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)