TBLASTX 2.0MP-WashU [12-Feb-2001] [linux-i686 01:36:08 31-Jan-2001] Copyright (C) 1996-2000 Washington University, Saint Louis, Missouri USA. All Rights Reserved. Reference: Gish, W. (1996-2000) http://blast.wustl.edu Notice: statistical significance is estimated under the assumption that the equivalent of one entire reading frame of the query sequence and one entire reading frame of the database code for protein and that significant alignments will only involve coding reading frames. Query= gi|142864|gb|M10040.1|BACDNAE B.subtilis dnaE gene encoding DNA primase, complete cds (2001 letters) Translating both strands of query sequence in all 6 reading frames Database: ecoli.nt 400 sequences; 4,662,239 total letters. Searching....10....20....30....40....50....60....70....80....90....100% done Smallest Sum Reading High Probability Sequences producing High-scoring Segment Pairs: Frame Score P(N) N gi|1789441|gb|AE000388.1|AE000388 Escherichia coli K-1... +2 318 6.4e-70 5 gi|2367383|gb|AE000509.1|AE000509 Escherichia coli K-1... -3 59 0.9992 2 >gi|1789441|gb|AE000388.1|AE000388 Escherichia coli K-12 MG1655 section 278 of 400 of the complete genome Length = 10,334 Plus Strand HSPs: Score = 318 (148.6 bits), Expect = 6.4e-70, Sum P(5) = 6.4e-70 Identities = 57/127 (44%), Positives = 81/127 (63%), Frame = +3 / +2 Query: 618 FDRFRNRVMFPIHDHHGAVVAFSGRALGSQQPKYMNSPETPLFHKSKLLYNFYKARLHIR 797 +DRFR RVMFPI D G V+ F GR LG+ PKY+NSPET +FHK + LY Y+A+ Sbjct: 5366 YDRFRERVMFPIRDKRGRVIGFGGRVLGNDTPKYLNSPETDIFHKGRQLYGLYEAQQDNA 5545 Query: 798 KQERAVLFEGFADVYTAVSSDVKESIATMGTSLTDDHVKILRRNVEEIILCYDSDKAGYE 977 + R ++ EG+ DV + ++A++GTS T DH+++L R +I CYD D+AG + Sbjct: 5546 EPNRLLVVEGYMDVVALAQYGINYAVASLGTSTTADHIQLLFRATNNVICCYDGDRAGRD 5725 Query: 978 ATLKASE 998 A +A E Sbjct: 5726 AAWRALE 5746 Score = 247 (116.1 bits), Expect = 6.4e-70, Sum P(5) = 6.4e-70 Identities = 44/98 (44%), Positives = 61/98 (62%), Frame = +3 / +2 Query: 21 MGNRIPDEIVDQVQKSADIVEVIGDYVQLKKQGRNYFGLCPFHGESTPSFSVSPDKQIFH 200 M RIP ++ + DIV++I V+LKKQG+N+ CPFH E TPSF+V+ +KQ +H Sbjct: 4778 MAGRIPRVFINDLLARTDIVDLIDARVKLKKQGKNFHACCPFHNEKTPSFTVNGEKQFYH 4957 Query: 201 CFGCGAGGNVFSFLRQMEGYSFAESVSHLADKYQIDFP 314 CFGCGA GN FL + F E+V LA + ++ P Sbjct: 4958 CFGCGAHGNAIDFLMNYDKLEFVETVEELAAMHNLEVP 5071 Score = 85 (41.8 bits), Expect = 6.4e-70, Sum P(5) = 6.4e-70 Identities = 19/59 (32%), Positives = 28/59 (47%), Frame = +3 / +2 Query: 441 ALDYLLSRGFTKELINEFQIGYALDSWDFITKFLVKRGFSEAQMEKAGLLIRREDGSGY 617 A YL RG + E+I F IG+A WD + K + + AG+L+ + G Y Sbjct: 5192 ARQYLEKRGLSHEVIARFAIGFAPPGWDNVLKRFGGNPENRQSLIDAGMLVTNDQGRSY 5368 Score = 65 (32.7 bits), Expect = 6.4e-70, Sum P(5) = 6.4e-70 Identities = 12/28 (42%), Positives = 18/28 (64%), Frame = +3 / +2 Query: 1014 GCKVRVAMIPDGLDPDDYIKKFGGEKFK 1097 G ++R +PDG DPD ++K G E F+ Sbjct: 5771 GRQLRFMFLPDGEDPDTLVRKEGKEAFE 5854 Score = 48 (24.9 bits), Expect = 0.89, Sum P(4) = 0.59 Identities = 15/49 (30%), Positives = 21/49 (42%), Frame = +3 / +2 Query: 639 VMFPIHDHHGAVVAFSGRALGSQQPKYMNSPETPLFHKSKLLYNFYKAR 785 V F HD V A R+ + P Y T LFH+ K F++ + Sbjct: 4046 VRFYAHDRGRPVQARRRRSQRAISPDYTIGWLTNLFHRRKWRCRFHRRK 4192 Score = 46 (24.0 bits), Expect = 1.5, Sum P(4) = 0.78 Identities = 8/17 (47%), Positives = 10/17 (58%), Frame = +3 / +2 Query: 150 GESTPSFSVSPDKQIFH 200 G TP + SP+ IFH Sbjct: 5447 GNDTPKYLNSPETDIFH 5497 Score = 42 (22.1 bits), Expect = 6.4e-70, Sum P(5) = 6.4e-70 Identities = 6/16 (37%), Positives = 10/16 (62%), Frame = +1 / +2 Query: 1129 WRSKCNISEKERTCPM 1176 W S + +K+R CP+ Sbjct: 7151 WNSTIVLKQKKRVCPI 7198 Score = 42 (22.1 bits), Expect = 2.0e-42, Sum P(5) = 2.0e-42 Identities = 6/18 (33%), Positives = 14/18 (77%), Frame = +3 / +2 Query: 21 MGNRIPDEIVDQVQKSAD 74 + R+PD++VD++++ D Sbjct: 206 ISTRMPDDVVDKLKQLKD 259 Minus Strand HSPs: Score = 102 (49.6 bits), Expect = 4.9e-08, Sum P(3) = 4.9e-08 Identities = 32/83 (38%), Positives = 42/83 (50%), Frame = -3 / -3 Query: 319 SSGKSIWYLSAR*ETDSAKE*PSICLKKEKTLPPAPQPKQ*KICLSGDTENEGVLSP*KG 140 S+G S ++A T S S ++K LP AP PKQ C S T +GV S G Sbjct: 5076 SNGTSRLCIAASSSTVSTNSSLS*FIRKSIALPCAPHPKQW*NCFSPLTVKDGVFSLWNG 4897 Query: 139 QSPK*FRPCFFN*T*SPMTSTIS 71 Q F PCFF+ T + + ST+S Sbjct: 4896 QHAWKFLPCFFSFTRASIRSTMS 4828 Score = 71 (35.4 bits), Expect = 4.9e-08, Sum P(3) = 4.9e-08 Identities = 18/35 (51%), Positives = 20/35 (57%), Frame = -3 / -3 Query: 724 FIYLGCWLPRALPEKATTAP**SWIGNMTRFLKRS 620 F YLG LP P K T P S +GN+TR KRS Sbjct: 5472 FRYLGVSLPSTRPPKPITRPRLSRMGNITRSRKRS 5368 Score = 65 (32.7 bits), Expect = 0.0034, Sum P(3) = 0.0034 Identities = 18/71 (25%), Positives = 34/71 (47%), Frame = -2 / -2 Query: 233 ENIAARSAAKAMKNLFVGRYGKRRCAFSMKRTESKVVSALLL*LNIITYDFNDICRLLHL 54 + +A R+ +KA+ LF+ G+ R ++ T + ALL L+ +D+ + Sbjct: 4990 DRVAVRATSKAVVKLFLTVNGEGRGFLVVEWTTRVEILALLFQLHTGIDQIDDVSACQQI 4811 Query: 53 IHNFIWYPISH 21 I+ + W SH Sbjct: 4810 INEYAWDSSSH 4778 Score = 42 (22.1 bits), Expect = 4.9e-08, Sum P(3) = 4.9e-08 Identities = 10/18 (55%), Positives = 12/18 (66%), Frame = -3 / -3 Query: 1093 NFSPPNFLM*SSGSNPSG 1040 N S P+F SGS+PSG Sbjct: 5850 NASLPSFRTSVSGSSPSG 5797 >gi|2367383|gb|AE000509.1|AE000509 Escherichia coli K-12 MG1655 section 399 of 400 of the complete genome Length = 10,589 Minus Strand HSPs: Score = 59 (29.9 bits), Expect = 7.1, Sum P(2) = 1.00 Identities = 15/40 (37%), Positives = 19/40 (47%), Frame = -3 / -3 Query: 706 WLPRALPEKATTAP**SWIGNMTRFLKRSKYPLPSSRLIR 587 WL R +T +P WI M L SK LPS++ R Sbjct: 4227 WLSRTTVGSSTVSPRTFWITRMKVKLSSSKVTLPSTKSTR 4108 Score = 51 (26.3 bits), Expect = 7.1, Sum P(2) = 1.00 Identities = 8/15 (53%), Positives = 10/15 (66%), Frame = -3 / -1 Query: 382 CASAIFCSPEDSGRA 338 C S + C P+D GRA Sbjct: 1097 CTSLMLCRPQDGGRA 1053 Parameters: novalidctxok nonnegok gapall Q=12 R=1 cpus=1 filter=seg nogaps matrix=blosum62 W=3 S2=41 gapS2=68 X=16 gapX=38 hitdist=40 gi gapL=0.27 gapK=0.047 gapH=0.23 ctxfactor=36.0 E=10 Query ----- As Used ----- ----- Computed ---- Frame MatID Matrix name Lambda K H Lambda K H +3 0 blosum62 0.318 0.135 0.401 0.324 0.139 0.405 +2 0 blosum62 0.318 0.135 0.401 0.365 0.163 0.618 +1 0 blosum62 0.318 0.135 0.401 0.356 0.155 0.528 -1 0 blosum62 0.318 0.135 0.401 0.350 0.155 0.543 -2 0 blosum62 0.318 0.135 0.401 0.350 0.155 0.505 -3 0 blosum62 0.318 0.135 0.401 0.358 0.157 0.543 Query Frame MatID Length Eff.Length E S W T X E2 S2 +3 0 666 666 10. 54 3 13 16 0.021 41 +2 0 666 666 10. 54 3 13 16 0.021 41 +1 0 667 667 10. 54 3 13 16 0.021 41 -1 0 667 667 10. 54 3 13 16 0.021 41 -2 0 666 666 10. 54 3 13 16 0.021 41 -3 0 666 666 10. 54 3 13 16 0.021 41 Statistics: Database: /home/jes12/db/ecoli.nt Title: ecoli.nt Posted: 3:16:20 PM EST Nov 18, 2001 Created: 10:10:31 AM EST Nov 18, 2001 Format: XDF-1 # of letters in database: 4,662,239 # of sequences in database: 400 # of database sequences satisfying E: 2 No. of states in DFA: 598 (64 KB) Total size of DFA: 416 KB (1196 KB) Time to generate neighborhood: 0.02u 0.02s 0.04t Elapsed: 00:00:00 No. of threads or processors used: 1 Search cpu time: 2.41u 0.01s 2.42t Elapsed: 00:00:05 Total cpu time: 2.44u 0.03s 2.47t Elapsed: 00:00:07 Start: Sat Apr 20 18:19:43 2002 End: Sat Apr 20 18:19:50 2002