RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|255764464|ref|YP_003064771.2| Cytidine/deoxycytidylate deaminase, zinc-binding region [Candidatus Liberibacter asiaticus str. psy62] (149 letters) >gnl|CDD|182786 PRK10860, PRK10860, tRNA-specific adenosine deaminase; Provisional. Length = 172 Score = 114 bits (286), Expect = 1e-26 Identities = 58/143 (40%), Positives = 77/143 (53%) Query: 7 FMSCALEEAQNAALRNEIPVGAVAVLNNKIISRAGNRNRELKDVTAHAEILAIRMGCRIL 66 +M AL A+ A E+PVGAV V NN++I NR D TAHAEI+A+R G +L Sbjct: 16 WMRHALTLAKRAWDEREVPVGAVLVHNNRVIGEGWNRPIGRHDPTAHAEIMALRQGGLVL 75 Query: 67 SQEILPEVDLYVTLEPCTMCAAAISLARIRRLYYGASNPKGGGIENGTQFYTLATCHHSP 126 L + LYVTLEPC MCA A+ +RI RL +GA + K G + +H Sbjct: 76 QNYRLLDATLYVTLEPCVMCAGAMVHSRIGRLVFGARDAKTGAAGSLMDVLHHPGMNHRV 135 Query: 127 EIYPGISEQRSRQIIQDFFKERR 149 EI G+ ++ DFF+ RR Sbjct: 136 EITEGVLADECAALLSDFFRMRR 158 >gnl|CDD|161819 TIGR00326, eubact_ribD, riboflavin biosynthesis protein RibD. This model describes the ribD protein as found in Escherichia coli. The N-terminal domain includes the conserved zinc-binding site region captured in the model dCMP_cyt_deam and shared by proteins such as cytosine deaminase, mammalian apolipoprotein B mRNA editing protein, blasticidin-S deaminase, and Bacillus subtilis competence protein comEB. The C-terminal domain is homologous to the full length of yeast HTP reductase, a protein required for riboflavin biosynthesis. A number of archaeal proteins believed related to riboflavin biosynthesis contain only this C-terminal domain and are not found as full-length matches to this model. Length = 344 Score = 53.3 bits (128), Expect = 2e-08 Identities = 34/116 (29%), Positives = 48/116 (41%), Gaps = 21/116 (18%) Query: 8 MSCALEEAQNAALRNEI--PVGAVAVLNNKIISRAGNRNRELKDVTAHAEILAIRMGCRI 65 M+ AL+ A+ VG V V N +I+ + K HAE+ A+R Sbjct: 1 MNRALDLAKKGQGTTHPNPLVGCVIVKNGEIVGEGAH----QKAGEPHAEVHALRQ---- 52 Query: 66 LSQEILPEVDLYVTLEPCTM------CAAAISLARIRRLYYGASNP----KGGGIE 111 + E YVTLEPC+ CA AI A I+++ +P G G E Sbjct: 53 -AGENAKGATAYVTLEPCSHQGRTPPCAEAIIEAGIKKVVVSMQDPNPLVAGRGAE 107 >gnl|CDD|177417 PHA02588, cd, deoxycytidylate deaminase; Provisional. Length = 168 Score = 40.1 bits (94), Expect = 3e-04 Identities = 18/49 (36%), Positives = 26/49 (53%), Gaps = 2/49 (4%) Query: 53 HAEILAIRMGCRILSQEILPEVDLYVTLEPCTMCAAAISLARIRRLYYG 101 HAE+ AI R + + +YVT PC CA AI+ + I++L Y Sbjct: 83 HAELNAILFAAR--NGISIEGATMYVTASPCPDCAKAIAQSGIKKLVYC 129 >gnl|CDD|182729 PRK10786, ribD, bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional. Length = 367 Score = 32.0 bits (73), Expect = 0.064 Identities = 33/114 (28%), Positives = 47/114 (41%), Gaps = 29/114 (25%) Query: 6 VFMSCALEEAQNAALRNEIP---VGAVAVLNNKIIS-----RAGNRNRELKDVTAHAEIL 57 +M+ AL+ AQ P VG V V + +I+ RAG HAE+ Sbjct: 5 FYMARALKLAQRGRFTTH-PNPNVGCVIVKDGEIVGEGYHQRAGE---------PHAEVH 54 Query: 58 AIRMGCRILSQEILPEVDLYVTLEPCTM------CAAAISLARIRRLYYGASNP 105 A+RM + E YVTLEPC+ C A+ A + R+ +P Sbjct: 55 ALRM-----AGEKAKGATAYVTLEPCSHHGRTPPCCDALIAAGVARVVAAMQDP 103 >gnl|CDD|149333 pfam08210, APOBEC_N, APOBEC-like N-terminal domain. A mechanism of generating protein diversity is mRNA editing. Members of this family are C-to-U editing enzymes. The N-terminal domain of APOBEC-1 like proteins is the catalytic domain, while the C-terminal domain is a pseudocatalyitc domain. More specifically, the catalytic domain is a zinc dependent deaminases domain and is essential for cytidine deamination.APOBEC-3 like members contain two copies of this domain. This family also includes the functionally homologous activation induced deaminase, which is essential for the development of antibody diversity in B lymphocytes. RNA editing by APOBEC-1 requires homodimerization and this complex interacts with RNA binding proteins to from the editosome (and references therein). Length = 116 Score = 31.5 bits (72), Expect = 0.086 Identities = 19/65 (29%), Positives = 26/65 (40%), Gaps = 19/65 (29%) Query: 52 AHAEILAIRMGCRILSQEILP-----EVDLYVTLEPCTMCAAAIS--LAR---------I 95 HAE+ + S +LP V YV+ PC CA ++ LA + Sbjct: 55 CHAELCFLEW---FGSLRLLPADQRYSVTWYVSWSPCANCAQKVAEFLAEHPNVTLTIFV 111 Query: 96 RRLYY 100 RLYY Sbjct: 112 ARLYY 116 >gnl|CDD|178404 PLN02807, PLN02807, diaminohydroxyphosphoribosylaminopyrimidine deaminase. Length = 380 Score = 31.3 bits (71), Expect = 0.093 Identities = 27/101 (26%), Positives = 42/101 (41%), Gaps = 29/101 (28%) Query: 26 VGAVAVLNNKIISR-----AGNRNRELKDVTAHAEILAIRMGCRILSQEILPEVDLYVTL 80 VG V V + +I+ AG HAE+ A+R + ++ YV+L Sbjct: 56 VGCVIVKDGRIVGEGFHPKAGQ---------PHAEVFALRD-----AGDLAENATAYVSL 101 Query: 81 EPCTM------CAAAISLARIRRLYYGASNPK----GGGIE 111 EPC C A+ A+++R+ G +P GIE Sbjct: 102 EPCNHYGRTPPCTEALIKAKVKRVVVGMVDPNPIVASKGIE 142 >gnl|CDD|131622 TIGR02571, ComEB, ComE operon protein 2. This protein is found in the ComE operon for "late competence" as characterized in B. subtilis. Proteins in this family contain homology to a cytidine/deoxycytidine deaminase domain family (pfam00383), and may carry out this activity. Length = 151 Score = 31.0 bits (70), Expect = 0.14 Identities = 28/93 (30%), Positives = 41/93 (44%), Gaps = 23/93 (24%) Query: 26 VGAVAVLNNKIISRAGNRNRELK-DV----------------TAHAEILAIRMGCRI-LS 67 VGA V + +II AG N + V T HAE+ A+ + +S Sbjct: 27 VGATIVRDKRII--AGGYNGSVAGGVHCIDEGCYVVDGHCVRTIHAEMNALLQCAKFGVS 84 Query: 68 QEILPEVDLYVTLEPCTMCAAAISLARIRRLYY 100 E ++YVT PC C +I A I+++YY Sbjct: 85 TE---GAEIYVTHFPCLQCTKSIIQAGIKKIYY 114 >gnl|CDD|139929 PRK13869, PRK13869, plasmid-partitioning protein RepA; Provisional. Length = 405 Score = 27.3 bits (60), Expect = 1.4 Identities = 34/122 (27%), Positives = 57/122 (46%), Gaps = 15/122 (12%) Query: 37 ISRAGNRNRELK---DVT--AHAEILAIRMGCRILSQEILPEVDLYVTLEPCTMCAAA-- 89 +S+A +R + DVT HAE L+ ++ + +S+ + P + +L T AA Sbjct: 1 MSKAAAISRNDRPSVDVTIGEHAEQLSSQL--QAMSEALFPPTS-HKSLRKFTSGEAARL 57 Query: 90 --ISLARIRRLYYGASNPKGGGIENGTQFYTLATCHHSPEIYPGISEQRSRQIIQDFFKE 147 IS + +R++ P+ NG +FYTL + ++ G R R+ I DF Sbjct: 58 MKISDSTLRKMTLAGEGPQPELASNGRRFYTLGQINEIRQMLAG--STRGRESI-DFVPH 114 Query: 148 RR 149 RR Sbjct: 115 RR 116 >gnl|CDD|181228 PRK08097, ligB, NAD-dependent DNA ligase LigB; Reviewed. Length = 562 Score = 26.4 bits (59), Expect = 3.0 Identities = 7/20 (35%), Positives = 11/20 (55%) Query: 130 PGISEQRSRQIIQDFFKERR 149 PGI + R+ Q+ F R+ Sbjct: 465 PGIGKARAEQLWHQFNLARQ 484 >gnl|CDD|183877 PRK13170, hisH, imidazole glycerol phosphate synthase subunit HisH; Provisional. Length = 196 Score = 26.4 bits (59), Expect = 3.5 Identities = 11/40 (27%), Positives = 19/40 (47%), Gaps = 12/40 (30%) Query: 97 RLYYGASNPKGGGIENGTQFY------------TLATCHH 124 ++ A +P GIE+G+ FY T+A C++ Sbjct: 120 QVTPQAGHPLFQGIEDGSYFYFVHSYAMPVNEYTIAQCNY 159 >gnl|CDD|177513 PHA03065, PHA03065, Hypothetical protein; Provisional. Length = 438 Score = 25.3 bits (56), Expect = 6.5 Identities = 18/76 (23%), Positives = 29/76 (38%), Gaps = 4/76 (5%) Query: 9 SCALEEAQNAAL--RNEIPVGAVAVLNNKIISRAGNRNRELKDVTAHAEILAIRMG-CRI 65 +L AL R EI V V L +I A N+ + D+ + A I + + Sbjct: 341 GVSLCAQLICALEPRKEISVEEVETLL-SLIDSARNKKVTINDIASVASIFGYELNKDKN 399 Query: 66 LSQEILPEVDLYVTLE 81 + IL +L + Sbjct: 400 IVFGILNLKNLMLCFN 415 >gnl|CDD|179984 PRK05269, PRK05269, transaldolase B; Provisional. Length = 318 Score = 25.1 bits (56), Expect = 7.7 Identities = 12/43 (27%), Positives = 23/43 (53%), Gaps = 10/43 (23%) Query: 38 SRAGNRNRELKDVTAHAEILAIRMGCRILSQEILP-----EVD 75 ++G+R +++ D + LA+ G IL +++P EVD Sbjct: 61 QQSGDRAQQIDDA---IDKLAVNFGLEIL--KLIPGRVSTEVD 98 >gnl|CDD|178293 PLN02690, PLN02690, Agmatine deiminase. Length = 374 Score = 25.1 bits (55), Expect = 8.4 Identities = 9/24 (37%), Positives = 11/24 (45%) Query: 81 EPCTMCAAAISLARIRRLYYGASN 104 EP T+CA+ R G SN Sbjct: 55 EPVTVCASPAQWENAREQLPGVSN 78 >gnl|CDD|184560 PRK14190, PRK14190, bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional. Length = 284 Score = 25.0 bits (55), Expect = 8.8 Identities = 10/38 (26%), Positives = 22/38 (57%) Query: 25 PVGAVAVLNNKIISRAGNRNRELKDVTAHAEILAIRMG 62 PVG + + N ++ ++ + L ++T A+IL + +G Sbjct: 173 PVGQLLLNENATVTYCHSKTKNLAELTKQADILIVAVG 210 >gnl|CDD|152200 pfam11764, N-SET, COMPASS (Complex proteins associated with Set1p) component N. The n-SET or N-SET domain is a component of the COMPASS complex, associated with SET1, conserved in yeasts and in other eukaryotes up to humans. The COMPASS complex functions to methylate the fourth lysine of Histone 3 and for the silencing of genes close to the telomeres of chromosomes. This domain promotes trimethylation in conjunction with an RRM domain and is necessary for binding of the Spp1 component of COMPASS into the complex. Length = 166 Score = 24.7 bits (54), Expect = 9.8 Identities = 16/51 (31%), Positives = 19/51 (37%), Gaps = 4/51 (7%) Query: 11 ALEEAQNAALRNEIPVGAVAVLNNKIISRAGNR--NREL-KDVTAHAEILA 58 A E Q +E A +K SR NR NR L D+ A L Sbjct: 111 ARETVQAHNKEDEKARLAAENSASKRSSRE-NRANNRRLVADINAQKAALG 160 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 0.321 0.135 0.394 Gapped Lambda K H 0.267 0.0617 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 2,472,071 Number of extensions: 151113 Number of successful extensions: 246 Number of sequences better than 10.0: 1 Number of HSP's gapped: 244 Number of HSP's successfully gapped: 16 Length of query: 149 Length of database: 5,994,473 Length adjustment: 85 Effective length of query: 64 Effective length of database: 4,157,793 Effective search space: 266098752 Effective search space used: 266098752 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 (21.9 bits) S2: 53 (24.4 bits)