RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddB 
           21,608 sequences; 5,994,473 total letters

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

Query= gi|254780611|ref|YP_003065024.1| RNA polymerase factor sigma-32
[Candidatus Liberibacter asiaticus str. psy62]
         (302 letters)



>gnl|CDD|180635 PRK06596, PRK06596, RNA polymerase factor sigma-32; Reviewed.
          Length = 284

 Score =  459 bits (1184), Expect = e-130
 Identities = 139/287 (48%), Positives = 187/287 (65%), Gaps = 6/287 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M +    + ++ E  L  YI  + KIPML  +EEY+LAKR REHGDL AA +LV SHLR 
Sbjct: 1   MTKALQLLALSPEGNLDAYIQAVNKIPMLTAEEEYMLAKRLREHGDLEAAKQLVLSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA GYRGYGLP ++++ EGNIGLM+AVK+FDPE G RL ++++ WIKA + EYILR+
Sbjct: 61  VVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L       L PE+V  +A++L VSE EV  M  RL
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKAKKRLGW-----LNPEEVEMVAEELGVSEEEVREMESRL 175

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +G D SL+A I+  D+ S   QD+L         VL E      RR +L  ++  L+ R 
Sbjct: 176 SGQDASLDAPIDDDDEESGAPQDYLEDKSSDPADVLEEDNWEDQRRALLADALEGLDERS 235

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R I EAR L ++  TL+ L++E+ VS ERVRQIE  A KK++ +I+ 
Sbjct: 236 RDIIEARWLDDDKSTLQELAAEYGVSAERVRQIEKNAMKKLKAAIEA 282


>gnl|CDD|162835 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.
          Length = 270

 Score =  382 bits (983), Expect = e-107
 Identities = 137/268 (51%), Positives = 184/268 (68%), Gaps = 5/268 (1%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L  YI  + +IPML  +EEY LAKR REHGDL AA +LV SHLR VVKIA GYRGYGLP
Sbjct: 2   SLDAYIRAVNRIPMLTPEEEYQLAKRLREHGDLDAAKKLVLSHLRFVVKIARGYRGYGLP 61

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
            ++++ EGNIGLM+AVK+FDPERG RL ++++ WIKA + EYILR+W LVK+ TT  Q++
Sbjct: 62  QADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYILRNWRLVKVATTKAQRK 121

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSS 193
           LFFNLR++K  LQ   +    PE+V AIA++L VSE EV  M  RL+G D SLNA I+  
Sbjct: 122 LFFNLRKMKKRLQGWLN----PEEVEAIAEELGVSEREVREMESRLSGQDMSLNASIDDD 177

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           + +      +LV      E  L E++  + +R  L  ++  L+ R RRI EAR L ++ +
Sbjct: 178 EDDGGAPIAYLVDKTSDPEDTLEEEQWEELQRQALANALGSLDARSRRIIEARWLDDDKL 237

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TL+ L++E+ VS ER+RQIE  A KK++
Sbjct: 238 TLQELAAEYGVSAERIRQIEKNAMKKLK 265


>gnl|CDD|181003 PRK07500, rpoH2, RNA polymerase factor sigma-32; Reviewed.
          Length = 289

 Score =  264 bits (678), Expect = 1e-71
 Identities = 115/264 (43%), Positives = 178/264 (67%), Gaps = 1/264 (0%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K P LE++EE+ LA R+++H D  A HR++++H+RLV+ +A  +R +GLP+++++ EG +
Sbjct: 17  KAPYLEREEEHALAYRWKDHRDEDALHRIISAHMRLVISMAGKFRRFGLPMNDLIQEGYV 76

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A  +F+P+R  R +TY+ WWI+A++Q+YILR+WS+V+ GT++ QK LFFNLRRL+ 
Sbjct: 77  GLLEAAARFEPDREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQKALFFNLRRLRA 136

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDW 203
            L    +   K E    IA  L VS S+V  M+ RL+G D SLNA  +  D+  S+  D+
Sbjct: 137 RLAQADEELTKQEIHREIATALGVSLSDVEMMDARLSGPDASLNAPQSEEDEGRSERMDF 196

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           LV D    ++ +    + + RR  LT+++  LN RE RI   RRL+E+  TLE L  E  
Sbjct: 197 LVDDSPLPDEQVESSIDGERRRRWLTQALQTLNERELRIIRERRLREDGATLEALGEELG 256

Query: 264 VSRERVRQIEARAFKKVQESIQKQ 287
           +S+ERVRQIEARA +K++ ++  Q
Sbjct: 257 ISKERVRQIEARALEKLRRALLSQ 280


>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).
          Length = 285

 Score =  134 bits (338), Expect = 4e-32
 Identities = 84/279 (30%), Positives = 139/279 (49%), Gaps = 29/279 (10%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD  A   ++ S+LRLVV IA  Y   GLP+ ++
Sbjct: 18  YLREIGFKPLLTAEEEIAYARRALA-GDFEARKVMIESNLRLVVSIAKHYVNRGLPLLDL 76

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 77  IEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIERAIMNQARTIRLPVHV-IKELNVY 135

Query: 139 LRRLKGHLQAITDNNLKPEQVVA--------IAKKLNVSESEVISMNCRLAGDESLNALI 190
           LR  +  L+         E++          +++ L ++E  + S++  L  D S + L 
Sbjct: 136 LRAAR-QLEKKLGREPSVEEIAELLDKPVEDVSRVLALNER-ITSLDAPLDDDSSKSLLD 193

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RL 248
             +D+                E ++   + ++     L      LN R+R +   R   L
Sbjct: 194 TIADEQ-----------SIDPESLVQNDDLKQLIEAWLAE----LNERQREVLARRFGLL 238

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              P TLE +++E  ++RERVRQI+  A KK++  +++ 
Sbjct: 239 GYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRILERD 277


>gnl|CDD|180185 PRK05657, PRK05657, RNA polymerase sigma factor RpoS; Validated.
          Length = 325

 Score =  125 bits (315), Expect = 2e-29
 Identities = 91/289 (31%), Positives = 144/289 (49%), Gaps = 49/289 (16%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A+R    GD +A  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 58  YLNEIGYSPLLTAEEEVYFARRALR-GDFAARQRMIESNLRLVVKIAKRYLNRGLALLDL 116

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+            NQ R    
Sbjct: 117 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIM------------NQTR---T 161

Query: 139 LR-------------RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE- 184
           +R             R    L+   D+    E+   IA+ L+    +V  M   LA +E 
Sbjct: 162 IRLPVHVVKELNVYLRAARELEHKLDHEPSAEE---IAELLDKPVDDVSRM---LALNER 215

Query: 185 --SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR-RNMLTRSMSVLNPRERR 241
             SL+  +   D   S   D L  + +   +   + ++ K      L      LN ++R 
Sbjct: 216 ITSLDTPL-GGDPEKS-LLDILADEQENGPEDTTQDDDMKQSIVKWLFE----LNDKQRE 269

Query: 242 IFEARRLQEN---PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +   RR         TLE+++ E  ++RERVRQI+  A ++++E +Q Q
Sbjct: 270 VLA-RRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLREILQTQ 317


>gnl|CDD|163097 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 =  119 bits (301), Expect = 9e-28
 Identities = 87/316 (27%), Positives = 143/316 (45%), Gaps = 80/316 (25%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYRE---------------HGDLS--------------- 48
           Y+ EI ++P+L  +EE  LA++ ++                 + S               
Sbjct: 6   YLQEIGRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAEL 65

Query: 49  ---------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
                    A  +++ ++LRLVV +A  Y+  GL + +++ EG++GL +AV+KFDP RG+
Sbjct: 66  RQRLRQGQRAKEKMIKANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGY 125

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD--NNLKPE 157
           + +TY+ WWI+  +   I            ANQ R      RL  H   IT+  N +K  
Sbjct: 126 KFSTYAYWWIRQGITRAI------------ANQSRTI----RLPIH---ITEKLNKIKKV 166

Query: 158 Q------------VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
           Q               IA+ L +   +V  +  R     SL+A +   +   ++  D L 
Sbjct: 167 QRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEED--TELGDLLE 224

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFE 263
            D +  E+ +    ER++ R  L   ++ L PRER++   R       P+TL  +     
Sbjct: 225 DDGESPEEQV----ERESLRQDLESLLAELTPRERQVLRLRFGLDGGEPLTLAEIGRRLN 280

Query: 264 VSRERVRQIEARAFKK 279
           +SRERVRQIEA+A +K
Sbjct: 281 LSRERVRQIEAKALRK 296


>gnl|CDD|162836 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.
          Length = 238

 Score =  107 bits (270), Expect = 3e-24
 Identities = 73/238 (30%), Positives = 119/238 (50%), Gaps = 22/238 (9%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +LV S+LRLVV IA  Y   GL   +++ EGNIGLM+AV+KFD  +G++ +TY+ WW
Sbjct: 1   AKKQLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWW 60

Query: 109 IKAAMQEYILRSWSLVKI----GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T N+      L + +  L          E+   +A+
Sbjct: 61  IRQAITRAIADQARTIRIPVHMVETINK------LIKAERQLTQELGREPTDEE---LAE 111

Query: 165 KLNVSESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           ++ +   +V  +  ++A +  SL   I   +   S   D+ + D   +     +   ++ 
Sbjct: 112 RMGMPAEKVREIK-KIAQEPISLETPIGEEED--SFLGDF-IEDTSIESP--DDYAAKEL 165

Query: 224 RRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
            R  L   +  L  RER++   R   L   P TLE +  EF V+RER+RQIE++A +K
Sbjct: 166 LREQLDEVLETLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRK 223


>gnl|CDD|181701 PRK09210, PRK09210, RNA polymerase sigma factor RpoD; Validated.
          Length = 367

 Score = 96.6 bits (241), Expect = 8e-21
 Identities = 46/94 (48%), Positives = 65/94 (69%), Gaps = 1/94 (1%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L  +EE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 101 YLKEIGRVPLLTAEEEIELAKRI-EEGDEEAKQRLAEANLRLVVSIAKRYVGRGMLFLDL 159

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           + EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A
Sbjct: 160 IQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQA 193



 Score = 41.1 bits (97), Expect = 3e-04
 Identities = 15/26 (57%), Positives = 20/26 (76%)

Query: 254 TLENLSSEFEVSRERVRQIEARAFKK 279
           TLE +   F V+RER+RQIEA+A +K
Sbjct: 327 TLEEVGKVFGVTRERIRQIEAKALRK 352


>gnl|CDD|181056 PRK07598, PRK07598, RNA polymerase sigma factor SigC; Validated.
          Length = 415

 Score = 88.0 bits (218), Expect = 3e-18
 Identities = 67/238 (28%), Positives = 127/238 (53%), Gaps = 13/238 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           L A   ++ ++LRLVV +A  Y+  GL + ++V EG +GL +AV+KFDP +G+R +TY+ 
Sbjct: 174 LRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAY 233

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   I      +++     +K     L ++K   + I+    +   +  IA++L
Sbjct: 234 WWIRQGITRAIATQSRTIRLPVHITEK-----LNKIKKAQRKISQEKGRTPTIEDIAQEL 288

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            ++ ++V  +  R+    SL   +   DK+ ++  D L  D    E++L+    R++ + 
Sbjct: 289 EMTPTQVREVLLRVPRSVSLETKV-GKDKD-TELGDLLETDDISPEEMLM----RESLQR 342

Query: 227 MLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            L   ++ L  RER +   R      +  +L  +    ++SRERVRQIE++A +K+++
Sbjct: 343 DLQHLLADLTSRERDVIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESKALQKLRQ 400


>gnl|CDD|181169 PRK07921, PRK07921, RNA polymerase sigma factor SigB; Reviewed.
          Length = 324

 Score = 84.4 bits (209), Expect = 3e-17
 Identities = 89/314 (28%), Positives = 135/314 (42%), Gaps = 82/314 (26%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH-----GDLSAAHR---------------- 52
           Y++ I K  +L   +E  LAKR     Y EH       LS A +                
Sbjct: 31  YLNGIGKTALLTAADEVELAKRIEAGLYAEHLLETRKRLSEARKRDLAAVVRDGEAARRH 90

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +GF+ +TY+ WWI+ A
Sbjct: 91  LLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQA 150

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
               I R          A+Q R      RL  HL          EQV     KL   + E
Sbjct: 151 ----ITRG--------MADQSRTI----RLPVHLV---------EQV----NKLARIKRE 181

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD--------GQEQV-----LIEKE 219
              ++ +L  + +   L   S     +  D L +  D        G ++       IE  
Sbjct: 182 ---LHQQLGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDS 238

Query: 220 ERKNRRNMLTRSM------SVLNPRERRIFEARRLQ-----ENPVTLENLSSEFEVSRER 268
           E  +  N +   +      SVL   + R  +  RL+       P TL+ +   F +SRER
Sbjct: 239 EATSAENAVIAGLLHTDIRSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRER 298

Query: 269 VRQIEARAFKKVQE 282
           VRQIE     K++ 
Sbjct: 299 VRQIEREVMSKLRN 312


>gnl|CDD|180310 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional.
          Length = 509

 Score = 79.3 bits (196), Expect = 1e-15
 Identities = 40/120 (33%), Positives = 62/120 (51%), Gaps = 26/120 (21%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR----------YREHGDLSAAHR---------------- 52
           Y+ +I K+ +L  +EE  LAKR            E   L    R                
Sbjct: 216 YLKQIGKVKLLNAEEEVELAKRIEAGLYAEELLAEGEKLDPELRRDLQWIGRDGKRAKNH 275

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y   GL   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A
Sbjct: 276 LLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQA 335



 Score = 41.1 bits (97), Expect = 3e-04
 Identities = 14/37 (37%), Positives = 25/37 (67%)

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           P TL+ +   + V+RER+RQIE++  +K++   + QV
Sbjct: 467 PKTLDEIGQVYGVTRERIRQIESKTLRKLRHPSRSQV 503


>gnl|CDD|180321 PRK05949, PRK05949, RNA polymerase sigma factor; Validated.
          Length = 327

 Score = 74.1 bits (182), Expect = 4e-14
 Identities = 68/299 (22%), Positives = 136/299 (45%), Gaps = 52/299 (17%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR--------------------------YREHGDLS---- 48
           Y+HEI ++P+L  ++E V  K+                          + E  +LS    
Sbjct: 23  YLHEIGRVPLLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETEL 82

Query: 49  ---------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
                    A  +++ ++LRLVV IA  Y+   +   +++ EG +GL + V+KFDP RG+
Sbjct: 83  KQTLKQGKRAKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGY 142

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY+ WWI+ A+   I +    +++     +K     L ++K   + ++    +    
Sbjct: 143 KFSTYAYWWIRQAITRAIAQQARTIRLPIHITEK-----LNKIKKTQRELSQKLGRSATP 197

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             IAK+L +  S++          + ++  +   D   ++  + L  +    +Q + ++ 
Sbjct: 198 AEIAKELELEPSQI--REYLSMARQPISLDVRVGDNQDTELSELLEDEGPSPDQYITQEL 255

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARA 276
            R++  N+L      L P++R +   R   E+   ++L  +     +SRERVRQ+E +A
Sbjct: 256 LRQDLNNLLAE----LTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQA 310


>gnl|CDD|180964 PRK07406, PRK07406, RNA polymerase sigma factor RpoD; Validated.
          Length = 373

 Score = 71.7 bits (176), Expect = 2e-13
 Identities = 34/97 (35%), Positives = 54/97 (55%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
            E       E  +  +   R R      A  ++V S+LRLVV IA  Y   GL   +++ 
Sbjct: 109 REPSDKEWAELVDMPLPKFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQ 168

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           EG++GL++A +KFD E+G++ +TY+ WWI+ A+   I
Sbjct: 169 EGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAI 205



 Score = 42.1 bits (99), Expect = 2e-04
 Identities = 22/51 (43%), Positives = 31/51 (60%), Gaps = 10/51 (19%)

Query: 235 LNPRERRIFEAR------RLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
           L+PRER +   R      R++    TLE +   F V+RER+RQIEA+A +K
Sbjct: 312 LSPRERDVLRLRYGLDDGRMK----TLEEIGQIFNVTRERIRQIEAKALRK 358


>gnl|CDD|180186 PRK05658, PRK05658, RNA polymerase sigma factor RpoD; Validated.
          Length = 619

 Score = 70.2 bits (173), Expect = 5e-13
 Identities = 32/69 (46%), Positives = 46/69 (66%), Gaps = 4/69 (5%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ 
Sbjct: 384 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 443

Query: 112 AMQEYILRS 120
           A    I RS
Sbjct: 444 A----ITRS 448



 Score = 42.5 bits (101), Expect = 1e-04
 Identities = 23/59 (38%), Positives = 36/59 (61%), Gaps = 2/59 (3%)

Query: 223 NRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVRQIEARAFKK 279
           + R   T  ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K
Sbjct: 545 SLREATTDVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRK 603


>gnl|CDD|163094 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 = 70.3 bits (173), Expect = 6e-13
 Identities = 64/240 (26%), Positives = 112/240 (46%), Gaps = 25/240 (10%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           +LV  +L LV  IA  +R  G P  ++V  G IGL++A+ +FDP  G + +T+++  I  
Sbjct: 7   KLVELNLPLVRSIARRFRNRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPTIMG 66

Query: 112 AMQEYILR--SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
            ++ +  R  +W+ V++     +  L     ++    + +T    +   +  IA++L VS
Sbjct: 67  EIKRF-FRDDTWA-VRVPRRLKELGL-----KINKATEELTQRLGRSPTIAEIAEELGVS 119

Query: 170 ESEVISMNCRLAGD----ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           E EV+      AG+     SL+A I   D +     D L  + D  E V          R
Sbjct: 120 EEEVVE--ALEAGNSYSALSLDAPIEDDDGDPIALLDTLGDEDDALETVE--------DR 169

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             L   ++ L  RERRI   R  ++   T   ++    +S+  V ++  RA KK++E + 
Sbjct: 170 LALKPLLAALPERERRILLLRFFED--KTQSEIAERLGISQMHVSRLLRRALKKLREQLL 227


>gnl|CDD|162877 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 = 65.4 bits (160), Expect = 2e-11
 Identities = 59/236 (25%), Positives = 103/236 (43%), Gaps = 21/236 (8%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPIS----EVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           L+  +L LV +IA      GLP S    +++  G  GL+ A++++DP RG +  TY++  
Sbjct: 1   LIRRYLPLVKRIAGRLSV-GLPSSVELDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQR 59

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ AM +  LR    V        ++    L R    L+A        E+   IA++L +
Sbjct: 60  IRGAMLDE-LRRLDWVPRSLRQKARK----LERAIRELEARLGREPTEEE---IAEELGM 111

Query: 169 SESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
              E       +      SL+ L+ S D   S          +  E+ L    ER+  R 
Sbjct: 112 DLKEYRQALNEINALSLVSLDELLESGDDGGSLIDRIEDDKSEDPEEEL----EREELRE 167

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            L  ++  L+ RE+ +      +E  + L+ +     ++  RV QI ++A KK++ 
Sbjct: 168 ALAEAIESLSEREQLVLSLYYYEE--LNLKEIGEVLGLTESRVSQIHSQALKKLRA 221


>gnl|CDD|180963 PRK07405, PRK07405, RNA polymerase sigma factor SigD; Validated.
          Length = 317

 Score = 63.6 bits (155), Expect = 5e-11
 Identities = 36/138 (26%), Positives = 63/138 (45%), Gaps = 39/138 (28%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS------------------------------ 48
           Y+ EI ++P+L  +EE +  K+ +    L                               
Sbjct: 13  YLREIGRVPLLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAAKLSEEEL 72

Query: 49  ---------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
                    A  ++V ++LRLVV +A  Y    + + +++ EG IG+ + V+KFDP +G+
Sbjct: 73  RSAIAEGEAAKRKMVEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGY 132

Query: 100 RLATYSMWWIKAAMQEYI 117
           R +TY+ WWI+ A+   I
Sbjct: 133 RFSTYAYWWIRQAITRAI 150



 Score = 38.2 bits (89), Expect = 0.003
 Identities = 21/61 (34%), Positives = 33/61 (54%), Gaps = 2/61 (3%)

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +  L R M  L P+++ +   R   E+  P+TL  +     +SRERVRQIE  A  K+++
Sbjct: 247 QLDLERLMEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRK 306

Query: 283 S 283
            
Sbjct: 307 R 307


>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.
          Length = 234

 Score = 63.3 bits (154), Expect = 7e-11
 Identities = 37/100 (37%), Positives = 57/100 (57%), Gaps = 2/100 (2%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
            E    P+  ++EE +L K     GD SA   L+  +LRLVV IA  +   G+ I ++VS
Sbjct: 27  SEALPPPLTGEEEEALLQKL--TQGDESAKSTLIERNLRLVVYIARKFENTGIGIEDLVS 84

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
            G IGL++AV  F+P +  +LATY+   I+  +  Y+ R+
Sbjct: 85  IGTIGLIKAVNTFNPSKKIKLATYASRCIENEILMYLRRN 124


>gnl|CDD|181367 PRK08301, PRK08301, sporulation sigma factor SigE; Reviewed.
          Length = 234

 Score = 62.6 bits (153), Expect = 1e-10
 Identities = 32/78 (41%), Positives = 47/78 (60%), Gaps = 1/78 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE  L  +    GD +    L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 32  PPLSKEEEEYLLNKL-PKGDEAVRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGL 90

Query: 87  MQAVKKFDPERGFRLATY 104
           ++AV  F+PE+  +LATY
Sbjct: 91  IKAVNTFNPEKKIKLATY 108



 Score = 28.3 bits (64), Expect = 2.8
 Identities = 8/22 (36%), Positives = 15/22 (68%)

Query: 225 RNMLTRSMSVLNPRERRIFEAR 246
           R +L +++  L+ RE++I E R
Sbjct: 169 RKLLKKALKKLSDREKQIMELR 190


>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.
          Length = 227

 Score = 60.1 bits (146), Expect = 6e-10
 Identities = 31/79 (39%), Positives = 50/79 (63%), Gaps = 2/79 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+ E++E+  L  R +E GD  A + L+  +LRLV  I   +   G  + +++S G IGL
Sbjct: 29  PLSEEEEKKYL-DRLKE-GDEEARNVLIERNLRLVAHIVKKFSNTGEDVDDLISIGTIGL 86

Query: 87  MQAVKKFDPERGFRLATYS 105
           ++A+  FDP++G RLATY+
Sbjct: 87  IKAIDSFDPDKGTRLATYA 105



 Score = 35.5 bits (82), Expect = 0.016
 Identities = 21/71 (29%), Positives = 32/71 (45%), Gaps = 2/71 (2%)

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERV 269
              +IE+ E       L + +SVL+ RER + E R         T   ++    +SR  V
Sbjct: 152 GDSVIEQVELNLEIKKLYKKLSVLDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYV 211

Query: 270 RQIEARAFKKV 280
            +IE RA  K+
Sbjct: 212 SRIEKRALMKL 222


>gnl|CDD|180266 PRK05803, PRK05803, sporulation sigma factor SigK; Reviewed.
          Length = 233

 Score = 60.0 bits (146), Expect = 7e-10
 Identities = 28/78 (35%), Positives = 47/78 (60%), Gaps = 2/78 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+ E++E   L +  +E GD  A + L+  +LRLV  I   +   G  + +++S G IGL
Sbjct: 30  PLSEEEERKYL-ELMKE-GDEEARNILIERNLRLVAHIVKKFENTGEDVDDLISIGTIGL 87

Query: 87  MQAVKKFDPERGFRLATY 104
           ++A++ FD  +G +LATY
Sbjct: 88  IKAIESFDAGKGTKLATY 105



 Score = 32.6 bits (75), Expect = 0.13
 Identities = 26/100 (26%), Positives = 43/100 (43%), Gaps = 13/100 (13%)

Query: 201 QDWLVYDHDGQEQVLI-----------EKEERKNRRNMLTRSMSVLNPRERRIFEARR-- 247
           QD +  D +G E  LI           E+ E K     L + + +L+ RE+ + E R   
Sbjct: 131 QDPIGVDKEGNEISLIDILGSEEDDVIEQVELKMEVEKLYKKIDILDEREKEVIEMRYGL 190

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
                 T   ++    +SR  V +IE RA KK+ + + + 
Sbjct: 191 GNGKEKTQREIAKALGISRSYVSRIEKRALKKLFKELYRA 230


>gnl|CDD|181489 PRK08583, PRK08583, RNA polymerase sigma factor SigB; Validated.
          Length = 257

 Score = 58.6 bits (142), Expect = 2e-09
 Identities = 64/272 (23%), Positives = 124/272 (45%), Gaps = 40/272 (14%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE-VVSEGNIGLM 87
           L K+E       Y+E+ D  A  +LV  +  LV  +A  Y   G    E +V  G +GL+
Sbjct: 10  LTKEEVNKWIAEYQENQDEEAQEKLVKHYKNLVESLAYKY-SKGQSHHEDLVQVGMVGLL 68

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWS------LVKIGTTANQKRLFFNLR 140
            A++++DP  G     +++  I   ++ Y+  ++WS      + ++G             
Sbjct: 69  GAIRRYDPSFGRSFEAFAVPTIIGEIKRYLRDKTWSVHVPRRIKELGP------------ 116

Query: 141 RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL-INSSDKNSSQ 199
           ++K  +  +T    +  ++  IA +L VSE EV+     +   +S  AL ++ S +  S 
Sbjct: 117 KIKKAVDELTTELQRSPKISEIADRLGVSEEEVLEA---MEMGKSYQALSVDHSIEADSD 173

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
                + D  GQ++   +  E   +R +L + + VL+ RE+ I +          +ENLS
Sbjct: 174 GSTVTLLDIVGQQE---DGYELTEQRMILEKILPVLSDREKSIIQC-------TFIENLS 223

Query: 260 SE-----FEVSRERVRQIEARAFKKVQESIQK 286
            +       +S+  V +++ +A KK++E+   
Sbjct: 224 QKETGERLGISQMHVSRLQRQAIKKLREAAFL 255


>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 = 57.6 bits (139), Expect = 4e-09
 Identities = 58/270 (21%), Positives = 120/270 (44%), Gaps = 36/270 (13%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L K++       ++++ +  A  +LV  +  LV  IA  Y   G    ++V  G +GL+ 
Sbjct: 10  LTKEDVIQWIAEFQQNQNGEAQEKLVDHYQNLVYSIAYKYSKGGPMHEDLVQVGMLGLLG 69

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           A++++D   G     +++  I   ++ Y+  ++WS+         +R+     ++K  + 
Sbjct: 70  AIRRYDYSIGNAFEPFAIPTIIGEIKRYLRDKTWSV------HVPRRIKELGPKIKKAID 123

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI------NSSDKNSSQWQ 201
            +TD+  +  +++ IA  L +SE EV+ +   +   +S  AL         SD ++    
Sbjct: 124 ELTDHLQRSPKIIEIADHLGLSEEEVLEI---MEMGQSYRALSVDDVIEADSDGSTVARL 180

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
           D +    DG +Q          RR +L + + +L+ RE+ I             ENLS +
Sbjct: 181 DSVGEVEDGYDQT--------ERRMVLEKILPILSEREKSIIHC-------TFEENLSQK 225

Query: 262 -----FEVSRERVRQIEARAFKKVQESIQK 286
                  +S+  V +++ +A  K++E+   
Sbjct: 226 ETGERLGISQMHVSRLQRQAISKLKEAAFL 255


>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.
          Length = 254

 Score = 55.6 bits (134), Expect = 2e-08
 Identities = 66/266 (24%), Positives = 114/266 (42%), Gaps = 29/266 (10%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+ QE   L  R +  GD +A  +L+  +LRLV+ +   +   G  + ++   G I
Sbjct: 12  KLPVLKNQEMRELFIRMQS-GDTTAREKLINGNLRLVLSVIQRFNNRGEYVDDLFQVGCI 70

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEY------ILRSWSLVKIGTTANQKRLFFN 138
           GLM+++  FD  +  + +TY++  I   ++ Y      I  S SL  I   A Q R    
Sbjct: 71  GLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNPIRVSRSLRDIAYKALQVR---- 126

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
                     +   N K   V  IAK+L V + EV+     +    SL   I +   +  
Sbjct: 127 --------DKLISENSKEPTVSEIAKELKVPQEEVVFALDAIQDPVSLFEPIYNDGGDPI 178

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
              D +  + +   Q L            L  +M  LN RE+ I   R  +    T   +
Sbjct: 179 YVMDQISDEKNKDSQWLEGIA--------LKEAMKRLNEREKMILNMRFFEGK--TQMEV 228

Query: 259 SSEFEVSRERVRQIEARAFKKVQESI 284
           + E  +S+ +V ++E  A K +++ +
Sbjct: 229 AEEIGISQAQVSRLEKAALKHMRKYV 254


>gnl|CDD|180512 PRK06288, PRK06288, RNA polymerase sigma factor WhiG; Reviewed.
          Length = 268

 Score = 54.3 bits (131), Expect = 4e-08
 Identities = 70/260 (26%), Positives = 119/260 (45%), Gaps = 21/260 (8%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP----ISEVV 79
            KIP   +Q+E  L + Y++ GD      L+  +  LV  +A G    G+P      ++V
Sbjct: 7   GKIPKYAQQDETELWREYKKTGDPKIREYLILKYSPLVKYVA-GRIAVGMPQNVEFDDLV 65

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
           S G  GL+ A++KFDPER  +  TY++  I+ A+ +  LR  S+  I  +  QK     +
Sbjct: 66  SYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIFDE-LR--SIDWIPRSVRQKAR--QI 120

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNS 197
            R    L+A        E+   IA +L +S  E  S+  +L+G    SLN L    D+  
Sbjct: 121 ERAIAMLEARLGRTPSDEE---IADELGISLEEYNSLLSKLSGTSVVSLNDLWFGGDEGD 177

Query: 198 S-QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
                D L          + E+EE K    ++  ++  L  RE+++      ++  +TL+
Sbjct: 178 EVSLMDTLESPAALNPDEIAEREEIK---RVIVEAIKTLPEREKKVLILYYYED--LTLK 232

Query: 257 NLSSEFEVSRERVRQIEARA 276
            +     V+  R+ Q+  +A
Sbjct: 233 EIGKVLGVTESRISQLHTKA 252


>gnl|CDD|181296 PRK08215, PRK08215, sporulation sigma factor SigG; Reviewed.
          Length = 258

 Score = 52.3 bits (126), Expect = 1e-07
 Identities = 75/281 (26%), Positives = 128/281 (45%), Gaps = 57/281 (20%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+ +E   L +R +  GD  A  +L+  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLKNEEMRELFERMQN-GDKEAREKLINGNLRLVLSVIQRFNNRGENVDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR-------SWSLVKIGTTANQKRLFF 137
           GLM+A+  FD  +  + +TY++  I   ++ Y LR       S SL  I   A Q R   
Sbjct: 74  GLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRY-LRDNNPIRVSRSLRDIAYKALQVR--- 129

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
                    + + + N K   V  IAK+L V   EV+          +L+A+        
Sbjct: 130 ---------EKLINENSKEPTVEEIAKELEVPREEVV---------FALDAI-------- 163

Query: 198 SQWQDWL-----VYDHDG------QEQVLIEKEERKN-RRNM-LTRSMSVLNPRERRIFE 244
              QD +     +Y HDG       +Q+  EK + +N    + L  +M  LN RE+ I  
Sbjct: 164 ---QDPVSLFEPIY-HDGGDPIYVMDQISDEKNKDENWLEEIALKEAMKKLNDREKLIL- 218

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             R  +    +E ++ E  +S+ +V ++E  A K +++ IQ
Sbjct: 219 NLRFFQGKTQME-VAEEIGISQAQVSRLEKAALKHMRKYIQ 258


>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.
          Length = 231

 Score = 47.4 bits (113), Expect = 4e-06
 Identities = 58/241 (24%), Positives = 111/241 (46%), Gaps = 18/241 (7%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A  +L+  +LRLV  I   +   G    ++   G IGL++A+ KFD     + +TY
Sbjct: 8   GDKEARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTY 67

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA-IA 163
           ++  I   ++ + LR   ++K+  +   K L   +R +K  L       L  E  +  +A
Sbjct: 68  AVPMIMGEIKRF-LRDDGIIKVSRSL--KELARKIRYMKEELS----KELGREPTINELA 120

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           + L VS  E++         +SL   ++  D +     D +  D   ++   +EK     
Sbjct: 121 EALGVSPEEIVMALESARSPQSLYDTVHQDDGDPIYLLDQIA-DKGSEDSDWLEKI---- 175

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
               L  ++S L+ RER+I   R  ++   T   +++   +S+ +V ++E +  KK++E 
Sbjct: 176 ---ALKEAISKLDERERQIIMLRYFKDK--TQTEVANMLGISQVQVSRLEKKVLKKMKEK 230

Query: 284 I 284
           +
Sbjct: 231 L 231


>gnl|CDD|163078 TIGR02937, sigma70-ECF, RNA polymerase sigma factor, sigma-70
           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 = 47.0 bits (112), Expect = 7e-06
 Identities = 17/70 (24%), Positives = 33/70 (47%), Gaps = 2/70 (2%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   L   +L L+ + A  Y G      ++V E  + L++A+ +FDPE  F+   +   
Sbjct: 1   EAFEELYERYLPLLYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFK--AWLFR 58

Query: 108 WIKAAMQEYI 117
             +  + +Y+
Sbjct: 59  IARNLILDYL 68



 Score = 41.6 bits (98), Expect = 2e-04
 Identities = 17/68 (25%), Positives = 35/68 (51%), Gaps = 2/68 (2%)

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
           E+ E++  R  L  ++  L  RER +   R L+   ++ + ++    +S   V++   RA
Sbjct: 93  EELEQEEEREALREALEKLPEREREVLVLRYLEG--LSYKEIAEILGISVGTVKRRLKRA 150

Query: 277 FKKVQESI 284
            KK++E +
Sbjct: 151 RKKLRELL 158


>gnl|CDD|180965 PRK07408, PRK07408, RNA polymerase sigma factor SigF; Reviewed.
          Length = 256

 Score = 44.1 bits (105), Expect = 5e-05
 Identities = 57/236 (24%), Positives = 110/236 (46%), Gaps = 32/236 (13%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGLPISEVVSEGNIGLMQAVKKFDP 95
           L + Y+++  ++  ++LV  +L LV K A  +      P  ++V  G++GL++A+++FDP
Sbjct: 14  LLRAYQQNPSIALRNQLVELNLGLVRKEAHRWSNQCSEPYEDLVQVGSLGLIRAIERFDP 73

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL-RRLKGHLQAITDNNL 154
            +G   +++++ +I+  +Q Y+      V+I       R +  L R+ K   Q +     
Sbjct: 74  SKGHAFSSFAIPYIRGEIQHYLRDKSPTVRI------PRRWQELQRQAKKVRQELRQELG 127

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDE----SLNALINSSDKNSSQWQDWLVYDHDG 210
           +      IA+ L++S  E      +LA       SL+A +N  +  S+   D L+ D   
Sbjct: 128 RQPTDQEIAQALDISLEEWQE--IKLALQNRTPLSLDAPVNQDEDGSTSLGD-LLPDPRY 184

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE------------ARRLQENPVT 254
           +   L +++     R  L ++++ L  R R + E            A RL  +PVT
Sbjct: 185 RSFQLAQED-----RIRLQQALAQLEERTREVLEFVFLHDLTQKEAAERLGISPVT 235


>gnl|CDD|181075 PRK07670, PRK07670, RNA polymerase sigma factor SigD; Validated.
          Length = 251

 Score = 42.0 bits (99), Expect = 2e-04
 Identities = 64/281 (22%), Positives = 127/281 (45%), Gaps = 63/281 (22%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVV----KIAMGYRGYGLPIS----EVVSEGNI 84
           EE  L  R++E  D  AA  L+  ++ LV     +I++G     LP S    ++ S G +
Sbjct: 7   EEQKLWDRWKEERDPDAADELIRRYMPLVHYHVQRISVG-----LPKSVSKDDLKSLGML 61

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGTTANQKRLFFN 138
           GL  A++KFDP R  +  TY+ + I+ A+      ++++ RS    K       K++   
Sbjct: 62  GLYDALEKFDPSRDLKFDTYASFRIRGAIIDGLRKEDWLPRS-MREKT------KKVEAA 114

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV------------ISMNCRLAG-DES 185
           + +L+         N+ P++V   A +L ++E EV            +S++ +    D+ 
Sbjct: 115 IEKLEQRYM----RNVTPKEV---AAELGMTEEEVEATMNEGFFANLLSIDEKTHDQDDG 167

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
            N  +   D  +   ++ L+      ++ LIE+         L   +  L+ +E+ +   
Sbjct: 168 ENVSVTIRDDKTPTPEEKLL------KEELIEE---------LAEKIKQLSEKEQLVISL 212

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              +E  +TL  +     +S  R+ QI ++A  K+++ ++K
Sbjct: 213 FYKEE--LTLTEIGQVLNLSTSRISQIHSKALFKLKKLLEK 251


>gnl|CDD|180137 PRK05572, PRK05572, sporulation sigma factor SigF; Validated.
          Length = 252

 Score = 40.0 bits (94), Expect = 8e-04
 Identities = 65/262 (24%), Positives = 119/262 (45%), Gaps = 41/262 (15%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           L K+ ++ GD  A   LV  +LRLV  +   +   G    ++   G IGL++AV KFD  
Sbjct: 22  LIKKSQD-GDQEARDTLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLS 80

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVK----IGTTANQKRLFFNLRRLKGHLQAITDN 152
              + +TY++  I   +Q + LR    VK    +  TAN+      +R+ K  L      
Sbjct: 81  YDVKFSTYAVPMIIGEIQRF-LRDDGTVKVSRSLKETANK------IRKDKDELSKE--L 131

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +P  +  +A+ L V+  EV+     LA + S           S Q     V+++DG  
Sbjct: 132 GREP-TIEELAEYLGVTPEEVV-----LAQEAS----------RSPQSIHETVHENDGDP 175

Query: 213 QVLIEK-----EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
             L+++     EE    +  L  ++  L+ RER I   R  ++   T   ++    +S+ 
Sbjct: 176 ITLLDQIADQSEEDWFDKIALKEAIRELDERERLIVYLRYFKDK--TQSEVAKRLGISQV 233

Query: 268 RVRQIEARAFKKVQESIQKQVE 289
           +V ++E    KK+ + ++++++
Sbjct: 234 QVSRLE----KKILKQMKEKLD 251


>gnl|CDD|180784 PRK06986, fliA, flagellar biosynthesis sigma factor; Validated.
          Length = 236

 Score = 38.7 bits (91), Expect = 0.002
 Identities = 62/251 (24%), Positives = 108/251 (43%), Gaps = 40/251 (15%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPIS----EVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             LV  +  LV +IA+  +   LP S    +++  G IGL++A +++D E+G    TY+ 
Sbjct: 11  DELVEQYAPLVKRIALRLKAR-LPASVDLDDLIQAGMIGLLEAARRYDGEQGASFETYAG 69

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ-AITDNNLKPEQVVAIAKK 165
             I+ AM +  LRS   V      N + +   +R+L+  L    TD          +A+K
Sbjct: 70  QRIRGAMLDE-LRSLDWVPRSVRRNAREVAQAIRQLEQELGREPTDTE--------VAEK 120

Query: 166 LNVSESEVISMNCRLAGDESLNALINSS----DKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           L +S  E   M         L     S     D+   +  D ++   D Q++  +++ E 
Sbjct: 121 LGLSLEEYREM---------LLDTNISQLFSIDELRGEHGDSILVTEDHQDEDPLQQLED 171

Query: 222 KNRRNMLTRSMSVLNPRERRI-----FEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
           +  R  L  ++  L  RE+ +      E   L+E    L        VS  RV QI ++A
Sbjct: 172 EELREALVEAIESLPEREQLVLSLYYQEELNLKEIGAVL-------GVSESRVSQIHSQA 224

Query: 277 FKKVQESIQKQ 287
            K+++  + + 
Sbjct: 225 IKRLRARLGEW 235


>gnl|CDD|135656 PRK05911, PRK05911, RNA polymerase sigma factor sigma-28; Reviewed.
          Length = 257

 Score = 38.4 bits (89), Expect = 0.002
 Identities = 55/251 (21%), Positives = 111/251 (44%), Gaps = 44/251 (17%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           L+  +L LV  +A      G+P      ++ + G  GL++AV++FDPE+  R   Y+++ 
Sbjct: 28  LIEFYLPLVKNVAHRLIS-GMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFL 86

Query: 109 IKAAMQEYILRS-WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           IKAA+ + + +  W    +   AN         +L   + ++  +  K      + + LN
Sbjct: 87  IKAAIIDDLRKQDWVPRSVHQKAN---------KLADAMDSLRQSLGKEPTDGELCEYLN 137

Query: 168 VSESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG-----QEQVLIEKEE 220
           +S+ E+     + R A   SLN             +++     D      +E++  E+ E
Sbjct: 138 ISQQELSGWFSSARPALILSLN-------------EEFPCQSDDEAGLALEERIADERAE 184

Query: 221 -------RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
                  +K   ++L  ++  L  +ER++      +E  + L+ +     VS  RV QI 
Sbjct: 185 TGYDVVDKKEFSSILAEAILALEEKERKVMALYYYEE--LVLKEIGKILGVSESRVSQIH 242

Query: 274 ARAFKKVQESI 284
           ++A  K++ ++
Sbjct: 243 SKALLKLRATL 253


>gnl|CDD|168831 PRK07122, PRK07122, RNA polymerase sigma factor SigF; Reviewed.
          Length = 264

 Score = 36.7 bits (85), Expect = 0.007
 Identities = 19/47 (40%), Positives = 26/47 (55%)

Query: 52 RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
          R+VT  L L   IA  + G G P  ++V    +GL+ AV +FD E G
Sbjct: 44 RIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETG 90


>gnl|CDD|180757 PRK06930, PRK06930, positive control sigma-like factor; Validated.
          Length = 170

 Score = 34.3 bits (79), Expect = 0.044
 Identities = 13/84 (15%), Positives = 34/84 (40%), Gaps = 2/84 (2%)

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEF 262
           +   +    +    E    +  +  +  ++SVL  RE+ ++   R     ++   ++   
Sbjct: 83  FRSMEDLEWDIEEPESVISEWDKIRIEDALSVLTEREKEVYLMHRGYG--LSYSEIADYL 140

Query: 263 EVSRERVRQIEARAFKKVQESIQK 286
            + +  V+ +  RA KK+   I +
Sbjct: 141 NIKKSTVQSMIERAEKKIARQINE 164


>gnl|CDD|180680 PRK06759, PRK06759, RNA polymerase factor sigma-70; Validated.
          Length = 154

 Score = 32.5 bits (74), Expect = 0.15
 Identities = 16/53 (30%), Positives = 30/53 (56%), Gaps = 2/53 (3%)

Query: 232 MSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           MSVL+ +E+ I   R       T+  ++ E E++  +VR I  +A +K++ S+
Sbjct: 104 MSVLDEKEKYIIFERFFVGK--TMGEIALETEMTYYQVRWIYRQALEKMRNSV 154


>gnl|CDD|162177 TIGR01054, rgy, reverse gyrase.  Generally, these gyrases are
           encoded as a single polypeptide. An exception was found
           in Methanopyrus kandleri, where enzyme is split within
           the topoisomerase domain, yielding a heterodimer of gene
           products designated RgyB and RgyA.
          Length = 1171

 Score = 29.8 bits (67), Expect = 0.78
 Identities = 22/80 (27%), Positives = 38/80 (47%), Gaps = 17/80 (21%)

Query: 228 LTRSMSVLNPRERRIFEA-------------RRLQENPVTLENLSSEFEVSRERVRQIEA 274
           LT+ +S++   +   FEA             +R+ E  V LE L  E +  RE+VR+I  
Sbjct: 535 LTKGLSIVLVDDPEAFEALKKRLKWTYEIEFKRIDE--VDLEKLIREIDEDREKVRRI-- 590

Query: 275 RAFKKVQESIQKQVELSSSP 294
           R  K  ++ ++  + +  SP
Sbjct: 591 REGKGRKDLVKTALLVVESP 610


>gnl|CDD|184892 PRK14898, PRK14898, DNA-directed RNA polymerase subunit A'';
           Provisional.
          Length = 858

 Score = 29.9 bits (67), Expect = 0.86
 Identities = 15/52 (28%), Positives = 24/52 (46%), Gaps = 4/52 (7%)

Query: 237 PRERRIFEARRLQENPVTLENLSSEFEVSRER----VRQIEARAFKKVQESI 284
           PR   I +AR+    P+   +L  E+   RE+     ++IE+     V  SI
Sbjct: 563 PRMIEIVDARKEPSTPIMTVHLKGEYATDREKAEEVAKKIESLTLGDVATSI 614


>gnl|CDD|181361 PRK08295, PRK08295, RNA polymerase factor sigma-70; Validated.
          Length = 208

 Score = 29.5 bits (67), Expect = 1.0
 Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 1/70 (1%)

Query: 28 MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            ++ E+  L +  R  GD  A   L+  +   V   A  Y   G    ++V EG IGL 
Sbjct: 5  DYDELEDEELVELARS-GDKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLY 63

Query: 88 QAVKKFDPER 97
          +A++ +D ++
Sbjct: 64 KAIRDYDKDK 73


>gnl|CDD|180589 PRK06489, PRK06489, hypothetical protein; Provisional.
          Length = 360

 Score = 29.2 bits (66), Expect = 1.4
 Identities = 11/24 (45%), Positives = 15/24 (62%), Gaps = 5/24 (20%)

Query: 49  AAHRLVT-----SHLRLVVKIAMG 67
           A +RLVT      HLRL++  +MG
Sbjct: 141 AQYRLVTEGLGVKHLRLILGTSMG 164


>gnl|CDD|116865 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 = 29.0 bits (66), Expect = 1.5
 Identities = 15/56 (26%), Positives = 28/56 (50%), Gaps = 2/56 (3%)

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
              L R++  L PR+R +F  R L+   ++   ++    +S   V+   +RA KK+
Sbjct: 1   LEALLRALEELPPRQREVFLLRYLEG--LSYAEIAELLGISEGTVKSRLSRARKKL 54


>gnl|CDD|181823 PRK09401, PRK09401, reverse gyrase; Reviewed.
          Length = 1176

 Score = 28.0 bits (63), Expect = 3.5
 Identities = 18/63 (28%), Positives = 32/63 (50%), Gaps = 12/63 (19%)

Query: 228 LTRSMSVLNPRERRIFEA--RRLQ----------ENPVTLENLSSEFEVSRERVRQIEAR 275
           LT+ +SVL   + ++FE+  ++L+           + V LE L  E +  RER+R++E  
Sbjct: 537 LTKGLSVLLVDDEKLFESLKKKLRWLLPEIEFKPLSEVDLEELLREIDEDRERIRRVERS 596

Query: 276 AFK 278
              
Sbjct: 597 KDL 599


>gnl|CDD|172374 PRK13850, PRK13850, type IV secretion system protein VirD4;
           Provisional.
          Length = 670

 Score = 27.1 bits (60), Expect = 5.1
 Identities = 14/46 (30%), Positives = 23/46 (50%), Gaps = 2/46 (4%)

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
           ++ E R +  N +    ++  P ERR  E RRL  N +T +   +E
Sbjct: 198 LDPERRTHCYNPVLDIAAL--PPERRFTETRRLAANLITAKGKGAE 241


>gnl|CDD|151092 pfam10547, P22_AR_N, P22_AR N-terminal domain.  This domain was
           identified by Iyer and colleagues.
          Length = 120

 Score = 27.3 bits (61), Expect = 5.6
 Identities = 15/41 (36%), Positives = 21/41 (51%), Gaps = 4/41 (9%)

Query: 121 WSLVKIGTTA----NQKRLFFNLRRLKGHLQAITDNNLKPE 157
            S+V I   A    N++ L   LR+L G L  I  N ++PE
Sbjct: 51  SSIVAIMIVASDGKNREMLCLPLRKLNGWLFTINPNKVRPE 91


>gnl|CDD|116863 pfam08279, HTH_11, HTH domain.  This family includes
           helix-turn-helix domains in a wide variety of proteins.
          Length = 55

 Score = 26.6 bits (60), Expect = 7.2
 Identities = 9/34 (26%), Positives = 17/34 (50%)

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           R  +I E       P++ + L+ +  VSR  +R+
Sbjct: 1   RLLQILELLLQAREPISGQELAEKLGVSRRTIRR 34


>gnl|CDD|182121 PRK09863, PRK09863, putative frv operon regulatory protein;
           Provisional.
          Length = 584

 Score = 26.7 bits (59), Expect = 7.4
 Identities = 13/42 (30%), Positives = 20/42 (47%), Gaps = 3/42 (7%)

Query: 234 VLNPRERRIFEARRLQENPVTLENLSSEFEVSRER-VRQIEA 274
           +LN RE +I     L++   +   L+ +  VSR   VR I  
Sbjct: 1   MLNERELKIV--DLLEQQDRSGGELAQQLGVSRRTIVRDIAY 40


>gnl|CDD|177533 PHA03119, PHA03119, helicase-primase primase subunit; Provisional.
          Length = 1085

 Score = 26.4 bits (58), Expect = 9.3
 Identities = 11/36 (30%), Positives = 19/36 (52%)

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           FN ++++ HL+A+T  ++     V  A  L  S  E
Sbjct: 358 FNRKQIRDHLRAVTLTDIALIPDVVSASSLGRSAIE 393


>gnl|CDD|182981 PRK11125, nrfA, cytochrome c nitrite reductase subunit c552;
           Provisional.
          Length = 480

 Score = 26.5 bits (59), Expect = 9.4
 Identities = 10/20 (50%), Positives = 13/20 (65%)

Query: 13  EIGLSRYIHEIRKIPMLEKQ 32
           EIG S + H + K PML+ Q
Sbjct: 245 EIGFSDWTHSLSKTPMLKAQ 264


  Database: CddB
    Posted date:  Feb 4, 2011  9:54 PM
  Number of letters in database: 5,994,473
  Number of sequences in database:  21,608
  
Lambda     K      H
   0.318    0.132    0.371 

Gapped
Lambda     K      H
   0.267   0.0763    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 4,934,523
Number of extensions: 317282
Number of successful extensions: 942
Number of sequences better than 10.0: 1
Number of HSP's gapped: 899
Number of HSP's successfully gapped: 94
Length of query: 302
Length of database: 5,994,473
Length adjustment: 93
Effective length of query: 209
Effective length of database: 3,984,929
Effective search space: 832850161
Effective search space used: 832850161
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: 57 (25.7 bits)