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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)
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