# ssearch34 -Q single.fa testset.fa SSEARCH searches a sequence data bank version 3.4t24 June 23, 2004 Please cite: T. F. Smith and M. S. Waterman, (1981) J. Mol. Biol. 147:195-197; W.R. Pearson (1991) Genomics 11:635-650 Query library single.fa vs testset.fa library searching testset.fa library 1>>>d1pfsa_ 2.24.6.1.2 Gene V protein [Pseudomonas phage pf3] - 78 aa vs testset.fa library opt E() < 20 0 0: 22 0 0: one = represents 1 library sequences 24 0 0: 26 0 0: 28 0 0: 30 0 0: 32 2 0:== 34 0 1:* 36 2 3:==* 38 3 5:=== * 40 4 6:==== * 42 2 8:== * 44 9 8:=======*= 46 10 9:========*= 48 8 8:=======* 50 8 8:=======* 52 5 7:===== * 54 8 6:=====*== 56 5 5:====* 58 7 4:===*=== 60 2 3:==* 62 4 3:==*= 64 3 2:=*= 66 2 2:=* 68 1 1:* 70 1 1:* 72 1 1:* 74 1 1:* 76 1 0:= 78 2 0:== 80 1 0:= 82 0 0: 84 0 0: 86 0 0: 88 0 0: 90 0 0: 92 0 0: 94 0 0: 96 0 0: 98 0 0: 100 0 0: 102 0 0: 104 0 0: 106 0 0: 108 0 0: 110 0 0: 112 0 0: 114 0 0: 116 0 0: 118 0 0: >120 1 0:= 13355 residues in 93 sequences Expectation_n fit: rho(ln(x))= 7.2437+/-0.0204; mu= -3.4950+/- 0.925 mean_var=32.6334+/- 9.107, 0's: 0 Z-trim: 1 B-trim: 0 in 0/19 Lambda= 0.224514 Kolmogorov-Smirnov statistic: 0.1096 (N=24) at 42 Smith-Waterman (PGopt) (4.2 Mar 2004) function [BL50 matrix (15:-5)], gap-penalty: -12/-2 Scan time: 0.020 The best scores are: s-w bits E(93) d1pfsa_ 2.24.6.1.2 Gene V protein [Pseudomonas ph ( 78) 534 177.3 2.4e-48 d1fus__ 4.1.1.1.2 RNase F1 [Fusarium moniliforme] ( 106) 48 19.6 0.97 d4ptp__ 2.29.1.2.1 Trypsin(ogen) [bovine (Bos tau ( 223) 52 20.2 1.3 d1jbc__ 2.18.1.1.1 Concanavalin A [jack bean (Can ( 237) 52 20.2 1.5 d1cyo__ 4.62.1.1.1 Cytochrome b5 [bovine (Bos tau ( 88) 44 18.5 1.8 d1ckaa_ 2.20.2.1.1 C-Crk, N-terminal SH3 domain [ ( 57) 40 17.6 2.1 d1rgea_ 4.1.1.1.1 RNase Sa [Streptomyces aureofac ( 96) 42 17.7 3.1 d2sga__ 2.29.1.1.2 Protease A [Streptomyces grise ( 181) 46 18.5 3.6 d1pls__ 2.35.1.1.5 Pleckstrin, N-terminal domain ( 113) 42 17.6 4.1 d1burs_ 4.35.1.1.2 Ribulose 1,5-bisphosphate carb ( 123) 41 17.2 5.8 d8rxna_ 7.34.3.1.1 Rubredoxin [Desulfovibrio vulg ( 52) 34 15.7 6.9 d2olba_ 3.68.1.1.1 Oligo-peptide binding protein ( 517) 50 18.8 7.9 d1xsoa_ 2.1.7.1.3 Cu,Zn superoxide dismutase, SOD ( 150) 41 17.0 7.9 d1ifc__ 2.39.1.2.2 Intestinal fatty acid binding ( 131) 40 16.8 8 d1lkka_ 4.47.1.1.1 p56-lck tyrosine kinase [human ( 105) 38 16.4 8.7 d3sdhb_ 1.1.1.1.1 Hemoglobin I [ark clam (Scaphar ( 145) 40 16.7 9.3 >>d1pfsa_ 2.24.6.1.2 Gene V protein [Pseudomonas phage p (78 aa) s-w opt: 534 Z-score: 935.7 bits: 177.3 E(): 2.4e-48 Smith-Waterman score: 534; 100.000% identity (100.000% similar) in 78 aa overlap (1-78:1-78) 10 20 30 40 50 60 d1pfsa MNIQITFTDSVRQGTSAKGNPYTFQEGFLHLEDKPHPLQCQFFVESVIPAGSYQVPYRIN :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: d1pfsa MNIQITFTDSVRQGTSAKGNPYTFQEGFLHLEDKPHPLQCQFFVESVIPAGSYQVPYRIN 10 20 30 40 50 60 70 d1pfsa VNNGRPELAFDFKAMKRA :::::::::::::::::: d1pfsa VNNGRPELAFDFKAMKRA 70 >>d1fus__ 4.1.1.1.2 RNase F1 [Fusarium moniliforme] (106 aa) s-w opt: 48 Z-score: 81.0 bits: 19.6 E(): 0.97 Smith-Waterman score: 48; 33.333% identity (51.515% similar) in 33 aa overlap (40-72:24-50) 10 20 30 40 50 60 d1pfsa SVRQGTSAKGNPYTFQEGFLHLEDKPHPLQCQFFVESVIPAGSYQVPYRINVNNGRPELA ::.. .. ::: :. : .: d1fus_ XSATTCGSTNYSASQVRAAANAACQYY-QNDDTAGSSTYPHTYNNYEG----- 10 20 30 40 70 d1pfsa FDFKAMKRA ::: d1fus_ FDFPVDGPYQEFPIKSGGVYTGGSPGADRVVINTNCEYAGAITHTGASGNNFVGCSGTN 50 60 70 80 90 100 >>d4ptp__ 2.29.1.2.1 Trypsin(ogen) [bovine (Bos taurus)] (223 aa) s-w opt: 52 Z-score: 78.6 bits: 20.2 E(): 1.3 Smith-Waterman score: 52; 42.857% identity (85.714% similar) in 14 aa overlap (51-64:8-21) 30 40 50 60 70 d1pfsa PYTFQEGFLHLEDKPHPLQCQFFVESVIPAGSYQVPYRINVNNGRPELAFDFKAMKRA :. :::....:.: d4ptp_ IVGGYTCGANTVPYQVSLNSGYHFCGGSLINSQWVVS 10 20 30 d4ptp_ AAHCYKSGIQVRLGEDNINVVEGNEQFISASKSIVHPSYNSNTLNNDIMLIKLKSAASLN 40 50 60 70 80 90 >>d1jbc__ 2.18.1.1.1 Concanavalin A [jack bean (Canavali (237 aa) s-w opt: 52 Z-score: 77.8 bits: 20.2 E(): 1.5 Smith-Waterman score: 52; 36.111% identity (55.556% similar) in 36 aa overlap (23-52:190-225) 10 20 30 40 d1pfsa MNIQITFTDSVRQGTSAKGNPYTFQEGFLHLEDKP--HPLQ-CQFFV---ES .:. : : .: :: . ::. .: d1jbc_ SSNGSPQGSSVGRALFYAPVHIWESSAVVASFEATFTFLIKSPDSHPADGIAFFISNIDS 160 170 180 190 200 210 50 60 70 d1pfsa VIPAGSYQVPYRINVNNGRPELAFDFKAMKRA ::.:: d1jbc_ SIPSGSTGRLLGLFPDAN 220 230 >>d1cyo__ 4.62.1.1.1 Cytochrome b5 [bovine (Bos taurus)] (88 aa) s-w opt: 44 Z-score: 76.4 bits: 18.5 E(): 1.8 Smith-Waterman score: 44; 39.286% identity (60.714% similar) in 28 aa overlap (7-34:58-84) 10 20 30 d1pfsa MNIQITFTDSVRQGTSAKGNPYTFQEGFLHLEDKPH : : : ..:.:. :: : :: .:. d1cyo_ KVYDLTKFLEEHPGGEEVLREQAGGDATENFED-VGHSTDARELSKTFIIGELHPDDRSK 30 40 50 60 70 80 40 50 60 70 d1pfsa PLQCQFFVESVIPAGSYQVPYRINVNNGRPELAFDFKAMKRA d1cyo_ IT >>d1ckaa_ 2.20.2.1.1 C-Crk, N-terminal SH3 domain [mouse (57 aa) s-w opt: 40 Z-score: 74.9 bits: 17.6 E(): 2.1 Smith-Waterman score: 40; 34.286% identity (57.143% similar) in 35 aa overlap (24-57:20-53) 10 20 30 40 50 d1pfsa MNIQITFTDSVRQGTSAKGNPYTFQEG-FLHLEDKPHPLQCQFFVESVIPAGSYQVPYRI :..: .:...:::. : .: : ::: d1ckaa AEYVRALFDFNGNDEEDLPFKKGDILRIRDKPEE-QWWNAEDSEGKRGMIPVPYVE 10 20 30 40 50 60 70 d1pfsa NVNNGRPELAFDFKAMKRA d1ckaa KY >>d1rgea_ 4.1.1.1.1 RNase Sa [Streptomyces aureofaciens] (96 aa) s-w opt: 42 Z-score: 71.8 bits: 17.7 E(): 3.1 Smith-Waterman score: 42; 40.000% identity (56.000% similar) in 25 aa overlap (33-53:25-49) 10 20 30 40 50 d1pfsa IQITFTDSVRQGTSAKGNPYTFQEGFLHLEDKPHPLQCQFFV----ESVIPAGSYQVPYR : : : . . : :::.:. :: d1rgea DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHE 10 20 30 40 50 60 70 d1pfsa INVNNGRPELAFDFKAMKRA d1rgea YTVITPGARTRGTRRIITGEATQEDYYTGDHYATFSLIDQTC 60 70 80 90 >>d2sga__ 2.29.1.1.2 Protease A [Streptomyces griseus, s (181 aa) s-w opt: 46 Z-score: 70.7 bits: 18.5 E(): 3.6 Smith-Waterman score: 46; 38.095% identity (71.429% similar) in 21 aa overlap (2-22:36-56) 10 20 30 d1pfsa MNIQITFTDSVRQGTSAKGNPYTFQEGFLHL ::. ... ..: ::: .: : d2sga_ AITTGGSRCSLGFNVSVNGVAHALTAGHCTNISASWSIGTRTGTSFPNNDYGIIRHSNPA 10 20 30 40 50 60 40 50 60 70 d1pfsa EDKPHPLQCQFFVESVIPAGSYQVPYRINVNNGRPELAFDFKAMKRA d2sga_ AADGRVYLYNGSYQDITTAGNAFVGQAVQRSGSTTGLRSGSVTGLNATVNYGSSGIVYGM 70 80 90 100 110 120 >>d1pls__ 2.35.1.1.5 Pleckstrin, N-terminal domain [Huma (113 aa) s-w opt: 42 Z-score: 69.7 bits: 17.6 E(): 4.1 Smith-Waterman score: 42; 36.842% identity (73.684% similar) in 19 aa overlap (15-33:72-90) 10 20 30 40 d1pfsa MNIQITFTDSVRQGTSAKGNPYTFQEGFLHLEDKPHPLQCQFFV :..: . . :: .::. .: d1pls_ NSPKGMIPLKGSTLTSPCQDFGKRMFVFKITTTKQQDHFFQAAFLEERDAWVRDINKAIK 50 60 70 80 90 100 50 60 70 d1pfsa ESVIPAGSYQVPYRINVNNGRPELAFDFKAMKRA d1pls_ CIEGLEHHHHHH 110 >>d1burs_ 4.35.1.1.2 Ribulose 1,5-bisphosphate carboxyla (123 aa) s-w opt: 41 Z-score: 66.9 bits: 17.2 E(): 5.8 Smith-Waterman score: 41; 35.714% identity (53.571% similar) in 28 aa overlap (49-73:20-47) 20 30 40 50 60 70 d1pfsa GNPYTFQEGFLHLEDKPHPLQCQFFVESVIPAGSYQVPYRIN---VNNGRPELAFDFKAM : . :. ..: ::: : : :. : d1burs MQVWPILGMKKYETLSYLPPLTTEQLLAEVNYLLVNNWIPCLEFEVKDG 10 20 30 40 d1pfsa KRA d1burs FVYREHLKSPGYYDGRYWTMWKLPMFGCTDPAQVLNELEECKKAYPDAFIRIIGFDNKRQ 50 60 70 80 90 100 >>d8rxna_ 7.34.3.1.1 Rubredoxin [Desulfovibrio vulgaris] (52 aa) s-w opt: 34 Z-score: 65.5 bits: 15.7 E(): 6.9 Smith-Waterman score: 34; 35.294% identity (64.706% similar) in 17 aa overlap (56-71:15-31) 30 40 50 60 70 d1pfsa EGFLHLEDKPHPLQCQFFVESVIPAGSYQVPYRINVNNG-RPELAFDFKAMKRA : . . .:: .: .:: d8rxna MKKYVCTVCGYEYDPAEGDPDNGVKPGTSFDDLPADWVCPVCGA 10 20 30 40 d8rxna PKSEFEAA 50 >>d2olba_ 3.68.1.1.1 Oligo-peptide binding protein (OPPA (517 aa) s-w opt: 50 Z-score: 64.4 bits: 18.8 E(): 7.9 Smith-Waterman score: 50; 36.667% identity (63.333% similar) in 30 aa overlap (48-77:312-340) 20 30 40 50 60 70 d1pfsa KGNPYTFQEGFLHLEDKPHPLQCQFFVESVIPAGSYQVPYRINVNNGRPELAFDFKAMKR .:: :: :: ... .:: : .. .:: d2olba APFNDVRVRTALKLALDRDIIVNKVKNQGDLPAYSYTPPYTDGAKLVEPEW-FKWSQQKR 290 300 310 320 330 340 d1pfsa A d2olba NEEAKKLLAEAGFTADKPLTFDLLYNTSDLHKKLAIAVASIWKKNLGVNVNLENQEWKTF 350 360 370 380 390 400 >>d1xsoa_ 2.1.7.1.3 Cu,Zn superoxide dismutase, SOD [Afr (150 aa) s-w opt: 41 Z-score: 64.4 bits: 17.0 E(): 7.9 Smith-Waterman score: 41; 30.769% identity (53.846% similar) in 39 aa overlap (31-66:36-72) 10 20 30 40 50 d1pfsa MNIQITFTDSVRQGTSAKGNPYTFQEGFLHLEDKPHPLQCQFFVESV---IPAGSYQVPY : : : .. . : ... . :::. : d1xsoa VLAGSGDVKGVVHFEQQDEGAVSVEGKIEGLTDGLHGFHIHVFGDNTNGCMSAGSHFNPE 10 20 30 40 50 60 60 70 d1pfsa RINVNNGRPELAFDFKAMKRA : :.: : d1xsoa --NKNHGAPGDTDRHVGDLGNVTAEGGVAQFKITDSLISLKGPNSIIGRTAVVHEKADDL 70 80 90 100 110 120 >>d1ifc__ 2.39.1.2.2 Intestinal fatty acid binding prote (131 aa) s-w opt: 40 Z-score: 64.3 bits: 16.8 E(): 8 Smith-Waterman score: 40; 27.778% identity (66.667% similar) in 18 aa overlap (9-26:34-51) 10 20 30 d1pfsa MNIQITFTDSVRQGTSAKGNPYTFQEGFLHLEDKPHPL :... . .:: .: .: d1ifc_ GTWKVDRNENYEKFMEKMGINVVKRKLGAHDNLKLTITQEGNKFTVKESSNFRNIDVVFE 10 20 30 40 50 60 40 50 60 70 d1pfsa QCQFFVESVIPAGSYQVPYRINVNNGRPELAFDFKAMKRA d1ifc_ LGVDFAYSLADGTELTGTWTMEGNKLVGKFKRVDNGKELIAVREISGNELIQTYTYEGVE 70 80 90 100 110 120 >>d1lkka_ 4.47.1.1.1 p56-lck tyrosine kinase [human (Hom (105 aa) s-w opt: 38 Z-score: 63.6 bits: 16.4 E(): 8.7 Smith-Waterman score: 38; 31.250% identity (62.500% similar) in 32 aa overlap (35-64:23-54) 10 20 30 40 50 60 d1pfsa ITFTDSVRQGTSAKGNPYTFQEGFLHLEDKPHPLQCQFFV-ESVIPAGSYQVPYR-INVN : . .:.. :: :::... : .. : d1lkka LEPEPWFFKNLSRKDAERQLLAPGNTHGSFLIRESESTAGSFSLSVRDFDQN 10 20 30 40 50 70 d1pfsa NGRPELAFDFKAMKRA .: d1lkka QGEVVKHYKIRNLDNGGFYISPRITFPGLHELVRHYTNASDGLCTRLSRPCQT 60 70 80 90 100 >>d3sdhb_ 1.1.1.1.1 Hemoglobin I [ark clam (Scapharca in (145 aa) s-w opt: 40 Z-score: 63.0 bits: 16.7 E(): 9.3 Smith-Waterman score: 40; 27.027% identity (54.054% similar) in 37 aa overlap (10-40:55-91) 10 20 30 d1pfsa MNIQITFTDSVRQGTSA---KGNPYTFQ---EGFLHLED .: :: . .:. :.. ..:. : d3sdhb GSDKKGNGVALMTTLFADNQETIGYFKRLGNVSQGMANDKLRGHSITLMYALQNFIDQLD 30 40 50 60 70 80 40 50 60 70 d1pfsa KPHPLQCQFFVESVIPAGSYQVPYRINVNNGRPELAFDFKAMKRA .: : : d3sdhb NPDDLVCVVEKFAVNHITRKISAAEFGKINGPIKKVLASKNFGDKYANAWAKLVAVVQAA 90 100 110 120 130 140 78 residues in 1 query sequences 13355 residues in 93 library sequences Scomplib [34t24] start: Tue Aug 15 22:46:28 2006 done: Tue Aug 15 22:46:28 2006 Total Scan time: 0.020 Total Display time: 0.010 Function used was SSEARCH [version 3.4t24 June 23, 2004]