RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780412|ref|YP_003064825.1| hypothetical protein CLIBASIA_01485 [Candidatus Liberibacter asiaticus str. psy62] (94 letters) >gnl|CDD|114945 pfam06253, MTTB, Trimethylamine methyltransferase (MTTB). This family consists of several trimethylamine methyltransferase (MTTB) (EC:2.1.1.-) proteins from numerous Rhizobium and Methanosarcina species. Length = 505 Score = 29.3 bits (66), Expect = 0.20 Identities = 9/56 (16%), Positives = 20/56 (35%), Gaps = 7/56 (12%) Query: 12 ASRLASCASDAFKDISKEAESFAQIKIQRTLNSMGVVRAEEIENVKRTTSHLREEI 67 A R A S ++ + ++ E++E + R + + EE+ Sbjct: 7 AGRRAMRGGPGAPQPS-------FPRLVNPIPPYQLLSDEQLERIHRASLRILEEV 55 >gnl|CDD|163223 TIGR03346, chaperone_ClpB, ATP-dependent chaperone ClpB. Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins. Length = 852 Score = 28.4 bits (64), Expect = 0.44 Identities = 19/63 (30%), Positives = 34/63 (53%), Gaps = 14/63 (22%) Query: 31 ESFAQIKIQRTLNSMGVVRAEEIENVKRTTSHLREEITAIGK--------RLEKIEQQLA 82 E+ A+I+++ ++S EE++ + R L E A+ K RLE +E++LA Sbjct: 391 EAAARIRME--IDSK----PEELDELDRRIIQLEIEREALKKEKDEASKERLEDLEKELA 444 Query: 83 DLE 85 +LE Sbjct: 445 ELE 447 >gnl|CDD|182605 PRK10636, PRK10636, putative ABC transporter ATP-binding protein; Provisional. Length = 638 Score = 28.2 bits (63), Expect = 0.49 Identities = 12/26 (46%), Positives = 16/26 (61%) Query: 60 TSHLREEITAIGKRLEKIEQQLADLE 85 T LR+EI + K +EK+ QLA E Sbjct: 558 TQPLRKEIARLEKEMEKLNAQLAQAE 583 >gnl|CDD|162062 TIGR00839, aspA, aspartate ammonia-lyase. Fumarate hydratase scores as high as 570 bits against this model. Length = 468 Score = 27.9 bits (62), Expect = 0.60 Identities = 22/87 (25%), Positives = 37/87 (42%), Gaps = 25/87 (28%) Query: 21 DAFKDISKEAESFAQIKIQRT-------------LNSMGVVRAEEIENVKRTTSHLRE-- 65 D F+ +KE +K+ RT + ++ EE++N+KRT L E Sbjct: 167 DGFEQKAKEFADI--LKMGRTQLQDAVPMTLGQEFEAFSILLEEEVKNIKRTAELLLEVN 224 Query: 66 -EITAIGKRL-------EKIEQQLADL 84 TAIG L + ++LA++ Sbjct: 225 LGATAIGTGLNTPPEYSPLVVKKLAEV 251 >gnl|CDD|177553 PHA03185, PHA03185, UL14 tegument protein; Provisional. Length = 214 Score = 27.3 bits (60), Expect = 0.94 Identities = 20/68 (29%), Positives = 36/68 (52%), Gaps = 1/68 (1%) Query: 19 ASDAFKDISKEAESFAQIKIQRTLNSMGVVRAEE-IENVKRTTSHLREEITAIGKRLEKI 77 A A +++ +S A++++ R + +R EE E +H R A+G+RL++ Sbjct: 50 AKAAHRELEARLKSRARLEMLRQHAACVKIRVEEQAERRDFLIAHRRYLDPALGERLDEA 109 Query: 78 EQQLADLE 85 E +LAD E Sbjct: 110 EDRLADQE 117 >gnl|CDD|180249 PRK05771, PRK05771, V-type ATP synthase subunit I; Validated. Length = 646 Score = 26.4 bits (59), Expect = 1.5 Identities = 15/87 (17%), Positives = 39/87 (44%), Gaps = 3/87 (3%) Query: 5 SNQFFQQASRLASCASDAFKDISKEAESFAQIKIQRTLNSMGVVRAEEIEN-VKRTTSHL 63 SN+ ++ L + S+A + ++ ++ + V EE+ V+ + Sbjct: 41 SNERLRKLRSLLTKLSEALDKLRSYLPKLNPLREEK--KKVSVKSLEELIKDVEEELEKI 98 Query: 64 REEITAIGKRLEKIEQQLADLELFINQ 90 +EI + + + ++E ++ +LE I + Sbjct: 99 EKEIKELEEEISELENEIKELEQEIER 125 >gnl|CDD|163162 TIGR03156, GTP_HflX, GTP-binding protein HflX. This protein family is one of a number of homologous small, well-conserved GTP-binding proteins with pleiotropic effects. Bacterial members are designated HflX, following the naming convention in Escherichia coli where HflX is encoded immediately downstream of the RNA chaperone Hfq, and immediately upstream of HflKC, a membrane-associated protease pair with an important housekeeping function. Over large numbers of other bacterial genomes, the pairing with hfq is more significant than with hflK and hlfC. The gene from Homo sapiens in this family has been named PGPL (pseudoautosomal GTP-binding protein-like). Length = 351 Score = 26.7 bits (60), Expect = 1.5 Identities = 9/19 (47%), Positives = 13/19 (68%) Query: 62 HLREEITAIGKRLEKIEQQ 80 +RE I + K LEK+E+Q Sbjct: 158 LIRERIAQLKKELEKVEKQ 176 >gnl|CDD|182934 PRK11058, PRK11058, GTPase HflX; Provisional. Length = 426 Score = 26.2 bits (58), Expect = 1.8 Identities = 9/18 (50%), Positives = 12/18 (66%) Query: 63 LREEITAIGKRLEKIEQQ 80 LR I I RLE++E+Q Sbjct: 167 LRNRIVQILSRLERVEKQ 184 >gnl|CDD|148090 pfam06273, eIF-4B, Plant specific eukaryotic initiation factor 4B. This family consists of several plant specific eukaryotic initiation factor 4B proteins. Length = 430 Score = 26.1 bits (57), Expect = 1.8 Identities = 21/61 (34%), Positives = 26/61 (42%), Gaps = 8/61 (13%) Query: 37 KIQRTLNSMGVVRAEEIENVKRTTSHLREEITAIGKRLEKIE---QQLADLELFINQKEK 93 KI L V R E E +L+EEI + K L+K E + I QKEK Sbjct: 294 KIDLELEHRRVDRPETEEE-----KNLKEEIELLKKELQKEEARXPKSKGSSELIRQKEK 348 Query: 94 E 94 E Sbjct: 349 E 349 >gnl|CDD|183393 PRK12273, aspA, aspartate ammonia-lyase; Provisional. Length = 472 Score = 26.2 bits (59), Expect = 1.9 Identities = 25/89 (28%), Positives = 39/89 (43%), Gaps = 29/89 (32%) Query: 21 DAFKDISKEAESFAQI-KIQRT-------------LNSMGVVRAEEIENVKRTTSHLREE 66 +AF+ +KE FA I K+ RT + V AE+ + + R LR E Sbjct: 171 EAFEAKAKE---FADILKMGRTQLQDAVPMTLGQEFGAYAVALAEDRKRLYRAAELLR-E 226 Query: 67 I----TAIGKRL-------EKIEQQLADL 84 + TAIG L E + ++LA++ Sbjct: 227 VNLGATAIGTGLNAPPGYIELVVEKLAEI 255 >gnl|CDD|163395 TIGR03683, A-tRNA_syn_arch, alanyl-tRNA synthetase. This family of alanyl-tRNA synthetases is limited to the archaea, and is a subset of those sequences identified by the model pfam07973 covering the second additional domain (SAD) of alanyl and threonyl tRNA synthetases. Length = 902 Score = 26.1 bits (58), Expect = 2.0 Identities = 19/81 (23%), Positives = 39/81 (48%), Gaps = 8/81 (9%) Query: 14 RLASCASDAFKDISKEAESFAQIKIQRTLNSMGVVRAEEIENVKRTTSHLREEITAIGKR 73 R+ A +A + +E E ++ + + + V + E VKR EE K Sbjct: 729 RIEFAAGEAALEYIQELED----LLRESSDILKVPPEQLPETVKR----FFEEWKEQRKE 780 Query: 74 LEKIEQQLADLELFINQKEKE 94 +E+++++LA+L+++ E E Sbjct: 781 IERLKKKLAELKIYELISEAE 801 >gnl|CDD|179074 PRK00591, prfA, peptide chain release factor 1; Validated. Length = 359 Score = 25.8 bits (58), Expect = 2.6 Identities = 9/30 (30%), Positives = 20/30 (66%) Query: 63 LREEITAIGKRLEKIEQQLADLELFINQKE 92 + +++ A+ +R E++E L+D E+ +QK Sbjct: 4 MLDKLEALEERYEELEALLSDPEVISDQKR 33 >gnl|CDD|178488 PLN02900, PLN02900, alanyl-tRNA synthetase. Length = 936 Score = 25.7 bits (57), Expect = 2.7 Identities = 14/40 (35%), Positives = 19/40 (47%) Query: 45 MGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQLADL 84 G V E +N KR T + EE + GK LEK ++ Sbjct: 360 SGDVFPEVKKNEKRITEIIAEEELSFGKTLEKGIEKFKKA 399 >gnl|CDD|184312 PRK13765, PRK13765, ATP-dependent protease Lon; Provisional. Length = 637 Score = 25.7 bits (57), Expect = 2.8 Identities = 26/70 (37%), Positives = 35/70 (50%), Gaps = 10/70 (14%) Query: 21 DAFKDISKEAESFAQIKIQRTL---NSMGVVR-AEEI---ENVKRTTSHLREEITAIGKR 73 DA ++I +EA+ A K TL + G+VR A +I E + TT E + K Sbjct: 343 DAVEEIIREAKRRAGRKGHLTLKLRDLGGLVRVAGDIARSEGAELTT---AEHVLEAKKI 399 Query: 74 LEKIEQQLAD 83 IEQQLAD Sbjct: 400 ARSIEQQLAD 409 >gnl|CDD|183309 PRK11778, PRK11778, putative inner membrane peptidase; Provisional. Length = 330 Score = 25.6 bits (57), Expect = 2.9 Identities = 8/11 (72%), Positives = 8/11 (72%) Query: 60 TSHLREEITAI 70 LREEITAI Sbjct: 106 VESLREEITAI 116 >gnl|CDD|182611 PRK10642, PRK10642, proline/glycine betaine transporter; Provisional. Length = 490 Score = 25.1 bits (55), Expect = 4.1 Identities = 7/23 (30%), Positives = 16/23 (69%) Query: 63 LREEITAIGKRLEKIEQQLADLE 85 L E I ++++ I+Q++A+L+ Sbjct: 454 LVEHYDNIEQKIDDIDQEIAELQ 476 >gnl|CDD|162740 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type. SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. Length = 1164 Score = 25.0 bits (55), Expect = 4.2 Identities = 21/84 (25%), Positives = 40/84 (47%), Gaps = 9/84 (10%) Query: 11 QASRLASCASDAFKDISKEAESFAQIKIQRTLNSMGVVRAEEIENVKRTTSHLREEITAI 70 + S+ S AS +I KE E Q + L E +E ++ S L +EI + Sbjct: 706 ELSQELSDASRKIGEIEKEIEQLEQE--EEKLK-------ERLEELEEDLSSLEQEIENV 756 Query: 71 GKRLEKIEQQLADLELFINQKEKE 94 L+++E ++ +LE +++ E+ Sbjct: 757 KSELKELEARIEELEEDLHKLEEA 780 Score = 25.0 bits (55), Expect = 4.4 Identities = 11/72 (15%), Positives = 37/72 (51%), Gaps = 4/72 (5%) Query: 23 FKDISKEAESFAQIKIQRTLNSMGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQLA 82 ++ + KE + ++ + ++ + E ++R + L EE+ + + + ++E++L Sbjct: 213 YQALLKEKREYEGYELLKEKEAL----ERQKEAIERQLASLEEELEKLTEEISELEKRLE 268 Query: 83 DLELFINQKEKE 94 ++E + + K+ Sbjct: 269 EIEQLLEELNKK 280 Score = 23.9 bits (52), Expect = 9.3 Identities = 10/44 (22%), Positives = 23/44 (52%) Query: 51 EEIENVKRTTSHLREEITAIGKRLEKIEQQLADLELFINQKEKE 94 E+ ++K + +EI + + E++E++L +LE + E Sbjct: 840 EQRIDLKEQIKSIEKEIENLNGKKEELEEELEELEAALRDLESR 883 >gnl|CDD|184382 PRK13902, alaS, alanyl-tRNA synthetase; Provisional. Length = 900 Score = 24.8 bits (55), Expect = 4.5 Identities = 13/58 (22%), Positives = 25/58 (43%), Gaps = 4/58 (6%) Query: 37 KIQRTLNSMGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQLADLELFINQKEKE 94 ++ +GV + + V+R EE K +EK+ ++LA+L + E Sbjct: 744 LLKEAAEILGVPPEQLPKTVER----FFEEWKEQKKEIEKLRKELAELLASELLSKAE 797 >gnl|CDD|149519 pfam08496, Peptidase_S49_N, Peptidase family S49 N-terminal. This domain is found to the N-terminus of bacterial signal peptidases of the S49 family (pfam01343). Length = 154 Score = 24.8 bits (55), Expect = 5.3 Identities = 8/11 (72%), Positives = 8/11 (72%) Query: 60 TSHLREEITAI 70 LREEITAI Sbjct: 113 VESLREEITAI 123 >gnl|CDD|161830 TIGR00344, alaS, alanine--tRNA ligase. The model describes alanine--tRNA ligase. This enzyme catalyzes the reaction (tRNAala + L-alanine + ATP = L-alanyl-tRNAala + pyrophosphate + AMP). Length = 851 Score = 24.7 bits (54), Expect = 6.4 Identities = 10/24 (41%), Positives = 14/24 (58%) Query: 40 RTLNSMGVVRAEEIENVKRTTSHL 63 R +N+ +R +IENV RT H Sbjct: 55 RLVNAQPCIRLNDIENVGRTARHH 78 >gnl|CDD|180144 PRK05580, PRK05580, primosome assembly protein PriA; Validated. Length = 679 Score = 24.0 bits (53), Expect = 8.1 Identities = 11/23 (47%), Positives = 15/23 (65%), Gaps = 4/23 (17%) Query: 67 ITAIGKRLEKIEQQLADLELFIN 89 + AI +RLE+ EQ L LF+N Sbjct: 356 LEAIKQRLERGEQVL----LFLN 374 >gnl|CDD|150352 pfam09660, DUF2397, Protein of unknown function (DUF2397). Proteins in this entry are encoded within a conserved gene four-gene neighbourhood found sporadically in a phylogenetically broad range of bacteria including: Nocardia farcinica, Symbiobacterium thermophilum, and Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. EbN1 and Ralstonia solanacearum (Betaproteobacteria). Length = 478 Score = 24.2 bits (53), Expect = 8.3 Identities = 9/28 (32%), Positives = 13/28 (46%) Query: 58 RTTSHLREEITAIGKRLEKIEQQLADLE 85 +LR+ I + +R KI L LE Sbjct: 187 LLIDYLRDFIRDLQRRSAKIAAALRALE 214 >gnl|CDD|179675 PRK03918, PRK03918, chromosome segregation protein; Provisional. Length = 880 Score = 23.9 bits (52), Expect = 9.0 Identities = 14/43 (32%), Positives = 22/43 (51%) Query: 51 EEIENVKRTTSHLREEITAIGKRLEKIEQQLADLELFINQKEK 93 E++E + L+EEI + K LE +E LE I + E+ Sbjct: 224 EKLEKEVKELEELKEEIEELEKELESLEGSKRKLEEKIRELEE 266 >gnl|CDD|131666 TIGR02617, tnaA_trp_ase, tryptophanase, leader peptide-associated. Members of this family belong to the beta-eliminating lyase family (pfam01212) and act as tryptophanase (L-tryptophan indole-lyase). The tryptophanases of this family, as a rule, are found with a tryptophanase leader peptide (TnaC) encoded upstream. Both tryptophanases (4.1.99.1) and tyrosine phenol-lyases (EC 4.1.99.2) are found between trusted and noise cutoffs, but this model captures nearly all tryptophanases for which the leader peptide gene tnaC can be found upstream. Length = 467 Score = 23.7 bits (51), Expect = 9.6 Identities = 10/18 (55%), Positives = 11/18 (61%) Query: 49 RAEEIENVKRTTSHLREE 66 R IE VKRTT RE+ Sbjct: 8 RIRVIEPVKRTTRAYREK 25 >gnl|CDD|179861 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional. Length = 572 Score = 23.8 bits (51), Expect = 9.9 Identities = 13/32 (40%), Positives = 17/32 (53%) Query: 60 TSHLREEITAIGKRLEKIEQQLADLELFINQK 91 T+ L EE AI E+ L D+E +I QK Sbjct: 348 TARLGEEGDAISFACERYAMSLPDIEAYIEQK 379 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 0.315 0.126 0.320 Gapped Lambda K H 0.267 0.0691 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 1,441,858 Number of extensions: 79750 Number of successful extensions: 486 Number of sequences better than 10.0: 1 Number of HSP's gapped: 469 Number of HSP's successfully gapped: 176 Length of query: 94 Length of database: 5,994,473 Length adjustment: 62 Effective length of query: 32 Effective length of database: 4,654,777 Effective search space: 148952864 Effective search space used: 148952864 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: 50 (23.1 bits)