RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9568
(248 letters)
>gnl|CDD|238011 cd00054, EGF_CA, Calcium-binding EGF-like domain, present in a
large number of membrane-bound and extracellular (mostly
animal) proteins. Many of these proteins require calcium
for their biological function and calcium-binding sites
have been found to be located at the N-terminus of
particular EGF-like domains; calcium-binding may be
crucial for numerous protein-protein interactions. Six
conserved core cysteines form three disulfide bridges as
in non calcium-binding EGF domains, whose structures are
very similar. EGF_CA can be found in tandem repeat
arrangements.
Length = 38
Score = 28.8 bits (65), Expect = 0.27
Identities = 15/29 (51%), Positives = 17/29 (58%), Gaps = 3/29 (10%)
Query: 88 PCLNGGRCK-GVN--KCRCPPGFLGDYCE 113
PC NGG C V +C CPPG+ G CE
Sbjct: 10 PCQNGGTCVNTVGSYRCSCPPGYTGRNCE 38
Score = 28.8 bits (65), Expect = 0.27
Identities = 15/29 (51%), Positives = 17/29 (58%), Gaps = 3/29 (10%)
Query: 126 PCLNGGRCK-GVN--KCRCPPGFLGDYCE 151
PC NGG C V +C CPPG+ G CE
Sbjct: 10 PCQNGGTCVNTVGSYRCSCPPGYTGRNCE 38
Score = 27.6 bits (62), Expect = 0.73
Identities = 12/28 (42%), Positives = 13/28 (46%), Gaps = 3/28 (10%)
Query: 25 CLNGGKCVQKD---TCECQKGFYGLRCE 49
C NGG CV C C G+ G CE
Sbjct: 11 CQNGGTCVNTVGSYRCSCPPGYTGRNCE 38
Score = 27.6 bits (62), Expect = 0.73
Identities = 12/28 (42%), Positives = 13/28 (46%), Gaps = 3/28 (10%)
Query: 57 CLNGGKCVQKD---TCECQKGFYGLRCE 81
C NGG CV C C G+ G CE
Sbjct: 11 CQNGGTCVNTVGSYRCSCPPGYTGRNCE 38
>gnl|CDD|153087 cd01678, PFL1, Pyruvate formate lyase 1. Pyruvate formate lyase
catalyzes a key step in anaerobic glycolysis, the
conversion of pyruvate and CoenzymeA to formate and
acetylCoA. The PFL mechanism involves an unusual radical
cleavage of pyruvate in which two cysteines and one
glycine form radicals that are required for catalysis.
PFL has a ten-stranded alpha/beta barrel domain that is
structurally similar to those of all three
ribonucleotide reductase (RNR) classes as well as
benzylsuccinate synthase and B12-independent glycerol
dehydratase.
Length = 738
Score = 30.4 bits (69), Expect = 0.93
Identities = 11/33 (33%), Positives = 16/33 (48%)
Query: 63 CVQKDTCECQKGFYGLRCEFSKCIIPCLNGGRC 95
CV Q F+G R +K ++ +NGGR
Sbjct: 406 CVSAMRIGKQMQFFGARANLAKALLYAINGGRD 438
>gnl|CDD|233331 TIGR01255, pyr_form_ly_1, formate acetyltransferase 1. Alternate
names: pyruvate formate-lyase; formate
C-acetyltransferase This enzyme converts formate +
acetyl-CoA into pyruvate + CoA. This model describes
formate acetyltransferase 1. More distantly related
putative formate acetyltransferases have also been
identified, including formate acetyltransferase 2 from
E. coli, which is excluded from this model [Energy
metabolism, Fermentation].
Length = 744
Score = 29.5 bits (66), Expect = 1.8
Identities = 9/31 (29%), Positives = 14/31 (45%)
Query: 63 CVQKDTCECQKGFYGLRCEFSKCIIPCLNGG 93
CV F+G R +K ++ +NGG
Sbjct: 404 CVSPMDVGKNMQFFGARVNLAKAMLTAINGG 434
>gnl|CDD|238010 cd00053, EGF, Epidermal growth factor domain, found in epidermal
growth factor (EGF) presents in a large number of
proteins, mostly animal; the list of proteins currently
known to contain one or more copies of an EGF-like
pattern is large and varied; the functional significance
of EGF-like domains in what appear to be unrelated
proteins is not yet clear; a common feature is that
these repeats are found in the extracellular domain of
membrane-bound proteins or in proteins known to be
secreted (exception: prostaglandin G/H synthase); the
domain includes six cysteine residues which have been
shown to be involved in disulfide bonds; the main
structure is a two-stranded beta-sheet followed by a
loop to a C-terminal short two-stranded sheet;
Subdomains between the conserved cysteines vary in
length; the region between the 5th and 6th cysteine
contains two conserved glycines of which at least one
is present in most EGF-like domains; a subset of
these bind calcium.
Length = 36
Score = 25.9 bits (57), Expect = 2.9
Identities = 16/30 (53%), Positives = 18/30 (60%), Gaps = 4/30 (13%)
Query: 88 PCLNGGRCK---GVNKCRCPPGFLGD-YCE 113
PC NGG C G +C CPPG+ GD CE
Sbjct: 7 PCSNGGTCVNTPGSYRCVCPPGYTGDRSCE 36
Score = 25.9 bits (57), Expect = 2.9
Identities = 16/30 (53%), Positives = 18/30 (60%), Gaps = 4/30 (13%)
Query: 126 PCLNGGRCK---GVNKCRCPPGFLGD-YCE 151
PC NGG C G +C CPPG+ GD CE
Sbjct: 7 PCSNGGTCVNTPGSYRCVCPPGYTGDRSCE 36
>gnl|CDD|219654 pfam07944, DUF1680, Putative glycosyl hydrolase of unknown function
(DUF1680). The members of this family are sequences
derived from hypothetical bacterial and eukaryotic
proteins of unknown function. One members of this family
is annotated as a possible arabinosidase, but no
references were found to back this. These proteins are
related to a large family of glycosyl hydrolases.
Length = 511
Score = 27.7 bits (62), Expect = 6.3
Identities = 21/87 (24%), Positives = 29/87 (33%), Gaps = 15/87 (17%)
Query: 143 PGFLGDYCEIWQRPYICPKPCKQGVCSAARTCACYE-GWFGRTCSQRSDSGEDKSTFYHD 201
G G E + PY P + TCA Y R + + + Y D
Sbjct: 268 TGGNGSRHEHFGPPYDLPNRL-----AYCETCASYNMLKLTRRMLEWTPDAK-----YAD 317
Query: 202 DEEGPPVRNLYSSLLGSDSGEDKSTFY 228
E R LY+ +L S + FY
Sbjct: 318 YYE----RALYNHILAGQSPDGGMFFY 340
>gnl|CDD|215652 pfam00008, EGF, EGF-like domain. There is no clear separation
between noise and signal. pfam00053 is very similar,
but has 8 instead of 6 conserved cysteines. Includes
some cytokine receptors. The EGF domain misses the
N-terminus regions of the Ca2+ binding EGF domains
(this is the main reason of discrepancy between
swiss-prot domain start/end and Pfam). The family is
hard to model due to many similar but different
sub-types of EGF domains. Pfam certainly misses a
number of EGF domains.
Length = 32
Score = 24.3 bits (53), Expect = 9.9
Identities = 13/26 (50%), Positives = 15/26 (57%), Gaps = 3/26 (11%)
Query: 25 CLNGGKCVQKD---TCECQKGFYGLR 47
C NGG CV TCEC +G+ G R
Sbjct: 7 CSNGGTCVDTPGGYTCECPEGYTGKR 32
Score = 24.3 bits (53), Expect = 9.9
Identities = 13/26 (50%), Positives = 15/26 (57%), Gaps = 3/26 (11%)
Query: 57 CLNGGKCVQKD---TCECQKGFYGLR 79
C NGG CV TCEC +G+ G R
Sbjct: 7 CSNGGTCVDTPGGYTCECPEGYTGKR 32
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
0.325 0.144 0.512
Gapped
Lambda K H
0.267 0.0678 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,775,684
Number of extensions: 1011765
Number of successful extensions: 971
Number of sequences better than 10.0: 1
Number of HSP's gapped: 922
Number of HSP's successfully gapped: 89
Length of query: 248
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 154
Effective length of database: 6,768,326
Effective search space: 1042322204
Effective search space used: 1042322204
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 58 (26.2 bits)