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)