RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 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|30914 COG0568, RpoD, DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]. Length = 342 Score = 235 bits (600), Expect = 1e-62 Identities = 106/295 (35%), Positives = 151/295 (51%), Gaps = 14/295 (4%) Query: 2 NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG-DLSAAHRLVTSHLRL 60 R+ LS YI I P+L +EE LA+R + DL A +LV S+LRL Sbjct: 55 GREPSERARRPAGRLSFYIRAIEAAPLLTPEEEKALARRLKRGERDLDAKKKLVESNLRL 114 Query: 61 VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120 VV IA Y G GLP +++ EGNIGLM+AV+KFDPE+GF+ +TY+ WWI+ A+ I Sbjct: 115 VVSIAKKYTGRGLPFLDLIQEGNIGLMKAVEKFDPEKGFKFSTYATWWIRQAITRAIADQ 174 Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180 ++I +Q L LRR+K L + IA++L VS +V M R Sbjct: 175 ARTIRIPV--HQVELINKLRRVKRELLQ---ELGREPTPEEIAEELGVSPDKVREMLKRA 229 Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDG-QEQVLIEKEERKNRRNMLTRSMSVLNPRE 239 + SL+ I + S+ D+L D E + + +++ +L L RE Sbjct: 230 SEPISLDTPIGDDE--DSELGDFLEDDKSVSPEDAVERESLKEDLNEVLA---EALTERE 284 Query: 240 RRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292 RR+ R P TLE L EF +SRERVRQIEA+A +K++ ++ L S Sbjct: 285 RRVIRLRFGLDDGEPKTLEELGEEFGISRERVRQIEAKALRKLRRHPERSALLRS 339 >gnl|CDD|31384 COG1191, FliA, DNA-directed RNA polymerase specialized sigma subunit [Transcription]. Length = 247 Score = 86.5 bits (214), Expect = 7e-18 Identities = 59/262 (22%), Positives = 120/262 (45%), Gaps = 19/262 (7%) Query: 27 PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP-ISEVVSEGNIG 85 L K+EE L + Y E + A RL+ +L LV IA + G +++ G IG Sbjct: 4 QPLSKEEEEKLLEYYAEGDE--EARRLIERYLPLVKSIARKFENRGPSEYDDLIQIGMIG 61 Query: 86 LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145 L++A++++DP +G + +TY++ I+ + +Y LR VK+ + L RR++ Sbjct: 62 LIKAIERYDPSKGTKFSTYAVRRIRGEILDY-LRKNDSVKV-----PRSLRELGRRIEEA 115 Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205 + + + IA++L + + E I + G + L+ + + D Sbjct: 116 IDELEQELGREPTDEEIAEELGIDKEEYIEALLAINGSQLLSLDEDVLKDDDDDVDD--- 172 Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265 Q + + E++ +L ++ L RE+ + R +E +T + ++ +S Sbjct: 173 -----QIENPDDGVEKEELLEILKEAIEPLPEREKLVLVLRYKEE--LTQKEIAEVLGIS 225 Query: 266 RERVRQIEARAFKKVQESIQKQ 287 RV ++ +A KK+++ + K Sbjct: 226 ESRVSRLHKKAIKKLRKELNKA 247 >gnl|CDD|146937 pfam04542, Sigma70_r2, Sigma-70 region 2. Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime. The aromatic residues of the recognition helix, found at the C-terminus of this domain are though to mediate strand separation, thereby allowing transcription initiation. Length = 71 Score = 74.9 bits (185), Expect = 2e-14 Identities = 25/69 (36%), Positives = 41/69 (59%) Query: 53 LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112 LV +L LV +A Y G G ++V EG +GL++AV++FDPERG +T+ I+ A Sbjct: 1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLLRAVERFDPERGVSFSTWLYTIIRNA 60 Query: 113 MQEYILRSW 121 + + + + Sbjct: 61 IIDALRKQR 69 >gnl|CDD|146939 pfam04545, Sigma70_r4, Sigma-70, region 4. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives. Length = 50 Score = 50.5 bits (122), Expect = 5e-07 Identities = 21/51 (41%), Positives = 32/51 (62%), Gaps = 2/51 (3%) Query: 232 MSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282 ++ L PRER + R + +TLE + +SRERVRQIE RA +K+++ Sbjct: 2 LASLPPREREVLVLRFGEG--LTLEEIGERLGISRERVRQIEKRALRKLRK 50 >gnl|CDD|100119 cd06171, Sigma70_r4, Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplasmic stress and pathogenesis. Ec sigmaE SR4 also contacts the -35 element, but recognizes a different consensus (a 7-base-pair GGAACTT). Plant SFs recognize sigma70 type promoters and direct transcription of the major plastid RNA polymerase, plastid-encoded RNA polymerase (PEP).. Length = 55 Score = 47.1 bits (113), Expect = 5e-06 Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 2/57 (3%) Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281 R L ++ L RER + R + ++ E ++ +SR VRQ RA KK++ Sbjct: 1 RERLEEALDKLPEREREVILLRFGEG--LSYEEIAEILGISRSTVRQRLHRALKKLR 55 >gnl|CDD|143911 pfam00140, Sigma70_r1_2, Sigma-70 factor, region 1.2. Length = 37 Score = 37.4 bits (88), Expect = 0.006 Identities = 11/32 (34%), Positives = 19/32 (59%) Query: 16 LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL 47 + Y+ EI ++P+L +EE LA+R +L Sbjct: 4 VRLYLREIGRVPLLTAEEEVELARRIEAGDEL 35 >gnl|CDD|38013 KOG2802, KOG2802, KOG2802, Membrane protein HUEL (cation efflux superfamily) [General function prediction only]. Length = 503 Score = 29.6 bits (66), Expect = 1.1 Identities = 11/36 (30%), Positives = 19/36 (52%) Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167 ++RLF N R L+ + + + +VVA A +N Sbjct: 181 RERLFRNQRILREYRDELGNTAKGSGRVVATAICIN 216 >gnl|CDD|145919 pfam03028, Dynein_heavy, Dynein heavy chain. This family represents the C-terminal region of dynein heavy chain. The chain also contains ATPase activity and microtubule binding ability and acts as a motor for the movement of organelles and vesicles along microtubules. Dynein is also involved in cilia and flagella movement. The dynein subunit consists of at least two heavy chains and a number of intermediate and light chains (see pfam01221). Length = 706 Score = 29.2 bits (66), Expect = 1.5 Identities = 13/50 (26%), Positives = 25/50 (50%), Gaps = 2/50 (4%) Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227 CRL+ E L + +KN+ +W+ W YD + E+ + +E + + Sbjct: 22 CRLSELEEFRGLDDDIEKNAKRWKKW--YDSEAPEEEKLPQEWKDRKSAF 69 >gnl|CDD|35530 KOG0309, KOG0309, KOG0309, Conserved WD40 repeat-containing protein [Function unknown]. Length = 1081 Score = 28.2 bits (62), Expect = 2.7 Identities = 22/80 (27%), Positives = 31/80 (38%), Gaps = 23/80 (28%) Query: 93 FDPERGFRLATY-----SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR------ 141 F P R T W A +I+ +T+NQK + +NL + Sbjct: 56 FTPPRWLHHITPWQVADVQWSPHPAKPYWIV---------STSNQKAIIWNLAKSSSNAI 106 Query: 142 ---LKGHLQAITDNNLKPEQ 158 L GH +AITD N P+ Sbjct: 107 EFVLHGHSRAITDINFNPQH 126 >gnl|CDD|37020 KOG1809, KOG1809, KOG1809, Vacuolar protein sorting-associated protein [Intracellular trafficking, secretion, and vesicular transport]. Length = 1827 Score = 28.1 bits (62), Expect = 3.3 Identities = 40/237 (16%), Positives = 75/237 (31%), Gaps = 29/237 (12%) Query: 65 AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124 + L S+ + + L+++V++ +R +WW A + SW + Sbjct: 272 NVEMHAEALTFSDAQYDDIMELLESVERVKTNLPYRKYRPRLWWKYAIQFVLEMWSWEHM 331 Query: 125 KIGTTANQKRLFFNLRRLKGHLQ----AITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180 K ++ R+ Q I + K V I +E E+ Sbjct: 332 K-KHRELRRSYAKLYRKKLTSAQLEAELIKEQLEKELDVFNIILSRQRAERELK------ 384 Query: 181 AGDESLNALINSSDKNSSQWQDWL---VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237 E N L++ + + W + +VL E+ LT Sbjct: 385 --REGKNKLLSKQPEEKAGWYSGFGGELTSKQKNGEVLQEETT----EAALTDE------ 432 Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSP 294 + ++F A EN L +VS R + ++E + V+LS Sbjct: 433 EKEKLFRAIGYSENAPELNLPK---DVSSSRSEVKLKKGSVVLREGKESLVKLSFLE 486 >gnl|CDD|39604 KOG4403, KOG4403, KOG4403, Cell surface glycoprotein STIM, contains SAM domain [General function prediction only]. Length = 575 Score = 27.8 bits (61), Expect = 3.5 Identities = 24/87 (27%), Positives = 46/87 (52%), Gaps = 7/87 (8%) Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPR-ERRIFEARRLQENPVTLENLSSEFEVSRERV- 269 EQ L + ++R + R+++V ER++ EA RL E +EN +S E+ + RV Sbjct: 258 EQSLEDLQKRLEKAREEQRNVAVEKLDLERKLDEAPRLSELREGVENETSRKELEQLRVA 317 Query: 270 -----RQIEARAFKKVQESIQKQVELS 291 +++EA + ++QK ++L+ Sbjct: 318 LEKAEKELEANSSWSAPLALQKWLQLT 344 >gnl|CDD|38888 KOG3684, KOG3684, KOG3684, Ca2+-activated K+ channel proteins (intermediate/small conductance classes) [Inorganic ion transport and metabolism]. Length = 489 Score = 26.8 bits (59), Expect = 7.1 Identities = 23/105 (21%), Positives = 50/105 (47%), Gaps = 11/105 (10%) Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEF 262 WL+Y H L+ K ++ R + + ++ +E R+L E +L +L+ Sbjct: 374 WLIYKH----TKLVSKGDQARLRKHQRKFLQAIHQFRSVKWEQRKLSEQANSLVDLAKTQ 429 Query: 263 EVSRERVRQIEAR--AFKKVQESIQKQVE-----LSSSPPLLQKP 300 + ++++ +R +K ++++ ++E LSS P LL +P Sbjct: 430 NDMYDLLQELHSRQEELEKQIDTLESKLEALTASLSSLPGLLAQP 474 Database: CddA Posted date: Feb 4, 2011 9:38 PM Number of letters in database: 6,263,737 Number of sequences in database: 21,609 Lambda K H 0.318 0.132 0.371 Gapped Lambda K H 0.267 0.0739 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 3,563,406 Number of extensions: 183501 Number of successful extensions: 572 Number of sequences better than 10.0: 1 Number of HSP's gapped: 561 Number of HSP's successfully gapped: 37 Length of query: 302 Length of database: 6,263,737 Length adjustment: 93 Effective length of query: 209 Effective length of database: 4,254,100 Effective search space: 889106900 Effective search space used: 889106900 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)