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)