RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780391|ref|YP_003064804.1| DNA polymerase III subunit chi [Candidatus Liberibacter asiaticus str. psy62] (141 letters) >gnl|CDD|180224 PRK05728, PRK05728, DNA polymerase III subunit chi; Validated. Length = 142 Score = 92.6 bits (231), Expect = 3e-20 Identities = 39/122 (31%), Positives = 60/122 (49%), Gaps = 7/122 (5%) Query: 17 LLVLLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWKKDGFLPHGVDVGDEGDFSSFQPVL 76 L L + G RV VQC E ++L+E LWT++ + FLPHG ++ QPVL Sbjct: 18 LCELAEKALRAGWRVLVQCEDEEQAEALDEALWTFRDESFLPHG---LAGEGPAAGQPVL 74 Query: 77 LTISSL-NANTSTIRFLVDEASMHIGDVDYYEKVVFIINTDDQGSLEWGRAHWRSLKNSG 135 LT NAN + +D A +E+VV + D+ + + R W++ + +G Sbjct: 75 LTWPGKRNANHRDLLINLDGA--VPAFAAAFERVVDFVGYDEA-AKQAARERWKAYRAAG 131 Query: 136 YA 137 YA Sbjct: 132 YA 133 >gnl|CDD|102480 PRK06646, PRK06646, DNA polymerase III subunit chi; Provisional. Length = 154 Score = 31.9 bits (72), Expect = 0.068 Identities = 14/53 (26%), Positives = 29/53 (54%), Gaps = 3/53 (5%) Query: 41 RDSLNEYLWTWKKDGFLPHGVDVGDEGDFSSFQPVLLTISSLNANTSTIRFLV 93 ++ LN+ LWT+ + F+PHG + + QP+ +T N N +++ ++ Sbjct: 42 QEMLNKNLWTYSRKQFIPHGSKLDPQ---PEKQPIYITDELQNPNNASVLVII 91 >gnl|CDD|130353 TIGR01286, nifK, nitrogenase molybdenum-iron protein beta chain. This model represents the majority of known sequences of the nitrogenase molybdenum-iron protein beta subunit. A distinct clade in a phylogenetic tree contains molybdenum-iron, vanadium-iron, and iron-iron forms of nitrogenase beta subunit and is excluded from this model. Nitrogenase, also called dinitrogenase, is responsible for nitrogen fixation. Note: the trusted cutoff score has recently been lowered to include an additional family in which the beta subunit is shorter by about 50 amino acids at the N-terminus. In species with the shorter form of the beta subunit, the alpha subunit has a novel insert of similar length. Length = 515 Score = 27.9 bits (62), Expect = 0.98 Identities = 13/33 (39%), Positives = 19/33 (57%) Query: 31 VSVQCGSERVRDSLNEYLWTWKKDGFLPHGVDV 63 VS C +E + D LN ++ KK+GF+P V Sbjct: 148 VSTTCMAEVIGDDLNAFIGNAKKEGFIPDDFPV 180 >gnl|CDD|177527 PHA03095, PHA03095, ankyrin-like protein; Provisional. Length = 471 Score = 26.5 bits (59), Expect = 2.3 Identities = 16/48 (33%), Positives = 22/48 (45%), Gaps = 2/48 (4%) Query: 57 LPHGVDVGDEGDFSSFQPVLLTISSLNANTSTIRFLVDEASMHIGDVD 104 L G DV D P+ + + S NAN +R L+D A + VD Sbjct: 139 LRKGADVNAL-DLYGMTPLAVLLKSRNANVELLRLLID-AGADVYAVD 184 >gnl|CDD|180659 PRK06690, PRK06690, acetyl-CoA acetyltransferase; Provisional. Length = 361 Score = 26.7 bits (59), Expect = 2.4 Identities = 11/46 (23%), Positives = 21/46 (45%), Gaps = 10/46 (21%) Query: 72 FQPVLLTISSL----------NANTSTIRFLVDEASMHIGDVDYYE 107 ++PVL + S + L++E +M + D+DY+E Sbjct: 237 YKPVLRFVRSAVVGVDPNLPGTGPIFAVNKLLNEMNMKVEDIDYFE 282 >gnl|CDD|151221 pfam10740, DUF2529, Protein of unknown function (DUF2529). This family is conserved in the Bacillales. The function is not known. Several members are annotated as being YWJG, a protein expressed downstream of pyrG, a gene encoding for cytidine triphosphate synthetase. Length = 172 Score = 26.5 bits (59), Expect = 2.5 Identities = 16/47 (34%), Positives = 24/47 (51%), Gaps = 2/47 (4%) Query: 2 RTLLFYRFKNDWEYNLLVLLQDEYEKGKRVSVQCGSERVRDSLNEYL 48 R LLF RF ND E + L + Y++G V + + DSL ++ Sbjct: 84 RVLLFSRFSNDEE--AVALAKKLYDQGIDVVAVSPNAKEGDSLADHA 128 >gnl|CDD|165290 PHA02987, PHA02987, Ig domain OX-2-like protein; Provisional. Length = 189 Score = 25.6 bits (56), Expect = 5.3 Identities = 17/52 (32%), Positives = 25/52 (48%), Gaps = 11/52 (21%) Query: 43 SLNEYLWTWKKD-----GFLPHGVDVGDEGDFSSFQPVLLTISSLNANTSTI 89 S N L TWKK+ G+ P G + D+ F+ + +S + N STI Sbjct: 42 SFNSILITWKKNNKTIAGYGPCGPVIVDK-----FKNKIEYLSK-SFNESTI 87 >gnl|CDD|151517 pfam11072, DUF2859, Protein of unknown function (DUF2859). This is a bacterial family of uncharacterized proteins. Length = 142 Score = 25.3 bits (56), Expect = 5.4 Identities = 12/68 (17%), Positives = 21/68 (30%), Gaps = 11/68 (16%) Query: 73 QPVLLTISSLNANTSTIRFLVDEASMHIGDVDYYEKV--------VFIINTDDQGSLEWG 124 +P S V + G V+ + +F+I D S +W Sbjct: 22 EPQPSPPSPPAGALEAAMLPVRSPRLSPGVVE--RRALNLPGLQPLFLIGDDPA-SRQWL 78 Query: 125 RAHWRSLK 132 + + LK Sbjct: 79 QQNADELK 86 >gnl|CDD|179773 PRK04184, PRK04184, DNA topoisomerase VI subunit B; Validated. Length = 535 Score = 25.2 bits (56), Expect = 6.7 Identities = 14/46 (30%), Positives = 21/46 (45%), Gaps = 11/46 (23%) Query: 58 PHGVDVGDEGDFSSFQPVLLTISSLNANTSTIRFLVDEASMHIGDV 103 PHGVD+G L +++ + FLV+E S +GD Sbjct: 238 PHGVDLGT----------LKRMAARTKRRTLKEFLVEEFS-RVGDK 272 >gnl|CDD|162338 TIGR01398, FlhA, flagellar biosynthesis protein FlhA. This model describes flagellar biosynthesis protein FlhA, one of a large number of genes associated with the biosynthesis of functional bacterial flagella. Homologs of many such proteins, including FlhA, function in type III protein secretion systems. A separate model describes InvA (Salmonella enterica), LcrD (Yersinia enterocolitica), HrcV (Xanthomonas), etc., all of which score below the noise cutoff for this model. Length = 678 Score = 24.5 bits (54), Expect = 9.0 Identities = 11/25 (44%), Positives = 16/25 (64%), Gaps = 2/25 (8%) Query: 68 DFSSFQPVLL--TISSLNANTSTIR 90 DFSSF +LL T+ L+ N ++ R Sbjct: 52 DFSSFPTLLLIATLFRLSLNVASTR 76 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 0.138 0.431 Gapped Lambda K H 0.267 0.0754 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 2,313,934 Number of extensions: 131649 Number of successful extensions: 242 Number of sequences better than 10.0: 1 Number of HSP's gapped: 240 Number of HSP's successfully gapped: 16 Length of query: 141 Length of database: 5,994,473 Length adjustment: 84 Effective length of query: 57 Effective length of database: 4,179,401 Effective search space: 238225857 Effective search space used: 238225857 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: 52 (23.8 bits)