TBLASTN 2.2.16 [Mar-25-2007]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= gi|1710680|sp|P00579.2|RPOD_ECOLI RecName: Full=RNA polymerase
sigma factor rpoD; AltName: Full=Sigma-70
         (613 letters)

Database: ecoli.nt 
           400 sequences; 4,662,239 total letters

Searching..................................................done



                                                             Score    E
Sequences producing significant alignments:                  (bits) Value  N

gb|AE000388.1|AE000388 Escherichia coli K-12 MG1655 section ...   933   0.0    2 
gb|AE000358.1|AE000358 Escherichia coli K-12 MG1655 section ...   240   1e-063  1 
gb|AE000422.1|AE000422 Escherichia coli K-12 MG1655 section ...    71   2e-016  2 
gb|AE000285.1|AE000285 Escherichia coli K-12 MG1655 section ...    42   1e-006  2 
gb|AE000397.1|AE000397 Escherichia coli K-12 MG1655 section ...    32   0.50   1 
gb|AE000436.1|AE000436 Escherichia coli K-12 MG1655 section ...    29   3.4    1 
gb|AE000375.1|AE000375 Escherichia coli K-12 MG1655 section ...    29   3.4    1 
gb|AE000405.1|AE000405 Escherichia coli K-12 MG1655 section ...    28   6.3    1 

>gb|AE000388.1|AE000388 Escherichia coli K-12 MG1655 section 278 of 400 of the complete
            genome
          Length = 10334

 Score =  933 bits (2038), Expect(2) = 0.0
 Identities = 404/404 (100%), Positives = 404/404 (100%)
 Frame = +1

Query: 210  NSIDPELAREKFAELRAQYVVTRDTIKAKGRSHATAQEEILKLSEVFKQFRLVPKQFDYL 269
            NSIDPELAREKFAELRAQYVVTRDTIKAKGRSHATAQEEILKLSEVFKQFRLVPKQFDYL
Sbjct: 7345 NSIDPELAREKFAELRAQYVVTRDTIKAKGRSHATAQEEILKLSEVFKQFRLVPKQFDYL 7524

Query: 270  VNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSDTWFNAAIAMNKPWSEK 329
            VNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSDTWFNAAIAMNKPWSEK
Sbjct: 7525 VNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSDTWFNAAIAMNKPWSEK 7704

Query: 330  LHDVSEEVHRALQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVIS 389
            LHDVSEEVHRALQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVIS
Sbjct: 7705 LHDVSEEVHRALQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVIS 7884

Query: 390  IAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 449
            IAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART
Sbjct: 7885 IAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 8064

Query: 450  IRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMET 509
            IRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMET
Sbjct: 8065 IRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMET 8244

Query: 510  PIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNT 569
            PIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNT
Sbjct: 8245 PIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNT 8424

Query: 570  DYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLDD 613
            DYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLDD
Sbjct: 8425 DYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLDD 8556



 Score =  404 bits (880), Expect(2) = 0.0
 Identities = 177/187 (94%), Positives = 177/187 (94%)
 Frame = +1

Query: 1    MEQNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAP 60
            MEQNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAP
Sbjct: 6718 MEQNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAP 6897

Query: 61   DADDLMLAENTXXXXXXXXXXQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 120
            DADDLMLAENT          QVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA
Sbjct: 6898 DADDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 7077

Query: 121  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATH 180
            KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATH
Sbjct: 7078 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATH 7257

Query: 181  VGSELSQ 187
            VGSELSQ
Sbjct: 7258 VGSELSQ 7278


>gb|AE000358.1|AE000358 Escherichia coli K-12 MG1655 section 248 of 400 of the complete
            genome
          Length = 11457

 Score =  240 bits (519), Expect = 1e-063
 Identities = 96/225 (42%), Positives = 157/225 (69%)
 Frame = -2

Query: 375  AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 434
            +++ M+E+NLRLV+ IA++Y NRGL  LDLI+EGN+GL++AV+KF+  RG++FSTYATWW
Sbjct: 2258 SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 2079

Query: 435  IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKI 494
            IRQ I R+I +Q RTIR+P+H+++ +N   R +R++  ++  EP+ EE+AE++  P D +
Sbjct: 2078 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 1899

Query: 495  RKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAR 554
             ++L++ +   S++TP+G D +  L D + D     P D+   + ++ +    L  L A+
Sbjct: 1898 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 1719

Query: 555  EAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLR 599
            + +VL  RFG+      TLE+VG++  +TRER+RQI+ + LR+LR
Sbjct: 1718 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLR 1584


>gb|AE000422.1|AE000422 Escherichia coli K-12 MG1655 section 312 of 400 of the complete
            genome
          Length = 10864

 Score = 71.0 bits (149), Expect(2) = 2e-016
 Identities = 31/78 (39%), Positives = 46/78 (58%)
 Frame = -3

Query: 375  AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 434
            A K ++ ++LR V+ IA+ Y   GL   DLIQEGNIGLMKAV +F    G +  ++A  W
Sbjct: 2759 AAKTLILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHW 2580

Query: 435  IRQAITRSIADQARTIRI 452
            I+  I   +    R +++
Sbjct: 2579 IKAEIHEYVLRNWRIVKV 2526



 Score = 38.6 bits (78), Expect(2) = 2e-016
 Identities = 14/35 (40%), Positives = 25/35 (71%)
 Frame = -3

Query: 565  IDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLR 599
            +D +   TL+E+  ++ V+ ER+RQ+E  A++KLR
Sbjct: 2171 LDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLR 2067


>gb|AE000285.1|AE000285 Escherichia coli K-12 MG1655 section 175 of 400 of the complete
            genome
          Length = 10165

 Score = 41.7 bits (85), Expect(2) = 1e-006
 Identities = 17/37 (45%), Positives = 26/37 (70%)
 Frame = -1

Query: 403  DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 439
            DL+Q G IGL+ AV++++  +G  F+TYA   IR A+
Sbjct: 1264 DLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAM 1154



 Score = 26.2 bits (51), Expect(2) = 1e-006
 Identities = 10/19 (52%), Positives = 14/19 (73%)
 Frame = -1

Query: 469  QMLQEMGREPTPEELAERM 487
            Q+ QE+GR  T  E+AER+
Sbjct: 1075 QLEQELGRNATETEVAERL 1019


>gb|AE000397.1|AE000397 Escherichia coli K-12 MG1655 section 287 of 400 of the complete genome
          Length = 14820

 Score = 31.7 bits (63), Expect = 0.50
 Identities = 12/37 (32%), Positives = 22/37 (59%)
 Frame = -3

Query: 505   ISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLR 541
             I++E    +DE  +LGD++ED    +  D  TT++ +
Sbjct: 13927 ITLEAARYEDESLNLGDYVEDQIESVTFDRITTQTAK 13817


>gb|AE000436.1|AE000436 Escherichia coli K-12 MG1655 section 326 of 400 of the complete
            genome
          Length = 11150

 Score = 29.0 bits (57), Expect = 3.4
 Identities = 12/26 (46%), Positives = 17/26 (65%)
 Frame = +1

Query: 535  ATTESLRAATHDVLAGLTAREAKVLR 560
            ATT +LR + H++  GL  R+ KV R
Sbjct: 1762 ATTRNLRWSWHEITWGLCLRQTKVCR 1839


>gb|AE000375.1|AE000375 Escherichia coli K-12 MG1655 section 265 of 400 of the complete
            genome
          Length = 10362

 Score = 29.0 bits (57), Expect = 3.4
 Identities = 11/41 (26%), Positives = 20/41 (48%)
 Frame = +3

Query: 426  KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRI 466
            K S+  TWW   A+ R +  +    R+P  +  ++   +RI
Sbjct: 5193 KLSSITTWWHLAALPRRVRRKPYPPRLPAELTNSMRPKSRI 5315


>gb|AE000405.1|AE000405 Escherichia coli K-12 MG1655 section 295 of 400 of the complete
            genome
          Length = 11095

 Score = 28.0 bits (55), Expect = 6.3
 Identities = 12/50 (24%), Positives = 24/50 (48%)
 Frame = +2

Query: 266  FDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSDTW 315
            F+  VNS  + +  V +Q+++  K   +  K   KN+     G + +D +
Sbjct: 1070 FEQRVNSDVLTVSTVNSQDQVTQKPLRDSVKQALKNYFAQLNGQDVNDLY 1219


  Database: ecoli.nt
    Posted date:  May 31, 2007 11:31 AM
  Number of letters in database: 4,662,239
  Number of sequences in database:  400
  
Lambda     K      H
   0.317    0.132    0.363 


Matrix: BLOSUM62
Number of Sequences: 400
Number of Hits to DB: 2,109,753
Number of extensions: 23326
Number of successful extensions: 120
Number of sequences better than 10.0: 8
Length of query: 613
Length of database: 1,554,079
Length adjustment: 43
Effective length of query: 570
Effective length of database: 1,536,879
Effective search space: 876021030
Effective search space used: 876021030
Neighboring words threshold: 13
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
S2: 52 (26.7 bits)
