RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2494
(166 letters)
>gnl|CDD|223372 COG0295, Cdd, Cytidine deaminase [Nucleotide transport and
metabolism].
Length = 134
Score = 142 bits (360), Expect = 3e-44
Identities = 58/104 (55%), Positives = 72/104 (69%), Gaps = 3/104 (2%)
Query: 16 EQNLANLSIQARDNAYCPYSKLQVGAALLCQDDTIFTGCNVENASYGMTICAEKTAISKA 75
L L+ +A NAY PYSK +VGAAL +D I+TG NVENASYG+T+CAE++AI KA
Sbjct: 5 GLELFALAPEAAANAYAPYSKFKVGAALRTKDGRIYTGANVENASYGLTVCAERSAIFKA 64
Query: 76 ISEGQTKFKRIAVSAILPDSNKFVSPCGSCRQVIAEFSSPACDI 119
ISEG+ KF + V A D+ K VSPCG+CRQV+AEF I
Sbjct: 65 ISEGKRKFDAVVVVA---DTGKPVSPCGACRQVLAEFCGDDTLI 105
>gnl|CDD|233371 TIGR01354, cyt_deam_tetra, cytidine deaminase, homotetrameric.
This small, homotetrameric zinc metalloprotein is found
in humans and most bacteria. A related, homodimeric form
with a much larger subunit is found in E. coli and in
Arabidopsis. Both types may act on deoxycytidine as well
as cytidine [Purines, pyrimidines, nucleosides, and
nucleotides, Salvage of nucleosides and nucleotides].
Length = 127
Score = 141 bits (358), Expect = 4e-44
Identities = 57/94 (60%), Positives = 67/94 (71%), Gaps = 3/94 (3%)
Query: 26 ARDNAYCPYSKLQVGAALLCQDDTIFTGCNVENASYGMTICAEKTAISKAISEGQTKFKR 85
AR NAY PYS +VGAALL +D IFTG NVENASY +TICAE++AI KAIS G KF
Sbjct: 10 ARKNAYAPYSNFKVGAALLTKDGRIFTGVNVENASYPLTICAERSAIGKAISAGYRKFVA 69
Query: 86 IAVSAILPDSNKFVSPCGSCRQVIAEFSSPACDI 119
IAV+ ++ VSPCG+CRQV+AEF P I
Sbjct: 70 IAVAD---SADDSVSPCGACRQVLAEFCGPDTPI 100
>gnl|CDD|180142 PRK05578, PRK05578, cytidine deaminase; Validated.
Length = 131
Score = 139 bits (353), Expect = 3e-43
Identities = 58/114 (50%), Positives = 73/114 (64%), Gaps = 5/114 (4%)
Query: 18 NLANLSIQARDNAYCPYSKLQVGAALLCQDDTIFTGCNVENASYGMTICAEKTAISKAIS 77
L +I+A + AY PYSK VGAALL D I+TGCN+ENASYG+T CAE+TAI KAIS
Sbjct: 5 ELIEAAIEASEKAYAPYSKFPVGAALLTDDGRIYTGCNIENASYGLTNCAERTAIFKAIS 64
Query: 78 EGQTKFKRIAVSAILPDSNKFVSPCGSCRQVIAEFSSPACDIQVLIVKSDRSQV 131
EG + IA ++ + +SPCG CRQV+AEF P D+ V +V D
Sbjct: 65 EGGGRLVAIACVG---ETGEPLSPCGRCRQVLAEFGGP--DLLVTLVAKDGPTG 113
>gnl|CDD|238610 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 = 127 bits (322), Expect = 8e-39
Identities = 50/96 (52%), Positives = 62/96 (64%), Gaps = 3/96 (3%)
Query: 24 IQARDNAYCPYSKLQVGAALLCQDDTIFTGCNVENASYGMTICAEKTAISKAISEGQTKF 83
+ A + AY PYS VGAALL +D IFTG NVENASYG+T+CAE+TAI KA+SEG ++
Sbjct: 5 LAAAEFAYAPYSNFTVGAALLTKDGRIFTGVNVENASYGLTLCAERTAIGKAVSEGLRRY 64
Query: 84 KRIAVSAILPDSNKFVSPCGSCRQVIAEFSSPACDI 119
+ D SPCG+CRQV+AEF I
Sbjct: 65 LVTWAVS---DEGGVWSPCGACRQVLAEFLPSRLYI 97
>gnl|CDD|183511 PRK12411, PRK12411, cytidine deaminase; Provisional.
Length = 132
Score = 125 bits (315), Expect = 1e-37
Identities = 53/99 (53%), Positives = 68/99 (68%), Gaps = 3/99 (3%)
Query: 17 QNLANLSIQARDNAYCPYSKLQVGAALLCQDDTIFTGCNVENASYGMTICAEKTAISKAI 76
+ L +I+AR AY PYSK QVGAALL QD ++ GCNVENASYG+ CAE+TA+ KA+
Sbjct: 4 KQLIQEAIEARKQAYVPYSKFQVGAALLTQDGKVYRGCNVENASYGLCNCAERTALFKAV 63
Query: 77 SEGQTKFKRIAVSAILPDSNKFVSPCGSCRQVIAEFSSP 115
SEG +F IA+ A D+ + V PCG+CRQV+ E
Sbjct: 64 SEGDKEFVAIAIVA---DTKRPVPPCGACRQVMVELCKQ 99
>gnl|CDD|215887 pfam00383, dCMP_cyt_deam_1, Cytidine and deoxycytidylate deaminase
zinc-binding region.
Length = 104
Score = 78.5 bits (194), Expect = 1e-19
Identities = 36/92 (39%), Positives = 45/92 (48%), Gaps = 7/92 (7%)
Query: 22 LSIQARDNAYCPYSKLQVGAALLCQDD-TIFTGCNVENASYGMTICAEKTAISKAISEGQ 80
L+++A AY PYS VGA ++ D I TG N ENA Y TI AE+ AI A G+
Sbjct: 10 LALEAAKRAYTPYSNFPVGAVIVKNDGGIIATGYNGENAGYDPTIHAERNAIRNAGRLGE 69
Query: 81 TKFKRIAVSAILPDSNKFVSPCGSCRQVIAEF 112
A + + PCG CRQ I E
Sbjct: 70 GIKLEGATLYV------TLEPCGMCRQAIIES 95
>gnl|CDD|238406 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 = 66.4 bits (162), Expect = 5e-15
Identities = 36/92 (39%), Positives = 51/92 (55%), Gaps = 11/92 (11%)
Query: 22 LSIQARDNAYCPYSKLQVGAALL--CQDDTIFTGCNVENASYGMTICAEKTAISKAISEG 79
+++A D Y S QVGA L+ + GCN+ENA+Y M AE+TA+ A SEG
Sbjct: 3 EALKAADLGYAKESNFQVGACLVNKKDGGKVGRGCNIENAAYSMCNHAERTALFNAGSEG 62
Query: 80 QTKFKRIAVSAILPDSNKFVSPCGSCRQVIAE 111
TK + + V+ +SPCG+C Q+I E
Sbjct: 63 DTKGQMLYVA---------LSPCGACAQLIIE 85
>gnl|CDD|235875 PRK06848, PRK06848, hypothetical protein; Validated.
Length = 139
Score = 65.1 bits (159), Expect = 4e-14
Identities = 33/85 (38%), Positives = 47/85 (55%), Gaps = 7/85 (8%)
Query: 34 YSKLQVGAALLCQDDTIFTGCNVENASYG-MTICAEKTAISKAISEGQTKFKRI-AVSAI 91
VGAAL + I+ ++E A G +T+CAE AI KAISEG + I AV
Sbjct: 24 NDWHHVGAALRTKTGRIYAAVHLE-AYVGRITVCAEAIAIGKAISEGDHEIDTIVAVRHP 82
Query: 92 LPDSN----KFVSPCGSCRQVIAEF 112
P + VSPCG+CR++I+++
Sbjct: 83 KPHEDDREIWVVSPCGACRELISDY 107
>gnl|CDD|233372 TIGR01355, cyt_deam_dimer, cytidine deaminase, homodimeric. This
homodimeric zinc metalloprotein is found in Arabidopis
and some Proteobacteria. A related, homotetrameric form
with a much smaller subunit is found most bacteria and
in animals. Both types may act on deoxycytidine as well
as cytidine [Purines, pyrimidines, nucleosides, and
nucleotides, Salvage of nucleosides and nucleotides].
Length = 283
Score = 53.3 bits (128), Expect = 5e-09
Identities = 31/106 (29%), Positives = 42/106 (39%), Gaps = 12/106 (11%)
Query: 26 ARDNAYCPYSKLQVGAALLCQDDTIFTGCNVE--NASYGMTICAEKTAISKAISEGQTKF 83
A A P SK VGA + G NVE +I AE+ IS G+
Sbjct: 32 AASYARAPISKFNVGAVGRGSSGRFYLGVNVEFPGLPLHHSIHAEQFLISHLALNGERGL 91
Query: 84 KRIAVSAILPDSNKFVSPCGSCRQVIAEFSSPACDIQVLIVKSDRS 129
+AVS +PCG CRQ + E + A I++L+
Sbjct: 92 NDLAVSF---------APCGHCRQFLNEIRN-ASSIKILLPDPHNK 127
Score = 47.1 bits (112), Expect = 7e-07
Identities = 28/128 (21%), Positives = 61/128 (47%), Gaps = 7/128 (5%)
Query: 1 MVGHDIMEFSALDPIE-----QNLANLSIQARDNAYCPYSKLQVGAALLCQDDTIFTGCN 55
H+ + D I +L +++A + +Y PYSK G AL ++ ++ G
Sbjct: 155 EERHNCLALIDPDSIRNSDICSDLKQQALKAANRSYAPYSKSPSGVALKDREGKVYRGWY 214
Query: 56 VENASYGMTICAEKTAISKAISEGQTK-FKRIAVSAILPDSNKFVSPCGSCRQVIAEFSS 114
+E+A++ ++ + A+ ++ G K F+ I V A+L + + + + E +
Sbjct: 215 IESAAFNPSLGPLQAALVDFMANGGGKGFEDI-VRAVLVEKADAKVSHEATARALLETIA 273
Query: 115 PACDIQVL 122
P+C+++V
Sbjct: 274 PSCELKVF 281
>gnl|CDD|178024 PLN02402, PLN02402, cytidine deaminase.
Length = 303
Score = 50.6 bits (121), Expect = 5e-08
Identities = 38/115 (33%), Positives = 50/115 (43%), Gaps = 12/115 (10%)
Query: 17 QNLANLSIQARDNAYCPYSKLQVGAALLCQDDTIFTGCNVE--NASYGMTICAEKTAISK 74
Q L +L A+ A P SK VGA L IF G N+E ++ AE+ I+
Sbjct: 26 QLLPSLVKSAQSLARPPISKYHVGAVGLGSSGRIFLGVNLEFPGLPLHHSVHAEQFLITN 85
Query: 75 AISEGQTKFKRIAVSAILPDSNKFVSPCGSCRQVIAEFSSPACDIQVLIVKSDRS 129
+ K +AVSA +PCG CRQ E A DI++LI S
Sbjct: 86 LTLNAEPHLKYVAVSA---------APCGHCRQFFQEIRD-APDIKILITGDSNS 130
Score = 35.6 bits (82), Expect = 0.006
Identities = 25/105 (23%), Positives = 57/105 (54%), Gaps = 2/105 (1%)
Query: 18 NLANLSIQARDNAYCPYSKLQVGAALLCQDDTIFTGCNVENASYGMTICAEKTAISKAIS 77
+L N +++A + ++ PYS G AL+ + ++ G +E+A+Y ++ + A+ ++
Sbjct: 194 DLKNEALEAANKSHAPYSNCPSGVALMDCEGKVYRGSYMESAAYNPSMGPVQAALVAYVA 253
Query: 78 EGQTK-FKRIAVSAILPDSNKFVSPCGSCRQVIAEFSSPACDIQV 121
G+ ++RI V+A+L + V +++ + SP C+ +V
Sbjct: 254 GGRGGGYERI-VAAVLVEKEGAVVRQEQTARLLLKEISPKCEFKV 297
>gnl|CDD|177837 PLN02182, PLN02182, cytidine deaminase.
Length = 339
Score = 47.4 bits (112), Expect = 8e-07
Identities = 37/112 (33%), Positives = 55/112 (49%), Gaps = 6/112 (5%)
Query: 13 DPIEQNLANLSIQARDNAYCPYSKLQVGAALLCQDDTIFTGCNVENASYGM--TICAEKT 70
DPI L NL +A A P SK +VGA ++ G NV+ + +I AE+
Sbjct: 44 DPIR--LPNLIRKAMCLARAPISKYKVGAVGRASSGRVYLGVNVDFPGLPLHHSIHAEQF 101
Query: 71 AISKAISEGQTKFKRIAVSAILPDSNKFVSPCGSCRQVIAEFSSPACDIQVL 122
++ + +AV AI D +F +PCG C Q + E S+ A DI++L
Sbjct: 102 LVTNLALNSEKDLCELAV-AISTDGKEFGTPCGHCLQFLMEMSN-ALDIKIL 151
Score = 40.0 bits (93), Expect = 2e-04
Identities = 29/131 (22%), Positives = 60/131 (45%), Gaps = 9/131 (6%)
Query: 23 SIQARDNAYCPYSKLQVGAALLCQDDTIFTGCNVENASYGMTICAEKTAISKAISEGQTK 82
++ A +N++ PY++ G ALL D + G +E+ + + + A+ ++ + K
Sbjct: 208 ALAAANNSFSPYTESPSGVALLDNDGKWYRGWYIESVASNPSFGPVQAALVDFVARSRGK 267
Query: 83 -FKRIAVSAILPDSNKFVSPCGSCRQVIAEFSSPACDIQVLIVKSD--------RSQVGL 133
F +I + ++ +N VS + + ++ ++P CD +V D R + +
Sbjct: 268 MFNKIVQAVLVEKNNAIVSQERTAKIILDTIAAPNCDFKVFHCSVDCAKRLKYLRDTLVI 327
Query: 134 ITIDGMYLTLH 144
T G Y LH
Sbjct: 328 DTSLGDYTGLH 338
>gnl|CDD|181614 PRK09027, PRK09027, cytidine deaminase; Provisional.
Length = 295
Score = 44.8 bits (107), Expect = 5e-06
Identities = 35/107 (32%), Positives = 47/107 (43%), Gaps = 12/107 (11%)
Query: 10 SALDPIEQNLANLSIQARDNAYCPYSKLQVGAALLCQDDTIFTGCNVE--NASYGMTICA 67
S LD LA L + A A P S VGA + G N+E A+ T+ A
Sbjct: 45 SGLDDDALALALLPLAA-ACAVTPISHFNVGAIARGVSGNFYFGANMEFAGAALQQTVHA 103
Query: 68 EKTAISKAISEGQTKFKRIAVSAILPDSNKFVSPCGSCRQVIAEFSS 114
E++AIS A G+ I V+ +PCG CRQ + E +S
Sbjct: 104 EQSAISHAWLRGEKAIADITVNY---------TPCGHCRQFMNELNS 141
Score = 39.4 bits (93), Expect = 3e-04
Identities = 21/58 (36%), Positives = 29/58 (50%), Gaps = 8/58 (13%)
Query: 12 LDPIEQNLA-----NLSIQARDNA---YCPYSKLQVGAALLCQDDTIFTGCNVENASY 61
+DP + LA L A D A + PYS+ G AL +D I+TG ENA++
Sbjct: 177 MDPQDHGLALDTGDPLIQAALDAANRSHAPYSQSYSGVALETKDGRIYTGRYAENAAF 234
>gnl|CDD|116797 pfam08211, dCMP_cyt_deam_2, Cytidine and deoxycytidylate deaminase
zinc-binding region.
Length = 124
Score = 36.9 bits (86), Expect = 0.001
Identities = 20/69 (28%), Positives = 37/69 (53%), Gaps = 2/69 (2%)
Query: 24 IQARDNAYCPYSKLQVGAALLCQDDTIFTGCNVENASYGMTICAEKTAISKAISEGQTKF 83
+ A + ++ PYSK G AL +D ++ G ENA++ ++ + A+ ++ G+ F
Sbjct: 41 LAAANRSHAPYSKSPSGVALEDKDGKVYAGRYAENAAFNPSLPPLQAALVDFVAAGKD-F 99
Query: 84 KRIAVSAIL 92
I V A+L
Sbjct: 100 NDI-VRAVL 107
>gnl|CDD|236225 PRK08298, PRK08298, cytidine deaminase; Validated.
Length = 136
Score = 35.9 bits (83), Expect = 0.002
Identities = 22/71 (30%), Positives = 33/71 (46%), Gaps = 7/71 (9%)
Query: 41 AALLCQDDTIFTGC--NVENASYGMTICAEKTAISKAISEGQTKFKRIAVSAILPDSNKF 98
AA+ +D TI T V NAS + C E AI +A + I V+ + ++
Sbjct: 27 AAMRVEDGTILTSVAPEVINASTEL--CMETGAICEAHKLQKRVTHSICVAR-ENEHSEL 83
Query: 99 V--SPCGSCRQ 107
SPCG C++
Sbjct: 84 KVLSPCGVCQE 94
>gnl|CDD|222748 pfam14431, YwqJ-deaminase, YwqJ-like deaminase. A member of the
nucleic acid/nucleotide deaminase superfamily prototyped
by Bacillus YwqJ. Members of this family are present in
a wide phyletic range of bacteria and a few
basidiomycetes. Bacterial versions are predicted to
function as toxins in bacterial polymorphic toxin
systems.
Length = 125
Score = 27.0 bits (60), Expect = 2.6
Identities = 14/62 (22%), Positives = 24/62 (38%), Gaps = 10/62 (16%)
Query: 61 YGMTICAEKTAISKAI----------SEGQTKFKRIAVSAILPDSNKFVSPCGSCRQVIA 110
YG AE A++ A+ +G +A P++ K PC +C ++
Sbjct: 62 YGAGNHAEVQAVNNALIDREAQARGLLDGARIMVITLRAAGTPENGKPFPPCPNCSGLLP 121
Query: 111 EF 112
F
Sbjct: 122 NF 123
>gnl|CDD|239748 cd03779, MATH_TRAF1, Tumor Necrosis Factor Receptor (TNFR)
Associated Factor (TRAF) family, TRAF1 subfamily, TRAF
domain, C-terminal MATH subdomain; TRAF molecules serve
as adapter proteins that link TNFRs and downstream
kinase cascades resulting in the activation of
transcription factors and the regulation of cell
survival, proliferation and stress responses. TRAF1
expression is the most restricted among the TRAFs. It is
found exclusively in activated lymphocytes, dendritic
cells and certain epithelia. TRAF1 associates, directly
or indirectly through heterodimerization with TRAF2,
with the TNFR family receptors TNFR-2, CD30, RANK, CD40
and LMP1, among others. It also binds the intracellular
proteins TRADD, TANK, TRIP, RIP1, RIP2 and FLIP. TRAF1
is unique among the TRAFs in that it lacks a RING
domain, which is critical for the activation of nuclear
factor-kappaB and Jun NH2-terminal kinase. Studies on
TRAF1-deficient mice suggest that TRAF1 has a negative
regulatory role in TNFR-mediated signaling events. TRAF1
contains one zinc finger and one TRAF domain. The TRAF
domain can be divided into a more divergent N-terminal
alpha helical region (TRAF-N), and a highly conserved
C-terminal MATH subdomain (TRAF-C) with an
eight-stranded beta-sandwich structure. TRAF-N mediates
trimerization while TRAF-C interacts with receptors.
Length = 147
Score = 26.8 bits (59), Expect = 4.2
Identities = 15/56 (26%), Positives = 24/56 (42%), Gaps = 9/56 (16%)
Query: 11 ALDPIEQNLANLSIQARDN---------AYCPYSKLQVGAALLCQDDTIFTGCNVE 57
+D +L++ S Q + + P KLQ C+DDTI+ C V+
Sbjct: 92 VIDAFRPDLSSASFQRPVSDMNVASGCPLFFPLKKLQSPKHAYCKDDTIYIKCVVD 147
>gnl|CDD|237769 PRK14616, PRK14616, 4-diphosphocytidyl-2-C-methyl-D-erythritol
kinase; Provisional.
Length = 287
Score = 27.0 bits (60), Expect = 5.1
Identities = 17/66 (25%), Positives = 28/66 (42%), Gaps = 14/66 (21%)
Query: 4 HDIMEFSALDPIEQNLANLSIQARDNAYCPYSKLQVGAALLCQDDTIFTGCNVENASYGM 63
+D + FS D I + NL + D+ C + AA Q+ + G S G+
Sbjct: 39 YDTLTFSPSDTISMSCTNLDLPVDDSNLC------IRAAKALQE---YAGV-----SKGV 84
Query: 64 TICAEK 69
+I +K
Sbjct: 85 SITLDK 90
>gnl|CDD|237869 PRK14962, PRK14962, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 472
Score = 26.3 bits (58), Expect = 10.0
Identities = 10/32 (31%), Positives = 16/32 (50%)
Query: 79 GQTKFKRIAVSAILPDSNKFVSPCGSCRQVIA 110
G+T RI ++ ++ K V PC CR +
Sbjct: 48 GKTTVARILAKSLNCENRKGVEPCNECRACRS 79
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.320 0.135 0.404
Gapped
Lambda K H
0.267 0.0655 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,786,626
Number of extensions: 652918
Number of successful extensions: 456
Number of sequences better than 10.0: 1
Number of HSP's gapped: 437
Number of HSP's successfully gapped: 25
Length of query: 166
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 76
Effective length of database: 6,945,742
Effective search space: 527876392
Effective search space used: 527876392
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 (21.8 bits)
S2: 55 (25.1 bits)