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)