RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4120
(95 letters)
>gnl|CDD|234692 PRK00222, PRK00222, methionine sulfoxide reductase B; Provisional.
Length = 142
Score = 119 bits (301), Expect = 2e-36
Identities = 51/123 (41%), Positives = 58/123 (47%), Gaps = 44/123 (35%)
Query: 14 KEELKKRLTPMQYHVTQEKGTER--------------Y--IGSNLLL------------- 44
KEE KK+LTP QY VTQE GTER Y I L
Sbjct: 7 KEEWKKQLTPEQYRVTQEHGTERPFTGEYLDNKEKGIYVCIVCGEPLFSSDTKFDSGCGW 66
Query: 45 -----------LITNPD----MVRTEVTCSKCDAHLGHVFNDGPAPTRRRFCINSASVDF 89
+ D MVRTEV C+ CD+HLGHVF DGP PT R+CINSAS+ F
Sbjct: 67 PSFTKPIDEEAIRELRDTSHGMVRTEVRCANCDSHLGHVFPDGPKPTGLRYCINSASLKF 126
Query: 90 VPD 92
+P
Sbjct: 127 IPK 129
>gnl|CDD|223307 COG0229, COG0229, Conserved domain frequently associated with
peptide methionine sulfoxide reductase
[Posttranslational modification, protein turnover,
chaperones].
Length = 140
Score = 101 bits (255), Expect = 2e-29
Identities = 49/124 (39%), Positives = 57/124 (45%), Gaps = 45/124 (36%)
Query: 15 EELKKRLTPMQYHVTQEKGTER--------------Y--IGSNLLL-------------- 44
EELK++LTP QY VTQ GTER Y I L
Sbjct: 7 EELKEKLTPEQYRVTQNHGTERPFTGEYLDNKEKGIYVCIVCGEPLFSSEDKFDSGCGWP 66
Query: 45 ----------LITNPD----MVRTEVTCSKCDAHLGHVFNDGPAPTRR-RFCINSASVDF 89
+ D MVRTEV C+ CD+HLGHVF DGP PT R+CINSAS+ F
Sbjct: 67 SFTKPISPDAITYKEDRSHGMVRTEVRCANCDSHLGHVFPDGPPPTGGLRYCINSASLRF 126
Query: 90 VPDH 93
+P
Sbjct: 127 IPKE 130
>gnl|CDD|129454 TIGR00357, TIGR00357, methionine-R-sulfoxide reductase. This model
describes a domain found in PilB, a protein important
for pilin expression, N-terminal to a domain coextensive
to with the known peptide methionine sulfoxide reductase
(MsrA), a protein repair enzyme, of E. coli. Among the
early completed genomes, this module is found if and
only if MsrA is also found, whether N-terminal to MsrA
(as for Helicobacter pylori), C-terminal (as for
Treponema pallidum), or in a separate polypeptide.
Although the function of this region is not clear, an
auxiliary function to MsrA is suggested [Protein fate,
Protein modification and repair, Cellular processes,
Adaptations to atypical conditions].
Length = 134
Score = 92.1 bits (229), Expect = 1e-25
Identities = 48/127 (37%), Positives = 57/127 (44%), Gaps = 44/127 (34%)
Query: 11 KIDKEELKKRLTPMQYHVTQEKGTER--------------Y--IGSNLLLLITNP----- 49
K EELKK+LTP+QY VTQ GTE Y I L +
Sbjct: 1 KPSDEELKKKLTPLQYEVTQNAGTEPPFTNEYWDNKEEGIYVDITCGEPLFSSEDKFDSG 60
Query: 50 -----------------------DMVRTEVTCSKCDAHLGHVFNDGPAPTRRRFCINSAS 86
M+RTEV C CDAHLGHVF+DGP PT R+CINSA+
Sbjct: 61 CGWPSFYKPISEEVVAYERDESHGMIRTEVRCRNCDAHLGHVFDDGPEPTGLRYCINSAA 120
Query: 87 VDFVPDH 93
+ F+P
Sbjct: 121 LKFIPLE 127
>gnl|CDD|201899 pfam01641, SelR, SelR domain. Methionine sulfoxide reduction is an
important process, by which cells regulate biological
processes and cope with oxidative stress. MsrA, a
protein involved in the reduction of methionine
sulfoxides in proteins, has been known for four decades
and has been extensively characterized with respect to
structure and function. However, recent studies revealed
that MsrA is only specific for methionine-S-sulfoxides.
Because oxidized methionines occur in a mixture of R and
S isomers in vivo, it was unclear how stereo-specific
MsrA could be responsible for the reduction of all
protein methionine sulfoxides. It appears that a second
methionine sulfoxide reductase, SelR, evolved that is
specific for methionine-R-sulfoxides, the activity that
is different but complementary to that of MsrA. Thus,
these proteins, working together, could reduce both
stereoisomers of methionine sulfoxide. This domain is
found both in SelR proteins and fused with the peptide
methionine sulfoxide reductase enzymatic domain
pfam01625. The domain has two conserved cysteine and
histidines. The domain binds both selenium and zinc. The
final cysteine is found to be replaced by the rare amino
acid selenocysteine in some members of the family. This
family has methionine-R-sulfoxide reductase activity.
Length = 124
Score = 91.2 bits (227), Expect = 2e-25
Identities = 45/124 (36%), Positives = 53/124 (42%), Gaps = 45/124 (36%)
Query: 14 KEELKKRLTPMQYHVTQEKGTER--------------Y--IGSNLLLLITN--------- 48
EE K L+P QY V + KGTE+ Y IG L +
Sbjct: 1 DEEWKAVLSPEQYRVLRNKGTEKPFTGEYDDHFEEGIYVCIGCGEPLFSSTTKFDSGCGW 60
Query: 49 ---------------PD----MVRTEVTCSKCDAHLGHVFNDGPA-PTRRRFCINSASVD 88
PD M RTEV C+ CD HLGHVF DGP P R+CINSAS+
Sbjct: 61 PSFFEPISGDAIKYTPDRSHGMRRTEVRCANCDGHLGHVFKDGPKEPGGLRYCINSASLK 120
Query: 89 FVPD 92
F+P
Sbjct: 121 FIPA 124
>gnl|CDD|235499 PRK05550, PRK05550, bifunctional methionine sulfoxide reductase B/A
protein; Provisional.
Length = 283
Score = 81.9 bits (203), Expect = 2e-20
Identities = 40/120 (33%), Positives = 52/120 (43%), Gaps = 42/120 (35%)
Query: 15 EELKKRLTPMQYHVTQEKGTER--------------YI----GSNLLL------------ 44
+ K LTP +Y V ++KGTER Y+ G+ L
Sbjct: 1 MDKMKSLTPFEYRVIEDKGTERPFSGEYYDHDEKGVYLCRRCGAPLFRSEDKFNSGCGWP 60
Query: 45 ---------LITNPDM--VRTEVTCSKCDAHLGHVF-NDGPAPTRRRFCINSASVDFVPD 92
+ PD RTE+ C+ C AHLGHVF +G P R C+NSAS+DFVP
Sbjct: 61 SFDDEIPGAVKRLPDADGRRTEIVCANCGAHLGHVFEGEGLTPKNTRHCVNSASLDFVPA 120
>gnl|CDD|184456 PRK14018, PRK14018, trifunctional thioredoxin/methionine sulfoxide
reductase A/B protein; Provisional.
Length = 521
Score = 69.9 bits (171), Expect = 1e-15
Identities = 41/126 (32%), Positives = 49/126 (38%), Gaps = 45/126 (35%)
Query: 11 KIDKEELKKRLTPMQYHVTQEKGTER--------------YI----GSNLLLL------- 45
K ELK+ LT QY +TQ TER Y+ G L
Sbjct: 379 KPSDAELKRTLTEEQYQITQNAATERAFSHEYDHLFKPGIYVDVVSGEPLFSSADKYDSG 438
Query: 46 -----ITNP--------------DMVRTEVTCSKCDAHLGHVFNDGP-APTRRRFCINSA 85
T P +M RTEV D+HLGHVF DGP R+CIN A
Sbjct: 439 CGWPSFTRPIDAKVVTEHDDFSYNMRRTEVRSRAADSHLGHVFPDGPRDKGGLRYCINGA 498
Query: 86 SVDFVP 91
S+ F+P
Sbjct: 499 SLKFIP 504
>gnl|CDD|180121 PRK05508, PRK05508, methionine sulfoxide reductase B; Provisional.
Length = 119
Score = 56.6 bits (137), Expect = 6e-12
Identities = 24/48 (50%), Positives = 30/48 (62%), Gaps = 1/48 (2%)
Query: 46 ITNPDMVRTEVTCSKCDAHLGHVF-NDGPAPTRRRFCINSASVDFVPD 92
I + D RTE+ C+ C HLGHVF +G P R C+NS S+ FVPD
Sbjct: 70 IPDADGRRTEIVCANCGGHLGHVFEGEGFTPKNTRHCVNSISLKFVPD 117
>gnl|CDD|220419 pfam09814, DUF2351, Uncharacterized conserved protein (DUF2351).
Members of this family of proteins have no known
function.
Length = 350
Score = 25.6 bits (56), Expect = 4.9
Identities = 9/41 (21%), Positives = 15/41 (36%), Gaps = 5/41 (12%)
Query: 37 YIGSNLLLLITN-----PDMVRTEVTCSKCDAHLGHVFNDG 72
+G L+ + T+V C +C A LG +
Sbjct: 169 LVGDTYFLVNKSDLSEVVVRDETKVICKRCKAMLGEKTSSE 209
>gnl|CDD|162820 TIGR02356, adenyl_thiF, thiazole biosynthesis adenylyltransferase
ThiF, E. coli subfamily. Members of the HesA/MoeB/ThiF
family of proteins (pfam00899) include a number of
members encoded in the midst of thiamine biosynthetic
operons. This mix of known and putative ThiF proteins
shows a deep split in phylogenetic trees, with the
Escherichia. coli ThiF and the E. coli MoeB proteins
seemingly more closely related than E. coli ThiF and
Campylobacter (for example) ThiF. This model represents
the more widely distributed clade of ThiF proteins such
found in E. coli [Biosynthesis of cofactors, prosthetic
groups, and carriers, Thiamine].
Length = 202
Score = 25.4 bits (56), Expect = 4.9
Identities = 13/38 (34%), Positives = 17/38 (44%)
Query: 15 EELKKRLTPMQYHVTQEKGTERYIGSNLLLLITNPDMV 52
E +RL + + ER NL LLI N D+V
Sbjct: 78 EVAAQRLRELNSDIQVTALKERVTAENLELLINNVDLV 115
>gnl|CDD|214521 smart00115, CASc, Caspase, interleukin-1 beta converting enzyme
(ICE) homologues. Cysteine aspartases that mediate
programmed cell death (apoptosis). Caspases are
synthesised as zymogens and activated by proteolysis of
the peptide backbone adjacent to an aspartate. The
resulting two subunits associate to form an
(alpha)2(beta)2-tetramer which is the active enzyme.
Activation of caspases can be mediated by other caspase
homologues.
Length = 241
Score = 25.3 bits (56), Expect = 5.0
Identities = 6/24 (25%), Positives = 10/24 (41%)
Query: 9 GCKIDKEELKKRLTPMQYHVTQEK 32
G +D E L + + Y V +
Sbjct: 27 GTDVDAENLTELFQSLGYEVQVKN 50
>gnl|CDD|224126 COG1205, COG1205, Distinct helicase family with a unique C-terminal
domain including a metal-binding cysteine cluster
[General function prediction only].
Length = 851
Score = 25.4 bits (56), Expect = 5.3
Identities = 12/40 (30%), Positives = 20/40 (50%), Gaps = 3/40 (7%)
Query: 15 EELKKRLTPMQYHVTQEKGTER--YIGSNLLLLITNPDMV 52
+L ++T +Y ER I + +L+TNPDM+
Sbjct: 140 SDLPGKVTFGRYT-GDTPPEERRAIIRNPPDILLTNPDML 178
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 0.136 0.427
Gapped
Lambda K H
0.267 0.0767 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,717,557
Number of extensions: 362244
Number of successful extensions: 315
Number of sequences better than 10.0: 1
Number of HSP's gapped: 310
Number of HSP's successfully gapped: 23
Length of query: 95
Length of database: 10,937,602
Length adjustment: 62
Effective length of query: 33
Effective length of database: 8,187,654
Effective search space: 270192582
Effective search space used: 270192582
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: 53 (24.1 bits)