSDaELLAIfLRTGtKGksV +++ Pe ++ +a SD+E + AAL27645.1 341 ------IANPPE---------HVCLAAMSDQEAV----------PYH 362 LeLskeLLeeFGsLraLleasveelssvpGlGlaKaiqlkaalElgkRil +++ +++ +++ L++Ll++s e ++ +G+ ++ ql +R AAL27645.1 363 VSTTDNMQVMLDQLHKLLDISSE--LQMEGVKVVDIEQLEP-----RRWE 405 aerlregivltsPeavreyLrqeLrgeerEvFavLfLDnqnRlIaketLF e+++++++++ ++ L+ L + + ++ +I++e+ AAL27645.1 406 YEAYLRRSAIRHISTASSTLQ-SLIKLLDQISYI--------VIDDEV-- 444 iGTinaaeVhPREVvKeALklNAAAvIlAHNHPSGdpePSqaDrriTeRL +AA + S+aD+ L AAL27645.1 445 ---------------------GAA------------ITNSYADI-----L 456 kqAleLvdirVLDHlIvGdgeyvSFaErGwL<-* + ++L++ r+ D ++ ++ +v ErG AAL27645.1 457 AAKAALLEHRLADASVLAKRAFVA-SERGFF 486 COG3265: domain 1 of 1, from 407 to 533: score -129.0, E = 91 *->mTEKHKtmmagksiVvMGVsGsGKStvA...seLakrlgaayPDLKF E a +i St++++ ++L+k+l ++ AAL27645.1 407 --EAYLRRSAIRHI----------STASstlQSLIKLLDQI------ 435 iEGDdLHPraNieKMsaGiPLtDeDRkPWLealrVDaltqaaqageklsv + +D aa ++ AAL27645.1 436 ------------------------------SYIVIDDEVGAAITN----- 450 vtCSALKkqYRDlLReanpeSEvhFiyLdgtkdvileR..mkaRkGHFMK +Y D+L a+ + + ++ v+++R +++ G F+ AAL27645.1 451 --------SYADIL--AAKA--ALLEHRLADASVLAKRafVASERG-FFD 487 asmLdSQFetLEePgiadEtdlkv...ididlpveevvekclaaiqvvke as+L + L P+ + +++ ++ ++i pv + ++q+ + AAL27645.1 488 ASLL----AQLYFPD-EQKYAIYIplfLPIMVPVLSSFNMLRGVLQARR- 531 avLsiee<-* +e AAL27645.1 532 -----KE 533 // 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: pig-s.AAL27645.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: AAL27645.1 SD10476p [Drosophila melanogaster]. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- COG0582 3.1 5.8 1 COG2814 2.4 8.4 1 COG0196 2.0 12 1 COG0425 1.5 76 1 COG2034 1.2 46 1 COG3031 0.8 25 1 COG0350 0.7 58 1 COG0769 0.6 19 1 COG2250 0.5 57 1 COG1579 -0.2 61 1 COG0792 -0.3 92 1 COG0134 -0.6 91 1 COG2974 -0.6 90 1 COG0602 -0.8 71 1 COG2431 -0.9 56 1 COG0074 -1.0 73 1 COG1426 -1.3 93 1 COG1053 -1.9 52 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- COG2034 1/1 18 41 .. 1 29 [. 1.2 46 COG1426 1/1 8 43 .. 105 141 .. -1.3 93 COG2974 1/1 40 51 .. 1 13 [. -0.6 90 COG0792 1/1 71 94 .. 105 129 .] -0.3 92 COG3031 1/1 100 108 .. 1 9 [. 0.8 25 COG0769 1/1 114 124 .. 383 393 .. 0.6 19 COG0134 1/1 154 172 .. 256 274 .] -0.6 91 COG2814 1/1 227 244 .. 237 254 .. 2.4 8.4 COG0350 1/1 327 381 .. 1 68 [. 0.7 58 COG1579 1/1 369 383 .. 1 15 [. -0.2 61 COG0602 1/1 373 383 .. 267 279 .] -0.8 71 COG1053 1/1 385 406 .. 624 644 .] -1.9 52 COG0425 1/1 381 414 .. 43 74 .] 1.5 76 COG2250 1/1 405 435 .. 116 146 .] 0.5 57 COG0074 1/1 443 466 .. 445 472 .] -1.0 73 COG0196 1/1 453 467 .. 298 312 .] 2.0 12 COG0582 1/1 400 481 .. 1 90 [. 3.1 5.8 COG2431 1/1 508 522 .. 307 321 .] -0.9 56 Alignments of top-scoring domains: COG2034: domain 1 of 1, from 18 to 41: score 1.2, E = 46 *->rEdmmrgesgiLIllGiiLIiiGfflvFl<-* Ed+ r+ +l +i +iiG+ ++++ AAL27645.1 18 -EDKFRIGA----TLAFIVVIIGIGVPMW 41 COG1426: domain 1 of 1, from 8 to 43: score -1.3, E = 93 *->psekaekergrrsmplvrskalvlfsliglsvllwwq<-* p+++++k ++ + +++++ a ++++ ig+ v++ww+ AAL27645.1 8 PVKPRRKDKDEDKFRIGATLAFIVVI-IGIGVPMWWR 43 COG2974: domain 1 of 1, from 40 to 51: score -0.6, E = 90 *->mMWFKNLmvYRLn<-* MW + +vYR+n AAL27645.1 40 -MWWRTTTVYRVN 51 COG0792: domain 1 of 1, from 71 to 94: score -0.3, E = 92 *->vavesep.ttgqNeveldwiknaFld<-* va++++ + +gq +++++naF d AAL27645.1 71 VAIYTQQtSRGQ--LLIAELQNAFSD 94 COG3031: domain 1 of 1, from 100 to 108: score 0.8, E = 25 *->mEFKqLmPl<-* +EFKqL P+ AAL27645.1 100 VEFKQLSPT 108 COG0769: domain 1 of 1, from 114 to 124: score 0.6, E = 19 *->AHTPDaLekvL<-* AHTP+aLek L AAL27645.1 114 AHTPAALEKLL 124 COG0134: domain 1 of 1, from 154 to 172: score -0.6, E = 91 *->tsLMkaedprealrelvga<-* ++LM+++ p +++ l+ a AAL27645.1 154 SALMRSDTPSNKIAQLLHA 172 COG2814: domain 1 of 1, from 227 to 244: score 2.4, E = 8.4 *->TYiaPfLqevaGfsgatv<-* TYi+P+L+ v+G+s+ tv AAL27645.1 227 TYIEPWLAKVSGVSNYTV 244 COG0350: domain 1 of 1, from 327 to 381: score 0.7, E = 58 *->lyyteiesplgelllvasesglc.ivfldqnsrletlklsplqkkkl + ++i+ p+g+++++ ++++c ++dq+ + AAL27645.1 327 DVDAFISPPWGGFIIANPPEHVClAAMSDQEAV-------------- 359 slgppedealeelvrqleeYfa<-* ++ + + +++ ++ql++ ++ AAL27645.1 360 PYHVSTTDNMQVMLDQLHKLLD 381 COG1579: domain 1 of 1, from 369 to 383: score -0.2, E = 61 *->MmmmntalksLlklq<-* M +m ++l Ll ++ AAL27645.1 369 MQVMLDQLHKLLDIS 383 COG0602: domain 1 of 1, from 373 to 383: score -0.8, E = 71 *->spQtHKllylgvr<-* ++Q+HK l++ AAL27645.1 373 LDQLHK--LLDIS 383 COG1053: domain 1 of 1, from 385 to 406: score -1.9, E = 52 *->kveyepvdeilit.fePkeRvY<-* ++ +e v+ + i + eP +++Y AAL27645.1 385 ELQMEGVKVVDIEqLEPRRWEY 406 COG0425: domain 1 of 1, from 381 to 414: score 1.5, E = 76 *->DIpkfakkeGhelleveqeggk..eyrilikKgk<-* DI + ++ eG +++++eq ++ + ey ++++ + AAL27645.1 381 DISSELQMEGVKVVDIEQLEPRrwEYEAYLRRSA 414 COG2250: domain 1 of 1, from 405 to 435: score 0.5, E = 57 *->PdeeysrrdAeevveaAervvefverfLeee<-* + e+y+rr+A ++++ A+ + + ++L+ + AAL27645.1 405 EYEAYLRRSAIRHISTASSTLQSLIKLLDQI 435 COG0074: domain 1 of 1, from 443 to 466: score -1.0, E = 73 *->eAGKEaavkVaespaeigellaelLkkr<-* e+G ++++ s+a+i ++ a+lL+ r AAL27645.1 443 EVG----AAITNSYADILAAKAALLEHR 466 COG0196: domain 1 of 1, from 453 to 467: score 2.0, E = 12 *->kDieqArewlnkqrl<-* +Di++A++ l ++rl AAL27645.1 453 ADILAAKAALLEHRL 467 COG0582: domain 1 of 1, from 400 to 481: score 3.1, E = 5.8 *->vdefleylkkergls.ntikaYrrdlrsflaflaphsakklgkksle +++ey+ r+ + + i++ + l+s++++l++ + ++ AAL27645.1 400 EPRRWEYEAYLRRSAiRHISTASSTLQSLIKLLDQ----ISYIVIDD 442 diteedesellkptrrdlrlflaelkerglsettiarrlsalks<-* ++ +++++ ++d+++ +a+l+e l+ +++ +++ + s AAL27645.1 443 EVGAAITNS-----YADILAAKAALLEHRLADASVLAKRAFVAS 481 COG2431: domain 1 of 1, from 508 to 522: score -0.9, E = 56 *->LLvPiLlpfFsSlgg<-* L +Pi++p++sS+ AAL27645.1 508 LFLPIMVPVLSSFNM 522 //