RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254781063|ref|YP_003065476.1| hypothetical protein CLIBASIA_04825 [Candidatus Liberibacter asiaticus str. psy62] (129 letters) >gnl|CDD|131990 TIGR02945, SUF_assoc, FeS assembly SUF system protein. Members of this family belong to the broader Pfam family pfam01883, or Domain of Unknown Function DUF59. Many members of DUF59 are candidate ring hydroxylating complex subunits. However, members of the narrower family defined here all are found in genomes that carry the FeS assembly SUF system. For 70 % of these species, the member of this protein family is found as part of the SUF locus, usually immediately downstream of the sufS gene. Length = 99 Score = 152 bits (386), Expect = 3e-38 Identities = 60/99 (60%), Positives = 75/99 (75%) Query: 31 RISNDIIAALKTVYDPEIPCDIFELGLIYKIDVENDYMVKILMTLTAPGCPVAGDMPKWI 90 R+ + +I ALKTVYDPEIP +I+ELGLIY IDV++D V I MTLTAP CPVAG MP + Sbjct: 1 RLKDAVIEALKTVYDPEIPVNIYELGLIYDIDVDDDGHVDIQMTLTAPNCPVAGSMPGEV 60 Query: 91 ENAVGAVEGISGVEVSITFDPPWTPDLMSEEAQIATGYY 129 ENAV AV G+ V V + +DPPWTP+ MSEEA++ G + Sbjct: 61 ENAVRAVPGVGSVTVELVWDPPWTPERMSEEARLELGMF 99 >gnl|CDD|132447 TIGR03406, FeS_long_SufT, probable FeS assembly SUF system protein SufT. The function is unknown for this protein family, but members are found almost always in operons for the the SUF system of iron-sulfur cluster biosynthesis. The SUF system is present elsewhere on the chromosome for those few species where SUF genes are not adjacent. This family shares this property of association with the SUF system with a related family, TIGR02945. TIGR02945 consists largely of a DUF59 domain (see Pfam family pfam01883), while this protein is about double the length, with a unique N-terminal domain and DUF59 C-terminal domain. A location immediately downstream of the cysteine desulfurase gene sufS in many contexts suggests the gene symbol sufT. Note that some other homologs of this family and of TIGR02945, but no actual members of this family, are found in operons associated with phenylacetic acid (or other ring-hydroxylating) degradation pathways. Length = 174 Score = 103 bits (260), Expect = 9e-24 Identities = 51/126 (40%), Positives = 69/126 (54%), Gaps = 15/126 (11%) Query: 13 ADKIALSP--ESTIPPEDLERISNDII-AALKTVYDPEIPCDIFELGLIYKIDVE----N 65 AD + P +P + D + L+TVYDPEIP +I +LGL+Y VE Sbjct: 52 ADALGKEPPPPLDLPENADGEDNEDQVWEQLRTVYDPEIPVNIVDLGLVYGCRVEKLGEG 111 Query: 66 DYMVKILMTLTAPGC---PV-AGDMPKWIENAVGAVEGISGVEVSITFDPPWTPDLMSEE 121 + V I MTLTAPGC PV D +E+ V AV + VEV + FDPPW+ ++MSE Sbjct: 112 QFRVDIEMTLTAPGCGMGPVLVED----VEDKVLAVPNVDEVEVELVFDPPWSREMMSEA 167 Query: 122 AQIATG 127 A++ G Sbjct: 168 AKLELG 173 >gnl|CDD|131214 TIGR02159, PA_CoA_Oxy4, phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA. Length = 146 Score = 57.1 bits (138), Expect = 1e-09 Identities = 33/82 (40%), Positives = 51/82 (62%), Gaps = 3/82 (3%) Query: 43 VYDPEIPC-DIFELGLIYKIDVENDYMVKILMTLTAPGCPVAGDMPKWIENAVGAVEGIS 101 V DPEIP + +LG++ ++DV+ V + T T GCP + + I +AV A+ G+ Sbjct: 1 VPDPEIPVVSVTDLGMVREVDVDGG-GVVVKFTPTYSGCPALEVIRQDIRDAVRAL-GVE 58 Query: 102 GVEVSITFDPPWTPDLMSEEAQ 123 VEVS + DPPWT D ++E+A+ Sbjct: 59 VVEVSTSLDPPWTTDWITEDAR 80 >gnl|CDD|183761 PRK12806, PRK12806, flagellin; Provisional. Length = 475 Score = 30.0 bits (67), Expect = 0.18 Identities = 24/125 (19%), Positives = 44/125 (35%), Gaps = 5/125 (4%) Query: 7 DTENNIADKIALSPESTIPPEDLERISNDIIAALKTVYDPEIPCDIFELGL----IYKID 62 ++ NN +D+ ++ E + +LERI+ + + + D F++G Sbjct: 101 NSTNNSSDRASIQSEISQLKSELERIAQNTEFNGQRILDGSFSGASFQVGANSNQTINFS 160 Query: 63 VENDYMVKILMTLTAPGCPVAGDMPKWIENAVGAVEGISGVEVSITFDPPWTPDLMSEEA 122 + + I TA G VAG I A+G + + S F + Sbjct: 161 IGSIKASSIGGIATATGTEVAGAAATDITIAIGGGA-ATSINSSANFTGALNGQDATSAY 219 Query: 123 QIATG 127 A Sbjct: 220 AKAAA 224 >gnl|CDD|179579 PRK03437, PRK03437, 3-isopropylmalate dehydrogenase; Provisional. Length = 344 Score = 27.2 bits (61), Expect = 1.2 Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 4/65 (6%) Query: 23 TIPPEDLERI-SNDIIAALKTVYDPEIPCDIFELGLIYKIDVENDYMVKILMTLTAPG-- 79 T+P L + +D I L + DP +P + E GL+ K+ D+ V + + PG Sbjct: 55 TLPDSVLAELRQHDAIL-LGAIGDPSVPSGVLERGLLLKLRFALDHYVNLRPSKLYPGVT 113 Query: 80 CPVAG 84 P+AG Sbjct: 114 SPLAG 118 >gnl|CDD|118064 pfam09528, Ehrlichia_rpt, Ehrlichia tandem repeat (Ehrlichia_rpt). This entry represents 77 residues of an 80 amino acid (240 nucleotide) tandem repeat, found in a variable number of copies in an immunodominant outer membrane protein of Ehrlichia chaffeensis, a tick-borne obligate intracellular pathogen. Length = 707 Score = 26.5 bits (57), Expect = 2.0 Identities = 10/43 (23%), Positives = 23/43 (53%) Query: 83 AGDMPKWIENAVGAVEGISGVEVSITFDPPWTPDLMSEEAQIA 125 A D+P +++++ G +V F + P++++E+ Q A Sbjct: 521 AEDLPPAVDDSLEHSIPEVGEKVDEMFAEEFNPEVIAEDLQPA 563 >gnl|CDD|184487 PRK14071, PRK14071, 6-phosphofructokinase; Provisional. Length = 360 Score = 26.2 bits (58), Expect = 2.5 Identities = 26/79 (32%), Positives = 32/79 (40%), Gaps = 20/79 (25%) Query: 33 SNDIIAALKTVYDPEIPCDIFELGLIYKIDVENDYMVKILMTLTAPG-CPVAGDMPKWIE 91 S +II LGL I + D + IL L G + G +PK I+ Sbjct: 96 SQEIIDGYH------------SLGLDALIGIGGDGSLAILRRLAQQGGINLVG-IPKTID 142 Query: 92 NAVGAVEGISGVEVSITFD 110 N VGA EVSI FD Sbjct: 143 NDVGA------TEVSIGFD 155 >gnl|CDD|131709 TIGR02661, MauD, methylamine dehydrogenase accessory protein MauD. This protein, MauD, appears critical to proper formation of the small subunit of methylamine dehydrogenase, which has both an unusual tryptophan tryptophylquinone cofactor and multiple disulfide bonds. MauD shares sequence similarity, including a CPxC motif, with a number of thiol:disulfide interchange proteins. In MauD mutants, the small subunit apparently does not form properly and is rapidly degraded. Length = 189 Score = 26.0 bits (57), Expect = 2.7 Identities = 11/35 (31%), Positives = 17/35 (48%), Gaps = 1/35 (2%) Query: 72 LMTLTAPGCPVAGDMPKWIENAVGAVEGISGVEVS 106 L+ TAP CPV + I+ ++ E V +S Sbjct: 78 LLMFTAPSCPVCDKLFPIIK-SIARAEETDVVMIS 111 >gnl|CDD|132287 TIGR03243, arg_catab_AOST, arginine and ornithine succinyltransferase subunits. In many bacteria, the sole member of this protein family is arginine N-succinyltransferase (EC 2.3.1.109), the AstA protein of the arginine succinyltransferase (ast) pathway. However, in Pseudomonas aeruginosa and several other species, a tandem gene pair encodes alpha and beta subunits of a heterodimer that is designated arginine and ornithine succinyltransferase (AOST). Length = 335 Score = 26.1 bits (58), Expect = 3.1 Identities = 7/19 (36%), Positives = 12/19 (63%) Query: 95 GAVEGISGVEVSITFDPPW 113 G V G+S +E ++ D P+ Sbjct: 66 GTVAGVSAIEAAVGLDEPF 84 >gnl|CDD|179052 PRK00513, minC, septum formation inhibitor; Reviewed. Length = 214 Score = 25.6 bits (57), Expect = 3.9 Identities = 11/28 (39%), Positives = 13/28 (46%), Gaps = 2/28 (7%) Query: 12 IADKIALSPESTIPPEDLE--RISNDII 37 IAD IA +PE P E I + I Sbjct: 174 IADVIARAPEDKEKPNYPEVAYIKDGGI 201 >gnl|CDD|173066 PRK14602, ruvA, Holliday junction DNA helicase RuvA; Provisional. Length = 203 Score = 25.4 bits (56), Expect = 4.5 Identities = 24/74 (32%), Positives = 33/74 (44%), Gaps = 4/74 (5%) Query: 15 KIALSPESTIPPEDLERI-SNDIIAALKTV--YDPEIPCDIFELGLIYKIDVENDYMVKI 71 K AL+ S P+DL R+ + + +AAL V + IF L L YK+ VE + Sbjct: 85 KTALAILSQFRPDDLRRLVAEEDVAALTRVSGIGKKTAQHIF-LELKYKLKVEGLPAAAV 143 Query: 72 LMTLTAPGCPVAGD 85 L A V D Sbjct: 144 LAGTGAVPGSVFRD 157 >gnl|CDD|179038 PRK00464, nrdR, transcriptional regulator NrdR; Validated. Length = 154 Score = 25.1 bits (56), Expect = 4.8 Identities = 6/26 (23%), Positives = 12/26 (46%) Query: 24 IPPEDLERISNDIIAALKTVYDPEIP 49 + E +E + I L+ + E+P Sbjct: 79 VSSEQIEAAVSRIERQLRASGEREVP 104 >gnl|CDD|148093 pfam06278, DUF1032, Protein of unknown function (DUF1032). This family consists of several conserved eukaryotic proteins of unknown function. Length = 565 Score = 25.3 bits (55), Expect = 5.2 Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 10/39 (25%) Query: 6 PDTENNIADK----------IALSPESTIPPEDLERISN 34 D+E N+ K I L P + +PPE++E+ SN Sbjct: 74 EDSEANVDLKDDQITSPVLIIPLLPMALVPPEEVEKNSN 112 >gnl|CDD|165553 PHA03296, PHA03296, envelope glycoprotein H; Provisional. Length = 814 Score = 25.0 bits (54), Expect = 6.0 Identities = 19/65 (29%), Positives = 29/65 (44%), Gaps = 2/65 (3%) Query: 15 KIALSPESTIPPEDLERISNDIIAALKTVYDPEIPCDIF--ELGLIYKIDVENDYMVKIL 72 KI LS E + L S IAA + + P+ D F EL + D+E+ + I Sbjct: 571 KIFLSGEGELETAALLDDSARAIAAAQALGGPKALADAFFPELAKCFDWDLEHHIVFFIA 630 Query: 73 MTLTA 77 ++ A Sbjct: 631 ISAHA 635 >gnl|CDD|181078 PRK07678, PRK07678, aminotransferase; Validated. Length = 451 Score = 25.0 bits (55), Expect = 6.4 Identities = 14/43 (32%), Positives = 21/43 (48%), Gaps = 6/43 (13%) Query: 4 KNPDT---ENNIADKIALSPESTIPPEDLERISNDIIAALKTV 43 KN DT NN+ + LSP I E++ I + AL+ + Sbjct: 411 KNGDTVAGYNNV---LTLSPPLVISSEEIAFIVGTLKTALERI 450 >gnl|CDD|147801 pfam05843, Suf, Suppressor of forked protein (Suf). This family consists of several eukaryotic suppressor of forked (Suf) like proteins. The Drosophila melanogaster Suppressor of forked [Su(f)] protein shares homology with the yeast RNA14 protein and the 77-kDa subunit of human cleavage stimulation factor, which are proteins involved in mRNA 3' end formation. This suggests a role for Su(f) in mRNA 3' end formation in Drosophila. The su(f) gene produces three transcripts; two of them are polyadenylated at the end of the transcription unit, and one is a truncated transcript, polyadenylated in intron 4. It is thought that su(f) plays a role in the regulation of poly(A) site utilisation and an important role of the GU-rich sequence for this regulation to occur. Length = 275 Score = 25.0 bits (55), Expect = 6.6 Identities = 8/13 (61%), Positives = 9/13 (69%) Query: 45 DPEIPCDIFELGL 57 DP+ IFELGL Sbjct: 51 DPKTAFKIFELGL 63 >gnl|CDD|183738 PRK12775, PRK12775, putative trifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta/ferritin domain-containing protein; Provisional. Length = 1006 Score = 24.9 bits (54), Expect = 6.9 Identities = 12/27 (44%), Positives = 16/27 (59%), Gaps = 5/27 (18%) Query: 79 GCPVAGDMPKWIENAV-----GAVEGI 100 GCPV D+P +I + V GA+E I Sbjct: 344 GCPVQIDIPVFIRHVVVRDFDGALEVI 370 >gnl|CDD|132288 TIGR03244, arg_catab_AstA, arginine N-succinyltransferase. In many bacteria, the arginine succinyltransferase (ast) pathway operon consists of five genes, including this protein, arginine N-succinyltransferase (EC 2.3.1.109). In a few species, such as Pseudomonas aeruginosa, the member of this family is encoded adjacent to a paralog, and the two polypeptides form a heterodimeric enzyme, active on both arginine and ornithine. In such species, this polypeptide may be treated as the beta subunit of an enzyme that may be named either arginine N-succinyltransferase (AST) or arginine and orthithine N-succinyltransferase (AOST). Length = 336 Score = 24.6 bits (54), Expect = 7.9 Identities = 6/19 (31%), Positives = 12/19 (63%) Query: 95 GAVEGISGVEVSITFDPPW 113 G V G+S +E ++ + P+ Sbjct: 66 GTVAGVSAIEAAVGLEEPF 84 >gnl|CDD|149445 pfam08385, DHC_N1, Dynein heavy chain, N-terminal region 1. Dynein heavy chains interact with other heavy chains to form dimers, and with intermediate chain-light chain complexes to form a basal cargo binding unit. The region featured in this family includes the sequences implicated in mediating these interactions. It is thought to be flexible and not to adopt a rigid conformation. Length = 577 Score = 24.5 bits (54), Expect = 7.9 Identities = 12/27 (44%), Positives = 16/27 (59%), Gaps = 3/27 (11%) Query: 29 LERISNDIIAALKTVYDPEIPCDIFEL 55 LE+ISND+I LK+ P D+ L Sbjct: 150 LEKISNDLIDQLKSYLSPS---DLMSL 173 >gnl|CDD|181589 PRK08943, PRK08943, lipid A biosynthesis (KDO)2-(lauroyl)-lipid IVA acyltransferase; Validated. Length = 314 Score = 24.4 bits (54), Expect = 8.1 Identities = 6/19 (31%), Positives = 9/19 (47%) Query: 107 ITFDPPWTPDLMSEEAQIA 125 I PP L +++ IA Sbjct: 260 IEIRPPMDDLLSADDETIA 278 >gnl|CDD|180329 PRK05964, PRK05964, adenosylmethionine--8-amino-7-oxononanoate transaminase; Provisional. Length = 423 Score = 24.4 bits (54), Expect = 8.2 Identities = 9/28 (32%), Positives = 15/28 (53%) Query: 16 IALSPESTIPPEDLERISNDIIAALKTV 43 I L P I E+L+RI++ I+ + Sbjct: 396 IYLMPPYIITAEELDRITDAIVEVADEL 423 >gnl|CDD|161821 TIGR00331, hrcA, heat shock gene repressor HrcA. In Bacillus subtilis, hrcA is the first gene of the dnaK operon and so is itself a heat shock gene. Length = 337 Score = 24.2 bits (53), Expect = 9.3 Identities = 16/50 (32%), Positives = 22/50 (44%) Query: 18 LSPESTIPPEDLERISNDIIAALKTVYDPEIPCDIFELGLIYKIDVENDY 67 + + I EDLER N + L+ EI I EL KI++E Sbjct: 161 IELPANISQEDLERAVNILNDRLRGRTLSEIREQIIELLSQLKIEIEEFE 210 >gnl|CDD|165212 PHA02884, PHA02884, ankyrin repeat protein; Provisional. Length = 300 Score = 24.2 bits (52), Expect = 9.5 Identities = 21/48 (43%), Positives = 25/48 (52%), Gaps = 5/48 (10%) Query: 35 DII-AALKTVYDPEIPCDIFELG----LIYKIDVENDYMVKILMTLTA 77 DII A LK DPE P + E LIY ID +ND K+L+ A Sbjct: 47 DIIDAILKLGADPEAPFPLSENSKTNPLIYAIDCDNDDAAKLLIRYGA 94 >gnl|CDD|182474 PRK10456, PRK10456, arginine succinyltransferase; Provisional. Length = 344 Score = 24.3 bits (53), Expect = 10.0 Identities = 8/19 (42%), Positives = 12/19 (63%) Query: 95 GAVEGISGVEVSITFDPPW 113 G V GI +EV++ + PW Sbjct: 68 GTVAGICAIEVAVGLNDPW 86 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 0.314 0.136 0.404 Gapped Lambda K H 0.267 0.0819 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 2,257,988 Number of extensions: 136224 Number of successful extensions: 251 Number of sequences better than 10.0: 1 Number of HSP's gapped: 249 Number of HSP's successfully gapped: 42 Length of query: 129 Length of database: 5,994,473 Length adjustment: 83 Effective length of query: 46 Effective length of database: 4,201,009 Effective search space: 193246414 Effective search space used: 193246414 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: 42 (21.9 bits) S2: 51 (23.3 bits)