RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1480
(126 letters)
>gnl|CDD|148383 pfam06747, CHCH, CHCH domain. we have identified a conserved
motif in the LOC118487 protein that we have called the
CHCH motif. Alignment of this protein with related
members showed the presence of three subgroups of
proteins, which are called the S (Small), N (N-terminal
extended) and C (C-terminal extended) subgroups. All
three sub-groups of proteins have in common that they
contain a predicted conserved [coiled coil 1]-[helix
1]-[coiled coil 2]-[helix 2] domain (CHCH domain).
Within each helix of the CHCH domain, there are two
cysteines present in a C-X9-C motif. The N-group
contains an additional double helix domain, and each
helix contains the C-X9-C motif. This family contains a
number of characterized proteins: Cox19 protein - a
nuclear gene of Saccharomyces cerevisiae, codes for an
11-kDa protein (Cox19p) required for expression of
cytochrome oxidase. Because cox19 mutants are able to
synthesise the mitochondrial and nuclear gene products
of cytochrome oxidase, Cox19p probably functions
post-translationally during assembly of the enzyme.
Cox19p is present in the cytoplasm and mitochondria,
where it exists as a soluble intermembrane protein.
This dual location is similar to what was previously
reported for Cox17p, a low molecular weight copper
protein thought to be required for maturation of the
CuA centre of subunit 2 of cytochrome oxidase. Cox19p
have four conserved potential metal ligands, these are
three cysteines and one histidine. Mrp10 - belongs to
the class of yeast mitochondrial ribosomal proteins
that are essential for translation. Eukaryotic
NADH-ubiquinone oxidoreductase 19 kDa (NDUFA8) subunit.
The CHCH domain was previously called DUF657.
Length = 35
Score = 35.3 bits (82), Expect = 4e-04
Identities = 11/32 (34%), Positives = 13/32 (40%)
Query: 53 CIQEMSMAFSCLKANDFVQTNCAKEIKDFIAC 84
C +E CLK N + C KE F C
Sbjct: 1 CGEEFKAFLKCLKENSDELSKCRKEFDAFRQC 32
>gnl|CDD|238961 cd02003, TPP_IolD, Thiamine pyrophosphate (TPP) family, IolD
subfamily, TPP-binding module; composed of proteins
similar to Rhizobium leguminosarum bv. viciae IolD. IolD
plays an important role in myo-inositol catabolism.
Length = 205
Score = 33.0 bits (76), Expect = 0.022
Identities = 12/58 (20%), Positives = 23/58 (39%)
Query: 11 MRNFRRLIKYSKDENRVKFDPILPLELKNRVSGKGGDSKKAGCIQEMSMAFSCLKAND 68
+F + E+ +LP++ G +K I+E+ A + KA+D
Sbjct: 117 SGSFGTEFRDRDQESGQLDGALLPVDFAANARSLGARVEKVKTIEELKAALAKAKASD 174
>gnl|CDD|233050 TIGR00609, recB, exodeoxyribonuclease V, beta subunit. The RecBCD
holoenzyme is a multifunctional nuclease with potent
ATP-dependent exodeoxyribonuclease activity. Ejection of
RecD, as occurs at chi recombinational hotspots,
cripples exonuclease activity in favor of recombinagenic
helicase activity. All proteins in this family for which
functions are known are DNA-DNA helicases that are used
as part of an exonuclease-helicase complex (made up of
RecBCD homologs) that function to generate substrates
for the initiation of recombination and recombinational
repair. This family is based on the phylogenomic
analysis of JA Eisen (1999, Ph.D. Thesis, Stanford
University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 1087
Score = 28.2 bits (63), Expect = 1.5
Identities = 14/55 (25%), Positives = 21/55 (38%), Gaps = 12/55 (21%)
Query: 74 CAKEIKDFIACADLRRSNKYIKKQEF------------HKKEISIGDKDLKAWEI 116
CA+EI ++A A L +N +KE + K LK +I
Sbjct: 440 CAREIALWLASAALGLANFIATFGGRPLRAGDIAVLVRGRKEANQIRKALKKAQI 494
>gnl|CDD|212507 cd11648, RsmI, Ribosomal RNA small subunit methyltransferase I,
also known as rRNA (cytidine-2'-O-)-methyltransferase
RsmI. Proteins in this family catalyze the
2-O-methylation of the ribose of cytidine 1402 (C1402)
in 16S rRNA using S-adenosyl-L-methionine (SAM or
Ado-Met) as the methyl donor. RsmI proteins employ the
30S subunit (not the 16S rRNA) as a substrate,
suggesting that the methylation reaction occurs at a
late step during 30S assembly in the cell.
Length = 218
Score = 27.3 bits (62), Expect = 2.1
Identities = 10/26 (38%), Positives = 12/26 (46%)
Query: 80 DFIACADLRRSNKYIKKQEFHKKEIS 105
D IAC D R + K + K IS
Sbjct: 26 DLIACEDTRHTKKLLNHYGIKKPLIS 51
>gnl|CDD|188452 TIGR03937, PgaC_IcaA, poly-beta-1,6 N-acetyl-D-glucosamine
synthase. Members of this protein family are
biofilm-forming enzymes that polymerize
N-acetyl-D-glucosamine residues in beta(1,6) linkage.
One named members is IcaA (intercellular adhesin protein
A), an enzyme that acts (with aid of subunit IcaD) in
Polysaccharide Intercellular Adhesin (PIA) biosynthesis
in Staphylococcus epidermis). The homologous member in
E. coli is designated PgaC. Members are often encoded
next to a polysaccharide deacetylase and involved in
biofilm formation. Note that chitin, although also made
from N-acetylglucosamine, is formed with beta-1,4
linkages.
Length = 407
Score = 27.2 bits (61), Expect = 2.7
Identities = 13/52 (25%), Positives = 22/52 (42%), Gaps = 7/52 (13%)
Query: 82 IAC----ADLRRSNKYIKKQEFHKKEISI---GDKDLKAWEIDALLKKYPRL 126
+ C A++ + ++ + EI G KD A +D L + PRL
Sbjct: 51 VPCYNEGANVEETISHLLALRYPNFEIIAINDGSKDNTAEILDRLAAQDPRL 102
>gnl|CDD|239570 cd03488, Topoisomer_IB_N_htopoI_like, Topoisomer_IB_N_htopoI_like :
N-terminal DNA binding fragment found in eukaryotic DNA
topoisomerase (topo) IB proteins similar to the
monomeric yeast and human topo I. Topo I enzymes are
divided into: topo type IA (bacterial) and type IB
(eukaryotic). Topo I relaxes superhelical tension in
duplex DNA by creating a single-strand nick, the broken
strand can then rotate around the unbroken strand to
remove DNA supercoils and, the nick is religated,
liberating topo I. These enzymes regulate the
topological changes that accompany DNA replication,
transcription and other nuclear processes. Human topo I
is the target of a diverse set of anticancer drugs
including camptothecins (CPTs). CPTs bind to the topo
I-DNA complex and inhibit religation of the
single-strand nick, resulting in the accumulation of
topo I-DNA adducts. This family may represent more than
one structural domain.
Length = 215
Score = 26.5 bits (59), Expect = 3.4
Identities = 21/60 (35%), Positives = 28/60 (46%), Gaps = 4/60 (6%)
Query: 67 NDF--VQTNCAKE-IKDFIACADLRRSNKYIKKQEFHKKEISIGDKDLKAWEIDALLKKY 123
DF V T K IKDF C D + Y K Q+ KK +S +K E + L ++Y
Sbjct: 65 KDFKKVMTKEEKVIIKDFSKC-DFTQMFAYFKAQKEEKKAMSKEEKKAIKAEKEKLEEEY 123
>gnl|CDD|192194 pfam08991, DUF1903, Domain of unknown function (DUF1903).
Members of this family adopt a coiled coil structure,
with two antiparallel alpha-helices that are tightly
strapped together by two disulfide bridges at each end.
The protein sequence shows a cysteine motif, required
for the stabilisation of the coiled-coil-like
structure. Additional inter-helix hydrophobic contacts
impart stability to this scaffold. The precise function
of this eukaryotic domain is, as yet, unknown.
Length = 67
Score = 24.9 bits (54), Expect = 5.0
Identities = 12/36 (33%), Positives = 17/36 (47%), Gaps = 6/36 (16%)
Query: 49 KKAGCIQEMSMAFSCLKANDFVQTNCAKEIKDFIAC 84
K+A IQ CL+AN + ++ C I D C
Sbjct: 6 KQACAIQ------DCLQANGYDESRCEDVIDDLYRC 35
>gnl|CDD|226091 COG3561, COG3561, Phage anti-repressor protein [Transcription].
Length = 110
Score = 25.4 bits (56), Expect = 5.6
Identities = 9/46 (19%), Positives = 20/46 (43%), Gaps = 5/46 (10%)
Query: 76 KEIKDFIACADLRRSNKYIKKQEF-----HKKEISIGDKDLKAWEI 116
E D+I C+D + ++ KEI++ +++ K +
Sbjct: 42 IENIDYIGCSDYGEEFSGVIGMDYALTIDMAKEIAMVERNEKGRQA 87
>gnl|CDD|216221 pfam00971, EIAV_GP90, EIAV coat protein, gp90. Equine infectious
anaemia (EIAV). EIAV belongs to the family Retroviridae.
EIAV gp90 is hypervariable in the carboxyl-end region
and more stable in the amino-end region. This
variability is a pathogenicity factor that allows the
evasion of the host's immune response.
Length = 385
Score = 26.2 bits (57), Expect = 5.6
Identities = 12/32 (37%), Positives = 21/32 (65%), Gaps = 1/32 (3%)
Query: 86 DLRRSNKYIKKQEFHKKEISIGDK-DLKAWEI 116
+L R NK I+ Q F++ SI +K +L+ W++
Sbjct: 342 ELPRPNKRIRNQSFNQYNCSINNKTELETWKL 373
>gnl|CDD|151559 pfam11115, DUF2623, Protein of unknown function (DUF2623). This
family is conserved in the Enterobacteriaceae family.
Several members are named as YghW. The function is not
known.
Length = 95
Score = 25.1 bits (55), Expect = 6.0
Identities = 14/49 (28%), Positives = 23/49 (46%), Gaps = 5/49 (10%)
Query: 75 AKEIKDFIACADLRRSNKYIKKQEFHKKEISIGDKDLKAWEIDALLKKY 123
A + +F C+D +R ++ E GD+ L AWE L ++Y
Sbjct: 21 ANNVANF--CSDYKRG--FVLGYAHRMAE-KTGDRQLSAWEAGILTRRY 64
>gnl|CDD|205253 pfam13072, DUF3936, Protein of unknown function (DUF3936). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria. Proteins in
this family are approximately 40 amino acids in length.
There is a conserved GKAW sequence motif. There is a
single completely conserved residue G that may be
functionally important.
Length = 38
Score = 24.3 bits (53), Expect = 6.1
Identities = 9/14 (64%), Positives = 11/14 (78%)
Query: 112 KAWEIDALLKKYPR 125
KAWEI A LK+Y +
Sbjct: 15 KAWEIRAKLKEYSK 28
>gnl|CDD|223390 COG0313, COG0313, Predicted methyltransferases [General function
prediction only].
Length = 275
Score = 26.0 bits (58), Expect = 6.3
Identities = 13/46 (28%), Positives = 19/46 (41%), Gaps = 2/46 (4%)
Query: 80 DFIACADLRRSNKYIKKQEFHKKEISIGDKDLKAW--EIDALLKKY 123
D IA D R + K + IS + + K ++ LLKK
Sbjct: 32 DVIAAEDTRVTRKLLSHLGIKTPLISYHEHNEKEKLPKLIPLLKKG 77
>gnl|CDD|224684 COG1770, PtrB, Protease II [Amino acid transport and metabolism].
Length = 682
Score = 26.1 bits (58), Expect = 7.1
Identities = 6/20 (30%), Positives = 6/20 (30%)
Query: 78 IKDFIACADLRRSNKYIKKQ 97
DFIA A Y
Sbjct: 508 FTDFIAAARHLVKEGYTSPD 527
>gnl|CDD|234713 PRK00283, xerD, site-specific tyrosine recombinase XerD; Reviewed.
Length = 299
Score = 25.5 bits (57), Expect = 9.1
Identities = 9/30 (30%), Positives = 14/30 (46%), Gaps = 3/30 (10%)
Query: 8 LSAMRNFRRLIKYSKDENRVKFDPILPLEL 37
LSA+R F + + E + DP L+
Sbjct: 77 LSALRRFFQ---FLLREGLREDDPSALLDS 103
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
0.321 0.136 0.403
Gapped
Lambda K H
0.267 0.0689 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,331,724
Number of extensions: 532031
Number of successful extensions: 403
Number of sequences better than 10.0: 1
Number of HSP's gapped: 403
Number of HSP's successfully gapped: 26
Length of query: 126
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 41
Effective length of database: 7,167,512
Effective search space: 293867992
Effective search space used: 293867992
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 (24.3 bits)