RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254781089|ref|YP_003065502.1| hypothetical protein CLIBASIA_04955 [Candidatus Liberibacter asiaticus str. psy62] (80 letters) >gnl|CDD|179385 PRK02224, PRK02224, chromosome segregation protein; Provisional. Length = 880 Score = 31.2 bits (71), Expect = 0.068 Identities = 11/20 (55%), Positives = 16/20 (80%), Gaps = 2/20 (10%) Query: 2 GLSESGKTTLLEAIF--LFG 19 G++ SGK++LLEA F L+G Sbjct: 30 GVNGSGKSSLLEACFFALYG 49 >gnl|CDD|132456 TIGR03415, ABC_choXWV_ATP, choline ABC transporter, ATP-binding protein. Members of this protein family are the ATP-binding subunit of a three-protein transporter. This family belongs, more broadly, to the family of proline and glycine-betaine transporters, but members have been identified by direct characterization and by bioinformatic means as choline transporters. Many species have several closely-related members of this family, probably with variable abilities to act additionally on related quaternary amines. Length = 382 Score = 29.8 bits (67), Expect = 0.15 Identities = 10/15 (66%), Positives = 13/15 (86%) Query: 1 MGLSESGKTTLLEAI 15 MGLS SGK++LL A+ Sbjct: 56 MGLSGSGKSSLLRAV 70 >gnl|CDD|178835 PRK00064, recF, recombination protein F; Reviewed. Length = 361 Score = 29.7 bits (68), Expect = 0.18 Identities = 9/14 (64%), Positives = 10/14 (71%) Query: 6 SGKTTLLEAIFLFG 19 GKT LLEAI+L Sbjct: 34 QGKTNLLEAIYLLA 47 >gnl|CDD|129679 TIGR00591, phr2, photolyase PhrII. All proteins in this family for which functions are known are DNA-photolyases used for the direct repair of UV irradiation induced DNA damage. Some repair 6-4 photoproducts while others repair cyclobutane pyrimidine dimers. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Length = 454 Score = 28.6 bits (64), Expect = 0.40 Identities = 16/70 (22%), Positives = 23/70 (32%), Gaps = 5/70 (7%) Query: 14 AIFLFGEALALALSNDPVSVFLKSDVFDGISKNQYGFFTGKIKVDAQFILSEKMDIPHVF 73 + + LAL F D F ++ Y F G + A E++ IP Sbjct: 39 WALIAAQTLALKKKLPLHVCFCLVDFFLAATRRHYFFMLGGLDEVAN--ECERLIIPFHL 96 Query: 74 L---PMVHFP 80 L P P Sbjct: 97 LDGPPKELLP 106 >gnl|CDD|168091 PRK05541, PRK05541, adenylylsulfate kinase; Provisional. Length = 176 Score = 28.1 bits (63), Expect = 0.54 Identities = 15/40 (37%), Positives = 22/40 (55%), Gaps = 6/40 (15%) Query: 1 MGLSESGKTTLLEAIFLFGEALALALSNDPVSVFLKSDVF 40 GL+ SGKTT+ +A++ E L L SN ++L D Sbjct: 13 TGLAGSGKTTIAKALY---ERLKLKYSN---VIYLDGDEL 46 >gnl|CDD|183713 PRK12740, PRK12740, elongation factor G; Reviewed. Length = 668 Score = 27.4 bits (62), Expect = 0.80 Identities = 12/18 (66%), Positives = 14/18 (77%), Gaps = 1/18 (5%) Query: 1 MGLSESGKTTLLEAIFLF 18 +G S +GKTTL EAI LF Sbjct: 1 VGHSGAGKTTLTEAI-LF 17 >gnl|CDD|172963 PRK14490, PRK14490, putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobB/MobA; Provisional. Length = 369 Score = 27.3 bits (61), Expect = 0.89 Identities = 9/14 (64%), Positives = 11/14 (78%) Query: 2 GLSESGKTTLLEAI 15 G S SGKTTL+ A+ Sbjct: 12 GYSGSGKTTLITAL 25 >gnl|CDD|179105 PRK00741, prfC, peptide chain release factor 3; Provisional. Length = 526 Score = 26.6 bits (60), Expect = 1.4 Identities = 11/19 (57%), Positives = 13/19 (68%) Query: 7 GKTTLLEAIFLFGEALALA 25 GKTTL E + LFG A+ A Sbjct: 22 GKTTLTEKLLLFGGAIQEA 40 >gnl|CDD|179932 PRK05092, PRK05092, PII uridylyl-transferase; Provisional. Length = 931 Score = 26.4 bits (59), Expect = 1.7 Identities = 13/35 (37%), Positives = 18/35 (51%), Gaps = 4/35 (11%) Query: 8 KTTLLEAIFLFGEALALALSNDPVSVFLKSDVFDG 42 +T LLEA FL G+ AL + + F +V G Sbjct: 178 RTALLEARFLAGDR---ALFEELETRF-DKEVVKG 208 >gnl|CDD|163179 TIGR03185, DNA_S_dndD, DNA sulfur modification protein DndD. This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria. Length = 650 Score = 26.2 bits (58), Expect = 1.8 Identities = 11/16 (68%), Positives = 14/16 (87%) Query: 2 GLSESGKTTLLEAIFL 17 GL+ +GKTTLL+AI L Sbjct: 35 GLNGAGKTTLLDAIQL 50 >gnl|CDD|161957 TIGR00611, recf, recF protein. All proteins in this family for which functions are known are DNA binding proteins that assist the filamentation of RecA onto DNA for the initiation of recombination or recombinational repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Length = 365 Score = 26.2 bits (58), Expect = 2.0 Identities = 11/28 (39%), Positives = 14/28 (50%) Query: 2 GLSESGKTTLLEAIFLFGEALALALSND 29 G + GKT LLEAI+ + S D Sbjct: 30 GPNGQGKTNLLEAIYYLALGRSHRTSRD 57 >gnl|CDD|129594 TIGR00503, prfC, peptide chain release factor 3. This translation releasing factor, RF-3 (prfC) was originally described as stop codon-independent, in contrast to peptide chain release factor 1 (RF-1, prfA) and RF-2 (prfB). RF-1 and RF-2 are closely related to each other, while RF-3 is similar to elongation factors EF-Tu and EF-G; RF-1 is active at UAA and UAG and RF-2 is active at UAA and UGA. More recently, RF-3 was shown to be active primarily at UGA stop codons in E. coli. All bacteria and organelles have RF-1. The Mycoplasmas and organelles, which translate UGA as Trp rather than as a stop codon, lack RF-2. RF-3, in contrast, seems to be rare among bacteria and is found so far only in Escherichia coli and some other gamma subdivision Proteobacteria, in Synechocystis PCC6803, and in Staphylococcus aureus. Length = 527 Score = 26.0 bits (57), Expect = 2.4 Identities = 9/21 (42%), Positives = 15/21 (71%) Query: 5 ESGKTTLLEAIFLFGEALALA 25 ++GKTT+ E + L+G A+ A Sbjct: 21 DAGKTTITEKVLLYGGAIQTA 41 >gnl|CDD|181780 PRK09328, PRK09328, N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional. Length = 275 Score = 25.9 bits (58), Expect = 2.5 Identities = 11/35 (31%), Positives = 17/35 (48%), Gaps = 7/35 (20%) Query: 20 EALALALSN------DPVSVFLKSDVFDGISKNQY 48 EALA+A N V FL+ D F+ + ++ Sbjct: 143 EALAVARRNAKHGLGARVE-FLQGDWFEPLPGGRF 176 >gnl|CDD|151168 pfam10662, PduV-EutP, Ethanolamine utilisation - propanediol utilisation. Members of this family function in ethanolamine and propanediol degradation pathways, however the exact roles of these proteins is poorly understood. Length = 143 Score = 25.7 bits (57), Expect = 2.7 Identities = 8/15 (53%), Positives = 11/15 (73%) Query: 1 MGLSESGKTTLLEAI 15 +G S GKTTL +A+ Sbjct: 7 IGRSGCGKTTLTQAL 21 >gnl|CDD|182330 PRK10246, PRK10246, exonuclease subunit SbcC; Provisional. Length = 1047 Score = 25.5 bits (56), Expect = 2.8 Identities = 10/16 (62%), Positives = 13/16 (81%) Query: 2 GLSESGKTTLLEAIFL 17 G + +GKTTLL+AI L Sbjct: 37 GPTGAGKTTLLDAICL 52 >gnl|CDD|150482 pfam09818, ABC_ATPase, Predicted ATPase of the ABC class. Members of this family include various bacterial predicted ABC class ATPases. Length = 447 Score = 25.6 bits (57), Expect = 3.1 Identities = 7/9 (77%), Positives = 9/9 (100%) Query: 7 GKTTLLEAI 15 GK+TLLEA+ Sbjct: 255 GKSTLLEAL 263 >gnl|CDD|162130 TIGR00955, 3a01204, The Eye Pigment Precursor Transporter (EPP) Family protein. Length = 617 Score = 25.4 bits (56), Expect = 3.3 Identities = 9/15 (60%), Positives = 12/15 (80%) Query: 1 MGLSESGKTTLLEAI 15 MG S +GKTTL+ A+ Sbjct: 57 MGSSGAGKTTLMNAL 71 >gnl|CDD|183990 PRK13351, PRK13351, elongation factor G; Reviewed. Length = 687 Score = 25.3 bits (56), Expect = 3.4 Identities = 9/18 (50%), Positives = 12/18 (66%), Gaps = 1/18 (5%) Query: 1 MGLSESGKTTLLEAIFLF 18 + ++GKTTL E I LF Sbjct: 14 LAHIDAGKTTLTERI-LF 30 >gnl|CDD|183280 PRK11701, phnK, phosphonate C-P lyase system protein PhnK; Provisional. Length = 258 Score = 25.3 bits (56), Expect = 3.5 Identities = 10/14 (71%), Positives = 11/14 (78%) Query: 2 GLSESGKTTLLEAI 15 G S SGKTTLL A+ Sbjct: 39 GESGSGKTTLLNAL 52 >gnl|CDD|183056 PRK11248, tauB, taurine transporter ATP-binding subunit; Provisional. Length = 255 Score = 25.4 bits (56), Expect = 3.5 Identities = 13/34 (38%), Positives = 18/34 (52%), Gaps = 2/34 (5%) Query: 1 MGLSESGKTTLLEAI--FLFGEALALALSNDPVS 32 +G S GKTTLL I F+ + ++ L PV Sbjct: 33 LGPSGCGKTTLLNLIAGFVPYQHGSITLDGKPVE 66 >gnl|CDD|161745 TIGR00176, mobB, molybdopterin-guanine dinucleotide biosynthesis protein MobB. This molybdenum cofactor biosynthesis enzyme is similar to the urease accessory protein UreG and to the hydrogenase accessory protein HypB, both GTP hydrolases involved in loading nickel into the metallocenters of their respective target enzymes. Length = 155 Score = 25.0 bits (55), Expect = 4.1 Identities = 8/14 (57%), Positives = 10/14 (71%) Query: 2 GLSESGKTTLLEAI 15 G SGKTTL+E + Sbjct: 6 GPKNSGKTTLIERL 19 >gnl|CDD|162131 TIGR00956, 3a01205, Pleiotropic Drug Resistance (PDR) Family protein. Length = 1394 Score = 24.7 bits (54), Expect = 5.5 Identities = 9/15 (60%), Positives = 11/15 (73%) Query: 1 MGLSESGKTTLLEAI 15 MG S +GKTTLL + Sbjct: 795 MGASGAGKTTLLNVL 809 >gnl|CDD|184491 PRK14079, recF, recombination protein F; Provisional. Length = 349 Score = 24.7 bits (54), Expect = 6.0 Identities = 10/16 (62%), Positives = 13/16 (81%) Query: 2 GLSESGKTTLLEAIFL 17 G + +GKT LLEAI+L Sbjct: 30 GENAAGKTNLLEAIYL 45 >gnl|CDD|182508 PRK10512, PRK10512, selenocysteinyl-tRNA-specific translation factor; Provisional. Length = 614 Score = 24.6 bits (54), Expect = 6.1 Identities = 8/9 (88%), Positives = 9/9 (100%) Query: 7 GKTTLLEAI 15 GKTTLL+AI Sbjct: 12 GKTTLLQAI 20 >gnl|CDD|181788 PRK09344, PRK09344, phosphoenolpyruvate carboxykinase; Provisional. Length = 526 Score = 24.4 bits (54), Expect = 6.4 Identities = 8/11 (72%), Positives = 9/11 (81%) Query: 1 MGLSESGKTTL 11 GLS +GKTTL Sbjct: 231 FGLSGTGKTTL 241 >gnl|CDD|179675 PRK03918, PRK03918, chromosome segregation protein; Provisional. Length = 880 Score = 24.3 bits (53), Expect = 7.9 Identities = 7/11 (63%), Positives = 10/11 (90%) Query: 6 SGKTTLLEAIF 16 SGK+++LEAI Sbjct: 34 SGKSSILEAIL 44 >gnl|CDD|182778 PRK10851, PRK10851, sulfate/thiosulfate transporter subunit; Provisional. Length = 353 Score = 23.9 bits (52), Expect = 8.7 Identities = 10/15 (66%), Positives = 11/15 (73%) Query: 1 MGLSESGKTTLLEAI 15 +G S SGKTTLL I Sbjct: 34 LGPSGSGKTTLLRII 48 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 0.324 0.142 0.407 Gapped Lambda K H 0.267 0.0771 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 1,311,872 Number of extensions: 70412 Number of successful extensions: 286 Number of sequences better than 10.0: 1 Number of HSP's gapped: 286 Number of HSP's successfully gapped: 52 Length of query: 80 Length of database: 5,994,473 Length adjustment: 50 Effective length of query: 30 Effective length of database: 4,914,073 Effective search space: 147422190 Effective search space used: 147422190 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 50 (23.0 bits)