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)