RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780237|ref|YP_003064650.1| DNA-directed RNA polymerase
subunit alpha [Candidatus Liberibacter asiaticus str. psy62]
(340 letters)
>gnl|CDD|179956 PRK05182, PRK05182, DNA-directed RNA polymerase subunit alpha;
Provisional.
Length = 310
Score = 446 bits (1150), Expect = e-126
Identities = 169/313 (53%), Positives = 232/313 (74%), Gaps = 3/313 (0%)
Query: 7 QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
E +KP IE + E++N + EPL RGF TLGNALRRVL+SSL GAA+T+V+ID
Sbjct: 1 TEFLKPQKIE-VEEESEDDNYGKFVLEPLERGFGTTLGNALRRVLLSSLPGAAVTSVKID 59
Query: 67 GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
GVLHE S+I GV ED+T+IILN+KG+ LK+ GD +T+ K+GPG VTAGDI+T D+E
Sbjct: 60 GVLHEFSTIPGVREDVTEIILNLKGLRLKLHGDEPVTLTLSKKGPGEVTAGDIETDGDVE 119
Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
++NPD VI L+ A + MELTV +G GYVPA+ ++ E+ PIG I +DA++SP+KKV+YT
Sbjct: 120 IVNPDLVIATLNEGAKLEMELTVERGRGYVPAEENK-EDAPIGRIPVDAIFSPVKKVNYT 178
Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
VE+ R GQ DYDKL + ++TDGSIT E+++ALA++IL +QL +F++ EE +E +E++
Sbjct: 179 VENTRVGQRTDYDKLILEVETDGSITPEEALALAAKILVEQLSVFVDLEEA-EEAEEEVE 237
Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
+ F+P LL+ +EELELSVRS NCL+ I +GDL+QRTE ++L+ N G+KSL EI
Sbjct: 238 EEEPEFDPILLRPIEELELSVRSYNCLKRAGINTIGDLVQRTEEELLKTRNLGKKSLEEI 297
Query: 307 KGVLGTMGLFLGM 319
K L +GL LGM
Sbjct: 298 KEKLAELGLSLGM 310
>gnl|CDD|162666 TIGR02027, rpoA, DNA-directed RNA polymerase, alpha subunit,
bacterial and chloroplast-type. This family consists of
the bacterial (and chloroplast) DNA-directed RNA
polymerase alpha subunit, encoded by the rpoA gene. The
RNA polymerase catalyzes the transcription of DNA into
RNA using the four ribonucleoside triphosphates as
substrates. The amino terminal domain is involved in
dimerizing and assembling the other RNA polymerase
subunits into a transcriptionally active enzyme. The
carboxy-terminal domain contains determinants for
interaction with DNA and with transcriptional activator
proteins.
Length = 297
Score = 365 bits (940), Expect = e-102
Identities = 149/293 (50%), Positives = 211/293 (72%), Gaps = 3/293 (1%)
Query: 31 IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIK 90
+ EPL RGF TLGNALRRVL+SS+ GAAITAV+IDGVLHE S+I+GV ED+T+IILN+K
Sbjct: 5 VLEPLERGFGITLGNALRRVLLSSIPGAAITAVKIDGVLHEFSTIEGVKEDVTEIILNLK 64
Query: 91 GINLKMSGDSHKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
+ +K GD + +T+ K+GPGVVTAGDI D+E++NPD VI L A + +EL V
Sbjct: 65 QLVVKSEGDGERTMTLSKKGPGVVTAGDIKAPPGDVEIVNPDLVIATLTEPADLEIELRV 124
Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
+G GYVPA+ +R E+ P+G+I +DA++SP+ KV+Y VE+ R GQ DYDKL + I+T+G
Sbjct: 125 ERGRGYVPAEENREEDRPVGVIAVDAIFSPVLKVNYEVENTRVGQRTDYDKLILEIETNG 184
Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK--SLPFNPALLKKVEELELSV 267
SIT +D++A A++IL + L F+N +E + +E+ + L L K+EEL+LSV
Sbjct: 185 SITPKDAIAEAAKILIEHLEPFVNLDEEIEAFEEEQEEEEEELEDAKLLSIKIEELDLSV 244
Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
RS NCL+ I +G+L+ ++E ++L++ NFG+KSL EIK L +GL LGM+
Sbjct: 245 RSYNCLKRAGIHTLGELVSKSEEELLKIKNFGKKSLTEIKEKLAELGLELGMD 297
>gnl|CDD|128908 smart00662, RPOLD, RNA polymerases D. DNA-directed RNA polymerase
subunit D and bacterial alpha chain.
Length = 224
Score = 182 bits (465), Expect = 1e-46
Identities = 76/224 (33%), Positives = 117/224 (52%), Gaps = 35/224 (15%)
Query: 37 RGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM 96
+ TL NALRRVL+SS+ G A+T V+I+G + GV +++ L +K +
Sbjct: 7 EPYGLTLANALRRVLLSSVPGMAVTEVEIEG------NTSGVQDEVLAHRLGLKPLASDP 60
Query: 97 SGDSHKR--------------VTIFKRGPGVVTAGDIQTV--NDIEVLNPDHVICNLDVD 140
GD ++R +T+ +GPG VTAGD+++ D+E++NPD I L
Sbjct: 61 DGDEYQRDCECEEGCEKCSVTLTLDVKGPGEVTAGDLKSDSDPDVEIVNPDIPIAKLREG 120
Query: 141 AVVRMELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
+ +E KG GYV AK E I I +DA +SP+ +V+Y VE R Q D
Sbjct: 121 QELELEARAEKGRGYVHAKWSPVSTVEYRYIPRIPVDASFSPVDRVAYQVECPRVVQRTD 180
Query: 198 ----------YDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
YDKL ++T+GS+ E++V A++IL+++L F
Sbjct: 181 CCRECDEGEEYDKLIFDVETNGSLKPEEAVLEAAKILKEKLEAF 224
>gnl|CDD|184899 PRK14906, PRK14906, DNA-directed RNA polymerase subunit beta'/alpha
domain fusion protein; Provisional.
Length = 1460
Score = 34.1 bits (78), Expect = 0.050
Identities = 20/55 (36%), Positives = 30/55 (54%)
Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
++L +S R N I +GDLI +TE D+LR+ G K++ E+K L L
Sbjct: 1317 DDLGVSQRWANKFSEAGIETVGDLIGKTEEDLLRIEGIGAKAIEELKDGLEAHNL 1371
>gnl|CDD|178686 PLN03141, PLN03141, 3-epi-6-deoxocathasterone 23-monooxygenase;
Provisional.
Length = 452
Score = 30.5 bits (69), Expect = 0.66
Identities = 23/74 (31%), Positives = 33/74 (44%), Gaps = 10/74 (13%)
Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIV---YMG-DLIQRTEADMLRMANF---- 298
VK L P L+++ E + ++ GE + YM Q + LRM N
Sbjct: 275 VKFLSDCPVALQQLTEENMKLKRLKADTGEPLYWTDYMSLPFTQNVITETLRMGNIINGV 334
Query: 299 GRKSL--VEIKGVL 310
RK++ VEIKG L
Sbjct: 335 MRKAMKDVEIKGYL 348
>gnl|CDD|151810 pfam11370, DUF3170, Protein of unknown function (DUF3170). This
bacterial family of proteins has no known function.
Length = 609
Score = 29.8 bits (67), Expect = 1.2
Identities = 20/52 (38%), Positives = 25/52 (48%), Gaps = 4/52 (7%)
Query: 22 QEEENRTLMIAEPLPRGFAHTLGNALRR-VLMSSLRGAAITAVQ--IDGVLH 70
E +R + I EP RG AH LG+ L R VL G + Q +D VL
Sbjct: 178 HERADRLVRIVEPGARG-AHALGDRLHRLVLADHALGQMLFHAQNLLDLVLE 228
>gnl|CDD|173409 PTZ00117, PTZ00117, malate dehydrogenase; Provisional.
Length = 319
Score = 27.8 bits (62), Expect = 4.5
Identities = 16/76 (21%), Positives = 32/76 (42%), Gaps = 6/76 (7%)
Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
++ +G+ LD S + ++ +I G ++ ++D + I +KE E
Sbjct: 38 IKGVPQGKALDLKHFSTLVGSNINILGTNNY----EDIKDSDVVVITAGVQRKE--EMTR 91
Query: 247 VKSLPFNPALLKKVEE 262
L N ++K V E
Sbjct: 92 EDLLTINGKIMKSVAE 107
>gnl|CDD|115422 pfam06763, Minor_tail_Z, Prophage minor tail protein Z (GPZ). This
family consists of several prophage minor tail protein Z
like sequences from Escherichia coli, Salmonella
typhimurium and Lambda-like bacteriophages.
Length = 183
Score = 27.4 bits (61), Expect = 5.9
Identities = 8/28 (28%), Positives = 13/28 (46%)
Query: 24 EENRTLMIAEPLPRGFAHTLGNALRRVL 51
E ++ E +P+ + L LR VL
Sbjct: 154 ETEVDRIMREEMPKELGYALKQQLRLVL 181
>gnl|CDD|184941 PRK14979, PRK14979, DNA-directed RNA polymerase subunit D;
Provisional.
Length = 195
Score = 27.1 bits (60), Expect = 6.2
Identities = 27/87 (31%), Positives = 40/87 (45%), Gaps = 19/87 (21%)
Query: 45 NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILN-------IKGINLKMS 97
+ALRR+++S + AI V +E SS + D IL IKG + S
Sbjct: 28 SALRRIMISEVPTYAIENVYF----YENSS------SMYDEILAHRLGLIPIKGKPV--S 75
Query: 98 GDSHKRVTIFKRGPGVVTAGDIQTVND 124
GD T+ K GP V + D+++ N
Sbjct: 76 GDEVITFTLSKEGPCTVYSSDLKSENG 102
>gnl|CDD|182764 PRK10833, PRK10833, putative assembly protein; Provisional.
Length = 617
Score = 27.2 bits (61), Expect = 6.4
Identities = 7/20 (35%), Positives = 16/20 (80%)
Query: 87 LNIKGINLKMSGDSHKRVTI 106
+N++ INL+M D+ ++V++
Sbjct: 167 INVRDINLQMEQDAQRQVSV 186
>gnl|CDD|177641 PHA03413, PHA03413, putative internal core protein; Provisional.
Length = 1304
Score = 27.3 bits (60), Expect = 6.5
Identities = 22/82 (26%), Positives = 36/82 (43%), Gaps = 3/82 (3%)
Query: 215 DSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLR 274
D ++ ++ + D LG IN + K + N F L K EE++L R+
Sbjct: 350 DHLSAGAKAILDALGDAINDIDFKL-MAASANRSRYTFAQQDLAKREEIKL--RAPAKAD 406
Query: 275 GENIVYMGDLIQRTEADMLRMA 296
G +GD + +AD R+A
Sbjct: 407 GSTFKTVGDALNAMDADTSRVA 428
>gnl|CDD|178139 PLN02524, PLN02524, S-adenosylmethionine decarboxylase.
Length = 355
Score = 26.5 bits (59), Expect = 9.0
Identities = 9/45 (20%), Positives = 23/45 (51%)
Query: 96 MSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
M+G ++ ++F + + +A ++ + I + P+ IC+ D
Sbjct: 185 MTGLDREKASVFFKDSSLSSAEEMTKASGIRKILPESEICDFAFD 229
>gnl|CDD|132285 TIGR03241, arg_catab_astB, succinylarginine dihydrolase. Members
of this family are succinylarginine dihydrolase (EC
3.5.3.23), the second of five enzymes in the arginine
succinyltransferase (AST) pathway.
Length = 443
Score = 26.6 bits (59), Expect = 9.9
Identities = 15/60 (25%), Positives = 23/60 (38%), Gaps = 1/60 (1%)
Query: 229 GMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENI-VYMGDLIQR 287
F+ E P EV V S FN LL + + + V C + Y+ +L+
Sbjct: 285 QQFVAIEVPDAEVSVADAVSSYLFNSQLLSREDGKMMLVVPEECRENAAVWAYLNELVAG 344
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
0.317 0.136 0.386
Gapped
Lambda K H
0.267 0.0661 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 5,543,694
Number of extensions: 361351
Number of successful extensions: 794
Number of sequences better than 10.0: 1
Number of HSP's gapped: 785
Number of HSP's successfully gapped: 21
Length of query: 340
Length of database: 5,994,473
Length adjustment: 94
Effective length of query: 246
Effective length of database: 3,963,321
Effective search space: 974976966
Effective search space used: 974976966
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 (21.6 bits)
S2: 57 (25.9 bits)