!!SEQUENCE_LIST 1.0 (Peptide) FASTA of: test.gcg from: 1 to: 146 August 25, 2003 13:25 REFORMAT of: b124_sp.pep check: -1 from: 1 to: 146 January 28, 1999 16:22 (No documentation) TO: PIR:* Sequences: 283,308 Symbols: 96,168,669 Word Size: 2 Databases searched: NBRF, Release 76.0, Released on 31Mar2003, Formatted on 7Apr2003 Scoring matrix: GenRunData:blosum50.cmp Variable pamfactor used Gap creation penalty: 12 Gap extension penalty: 2 Histogram Key: Each histogram symbol represents 474 search set sequences Each inset symbol represents 4 search set sequences z-scores computed from opt scores z-score obs exp (=) (*) < 20 789 0:== 22 0 0: 24 4 0:= 26 8 6:* 28 9 64:* 30 101 390:* 32 407 1509:= * 34 2185 4092:===== * 36 7555 8404:================ * 38 16600 13889:=============================*====== 40 25000 19373:========================================*============ 42 27813 23681:=================================================*========= 44 28394 26123:=======================================================*==== 46 26152 26607:========================================================* 48 23191 25473:================================================= * 50 20419 23244:============================================ * 52 18108 20435:======================================= * 54 15701 17455:================================== * 56 13874 14581:==============================* 58 11026 11970:======================== * 60 9392 9697:====================* 62 7678 7774:================* 64 6295 6183:=============* 66 4986 4887:==========* 68 3909 3844:========* 70 3131 3012:======* 72 2497 2354:====*= 74 1858 1835:===* 76 1469 1428:===* 78 1160 1110:==* 80 845 862:=* 82 665 659:=* 84 515 522:=* 86 376 404:* 88 261 313:* 90 225 242:* 92 157 187:* :=======================================* 94 132 145:* :================================= * 96 93 112:* :======================== * 98 63 87:* :================ * 100 73 67:* :================*== 102 44 52:* :=========== * 104 32 40:* :======== * 106 27 31:* :=======* 108 18 24:* :=====* 110 18 19:* :====* 112 11 14:* :===* 114 11 11:* :==* 116 10 9:* :==* 118 8 7:* :=* >120 13 5:* :=*== Joining threshold: 36, opt. threshold: 24, opt. width: 16, reg.-scaled The best scores are: init1 initn opt z-sc E(283250).. PIR2:S44629 Begin: 342 End: 470 ! F22B7.10 protein - Caenorhabditis e... 108 143 241 304.1 1.1e-09 PIR1:WMBELM Begin: 307 End: 385 ! membrane protein LMP-2A - human her... 59 91 99 130.6 5.1 PIR2:AG0762 Begin: 63 End: 144 ! probable membrane protein STY2265 [... 65 65 96 128.9 6.4 PIR2:B83179 Begin: 9 End: 86 ! hypothetical protein PA3730 [import... 40 40 92 127.0 8.2 \\End of List test.gcg PIR2:S44629 P1;S44629 - F22B7.10 protein - Caenorhabditis elegans C;Species: Caenorhabditis elegans C;Date: 20-Feb-1995 #sequence_revision 20-Feb-1995 #text_change 04-Mar-2000 C;Accession: S44629 R;Anderson, K. submitted to the EMBL Data Library, March 1993 . . . SCORES Init1: 108 Initn: 143 Opt: 241 z-score: 304.1 E(): 1.1e-09 >>PIR2:S44629 (628 aa) initn: 143 init1: 108 opt: 241 Z-score: 304.1 expect(): 1.1e-09 Smith-Waterman score: 241; 32.6% identity in 135 aa overlap (3-135:342-470) 10 20 30 test.gcg VXCAAEFDFMEKETPLRYTKTLLLPVVLVVFV |:|||||:: | : |||:|::|: :| S44629 GLGIEDDAHIFDILRSKFTSFANFHTRLYTCSAEFDFIQYSTIEKLCGTLLIPLALISLV 320 330 340 350 360 370 40 50 60 70 80 90 test.gcg AIVRKIISDMWGVLAKQQTHVRKHQFDHGELVYHALQLLAYTALGILIMRLKLFLTPYMC ::| ::::: ::| ::: :: ::||::|:::|| |::::||||||||:||::| S44629 TFVFNFVKNT-NLLWRNSEEIG----ENGEILYNVVQLCCSTVMAFLIMRLKLFMTPHLC 380 390 400 410 420 100 110 120 130 140 test.gcg VMASLICSRQLFG--WLFCKVHPGAIVFVILAAMSIQGSANLQTQWKSTASLALET ::|:|: : :|:| : :: :|:| || | : :| |:: | S44629 IVAALFANSKLLGGDRISKTIRVSALVGVI-AILFYRGIPNIRQQLNVKGEYSNPDQEML 430 440 450 460 470 480 S44629 FDWIQHNTKQDAVFAGTMPVMANVKLTTLRPIVNHPHYEHVGIRERTLKVYSMFSKKPIA 490 500 510 520 530 540 test.gcg PIR1:WMBELM P1;WMBELM - membrane protein LMP-2A - human herpesvirus 4 N;Contains: membrane protein LMP-2B C;Species: human herpesvirus 4, Epstein-Barr virus A;Note: host Homo sapiens (man) C;Date: 31-Dec-1989 #sequence_revision 31-Dec-1989 #text_change 16-Jul-1999 C;Accession: A30178; B30178; S00392 . . . SCORES Init1: 59 Initn: 91 Opt: 99 z-score: 130.6 E(): 5.1 >>PIR1:WMBELM (497 aa) initn: 91 init1: 59 opt: 99 Z-score: 130.6 expect(): 5.1 Smith-Waterman score: 99; 32.9% identity in 79 aa overlap (67-141:307-385) 40 50 60 70 80 90 test.gcg KIISDMWGVLAKQQTHVRKHQFDHGELVYHALQLLAYTALGILIMRLKLFLTPYMCVMAS || ||| || | : ::| ::: WMBELM MTLLLLAFVLWLSSPGGLGTLGAALLTLAAALALLASLILGTLNLTTMFLLMLLWTLVVL 280 290 300 310 320 330 100 110 120 130 140 test.gcg LICSR----QLFGWLFCKVHPGAIVFVILAAMSIQGSANLQTQWKSTASLALET |||| | |: :: |:::::||: | |:: |||::|| :| WMBELM LICSSCSSCPLSKILLARLFLYALALLLLASALIAGGSILQTNFKSLSSTEFIPNLFCML 340 350 360 370 380 390 WMBELM LLIVAGILFILAILTEWGSGNRTYGPVFMCLGGLLTMVAGAVWLTVMSNTLLSAWILTAG 400 410 420 430 440 450 test.gcg PIR2:AG0762 P1;AG0762 - probable membrane protein STY2265 [imported] - Salmonella enterica subsp. enterica serovar Typhi (strain CT18) C;Species: Salmonella enterica subsp. enterica serovar Typhi A;Note: this species has also been called Salmonella typhi C;Date: 09-Nov-2001 #sequence_revision 09-Nov-2001 #text_change 18-Nov-2002 C;Accession: AG0762 R;Parkhill, J.; Dougan, G.; James, K.D.; Thomson, N.R.; Pickard, D.; Wain, J.; Churcher, C.; Mungall, K.L.; Bentley, S.D.; Holden, M.T.G.; Sebaihia, M.; Baker, S.; Basham, D.; Brooks, K.; Chillingworth, T.; Connerton, P.; Cronin, A.; Davis, P.; Davies, R.M.; Dowd, L.; White, N.; Farrar, J.; Feltwell, T.; Hamlin, N.; Haque, A.; Hien, T.T.; Holroyd, S.; Jagels, K.; Krogh, A.; Larsen, T.S.; Leather, S.; Moule, S.; O'Gaora, P SCORES Init1: 65 Initn: 65 Opt: 96 z-score: 128.9 E(): 6.4 >>PIR2:AG0762 (352 aa) initn: 65 init1: 65 opt: 96 Z-score: 128.9 expect(): 6.4 Smith-Waterman score: 96; 27.6% identity in 87 aa overlap (61-137:63-144) 40 50 60 70 80 test.gcg FVAIVRKIISDMWGVLAKQQTHVRKHQFDHGELVYHALQLLAYT----ALGILIMRLKLF |::| :|:: :: | |||:: :||:|| AG0762 TFLLVRLFSIPEGTWPLITLVVIMGPISFWGNVVPRAFERIGGTILGAALGLVALRLELF 40 50 60 70 80 90 90 100 110 120 130 140 test.gcg LTPYM---CVMASLICSRQLFGWLFCKVHP--GAIVFVILAAMSIQGSANLQTQ-WKSTA | | |::| ::| ||| :| : :: : ||:: :::::| |:: AG0762 SLPLMLVWCAIAMFLC-----GWLALGKKPYQALLIGITLAVVVGAPAGDMNTALWRGGD 100 110 120 130 140 test.gcg SLALET AG0762 VILGALLAMLFTGIWPQRAFLHWRIQLAHCVTAYNRVYQAALSPNLLERPRLDKYLQRLL 150 160 170 180 190 200 test.gcg PIR2:B83179 P1;B83179 - hypothetical protein PA3730 [imported] - Pseudomonas aeruginosa (strain PAO1) C;Species: Pseudomonas aeruginosa C;Date: 15-Sep-2000 #sequence_revision 15-Sep-2000 #text_change 31-Dec-2000 C;Accession: B83179 R;Stover, C.K.; Pham, X.Q.; Erwin, A.L.; Mizoguchi, S.D.; Warrener, P.; Hickey, M.J.; Brinkman, F.S.L.; Hufnagle, W.O.; Kowalik, D.J.; Lagrou, M.; Garber, R.L.; Goltry, L.; Tolentino, E.; Westbrook-Wadman, S.; Yuan, Y.; Brody, L.L.; Coulter, S.N.; Folger, K.R.; Kas, A.; Larbig, K.; Lim, R.M.; Smith, K.A.; Spencer, D.H.; Wong, G.K.S.; Wu, Z.; Paulsen, I.T.; Reizer, J.; Saier, M.H.; Hancock, R.E.W.; Lory, S.; Olson, M.V. Nature 406, 959-964, 2000 . . . SCORES Init1: 40 Initn: 40 Opt: 92 z-score: 127.0 E(): 8.2 >>PIR2:B83179 (213 aa) initn: 40 init1: 40 opt: 92 Z-score: 127.0 expect(): 8.2 Smith-Waterman score: 92; 28.4% identity in 88 aa overlap (22-109:9-86) 10 20 30 40 50 60 test.gcg VXCAAEFDFMEKETPLRYTKTLLLPVVLVVFVAIVRKIISDMWGVLAKQQTHVRKHQFDH | :|:|| |: |: | :||::| :::: ::| B83179 MEGFLQTALSFPTVLFSFLLILAII---YWGIVALGMVEIDVLDLDA 10 20 30 40 70 80 90 100 110 120 test.gcg GELVYHALQLLAYTALGILIMRLKLFLTPYMCVMASLICSRQLFGWLFCKVHPGAIVFVI :| | | :|: |: :||| :| |:: | ::|:|::| B83179 ESVVDGAGQA---EGLAALLAKLKLNGVPVTLVLTLL----SFFAWFLCYFVQLWLLSAL 50 60 70 80 90 130 140 test.gcg LAAMSIQGSANLQTQWKSTASLALET B83179 PLGWLRYPLGAVVAVGALFLAAPLAATLCRPLRPLFRKLESTSSKSVLGQVAVVRSGRVT 100 110 120 130 140 150 ! Distributed over 1 thread. ! Start time: Mon Aug 25 13:23:54 2003 ! Completion time: Mon Aug 25 13:25:12 2003 ! CPU time used: ! Database scan: 0:01:34.1 ! Post-scan processing: 0:00:00.6 ! Total CPU time: 0:01:34.7 ! Output File: test.fasta