RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780410|ref|YP_003064823.1| hypothetical protein CLIBASIA_01475 [Candidatus Liberibacter asiaticus str. psy62] (362 letters) >gnl|CDD|180916 PRK07276, PRK07276, DNA polymerase III subunit delta'; Validated. Length = 290 Score = 30.8 bits (70), Expect = 0.59 Identities = 14/56 (25%), Positives = 26/56 (46%), Gaps = 2/56 (3%) Query: 295 LTTQGKFLEGLGIWQRAFSLMKQTARKDILLDSVKRLVSTSADKKSMGELFKILVV 350 L KFLE + +R +++ KD V RLV + +K+ ++ +L + Sbjct: 197 LAQNKKFLELIDQAERFVTILL--KDKDEAYLQVARLVQLADEKEEQDQVLTLLTL 250 >gnl|CDD|152432 pfam11997, DUF3492, Domain of unknown function (DUF3492). This presumed domain is functionally uncharacterized. This domain is found in bacteria, archaea and eukaryotes. This domain is typically between 259 to 282 amino acids in length. This domain is found associated with pfam00534. This domain has two conserved sequence motifs: GGVS and EHGIY. Length = 268 Score = 29.9 bits (68), Expect = 0.97 Identities = 11/21 (52%), Positives = 15/21 (71%), Gaps = 2/21 (9%) Query: 167 FVMTEHGI--RERMIDIDQHD 185 ++TEHGI RER I++ Q D Sbjct: 199 LLLTEHGIYTRERKIELLQAD 219 >gnl|CDD|150552 pfam09892, DUF2119, Uncharacterized protein conserved in archaea (DUF2119). This domain, found in various hypothetical archaeal proteins, has no known function. Length = 193 Score = 29.3 bits (66), Expect = 1.5 Identities = 15/35 (42%), Positives = 20/35 (57%) Query: 89 RGIMMLDILRVICKLKPDFFSVLSIYMVETSERLT 123 + M ILR+I K KPDF+ L Y E ++LT Sbjct: 61 KSEMGKKILRLIEKYKPDFYFELHSYSKENYDKLT 95 >gnl|CDD|173552 PTZ00359, PTZ00359, hypothetical protein; Provisional. Length = 443 Score = 29.0 bits (65), Expect = 1.8 Identities = 15/41 (36%), Positives = 22/41 (53%), Gaps = 7/41 (17%) Query: 42 PFGAVGDFVTAPEISQIFGEMLAIFLICAWEQHGFPSCVRL 82 +GA+G T E+ +FG F+ICA + H F C+ L Sbjct: 147 VYGAMG--FTGLELLAMFG-----FIICAMKTHCFGGCMTL 180 >gnl|CDD|129416 TIGR00316, cdhC, CO dehydrogenase/CO-methylating acetyl-CoA synthase complex, beta subunit. Nomenclature follows the description for Methanosarcina thermophila. The CO-methylating acetyl-CoA synthase is considered the defining enzyme of the Wood-Ljungdahl pathway, used for acetate catabolism by sulfate reducing bacteria but for acetate biosynthesis by acetogenic bacteria such as oorella thermoacetica (f. Clostridium thermoaceticum). Length = 458 Score = 29.1 bits (65), Expect = 2.0 Identities = 16/51 (31%), Positives = 27/51 (52%), Gaps = 2/51 (3%) Query: 300 KFLEGLGIWQRAFSLMKQTAR--KDILLDSVKRLVSTSADKKSMGELFKIL 348 KFL+ G W+R + K+ KD + + ++ ++T D K+ EL K L Sbjct: 338 KFLQADGGWERVVWMPKELKERVKDAIPEDLRDKIATEEDAKTTDELRKFL 388 >gnl|CDD|150938 pfam10344, Fmp27, Mitochondrial protein from FMP27. This family contains mitochondrial FMP27 proteins which in yeasts together with SEN1 are long genes that exist in a looped conformation, effectively bringing together their promoter and terminator regions. Pol-II is located at both ends of FMP27 when this gene is transcribed from a GAL1 promoter under induced and non-induced conditions. The exact function of the Fmp27 protein is not certain. Length = 859 Score = 28.6 bits (64), Expect = 2.9 Identities = 18/87 (20%), Positives = 34/87 (39%), Gaps = 8/87 (9%) Query: 261 VSPLVNPGQADLSSHVDFQRLSSIAILYKLYINGLTTQGKFLEGLGIWQRAFSLMKQTAR 320 VS L + L ++ ++ LY+++ + L + + F T + Sbjct: 756 VSTLSDDSGPKLHLNLHIPKIDGQYSLYRVFC--------IIYALSLLKSFFGKPISTVK 807 Query: 321 KDILLDSVKRLVSTSADKKSMGELFKI 347 + D +K L S S D K + EL + Sbjct: 808 RPSTKDEIKSLSSISKDWKGLKELLTL 834 >gnl|CDD|181269 PRK08176, pdxK, pyridoxal-pyridoxamine kinase/hydroxymethylpyrimidine kinase; Reviewed. Length = 281 Score = 27.3 bits (61), Expect = 7.2 Identities = 14/47 (29%), Positives = 26/47 (55%), Gaps = 2/47 (4%) Query: 317 QTARKDILLDSVKRLVSTSADKKSMGELFKILVVSHEKVELM--PFV 361 A K +L D++K +V TSA + +++VV+ + V ++ P V Sbjct: 178 IAAAKSLLSDTLKWVVITSAAGNEENQEMQVVVVTADSVNVISHPRV 224 >gnl|CDD|162909 TIGR02539, SepCysS, Sep-tRNA:Cys-tRNA synthase. Aminoacylation of tRNA(Cys) with Cys, and cysteine biosynthesis in the process, happens in Methanocaldococcus jannaschii and several other archaea by misacylation of tRNA(Cys) with O-phosphoserine (Sep), followed by modification of the phosphoserine to cysteine. In some species, direct tRNA-cys aminoacylation also occurs but this pathway is required for Cys biosynthesis. Members of this protein catalyze the second step in this two step pathway, using pyridoxal phosphate and a sulfur donor to synthesize Cys from Sep while attached to the tRNA. Length = 370 Score = 27.1 bits (60), Expect = 7.3 Identities = 25/69 (36%), Positives = 33/69 (47%), Gaps = 8/69 (11%) Query: 4 KLIRKIVNL--IKKNGQMTVDQYFALCVADPEFG-YYSTCNPFGAVGDFVTAPEISQIFG 60 +L R +NL +++ G +T AL EFG YS C+ G D +T P I F Sbjct: 3 RLTRGSINLNPLQRGGVLTEAARKALV----EFGDGYSVCDFCGGRLDQITKPPIHD-FL 57 Query: 61 EMLAIFLIC 69 E LA FL Sbjct: 58 EDLAEFLGM 66 >gnl|CDD|129953 TIGR00875, fsa_talC_mipB, fructose-6-phosphate aldolase, TalC/MipB family. This model represents a family that includes the E. coli transaldolase homologs TalC and MipB, both shown to be fructose-6-phosphate aldolases rather than transaldolases as previously thought. It is related to but distinct from the transaldolase family of E. coli TalA and TalB. The member from Bacillus subtilis becomes phosphorylated during early stationary phase but not during exponential growth. Length = 213 Score = 27.1 bits (60), Expect = 7.4 Identities = 11/40 (27%), Positives = 19/40 (47%), Gaps = 2/40 (5%) Query: 252 LQAVKGHTYVSPLVNPGQADLSSHVDFQRLSSIAILYKLY 291 L A G TYVSP V G+ D + + + +++ + Sbjct: 117 LAAKAGATYVSPFV--GRLDDIGGDGMKLIEEVKTIFENH 154 >gnl|CDD|129801 TIGR00718, sda_alpha, L-serine dehydratase, iron-sulfur-dependent, alpha subunit. This enzyme is also called serine deaminase. L-serine dehydratase converts serine into pyruvate in the gluconeogenesis pathway from serine. This model describes the alpha chain of an iron-sulfur-dependent L-serine dehydratase, found in Bacillus subtilis. A fairly deep split in a UPGMA tree separates members of this family of alpha chains from the homologous region of single chain forms such as found in Escherichia coli. This family of enzymes is not homologous to the pyridoxal phosphate-dependent threonine deaminases and eukaryotic serine deaminases. Length = 294 Score = 26.9 bits (59), Expect = 8.4 Identities = 9/51 (17%), Positives = 27/51 (52%) Query: 294 GLTTQGKFLEGLGIWQRAFSLMKQTARKDILLDSVKRLVSTSADKKSMGEL 344 G T++ ++G +A++ ++ D + D++ + +T+ +MG++ Sbjct: 60 GDTSETGLIDGDAKKLQAYANSGKSISGDFIADAMAKAFATNEVNAAMGKI 110 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 0.140 0.417 Gapped Lambda K H 0.267 0.0640 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 5,920,997 Number of extensions: 381885 Number of successful extensions: 771 Number of sequences better than 10.0: 1 Number of HSP's gapped: 771 Number of HSP's successfully gapped: 13 Length of query: 362 Length of database: 5,994,473 Length adjustment: 95 Effective length of query: 267 Effective length of database: 3,941,713 Effective search space: 1052437371 Effective search space used: 1052437371 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: 40 (21.6 bits) S2: 58 (26.3 bits)