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