RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15215
(1432 letters)
>gnl|CDD|235549 PRK05658, PRK05658, RNA polymerase sigma factor RpoD; Validated.
Length = 619
Score = 854 bits (2209), Expect = 0.0
Identities = 332/616 (53%), Positives = 438/616 (71%), Gaps = 12/616 (1%)
Query: 824 EEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV 883
++N + + K LIK GKERGYLT++E+ND LPEDI+D E IE II M I V E
Sbjct: 4 PMLDNPQSQLKKLIKRGKERGYLTYAELNDHLPEDIVDSEQIEDIIAMLNDMGIQVVEEA 63
Query: 884 LDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDG 939
D + L+L+ +D+D EE AALS+V+S+ GRT DP++MY+REMG+VELLTR+G
Sbjct: 64 PDADDLLLAENEADAQTDEDAEEEAAAALSSVESEIGRTDDPVRMYLREMGTVELLTREG 123
Query: 940 EIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNR 999
EIEIAKRIE G MI A+ P TI IL D++ E ++ E++DG +D N +
Sbjct: 124 EIEIAKRIEAGENIMIAALCESPLTIDAILEWYDRLENGERRLRELIDGFVDPNAEEDPA 183
Query: 1000 VI---KGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGY 1056
+ +++E++ E + D +L + L KF ++ + K+RKA EK+
Sbjct: 184 HVGSELEELDDDEDEEEEEDENDDSLAADESELPEKVLEKFKALAKQYKKLRKAQEKKVE 243
Query: 1057 N----SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCG 1112
+ Y K + E+ +R T+K I++L + LR+ +V E+++L +V +
Sbjct: 244 GRLAQHKKYAKLREKLKEELKSLRLTSKQIDELVEQLRDINKRVRGQERELLRLV-ERLK 302
Query: 1113 MPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLN 1172
MPR F+K+F NE+++ W++ E ++ L R IK+LQQ+L ++ + L +
Sbjct: 303 MPRKDFLKLFQGNELDITWLEKEIASGKPWSEFLVRVYDEIKKLQQELEAIEEETGLTIE 362
Query: 1173 DLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAV 1232
+L++INR++ GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAV
Sbjct: 363 ELKEINRQISKGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 422
Query: 1233 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGS 1292
DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G
Sbjct: 423 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEIGR 482
Query: 1293 EPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAAL 1352
EP P +A ++ MPE+K+RK++KIAKEP+S+E+P+GDDEDSHLGDFIED+N P DAA+
Sbjct: 483 EPTPEELAERLGMPEDKVRKVLKIAKEPISLETPIGDDEDSHLGDFIEDKNAELPIDAAI 542
Query: 1353 NASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALR 1412
S+R D+L SLTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALR
Sbjct: 543 QESLREATTDVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 602
Query: 1413 KLRHPSRYYKLKIFLE 1428
KLRHPSR KL+ FL+
Sbjct: 603 KLRHPSRSRKLRSFLD 618
Score = 835 bits (2161), Expect = 0.0
Identities = 324/603 (53%), Positives = 428/603 (70%), Gaps = 12/603 (1%)
Query: 34 EEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV 93
++N + + K LIK GKERGYLT++E+ND LPEDI+D E IE II M I V E
Sbjct: 4 PMLDNPQSQLKKLIKRGKERGYLTYAELNDHLPEDIVDSEQIEDIIAMLNDMGIQVVEEA 63
Query: 94 LDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDG 149
D + L+L+ +D+D EE AALS+V+S+ GRT DP++MY+REMG+VELLTR+G
Sbjct: 64 PDADDLLLAENEADAQTDEDAEEEAAAALSSVESEIGRTDDPVRMYLREMGTVELLTREG 123
Query: 150 EIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNR 209
EIEIAKRIE G MI A+ P TI IL D++ E ++ E++DG +D N +
Sbjct: 124 EIEIAKRIEAGENIMIAALCESPLTIDAILEWYDRLENGERRLRELIDGFVDPNAEEDPA 183
Query: 210 VI---KGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGY 266
+ +++E++ E + D +L + L KF ++ + K+RKA EK+
Sbjct: 184 HVGSELEELDDDEDEEEEEDENDDSLAADESELPEKVLEKFKALAKQYKKLRKAQEKKVE 243
Query: 267 N----SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCG 322
+ Y K + E+ +R T+K I++L + LR+ +V E+++L +V +
Sbjct: 244 GRLAQHKKYAKLREKLKEELKSLRLTSKQIDELVEQLRDINKRVRGQERELLRLV-ERLK 302
Query: 323 MPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLN 382
MPR F+K+F NE+++ W++ E ++ L R IK+LQQ+L ++ + L +
Sbjct: 303 MPRKDFLKLFQGNELDITWLEKEIASGKPWSEFLVRVYDEIKKLQQELEAIEEETGLTIE 362
Query: 383 DLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAV 442
+L++INR++ GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAV
Sbjct: 363 ELKEINRQISKGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 422
Query: 443 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGS 502
DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G
Sbjct: 423 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEIGR 482
Query: 503 EPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAAL 562
EP P +A ++ MPE+K+RK++KIAKEP+S+E+P+GDDEDSHLGDFIED+N P DAA+
Sbjct: 483 EPTPEELAERLGMPEDKVRKVLKIAKEPISLETPIGDDEDSHLGDFIEDKNAELPIDAAI 542
Query: 563 NASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALR 622
S+R D+L SLTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALR
Sbjct: 543 QESLREATTDVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 602
Query: 623 KLR 625
KLR
Sbjct: 603 KLR 605
>gnl|CDD|236413 PRK09210, PRK09210, RNA polymerase sigma factor RpoD; Validated.
Length = 367
Score = 414 bits (1067), Expect = e-133
Identities = 161/244 (65%), Positives = 204/244 (83%)
Query: 1185 EMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 1244
E +AK+ + EANLRLV+SIAK+Y RG+ FLDLIQEGN+GLMKAV+KF+YR+G+KFS
Sbjct: 124 EEGDEEAKQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFS 183
Query: 1245 TYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKME 1304
TYATWWIRQAITR+IADQARTIRIPVHM+ETINK+ R+ RQ+LQE G EP P IA +M+
Sbjct: 184 TYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQELGREPTPEEIAEEMD 243
Query: 1305 MPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDIL 1364
MP EK+R+I+KIA+EPVS+E+P+G+++DSHLGDFIED++ +P+D A ++ ++D+L
Sbjct: 244 MPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPADHAAYELLKEQLEDVL 303
Query: 1365 NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLK 1424
++LT RE VLR+RFG++ TLEEVGK F VTRERIRQIEAKALRKLRHPSR +LK
Sbjct: 304 DTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLK 363
Query: 1425 IFLE 1428
FLE
Sbjct: 364 DFLE 367
Score = 395 bits (1016), Expect = e-126
Identities = 152/231 (65%), Positives = 194/231 (83%)
Query: 395 EMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 454
E +AK+ + EANLRLV+SIAK+Y RG+ FLDLIQEGN+GLMKAV+KF+YR+G+KFS
Sbjct: 124 EEGDEEAKQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFS 183
Query: 455 TYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKME 514
TYATWWIRQAITR+IADQARTIRIPVHM+ETINK+ R+ RQ+LQE G EP P IA +M+
Sbjct: 184 TYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQELGREPTPEEIAEEMD 243
Query: 515 MPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDIL 574
MP EK+R+I+KIA+EPVS+E+P+G+++DSHLGDFIED++ +P+D A ++ ++D+L
Sbjct: 244 MPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPADHAAYELLKEQLEDVL 303
Query: 575 NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
++LT RE VLR+RFG++ TLEEVGK F VTRERIRQIEAKALRKLR
Sbjct: 304 DTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 354
Score = 77.7 bits (192), Expect = 6e-15
Identities = 39/132 (29%), Positives = 69/132 (52%), Gaps = 6/132 (4%)
Query: 29 KSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDIS 88
K ++E L + K LI+ GK+RG LT+ EI + L +D + I+ + + IS
Sbjct: 1 KKTKKKETTTLEQVVKELIEKGKKRGTLTYDEIAEKLIPFELDSDQIDDLYERLEDAGIS 60
Query: 89 VSEHVLDTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRD 148
+ + + + + +++++ + DP++MY++E+G V LLT +
Sbjct: 61 IVDEEGNPSSAQVVEEEEEEELDNDLSVPPGV------KINDPVRMYLKEIGRVPLLTAE 114
Query: 149 GEIEIAKRIEEG 160
EIE+AKRIEEG
Sbjct: 115 EEIELAKRIEEG 126
Score = 77.7 bits (192), Expect = 6e-15
Identities = 39/132 (29%), Positives = 69/132 (52%), Gaps = 6/132 (4%)
Query: 819 KSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDIS 878
K ++E L + K LI+ GK+RG LT+ EI + L +D + I+ + + IS
Sbjct: 1 KKTKKKETTTLEQVVKELIEKGKKRGTLTYDEIAEKLIPFELDSDQIDDLYERLEDAGIS 60
Query: 879 VSEHVLDTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRD 938
+ + + + + +++++ + DP++MY++E+G V LLT +
Sbjct: 61 IVDEEGNPSSAQVVEEEEEEELDNDLSVPPGV------KINDPVRMYLKEIGRVPLLTAE 114
Query: 939 GEIEIAKRIEEG 950
EIE+AKRIEEG
Sbjct: 115 EEIELAKRIEEG 126
>gnl|CDD|213709 TIGR02393, RpoD_Cterm, RNA polymerase sigma factor RpoD, C-terminal
domain. This model represents the well-conserved
C-terminal region of the major, essential sigma factor of
most bacteria. Members of this clade show considerable
variability in domain architecture and molecular weight,
as well as in nomenclature: RpoD in E. coli and other
Proteobacteria, SigA in Bacillus subtilis and many other
Gram-positive bacteria, HrdB in Streptomyces, MysA in
Mycobacterium smegmatis, etc [Transcription,
Transcription factors].
Length = 238
Score = 406 bits (1045), Expect = e-132
Identities = 160/238 (67%), Positives = 199/238 (83%)
Query: 1191 AKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 1250
AK+++ E+NLRLV+SIAKKYT+RGL FLDLIQEGNIGLMKAV+KF+YR+GYKFSTYATWW
Sbjct: 1 AKKQLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWW 60
Query: 1251 IRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKI 1310
IRQAITR+IADQARTIRIPVHM+ETINK+ + RQ+ QE G EP +A +M MP EK+
Sbjct: 61 IRQAITRAIADQARTIRIPVHMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKV 120
Query: 1311 RKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPR 1370
R+I KIA+EP+S+E+P+G++EDS LGDFIED ++ +P D A +R + ++L +LT R
Sbjct: 121 REIKKIAQEPISLETPIGEEEDSFLGDFIEDTSIESPDDYAAKELLREQLDEVLETLTER 180
Query: 1371 ESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
E KVLRMR+G+ HTLEEVGK+F+VTRERIRQIE+KALRKLRHPSR KLK FL+
Sbjct: 181 EEKVLRMRYGLLDGQPHTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKKLKSFLD 238
Score = 390 bits (1003), Expect = e-126
Identities = 151/225 (67%), Positives = 189/225 (84%)
Query: 401 AKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 460
AK+++ E+NLRLV+SIAKKYT+RGL FLDLIQEGNIGLMKAV+KF+YR+GYKFSTYATWW
Sbjct: 1 AKKQLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWW 60
Query: 461 IRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKI 520
IRQAITR+IADQARTIRIPVHM+ETINK+ + RQ+ QE G EP +A +M MP EK+
Sbjct: 61 IRQAITRAIADQARTIRIPVHMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKV 120
Query: 521 RKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPR 580
R+I KIA+EP+S+E+P+G++EDS LGDFIED ++ +P D A +R + ++L +LT R
Sbjct: 121 REIKKIAQEPISLETPIGEEEDSFLGDFIEDTSIESPDDYAAKELLREQLDEVLETLTER 180
Query: 581 ESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
E KVLRMR+G+ HTLEEVGK+F+VTRERIRQIE+KALRKLR
Sbjct: 181 EEKVLRMRYGLLDGQPHTLEEVGKEFNVTRERIRQIESKALRKLR 225
>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional.
Length = 509
Score = 392 bits (1009), Expect = e-123
Identities = 140/254 (55%), Positives = 191/254 (75%)
Query: 1175 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDK 1234
++ R + ++AK + EANLRLV+S+AK+YT+RGL FLDLIQEGN+GL+KAV+K
Sbjct: 256 PELRRDLQWIGRDGKRAKNHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEK 315
Query: 1235 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEP 1294
F+Y +GYKFSTYATWWIRQAITR++ADQARTIRIPVHM+ETINK+ RI R++LQE G EP
Sbjct: 316 FDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVETINKLGRIERELLQELGREP 375
Query: 1295 DPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNA 1354
P +A +M EK+R+I K +EP+S++ +G + DS GDFIED ++P DA
Sbjct: 376 TPEELAKEMGFTPEKVREIQKYNREPISLDKTIGKEGDSQFGDFIEDSEAVSPVDAVSFT 435
Query: 1355 SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 1414
++ ++++L +L+ RE+ V+RMRFG+ TL+E+G+ + VTRERIRQIE+K LRKL
Sbjct: 436 LLQDQLQEVLETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKL 495
Query: 1415 RHPSRYYKLKIFLE 1428
RHPSR L+ FL+
Sbjct: 496 RHPSRSQVLRDFLD 509
Score = 377 bits (970), Expect = e-117
Identities = 133/241 (55%), Positives = 182/241 (75%)
Query: 385 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDK 444
++ R + ++AK + EANLRLV+S+AK+YT+RGL FLDLIQEGN+GL+KAV+K
Sbjct: 256 PELRRDLQWIGRDGKRAKNHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEK 315
Query: 445 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEP 504
F+Y +GYKFSTYATWWIRQAITR++ADQARTIRIPVHM+ETINK+ RI R++LQE G EP
Sbjct: 316 FDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVETINKLGRIERELLQELGREP 375
Query: 505 DPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNA 564
P +A +M EK+R+I K +EP+S++ +G + DS GDFIED ++P DA
Sbjct: 376 TPEELAKEMGFTPEKVREIQKYNREPISLDKTIGKEGDSQFGDFIEDSEAVSPVDAVSFT 435
Query: 565 SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 624
++ ++++L +L+ RE+ V+RMRFG+ TL+E+G+ + VTRERIRQIE+K LRKL
Sbjct: 436 LLQDQLQEVLETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKL 495
Query: 625 R 625
R
Sbjct: 496 R 496
Score = 63.1 bits (154), Expect = 7e-10
Identities = 39/160 (24%), Positives = 65/160 (40%), Gaps = 5/160 (3%)
Query: 6 KKTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFL 65
K K K+ + S + + + ++ K + L + + +D
Sbjct: 84 KAAAAKAPAKKKLKDELDSSKKAEKKNALDKDDDLNYVKDIDVLNQADDDDDDDDDDDLD 143
Query: 66 PEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNITSDDDVEEATE--AALSTVDS 123
+DI D + E + D E E L ++ DDD + AL
Sbjct: 144 DDDIDDDDDDEDDDEDDD-DDDVDDEDEEKKEAKELEKLSDDDDFVWDEDDSEALRQARK 202
Query: 124 DFGRTK--DPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
D T DP+K Y++++G V+LL + E+E+AKRIE GL
Sbjct: 203 DAKLTATADPVKAYLKQIGKVKLLNAEEEVELAKRIEAGL 242
Score = 57.3 bits (139), Expect = 4e-08
Identities = 35/137 (25%), Positives = 59/137 (43%), Gaps = 5/137 (3%)
Query: 819 KSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDIS 878
+ + + ++ K + L + + +D +DI D + E + D
Sbjct: 107 EKKNALDKDDDLNYVKDIDVLNQADDDDDDDDDDDLDDDDIDDDDDDEDDDEDDD-DDDV 165
Query: 879 VSEHVLDTETLMLSNITSDDDVEEATE--AALSTVDSDFGRTK--DPIKMYMREMGSVEL 934
E E L ++ DDD + AL D T DP+K Y++++G V+L
Sbjct: 166 DDEDEEKKEAKELEKLSDDDDFVWDEDDSEALRQARKDAKLTATADPVKAYLKQIGKVKL 225
Query: 935 LTRDGEIEIAKRIEEGL 951
L + E+E+AKRIE GL
Sbjct: 226 LNAEEEVELAKRIEAGL 242
>gnl|CDD|223642 COG0568, RpoD, DNA-directed RNA polymerase, sigma subunit
(sigma70/sigma32) [Transcription].
Length = 342
Score = 362 bits (930), Expect = e-114
Identities = 147/283 (51%), Positives = 208/283 (73%), Gaps = 3/283 (1%)
Query: 1148 RNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIA 1207
R L + ++ +L + + + R++ GE + AK+++ E+NLRLV+SIA
Sbjct: 61 RARRPAGRLSFYIRAIEAAPLLTPEEEKALARRLKRGE-RDLDAKKKLVESNLRLVVSIA 119
Query: 1208 KKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIR 1267
KKYT RGL FLDLIQEGNIGLMKAV+KF+ +G+KFSTYATWWIRQAITR+IADQARTIR
Sbjct: 120 KKYTGRGLPFLDLIQEGNIGLMKAVEKFDPEKGFKFSTYATWWIRQAITRAIADQARTIR 179
Query: 1268 IPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPV 1327
IPVH +E INK+ R+ R++LQE G EP P IA ++ + +K+R+++K A EP+S+++P+
Sbjct: 180 IPVHQVELINKLRRVKRELLQELGREPTPEEIAEELGVSPDKVREMLKRASEPISLDTPI 239
Query: 1328 GDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNS-LTPRESKVLRMRFGIEMSSD 1386
GDDEDS LGDF+ED+ ++P DA S++ + ++L LT RE +V+R+RFG++
Sbjct: 240 GDDEDSELGDFLEDDKSVSPEDAVERESLKEDLNEVLAEALTERERRVIRLRFGLDDGEP 299
Query: 1387 HTLEEVGKQFDVTRERIRQIEAKALRKLR-HPSRYYKLKIFLE 1428
TLEE+G++F ++RER+RQIEAKALRKLR HP R L+ +L+
Sbjct: 300 KTLEELGEEFGISRERVRQIEAKALRKLRRHPERSALLRSYLD 342
Score = 356 bits (917), Expect = e-112
Identities = 142/269 (52%), Positives = 200/269 (74%), Gaps = 2/269 (0%)
Query: 358 RNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIA 417
R L + ++ +L + + + R++ GE + AK+++ E+NLRLV+SIA
Sbjct: 61 RARRPAGRLSFYIRAIEAAPLLTPEEEKALARRLKRGE-RDLDAKKKLVESNLRLVVSIA 119
Query: 418 KKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIR 477
KKYT RGL FLDLIQEGNIGLMKAV+KF+ +G+KFSTYATWWIRQAITR+IADQARTIR
Sbjct: 120 KKYTGRGLPFLDLIQEGNIGLMKAVEKFDPEKGFKFSTYATWWIRQAITRAIADQARTIR 179
Query: 478 IPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPV 537
IPVH +E INK+ R+ R++LQE G EP P IA ++ + +K+R+++K A EP+S+++P+
Sbjct: 180 IPVHQVELINKLRRVKRELLQELGREPTPEEIAEELGVSPDKVREMLKRASEPISLDTPI 239
Query: 538 GDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNS-LTPRESKVLRMRFGIEMSSD 596
GDDEDS LGDF+ED+ ++P DA S++ + ++L LT RE +V+R+RFG++
Sbjct: 240 GDDEDSELGDFLEDDKSVSPEDAVERESLKEDLNEVLAEALTERERRVIRLRFGLDDGEP 299
Query: 597 HTLEEVGKQFDVTRERIRQIEAKALRKLR 625
TLEE+G++F ++RER+RQIEAKALRKLR
Sbjct: 300 KTLEELGEEFGISRERVRQIEAKALRKLR 328
>gnl|CDD|234082 TIGR02997, Sig70-cyanoRpoD, RNA polymerase sigma factor,
cyanobacterial RpoD-like family. This family includes a
number of closely related sigma-70 (TIGR02937) factors
in the cyanobacteria. All appear most closely related to
the essential sigma-70 factor RpoD, and some score above
trusted to the RpoD C-terminal domain model (TIGR02393).
Length = 298
Score = 324 bits (834), Expect = e-101
Identities = 118/227 (51%), Positives = 177/227 (77%), Gaps = 1/227 (0%)
Query: 399 RKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 458
++AK +M +ANLRLV+S+AKKY +RGL+ LDLIQEG++GL +AV+KF+ RGYKFSTYA
Sbjct: 73 QRAKEKMIKANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAY 132
Query: 459 WWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEE 518
WWIRQ ITR+IA+Q+RTIR+P+H+ E +NKI ++ R++ Q+ G P + IA +E+ E
Sbjct: 133 WWIRQGITRAIANQSRTIRLPIHITEKLNKIKKVQRELSQKLGRTPSEAEIAEALELEPE 192
Query: 519 KIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLT 578
++R++++ A++PVS+++PVGD+ED+ LGD +ED+ P + S+R ++ +L LT
Sbjct: 193 QVRELLQRARQPVSLDAPVGDEEDTELGDLLEDDGES-PEEQVERESLRQDLESLLAELT 251
Query: 579 PRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
PRE +VLR+RFG++ TL E+G++ +++RER+RQIEAKALRKLR
Sbjct: 252 PRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKLR 298
Score = 324 bits (834), Expect = e-101
Identities = 118/227 (51%), Positives = 177/227 (77%), Gaps = 1/227 (0%)
Query: 1189 RKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 1248
++AK +M +ANLRLV+S+AKKY +RGL+ LDLIQEG++GL +AV+KF+ RGYKFSTYA
Sbjct: 73 QRAKEKMIKANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAY 132
Query: 1249 WWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEE 1308
WWIRQ ITR+IA+Q+RTIR+P+H+ E +NKI ++ R++ Q+ G P + IA +E+ E
Sbjct: 133 WWIRQGITRAIANQSRTIRLPIHITEKLNKIKKVQRELSQKLGRTPSEAEIAEALELEPE 192
Query: 1309 KIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLT 1368
++R++++ A++PVS+++PVGD+ED+ LGD +ED+ P + S+R ++ +L LT
Sbjct: 193 QVRELLQRARQPVSLDAPVGDEEDTELGDLLEDDGES-PEEQVERESLRQDLESLLAELT 251
Query: 1369 PRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415
PRE +VLR+RFG++ TL E+G++ +++RER+RQIEAKALRKLR
Sbjct: 252 PRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKLR 298
Score = 35.7 bits (83), Expect = 0.13
Identities = 12/30 (40%), Positives = 25/30 (83%)
Query: 130 DPIKMYMREMGSVELLTRDGEIEIAKRIEE 159
D +++Y++E+G V LLT + EIE+A+++++
Sbjct: 1 DLVRLYLQEIGRVPLLTPEEEIELARQVQQ 30
Score = 35.7 bits (83), Expect = 0.13
Identities = 12/30 (40%), Positives = 25/30 (83%)
Query: 920 DPIKMYMREMGSVELLTRDGEIEIAKRIEE 949
D +++Y++E+G V LLT + EIE+A+++++
Sbjct: 1 DLVRLYLQEIGRVPLLTPEEEIELARQVQQ 30
>gnl|CDD|236012 PRK07406, PRK07406, RNA polymerase sigma factor RpoD; Validated.
Length = 373
Score = 312 bits (801), Expect = 1e-95
Identities = 136/245 (55%), Positives = 184/245 (75%), Gaps = 5/245 (2%)
Query: 1186 MKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 1245
M R+AK +M ++NLRLV+SIAKKY +RGL F DLIQEG++GL++A +KF++ +GYKFST
Sbjct: 132 MLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFST 191
Query: 1246 YATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEM 1305
YATWWIRQAITR+IADQ+RTIR+PVH+ ETI++I + ++ + QE G +P IA MEM
Sbjct: 192 YATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEM 251
Query: 1306 PEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIED--ENMLAPSDAALNASMRSVVKDI 1363
EK+R I K A+ P+S+E+P+G +EDS LGDFIE E P D +R ++ +
Sbjct: 252 TIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIEADGET---PEDDVAKNLLREDLEGV 308
Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423
L +L+PRE VLR+R+G++ TLEE+G+ F+VTRERIRQIEAKALRKLRHP+R L
Sbjct: 309 LATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSVL 368
Query: 1424 KIFLE 1428
K ++
Sbjct: 369 KEYIR 373
Score = 302 bits (774), Expect = 7e-92
Identities = 131/232 (56%), Positives = 176/232 (75%), Gaps = 5/232 (2%)
Query: 396 MKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 455
M R+AK +M ++NLRLV+SIAKKY +RGL F DLIQEG++GL++A +KF++ +GYKFST
Sbjct: 132 MLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFST 191
Query: 456 YATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEM 515
YATWWIRQAITR+IADQ+RTIR+PVH+ ETI++I + ++ + QE G +P IA MEM
Sbjct: 192 YATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEM 251
Query: 516 PEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIED--ENMLAPSDAALNASMRSVVKDI 573
EK+R I K A+ P+S+E+P+G +EDS LGDFIE E P D +R ++ +
Sbjct: 252 TIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIEADGET---PEDDVAKNLLREDLEGV 308
Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
L +L+PRE VLR+R+G++ TLEE+G+ F+VTRERIRQIEAKALRKLR
Sbjct: 309 LATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLR 360
Score = 36.7 bits (85), Expect = 0.085
Identities = 18/64 (28%), Positives = 32/64 (50%), Gaps = 1/64 (1%)
Query: 95 DTETLMLSNITSDDDVEEATEAALS-TVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 153
+ E N + E +A + T+D I++Y++E+G + LL D EIE+
Sbjct: 27 EDEESSSENADELSEKEAKAKALARIKIGPKKVYTEDSIRVYLQEIGRIRLLRPDEEIEL 86
Query: 154 AKRI 157
A++I
Sbjct: 87 ARKI 90
Score = 36.7 bits (85), Expect = 0.085
Identities = 18/64 (28%), Positives = 32/64 (50%), Gaps = 1/64 (1%)
Query: 885 DTETLMLSNITSDDDVEEATEAALS-TVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 943
+ E N + E +A + T+D I++Y++E+G + LL D EIE+
Sbjct: 27 EDEESSSENADELSEKEAKAKALARIKIGPKKVYTEDSIRVYLQEIGRIRLLRPDEEIEL 86
Query: 944 AKRI 947
A++I
Sbjct: 87 ARKI 90
>gnl|CDD|181169 PRK07921, PRK07921, RNA polymerase sigma factor SigB; Reviewed.
Length = 324
Score = 304 bits (781), Expect = 2e-93
Identities = 116/255 (45%), Positives = 184/255 (72%), Gaps = 2/255 (0%)
Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
L++ R + + + A+R + EANLRLV+S+AK+YT RG+ LDLIQEGN+GL+
Sbjct: 68 RLSEARKRDLAAVVRD--GEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLI 125
Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
+A++KF+Y +G+KFSTYATWWIRQAITR +ADQ+RTIR+PVH++E +NK++RI R++ Q+
Sbjct: 126 RAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKRELHQQ 185
Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
G E +A + +PEEKI +++ +++PVS++ PVG DE++ LGDFIED + +
Sbjct: 186 LGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDSEATSAEN 245
Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
A + + + ++ +L +L RE +V+R+RFG++ TL+++GK F ++RER+RQIE +
Sbjct: 246 AVIAGLLHTDIRSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERE 305
Query: 1410 ALRKLRHPSRYYKLK 1424
+ KLR+ R +L+
Sbjct: 306 VMSKLRNGERADRLR 320
Score = 298 bits (764), Expect = 3e-91
Identities = 114/246 (46%), Positives = 179/246 (72%), Gaps = 2/246 (0%)
Query: 380 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 439
L++ R + + + A+R + EANLRLV+S+AK+YT RG+ LDLIQEGN+GL+
Sbjct: 68 RLSEARKRDLAAVVRD--GEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLI 125
Query: 440 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 499
+A++KF+Y +G+KFSTYATWWIRQAITR +ADQ+RTIR+PVH++E +NK++RI R++ Q+
Sbjct: 126 RAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKRELHQQ 185
Query: 500 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 559
G E +A + +PEEKI +++ +++PVS++ PVG DE++ LGDFIED + +
Sbjct: 186 LGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDSEATSAEN 245
Query: 560 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 619
A + + + ++ +L +L RE +V+R+RFG++ TL+++GK F ++RER+RQIE +
Sbjct: 246 AVIAGLLHTDIRSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERE 305
Query: 620 ALRKLR 625
+ KLR
Sbjct: 306 VMSKLR 311
Score = 36.6 bits (85), Expect = 0.082
Identities = 19/57 (33%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 105 TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
+D T S +D+ D +++Y+ +G LLT E+E+AKRIE GL
Sbjct: 2 MADATARATTSRVDSDLDAQ-SPAADLVRVYLNGIGKTALLTAADEVELAKRIEAGL 57
Score = 36.6 bits (85), Expect = 0.082
Identities = 19/57 (33%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 895 TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
+D T S +D+ D +++Y+ +G LLT E+E+AKRIE GL
Sbjct: 2 MADATARATTSRVDSDLDAQ-SPAADLVRVYLNGIGKTALLTAADEVELAKRIEAGL 57
>gnl|CDD|236067 PRK07598, PRK07598, RNA polymerase sigma factor SigC; Validated.
Length = 415
Score = 267 bits (685), Expect = 3e-79
Identities = 114/239 (47%), Positives = 172/239 (71%), Gaps = 1/239 (0%)
Query: 1190 KAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 1249
+AK M +ANLRLV+S+AKKY +RGL+ LDL+QEG +GL +AV+KF+ +GY+FSTYA W
Sbjct: 175 RAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYW 234
Query: 1250 WIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEK 1309
WIRQ ITR+IA Q+RTIR+PVH+ E +NKI + R+I QE G P IA ++EM +
Sbjct: 235 WIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQ 294
Query: 1310 IRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTP 1369
+R+++ VS+E+ VG D+D+ LGD +E ++ ++P + + S++ ++ +L LT
Sbjct: 295 VREVLLRVPRSVSLETKVGKDKDTELGDLLETDD-ISPEEMLMRESLQRDLQHLLADLTS 353
Query: 1370 RESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
RE V+RMRFG+ ++L E+G+ D++RER+RQIE+KAL+KLR P R +++ +LE
Sbjct: 354 RERDVIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESKALQKLRQPKRRNRIRDYLE 412
Score = 257 bits (657), Expect = 2e-75
Identities = 110/226 (48%), Positives = 164/226 (72%), Gaps = 1/226 (0%)
Query: 400 KAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 459
+AK M +ANLRLV+S+AKKY +RGL+ LDL+QEG +GL +AV+KF+ +GY+FSTYA W
Sbjct: 175 RAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYW 234
Query: 460 WIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEK 519
WIRQ ITR+IA Q+RTIR+PVH+ E +NKI + R+I QE G P IA ++EM +
Sbjct: 235 WIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQ 294
Query: 520 IRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTP 579
+R+++ VS+E+ VG D+D+ LGD +E ++ ++P + + S++ ++ +L LT
Sbjct: 295 VREVLLRVPRSVSLETKVGKDKDTELGDLLETDD-ISPEEMLMRESLQRDLQHLLADLTS 353
Query: 580 RESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
RE V+RMRFG+ ++L E+G+ D++RER+RQIE+KAL+KLR
Sbjct: 354 RERDVIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESKALQKLR 399
Score = 42.2 bits (99), Expect = 0.002
Identities = 17/63 (26%), Positives = 35/63 (55%), Gaps = 6/63 (9%)
Query: 106 SDDDVEEATEAALSTVDSDF------GRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEE 159
DD +++ E ++ D R+ D +++Y++E+G V LL RD E+ A++++
Sbjct: 30 PDDSLDDVQELEIAAADEAVETAARNRRSTDLVRLYLQEIGRVRLLGRDEEVSEAQKVQR 89
Query: 160 GLK 162
+K
Sbjct: 90 YMK 92
Score = 42.2 bits (99), Expect = 0.002
Identities = 17/63 (26%), Positives = 35/63 (55%), Gaps = 6/63 (9%)
Query: 896 SDDDVEEATEAALSTVDSDF------GRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEE 949
DD +++ E ++ D R+ D +++Y++E+G V LL RD E+ A++++
Sbjct: 30 PDDSLDDVQELEIAAADEAVETAARNRRSTDLVRLYLQEIGRVRLLGRDEEVSEAQKVQR 89
Query: 950 GLK 952
+K
Sbjct: 90 YMK 92
>gnl|CDD|131447 TIGR02394, rpoS_proteo, RNA polymerase sigma factor RpoS. A sigma
factor is a DNA-binding protein protein that binds to the
DNA-directed RNA polymerase core to produce the
holoenzyme capable of initiating transcription at
specific sites. Different sigma factors act in vegetative
growth, heat shock, extracytoplasmic functions (ECF),
etc. This model represents the clade of sigma factors
called RpoS (also called sigma-38, KatF, etc.), found
only in Proteobacteria. This sigma factor is induced in
stationary phase (in response to the stress of nutrient
limitation) and becomes the second prinicipal sigma
factor at that time. RpoS is a member of the larger
Sigma-70 subfamily (TIGR02937) and most closely related
to RpoD (TIGR02393) [Cellular processes, Adaptations to
atypical conditions, Transcription, Transcription
factors].
Length = 285
Score = 260 bits (665), Expect = 2e-78
Identities = 108/238 (45%), Positives = 158/238 (66%), Gaps = 3/238 (1%)
Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
R+ +AG+ +ARK M E+NLRLV+SIAK Y +RGL LDLI+EGN+GLM AV+KF+
Sbjct: 38 RRALAGDFEARKV---MIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPE 94
Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
RG++FSTYATWWIRQ I R+I +QARTIR+PVH+I+ +N R +RQ+ ++ G EP
Sbjct: 95 RGFRFSTYATWWIRQTIERAIMNQARTIRLPVHVIKELNVYLRAARQLEKKLGREPSVEE 154
Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
IA ++ P E + +++ + + S+++P+ DD L D I DE + P N ++
Sbjct: 155 IAELLDKPVEDVSRVLALNERITSLDAPLDDDSSKSLLDTIADEQSIDPESLVQNDDLKQ 214
Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416
+++ L L R+ +VL RFG+ TLEEV + +TRER+RQI+ +AL+KLR
Sbjct: 215 LIEAWLAELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLRR 272
Score = 258 bits (662), Expect = 8e-78
Identities = 108/237 (45%), Positives = 158/237 (66%), Gaps = 3/237 (1%)
Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
R+ +AG+ +ARK M E+NLRLV+SIAK Y +RGL LDLI+EGN+GLM AV+KF+
Sbjct: 38 RRALAGDFEARKV---MIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPE 94
Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
RG++FSTYATWWIRQ I R+I +QARTIR+PVH+I+ +N R +RQ+ ++ G EP
Sbjct: 95 RGFRFSTYATWWIRQTIERAIMNQARTIRLPVHVIKELNVYLRAARQLEKKLGREPSVEE 154
Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
IA ++ P E + +++ + + S+++P+ DD L D I DE + P N ++
Sbjct: 155 IAELLDKPVEDVSRVLALNERITSLDAPLDDDSSKSLLDTIADEQSIDPESLVQNDDLKQ 214
Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
+++ L L R+ +VL RFG+ TLEEV + +TRER+RQI+ +AL+KLR
Sbjct: 215 LIEAWLAELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLR 271
>gnl|CDD|180321 PRK05949, PRK05949, RNA polymerase sigma factor; Validated.
Length = 327
Score = 248 bits (636), Expect = 8e-74
Identities = 106/229 (46%), Positives = 167/229 (72%), Gaps = 1/229 (0%)
Query: 397 KARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 456
+ ++AK++M EANLRLV++IAKKY R ++FLDLIQEG +GL + V+KF+ RGYKFSTY
Sbjct: 88 QGKRAKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTY 147
Query: 457 ATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMP 516
A WWIRQAITR+IA QARTIR+P+H+ E +NKI + R++ Q+ G P+ IA ++E+
Sbjct: 148 AYWWIRQAITRAIAQQARTIRLPIHITEKLNKIKKTQRELSQKLGRSATPAEIAKELELE 207
Query: 517 EEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNS 576
+IR+ + +A++P+S++ VGD++D+ L + +EDE +P +R + ++L
Sbjct: 208 PSQIREYLSMARQPISLDVRVGDNQDTELSELLEDEG-PSPDQYITQELLRQDLNNLLAE 266
Query: 577 LTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
LTP++ +VL +RFG+E + +L +VG++ +++RER+RQ+E +AL LR
Sbjct: 267 LTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLR 315
Score = 248 bits (636), Expect = 8e-74
Identities = 106/229 (46%), Positives = 167/229 (72%), Gaps = 1/229 (0%)
Query: 1187 KARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 1246
+ ++AK++M EANLRLV++IAKKY R ++FLDLIQEG +GL + V+KF+ RGYKFSTY
Sbjct: 88 QGKRAKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTY 147
Query: 1247 ATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMP 1306
A WWIRQAITR+IA QARTIR+P+H+ E +NKI + R++ Q+ G P+ IA ++E+
Sbjct: 148 AYWWIRQAITRAIAQQARTIRLPIHITEKLNKIKKTQRELSQKLGRSATPAEIAKELELE 207
Query: 1307 EEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNS 1366
+IR+ + +A++P+S++ VGD++D+ L + +EDE +P +R + ++L
Sbjct: 208 PSQIREYLSMARQPISLDVRVGDNQDTELSELLEDEG-PSPDQYITQELLRQDLNNLLAE 266
Query: 1367 LTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415
LTP++ +VL +RFG+E + +L +VG++ +++RER+RQ+E +AL LR
Sbjct: 267 LTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLR 315
>gnl|CDD|180963 PRK07405, PRK07405, RNA polymerase sigma factor SigD; Validated.
Length = 317
Score = 239 bits (612), Expect = 1e-70
Identities = 104/241 (43%), Positives = 171/241 (70%), Gaps = 5/241 (2%)
Query: 385 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDK 444
++ + GE AKR+M EANLRLV+S+AKKY R + LDLIQEG IG+ + V+K
Sbjct: 70 EELRSAIAEGE----AAKRKMVEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEK 125
Query: 445 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEP 504
F+ +GY+FSTYA WWIRQAITR+IA+++RTIR+P+H+ E +NKI + RQ+ Q+ G
Sbjct: 126 FDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEKLNKIKKAQRQLSQQLGRAA 185
Query: 505 DPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNA 564
+A ++E+ +++R+ ++ A++P+S++ VGD++D+ LG+ +ED +P D A +
Sbjct: 186 TIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELGELLEDTG-ASPEDFATQS 244
Query: 565 SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 624
S++ ++ ++ LTP++ +V+ +RFG+E TL ++G++ +++RER+RQIE +AL KL
Sbjct: 245 SLQLDLERLMEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKL 304
Query: 625 R 625
R
Sbjct: 305 R 305
Score = 239 bits (612), Expect = 1e-70
Identities = 104/241 (43%), Positives = 171/241 (70%), Gaps = 5/241 (2%)
Query: 1175 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDK 1234
++ + GE AKR+M EANLRLV+S+AKKY R + LDLIQEG IG+ + V+K
Sbjct: 70 EELRSAIAEGE----AAKRKMVEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEK 125
Query: 1235 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEP 1294
F+ +GY+FSTYA WWIRQAITR+IA+++RTIR+P+H+ E +NKI + RQ+ Q+ G
Sbjct: 126 FDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEKLNKIKKAQRQLSQQLGRAA 185
Query: 1295 DPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNA 1354
+A ++E+ +++R+ ++ A++P+S++ VGD++D+ LG+ +ED +P D A +
Sbjct: 186 TIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELGELLEDTG-ASPEDFATQS 244
Query: 1355 SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 1414
S++ ++ ++ LTP++ +V+ +RFG+E TL ++G++ +++RER+RQIE +AL KL
Sbjct: 245 SLQLDLERLMEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKL 304
Query: 1415 R 1415
R
Sbjct: 305 R 305
Score = 35.9 bits (83), Expect = 0.12
Identities = 12/31 (38%), Positives = 21/31 (67%)
Query: 128 TKDPIKMYMREMGSVELLTRDGEIEIAKRIE 158
+ D ++ Y+RE+G V LLT + EI K+++
Sbjct: 6 STDLVRTYLREIGRVPLLTHEEEILYGKQVQ 36
Score = 35.9 bits (83), Expect = 0.12
Identities = 12/31 (38%), Positives = 21/31 (67%)
Query: 918 TKDPIKMYMREMGSVELLTRDGEIEIAKRIE 948
+ D ++ Y+RE+G V LLT + EI K+++
Sbjct: 6 STDLVRTYLREIGRVPLLTHEEEILYGKQVQ 36
>gnl|CDD|235548 PRK05657, PRK05657, RNA polymerase sigma factor RpoS; Validated.
Length = 325
Score = 234 bits (599), Expect = 8e-69
Identities = 97/237 (40%), Positives = 154/237 (64%), Gaps = 3/237 (1%)
Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
R+ + G+ AR+ M E+NLRLV+ IAK+Y +RGL LDLI+EGN+GL++AV+KF+
Sbjct: 78 RRALRGDFAARQ---RMIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPE 134
Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
RG++FSTYATWWIRQ I R+I +Q RTIR+PVH+++ +N R +R++ + EP
Sbjct: 135 RGFRFSTYATWWIRQTIERAIMNQTRTIRLPVHVVKELNVYLRAARELEHKLDHEPSAEE 194
Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
IA ++ P + + +++ + + S+++P+G D + L D + DE P D + M+
Sbjct: 195 IAELLDKPVDDVSRMLALNERITSLDTPLGGDPEKSLLDILADEQENGPEDTTQDDDMKQ 254
Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
+ L L ++ +VL RFG+ TLE+V ++ +TRER+RQI+ +ALR+LR
Sbjct: 255 SIVKWLFELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLR 311
Score = 234 bits (599), Expect = 8e-69
Identities = 97/237 (40%), Positives = 154/237 (64%), Gaps = 3/237 (1%)
Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
R+ + G+ AR+ M E+NLRLV+ IAK+Y +RGL LDLI+EGN+GL++AV+KF+
Sbjct: 78 RRALRGDFAARQ---RMIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPE 134
Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
RG++FSTYATWWIRQ I R+I +Q RTIR+PVH+++ +N R +R++ + EP
Sbjct: 135 RGFRFSTYATWWIRQTIERAIMNQTRTIRLPVHVVKELNVYLRAARELEHKLDHEPSAEE 194
Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
IA ++ P + + +++ + + S+++P+G D + L D + DE P D + M+
Sbjct: 195 IAELLDKPVDDVSRMLALNERITSLDTPLGGDPEKSLLDILADEQENGPEDTTQDDDMKQ 254
Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415
+ L L ++ +VL RFG+ TLE+V ++ +TRER+RQI+ +ALR+LR
Sbjct: 255 SIVKWLFELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLR 311
>gnl|CDD|203043 pfam04546, Sigma70_ner, Sigma-70, non-essential region. The domain
is found in the primary vegetative sigma factor. The
function of this domain is unclear and can be removed
without loss of function.
Length = 211
Score = 171 bits (436), Expect = 2e-48
Identities = 59/211 (27%), Positives = 100/211 (47%), Gaps = 7/211 (3%)
Query: 171 CPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVI-------KGNKNNNEEKIL 223
P I +L D++ E ++ +++ G ID N ++ +++
Sbjct: 1 YPGAIAYLLEQYDRVEAGEGRLSDLISGFIDPNAAAAAATAAAIESELDEEDLEDDDDDD 60
Query: 224 IESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEML 283
+ D L E+ +F+ + ++K RKA EK G S+ KA ++ E +
Sbjct: 61 EDEDEDDEEEADLGPDPEEARERFAELREQYEKTRKAIEKHGRGSKKAQKAREALAEEFM 120
Query: 284 GIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVD 343
R K ++L D LR +++V E+QI+++ V + MPR FIK FP NE NL+W+D
Sbjct: 121 QFRLVPKQFDRLVDNLRGMVDRVRAQERQIMKLCVERAKMPRKDFIKSFPGNETNLDWLD 180
Query: 344 NETKIQHDYNLILCRNIPSIKELQQKLINLQ 374
+ Y L R P I+ QQKLI+++
Sbjct: 181 ELLAAKKPYAEALERVKPDIQRAQQKLIDIE 211
Score = 171 bits (436), Expect = 2e-48
Identities = 59/211 (27%), Positives = 100/211 (47%), Gaps = 7/211 (3%)
Query: 961 CPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVI-------KGNKNNNEEKIL 1013
P I +L D++ E ++ +++ G ID N ++ +++
Sbjct: 1 YPGAIAYLLEQYDRVEAGEGRLSDLISGFIDPNAAAAAATAAAIESELDEEDLEDDDDDD 60
Query: 1014 IESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEML 1073
+ D L E+ +F+ + ++K RKA EK G S+ KA ++ E +
Sbjct: 61 EDEDEDDEEEADLGPDPEEARERFAELREQYEKTRKAIEKHGRGSKKAQKAREALAEEFM 120
Query: 1074 GIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVD 1133
R K ++L D LR +++V E+QI+++ V + MPR FIK FP NE NL+W+D
Sbjct: 121 QFRLVPKQFDRLVDNLRGMVDRVRAQERQIMKLCVERAKMPRKDFIKSFPGNETNLDWLD 180
Query: 1134 NETKIQHDYNLILCRNIPSIKELQQKLINLQ 1164
+ Y L R P I+ QQKLI+++
Sbjct: 181 ELLAAKKPYAEALERVKPDIQRAQQKLIDIE 211
>gnl|CDD|235551 PRK05667, dnaG, DNA primase; Validated.
Length = 580
Score = 142 bits (360), Expect = 6e-35
Identities = 53/120 (44%), Positives = 64/120 (53%), Gaps = 21/120 (17%)
Query: 706 ETPLFHKSNELYGLFEAKNAIGKSGYVLITEGYMDVIGLSQFGF---------------- 749
ETPLFHK LYGL EA+ AI K V++ EGYMDVI L Q G
Sbjct: 230 ETPLFHKGRVLYGLDEARKAIAKKKQVIVVEGYMDVIALHQAGITNAVASLGTALTEEHL 289
Query: 750 -----FANSSYTCFDGDQAGRRAARRALEVCLLYATDDKIIKFLFLPDKYDPDSYIRKFG 804
+ CFDGD+AGR+AA RALE+ L D + ++ FLPD DPD +RK G
Sbjct: 290 KLLRRLTDEVILCFDGDKAGRKAALRALELALPLLKDGRQVRVAFLPDGKDPDDLVRKEG 349
>gnl|CDD|234078 TIGR02980, SigBFG, RNA polymerase sigma-70 factor, sigma-B/F/G
subfamily. This group of similar sigma-70 factors
includes clades found in Bacilli (including the
sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as
well as SigB:TIGR02941), and the high GC gram positive
bacteria (Actinobacteria) where a variable number of
them are found depending on the lineage.
Length = 227
Score = 130 bits (328), Expect = 7e-34
Identities = 73/233 (31%), Positives = 126/233 (54%), Gaps = 17/233 (7%)
Query: 399 RKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 458
++A+ ++ E NL LV SIA+++ +RG DL+Q G IGL+KA+D+F+ G KFST+A
Sbjct: 2 KEAREKLVELNLPLVRSIARRFRNRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAV 61
Query: 459 WWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEE 518
I I R D +R+P + E KI++ + ++ Q G P + IA ++ + EE
Sbjct: 62 PTIMGEIKRFFRDDTWAVRVPRRLKELGVKINKATEELTQRLGRSPTIAEIAERLGVSEE 121
Query: 519 KIRKIMKIAK--EPVSMESPVGDDEDS--HLGDFIEDENMLAPSDAALN-ASMRSVVKDI 573
++ + ++ + +S+++ + DD+ L D + DE D AL R +K +
Sbjct: 122 EVVEALEAGNAYQALSLDASIEDDDGDPIALLDTLGDE------DDALETVEDRLALKPL 175
Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVG-KQFDVTRERIRQIEAKALRKLR 625
L +L RE ++L +RF + + E +G Q V+R + +AL+KLR
Sbjct: 176 LAALPERERRILLLRFFEDKTQSEIAERLGISQMHVSR-----LLRRALKKLR 223
Score = 130 bits (328), Expect = 7e-34
Identities = 73/233 (31%), Positives = 126/233 (54%), Gaps = 17/233 (7%)
Query: 1189 RKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 1248
++A+ ++ E NL LV SIA+++ +RG DL+Q G IGL+KA+D+F+ G KFST+A
Sbjct: 2 KEAREKLVELNLPLVRSIARRFRNRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAV 61
Query: 1249 WWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEE 1308
I I R D +R+P + E KI++ + ++ Q G P + IA ++ + EE
Sbjct: 62 PTIMGEIKRFFRDDTWAVRVPRRLKELGVKINKATEELTQRLGRSPTIAEIAERLGVSEE 121
Query: 1309 KIRKIMKIAK--EPVSMESPVGDDEDS--HLGDFIEDENMLAPSDAALN-ASMRSVVKDI 1363
++ + ++ + +S+++ + DD+ L D + DE D AL R +K +
Sbjct: 122 EVVEALEAGNAYQALSLDASIEDDDGDPIALLDTLGDE------DDALETVEDRLALKPL 175
Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVG-KQFDVTRERIRQIEAKALRKLR 1415
L +L RE ++L +RF + + E +G Q V+R + +AL+KLR
Sbjct: 176 LAALPERERRILLLRFFEDKTQSEIAERLGISQMHVSR-----LLRRALKKLR 223
>gnl|CDD|224112 COG1191, FliA, DNA-directed RNA polymerase specialized sigma subunit
[Transcription].
Length = 247
Score = 118 bits (297), Expect = 2e-29
Identities = 68/248 (27%), Positives = 126/248 (50%), Gaps = 17/248 (6%)
Query: 1172 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFL-DLIQEGNIGLMK 1230
+ + G+ +AR+ + E L LV SIA+K+ +RG DLIQ G IGL+K
Sbjct: 9 EEEEKLLEYYAEGDEEARR----LIERYLPLVKSIARKFENRGPSEYDDLIQIGMIGLIK 64
Query: 1231 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET 1290
A+++++ +G KFSTYA IR I + ++++P + E +I ++ QE
Sbjct: 65 AIERYDPSKGTKFSTYAVRRIRGEILDYLRKND-SVKVPRSLRELGRRIEEAIDELEQEL 123
Query: 1291 GSEPDPSVIAIKMEMPEEKIRKIMKIAK--EPVSMESPVGDDEDSHLGDFIEDENMLAPS 1348
G EP IA ++ + +E+ + + + +S++ V D+D + D IE+ +
Sbjct: 124 GREPTDEEIAEELGIDKEEYIEALLAINGSQLLSLDEDVLKDDDDDVDDQIENPD----- 178
Query: 1349 DAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 1408
D + ++K+ + L RE VL +R+ E+ T +E+ + ++ R+ ++
Sbjct: 179 DGVEKEELLEILKEAIEPLPEREKLVLVLRYKEEL----TQKEIAEVLGISESRVSRLHK 234
Query: 1409 KALRKLRH 1416
KA++KLR
Sbjct: 235 KAIKKLRK 242
Score = 117 bits (294), Expect = 4e-29
Identities = 68/247 (27%), Positives = 126/247 (51%), Gaps = 17/247 (6%)
Query: 382 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFL-DLIQEGNIGLMK 440
+ + G+ +AR+ + E L LV SIA+K+ +RG DLIQ G IGL+K
Sbjct: 9 EEEEKLLEYYAEGDEEARR----LIERYLPLVKSIARKFENRGPSEYDDLIQIGMIGLIK 64
Query: 441 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET 500
A+++++ +G KFSTYA IR I + ++++P + E +I ++ QE
Sbjct: 65 AIERYDPSKGTKFSTYAVRRIRGEILDYLRKND-SVKVPRSLRELGRRIEEAIDELEQEL 123
Query: 501 GSEPDPSVIAIKMEMPEEKIRKIMKIAK--EPVSMESPVGDDEDSHLGDFIEDENMLAPS 558
G EP IA ++ + +E+ + + + +S++ V D+D + D IE+ +
Sbjct: 124 GREPTDEEIAEELGIDKEEYIEALLAINGSQLLSLDEDVLKDDDDDVDDQIENPD----- 178
Query: 559 DAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 618
D + ++K+ + L RE VL +R+ E+ T +E+ + ++ R+ ++
Sbjct: 179 DGVEKEELLEILKEAIEPLPEREKLVLVLRYKEEL----TQKEIAEVLGISESRVSRLHK 234
Query: 619 KALRKLR 625
KA++KLR
Sbjct: 235 KAIKKLR 241
>gnl|CDD|236033 PRK07500, rpoH2, RNA polymerase factor sigma-32; Reviewed.
Length = 289
Score = 118 bits (297), Expect = 6e-29
Identities = 75/252 (29%), Positives = 125/252 (49%), Gaps = 41/252 (16%)
Query: 399 RKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 458
A + A++RLVIS+A K+ GL DLIQEG +GL++A +FE R +FSTYAT
Sbjct: 39 EDALHRIISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYAT 98
Query: 459 WWIRQAITRSI-------------ADQA-----RTIRIPVHMIETINKISRISRQILQET 500
WWIR +I I A +A R +R +R+++ + T
Sbjct: 99 WWIRASIQDYILRNWSIVRGGTSSAQKALFFNLRRLR------------ARLAQADEELT 146
Query: 501 GSEPDPSVIAIKMEMPEEKIRKIM--KIAKEPVSMESPVGDDEDSHLG--DFIEDENMLA 556
E IA + + + ++M +++ S+ +P ++++ DF+ D++ L
Sbjct: 147 KQEIHRE-IATALGVSLSDV-EMMDARLSGPDASLNAPQSEEDEGRSERMDFLVDDSPLP 204
Query: 557 P---SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERI 613
+ R + L +L RE +++R R E + TLE +G++ +++ER+
Sbjct: 205 DEQVESSIDGERRRRWLTQALQTLNERELRIIRERRLREDGA--TLEALGEELGISKERV 262
Query: 614 RQIEAKALRKLR 625
RQIEA+AL KLR
Sbjct: 263 RQIEARALEKLR 274
Score = 118 bits (297), Expect = 6e-29
Identities = 75/252 (29%), Positives = 125/252 (49%), Gaps = 41/252 (16%)
Query: 1189 RKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 1248
A + A++RLVIS+A K+ GL DLIQEG +GL++A +FE R +FSTYAT
Sbjct: 39 EDALHRIISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYAT 98
Query: 1249 WWIRQAITRSI-------------ADQA-----RTIRIPVHMIETINKISRISRQILQET 1290
WWIR +I I A +A R +R +R+++ + T
Sbjct: 99 WWIRASIQDYILRNWSIVRGGTSSAQKALFFNLRRLR------------ARLAQADEELT 146
Query: 1291 GSEPDPSVIAIKMEMPEEKIRKIM--KIAKEPVSMESPVGDDEDSHLG--DFIEDENMLA 1346
E IA + + + ++M +++ S+ +P ++++ DF+ D++ L
Sbjct: 147 KQEIHRE-IATALGVSLSDV-EMMDARLSGPDASLNAPQSEEDEGRSERMDFLVDDSPLP 204
Query: 1347 P---SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERI 1403
+ R + L +L RE +++R R E + TLE +G++ +++ER+
Sbjct: 205 DEQVESSIDGERRRRWLTQALQTLNERELRIIRERRLREDGA--TLEALGEELGISKERV 262
Query: 1404 RQIEAKALRKLR 1415
RQIEA+AL KLR
Sbjct: 263 RQIEARALEKLR 274
>gnl|CDD|233844 TIGR02392, rpoH_proteo, alternative sigma factor RpoH. A sigma
factor is a DNA-binding protein protein that binds to
the DNA-directed RNA polymerase core to produce the
holoenzyme capable of initiating transcription at
specific sites. Different sigma factors act in
vegetative growth, heat shock, extracytoplasmic
functions (ECF), etc. This model represents the clade of
sigma factors called RpoH and further restricted to the
Proteobacteria. This protein may be called sigma-32,
sigma factor H, heat shock sigma factor, and alternative
sigma factor RpoH. Note that in some species the single
locus rpoH may be replaced by two or more differentially
regulated stress response sigma factors [Cellular
processes, Adaptations to atypical conditions,
Transcription, Transcription factors].
Length = 270
Score = 116 bits (293), Expect = 1e-28
Identities = 72/240 (30%), Positives = 124/240 (51%), Gaps = 21/240 (8%)
Query: 399 RKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 458
A +++ ++LR V+ IA+ Y GL DLIQEGNIGLMKAV +F+ RG + ++A
Sbjct: 34 LDAAKKLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAV 93
Query: 459 WWIRQAITRSIADQARTIRIPVHMIETINKIS-----RISRQILQETGSEPDPSVIAIKM 513
WI+ I I R R+ V + T + R ++ LQ + + IA ++
Sbjct: 94 HWIKAEIHEYI---LRNWRL-VKVATTKAQRKLFFNLRKMKKRLQGWLNPEEVEAIAEEL 149
Query: 514 EMPEEKIRKI-MKIAKEPVSMESPVGDDEDS------HLGDFIED-ENMLAPSDAALNAS 565
+ E ++R++ +++ + +S+ + + DDED +L D D E+ L
Sbjct: 150 GVSEREVREMESRLSGQDMSLNASIDDDEDDGGAPIAYLVDKRSDPEDTLEEEQWEELQ- 208
Query: 566 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
R + + L SL R +++ R+ + TL+E+ ++ V+ ERIRQIE A++KL+
Sbjct: 209 -RQALANALGSLDARSRRIIEARWLDDDKL--TLQELAAEYGVSAERIRQIEKNAMKKLK 265
Score = 116 bits (293), Expect = 1e-28
Identities = 72/240 (30%), Positives = 124/240 (51%), Gaps = 21/240 (8%)
Query: 1189 RKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 1248
A +++ ++LR V+ IA+ Y GL DLIQEGNIGLMKAV +F+ RG + ++A
Sbjct: 34 LDAAKKLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAV 93
Query: 1249 WWIRQAITRSIADQARTIRIPVHMIETINKIS-----RISRQILQETGSEPDPSVIAIKM 1303
WI+ I I R R+ V + T + R ++ LQ + + IA ++
Sbjct: 94 HWIKAEIHEYI---LRNWRL-VKVATTKAQRKLFFNLRKMKKRLQGWLNPEEVEAIAEEL 149
Query: 1304 EMPEEKIRKI-MKIAKEPVSMESPVGDDEDS------HLGDFIED-ENMLAPSDAALNAS 1355
+ E ++R++ +++ + +S+ + + DDED +L D D E+ L
Sbjct: 150 GVSEREVREMESRLSGQDMSLNASIDDDEDDGGAPIAYLVDKRSDPEDTLEEEQWEELQ- 208
Query: 1356 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415
R + + L SL R +++ R+ + TL+E+ ++ V+ ERIRQIE A++KL+
Sbjct: 209 -RQALANALGSLDARSRRIIEARWLDDDKL--TLQELAAEYGVSAERIRQIEKNAMKKLK 265
>gnl|CDD|233392 TIGR01391, dnaG, DNA primase, catalytic core. Members of this
family are DNA primase, a ubiquitous bacteria protein.
Most members of this family contain nearly two hundred
additional residues C-terminal to the region represented
here, but conservation between species is poor and the
C-terminal region was not included in the seed
alignment. This protein contains a CHC2 zinc finger
(pfam01807) and a Toprim domain (pfam01751) [DNA
metabolism, DNA replication, recombination, and repair].
Length = 415
Score = 113 bits (285), Expect = 2e-26
Identities = 59/167 (35%), Positives = 79/167 (47%), Gaps = 36/167 (21%)
Query: 706 ETPLFHKSNELYGLFEAKNAIGKSGYVLITEGYMDVIGLSQFGF---------------- 749
ETPLF KS LYGL +A+ I K +++ EGYMDVI L Q G
Sbjct: 234 ETPLFKKSELLYGLHKARKEIRKEKELILVEGYMDVIALHQAGIKNAVASLGTALTEEHI 293
Query: 750 -----FANSSYTCFDGDQAGRRAARRALEVCLLYATDDKIIKFLFLPDKYDPDSYIRKFG 804
+A+ CFDGD+AGR+AA RA+E+ L +K + LP DPD Y+RK G
Sbjct: 294 KLLKRYADEIILCFDGDKAGRKAALRAIELLLPLG---INVKVIKLPGGKDPDEYLRKEG 350
Query: 805 YKIFSK-----KNAFSFDIKS-------NSREEIENLRKKFKILIKL 839
+ K K+ F I ++ EE L ++ LIK
Sbjct: 351 VEALKKLLENSKSLIEFLIARLLSNYNLDTPEEKAKLVEELLPLIKK 397
>gnl|CDD|233885 TIGR02479, FliA_WhiG, RNA polymerase sigma factor, FliA/WhiG
family. Most members of this family are the flagellar
operon sigma factor FliA, controlling transcription of
bacterial flagellar genes by RNA polymerase. An
exception is the sigma factor WhiG in the genus
Streptomyces, involved in the production of sporulating
aerial mycelium.
Length = 224
Score = 104 bits (262), Expect = 5e-25
Identities = 61/203 (30%), Positives = 102/203 (50%), Gaps = 16/203 (7%)
Query: 429 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI---TRSIADQARTIRIPVHMIET 485
DLIQ G GL+ A+++++ RG KF TYA IR A+ R + R++R +E
Sbjct: 28 DLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMLDELRRLDWVPRSLRQKARKLE- 86
Query: 486 INKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMK--IAKEPVSMESPVGDDEDS 543
R R++ G EP IA ++ M ++ R+ + A VS++ + +D
Sbjct: 87 -----RAIRELEARLGREPTEEEIAEELGMDLKEYRQALNEINALSLVSLDELLESGDDG 141
Query: 544 H-LGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEV 602
L D IED+ P + +R + + + SL+ RE VL + + E+ L+E+
Sbjct: 142 GSLIDRIEDDKSEDPEEELEREELREALAEAIESLSEREQLVLSLYYYEEL----NLKEI 197
Query: 603 GKQFDVTRERIRQIEAKALRKLR 625
G+ +T R+ QI ++AL+KLR
Sbjct: 198 GEVLGLTESRVSQIHSQALKKLR 220
Score = 104 bits (262), Expect = 5e-25
Identities = 61/203 (30%), Positives = 102/203 (50%), Gaps = 16/203 (7%)
Query: 1219 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI---TRSIADQARTIRIPVHMIET 1275
DLIQ G GL+ A+++++ RG KF TYA IR A+ R + R++R +E
Sbjct: 28 DLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMLDELRRLDWVPRSLRQKARKLE- 86
Query: 1276 INKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMK--IAKEPVSMESPVGDDEDS 1333
R R++ G EP IA ++ M ++ R+ + A VS++ + +D
Sbjct: 87 -----RAIRELEARLGREPTEEEIAEELGMDLKEYRQALNEINALSLVSLDELLESGDDG 141
Query: 1334 H-LGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEV 1392
L D IED+ P + +R + + + SL+ RE VL + + E+ L+E+
Sbjct: 142 GSLIDRIEDDKSEDPEEELEREELREALAEAIESLSEREQLVLSLYYYEEL----NLKEI 197
Query: 1393 GKQFDVTRERIRQIEAKALRKLR 1415
G+ +T R+ QI ++AL+KLR
Sbjct: 198 GEVLGLTESRVSQIHSQALKKLR 220
>gnl|CDD|146934 pfam04539, Sigma70_r3, Sigma-70 region 3. Region 3 forms a
discrete compact three helical domain within the
sigma-factor. Region is not normally involved in the
recognition of promoter DNA, but as some specific
bacterial promoters containing an extended -10 promoter
element, residues within region 3 play an important
role. Region 3 primarily is involved in binding the core
RNA polymerase in the holoenzyme.
Length = 78
Score = 95.4 bits (238), Expect = 1e-23
Identities = 36/78 (46%), Positives = 56/78 (71%)
Query: 484 ETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDS 543
E +NKI R R++ QE G EP P IA ++ + EEK+R++++ A+EPVS++ PVG++ED
Sbjct: 1 ELLNKIKRAQRELEQELGREPTPEEIAEELGISEEKVREVLEAAREPVSLDLPVGEEEDG 60
Query: 544 HLGDFIEDENMLAPSDAA 561
LGD +ED++ +P DA
Sbjct: 61 ELGDLLEDDDAESPEDAV 78
Score = 95.4 bits (238), Expect = 1e-23
Identities = 36/78 (46%), Positives = 56/78 (71%)
Query: 1274 ETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDS 1333
E +NKI R R++ QE G EP P IA ++ + EEK+R++++ A+EPVS++ PVG++ED
Sbjct: 1 ELLNKIKRAQRELEQELGREPTPEEIAEELGISEEKVREVLEAAREPVSLDLPVGEEEDG 60
Query: 1334 HLGDFIEDENMLAPSDAA 1351
LGD +ED++ +P DA
Sbjct: 61 ELGDLLEDDDAESPEDAV 78
>gnl|CDD|131897 TIGR02850, spore_sigG, RNA polymerase sigma-G factor. Members of
this family comprise the Firmicutes lineage endospore
formation-specific sigma factor SigG. It is also
desginated stage III sporulation protein G (SpoIIIG).
This protein is rather closely related to sigma-F
(SpoIIAC), another sporulation sigma factor
[Transcription, Transcription factors, Cellular
processes, Sporulation and germination].
Length = 254
Score = 100 bits (250), Expect = 3e-23
Identities = 71/250 (28%), Positives = 132/250 (52%), Gaps = 15/250 (6%)
Query: 378 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 437
VL ++R++ +M +G+ AR+ ++ NLRLV+S+ +++ +RG DL Q G IG
Sbjct: 15 VLKNQEMRELFIRMQSGDTTARE---KLINGNLRLVLSVIQRFNNRGEYVDDLFQVGCIG 71
Query: 438 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 497
LMK++D F+ + KFSTYA I I R + D IR+ + + K ++ +++
Sbjct: 72 LMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDN-NPIRVSRSLRDIAYKALQVRDKLI 130
Query: 498 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDD--EDSHLGDFIEDENML 555
E EP S IA ++++P+E++ + ++PVS+ P+ +D + ++ D I DE
Sbjct: 131 SENSKEPTVSEIAKELKVPQEEVVFALDAIQDPVSLFEPIYNDGGDPIYVMDQISDE--- 187
Query: 556 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 615
+ +K+ + L RE +L MRF T EV ++ +++ ++ +
Sbjct: 188 --KNKDSQWLEGIALKEAMKRLNEREKMILNMRF----FEGKTQMEVAEEIGISQAQVSR 241
Query: 616 IEAKALRKLR 625
+E AL+ +R
Sbjct: 242 LEKAALKHMR 251
Score = 100 bits (250), Expect = 3e-23
Identities = 71/250 (28%), Positives = 132/250 (52%), Gaps = 15/250 (6%)
Query: 1168 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 1227
VL ++R++ +M +G+ AR+ ++ NLRLV+S+ +++ +RG DL Q G IG
Sbjct: 15 VLKNQEMRELFIRMQSGDTTARE---KLINGNLRLVLSVIQRFNNRGEYVDDLFQVGCIG 71
Query: 1228 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 1287
LMK++D F+ + KFSTYA I I R + D IR+ + + K ++ +++
Sbjct: 72 LMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDN-NPIRVSRSLRDIAYKALQVRDKLI 130
Query: 1288 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDD--EDSHLGDFIEDENML 1345
E EP S IA ++++P+E++ + ++PVS+ P+ +D + ++ D I DE
Sbjct: 131 SENSKEPTVSEIAKELKVPQEEVVFALDAIQDPVSLFEPIYNDGGDPIYVMDQISDE--- 187
Query: 1346 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 1405
+ +K+ + L RE +L MRF T EV ++ +++ ++ +
Sbjct: 188 --KNKDSQWLEGIALKEAMKRLNEREKMILNMRF----FEGKTQMEVAEEIGISQAQVSR 241
Query: 1406 IEAKALRKLR 1415
+E AL+ +R
Sbjct: 242 LEKAALKHMR 251
>gnl|CDD|218138 pfam04542, Sigma70_r2, Sigma-70 region 2. Region 2 of sigma-70 is
the most conserved region of the entire protein. All
members of this class of sigma-factor contain region 2.
The high conservation is due to region 2 containing both
the -10 promoter recognition helix and the primary core
RNA polymerase binding determinant. The core binding
helix, interacts with the clamp domain of the largest
polymerase subunit, beta prime. The aromatic residues of
the recognition helix, found at the C-terminus of this
domain are though to mediate strand separation, thereby
allowing transcription initiation.
Length = 71
Score = 94.2 bits (235), Expect = 3e-23
Identities = 30/71 (42%), Positives = 44/71 (61%)
Query: 405 MTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 464
+ E L LV S+A++Y G DL+QEG +GL++AV++F+ RG FST+ IR A
Sbjct: 1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLLRAVERFDPERGVSFSTWLYTIIRNA 60
Query: 465 ITRSIADQART 475
I ++ Q RT
Sbjct: 61 IIDALRKQRRT 71
Score = 94.2 bits (235), Expect = 3e-23
Identities = 30/71 (42%), Positives = 44/71 (61%)
Query: 1195 MTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 1254
+ E L LV S+A++Y G DL+QEG +GL++AV++F+ RG FST+ IR A
Sbjct: 1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLLRAVERFDPERGVSFSTWLYTIIRNA 60
Query: 1255 ITRSIADQART 1265
I ++ Q RT
Sbjct: 61 IIDALRKQRRT 71
>gnl|CDD|223435 COG0358, DnaG, DNA primase (bacterial type) [DNA replication,
recombination, and repair].
Length = 568
Score = 104 bits (261), Expect = 7e-23
Identities = 76/354 (21%), Positives = 130/354 (36%), Gaps = 37/354 (10%)
Query: 706 ETPLFHKSNELYGLFEAKNAIGKSGYVLITEGYMDVIGLSQFGF---------------- 749
ET LF K ELYGL A+ I K+ +++ EGYMDVI L + G
Sbjct: 224 ETELFKKGEELYGLDPARKKIAKADQIIVVEGYMDVIALHKAGIKNAVASLGTALTEEHI 283
Query: 750 -----FANSSYTCFDGDQAGRRAARRALEVCLLYATDDKIIKFLFLPDKYDPDSYIRKFG 804
CFDGD+AGR+AA+RAL++ L + + LPD DPD IRK G
Sbjct: 284 KLLSRGKKKVILCFDGDRAGRKAAKRALQLVLPLDFV--GVFVILLPDGKDPDELIRKEG 341
Query: 805 YKIFSKKNAFSFDIKSNSREEIENLRKKFK--ILIKLGKERGYLTFSEINDFLPEDIIDH 862
A + + IE L + L GK R + +P++++
Sbjct: 342 ------AEALRKKLPNERLPLIEFLIEYLIPSNLDTEGKARLVEEAVPLIKVIPDEVLRD 395
Query: 863 EIIESIIKTFRYMD--ISVSEHVLDTETLMLSNITSDDDVEEATEAALSTVDSDFG-RTK 919
++ + + D + + + + + + A +
Sbjct: 396 YYLQKLAELLGISDDALLQLQVQPEKKATQSPFKQNPGRIAIALLVQNPVLAPKQPILKA 455
Query: 920 DPIKMYMREMGSVELLTRD-GEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKN 978
+ ++ + ELL G EI R + L + + ++E+L +SK
Sbjct: 456 LLERPLLKLLLFEELLLELFGTPEIDARFLDELFQSLFEVLL--EELVELLDINLLVSKA 513
Query: 979 EIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYE 1032
I D ++ L + + +K ++ L + DL+ +
Sbjct: 514 AIVFDGVITLLQRLLDQALEKGLKNLIGAKKKSGLNKKPKEDLNVLTKDLQLEL 567
>gnl|CDD|181296 PRK08215, PRK08215, sporulation sigma factor SigG; Reviewed.
Length = 258
Score = 94.6 bits (236), Expect = 3e-21
Identities = 74/259 (28%), Positives = 129/259 (49%), Gaps = 33/259 (12%)
Query: 378 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 437
VL ++R++ +M G+ +AR+ ++ NLRLV+S+ +++ +RG DL Q G IG
Sbjct: 18 VLKNEEMRELFERMQNGDKEARE---KLINGNLRLVLSVIQRFNNRGENVDDLFQVGCIG 74
Query: 438 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 497
LMKA+D F+ + KFSTYA I I R + D IR+ + + K ++ +++
Sbjct: 75 LMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDN-NPIRVSRSLRDIAYKALQVREKLI 133
Query: 498 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFI-------- 549
E EP IA ++E+P E++ + ++PVS+ P+ D GD I
Sbjct: 134 NENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEPIYHDG----GDPIYVMDQISD 189
Query: 550 ---EDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQF 606
+DEN L +K+ + L RE +L +RF T EV ++
Sbjct: 190 EKNKDENWLE----------EIALKEAMKKLNDREKLILNLRF----FQGKTQMEVAEEI 235
Query: 607 DVTRERIRQIEAKALRKLR 625
+++ ++ ++E AL+ +R
Sbjct: 236 GISQAQVSRLEKAALKHMR 254
Score = 94.6 bits (236), Expect = 3e-21
Identities = 74/259 (28%), Positives = 129/259 (49%), Gaps = 33/259 (12%)
Query: 1168 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 1227
VL ++R++ +M G+ +AR+ ++ NLRLV+S+ +++ +RG DL Q G IG
Sbjct: 18 VLKNEEMRELFERMQNGDKEARE---KLINGNLRLVLSVIQRFNNRGENVDDLFQVGCIG 74
Query: 1228 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 1287
LMKA+D F+ + KFSTYA I I R + D IR+ + + K ++ +++
Sbjct: 75 LMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDN-NPIRVSRSLRDIAYKALQVREKLI 133
Query: 1288 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFI-------- 1339
E EP IA ++E+P E++ + ++PVS+ P+ D GD I
Sbjct: 134 NENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEPIYHDG----GDPIYVMDQISD 189
Query: 1340 ---EDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQF 1396
+DEN L +K+ + L RE +L +RF T EV ++
Sbjct: 190 EKNKDENWLE----------EIALKEAMKKLNDREKLILNLRF----FQGKTQMEVAEEI 235
Query: 1397 DVTRERIRQIEAKALRKLR 1415
+++ ++ ++E AL+ +R
Sbjct: 236 GISQAQVSRLEKAALKHMR 254
>gnl|CDD|168831 PRK07122, PRK07122, RNA polymerase sigma factor SigF; Reviewed.
Length = 264
Score = 93.7 bits (233), Expect = 8e-21
Identities = 64/243 (26%), Positives = 115/243 (47%), Gaps = 17/243 (6%)
Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
+ AG + ++ + + L L IA+++ RG DL+Q +GL+ AV++F+
Sbjct: 29 AGLPAGSPEFQRQRDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVE 88
Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
G F ++A I + R D + ++++P + E ++ R + ++ Q G P S
Sbjct: 89 TGSDFVSFAVPTIMGEVRRHFRDNSWSVKVPRRLKELHLRLGRATAELSQRLGRAPTASE 148
Query: 509 IAIKMEMPEEKIRK--IMKIAKEPVSMESPVG--DDEDSHLGDFIEDENMLAPSDAAL-N 563
+A ++ M E++ + + A +S++S G DD+ + D + D DA L
Sbjct: 149 LAAELGMDREEVVEGLVAGSAYNTLSIDSGGGSGDDDARAIADTLGDV------DAGLDQ 202
Query: 564 ASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVG-KQFDVTRERIRQIEAKALR 622
R ++ +L +L RE VL +RF M+ E VG Q V+R + AK L
Sbjct: 203 IENREALRPLLAALPERERTVLVLRFFESMTQTQIAERVGISQMHVSR-----LLAKTLA 257
Query: 623 KLR 625
+LR
Sbjct: 258 RLR 260
Score = 93.7 bits (233), Expect = 8e-21
Identities = 64/243 (26%), Positives = 115/243 (47%), Gaps = 17/243 (6%)
Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
+ AG + ++ + + L L IA+++ RG DL+Q +GL+ AV++F+
Sbjct: 29 AGLPAGSPEFQRQRDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVE 88
Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
G F ++A I + R D + ++++P + E ++ R + ++ Q G P S
Sbjct: 89 TGSDFVSFAVPTIMGEVRRHFRDNSWSVKVPRRLKELHLRLGRATAELSQRLGRAPTASE 148
Query: 1299 IAIKMEMPEEKIRK--IMKIAKEPVSMESPVG--DDEDSHLGDFIEDENMLAPSDAAL-N 1353
+A ++ M E++ + + A +S++S G DD+ + D + D DA L
Sbjct: 149 LAAELGMDREEVVEGLVAGSAYNTLSIDSGGGSGDDDARAIADTLGDV------DAGLDQ 202
Query: 1354 ASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVG-KQFDVTRERIRQIEAKALR 1412
R ++ +L +L RE VL +RF M+ E VG Q V+R + AK L
Sbjct: 203 IENREALRPLLAALPERERTVLVLRFFESMTQTQIAERVGISQMHVSR-----LLAKTLA 257
Query: 1413 KLR 1415
+LR
Sbjct: 258 RLR 260
>gnl|CDD|131931 TIGR02885, spore_sigF, RNA polymerase sigma-F factor. Members of
this protein family are the RNA polymerase sigma factor
F. Sigma-F is specifically and universally a component
of the Firmicutes lineage endospore formation program,
and is expressed in the forespore to turn on expression
of dozens of genes. It is closely homologous to sigma-G,
which is also expressed in the forespore [Transcription,
Transcription factors, Cellular processes, Sporulation
and germination].
Length = 231
Score = 89.0 bits (221), Expect = 1e-19
Identities = 67/228 (29%), Positives = 120/228 (52%), Gaps = 10/228 (4%)
Query: 399 RKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 458
++A+ ++ E NLRLV SI K++ +RG + DL Q G IGL+KA+DKF+ KFSTYA
Sbjct: 10 KEARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAV 69
Query: 459 WWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEE 518
I I R + D I++ + E KI + ++ +E G EP + +A + + E
Sbjct: 70 PMIMGEIKRFLRDDG-IIKVSRSLKELARKIRYMKEELSKELGREPTINELAEALGVSPE 128
Query: 519 KIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLA-PSDAALNASMRSVVKDILNSL 577
+I ++ A+ P S+ V D+ GD I + +A + + +K+ ++ L
Sbjct: 129 EIVMALESARSPQSLYDTVHQDD----GDPIYLLDQIADKGSEDSDWLEKIALKEAISKL 184
Query: 578 TPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
RE +++ +R+ D T EV +++ ++ ++E K L+K++
Sbjct: 185 DERERQIIMLRY----FKDKTQTEVANMLGISQVQVSRLEKKVLKKMK 228
Score = 89.0 bits (221), Expect = 1e-19
Identities = 67/228 (29%), Positives = 120/228 (52%), Gaps = 10/228 (4%)
Query: 1189 RKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 1248
++A+ ++ E NLRLV SI K++ +RG + DL Q G IGL+KA+DKF+ KFSTYA
Sbjct: 10 KEARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAV 69
Query: 1249 WWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEE 1308
I I R + D I++ + E KI + ++ +E G EP + +A + + E
Sbjct: 70 PMIMGEIKRFLRDDG-IIKVSRSLKELARKIRYMKEELSKELGREPTINELAEALGVSPE 128
Query: 1309 KIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLA-PSDAALNASMRSVVKDILNSL 1367
+I ++ A+ P S+ V D+ GD I + +A + + +K+ ++ L
Sbjct: 129 EIVMALESARSPQSLYDTVHQDD----GDPIYLLDQIADKGSEDSDWLEKIALKEAISKL 184
Query: 1368 TPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415
RE +++ +R+ D T EV +++ ++ ++E K L+K++
Sbjct: 185 DERERQIIMLRY----FKDKTQTEVANMLGISQVQVSRLEKKVLKKMK 228
>gnl|CDD|235770 PRK06288, PRK06288, RNA polymerase sigma factor WhiG; Reviewed.
Length = 268
Score = 89.7 bits (223), Expect = 2e-19
Identities = 65/215 (30%), Positives = 100/215 (46%), Gaps = 32/215 (14%)
Query: 426 QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI----------TRSIADQART 475
+F DL+ G GL+ A++KF+ R KF TYA IR AI RS+ +AR
Sbjct: 60 EFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIFDELRSIDWIPRSVRQKARQ 119
Query: 476 IRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMK--IAKEPVSM 533
I + M+E +R+ R P IA ++ + E+ ++ VS+
Sbjct: 120 IERAIAMLE-----ARLGRT--------PSDEEIADELGISLEEYNSLLSKLSGTSVVSL 166
Query: 534 ES--PVGDDEDS-HLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFG 590
GD+ D L D +E L P + A ++ V+ + + +L RE KVL + +
Sbjct: 167 NDLWFGGDEGDEVSLMDTLESPAALNPDEIAEREEIKRVIVEAIKTLPEREKKVLILYY- 225
Query: 591 IEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
D TL+E+GK VT RI Q+ KA+ +LR
Sbjct: 226 ---YEDLTLKEIGKVLGVTESRISQLHTKAVLQLR 257
Score = 89.7 bits (223), Expect = 2e-19
Identities = 65/215 (30%), Positives = 100/215 (46%), Gaps = 32/215 (14%)
Query: 1216 QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI----------TRSIADQART 1265
+F DL+ G GL+ A++KF+ R KF TYA IR AI RS+ +AR
Sbjct: 60 EFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIFDELRSIDWIPRSVRQKARQ 119
Query: 1266 IRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMK--IAKEPVSM 1323
I + M+E +R+ R P IA ++ + E+ ++ VS+
Sbjct: 120 IERAIAMLE-----ARLGRT--------PSDEEIADELGISLEEYNSLLSKLSGTSVVSL 166
Query: 1324 ES--PVGDDEDS-HLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFG 1380
GD+ D L D +E L P + A ++ V+ + + +L RE KVL + +
Sbjct: 167 NDLWFGGDEGDEVSLMDTLESPAALNPDEIAEREEIKRVIVEAIKTLPEREKKVLILYY- 225
Query: 1381 IEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415
D TL+E+GK VT RI Q+ KA+ +LR
Sbjct: 226 ---YEDLTLKEIGKVLGVTESRISQLHTKAVLQLR 257
>gnl|CDD|235838 PRK06596, PRK06596, RNA polymerase factor sigma-32; Reviewed.
Length = 284
Score = 85.2 bits (212), Expect = 7e-18
Identities = 29/67 (43%), Positives = 43/67 (64%)
Query: 399 RKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 458
+A +++ ++LR V+ IA+ Y GL DLIQEGNIGLMKAV +F+ G + ++A
Sbjct: 47 LEAAKQLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAV 106
Query: 459 WWIRQAI 465
WI+ I
Sbjct: 107 HWIKAEI 113
Score = 85.2 bits (212), Expect = 7e-18
Identities = 29/67 (43%), Positives = 43/67 (64%)
Query: 1189 RKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 1248
+A +++ ++LR V+ IA+ Y GL DLIQEGNIGLMKAV +F+ G + ++A
Sbjct: 47 LEAAKQLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAV 106
Query: 1249 WWIRQAI 1255
WI+ I
Sbjct: 107 HWIKAEI 113
Score = 58.3 bits (142), Expect = 8e-09
Identities = 31/116 (26%), Positives = 56/116 (48%), Gaps = 22/116 (18%)
Query: 528 KEPVSMES-----------PVGDDEDSH--LGDFIED-----ENMLAPSDAALNASMRSV 569
+E MES P+ DD++ D++ED ++L + R++
Sbjct: 166 EEVREMESRLSGQDASLDAPIDDDDEESGAPQDYLEDKSSDPADVLEEDNWEDQR--RAL 223
Query: 570 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
+ D L L R ++ R+ + S TL+E+ ++ V+ ER+RQIE A++KL+
Sbjct: 224 LADALEGLDERSRDIIEARWLDDDKS--TLQELAAEYGVSAERVRQIEKNAMKKLK 277
Score = 58.3 bits (142), Expect = 8e-09
Identities = 31/116 (26%), Positives = 56/116 (48%), Gaps = 22/116 (18%)
Query: 1318 KEPVSMES-----------PVGDDEDSH--LGDFIED-----ENMLAPSDAALNASMRSV 1359
+E MES P+ DD++ D++ED ++L + R++
Sbjct: 166 EEVREMESRLSGQDASLDAPIDDDDEESGAPQDYLEDKSSDPADVLEEDNWEDQR--RAL 223
Query: 1360 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415
+ D L L R ++ R+ + S TL+E+ ++ V+ ER+RQIE A++KL+
Sbjct: 224 LADALEGLDERSRDIIEARWLDDDKS--TLQELAAEYGVSAERVRQIEKNAMKKLK 277
>gnl|CDD|181075 PRK07670, PRK07670, RNA polymerase sigma factor SigD; Validated.
Length = 251
Score = 84.3 bits (209), Expect = 8e-18
Identities = 55/202 (27%), Positives = 94/202 (46%), Gaps = 12/202 (5%)
Query: 1219 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTI-RIPVHMIETIN 1277
DL G +GL A++KF+ R KF TYA++ IR AI D R +P M E
Sbjct: 54 DLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAII----DGLRKEDWLPRSMREKTK 109
Query: 1278 KISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMK--IAKEPVSM-ESPVGDDEDSH 1334
K+ ++ Q P +A ++ M EE++ M +S+ E D+ +
Sbjct: 110 KVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMNEGFFANLLSIDEKTHDQDDGEN 169
Query: 1335 LGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGK 1394
+ I D+ P + L + + + + L+ +E V+ + + E+ TL E+G+
Sbjct: 170 VSVTIRDDKTPTPEEKLLKEELIEELAEKIKQLSEKEQLVISLFYKEEL----TLTEIGQ 225
Query: 1395 QFDVTRERIRQIEAKALRKLRH 1416
+++ RI QI +KAL KL+
Sbjct: 226 VLNLSTSRISQIHSKALFKLKK 247
Score = 82.4 bits (204), Expect = 4e-17
Identities = 56/203 (27%), Positives = 95/203 (46%), Gaps = 12/203 (5%)
Query: 429 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTI-RIPVHMIETIN 487
DL G +GL A++KF+ R KF TYA++ IR AI D R +P M E
Sbjct: 54 DLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAII----DGLRKEDWLPRSMREKTK 109
Query: 488 KISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMK--IAKEPVSM-ESPVGDDEDSH 544
K+ ++ Q P +A ++ M EE++ M +S+ E D+ +
Sbjct: 110 KVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMNEGFFANLLSIDEKTHDQDDGEN 169
Query: 545 LGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGK 604
+ I D+ P + L + + + + L+ +E V+ + + E+ TL E+G+
Sbjct: 170 VSVTIRDDKTPTPEEKLLKEELIEELAEKIKQLSEKEQLVISLFYKEEL----TLTEIGQ 225
Query: 605 QFDVTRERIRQIEAKALRKLRPL 627
+++ RI QI +KAL KL+ L
Sbjct: 226 VLNLSTSRISQIHSKALFKLKKL 248
>gnl|CDD|180266 PRK05803, PRK05803, sporulation sigma factor SigK; Reviewed.
Length = 233
Score = 83.1 bits (206), Expect = 1e-17
Identities = 60/230 (26%), Positives = 96/230 (41%), Gaps = 58/230 (25%)
Query: 1191 AKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 1250
A+ + E NLRLV I KK+ + G DLI G IGL+KA++ F+ +G K +TYA
Sbjct: 50 ARNILIERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYA--- 106
Query: 1251 IRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKI 1310
AR I + M +
Sbjct: 107 ------------ARCIENEILMH------------------------------------L 118
Query: 1311 RKIMKIAKEPVSMESPVGDDEDSH---LGDFIEDENMLAPSDAALNASMR-SVVKDILNS 1366
R + K KE VS++ P+G D++ + L D + E + M + ++
Sbjct: 119 RNLKKTKKE-VSLQDPIGVDKEGNEISLIDILGSEE--DDVIEQVELKMEVEKLYKKIDI 175
Query: 1367 LTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416
L RE +V+ MR+G+ + T E+ K ++R + +IE +AL+KL
Sbjct: 176 LDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKLFK 225
Score = 82.3 bits (204), Expect = 3e-17
Identities = 60/228 (26%), Positives = 96/228 (42%), Gaps = 58/228 (25%)
Query: 401 AKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 460
A+ + E NLRLV I KK+ + G DLI G IGL+KA++ F+ +G K +TYA
Sbjct: 50 ARNILIERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYA--- 106
Query: 461 IRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKI 520
AR I + M +
Sbjct: 107 ------------ARCIENEILMH------------------------------------L 118
Query: 521 RKIMKIAKEPVSMESPVGDDEDSH---LGDFIEDENMLAPSDAALNASMR-SVVKDILNS 576
R + K KE VS++ P+G D++ + L D + E + M + ++
Sbjct: 119 RNLKKTKKE-VSLQDPIGVDKEGNEISLIDILGSEE--DDVIEQVELKMEVEKLYKKIDI 175
Query: 577 LTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 624
L RE +V+ MR+G+ + T E+ K ++R + +IE +AL+KL
Sbjct: 176 LDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKL 223
>gnl|CDD|180137 PRK05572, PRK05572, sporulation sigma factor SigF; Validated.
Length = 252
Score = 82.7 bits (205), Expect = 4e-17
Identities = 71/252 (28%), Positives = 130/252 (51%), Gaps = 23/252 (9%)
Query: 380 PLNDLRDINRKMIA----GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 435
L D + N+++I G+ +AR + E NLRLV S+ +++ +RG + DL Q G
Sbjct: 13 QLKD--EENKELIKKSQDGDQEARD---TLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGC 67
Query: 436 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 495
IGL+KAVDKF+ KFSTYA I I R + D T+++ + ET NKI + +
Sbjct: 68 IGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKETANKIRKDKDE 126
Query: 496 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDS--HLGDFIEDEN 553
+ +E G EP +A + + E++ + ++ P S+ V +++ L D I D+
Sbjct: 127 LSKELGREPTIEELAEYLGVTPEEVVLAQEASRSPQSIHETVHENDGDPITLLDQIADQ- 185
Query: 554 MLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERI 613
+ + + +K+ + L RE ++ +R+ D T EV K+ +++ ++
Sbjct: 186 ---SEEDWFD---KIALKEAIRELDERERLIVYLRY----FKDKTQSEVAKRLGISQVQV 235
Query: 614 RQIEAKALRKLR 625
++E K L++++
Sbjct: 236 SRLEKKILKQMK 247
Score = 82.7 bits (205), Expect = 4e-17
Identities = 71/252 (28%), Positives = 130/252 (51%), Gaps = 23/252 (9%)
Query: 1170 PLNDLRDINRKMIA----GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 1225
L D + N+++I G+ +AR + E NLRLV S+ +++ +RG + DL Q G
Sbjct: 13 QLKD--EENKELIKKSQDGDQEARD---TLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGC 67
Query: 1226 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 1285
IGL+KAVDKF+ KFSTYA I I R + D T+++ + ET NKI + +
Sbjct: 68 IGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKETANKIRKDKDE 126
Query: 1286 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDS--HLGDFIEDEN 1343
+ +E G EP +A + + E++ + ++ P S+ V +++ L D I D+
Sbjct: 127 LSKELGREPTIEELAEYLGVTPEEVVLAQEASRSPQSIHETVHENDGDPITLLDQIADQ- 185
Query: 1344 MLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERI 1403
+ + + +K+ + L RE ++ +R+ D T EV K+ +++ ++
Sbjct: 186 ---SEEDWFD---KIALKEAIRELDERERLIVYLRY----FKDKTQSEVAKRLGISQVQV 235
Query: 1404 RQIEAKALRKLR 1415
++E K L++++
Sbjct: 236 SRLEKKILKQMK 247
>gnl|CDD|218139 pfam04545, Sigma70_r4, Sigma-70, region 4. Region 4 of sigma-70 like
sigma-factors are involved in binding to the -35 promoter
element via a helix-turn-helix motif. Due to the way Pfam
works, the threshold has been set artificially high to
prevent overlaps with other helix-turn-helix families.
Therefore there are many false negatives.
Length = 50
Score = 70.9 bits (175), Expect = 2e-15
Identities = 29/53 (54%), Positives = 38/53 (71%), Gaps = 4/53 (7%)
Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416
L SL PRE +VL +RFG TLEE+G++ ++RER+RQIE +ALRKLR
Sbjct: 2 LASLPPREREVLVLRFG----EGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
Score = 69.4 bits (171), Expect = 8e-15
Identities = 29/52 (55%), Positives = 38/52 (73%), Gaps = 4/52 (7%)
Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
L SL PRE +VL +RFG TLEE+G++ ++RER+RQIE +ALRKLR
Sbjct: 2 LASLPPREREVLVLRFG----EGLTLEEIGERLGISRERVRQIEKRALRKLR 49
>gnl|CDD|180965 PRK07408, PRK07408, RNA polymerase sigma factor SigF; Reviewed.
Length = 256
Score = 77.3 bits (191), Expect = 3e-15
Identities = 48/151 (31%), Positives = 93/151 (61%), Gaps = 7/151 (4%)
Query: 407 EANLRLVISIAKKYTDRGLQ-FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 465
E NL LV A +++++ + + DL+Q G++GL++A+++F+ +G+ FS++A +IR I
Sbjct: 32 ELNLGLVRKEAHRWSNQCSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEI 91
Query: 466 TRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMK 525
+ D++ T+RIP E + ++ +++ QE G +P IA +++ E+ ++I K
Sbjct: 92 QHYLRDKSPTVRIPRRWQELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEI-K 150
Query: 526 IA---KEPVSMESPVGDDEDSH--LGDFIED 551
+A + P+S+++PV DED LGD + D
Sbjct: 151 LALQNRTPLSLDAPVNQDEDGSTSLGDLLPD 181
Score = 77.3 bits (191), Expect = 3e-15
Identities = 48/151 (31%), Positives = 93/151 (61%), Gaps = 7/151 (4%)
Query: 1197 EANLRLVISIAKKYTDRGLQ-FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 1255
E NL LV A +++++ + + DL+Q G++GL++A+++F+ +G+ FS++A +IR I
Sbjct: 32 ELNLGLVRKEAHRWSNQCSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEI 91
Query: 1256 TRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMK 1315
+ D++ T+RIP E + ++ +++ QE G +P IA +++ E+ ++I K
Sbjct: 92 QHYLRDKSPTVRIPRRWQELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEI-K 150
Query: 1316 IA---KEPVSMESPVGDDEDSH--LGDFIED 1341
+A + P+S+++PV DED LGD + D
Sbjct: 151 LALQNRTPLSLDAPVNQDEDGSTSLGDLLPD 181
>gnl|CDD|235901 PRK06986, fliA, flagellar biosynthesis sigma factor; Validated.
Length = 236
Score = 76.4 bits (189), Expect = 3e-15
Identities = 56/215 (26%), Positives = 96/215 (44%), Gaps = 35/215 (16%)
Query: 425 LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI----------TRSIADQAR 474
+ DLIQ G IGL++A +++ +G F TYA IR A+ RS+ AR
Sbjct: 36 VDLDDLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMLDELRSLDWVPRSVRRNAR 95
Query: 475 TIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSME 534
+ + RQ+ QE G EP + +A K+ + E+ R+ M + ++
Sbjct: 96 EVAQAI-------------RQLEQELGREPTDTEVAEKLGLSLEEYRE-MLLD---TNIS 138
Query: 535 SPVG-DDEDSHLGDFIEDENMLA---PSDAALNASMRSVVKDILNSLTPRESKVLRMRFG 590
D+ GD I P + +R + + + SL RE VL + +
Sbjct: 139 QLFSIDELRGEHGDSILVTEDHQDEDPLQQLEDEELREALVEAIESLPEREQLVLSLYYQ 198
Query: 591 IEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
E++ L+E+G V+ R+ QI ++A+++LR
Sbjct: 199 EELN----LKEIGAVLGVSESRVSQIHSQAIKRLR 229
Score = 76.4 bits (189), Expect = 3e-15
Identities = 56/215 (26%), Positives = 96/215 (44%), Gaps = 35/215 (16%)
Query: 1215 LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI----------TRSIADQAR 1264
+ DLIQ G IGL++A +++ +G F TYA IR A+ RS+ AR
Sbjct: 36 VDLDDLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMLDELRSLDWVPRSVRRNAR 95
Query: 1265 TIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSME 1324
+ + RQ+ QE G EP + +A K+ + E+ R+ M + ++
Sbjct: 96 EVAQAI-------------RQLEQELGREPTDTEVAEKLGLSLEEYRE-MLLD---TNIS 138
Query: 1325 SPVG-DDEDSHLGDFIEDENMLA---PSDAALNASMRSVVKDILNSLTPRESKVLRMRFG 1380
D+ GD I P + +R + + + SL RE VL + +
Sbjct: 139 QLFSIDELRGEHGDSILVTEDHQDEDPLQQLEDEELREALVEAIESLPEREQLVLSLYYQ 198
Query: 1381 IEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415
E++ L+E+G V+ R+ QI ++A+++LR
Sbjct: 199 EELN----LKEIGAVLGVSESRVSQIHSQAIKRLR 229
>gnl|CDD|131987 TIGR02941, Sigma_B, RNA polymerase sigma-B factor. This sigma
factor is restricted to certain lineages of the order
Bacillales including Staphylococcus , Listeria and
Bacillus.
Length = 255
Score = 76.5 bits (188), Expect = 4e-15
Identities = 57/222 (25%), Positives = 104/222 (46%), Gaps = 10/222 (4%)
Query: 411 RLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 470
LV SIA KY+ G DL+Q G +GL+ A+ +++Y G F +A I I R +
Sbjct: 40 NLVYSIAYKYSKGGPMHEDLVQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIIGEIKRYLR 99
Query: 471 DQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAK-- 528
D+ ++ +P + E KI + ++ P IA + + EE++ +IM++ +
Sbjct: 100 DKTWSVHVPRRIKELGPKIKKAIDELTDHLQRSPKIIEIADHLGLSEEEVLEIMEMGQSY 159
Query: 529 EPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMR 588
+S++ + D D + +++ D R V++ IL L+ RE ++
Sbjct: 160 RALSVDDVIEADSDGSTVARL--DSVGEVEDGYDQTERRMVLEKILPILSEREKSIIHCT 217
Query: 589 FGIEMSSDHTLEEVG-KQFDVTRERIRQIEAKALRKLRPLAH 629
F +S T E +G Q V+R ++ +A+ KL+ A
Sbjct: 218 FEENLSQKETGERLGISQMHVSR-----LQRQAISKLKEAAF 254
Score = 74.6 bits (183), Expect = 2e-14
Identities = 56/218 (25%), Positives = 103/218 (47%), Gaps = 10/218 (4%)
Query: 1201 RLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 1260
LV SIA KY+ G DL+Q G +GL+ A+ +++Y G F +A I I R +
Sbjct: 40 NLVYSIAYKYSKGGPMHEDLVQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIIGEIKRYLR 99
Query: 1261 DQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAK-- 1318
D+ ++ +P + E KI + ++ P IA + + EE++ +IM++ +
Sbjct: 100 DKTWSVHVPRRIKELGPKIKKAIDELTDHLQRSPKIIEIADHLGLSEEEVLEIMEMGQSY 159
Query: 1319 EPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMR 1378
+S++ + D D + +++ D R V++ IL L+ RE ++
Sbjct: 160 RALSVDDVIEADSDGSTVARL--DSVGEVEDGYDQTERRMVLEKILPILSEREKSIIHCT 217
Query: 1379 FGIEMSSDHTLEEVG-KQFDVTRERIRQIEAKALRKLR 1415
F +S T E +G Q V+R ++ +A+ KL+
Sbjct: 218 FEENLSQKETGERLGISQMHVSR-----LQRQAISKLK 250
>gnl|CDD|131893 TIGR02846, spore_sigmaK, RNA polymerase sigma-K factor. The
sporulation-specific transcription factor sigma-K (also
called sigma-27) is expressed in the mother cell
compartment of endospore-forming bacteria such as
Bacillus subtilis. Like its close homolog sigma-E
(sigma-29) (see TIGR02835), also specific to the mother
cell compartment, it must be activated by a proteolytic
cleavage. Note that in Bacillus subtilis (and apparently
also Clostridium tetani), but not in other endospore
forming species such as Bacillus anthracis, the sigK gene
is generated by a non-germline (mother cell only)
chromosomal rearrangement that recombines coding regions
for the N-terminal and C-terminal regions of sigma-K
[Transcription, Transcription factors, Cellular
processes, Sporulation and germination].
Length = 227
Score = 74.8 bits (184), Expect = 9e-15
Identities = 59/234 (25%), Positives = 97/234 (41%), Gaps = 62/234 (26%)
Query: 1189 RKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 1248
+A+ + E NLRLV I KK+++ G DLI G IGL+KA+D F+ +G + +TYA
Sbjct: 47 EEARNVLIERNLRLVAHIVKKFSNTGEDVDDLISIGTIGLIKAIDSFDPDKGTRLATYAA 106
Query: 1249 WWIRQAITRSIADQARTIRIPVHMIETI------NKISRISRQILQETGSEPDPSVIAIK 1302
I I + +T + V + + I N+IS I IL GS+ D + ++
Sbjct: 107 RCIENEILMHLRALKKT-KGEVSLQDPIGVDKEGNEISLID--IL---GSDGDSVIEQVE 160
Query: 1303 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 1362
+ + +K+ K + +
Sbjct: 161 LNLEIKKLYKKLSV---------------------------------------------- 174
Query: 1363 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416
L RE +V+ MR+G+ T E+ K ++R + +IE +AL KL
Sbjct: 175 ----LDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRALMKLYK 224
Score = 74.0 bits (182), Expect = 2e-14
Identities = 59/232 (25%), Positives = 97/232 (41%), Gaps = 62/232 (26%)
Query: 399 RKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 458
+A+ + E NLRLV I KK+++ G DLI G IGL+KA+D F+ +G + +TYA
Sbjct: 47 EEARNVLIERNLRLVAHIVKKFSNTGEDVDDLISIGTIGLIKAIDSFDPDKGTRLATYAA 106
Query: 459 WWIRQAITRSIADQARTIRIPVHMIETI------NKISRISRQILQETGSEPDPSVIAIK 512
I I + +T + V + + I N+IS I IL GS+ D + ++
Sbjct: 107 RCIENEILMHLRALKKT-KGEVSLQDPIGVDKEGNEISLID--IL---GSDGDSVIEQVE 160
Query: 513 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 572
+ + +K+ K + +
Sbjct: 161 LNLEIKKLYKKLSV---------------------------------------------- 174
Query: 573 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 624
L RE +V+ MR+G+ T E+ K ++R + +IE +AL KL
Sbjct: 175 ----LDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRALMKL 222
>gnl|CDD|217827 pfam03979, Sigma70_r1_1, Sigma-70 factor, region 1.1. Region 1.1
modulates DNA binding by region 2 and 4 when sigma is
unbound by the core RNA polymerase. Region 1.1 is also
involved in promoter binding.
Length = 79
Score = 65.8 bits (161), Expect = 3e-13
Identities = 32/80 (40%), Positives = 44/80 (55%), Gaps = 1/80 (1%)
Query: 35 EIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVL 94
+ + + K LI+ GK+RGYLT+ EIN+ LP D +D E I+ II M I V E
Sbjct: 1 LEDLSQAQVKKLIEQGKKRGYLTYDEINEALPPDDVDSEQIDDIISMLEDMGIEVVE-EA 59
Query: 95 DTETLMLSNITSDDDVEEAT 114
D+E L + +D EEA
Sbjct: 60 DSEELDEETSSDEDAEEEAE 79
Score = 65.8 bits (161), Expect = 3e-13
Identities = 32/80 (40%), Positives = 44/80 (55%), Gaps = 1/80 (1%)
Query: 825 EIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVL 884
+ + + K LI+ GK+RGYLT+ EIN+ LP D +D E I+ II M I V E
Sbjct: 1 LEDLSQAQVKKLIEQGKKRGYLTYDEINEALPPDDVDSEQIDDIISMLEDMGIEVVE-EA 59
Query: 885 DTETLMLSNITSDDDVEEAT 904
D+E L + +D EEA
Sbjct: 60 DSEELDEETSSDEDAEEEAE 79
>gnl|CDD|100119 cd06171, Sigma70_r4, Sigma70, region (SR) 4 refers to the most
C-terminal of four conserved domains found in
Escherichia coli (Ec) sigma70, the main housekeeping
sigma, and related sigma-factors (SFs). A SF is a
dissociable subunit of RNA polymerase, it directs
bacterial or plastid core RNA polymerase to specific
promoter elements located upstream of transcription
initiation points. The SR4 of Ec sigma70 and other
essential primary SFs contact promoter sequences located
35 base-pairs upstream of the initiation point,
recognizing a 6-base-pair -35 consensus TTGACA. Sigma70
related SFs also include SFs which are dispensable for
bacterial cell growth for example Ec sigmaS, SFs which
activate regulons in response to a specific signal for
example heat-shock Ec sigmaH, and a group of SFs which
includes the extracytoplasmic function (ECF) SFs and is
typified by Ec sigmaE which contains SR2 and -4 only.
ECF SFs direct the transcription of genes that regulate
various responses including periplasmic stress and
pathogenesis. Ec sigmaE SR4 also contacts the -35
element, but recognizes a different consensus (a
7-base-pair GGAACTT). Plant SFs recognize sigma70 type
promoters and direct transcription of the major plastid
RNA polymerase, plastid-encoded RNA polymerase (PEP).
Length = 55
Score = 62.5 bits (153), Expect = 2e-12
Identities = 19/59 (32%), Positives = 34/59 (57%), Gaps = 4/59 (6%)
Query: 567 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
R +++ L+ L RE +V+ +RFG + EE+ + ++R +RQ +AL+KLR
Sbjct: 1 RERLEEALDKLPEREREVILLRFG----EGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
Score = 62.5 bits (153), Expect = 2e-12
Identities = 19/59 (32%), Positives = 34/59 (57%), Gaps = 4/59 (6%)
Query: 1357 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415
R +++ L+ L RE +V+ +RFG + EE+ + ++R +RQ +AL+KLR
Sbjct: 1 RERLEEALDKLPEREREVILLRFG----EGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
>gnl|CDD|236306 PRK08583, PRK08583, RNA polymerase sigma factor SigB; Validated.
Length = 257
Score = 67.0 bits (164), Expect = 7e-12
Identities = 57/220 (25%), Positives = 106/220 (48%), Gaps = 16/220 (7%)
Query: 412 LVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD 471
LV S+A KY+ DL+Q G +GL+ A+ +++ G F +A I I R + D
Sbjct: 41 LVESLAYKYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEIKRYLRD 100
Query: 472 QARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAK--E 529
+ ++ +P + E KI + ++ E P S IA ++ + EE++ + M++ K +
Sbjct: 101 KTWSVHVPRRIKELGPKIKKAVDELTTELQRSPKISEIADRLGVSEEEVLEAMEMGKSYQ 160
Query: 530 PVSMESPVGDDEDSH---LGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLR 586
+S++ + D D L D + + D R +++ IL L+ RE +++
Sbjct: 161 ALSVDHSIEADSDGSTVTLLDIVGQQE-----DGYELTEQRMILEKILPVLSDREKSIIQ 215
Query: 587 MRFGIEMSSDHTLEEVG-KQFDVTRERIRQIEAKALRKLR 625
F +S T E +G Q V+R ++ +A++KLR
Sbjct: 216 CTFIENLSQKETGERLGISQMHVSR-----LQRQAIKKLR 250
Score = 67.0 bits (164), Expect = 7e-12
Identities = 57/220 (25%), Positives = 106/220 (48%), Gaps = 16/220 (7%)
Query: 1202 LVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD 1261
LV S+A KY+ DL+Q G +GL+ A+ +++ G F +A I I R + D
Sbjct: 41 LVESLAYKYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEIKRYLRD 100
Query: 1262 QARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAK--E 1319
+ ++ +P + E KI + ++ E P S IA ++ + EE++ + M++ K +
Sbjct: 101 KTWSVHVPRRIKELGPKIKKAVDELTTELQRSPKISEIADRLGVSEEEVLEAMEMGKSYQ 160
Query: 1320 PVSMESPVGDDEDSH---LGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLR 1376
+S++ + D D L D + + D R +++ IL L+ RE +++
Sbjct: 161 ALSVDHSIEADSDGSTVTLLDIVGQQE-----DGYELTEQRMILEKILPVLSDREKSIIQ 215
Query: 1377 MRFGIEMSSDHTLEEVG-KQFDVTRERIRQIEAKALRKLR 1415
F +S T E +G Q V+R ++ +A++KLR
Sbjct: 216 CTFIENLSQKETGERLGISQMHVSR-----LQRQAIKKLR 250
>gnl|CDD|173784 cd03364, TOPRIM_DnaG_primases, TOPRIM_DnaG_primases: The
topoisomerase-primase (TORPIM) nucleotidyl
transferase/hydrolase domain found in the active site
regions of proteins similar to Escherichia coli DnaG.
Primases synthesize RNA primers for the initiation of
DNA replication. DnaG type primases are often closely
associated with DNA helicases in primosome assemblies.
The TOPRIM domain has two conserved motifs, one of which
centers at a conserved glutamate and the other one at
two conserved aspartates (DxD). This glutamate and two
aspartates, cluster together to form a highly acid
surface patch. The conserved glutamate may act as a
general base in nucleotide polymerization by primases.
The DXD motif may co-ordinate Mg2+, a cofactor required
for full catalytic function. E. coli DnaG is a single
subunit enzyme.
Length = 79
Score = 59.1 bits (144), Expect = 7e-11
Identities = 27/80 (33%), Positives = 35/80 (43%), Gaps = 24/80 (30%)
Query: 732 VLITEGYMDVIGLSQFGF---------------------FANSSYTCFDGDQAGRRAARR 770
V++ EGYMDVI L Q G A FDGD+AG++AA R
Sbjct: 3 VILVEGYMDVIALHQAGIKNVVASLGTALTEEQAELLKRLAKEVILAFDGDEAGQKAALR 62
Query: 771 ALEVCLLYATDDKIIKFLFL 790
ALE+ L ++ L L
Sbjct: 63 ALELLL---KLGLNVRVLTL 79
>gnl|CDD|201030 pfam00140, Sigma70_r1_2, Sigma-70 factor, region 1.2.
Length = 37
Score = 56.3 bits (137), Expect = 2e-10
Identities = 16/33 (48%), Positives = 26/33 (78%)
Query: 130 DPIKMYMREMGSVELLTRDGEIEIAKRIEEGLK 162
D +++Y+RE+G V LLT + E+E+A+RIE G +
Sbjct: 2 DSVRLYLREIGRVPLLTAEEEVELARRIEAGDE 34
Score = 56.3 bits (137), Expect = 2e-10
Identities = 16/33 (48%), Positives = 26/33 (78%)
Query: 920 DPIKMYMREMGSVELLTRDGEIEIAKRIEEGLK 952
D +++Y+RE+G V LLT + E+E+A+RIE G +
Sbjct: 2 DSVRLYLREIGRVPLLTAEEEVELARRIEAGDE 34
>gnl|CDD|131882 TIGR02835, spore_sigmaE, RNA polymerase sigma-E factor. Members of
this family comprise the Firmicutes lineage endospore
formation-specific sigma factor SigE, also called
SpoIIGB and sigma-29. As characterized in Bacillus
subtilis, this protein is synthesized as a precursor,
specifically in the mother cell compartment, and must
cleaved by the SpoIIGA protein to be made active
[Transcription, Transcription factors, Cellular
processes, Sporulation and germination].
Length = 234
Score = 61.4 bits (149), Expect = 4e-10
Identities = 55/226 (24%), Positives = 97/226 (42%), Gaps = 52/226 (23%)
Query: 401 AKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 460
AK + E NLRLV+ IA+K+ + G+ DL+ G IGL+KAV+ F + K +TYA+
Sbjct: 53 AKSTLIERNLRLVVYIARKFENTGIGIEDLVSIGTIGLIKAVNTFNPSKKIKLATYASRC 112
Query: 461 IRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET-GSEPDPSVIAIKMEMPEEK 519
I I + +T R V E +N + +L + G++ D + + EE
Sbjct: 113 IENEILMYLRRNNKT-RSEVSFDEPLNVDWDGNELLLSDVLGTDSD----IVYKYLEEEV 167
Query: 520 IRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTP 579
R++++ A L L
Sbjct: 168 DRELLRKA----------------------------------------------LAKLND 181
Query: 580 RESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
RE K++ +RFG+ ++ T +EV +++ I ++E + L++L+
Sbjct: 182 REKKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEKRILKRLK 227
Score = 61.4 bits (149), Expect = 4e-10
Identities = 55/226 (24%), Positives = 97/226 (42%), Gaps = 52/226 (23%)
Query: 1191 AKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 1250
AK + E NLRLV+ IA+K+ + G+ DL+ G IGL+KAV+ F + K +TYA+
Sbjct: 53 AKSTLIERNLRLVVYIARKFENTGIGIEDLVSIGTIGLIKAVNTFNPSKKIKLATYASRC 112
Query: 1251 IRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET-GSEPDPSVIAIKMEMPEEK 1309
I I + +T R V E +N + +L + G++ D + + EE
Sbjct: 113 IENEILMYLRRNNKT-RSEVSFDEPLNVDWDGNELLLSDVLGTDSD----IVYKYLEEEV 167
Query: 1310 IRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTP 1369
R++++ A L L
Sbjct: 168 DRELLRKA----------------------------------------------LAKLND 181
Query: 1370 RESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415
RE K++ +RFG+ ++ T +EV +++ I ++E + L++L+
Sbjct: 182 REKKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEKRILKRLK 227
>gnl|CDD|234065 TIGR02937, sigma70-ECF, RNA polymerase sigma factor, sigma-70
family. This model encompasses all varieties of the
sigma-70 type sigma factors including the ECF subfamily.
A number of sigma factors have names with a different
number than 70 (i.e. sigma-38), but in fact, all except
for the Sigma-54 family (TIGR02395) are included within
this family. Several PFAM models hit segments of these
sequences including Sigma-70 region 2 (pfam04542) and
Sigma-70, region 4 (pfam04545), but not always above
their respective trusted cutoffs.
Length = 158
Score = 58.5 bits (142), Expect = 8e-10
Identities = 24/100 (24%), Positives = 43/100 (43%), Gaps = 2/100 (2%)
Query: 400 KAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 459
+A E+ E L LV A++Y DL+QE + L++A+D+F+ F +
Sbjct: 1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPE--GSFKAWLFR 58
Query: 460 WIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 499
R I + + R R + E ++ ++ QE
Sbjct: 59 IARNLILDYLRRKRRLRRELDLLEELLDSDPSPEEELEQE 98
Score = 58.5 bits (142), Expect = 8e-10
Identities = 24/100 (24%), Positives = 43/100 (43%), Gaps = 2/100 (2%)
Query: 1190 KAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 1249
+A E+ E L LV A++Y DL+QE + L++A+D+F+ F +
Sbjct: 1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPE--GSFKAWLFR 58
Query: 1250 WIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
R I + + R R + E ++ ++ QE
Sbjct: 59 IARNLILDYLRRKRRLRRELDLLEELLDSDPSPEEELEQE 98
Score = 50.4 bits (121), Expect = 5e-07
Identities = 15/76 (19%), Positives = 36/76 (47%), Gaps = 4/76 (5%)
Query: 550 EDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVT 609
++ +P + R +++ L L RE +VL +R+ +S +E+ + ++
Sbjct: 84 LLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLS----YKEIAEILGIS 139
Query: 610 RERIRQIEAKALRKLR 625
+++ +A +KLR
Sbjct: 140 VGTVKRRLKRARKKLR 155
Score = 50.4 bits (121), Expect = 5e-07
Identities = 15/76 (19%), Positives = 36/76 (47%), Gaps = 4/76 (5%)
Query: 1340 EDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVT 1399
++ +P + R +++ L L RE +VL +R+ +S +E+ + ++
Sbjct: 84 LLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLS----YKEIAEILGIS 139
Query: 1400 RERIRQIEAKALRKLR 1415
+++ +A +KLR
Sbjct: 140 VGTVKRRLKRARKKLR 155
>gnl|CDD|235644 PRK05911, PRK05911, RNA polymerase sigma factor sigma-28; Reviewed.
Length = 257
Score = 59.6 bits (144), Expect = 2e-09
Identities = 52/203 (25%), Positives = 97/203 (47%), Gaps = 13/203 (6%)
Query: 429 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 488
DL G GL++AV++F+ + +F YA + I+ AI I D + +P + + NK
Sbjct: 55 DLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAI---IDDLRKQDWVPRSVHQKANK 111
Query: 489 ISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSM----ESPVGDDEDS- 543
++ + Q G EP + + + ++++ A+ + + E P D+++
Sbjct: 112 LADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPALILSLNEEFPCQSDDEAG 171
Query: 544 -HLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEV 602
L + I DE D S++ + + +L +E KV+ + + E+ L+E+
Sbjct: 172 LALEERIADERAETGYDVVDKKEFSSILAEAILALEEKERKVMALYYYEEL----VLKEI 227
Query: 603 GKQFDVTRERIRQIEAKALRKLR 625
GK V+ R+ QI +KAL KLR
Sbjct: 228 GKILGVSESRVSQIHSKALLKLR 250
Score = 59.6 bits (144), Expect = 2e-09
Identities = 52/203 (25%), Positives = 97/203 (47%), Gaps = 13/203 (6%)
Query: 1219 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 1278
DL G GL++AV++F+ + +F YA + I+ AI I D + +P + + NK
Sbjct: 55 DLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAI---IDDLRKQDWVPRSVHQKANK 111
Query: 1279 ISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSM----ESPVGDDEDS- 1333
++ + Q G EP + + + ++++ A+ + + E P D+++
Sbjct: 112 LADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPALILSLNEEFPCQSDDEAG 171
Query: 1334 -HLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEV 1392
L + I DE D S++ + + +L +E KV+ + + E+ L+E+
Sbjct: 172 LALEERIADERAETGYDVVDKKEFSSILAEAILALEEKERKVMALYYYEEL----VLKEI 227
Query: 1393 GKQFDVTRERIRQIEAKALRKLR 1415
GK V+ R+ QI +KAL KLR
Sbjct: 228 GKILGVSESRVSQIHSKALLKLR 250
>gnl|CDD|173779 cd01029, TOPRIM_primases, TOPRIM_primases: The
topoisomerase-primase (TORPIM) nucleotidyl
transferase/hydrolase domain found in the active site
regions of bacterial DnaG-type primases and their
homologs. Primases synthesize RNA primers for the
initiation of DNA replication. DnaG type primases are
often closely associated with DNA helicases in primosome
assemblies. The TOPRIM domain has two conserved motifs,
one of which centers at a conserved glutamate and the
other one at two conserved aspartates (DxD). This
glutamate and two aspartates, cluster together to form a
highly acid surface patch. The conserved glutamate may
act as a general base in nucleotide polymerization by
primases. The DXD motif may co-ordinate Mg2+, a cofactor
required for full catalytic function. The prototypical
bacterial primase. Escherichia coli DnaG is a single
subunit enzyme.
Length = 79
Score = 54.6 bits (132), Expect = 3e-09
Identities = 26/80 (32%), Positives = 35/80 (43%), Gaps = 24/80 (30%)
Query: 732 VLITEGYMDVIGLSQFGFF--------ANSSYT-------------CFDGDQAGRRAARR 770
V+I EGYMDV+ L Q G AN+ FD D+AG++AA R
Sbjct: 3 VIIVEGYMDVLALHQAGIKNVVAALGTANTEEQLRLLKRFARTVILAFDNDEAGKKAAAR 62
Query: 771 ALEVCLLYATDDKIIKFLFL 790
ALE+ L ++ L
Sbjct: 63 ALELLLAL---GGRVRVPPL 79
>gnl|CDD|236228 PRK08301, PRK08301, sporulation sigma factor SigE; Reviewed.
Length = 234
Score = 52.9 bits (128), Expect = 3e-07
Identities = 28/68 (41%), Positives = 40/68 (58%), Gaps = 3/68 (4%)
Query: 390 KMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRR 449
K+ G+ R + E NLRLV+ IA+K+ + G+ DLI G IGL+KAV+ F +
Sbjct: 45 KLPKGDEAVRS---LLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEK 101
Query: 450 GYKFSTYA 457
K +TYA
Sbjct: 102 KIKLATYA 109
Score = 52.9 bits (128), Expect = 3e-07
Identities = 28/68 (41%), Positives = 40/68 (58%), Gaps = 3/68 (4%)
Query: 1180 KMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRR 1239
K+ G+ R + E NLRLV+ IA+K+ + G+ DLI G IGL+KAV+ F +
Sbjct: 45 KLPKGDEAVRS---LLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEK 101
Query: 1240 GYKFSTYA 1247
K +TYA
Sbjct: 102 KIKLATYA 109
>gnl|CDD|221942 pfam13155, Toprim_2, Toprim-like. This is a family or Toprim-like
proteins.
Length = 90
Score = 42.6 bits (101), Expect = 7e-05
Identities = 22/92 (23%), Positives = 35/92 (38%), Gaps = 28/92 (30%)
Query: 734 ITEGYMDVIGLSQFGF------FANSSYT-------------------CFDGDQAGRRAA 768
+ EG +D + L Q G + T FD D+AGR+AA
Sbjct: 2 VFEGAIDALSLYQLGQENNKAVVVATLGTALTEAQAKLLKRYAKEVILAFDNDKAGRKAA 61
Query: 769 RRALEVCLLYATDDKIIKFLFLPDKYDPDSYI 800
R + + + +K + LPD D + Y+
Sbjct: 62 ERLQK---ILKEEGLEVKVVLLPDGKDWNDYL 90
>gnl|CDD|222298 pfam13662, Toprim_4, Toprim domain. The toprim domain is found in
a wide variety of enzymes involved in nucleic acid
manipulation.
Length = 81
Score = 39.1 bits (92), Expect = 0.001
Identities = 20/80 (25%), Positives = 28/80 (35%), Gaps = 24/80 (30%)
Query: 730 GYVLITEGYMDVIGLSQFGF-----FANSSYT-------------------CFDGDQAGR 765
+ I EGY DV+ L Q G+ + + FDGD AG
Sbjct: 1 STICIVEGYADVLALEQAGYKGVVAVLGGALSPLDGIGPEDLNIDVKEVILAFDGDVAGE 60
Query: 766 RAARRALEVCLLYATDDKII 785
+AA R E+ L +
Sbjct: 61 KAALRLAELLLALGVKVTRL 80
>gnl|CDD|181361 PRK08295, PRK08295, RNA polymerase factor sigma-70; Validated.
Length = 208
Score = 39.1 bits (92), Expect = 0.007
Identities = 20/56 (35%), Positives = 30/56 (53%), Gaps = 1/56 (1%)
Query: 412 LVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI-RQAIT 466
V + A+ Y G D++QEG IGL KA+ ++ + F ++A I RQ IT
Sbjct: 36 FVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCITRQIIT 91
Score = 39.1 bits (92), Expect = 0.007
Identities = 20/56 (35%), Positives = 30/56 (53%), Gaps = 1/56 (1%)
Query: 1202 LVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI-RQAIT 1256
V + A+ Y G D++QEG IGL KA+ ++ + F ++A I RQ IT
Sbjct: 36 FVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCITRQIIT 91
>gnl|CDD|240578 cd12951, RRP7_Rrp7A, RRP7 domain ribosomal RNA-processing protein 7
homolog A (Rrp7A) and similar proteins. The family
corresponds to the RRP7 domain of Rrp7A, also termed
gastric cancer antigen Zg14, and similar proteins which
are yeast ribosomal RNA-processing protein 7 (Rrp7p)
homologs mainly found in Metazoans. The cellular
function of Rrp7A remains unclear currently. Rrp7A
harbors an N-terminal RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal RRP7
domain.
Length = 129
Score = 36.9 bits (86), Expect = 0.016
Identities = 16/40 (40%), Positives = 23/40 (57%)
Query: 4 INKKTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKF 43
K + + KK K+ LKN + F I+ + R E+ LRKKF
Sbjct: 71 AAKAAEKEKKKKKKKELKNFYRFQIRESKRNELAELRKKF 110
Score = 29.2 bits (66), Expect = 8.1
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 811 KNAFSFDIKSNSREEIENLRKKF 833
KN + F I+ + R E+ LRKKF
Sbjct: 88 KNFYRFQIRESKRNELAELRKKF 110
>gnl|CDD|183523 PRK12427, PRK12427, flagellar biosynthesis sigma factor;
Provisional.
Length = 231
Score = 38.3 bits (89), Expect = 0.017
Identities = 48/208 (23%), Positives = 91/208 (43%), Gaps = 37/208 (17%)
Query: 429 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT---RSIADQARTIRIPVHMIET 485
D+ Q +GL++A+ ++ + +F+ YA IR AI R + + R +R H
Sbjct: 47 DMEQIALMGLLEALRRYGHPDE-QFAAYAVHRIRGAILDELRELDWRPRRLRQKTH---- 101
Query: 486 INKISRISRQILQETGSEPDPSVIAIKMEMPEEKIR--------KIMKIAKEPVSMESPV 537
K + R+I + G EP+ I+ ++ + E+ + ++ E +++E+
Sbjct: 102 --KTNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEYLLLENAGTLESLDELLALEAHN 159
Query: 538 GDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDH 597
+ L + I E+ L K L+ L RE +L + + EMS
Sbjct: 160 DILQSRDLEENIIIEDNL---------------KQALSQLDEREQLILHLYYQHEMS--- 201
Query: 598 TLEEVGKQFDVTRERIRQIEAKALRKLR 625
L+E+ D+T RI Q+ K +K++
Sbjct: 202 -LKEIALVLDLTEARICQLNKKIAQKIK 228
Score = 38.3 bits (89), Expect = 0.017
Identities = 48/208 (23%), Positives = 91/208 (43%), Gaps = 37/208 (17%)
Query: 1219 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT---RSIADQARTIRIPVHMIET 1275
D+ Q +GL++A+ ++ + +F+ YA IR AI R + + R +R H
Sbjct: 47 DMEQIALMGLLEALRRYGHPDE-QFAAYAVHRIRGAILDELRELDWRPRRLRQKTH---- 101
Query: 1276 INKISRISRQILQETGSEPDPSVIAIKMEMPEEKIR--------KIMKIAKEPVSMESPV 1327
K + R+I + G EP+ I+ ++ + E+ + ++ E +++E+
Sbjct: 102 --KTNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEYLLLENAGTLESLDELLALEAHN 159
Query: 1328 GDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDH 1387
+ L + I E+ L K L+ L RE +L + + EMS
Sbjct: 160 DILQSRDLEENIIIEDNL---------------KQALSQLDEREQLILHLYYQHEMS--- 201
Query: 1388 TLEEVGKQFDVTRERIRQIEAKALRKLR 1415
L+E+ D+T RI Q+ K +K++
Sbjct: 202 -LKEIALVLDLTEARICQLNKKIAQKIK 228
>gnl|CDD|219773 pfam08275, Toprim_N, DNA primase catalytic core, N-terminal domain.
Length = 128
Score = 36.5 bits (85), Expect = 0.024
Identities = 13/18 (72%), Positives = 13/18 (72%)
Query: 706 ETPLFHKSNELYGLFEAK 723
ETPLF K LYGL EAK
Sbjct: 111 ETPLFKKGKVLYGLDEAK 128
>gnl|CDD|236602 PRK09639, PRK09639, RNA polymerase sigma factor SigX; Provisional.
Length = 166
Score = 35.7 bits (83), Expect = 0.068
Identities = 17/79 (21%), Positives = 38/79 (48%), Gaps = 5/79 (6%)
Query: 547 DFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQF 606
+ E +N +P + + + V+++L +T R+ VL +RF S ++ +E+ +
Sbjct: 83 QWQEVDNEPSPEEIWIRKEEITKVQEVLAKMTERDRTVLLLRF-----SGYSYKEIAEAL 137
Query: 607 DVTRERIRQIEAKALRKLR 625
+ + A+A +K R
Sbjct: 138 GIKESSVGTTLARAKKKFR 156
Score = 35.7 bits (83), Expect = 0.068
Identities = 17/79 (21%), Positives = 38/79 (48%), Gaps = 5/79 (6%)
Query: 1337 DFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQF 1396
+ E +N +P + + + V+++L +T R+ VL +RF S ++ +E+ +
Sbjct: 83 QWQEVDNEPSPEEIWIRKEEITKVQEVLAKMTERDRTVLLLRF-----SGYSYKEIAEAL 137
Query: 1397 DVTRERIRQIEAKALRKLR 1415
+ + A+A +K R
Sbjct: 138 GIKESSVGTTLARAKKKFR 156
>gnl|CDD|225360 COG2771, CsgD, DNA-binding HTH domain-containing proteins
[Transcription].
Length = 65
Score = 33.1 bits (76), Expect = 0.100
Identities = 14/62 (22%), Positives = 30/62 (48%), Gaps = 5/62 (8%)
Query: 1367 LTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIF 1426
LTPRE ++LR+ ++ + +E+ + ++ E ++ RKL +R + +
Sbjct: 5 LTPREREILRL-----VAQGKSNKEIARILGISEETVKTHLRNIYRKLGVKNRVELVALA 59
Query: 1427 LE 1428
L
Sbjct: 60 LR 61
>gnl|CDD|234079 TIGR02984, Sig-70_plancto1, RNA polymerase sigma-70 factor,
Planctomycetaceae-specific subfamily 1. This group of
sigma factors are members of the sigma-70 family
(TIGR02937) and are apparently found only in the
Planctomycetaceae family including the genuses Gemmata
and Pirellula (in which seven sequences are found).
Length = 189
Score = 35.4 bits (82), Expect = 0.10
Identities = 19/100 (19%), Positives = 38/100 (38%), Gaps = 6/100 (6%)
Query: 531 VSMESPVGDDEDS-HLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRF 589
S+++ DE S L + + +PS A + L L +V+ +R
Sbjct: 95 QSLDAGGRLDESSVRLEAQLAADGP-SPSQVAARRESAVRLAQALAKLPEDYREVILLRH 153
Query: 590 GIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLAH 629
+S EV ++ D + + + + L +LR +
Sbjct: 154 LEGLS----FAEVAERMDRSEGAVSMLWVRGLARLRQILE 189
Score = 34.2 bits (79), Expect = 0.23
Identities = 19/96 (19%), Positives = 37/96 (38%), Gaps = 6/96 (6%)
Query: 1321 VSMESPVGDDEDS-HLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRF 1379
S+++ DE S L + + +PS A + L L +V+ +R
Sbjct: 95 QSLDAGGRLDESSVRLEAQLAADGP-SPSQVAARRESAVRLAQALAKLPEDYREVILLRH 153
Query: 1380 GIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415
+S EV ++ D + + + + L +LR
Sbjct: 154 LEGLS----FAEVAERMDRSEGAVSMLWVRGLARLR 185
>gnl|CDD|173773 cd00188, TOPRIM, Topoisomerase-primase domain. This is a
nucleotidyl transferase/hydrolase domain found in type
IA, type IIA and type IIB topoisomerases, bacterial
DnaG-type primases, small primase-like proteins from
bacteria and archaea, OLD family nucleases from
bacterial and archaea, and bacterial DNA repair proteins
of the RecR/M family. This domain has two conserved
motifs, one of which centers at a conserved glutamate
and the other one at two conserved aspartates (DxD).
This glutamate and two aspartates, cluster together to
form a highly acid surface patch. The conserved
glutamate may act as a general base in nucleotide
polymerization by primases and in strand joining in
topoisomerases and, as a general acid in strand cleavage
by topisomerases and nucleases. The DXD motif may
co-ordinate Mg2+, a cofactor required for full catalytic
function.
Length = 83
Score = 33.2 bits (76), Expect = 0.13
Identities = 14/82 (17%), Positives = 24/82 (29%), Gaps = 25/82 (30%)
Query: 731 YVLITEGYMDVIGLSQFGFFANSS-------------------------YTCFDGDQAGR 765
++I EG D + L+Q G + + D D+ G
Sbjct: 2 KLIIVEGPSDALALAQAGGYGGAVVALGGHALNKTRELLKRLLGEAKEVIIATDADREGE 61
Query: 766 RAARRALEVCLLYATDDKIIKF 787
A R LE+ + +
Sbjct: 62 AIALRLLELLKSLGKKVRRLLL 83
>gnl|CDD|214695 smart00493, TOPRIM, topoisomerases, DnaG-type primases, OLD family
nucleases and RecR proteins.
Length = 75
Score = 33.0 bits (76), Expect = 0.14
Identities = 12/70 (17%), Positives = 17/70 (24%), Gaps = 25/70 (35%)
Query: 732 VLITEGYMDVIGLSQFGFFAN----SSYT---------------------CFDGDQAGRR 766
++I EG D I L + G D D+ G
Sbjct: 3 LIIVEGPADAIALEKAGGKRGNVVALGGHLLSKEQIKLLKKLAKKAEVILATDPDREGEA 62
Query: 767 AARRALEVCL 776
A E+
Sbjct: 63 IAWELAELLK 72
>gnl|CDD|131906 TIGR02859, spore_sigH, RNA polymerase sigma-H factor. Members of
this protein family are RNA polymerase sigma-H factor
for sporulation in endospore-forming bacteria. This
protein is also called Sigma-30 and SigH. Although
rather close homologs in Listeria score above the noise
cutoff to This model, Listeria does not form spores and
the role of the related sigma factor in that genus is in
doubt [Transcription, Transcription factors, Cellular
processes, Sporulation and germination].
Length = 198
Score = 34.4 bits (79), Expect = 0.28
Identities = 24/76 (31%), Positives = 37/76 (48%)
Query: 413 VISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ 472
V + A+ Y G D+IQEG IGL KA+ F + F +A + + I +I
Sbjct: 32 VRAKARSYFLIGADKEDIIQEGMIGLYKAIRDFRPDKLSSFKAFAELCVTRQIITAIKTA 91
Query: 473 ARTIRIPVHMIETINK 488
R IP++ ++NK
Sbjct: 92 TRQKHIPLNSYVSLNK 107
Score = 34.4 bits (79), Expect = 0.28
Identities = 24/76 (31%), Positives = 37/76 (48%)
Query: 1203 VISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ 1262
V + A+ Y G D+IQEG IGL KA+ F + F +A + + I +I
Sbjct: 32 VRAKARSYFLIGADKEDIIQEGMIGLYKAIRDFRPDKLSSFKAFAELCVTRQIITAIKTA 91
Query: 1263 ARTIRIPVHMIETINK 1278
R IP++ ++NK
Sbjct: 92 TRQKHIPLNSYVSLNK 107
>gnl|CDD|131997 TIGR02952, Sig70_famx2, RNA polymerase sigma-70 factor, TIGR02952
family. This group of sigma factors are members of the
sigma-70 family (TIGR02937). They and appear by
homology, tree building, bidirectional best hits and
one-to-a-genome distribution, to represent a conserved
family. This family is found in a limited number of
Gram-positive bacterial lineages.
Length = 170
Score = 33.6 bits (77), Expect = 0.33
Identities = 17/69 (24%), Positives = 33/69 (47%), Gaps = 4/69 (5%)
Query: 557 PSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQI 616
P +A L + L LTP++ V+ +RFG + + EV + T ++ +
Sbjct: 103 PEEAILKEEANEKLLKALKILTPKQQHVIALRFG----QNLPIAEVARILGKTEGAVKIL 158
Query: 617 EAKALRKLR 625
+ +A++KL
Sbjct: 159 QFRAIKKLA 167
Score = 33.6 bits (77), Expect = 0.33
Identities = 17/69 (24%), Positives = 33/69 (47%), Gaps = 4/69 (5%)
Query: 1347 PSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQI 1406
P +A L + L LTP++ V+ +RFG + + EV + T ++ +
Sbjct: 103 PEEAILKEEANEKLLKALKILTPKQQHVIALRFG----QNLPIAEVARILGKTEGAVKIL 158
Query: 1407 EAKALRKLR 1415
+ +A++KL
Sbjct: 159 QFRAIKKLA 167
>gnl|CDD|221857 pfam12923, RRP7, Ribosomal RNA-processing protein 7 (RRP7). RRP7
is an essential protein in yeast that is involved in
pre-rRNA processing and ribosome assembly. It is
speculated to be required for correct assembly of rpS27
into the pre-ribosomal particle.
Length = 131
Score = 33.0 bits (76), Expect = 0.36
Identities = 17/39 (43%), Positives = 24/39 (61%), Gaps = 2/39 (5%)
Query: 6 KKTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFK 44
K + K KK KE L+N + F I+ +EE+ LRKKF+
Sbjct: 77 KLKEKKKKKKKE--LENFYRFQIREKKKEELAELRKKFE 113
>gnl|CDD|240576 cd12932, RRP7_like, RRP7 domain ribosomal RNA-processing protein 7
(Rrp7p), ribosomal RNA-processing protein 7 homolog A
(Rrp7A), and similar proteins. This CD corresponds to
the RRP7 domain of Rrp7p and Rrp7A. Rrp7p is encoded by
YCL031C gene from Saccharomyces cerevisiae. It is an
essential yeast protein involved in pre-rRNA processing
and ribosome assembly, and is speculated to be required
for correct assembly of rpS27 into the pre-ribosomal
particle. Rrp7A, also termed gastric cancer antigen
Zg14, is the Rrp7p homolog mainly found in Metazoans.
The cellular function of Rrp7A remains unclear
currently. Both Rrp7p and Rrp7A harbor an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal RRP7 domain.
Length = 118
Score = 32.6 bits (75), Expect = 0.41
Identities = 14/41 (34%), Positives = 24/41 (58%)
Query: 4 INKKTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFK 44
K + + KK K+ L++ + F I+ +EE+ LRKKF+
Sbjct: 72 EAKAKEKEKKKKKKKELEDFYRFQIREKKKEELAELRKKFE 112
>gnl|CDD|132028 TIGR02983, SigE-fam_strep, RNA polymerase sigma-70 factor, sigma-E
family. This group of similar sigma-70 factors includes
the sigE factor from Streptomyces coelicolor. The family
appears to include a paralagous expansion in the
Streptomycetes lineage, while related Actinomycetales
have at most two representatives.
Length = 162
Score = 33.1 bits (76), Expect = 0.52
Identities = 16/68 (23%), Positives = 33/68 (48%), Gaps = 4/68 (5%)
Query: 1349 DAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 1408
D A + ++R+ + L L R+ V+ +R+ ++S E +G + R+ +
Sbjct: 93 DPAPDVALRAALARALRRLPARQRAVVVLRYYEDLSEAQVAEALGISVGTVKSRL----S 148
Query: 1409 KALRKLRH 1416
+AL +LR
Sbjct: 149 RALARLRE 156
Score = 32.4 bits (74), Expect = 0.85
Identities = 17/70 (24%), Positives = 34/70 (48%), Gaps = 4/70 (5%)
Query: 559 DAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 618
D A + ++R+ + L L R+ V+ +R+ ++S E +G + R+ +
Sbjct: 93 DPAPDVALRAALARALRRLPARQRAVVVLRYYEDLSEAQVAEALGISVGTVKSRL----S 148
Query: 619 KALRKLRPLA 628
+AL +LR L
Sbjct: 149 RALARLRELL 158
>gnl|CDD|224511 COG1595, RpoE, DNA-directed RNA polymerase specialized sigma
subunit, sigma24 homolog [Transcription].
Length = 182
Score = 32.8 bits (75), Expect = 0.66
Identities = 14/76 (18%), Positives = 33/76 (43%), Gaps = 4/76 (5%)
Query: 550 EDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVT 609
E + ++ L ++ L L PR+ + +R+ +E + EE+ + ++
Sbjct: 101 EADPAPDLAELLLAEEELERLRRALARLPPRQREAFLLRY-LE---GLSYEEIAEILGIS 156
Query: 610 RERIRQIEAKALRKLR 625
++ +A +KLR
Sbjct: 157 VGTVKSRLHRARKKLR 172
Score = 32.8 bits (75), Expect = 0.66
Identities = 14/76 (18%), Positives = 33/76 (43%), Gaps = 4/76 (5%)
Query: 1340 EDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVT 1399
E + ++ L ++ L L PR+ + +R+ +E + EE+ + ++
Sbjct: 101 EADPAPDLAELLLAEEELERLRRALARLPPRQREAFLLRY-LE---GLSYEEIAEILGIS 156
Query: 1400 RERIRQIEAKALRKLR 1415
++ +A +KLR
Sbjct: 157 VGTVKSRLHRARKKLR 172
>gnl|CDD|235857 PRK06759, PRK06759, RNA polymerase factor sigma-70; Validated.
Length = 154
Score = 31.7 bits (72), Expect = 1.5
Identities = 16/57 (28%), Positives = 30/57 (52%), Gaps = 4/57 (7%)
Query: 570 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRP 626
VKD ++ L +E ++ RF T+ E+ + ++T ++R I +AL K+R
Sbjct: 100 VKDFMSVLDEKEKYIIFERF----FVGKTMGEIALETEMTYYQVRWIYRQALEKMRN 152
Score = 29.8 bits (67), Expect = 5.5
Identities = 16/56 (28%), Positives = 30/56 (53%), Gaps = 4/56 (7%)
Query: 1360 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415
VKD ++ L +E ++ RF T+ E+ + ++T ++R I +AL K+R
Sbjct: 100 VKDFMSVLDEKEKYIIFERF----FVGKTMGEIALETEMTYYQVRWIYRQALEKMR 151
>gnl|CDD|197715 smart00421, HTH_LUXR, helix_turn_helix, Lux Regulon. lux regulon
(activates the bioluminescence operon.
Length = 58
Score = 28.3 bits (64), Expect = 4.4
Identities = 15/51 (29%), Positives = 30/51 (58%), Gaps = 5/51 (9%)
Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 624
L SLTPRE +VLR+ ++ T +E+ ++ ++ + ++ + +RKL
Sbjct: 1 LASLTPREREVLRL-----LAEGLTNKEIAERLGISEKTVKTHLSNIMRKL 46
Score = 28.3 bits (64), Expect = 4.4
Identities = 15/51 (29%), Positives = 30/51 (58%), Gaps = 5/51 (9%)
Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 1414
L SLTPRE +VLR+ ++ T +E+ ++ ++ + ++ + +RKL
Sbjct: 1 LASLTPREREVLRL-----LAEGLTNKEIAERLGISEKTVKTHLSNIMRKL 46
>gnl|CDD|214710 smart00533, MUTSd, DNA-binding domain of DNA mismatch repair MUTS
family.
Length = 308
Score = 31.1 bits (71), Expect = 4.5
Identities = 32/175 (18%), Positives = 66/175 (37%), Gaps = 25/175 (14%)
Query: 159 EGLKDMIHAISSCPTTIMEIL---IAADKISKNEIKIDEIVD---------GLIDKNFSS 206
EGLK++ + S ++ +L I + E+ ++ + D GLI F
Sbjct: 89 EGLKEIRQLLESLDGPLLGLLLKVILEPLLELLELLLELLNDDDPLEVNDGGLIKDGFDP 148
Query: 207 NNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFE-KEG 265
++ EE++ E L+K + E I + ++ E +
Sbjct: 149 ELDELREKLEELEEELE----------ELLKKEREELGIDSLKLGYN-KVHGYYIEVTKS 197
Query: 266 YNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNK 320
+ S + RFT +++L + L ++ ++EK+IL ++ K
Sbjct: 198 EAKKVPKDFIRRSSLKN-TERFTTPELKELENELLEAKEEIERLEKEILRELLEK 251
Score = 31.1 bits (71), Expect = 4.5
Identities = 32/175 (18%), Positives = 66/175 (37%), Gaps = 25/175 (14%)
Query: 949 EGLKDMIHAISSCPTTIMEIL---IAADKISKNEIKIDEIVD---------GLIDKNFSS 996
EGLK++ + S ++ +L I + E+ ++ + D GLI F
Sbjct: 89 EGLKEIRQLLESLDGPLLGLLLKVILEPLLELLELLLELLNDDDPLEVNDGGLIKDGFDP 148
Query: 997 NNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFE-KEG 1055
++ EE++ E L+K + E I + ++ E +
Sbjct: 149 ELDELREKLEELEEELE----------ELLKKEREELGIDSLKLGYN-KVHGYYIEVTKS 197
Query: 1056 YNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNK 1110
+ S + RFT +++L + L ++ ++EK+IL ++ K
Sbjct: 198 EAKKVPKDFIRRSSLKN-TERFTTPELKELENELLEAKEEIERLEKEILRELLEK 251
>gnl|CDD|203898 pfam08281, Sigma70_r4_2, Sigma-70, region 4. Region 4 of sigma-70
like sigma-factors are involved in binding to the -35
promoter element via a helix-turn-helix motif.
Length = 54
Score = 27.8 bits (63), Expect = 5.2
Identities = 11/55 (20%), Positives = 26/55 (47%), Gaps = 4/55 (7%)
Query: 570 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 624
+ L L PR+ +V +R+ +S E+ + ++ ++ ++A +KL
Sbjct: 4 LLRALEELPPRQREVFLLRYLEGLSY----AEIAELLGISEGTVKSRLSRARKKL 54
Score = 27.8 bits (63), Expect = 5.2
Identities = 11/55 (20%), Positives = 26/55 (47%), Gaps = 4/55 (7%)
Query: 1360 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 1414
+ L L PR+ +V +R+ +S E+ + ++ ++ ++A +KL
Sbjct: 4 LLRALEELPPRQREVFLLRYLEGLSY----AEIAELLGISEGTVKSRLSRARKKL 54
>gnl|CDD|236608 PRK09652, PRK09652, RNA polymerase sigma factor RpoE; Provisional.
Length = 182
Score = 30.2 bits (69), Expect = 5.3
Identities = 27/115 (23%), Positives = 47/115 (40%), Gaps = 10/115 (8%)
Query: 520 IRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTP 579
I + K + P + + + ED L D + D + P + L+A + V+ + SL
Sbjct: 74 INYLRKQGRRPPASDVDAEEAEDFDLADALRDIS--TPENELLSAELEQRVRAAIESLPE 131
Query: 580 RESKVLRMRFGIEMSSDHTLEEVGKQFDV---T-RERIRQIEAKALRKLRPLAHD 630
+ +R IE + EE+ + T R RI + KL+PL +
Sbjct: 132 ELRTAITLRE-IE---GLSYEEIAEIMGCPIGTVRSRIFRAREALRAKLQPLLDE 182
Score = 29.4 bits (67), Expect = 8.3
Identities = 26/111 (23%), Positives = 44/111 (39%), Gaps = 14/111 (12%)
Query: 1310 IRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTP 1369
I + K + P + + + ED L D + D + P + L+A + V+ + SL
Sbjct: 74 INYLRKQGRRPPASDVDAEEAEDFDLADALRDIS--TPENELLSAELEQRVRAAIESLPE 131
Query: 1370 RESKVLRMRFGIEMSSDHTLEEVGKQFDV---T-RERIRQIEAKALRKLRH 1416
+ +R IE + EE+ + T R RI +A LR
Sbjct: 132 ELRTAITLRE-IE---GLSYEEIAEIMGCPIGTVRSRIF----RAREALRA 174
>gnl|CDD|205895 pfam13720, Acetyltransf_11, Udp N-acetylglucosamine
O-acyltransferase; Domain 2. This is domain 2, or the
C-terminal domain, of Udp N-acetylglucosamine
O-acyltransferase. This enzyme is a zinc-dependent
enzyme that catalyzes the deacetylation of
UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine to
form UDP-3-O-(R-hydroxymyristoyl)glucosamine and
acetate.
Length = 82
Score = 28.2 bits (64), Expect = 6.9
Identities = 14/48 (29%), Positives = 26/48 (54%), Gaps = 5/48 (10%)
Query: 32 SREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESII 79
S+EEI L++ +++L + G LT E + L E+ D ++ +I
Sbjct: 29 SKEEIRALKRAYRLLYRSG-----LTLEEALEELEEEAPDSPEVQELI 71
Score = 28.2 bits (64), Expect = 6.9
Identities = 14/48 (29%), Positives = 26/48 (54%), Gaps = 5/48 (10%)
Query: 822 SREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESII 869
S+EEI L++ +++L + G LT E + L E+ D ++ +I
Sbjct: 29 SKEEIRALKRAYRLLYRSG-----LTLEEALEELEEEAPDSPEVQELI 71
>gnl|CDD|216500 pfam01432, Peptidase_M3, Peptidase family M3. This is the Thimet
oligopeptidase family, large family of mammalian and
bacterial oligopeptidases that cleave medium sized
peptides. The group also contains mitochondrial
intermediate peptidase which is encoded by nuclear DNA
but functions within the mitochondria to remove the
leader sequence.
Length = 450
Score = 30.4 bits (69), Expect = 7.5
Identities = 16/58 (27%), Positives = 25/58 (43%), Gaps = 4/58 (6%)
Query: 793 KYDPDSYIRKFGYKIFSKKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSE 850
K PD RK Y+ F + N+ E L + K+ +L K GY +++E
Sbjct: 3 KESPDRETRKKAYRAFYSRAEAY----RNTLENSALLEELLKLRAELAKLLGYPSYAE 56
>gnl|CDD|107310 cd06315, PBP1_ABC_sugar_binding_like_6, Periplasmic sugar-binding
domain of uncharacterized ABC-type transport systems.
Periplasmic sugar-binding domain of uncharacterized
ABC-type transport systems that share homology with a
family of pentose/hexose sugar-binding proteins of the
type I periplasmic binding protein superfamily, which
consists of two domains connected by a three-stranded
hinge. The substrate specificity of this group is not
known, but it is predicted to be involved in the
transport of sugar-containing molecules and chemotaxis.
Length = 280
Score = 30.0 bits (68), Expect = 7.9
Identities = 25/109 (22%), Positives = 43/109 (39%), Gaps = 20/109 (18%)
Query: 95 DTETLMLSNITSD-DDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 153
E + N+T+D V E AAL + + G+ V + T D I
Sbjct: 96 IEEPGIFYNVTTDPLAVAEV--AALYAIANSGGKAG------------VVIFT-DSRFSI 140
Query: 154 AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDK 202
AK +K++I A C T++ I IS+ ++ + L+ +
Sbjct: 141 AKAKANAMKEIIEACKGC--TVLSIEDVP--ISRTATRMPALTARLLQR 185
Score = 30.0 bits (68), Expect = 7.9
Identities = 25/109 (22%), Positives = 43/109 (39%), Gaps = 20/109 (18%)
Query: 885 DTETLMLSNITSD-DDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 943
E + N+T+D V E AAL + + G+ V + T D I
Sbjct: 96 IEEPGIFYNVTTDPLAVAEV--AALYAIANSGGKAG------------VVIFT-DSRFSI 140
Query: 944 AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDK 992
AK +K++I A C T++ I IS+ ++ + L+ +
Sbjct: 141 AKAKANAMKEIIEACKGC--TVLSIEDVP--ISRTATRMPALTARLLQR 185
>gnl|CDD|181072 PRK07661, PRK07661, acetyl-CoA acetyltransferase; Provisional.
Length = 391
Score = 30.1 bits (68), Expect = 8.8
Identities = 23/82 (28%), Positives = 33/82 (40%), Gaps = 20/82 (24%)
Query: 554 MLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIE-------MSSDHTLEEVGKQF 606
ML S+A + S+ SL P V+R + M HT E+V ++
Sbjct: 105 MLGHSEAVIAGGAESM------SLVPMMGHVVRPNPRLVEAAPEYYMGMGHTAEQVAVKY 158
Query: 607 DVTRE-------RIRQIEAKAL 621
++RE R Q AKAL
Sbjct: 159 GISREDQDAFAVRSHQRAAKAL 180
Score = 30.1 bits (68), Expect = 8.8
Identities = 23/82 (28%), Positives = 33/82 (40%), Gaps = 20/82 (24%)
Query: 1344 MLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIE-------MSSDHTLEEVGKQF 1396
ML S+A + S+ SL P V+R + M HT E+V ++
Sbjct: 105 MLGHSEAVIAGGAESM------SLVPMMGHVVRPNPRLVEAAPEYYMGMGHTAEQVAVKY 158
Query: 1397 DVTRE-------RIRQIEAKAL 1411
++RE R Q AKAL
Sbjct: 159 GISREDQDAFAVRSHQRAAKAL 180
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.318 0.135 0.372
Gapped
Lambda K H
0.267 0.0735 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 74,116,806
Number of extensions: 7757221
Number of successful extensions: 10450
Number of sequences better than 10.0: 1
Number of HSP's gapped: 10270
Number of HSP's successfully gapped: 331
Length of query: 1432
Length of database: 10,937,602
Length adjustment: 109
Effective length of query: 1323
Effective length of database: 6,103,016
Effective search space: 8074290168
Effective search space used: 8074290168
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 65 (28.8 bits)