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
