RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9259
(489 letters)
>gnl|CDD|198427 cd10029, UDG_F3_SMUG, SMUG: single-strand-selective monofunctional
uracil-DNA glycosylase. SMUG (single-strand-selective
monofunctional uracil-DNA glycosylase) is classified as
Family 3 of Uracil-DNA glycosylase (UDG) enzymes. SMUG
is a DNA repair enzyme that catalyzes the removal of
mismatched uracil and its derivatives from DNA to
initiate DNA base excision repair pathway. Uracil in DNA
can arise as a result of mis-incorporation of dUMP
residues by DNA polymerase or deamination of cytosine.
Uracil mispaired with guanine in DNA is one of the major
pro-mutagenic events, causing G:C->A:T mutations. Thus,
DNA repair enzymes are essential for maintaining the
integrity of genetic information. A Family 3 UDG from
human was first characterized to remove Uracil from
ssDNA, hence the name hSMUG (single-strand-selective
monofunctional uracil-DNA glycosylase). However,
subsequent research has shown that hSMUG1 and its rat
ortholog can remove Uracil and its oxidized pyrimidine
derivatives from both, ssDNA and dsDNA. The SMUG
targeted mismatched uracil derivatives include
5-hydroxyuracil (hoU), 5-hydroxymethyluracil (hmU) and
5-formyluracil (fU). SMUGs are found in Eubacteria and
Eukarya.
Length = 233
Score = 301 bits (773), Expect = e-100
Identities = 113/239 (47%), Positives = 157/239 (65%), Gaps = 6/239 (2%)
Query: 65 EGVLNIEKQLIHELTNSNITYEFPVEYVYNPLDYAFELHSKYVYKYCNSKKKILFLGMNP 124
+ +L+IE +L +L N+++ PV +VYNPL+YA+E H Y+ +Y KK+LF+GMNP
Sbjct: 1 QKLLSIELELNEKL--DNLSFSAPVAHVYNPLEYAWEPHEAYLRRYGKGPKKVLFVGMNP 58
Query: 125 GPWGMVQCGIPFGEVKAVKGFLNIEGKVNQPEKFHKDRPIKGLDCPRSEISGKRLWELAS 184
GPWGM Q G+PFGEV AV+ +L IEG V +PE H RP++G DCPRSE+SG+RLW L
Sbjct: 59 GPWGMAQTGVPFGEVAAVRDWLGIEGPVGKPEVEHPKRPVEGFDCPRSEVSGRRLWGLFR 118
Query: 185 QLSDGKAADFFKHAYVHNYFPLAFVSKTATNITPAELKNKTTIEKLNSICDKSLSDIVKH 244
+ G +FF+H +VHNY PLAF+ ++ NITP +L K L CD++L V+
Sbjct: 119 ERF-GTPENFFRHCFVHNYCPLAFMEESGRNITPDKLP-KAERGPLFEACDEALRRTVEL 176
Query: 245 LGIETVIAIGKFAETRAEKALKSNRIFTVKVTSISHPSPRNPASNKNWVENTTKKLKDL 303
L E V+ +G FAE RA+ AL V V I HPSP +PA+N+ W E T++L++L
Sbjct: 177 LQPEWVVGVGAFAEQRAKAALS--AKLDVTVGRILHPSPASPAANRGWAEKATRQLEEL 233
>gnl|CDD|238612 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 = 74.6 bits (184), Expect = 2e-16
Identities = 25/96 (26%), Positives = 37/96 (38%), Gaps = 26/96 (27%)
Query: 338 RGMNEVNATKNATRHAEMVCIDHIVRQYPSTYRRVFESITVIVNVEPCIMCMAALLRVFE 397
RG N V + T HAE+V I + R+ S +
Sbjct: 33 RGHNRVEQDGDPTAHAEIVAIRNAARRLGS--------------------------YLLS 66
Query: 398 SITVIVNVEPCIMCMAALLSLNIRTIVFACSNDRFG 433
T+ +EPC MC ALL I+ +V+ S+ + G
Sbjct: 67 GCTLYTTLEPCPMCAGALLWARIKRVVYGASDPKLG 102
>gnl|CDD|223663 COG0590, CumB, Cytosine/adenosine deaminases [Nucleotide transport
and metabolism / Translation, ribosomal structure and
biogenesis].
Length = 152
Score = 65.8 bits (161), Expect = 7e-13
Identities = 22/96 (22%), Positives = 35/96 (36%), Gaps = 26/96 (27%)
Query: 338 RGMNEVNATKNATRHAEMVCIDHIVRQYPSTYRRVFESITVIVNVEPCIMCMAALLRVFE 397
RG N + T HAE++ I + YR +
Sbjct: 44 RGHNRREEDNDPTAHAEILAIRAAAETLGN-YR-------------------------LK 77
Query: 398 SITVIVNVEPCIMCMAALLSLNIRTIVFACSNDRFG 433
T+ V +EPC MC A++ I +V+ S+ + G
Sbjct: 78 DCTLYVTLEPCPMCAGAIIWARIDRVVYGASDPKTG 113
>gnl|CDD|215887 pfam00383, dCMP_cyt_deam_1, Cytidine and deoxycytidylate deaminase
zinc-binding region.
Length = 104
Score = 50.8 bits (122), Expect = 4e-08
Identities = 19/56 (33%), Positives = 25/56 (44%), Gaps = 3/56 (5%)
Query: 338 RGMNEVNATKNATRHAEMVCIDHIVRQYPSTYRRVFESITVIVNVEPCIMCMAALL 393
G N NA + T HAE I + R E T+ V +EPC MC A++
Sbjct: 41 TGYNGENAGYDPTIHAERNAIRNAGR---LGEGIKLEGATLYVTLEPCGMCRQAII 93
>gnl|CDD|217399 pfam03167, UDG, Uracil DNA glycosylase superfamily.
Length = 143
Score = 51.6 bits (124), Expect = 5e-08
Identities = 36/200 (18%), Positives = 58/200 (29%), Gaps = 64/200 (32%)
Query: 110 YCNSKKKILFLGMNPGPWGMVQCGIPFGEVKAVKGFLNIEGKVNQPEKFHKDRPIKGLDC 169
+ K+L +G PGP G G+PF
Sbjct: 2 FGPPNAKVLIVGEAPGP-GEDATGLPFAGR------------------------------ 30
Query: 170 PRSEISGKRLWELASQLSDGKAADFFKHAYVHNYFPLAFVSKTATNITPAELKNKTTIEK 229
+G LW++ A + Y TN+ +K + +
Sbjct: 31 -----AGNLLWKIL------AEAGLARQGV---YI---------TNV----VKCPRPVGR 63
Query: 230 LNS-----ICDKSLSDIVKHLGIETVIAIGKFAETRAEKALKSNRIFT-VKVTSISHPSP 283
+ C L + + L + V+ +GK A K + V + HPSP
Sbjct: 64 KPTRSEIAACRPYLLEELALLRPKVVVLLGKTAAKAFLGLGKKEADGGGIPVLPLPHPSP 123
Query: 284 RNPASNKNWVENTTKKLKDL 303
N E + L+DL
Sbjct: 124 LNRNPGFKRPEAFKEALEDL 143
>gnl|CDD|214957 smart00987, UreE_C, UreE urease accessory protein, C-terminal
domain. UreE is a urease accessory protein. Urease
hydrolyses urea into ammonia and carbamic acid. The
C-terminal region of members of this family contains a
His rich Nickel binding site.
Length = 135
Score = 42.6 bits (101), Expect = 6e-05
Identities = 35/184 (19%), Positives = 56/184 (30%), Gaps = 58/184 (31%)
Query: 110 YCNSKKKILFLGMNPGPWGMVQCGIPFGEVKAVKGFLNIEGKVNQPEKFHKDRPIKGLDC 169
+ + ++L +G PG G+PF G
Sbjct: 3 FGDPDARVLIVGQAPGHGEDAT-GLPFV------------GP------------------ 31
Query: 170 PRSEISGKRLWELASQLSDGKAADFFKHAYVHN---YFPLAFVSKTATNITPAELKNKTT 226
+G LW + +A + Y+ N P N+TP T
Sbjct: 32 -----AGNLLWNIL-----KEAGLDREDGYITNLVKCRPG----VLNGNLTP-------T 70
Query: 227 IEKLNSICDKSLSDIVKHLGIETVIAIGKFAETRA-EKALKSNRIFTVKVTSISHPSP-- 283
++ S L + L + ++ +GK A K + R +V HPSP
Sbjct: 71 AGEIASCAPGWLDAEIALLRPKVIVLLGKTAAKALLTKLIGRLRGRLPRVLPSPHPSPLL 130
Query: 284 RNPA 287
RNP
Sbjct: 131 RNPG 134
>gnl|CDD|198424 cd09593, UDG_like, Uracil-DNA glycosylases (UDG) and related
enzymes. Uracil-DNA glycosylases (UDG) catalyzes the
removal of uracil from DNA, which initiates the DNA base
excision repair pathway. Uracil in DNA can arise as a
result of mis-incorporation of dUMP residues by DNA
polymerase or via deamination of cytosine. Uracil in DNA
mispaired with guanine is one of the major pro-mutagenic
events, causing G:C->A:T mutations. Thus, UDG is an
essential enzyme for maintaining the integrity of
genetic information. At least five UDG families have
been characterized so far; these families share similar
overall folds and common active site motifs. They
demonstrate different substrate specificities, but often
the function of one enzyme can be complemented by the
other. Family 1 enzymes are active against uracil in
both ssDNA and dsDNA, and recognize uracil explicitly in
an extrahelical conformation via a combination of
protein and bound-water interactions. Family 2 enzymes
are mismatch specific and explicitly recognize the
widowed guanine on the complementary strand, rather than
the extrahelical scissile pyrimidine. This allows a
broader specificity so that some Family 2 enzymes can
excise uracil as well as 3, N(4)-ethenocytosine from
mismatches with guanine. A Family 3 UDG from human was
first characterized to remove Uracil from ssDNA, hence
the name hSMUG (single-strand-selective monofunctional
uracil-DNA glycosylase). However, subsequent research
has shown that hSMUG1 and its rat ortholog can remove
uracil and its oxidized pyrimidine derivatives from
both, ssDNA and dsDNA. Enzymes in Families 4 and 5 are
both thermostable. Family 4 enzymes specifically
recognize uracil in a manner similar to human UDG
(Family 1), rather than guanine in the complementary
strand DNA, as does E. coli MUG (Family 2). These
results suggest that the mechanism by which Family 4
UDGs remove uracils from DNA is similar to that of
Family 1 enzyme. Although Family 5 enzymes are close
relatives of Family 4, they show different substrate
specificities.
Length = 125
Score = 41.6 bits (98), Expect = 1e-04
Identities = 33/173 (19%), Positives = 46/173 (26%), Gaps = 55/173 (31%)
Query: 117 ILFLGMNPGPWGMVQCGIPFGEVKAVKGFLNIEGKVNQPEKFHKDRPIKGLDCPRSEISG 176
+L +G PG M Q G PF SG
Sbjct: 1 VLIVGQAPGIHEM-QAGGPFYGN-----------------------------------SG 24
Query: 177 KRLWELASQLSDGKAADFFKHAYVHNYFPLAFVSKTATNITPAELKNKTTIEKLNSICDK 236
K LW + G+ F Y+ N A + P EL C +
Sbjct: 25 KLLWRWLNAA-GGEFELFRYGVYLTNVVRCFPGKNKAGHRPP-ELAF----------CSE 72
Query: 237 SLSDIVKHLGIETVIAIGKFAETRAEKALKSNRIFTVKVTSIS-------HPS 282
L ++ L VI +G+ A ++ T HPS
Sbjct: 73 WLRREIELLKPRLVILLGRDAAEYLLPFRPLKKLVRQTYTGGGTDVLVLPHPS 125
>gnl|CDD|182786 PRK10860, PRK10860, tRNA-specific adenosine deaminase; Provisional.
Length = 172
Score = 36.7 bits (85), Expect = 0.009
Identities = 17/56 (30%), Positives = 28/56 (50%), Gaps = 5/56 (8%)
Query: 400 TVIVNVEPCIMCMAALLSLNIRTIVFACSNDRFG-----YNVLGSDEKTNYIEIVE 450
T+ V +EPC+MC A++ I +VF + + G +VL + +EI E
Sbjct: 84 TLYVTLEPCVMCAGAMVHSRIGRLVFGARDAKTGAAGSLMDVLHHPGMNHRVEITE 139
Score = 29.0 bits (65), Expect = 3.7
Identities = 14/47 (29%), Positives = 28/47 (59%), Gaps = 9/47 (19%)
Query: 350 TRHAEMVCIDH---IVRQYPSTYRRVFESITVIVNVEPCIMCMAALL 393
T HAE++ + +++ Y R+ ++ T+ V +EPC+MC A++
Sbjct: 60 TAHAEIMALRQGGLVLQNY-----RLLDA-TLYVTLEPCVMCAGAMV 100
>gnl|CDD|235426 PRK05352, PRK05352, Na(+)-translocating NADH-quinone reductase
subunit A; Provisional.
Length = 448
Score = 32.5 bits (75), Expect = 0.57
Identities = 13/50 (26%), Positives = 24/50 (48%), Gaps = 8/50 (16%)
Query: 237 SLSDIVKHLGIETVIAIGKFAETRAEKALKSNRIFTVKVTSISHPSPRNP 286
S V +G + VIAIGK + ++T +V +++ P+ + P
Sbjct: 233 SAGKTVWTIGYQDVIAIGKL--------FLTGELYTERVVALAGPAVKKP 274
>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 = 30.0 bits (68), Expect = 0.94
Identities = 15/54 (27%), Positives = 18/54 (33%), Gaps = 6/54 (11%)
Query: 338 RGMNEVNATKNATRHAEMVCIDHIVRQYPSTYRRVFESITV---IVNVEPCIMC 388
G+N NA+ T AE I V RR + V PC C
Sbjct: 33 TGVNVENASYGLTLCAERTAIGKAV---SEGLRRYLVTWAVSDEGGVWSPCGAC 83
>gnl|CDD|206605 pfam14439, Bd3614-deam, Bd3614-like deaminase. A member of the
nucleic acid/nucleotide deaminase superfamily prototyped
by Bdellovibrio Bd3614. They are typified by a distinct
N-terminal globular domain. The Bdellovibrio version
occurs in a predicted operon with a 23S rRNA
G2445-modifying methylase suggesting that it might be
involved in RNA editing.
Length = 113
Score = 29.8 bits (67), Expect = 1.2
Identities = 16/49 (32%), Positives = 22/49 (44%), Gaps = 5/49 (10%)
Query: 343 VNATKNATRHAEMVCIDHIVRQYPSTYRRVFESITVI-VNVEPCIMCMA 390
NA KN T HAE+ + + T RR + V ++ C MC A
Sbjct: 28 TNA-KNKTLHAEV---NLLQPLLRETARRPIPPGARLLVTLQCCKMCAA 72
>gnl|CDD|100616 PRK00611, PRK00611, putative disulfide oxidoreductase; Provisional.
Length = 135
Score = 29.8 bits (67), Expect = 1.5
Identities = 11/26 (42%), Positives = 18/26 (69%), Gaps = 2/26 (7%)
Query: 386 IMCMAALLRVFESITVIVNVEPCIMC 411
I C+ L+ ++ S I+NVEPC++C
Sbjct: 16 ISCIGTLMSIYYS--YILNVEPCVLC 39
>gnl|CDD|220656 pfam10256, Erf4, Golgin subfamily A member 7/ERF4 family. This
family of proteins includes Golgin subfamily A member 7
proteins as well as Ras modification protein ERF4.
Length = 118
Score = 29.5 bits (67), Expect = 1.6
Identities = 7/53 (13%), Positives = 18/53 (33%), Gaps = 6/53 (11%)
Query: 201 HNYFPLAFVSKTATNITPAELKNKTTIEKLNSICDKSLSDIVKHLGIETVIAI 253
+P + I+ E + I ++N ++ I +E ++
Sbjct: 19 STLYPGELEGR----ISEEEFE--EIINRINDYLAEAFEPISWRNLLEGILGC 65
>gnl|CDD|238613 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 = 29.2 bits (66), Expect = 2.3
Identities = 9/27 (33%), Positives = 16/27 (59%)
Query: 400 TVIVNVEPCIMCMAALLSLNIRTIVFA 426
T+ V + PCI C ++ I+ +V+A
Sbjct: 90 TLYVTLFPCIECAKLIIQAGIKKVVYA 116
>gnl|CDD|181196 PRK08010, PRK08010, pyridine nucleotide-disulfide oxidoreductase;
Provisional.
Length = 441
Score = 30.0 bits (67), Expect = 3.4
Identities = 30/114 (26%), Positives = 47/114 (41%), Gaps = 9/114 (7%)
Query: 208 FVSKTATNITPAELKNKTTIEKLNSICDKSLSDIVKHLGIETVIAIG-KFAETRAEKALK 266
F++ A + P TT +S +L ++ HLGI IG +FA A
Sbjct: 124 FINTGAQTVVPPIPGITTTPGVYDSTGLLNLKELPGHLGILGGGYIGVEFASMFAN---- 179
Query: 267 SNRIFTVKVTSISHPSPRNPASNKNWVENTTKKLKDLGVLHYFTSESQNIPNHE 320
F KVT + S P +++ +N L+D GV + + I +HE
Sbjct: 180 ----FGSKVTILEAASLFLPREDRDIADNIATILRDQGVDIILNAHVERISHHE 229
>gnl|CDD|114907 pfam06215, ISAV_HA, Infectious salmon anaemia virus haemagglutinin.
This family consists of several infectious salmon
anaemia virus haemagglutinin proteins. Infectious salmon
anaemia virus (ISAV), an orthomyxovirus-like virus, is
an important fish pathogen in marine aquaculture.
Length = 391
Score = 28.8 bits (64), Expect = 7.6
Identities = 13/33 (39%), Positives = 21/33 (63%)
Query: 6 IIQNIKVDSAITNPNTPIEKPTDGIMSIFMSAS 38
I++N+++D + PNT P+DG S+ SAS
Sbjct: 236 IMRNVELDEYVDTPNTGGVYPSDGFDSLHGSAS 268
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
0.317 0.132 0.386
Gapped
Lambda K H
0.267 0.0756 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 24,150,234
Number of extensions: 2286782
Number of successful extensions: 1885
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1876
Number of HSP's successfully gapped: 28
Length of query: 489
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 388
Effective length of database: 6,457,848
Effective search space: 2505645024
Effective search space used: 2505645024
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 61 (27.2 bits)