RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 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|30935 COG0590, CumB, Cytosine/adenosine deaminases [Nucleotide transport and metabolism / Translation, ribosomal structure and biogenesis]. Length = 152 Score = 154 bits (391), Expect = 8e-39 Identities = 66/142 (46%), Positives = 83/142 (58%), Gaps = 1/142 (0%) Query: 7 FMSCALEEAQNAALRNEIPVGAVAV-LNNKIISRAGNRNRELKDVTAHAEILAIRMGCRI 65 FM AL+EA+ A E+PVGAV V + +II+R NR E D TAHAEILAIR Sbjct: 11 FMREALKEAKKAGDEGEVPVGAVIVDADGEIIARGHNRREEDNDPTAHAEILAIRAAAET 70 Query: 66 LSQEILPEVDLYVTLEPCTMCAAAISLARIRRLYYGASNPKGGGIENGTQFYTLATCHHS 125 L L + LYVTLEPC MCA AI ARI R+ YGAS+PK G I + +H Sbjct: 71 LGNYRLKDCTLYVTLEPCPMCAGAIIWARIDRVVYGASDPKTGAIGSLLDILKDPRLNHR 130 Query: 126 PEIYPGISEQRSRQIIQDFFKE 147 E+Y GI E+ ++ +FF+ Sbjct: 131 VEVYGGILEEECSALLSEFFRR 152 >gnl|CDD|29828 cd01285, nucleoside_deaminase, Nucleoside deaminases include adenosine, guanine and cytosine deaminases. These enzymes are Zn dependent and catalyze the deamination of nucleosides. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on the substrate. The functional enzyme is a homodimer. Cytosine deaminase catalyzes the deamination of cytosine to uracil and ammonia and is a member of the pyrimidine salvage pathway. Cytosine deaminase is found in bacteria and fungi but is not present in mammals; for this reason, the enzyme is currently of interest for antimicrobial drug design and gene therapy applications against tumors. Some members of this family are tRNA-specific adenosine deaminases that generate inosine at the first position of their anticodon (position 34) of specific tRNAs; this modification is thought to enlarge the codon recognition capacity during protein synthesis. Other members of the family are guanine deaminases which deaminate guanine to xanthine as part of the utilization of guanine as a nitrogen source.. Length = 109 Score = 122 bits (307), Expect = 4e-29 Identities = 53/104 (50%), Positives = 67/104 (64%), Gaps = 1/104 (0%) Query: 8 MSCALEEAQNAALRNEIPVGAVAVLNN-KIISRAGNRNRELKDVTAHAEILAIRMGCRIL 66 M A+E A+ A E+P GAV V ++ K+I+R NR + D TAHAEI+AIR R L Sbjct: 1 MRLAIELARKALAEGEVPFGAVIVDDDGKVIARGHNRVEQDGDPTAHAEIVAIRNAARRL 60 Query: 67 SQEILPEVDLYVTLEPCTMCAAAISLARIRRLYYGASNPKGGGI 110 +L LY TLEPC MCA A+ ARI+R+ YGAS+PK GGI Sbjct: 61 GSYLLSGCTLYTTLEPCPMCAGALLWARIKRVVYGASDPKLGGI 104 >gnl|CDD|36236 KOG1018, KOG1018, KOG1018, Cytosine deaminase FCY1 and related enzymes [Nucleotide transport and metabolism]. Length = 169 Score = 100 bits (249), Expect = 2e-22 Identities = 56/154 (36%), Positives = 85/154 (55%), Gaps = 7/154 (4%) Query: 2 KKGNVFMSCALEEAQNAA-LRNEIPVGAVAV-LNNKIISRAGNRNRELKDVTAHAEILAI 59 FM A+EEA+ A +E+PVGAV V ++ K+++ GN E KD TAHAE++AI Sbjct: 9 DHDIAFMVEAVEEAKKALDEGDEVPVGAVLVHMDGKVLASGGNMVNEKKDPTAHAEVIAI 68 Query: 60 RM---GCRILSQEILPEVDLYVTLEPCTMCAAAISLARIRRLYYGASNPKGGGIENGTQF 116 R C+ L L E LYVT EPC MCA A++ + ++R+ +GASN + GGI + Sbjct: 69 REEEVMCKSLRTIDLSETTLYVTCEPCPMCAGALAQSGVKRVVFGASNERFGGIGFVLRG 128 Query: 117 Y--TLATCHHSPEIYPGISEQRSRQIIQDFFKER 148 L S GI ++ +++++ F+ Sbjct: 129 NKDFLKRLGASVISRDGIEKKEAQKLLIAFYVRD 162 >gnl|CDD|144101 pfam00383, dCMP_cyt_deam_1, Cytidine and deoxycytidylate deaminase zinc-binding region. Length = 104 Score = 95.1 bits (237), Expect = 6e-21 Identities = 40/98 (40%), Positives = 50/98 (51%), Gaps = 2/98 (2%) Query: 7 FMSCALEEAQNAALR-NEIPVGAVAV-LNNKIISRAGNRNRELKDVTAHAEILAIRMGCR 64 FM ALE A+ A + PVGAV V + II+ N D T HAE AIR R Sbjct: 7 FMRLALEAAKRAYTPYSNFPVGAVIVKNDGGIIATGYNGENAGYDPTIHAERNAIRNAGR 66 Query: 65 ILSQEILPEVDLYVTLEPCTMCAAAISLARIRRLYYGA 102 + L LYVTLEPC MC AI + I+++ +G Sbjct: 67 LGEGIKLEGATLYVTLEPCGMCRQAIIESGIKKVVFGT 104 >gnl|CDD|30466 COG0117, RibD, Pyrimidine deaminase [Coenzyme metabolism]. Length = 146 Score = 62.2 bits (151), Expect = 5e-11 Identities = 41/155 (26%), Positives = 62/155 (40%), Gaps = 29/155 (18%) Query: 7 FMSCALEEAQNAALRNEI--PVGAVAVLNNKIISRAGNRNRELKDVTAHAEILAIRMGCR 64 +M ALE A+ VG V V + +I+ + K HAE+ A+RM Sbjct: 9 YMERALELAEKGQGTTSPNPSVGCVIVKDGEIVGEGYHE----KAGGPHAEVCALRM--- 61 Query: 65 ILSQEILPEVDLYVTLEPCTM------CAAAISLARIRRLYYGASNP----KGGGIENGT 114 + E YVTLEPC+ CA A+ A + R+ +P GGG+ Sbjct: 62 --AGEAARGATAYVTLEPCSHYGRTPPCADALIKAGVARVVVAMLDPNPLVAGGGLARLR 119 Query: 115 QFYTLATCHHSPEIYPGISEQRSRQIIQDFFKERR 149 E+ GI E+ + ++ + F K R Sbjct: 120 A--------AGIEVEVGILEEEAEKLNEGFLKRMR 146 >gnl|CDD|29827 cd01284, Riboflavin_deaminase-reductase, Riboflavin-specific deaminase. Riboflavin biosynthesis protein RibD (Diaminohydroxyphosphoribosylaminopyrimidine deaminase) catalyzes the deamination of 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate, which is an intermediate step in the biosynthesis of riboflavin.The ribG gene of Bacillus subtilis and the ribD gene of E. coli are bifunctional and contain this deaminase domain and a reductase domain which catalyzes the subsequent reduction of the ribosyl side chain.. Length = 115 Score = 54.9 bits (132), Expect = 9e-09 Identities = 36/117 (30%), Positives = 51/117 (43%), Gaps = 21/117 (17%) Query: 8 MSCALEEAQNAALRNEI--PVGAVAVLNN-KIISRAGNRNRELKDVTAHAEILAIRMGCR 64 M ALE A+ PVG V V ++ +I+ +R K HAE+ A+ Sbjct: 1 MRRALELAEKGRGLTSPNPPVGCVIVDDDGEIVGEGYHR----KAGGPHAEVNALAS--- 53 Query: 65 ILSQEILPEVDLYVTLEPCTM------CAAAISLARIRRLYYGASNP----KGGGIE 111 +++ LYVTLEPC+ C AI A I+R+ G +P G G E Sbjct: 54 -AGEKLARGATLYVTLEPCSHHGKTPPCVDAIIEAGIKRVVVGVRDPNPLVAGKGAE 109 >gnl|CDD|37982 KOG2771, KOG2771, KOG2771, Subunit of tRNA-specific adenosine-34 deaminase [RNA processing and modification]. Length = 344 Score = 51.2 bits (122), Expect = 1e-07 Identities = 18/65 (27%), Positives = 35/65 (53%) Query: 75 DLYVTLEPCTMCAAAISLARIRRLYYGASNPKGGGIENGTQFYTLATCHHSPEIYPGISE 134 D+Y+ EPC MC+ A+ +RI+R++Y GG+ + + + + +H E++ G E Sbjct: 275 DVYLLHEPCAMCSMALVHSRIKRVFYCKPMSTAGGLGSLYRIHQRKSLNHRYEVFRGYLE 334 Query: 135 QRSRQ 139 + Sbjct: 335 EDPIP 339 >gnl|CDD|29829 cd01286, deoxycytidylate_deaminase, Deoxycytidylate deaminase domain. Deoxycytidylate deaminase catalyzes the deamination of dCMP to dUMP, providing the nucleotide substrate for thymidylate synthase. The enzyme binds Zn++, which is required for catalytic activity. The activity of the enzyme is allosterically regulated by the ratio of dCTP to dTTP not only in eukaryotic cells but also in T-even phage-infected Escherichia coli, with dCTP acting as an activator and dTTP as an inhibitor.. Length = 131 Score = 46.4 bits (110), Expect = 3e-06 Identities = 37/125 (29%), Positives = 46/125 (36%), Gaps = 26/125 (20%) Query: 12 LEEAQNAALRNEIP---VGAVAVLNNKIISRA--------------GNRNRELKD----- 49 + A+ AALR+ P VGAV V + +IIS G +L Sbjct: 5 MAIARLAALRSTCPRRQVGAVIVKDKRIISTGYNGSPSGLPHCAEVGCERDDLPSGEDQK 64 Query: 50 --VTAHAEILAIRMGCRILSQEILPEVDLYVTLEPCTMCAAAISLARIRRLYYGASNPKG 107 T HAE AI R L LYVTL PC CA I A I+++ Y Sbjct: 65 CCRTVHAEQNAILQAAR--HGVSLEGATLYVTLFPCIECAKLIIQAGIKKVVYAEPYDDD 122 Query: 108 GGIEN 112 Sbjct: 123 DPAAA 127 >gnl|CDD|29825 cd00786, cytidine_deaminase-like, Cytidine and deoxycytidylate deaminase zinc-binding region. The family contains cytidine deaminases, nucleoside deaminases, deoxycytidylate deaminases and riboflavin deaminases. Also included are the apoBec family of mRNA editing enzymes. All members are Zn dependent. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on the substrate.. Length = 96 Score = 45.4 bits (107), Expect = 7e-06 Identities = 27/94 (28%), Positives = 37/94 (39%), Gaps = 8/94 (8%) Query: 8 MSCALEEA-QNAALRNEIPVGAVAVLNNK---IISRAGNRNRELKDVTAHAEILAIRMGC 63 M+ AL+ A A + VGA ++N K + R N + HAE A+ Sbjct: 1 MTEALKAADLGYAKESNFQVGA-CLVNKKDGGKVGRGCNIENAAYSMCNHAERTALFNA- 58 Query: 64 RILSQEILPEVDLYVTLEPCTMCAAAISLARIRR 97 S+ LYV L PC CA I I+ Sbjct: 59 --GSEGDTKGQMLYVALSPCGACAQLIIELGIKD 90 >gnl|CDD|32314 COG2131, ComEB, Deoxycytidylate deaminase [Nucleotide transport and metabolism]. Length = 164 Score = 44.2 bits (104), Expect = 1e-05 Identities = 36/143 (25%), Positives = 53/143 (37%), Gaps = 27/143 (18%) Query: 1 MKKGNVFMSCALEEAQNAALRNEIP---VGAVAVLNNKIIS--------------RAGNR 43 M++ +++ + A+ ALR+ P VGAV V + +II+ G Sbjct: 2 MERPSMWDEYFMAIAELVALRSTCPRRQVGAVIVKDGRIIATGYNGAPSGEDHCIDRGCL 61 Query: 44 NRELKDVTA--------HAEILAIRMGCRILSQEILPEVDLYVTLEPCTMCAAAISLARI 95 ++ VT HAE AI R L LYVT PC+ CA I A I Sbjct: 62 RDKVVFVTTCGHCCRTLHAEQNAILQAARHG--VGLEGATLYVTHFPCSNCAKLIIQAGI 119 Query: 96 RRLYYGASNPKGGGIENGTQFYT 118 + + Y P + Sbjct: 120 KEVVYAEPYPTETVAPYSQELLE 142 >gnl|CDD|38337 KOG3127, KOG3127, KOG3127, Deoxycytidylate deaminase [Nucleotide transport and metabolism]. Length = 230 Score = 40.8 bits (95), Expect = 1e-04 Identities = 36/116 (31%), Positives = 48/116 (41%), Gaps = 28/116 (24%) Query: 12 LEEAQNAALRNEIP---VGAVAVL-NNKIIS-------------------RAGNRNRELK 48 + A +A R++ P VGA V N+I+ A + N +LK Sbjct: 71 MAIAFLSAKRSKDPNTQVGACIVDRENRIVGTGYNGFPRGCSDDVFPWCKAALSTNLDLK 130 Query: 49 D-VTAHAEILAIRMGCRILSQEILPEVDLYVTLEPCTMCAAAISLARIRRLYYGAS 103 HAE AI R E + LYVTL PC CA I A I+ +YY +S Sbjct: 131 YCYVVHAEENAILNKGR----ERVGGCSLYVTLCPCNECAKLIIQAGIKEVYYSSS 182 >gnl|CDD|29826 cd01283, cytidine_deaminase, Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on the substrate. Cytidine deaminases catalyze the deamination of cytidine to uridine and are important in the pyrimadine salvage pathway in many cell types, from bacteria to humans. This family also includes the apoBec proteins, which are a mammal specific expansion of RNA editing enzymes, and the closely related phorbolins, and the AID (activation-induced) enzymes.. Length = 112 Score = 27.3 bits (60), Expect = 1.6 Identities = 24/92 (26%), Positives = 31/92 (33%), Gaps = 7/92 (7%) Query: 25 PVGAVAVLNNKIISRAGNRNRELKDVTAHAEILAIRMGCRILSQEILPEVDLYVTLE--- 81 VGA + + I N +T AE AI G + V V+ E Sbjct: 19 TVGAALLTKDGRIFTGVNVENASYGLTLCAERTAI--GKAVSEGLRRYLVTWAVSDEGGV 76 Query: 82 --PCTMCAAAISLARIRRLYYGASNPKGGGIE 111 PC C ++ RLY NPKG Sbjct: 77 WSPCGACRQVLAEFLPSRLYIIIDNPKGEEFA 108 >gnl|CDD|143857 pfam00075, RnaseH, RNase H. RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral replication cycle, and often found as a domain associated with reverse transcriptases. Structure is a mixed alpha+beta fold with three a/b/a layers. Length = 126 Score = 26.1 bits (58), Expect = 3.5 Identities = 13/56 (23%), Positives = 19/56 (33%), Gaps = 12/56 (21%) Query: 18 AALRNEIPVGAVAVLN-NKIISRAGNR---NRELKDVTAHAEILAIRMGCRILSQE 69 + N GA V + K S+ R AE+LA+ LS + Sbjct: 11 SCNGNPGTGGAGYVTDGGKQRSKPLPGTTNQR--------AELLALIEALEALSGQ 58 >gnl|CDD|145524 pfam02423, OCD_Mu_crystall, Ornithine cyclodeaminase/mu-crystallin family. This family contains the bacterial Ornithine cyclodeaminase enzyme EC:4.3.1.12, which catalyses the deamination of ornithine to proline. This family also contains mu-Crystallin the major component of the eye lens in several Australian marsupials, mRNA for this protein has also been found in human retina. Length = 312 Score = 25.8 bits (57), Expect = 5.2 Identities = 11/52 (21%), Positives = 15/52 (28%), Gaps = 3/52 (5%) Query: 50 VTAHAEILAIRMGC---RILSQEILPEVDLYVTLEPCTMCAAAISLARIRRL 98 V I A+ C L +IL D++V P I Sbjct: 214 VKPGVHINAVGADCPGKTELDPDILLRADIFVDYPPQARIEGEIQQLPDDAP 265 >gnl|CDD|37378 KOG2167, KOG2167, KOG2167, Cullins [Cell cycle control, cell division, chromosome partitioning]. Length = 661 Score = 25.3 bits (55), Expect = 6.2 Identities = 9/29 (31%), Positives = 15/29 (51%), Gaps = 3/29 (10%) Query: 89 AISLARIRRLYYGASNPKGGGIENGTQFY 117 +++ R R L PKG +E+G +F Sbjct: 535 SLACGRARVL---QKVPKGKEVEDGDKFI 560 >gnl|CDD|119393 cd06222, RnaseH, RNase H (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a not sequence-specific manner. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H knockout mice lack mitochondrial DNA replication and die as embryos. The retroviral reverse transcriptase contains an RNase H domain that plays an important role in converting a single stranded retroviral genomic RNA into a dsDNA for integration into host chromosomes. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.. Length = 130 Score = 25.0 bits (55), Expect = 9.7 Identities = 13/61 (21%), Positives = 25/61 (40%), Gaps = 1/61 (1%) Query: 18 AALRNEIPVGAVAVLNNKIISRAGNRNRELKDVTAH-AEILAIRMGCRILSQEILPEVDL 76 + N P GA VL + + + T + AE+LA+ + + +V++ Sbjct: 7 SCRGNPGPAGAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELALELGGKKVNI 66 Query: 77 Y 77 Y Sbjct: 67 Y 67 Database: CddA Posted date: Feb 4, 2011 9:38 PM Number of letters in database: 6,263,737 Number of sequences in database: 21,609 Lambda K H 0.321 0.135 0.394 Gapped Lambda K H 0.267 0.0698 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 1,777,642 Number of extensions: 86993 Number of successful extensions: 161 Number of sequences better than 10.0: 1 Number of HSP's gapped: 150 Number of HSP's successfully gapped: 19 Length of query: 149 Length of database: 6,263,737 Length adjustment: 85 Effective length of query: 64 Effective length of database: 4,426,972 Effective search space: 283326208 Effective search space used: 283326208 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 (24.3 bits)