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)