RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780305|ref|YP_003064718.1| hypothetical protein CLIBASIA_00950 [Candidatus Liberibacter asiaticus str. psy62] (95 letters) >gnl|CDD|184876 PRK14876, PRK14876, conjugal transfer mating pair stabilization protein TraN; Provisional. Length = 928 Score = 33.7 bits (77), Expect = 0.010 Identities = 16/56 (28%), Positives = 27/56 (48%), Gaps = 4/56 (7%) Query: 6 IEQNFFSSQSDTNHTKNINITHYPEYTQCERVRIKQSLNNVPIH---IDDIIHHTG 58 I F ++T +N H PEY +C+RV + QS + +H + H++G Sbjct: 184 IAGGFGDCSAETTINQNTINAHIPEYERCQRV-VDQSGDCEVVHDYDAGVVKHYSG 238 >gnl|CDD|184948 PRK14986, PRK14986, glycogen phosphorylase; Provisional. Length = 815 Score = 27.1 bits (60), Expect = 1.1 Identities = 14/49 (28%), Positives = 28/49 (57%), Gaps = 2/49 (4%) Query: 9 NFFSSQSDTNHTKNINITHYP-EYTQCER-VRIKQSLNNVPIHIDDIIH 55 ++F++ D NH++N++ YP + T R +R++Q V + DI+ Sbjct: 251 DYFAAVEDKNHSENVSRVLYPDDSTYSGRELRLRQEYFLVSATVQDILS 299 >gnl|CDD|149509 pfam08482, HrpB_C, ATP-dependent helicase C-terminal. This domain is found near the C-terminus of bacterial ATP-dependent helicases such as HrpB. Length = 133 Score = 26.7 bits (60), Expect = 1.3 Identities = 18/44 (40%), Positives = 24/44 (54%), Gaps = 6/44 (13%) Query: 54 IHHTGIEAPVVYLVLLELDLAGRLCHHP---EGKVSLTMHLPSP 94 I ++G PV+ + L EL G L P G+V LT+HL SP Sbjct: 54 IDYSGDGGPVLAVRLQEL--FG-LTETPTIAGGRVPLTLHLLSP 94 >gnl|CDD|162630 TIGR01970, DEAH_box_HrpB, ATP-dependent helicase HrpB. This model represents HrpB, one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria, but also in a few species of other lineages. The member from Rhizobium meliloti has been designated HelO. HrpB is typically about 800 residues in length, while its paralog HrpA (TIGR01967), also uncharacterized, is about 1300 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing. Length = 819 Score = 26.3 bits (58), Expect = 1.8 Identities = 15/47 (31%), Positives = 20/47 (42%), Gaps = 9/47 (19%) Query: 57 TGIEAPVVYLVLLELDLAGRL------CHHP---EGKVSLTMHLPSP 94 TG + Y + LA RL P +G+V LT+ L SP Sbjct: 721 TGNFIAIRYSLDGPPLLAVRLQELFGLAESPRVAQGRVPLTLELLSP 767 >gnl|CDD|161893 TIGR00468, pheS, phenylalanyl-tRNA synthetase, alpha subunit. Most phenylalanyl-tRNA synthetases are heterodimeric, with 2 alpha (pheS) and 2 beta (pheT) subunits. This model describes the alpha subunit, which shows some similarity to class II aminoacyl-tRNA ligases. Mitochondrial phenylalanyl-tRNA synthetase is a single polypeptide chain, active as a monomer, and similar to this chain rather than to the beta chain, but excluded from this model. An interesting feature of the alignment of all sequences captured by this model is a deep split between non-spirochete bacterial examples and all other examples; supporting this split is a relative deletion of about 50 residues in the former set between two motifs well conserved throughout the alignment. Length = 294 Score = 25.7 bits (57), Expect = 2.7 Identities = 10/44 (22%), Positives = 21/44 (47%), Gaps = 2/44 (4%) Query: 22 NINITHYPEYTQCERVRIKQ--SLNNVPIHIDDIIHHTGIEAPV 63 ++ TH PE+ Q E + I + S N+ +++ + E + Sbjct: 164 TVDATHLPEFHQVEGLVIDKNVSFTNLKGFLEEFLKKMFGETEI 207 >gnl|CDD|178382 PLN02785, PLN02785, Protein HOTHEAD. Length = 587 Score = 25.5 bits (56), Expect = 2.8 Identities = 14/65 (21%), Positives = 27/65 (41%), Gaps = 16/65 (24%) Query: 4 PQIEQNFFSSQSDTNH--------TKNINITHYPEYTQCER--------VRIKQSLNNVP 47 P + N+F D K + H+ +TQC++ + +K ++N +P Sbjct: 441 PSVTFNYFKHPQDLQRCVYGIRTIEKIVKTNHFTNFTQCDKQTMEKVLNMSVKANINLIP 500 Query: 48 IHIDD 52 H +D Sbjct: 501 KHTND 505 >gnl|CDD|178973 PRK00311, panB, 3-methyl-2-oxobutanoate hydroxymethyltransferase; Reviewed. Length = 264 Score = 25.8 bits (58), Expect = 2.8 Identities = 9/24 (37%), Positives = 13/24 (54%), Gaps = 8/24 (33%) Query: 42 SLNNV--------PIHIDDIIHHT 57 SL V P+ +DD+I+HT Sbjct: 44 SLGMVVLGYDSTLPVTLDDMIYHT 67 >gnl|CDD|116156 pfam07537, CamS, CamS sex pheromone cAM373 precursor. This family includes CamS, from which Staphylococcus aureus sex pheromone staph-cAM373 is processed. Length = 318 Score = 25.5 bits (56), Expect = 2.8 Identities = 7/16 (43%), Positives = 9/16 (56%) Query: 35 ERVRIKQSLNNVPIHI 50 R+R +L NVPI Sbjct: 154 NRIRQNDNLKNVPITF 169 >gnl|CDD|183810 PRK12881, acnA, aconitate hydratase; Provisional. Length = 889 Score = 24.9 bits (55), Expect = 4.8 Identities = 6/12 (50%), Positives = 9/12 (75%) Query: 2 VHPQIEQNFFSS 13 +HP I+ NF +S Sbjct: 536 IHPNIKANFLAS 547 >gnl|CDD|178118 PLN02502, PLN02502, lysyl-tRNA synthetase. Length = 553 Score = 25.0 bits (55), Expect = 4.9 Identities = 7/13 (53%), Positives = 9/13 (69%) Query: 23 INITHYPEYTQCE 35 I+ H PE+T CE Sbjct: 312 ISTRHNPEFTTCE 324 >gnl|CDD|181987 PRK09607, rps11p, 30S ribosomal protein S11P; Reviewed. Length = 132 Score = 24.6 bits (54), Expect = 5.9 Identities = 10/24 (41%), Positives = 11/24 (45%), Gaps = 3/24 (12%) Query: 37 VRIKQSLNNVPIHIDDIIHHTGIE 60 I S NN I I D+ TG E Sbjct: 12 AHIYASFNNTIITITDL---TGAE 32 >gnl|CDD|163018 TIGR02784, addA_alphas, double-strand break repair helicase AddA, alphaproteobacterial type. AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination. The term AddAB is used broadly, with AddA homologous between the alphaproteobacteria (as modeled here) and the Firmicutes, while the partner AddB proteins show no strong homology across the two groups of species. Length = 1141 Score = 24.3 bits (53), Expect = 6.5 Identities = 8/10 (80%), Positives = 10/10 (100%) Query: 58 GIEAPVVYLV 67 G+EAPVV+LV Sbjct: 786 GLEAPVVFLV 795 >gnl|CDD|178385 PLN02788, PLN02788, phenylalanine-tRNA synthetase. Length = 402 Score = 24.0 bits (52), Expect = 9.5 Identities = 9/17 (52%), Positives = 12/17 (70%) Query: 23 INITHYPEYTQCERVRI 39 I+ THYP + Q E VR+ Sbjct: 162 IDATHYPVFHQMEGVRV 178 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 0.320 0.136 0.415 Gapped Lambda K H 0.267 0.0690 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 1,551,551 Number of extensions: 83127 Number of successful extensions: 137 Number of sequences better than 10.0: 1 Number of HSP's gapped: 137 Number of HSP's successfully gapped: 19 Length of query: 95 Length of database: 5,994,473 Length adjustment: 63 Effective length of query: 32 Effective length of database: 4,633,169 Effective search space: 148261408 Effective search space used: 148261408 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.1 bits)