RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780788|ref|YP_003065201.1| transcription elongation factor NusA [Candidatus Liberibacter asiaticus str. psy62] (526 letters) >gnl|CDD|30544 COG0195, NusA, Transcription elongation factor [Transcription]. Length = 190 Score = 181 bits (462), Expect = 3e-46 Identities = 98/188 (52%), Positives = 131/188 (69%), Gaps = 7/188 (3%) Query: 160 NSDGVIRRDETISRENLRPGDRVKSYIYDVRREQRGPQVLLSRTHPQFMVKLFHMEVPEI 219 + ++ + E I EN + GDR+++ +Y+V++E +G Q+ LSRT P+ + KLF +EVPEI Sbjct: 1 KVEAILPKREQIPGENFKVGDRIRALLYEVQKEAKG-QIELSRTIPELLEKLFEIEVPEI 59 Query: 220 YNGIVQVKAVSRDPGSRAKLAVFSSDSSIDPVGACVGMRGSRVQAVVTELRDEKIDIVVW 279 +G++++K V+RDP + AV S+ IDPVGAC+G RGSRV+AV EL EKID+V W Sbjct: 60 GDGVIEIKCVARDPRA----AVVSNVVKIDPVGACIGKRGSRVKAVSEEL-GEKIDVVEW 114 Query: 280 SPDSATFVINALRPAIVTKVVLDE-DVGRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWT 338 S D A F+ NAL PA V V + E D V+VP +QLSLAIG+ GQNVRLASQLTGW Sbjct: 115 SEDPAEFIKNALAPAEVLSVNIKEDDGHVAIVVVPPDQLSLAIGKGGQNVRLASQLTGWE 174 Query: 339 IDIITEEE 346 IDI T E Sbjct: 175 IDIETISE 182 Score = 27.5 bits (61), Expect = 9.3 Identities = 16/55 (29%), Positives = 24/55 (43%), Gaps = 1/55 (1%) Query: 294 AIVTKVVLDEDVGRIEVIVPKE-QLSLAIGRRGQNVRLASQLTGWTIDIITEEED 347 I K V + + V K + IG+RG V+ S+ G ID++ ED Sbjct: 63 VIEIKCVARDPRAAVVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWSED 117 >gnl|CDD|88421 cd04455, S1_NusA, S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three RNA binding domains (RBD's). The RBD's include one S1 domain and two KH domains that form an RNA binding surface. DNA transcription by RNA polymerase (RNAP) includes three phases - initiation, elongation, and termination. During initiation, sigma factors bind RNAP and target RNAP to specific promoters. During elongation, N-utilization substances (NusA, B, E, and G) replace sigma factors and regulate pausing, termination, and antitermination. NusA is cold-shock-inducible.. Length = 67 Score = 91.6 bits (228), Expect = 4e-19 Identities = 35/67 (52%), Positives = 52/67 (77%) Query: 136 DKVGEIISGTVKRVEYGNVIVDLGNSDGVIRRDETISRENLRPGDRVKSYIYDVRREQRG 195 D+ GEI++G VKRV+ GNVIVDLG + ++ + E I E+ RPGDR+K+Y+ +VR+ +G Sbjct: 1 DREGEIVTGIVKRVDRGNVIVDLGKVEAILPKKEQIPGESYRPGDRIKAYVLEVRKTSKG 60 Query: 196 PQVLLSR 202 PQ++LSR Sbjct: 61 PQIILSR 67 >gnl|CDD|48406 cd02134, NusA_KH, NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.. Length = 61 Score = 67.5 bits (165), Expect = 8e-12 Identities = 34/61 (55%), Positives = 42/61 (68%), Gaps = 1/61 (1%) Query: 283 SATFVINALRPAIVTKVVLDEDVG-RIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDI 341 A F+ NAL PA VT V + +D R V+VP +QL LAIG+ GQNVRLAS+L G IDI Sbjct: 1 PAEFIRNALSPAKVTSVTVLDDEEKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 Query: 342 I 342 + Sbjct: 61 V 61 Score = 30.2 bits (68), Expect = 1.5 Identities = 17/56 (30%), Positives = 26/56 (46%), Gaps = 8/56 (14%) Query: 224 VQVKAVSRDPGS--RAKLAVFSSDSSIDPVGACVGMRGSRVQAVVTELRDEKIDIV 277 +V +V+ RA++ V D +G +G G V+ +L EKIDIV Sbjct: 12 AKVTSVTVLDDEEKRARVVV-----PDDQLGLAIGKGGQNVRLAS-KLLGEKIDIV 61 >gnl|CDD|48407 cd02409, KH-II, KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.. Length = 68 Score = 46.8 bits (111), Expect = 2e-05 Identities = 17/57 (29%), Positives = 30/57 (52%), Gaps = 2/57 (3%) Query: 286 FVINALRPAIVTKVVLDE--DVGRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTID 340 F+ L PA ++ V ++ D I ++V + Q L IG++GQN+R +L + Sbjct: 3 FLKKLLAPAGISGVEIERTPDRIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLLR 59 >gnl|CDD|144242 pfam00575, S1, S1 RNA binding domain. The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure. Length = 74 Score = 43.4 bits (103), Expect = 1e-04 Identities = 23/71 (32%), Positives = 34/71 (47%), Gaps = 7/71 (9%) Query: 135 KDKVGEIISGTVKRVEYGNVIVDLGN-SDGVIRRDETISR------ENLRPGDRVKSYIY 187 K + G+++ GTV RV G VDLGN +G I E E L+ GD V+ + Sbjct: 1 KPEEGDVVKGTVTRVTKGGAFVDLGNGVEGFIPISEISDDRVEDPDEVLKVGDEVEVKVL 60 Query: 188 DVRREQRGPQV 198 V +E+ + Sbjct: 61 KVDKERGRIIL 71 >gnl|CDD|31968 COG1782, COG1782, Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]. Length = 637 Score = 40.2 bits (94), Expect = 0.002 Identities = 25/92 (27%), Positives = 42/92 (45%), Gaps = 12/92 (13%) Query: 280 SPDSATFVINALRP--AIVTKVVLDEDVGRIEVIVPKEQLSLAIGRRGQNVRLASQLTGW 337 P+ A +I + P A +T + D+D G EVI+ ++ L IG+ G +R + TGW Sbjct: 73 PPEEARKIILEIVPEEAGITDIYFDDDTG--EVIIEAKKPGLVIGKGGSTLREITAETGW 130 Query: 338 TIDII------TEEEDSINR--QKDFNERTQF 361 I+ + SI + + ER + Sbjct: 131 APKIVRTPPIQSRTIKSIREILRSERKERREI 162 >gnl|CDD|88442 cd05687, S1_RPS1_repeat_ec1_hs1, S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.. Length = 70 Score = 35.1 bits (81), Expect = 0.053 Identities = 23/71 (32%), Positives = 37/71 (52%), Gaps = 9/71 (12%) Query: 139 GEIISGTVKRVEYGNVIVDLGN-SDGVIRRDETISREN------LRPGDRVKSYIYDVRR 191 G+I+ GTV V+ V+VD+G S+G+I E ++ GD V+ Y+ +R Sbjct: 1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYV--LRV 58 Query: 192 EQRGPQVLLSR 202 E V+LS+ Sbjct: 59 EDEEGNVVLSK 69 >gnl|CDD|48408 cd02410, archeal_CPSF_KH, The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.. Length = 145 Score = 34.8 bits (80), Expect = 0.056 Identities = 21/65 (32%), Positives = 35/65 (53%), Gaps = 4/65 (6%) Query: 280 SPDSATFVINALRP--AIVTKVVLDEDVGRIEVIVPKEQLSLAIGRRGQNVRLASQLTGW 337 P+ A +I + P A +T + D+D G EVI+ E+ L IG+ G +R ++ TGW Sbjct: 50 PPEEAIKIILEIVPEEAGITDIYFDDDTG--EVIIEAEKPGLVIGKGGSTLREITRETGW 107 Query: 338 TIDII 342 ++ Sbjct: 108 APKVV 112 >gnl|CDD|30885 COG0539, RpsA, Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]. Length = 541 Score = 34.5 bits (79), Expect = 0.067 Identities = 25/87 (28%), Positives = 42/87 (48%), Gaps = 10/87 (11%) Query: 117 VIIQKVREAERDRQYLEFKD--KVGEIISGTVKRVEYGNVIVDLGNSDGVI-------RR 167 + + V E ER Q E + +VGE++ G VK + VD+G DG++ +R Sbjct: 169 LSRRAVLEEERSEQREELLNKLEVGEVVEGVVKNITDYGAFVDIGGVDGLLHISEISWKR 228 Query: 168 DETISRENLRPGDRVKSYIYDVRREQR 194 + S E ++ GD VK + + E+ Sbjct: 229 VDHPS-EVVKVGDEVKVKVISLDEERG 254 Score = 34.5 bits (79), Expect = 0.082 Identities = 20/59 (33%), Positives = 35/59 (59%), Gaps = 2/59 (3%) Query: 137 KVGEIISGTVKRVEYGNVIVDLGNS-DGVIRRDETISRENLRPGDRVKSYIYDVRREQR 194 K G ++ G VK V+ V+LG +G+IR E +SR+ L+ GD V++ + + ++ R Sbjct: 448 KKGSVVKGKVKSVKDKGAFVELGGGVEGLIRLSE-LSRDVLKVGDEVEAVVVSIDKKNR 505 Score = 31.4 bits (71), Expect = 0.70 Identities = 22/76 (28%), Positives = 41/76 (53%), Gaps = 6/76 (7%) Query: 137 KVGEIISGTVKRVEYGNVIVDLGN-SDGVIRRDETISR---ENLRPGDRVKSYIYDVRRE 192 + G+++ GTV +E V+VD+G S+GVI E + + ++ GD V+ + +R E Sbjct: 20 EPGDVVKGTVVSIEKDGVLVDIGGKSEGVIPISEFSNEPVEDVVQVGDEVEVLV--LRVE 77 Query: 193 QRGPQVLLSRTHPQFM 208 +++LSR + Sbjct: 78 DGEGELVLSRRKAERE 93 >gnl|CDD|88443 cd05688, S1_RPS1_repeat_ec3, S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.. Length = 68 Score = 34.4 bits (79), Expect = 0.077 Identities = 17/63 (26%), Positives = 31/63 (49%), Gaps = 8/63 (12%) Query: 138 VGEIISGTVKRVEYGNVIVDLGNSDGVIRRDETIS-------RENLRPGDRVKSYIYDVR 190 G+++ GTVK + VDLG DG++ + +S E + GD V+ + + Sbjct: 1 EGDVVEGTVKSITDFGAFVDLGGVDGLLHISD-MSWGRVKHPSEVVNVGDEVEVKVLKID 59 Query: 191 REQ 193 +E+ Sbjct: 60 KER 62 >gnl|CDD|146090 pfam03283, PAE, Pectinacetylesterase. Length = 366 Score = 34.2 bits (79), Expect = 0.091 Identities = 20/77 (25%), Positives = 33/77 (42%), Gaps = 19/77 (24%) Query: 213 HMEVPEIYNGIVQVKAVSRDPGS--------RAKL-----AVFSSDSSIDPVGACVGMRG 259 +ME ++GI+ S +P R K+ A FS DS + G + RG Sbjct: 82 YMEKTLTFSGIL-----SNNPEENPDFYNWNRVKIRYCDGASFSGDSEVVYKGTTLYFRG 136 Query: 260 SR-VQAVVTELRDEKID 275 R +AV+ +L + + Sbjct: 137 QRIWEAVIDDLLSKGMK 153 >gnl|CDD|144530 pfam00965, TIMP, Tissue inhibitor of metalloproteinase. Members of this family are common in extracellular regions of vertebrate species. Length = 174 Score = 32.0 bits (73), Expect = 0.46 Identities = 11/50 (22%), Positives = 18/50 (36%), Gaps = 4/50 (8%) Query: 160 NSDGVIRRDETISRENLR--PGDRVKSYIYDVRREQRGPQVLLSRTHPQF 207 N+D VIR + + L D+ Y + +G S Q+ Sbjct: 14 NADFVIRA--KVVGKKLVEQGNDKRIRYKVKQTKMFKGFSKAGSSLDIQY 61 >gnl|CDD|30738 COG0389, DinP, Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]. Length = 354 Score = 31.8 bits (72), Expect = 0.46 Identities = 13/56 (23%), Positives = 22/56 (39%) Query: 418 EGIDITLQKKIRELGVSEELCSIPGIDSKIKVALGENGIKTMEDLAGCSVDDLLGW 473 +GI + +++ L + G+ L GI T+ DLA +D L Sbjct: 159 DGITVIEPEEVPALLWQLPVLEFWGVGKVTAEKLRRLGISTIGDLAETDLDALKKR 214 >gnl|CDD|143804 pfam00013, KH_1, KH domain. KH motifs can bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia. Q4R966.1/333-392;. Length = 57 Score = 31.0 bits (71), Expect = 0.87 Identities = 10/34 (29%), Positives = 18/34 (52%) Query: 308 IEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDI 341 E+++P + IG+ G N++ + TG I I Sbjct: 2 EEILIPSSLVGRIIGKGGSNIKEIREETGAKIRI 35 >gnl|CDD|88463 cd05708, S1_Rrp5_repeat_sc12, S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.. Length = 77 Score = 31.0 bits (70), Expect = 0.93 Identities = 19/66 (28%), Positives = 36/66 (54%), Gaps = 8/66 (12%) Query: 137 KVGEIISGTVKRVEYGNVIVDLGNSD--GVIRRDETI------SRENLRPGDRVKSYIYD 188 KVG+ I GTV+RVE V +D+ ++ G+ + E + + R GD+V++ + Sbjct: 1 KVGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLK 60 Query: 189 VRREQR 194 + E++ Sbjct: 61 IDAEKK 66 >gnl|CDD|31378 COG1185, Pnp, Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]. Length = 692 Score = 29.8 bits (67), Expect = 1.8 Identities = 25/93 (26%), Positives = 42/93 (45%), Gaps = 20/93 (21%) Query: 110 AVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTVKRVE-YGNVIVDLGNSDGVIR-- 166 + + AK+ I RE E VGE+ GTV R+ +G + L DG++ Sbjct: 602 SAKKAKERIEAITREVE-----------VGEVYEGTVVRIVDFGAFVELLPGKDGLVHIS 650 Query: 167 -----RDETISRENLRPGDRVKSYIYDVRREQR 194 R E + + L+ GD VK + ++ ++ R Sbjct: 651 QLAKERVEKVE-DVLKEGDEVKVKVIEIDKQGR 682 >gnl|CDD|29002 cd00105, KH-I, K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.. Length = 64 Score = 29.8 bits (67), Expect = 2.1 Identities = 12/44 (27%), Positives = 18/44 (40%) Query: 308 IEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEEDSINR 351 V+VP + IG+ G ++ + TG I I S R Sbjct: 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEER 45 >gnl|CDD|176459 cd03586, PolY_Pol_IV_kappa, DNA Polymerase IV/Kappa. Pol IV, also known as Pol kappa, DinB, and Dpo4, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Known primarily as Pol IV in prokaryotes and Pol kappa in eukaryotes, this polymerase has a propensity for generating frameshift mutations. The eukaryotic Pol kappa differs from Pol IV and Dpo4 by an N-terminal extension of ~75 residues known as the "N-clasp" region. The structure of Pol kappa shows DNA that is almost totally encircled by Pol kappa, with the N-clasp region augmenting the interactions between DNA and the polymerase. Pol kappa is more resistant than Pol eta and Pol iota to bulky guanine adducts and is efficient at catalyzing the incorporation of dCTP. Bacterial pol IV has a higher error rate than other Y-family polymerases. Length = 334 Score = 29.0 bits (66), Expect = 3.0 Identities = 17/54 (31%), Positives = 24/54 (44%), Gaps = 4/54 (7%) Query: 425 QKKIRELGVSEELCSIPGIDSKIKVALGENGIKTMEDLAGCSVDDLLGWSENKG 478 ++ + L V + IPG+ L E GIKT+ DLA V+ L G Sbjct: 165 EEFLAPLPVRK----IPGVGKVTAEKLKELGIKTIGDLAKLDVELLKKLFGKSG 214 >gnl|CDD|38787 KOG3580, KOG3580, KOG3580, Tight junction proteins [Signal transduction mechanisms]. Length = 1027 Score = 28.9 bits (64), Expect = 3.1 Identities = 18/62 (29%), Positives = 26/62 (41%), Gaps = 2/62 (3%) Query: 136 DKVGEIISGTVKRVEYGNVIVDLGNSDGVIRRDETISRENLRPGDRVKSYIYDVRREQRG 195 + + G R Y NS G R S E RP +R +S D+ R++RG Sbjct: 118 FEDEDEFDGRSFRSGYSER--SRLNSHGGRSRSWEDSPERGRPHERARSRERDLSRDRRG 175 Query: 196 PQ 197 P+ Sbjct: 176 PR 177 >gnl|CDD|30441 COG0092, RpsC, Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]. Length = 233 Score = 29.1 bits (65), Expect = 3.4 Identities = 10/44 (22%), Positives = 20/44 (45%) Query: 286 FVINALRPAIVTKVVLDEDVGRIEVIVPKEQLSLAIGRRGQNVR 329 F+ L A ++ V ++ V + + L IG++G N+ Sbjct: 31 FLEKELSNAGISGVEIERTPKGTRVTIHAARPGLVIGKKGSNIE 74 >gnl|CDD|37490 KOG2279, KOG2279, KOG2279, Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]. Length = 608 Score = 28.9 bits (64), Expect = 3.5 Identities = 17/38 (44%), Positives = 27/38 (71%) Query: 308 IEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEE 345 IE++VP+E + L IGR+G N++ + TG ID+ TE+ Sbjct: 70 IEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTED 107 >gnl|CDD|34769 COG5169, HSF1, Heat shock transcription factor [Transcription]. Length = 282 Score = 28.5 bits (63), Expect = 4.8 Identities = 18/52 (34%), Positives = 26/52 (50%), Gaps = 7/52 (13%) Query: 255 VGMRGSRVQAVVTEL-----RDEKIDIVVWSPDSATFVINALRPAIVTKVVL 301 + R S+ + V +L E ++ WSPD +FVI L P TKV+L Sbjct: 3 MSSRWSQPKEFVHKLYQILEEPEYYKLIQWSPDGRSFVI--LDPEEFTKVIL 52 >gnl|CDD|28890 cd00006, PTS_IIA_man, PTS_IIA, PTS system, mannose/sorbose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation. IIA subunits receive phosphoryl groups from HPr and transfer them to IIB subunits, which in turn phosphorylate the substrate.. Length = 122 Score = 28.3 bits (63), Expect = 5.8 Identities = 9/51 (17%), Positives = 21/51 (41%) Query: 371 IIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRAREYLEGID 421 I H A G + E+ + + +I+ E+ ++ + + L +D Sbjct: 5 IATHGGFASGLLNSAEMILGEQENVEAIDFPPGESPDDLLEKIKAALAELD 55 >gnl|CDD|100033 cd02197, HypE, HypE (Hydrogenase expression/formation protein). HypE is involved in Ni-Fe hydrogenase biosynthesis. HypE dehydrates its own carbamoyl moiety in an ATP-dependent process to yield the enzyme thiocyanate. The N-terminal domain of HypE is related to the ATP-binding domains of the AIR synthases, selenophosphate synthetase (SelD), and FGAM synthase and is thought to bind ATP.. Length = 293 Score = 28.2 bits (64), Expect = 6.6 Identities = 11/20 (55%), Positives = 14/20 (70%) Query: 163 GVIRRDETISRENLRPGDRV 182 GVI R IS N+RPGD++ Sbjct: 137 GVIPRGVIISPSNIRPGDKI 156 >gnl|CDD|31292 COG1095, RPB7, DNA-directed RNA polymerase, subunit E' [Transcription]. Length = 183 Score = 27.9 bits (62), Expect = 6.6 Identities = 15/57 (26%), Positives = 26/57 (45%), Gaps = 1/57 (1%) Query: 132 LEFKDKVGEIISGTVKRVEYGNVIVDLGNSDGVIRRDETISRENLRPGDRVKSYIYD 188 L FK GE++ G V V V +G DG++ + I + + ++ K I + Sbjct: 75 LVFKPFRGEVVEGEVVEVVEFGAFVRIGPLDGLVHVSQ-IMDDYIDYDEKNKVLIGE 130 >gnl|CDD|32040 COG1855, COG1855, ATPase (PilT family) [General function prediction only]. Length = 604 Score = 27.9 bits (62), Expect = 6.7 Identities = 13/43 (30%), Positives = 23/43 (53%) Query: 306 GRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEEDS 348 GR V VP++ + IG+ G+ ++ + G ID+ EE+ Sbjct: 486 GRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLEEEE 528 >gnl|CDD|35793 KOG0573, KOG0573, KOG0573, Asparagine synthase [Amino acid transport and metabolism]. Length = 520 Score = 28.0 bits (62), Expect = 6.8 Identities = 20/85 (23%), Positives = 31/85 (36%), Gaps = 1/85 (1%) Query: 219 IYNGIVQVKAVSRDPGSRAKLAVFSSDSSIDPVGACVGMRGSRVQAVVTELRDEKIDIVV 278 Y+ RD R L + V + VG G + V R++ D V Sbjct: 122 YYDVRSDKLYFGRDDIGRRSLLYSLDPFNFSLVLSTVGTSGKLIYEVPPVFRNKLTDRVP 181 Query: 279 WSPDSATFVINALRPAIVTKVVLDE 303 W S T + N+L P++ + E Sbjct: 182 WPYLS-TKLENSLGPSLPPLCDISE 205 >gnl|CDD|88446 cd05691, S1_RPS1_repeat_ec6, S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.. Length = 73 Score = 27.8 bits (62), Expect = 7.1 Identities = 20/64 (31%), Positives = 33/64 (51%), Gaps = 9/64 (14%) Query: 139 GEIISGTVKRVEYGNVIVDLGNS-DGVIRRDETISRE-------NLRPGDRVKSYIYDVR 190 G I++G V V+ V LG+ +G +R E +SR+ + GD V++ I +V Sbjct: 1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAE-LSRDRVEDATERFKVGDEVEAKITNVD 59 Query: 191 REQR 194 R+ R Sbjct: 60 RKNR 63 >gnl|CDD|31304 COG1107, COG1107, Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]. Length = 715 Score = 28.0 bits (62), Expect = 7.3 Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 3/60 (5%) Query: 137 KVGEIISGTVKRVEYGNVIVDLGNSD--GVIRRDETISRENLRPGDRVKSYIYDVRREQR 194 + G+ G V RVE V V+L NS G+I R + + GD + + DVR E+ Sbjct: 121 EAGKYYKGIVSRVEKYGVFVEL-NSHVRGLIHRRDLGGDPDYAVGDEIIVQVSDVRPEKG 179 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 0.317 0.136 0.375 Gapped Lambda K H 0.267 0.0643 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 6,170,171 Number of extensions: 337363 Number of successful extensions: 973 Number of sequences better than 10.0: 1 Number of HSP's gapped: 966 Number of HSP's successfully gapped: 55 Length of query: 526 Length of database: 6,263,737 Length adjustment: 98 Effective length of query: 428 Effective length of database: 4,146,055 Effective search space: 1774511540 Effective search space used: 1774511540 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: 60 (27.1 bits)