RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2080
(93 letters)
>gnl|CDD|221996 pfam13232, Complex1_LYR_1, Complex1_LYR-like. This is a family
of proteins carrying the LYR motif of family
Complex1_LYR, pfam05347, likely to be involved in Fe-S
cluster biogenesis in mitochondria.
Length = 61
Score = 70.7 bits (174), Expect = 4e-18
Identities = 29/59 (49%), Positives = 42/59 (71%)
Query: 8 ILKLYKALLRESSKFPAYNYRMYFLRRTREKFQSNKNVDNNEQISLLYNEGLKELEVLK 66
+L LY+ LLR + KFP YN+R Y RR R++F+ NK++ + E+I L EG K+LE+LK
Sbjct: 3 VLSLYRQLLRAARKFPDYNFREYIRRRIRDEFRKNKDLTDPEKIEKLLKEGKKQLELLK 61
>gnl|CDD|203236 pfam05347, Complex1_LYR, Complex 1 protein (LYR family).
Proteins in this family have been identified as a
component of the higher eukaryotic NADH complex. In
Saccharomyces cerevisiae, the Isd11 protein has been
shown to play a role in Fe/S cluster biogenesis in
mitochondria. We have named this family LYR after a
highly conserved tripeptide motif close to the
N-terminus of these proteins.
Length = 59
Score = 67.2 bits (165), Expect = 9e-17
Identities = 31/57 (54%), Positives = 41/57 (71%)
Query: 8 ILKLYKALLRESSKFPAYNYRMYFLRRTREKFQSNKNVDNNEQISLLYNEGLKELEV 64
+L LY+ LLRE+ KFP YN R YF RR R++F+ NKN+ + E+I L EG K+LEV
Sbjct: 3 VLSLYRQLLREARKFPDYNAREYFRRRIRDEFRKNKNLTDPEKIEALLKEGKKQLEV 59
>gnl|CDD|233994 TIGR02746, TraC-F-type, type-IV secretion system protein TraC. The
protein family described here is common among the F, P
and I-like type IV secretion systems. Gene symbols
include TraC (F-type), TrbE/VirB4 (P-type) and TraU
(I-type). The protein conyains the Walker A and B motifs
and so is a putative nucleotide triphosphatase.
Length = 797
Score = 28.1 bits (63), Expect = 0.72
Identities = 12/51 (23%), Positives = 23/51 (45%), Gaps = 5/51 (9%)
Query: 39 FQSNKNVDNNEQISLLYNEGLKELEVLKRQVLISQLFKPDKLVIETQMQNS 89
F N+D + + +L E L++ L+ VL S + + I +M +
Sbjct: 588 FNGPNNLDFSNRFVVLELEELEDRPDLQAVVLFSLMVR-----ITGEMYLT 633
>gnl|CDD|221997 pfam13233, Complex1_LYR_2, Complex1_LYR-like. This is a family
of proteins carrying the LYR motif of family
Complex1_LYR, pfam05347, likely to be involved in Fe-S
cluster biogenesis in mitochondria.
Length = 97
Score = 26.6 bits (59), Expect = 1.0
Identities = 17/73 (23%), Positives = 31/73 (42%), Gaps = 4/73 (5%)
Query: 8 ILKLYKALLRE----SSKFPAYNYRMYFLRRTREKFQSNKNVDNNEQISLLYNEGLKELE 63
+L+LY+ LLRE ++ + R R++F+ + ++E E L
Sbjct: 1 VLRLYRELLRELPKYPLRYNLLSSLSLGRRYVRKEFRRHAGATDDELAKEFLQEAENYLA 60
Query: 64 VLKRQVLISQLFK 76
LK Q +L +
Sbjct: 61 YLKAQRHYLELLE 73
>gnl|CDD|221876 pfam12969, DUF3857, Domain of Unknown Function with PDB structure
(DUF3857). This family is based on the first domain of
the PDB structure PDB:3KD4(residues 1-228). It is
structurally similar to domains in other hydrolases,
eg. M1 family aminopeptidase (3ebi, Z=10, rmsd 3.6A for
152 CA, seq id 12%), despite lack of any significant
sequence similarity.
Length = 177
Score = 26.9 bits (60), Expect = 1.3
Identities = 15/40 (37%), Positives = 22/40 (55%), Gaps = 5/40 (12%)
Query: 45 VDNNEQISLLYNEGLKELEVLKRQVLISQLFKPDKLVIET 84
V+ QISL Y+ + LEV K +V+ +PD +IE
Sbjct: 24 VEEYSQISLSYDPDYETLEVHKARVI-----RPDGKIIEL 58
>gnl|CDD|111823 pfam02976, MutH, DNA mismatch repair enzyme MutH.
Length = 100
Score = 25.6 bits (57), Expect = 2.8
Identities = 5/32 (15%), Positives = 17/32 (53%)
Query: 48 NEQISLLYNEGLKELEVLKRQVLISQLFKPDK 79
+++ + EG +++ + R++ L+ P +
Sbjct: 60 LKRVLWIPYEGERDIPLADRKIGSPFLWSPSE 91
>gnl|CDD|197320 cd09086, ExoIII-like_AP-endo, Escherichia coli exonuclease III
(ExoIII) and Neisseria meningitides NExo-like subfamily
of the ExoIII family purinic/apyrimidinic (AP)
endonucleases. This subfamily includes Escherichia coli
ExoIII, Neisseria meningitides NExo,and related
proteins. These are ExoIII family AP endonucleases and
they belong to the large EEP
(exonuclease/endonuclease/phosphatase) superfamily that
contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds. AP endonucleases participate in the DNA base
excision repair (BER) pathway. AP sites are one of the
most common lesions in cellular DNA. During BER, the
damaged DNA is first recognized by DNA glycosylase. AP
endonucleases then catalyze the hydrolytic cleavage of
the phosphodiester bond 5' to the AP site, and this is
followed by the coordinated actions of DNA polymerase,
deoxyribose phosphatase, and DNA ligase. If left
unrepaired, AP sites block DNA replication, and have
both mutagenic and cytotoxic effects. AP endonucleases
can carry out a variety of excision and incision
reactions on DNA, including 3'-5' exonuclease,
3'-deoxyribose phosphodiesterase, 3'-phosphatase, and
occasionally, nonspecific DNase activities. Different AP
endonuclease enzymes catalyze the different reactions
with different efficiencies. Many organisms have two AP
endonucleases, usually one is the dominant AP
endonuclease, the other has weak AP endonuclease
activity. For example, Neisseria meningitides Nape and
NExo, and exonuclease III (ExoIII) and endonuclease IV
(EndoIV) in Escherichia coli. NExo and ExoIII are found
in this subfamily. NExo is the non-dominant AP
endonuclease. It exhibits strong 3'-5' exonuclease and
3'-deoxyribose phosphodiesterase activities. Escherichia
coli ExoIII is an active AP endonuclease, and in
addition, it exhibits double strand (ds)-specific 3'-5'
exonuclease, exonucleolytic RNase H,
3'-phosphomonoesterase and 3'-phosphodiesterase
activities, all catalyzed by a single active site. Class
II AP endonucleases have been classified into two
families, designated ExoIII and EndoIV, based on their
homology to the Escherichia coli enzymes ExoIII and
endonuclease IV (EndoIV). This subfamily belongs to the
ExoIII family; the EndoIV family belongs to a different
superfamily.
Length = 254
Score = 24.8 bits (55), Expect = 8.6
Identities = 6/26 (23%), Positives = 11/26 (42%)
Query: 23 PAYNYRMYFLRRTREKFQSNKNVDNN 48
P + Y++ +L R Q D+
Sbjct: 115 PKFAYKLDWLDRLIRYLQKLLKPDDP 140
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 0.349
Gapped
Lambda K H
0.267 0.0668 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,418,300
Number of extensions: 355666
Number of successful extensions: 357
Number of sequences better than 10.0: 1
Number of HSP's gapped: 356
Number of HSP's successfully gapped: 27
Length of query: 93
Length of database: 10,937,602
Length adjustment: 60
Effective length of query: 33
Effective length of database: 8,276,362
Effective search space: 273119946
Effective search space used: 273119946
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: 53 (24.3 bits)