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)