RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12432
(229 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 = 33.4 bits (77), Expect = 0.005
Identities = 13/32 (40%), Positives = 14/32 (43%), Gaps = 4/32 (12%)
Query: 37 CLNGATCFTVKIGESLLYNCECADGYMGQRCE 68
C NG TC Y C C GY G+ CE
Sbjct: 11 CQNGGTCVNTVGS----YRCSCPPGYTGRNCE 38
>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 = 30.5 bits (69), Expect = 0.051
Identities = 16/39 (41%), Positives = 18/39 (46%), Gaps = 7/39 (17%)
Query: 28 CPPTYATWYCLNGATCFTVKIGESLLYNCECADGYMGQR 66
C P C NG TC G Y CEC +GY G+R
Sbjct: 1 CSPNN---PCSNGGTCVDTPGG----YTCECPEGYTGKR 32
>gnl|CDD|214542 smart00179, EGF_CA, Calcium-binding EGF-like domain.
Length = 39
Score = 29.5 bits (67), Expect = 0.12
Identities = 17/34 (50%), Positives = 18/34 (52%), Gaps = 7/34 (20%)
Query: 37 CLNGATCF-TVKIGESLLYNCECADGYM-GQRCE 68
C NG TC TV S Y CEC GY G+ CE
Sbjct: 11 CQNGGTCVNTV---GS--YRCECPPGYTDGRNCE 39
>gnl|CDD|165214 PHA02887, PHA02887, EGF-like protein; Provisional.
Length = 126
Score = 31.4 bits (71), Expect = 0.15
Identities = 11/33 (33%), Positives = 16/33 (48%), Gaps = 3/33 (9%)
Query: 36 YCLNGATCFTVKIGESLLYNCECADGYMGQRCE 68
+C+NG + + E C C GY G RC+
Sbjct: 93 FCINGECMNIIDLDEKF---CICNKGYTGIRCD 122
>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 = 29.0 bits (65), Expect = 0.23
Identities = 13/33 (39%), Positives = 13/33 (39%), Gaps = 5/33 (15%)
Query: 37 CLNGATCFTVKIGESLLYNCECADGYMGQ-RCE 68
C NG TC Y C C GY G CE
Sbjct: 8 CSNGGTCVNTPGS----YRCVCPPGYTGDRSCE 36
>gnl|CDD|220647 pfam10242, L_HGMIC_fpl, Lipoma HMGIC fusion partner-like protein.
This is a group of proteins expressed from a series of
genes referred to as Lipoma HGMIC fusion partner-like.
The proteins carry four highly conserved transmembrane
domains in this entry. In certain instances, eg in
LHFPL5, mutations cause deafness in humans and
hypospadias, and LHFPL1 is transcribed in six liver
tumour cell lines.
Length = 181
Score = 31.1 bits (71), Expect = 0.28
Identities = 19/75 (25%), Positives = 27/75 (36%), Gaps = 5/75 (6%)
Query: 53 LYN-CECADGYMGQRCEFKDLDGSYLPSRKQVMLETASIASGASIAVFLVVILCFSLYVH 111
LY C M C LD +PS + A G A+ L+ I C SL+
Sbjct: 40 LYRRCIGLMDQMELTCGGYALDFLAIPSS---AWQAAMFFVGLGTALLLL-IACLSLFTF 95
Query: 112 CQRRKKQAQAASVCC 126
C++ +C
Sbjct: 96 CRQSIISKSVFKICG 110
>gnl|CDD|218597 pfam05466, BASP1, Brain acid soluble protein 1 (BASP1 protein).
This family consists of several brain acid soluble
protein 1 (BASP1) or neuronal axonal membrane protein
NAP-22. The BASP1 is a neuron enriched Ca(2+)-dependent
calmodulin-binding protein of unknown function.
Length = 233
Score = 31.0 bits (69), Expect = 0.37
Identities = 20/60 (33%), Positives = 26/60 (43%)
Query: 157 TEAPRAADTRTSITITGKGDSVSASQLYHQSSPPLPHMSHPPSCTPLPPAPSQPPDDIKA 216
TEAP AA T DS +S SS P + PS T AP+ P +++K
Sbjct: 158 TEAPAAAAQETKSDAAPASDSKPSSSEAAPSSKETPAATEAPSSTAKASAPAAPAEEVKP 217
>gnl|CDD|147197 pfam04906, Tweety, Tweety. The tweety (tty) gene has not been
characterized at the protein level. However, it is
thought to form a membrane protein with five potential
membrane-spanning regions. A number of potential
functions have been suggested in.
Length = 406
Score = 30.4 bits (69), Expect = 0.86
Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 6/60 (10%)
Query: 69 FKDLDGSYLPSRKQVMLETASIASGASIAVFLVVILCFSLYVHCQRRKKQA-QAASVCCT 127
F+ D SY Q +L AS+A A +A+ L+ +L + + + C RRK++ CC
Sbjct: 8 FRPEDESYQ----QSLLFLASVA-AACLALSLLFLLFYLITLCCCRRKREEHSNKDCCCV 62
>gnl|CDD|216503 pfam01435, Peptidase_M48, Peptidase family M48.
Length = 223
Score = 29.3 bits (66), Expect = 1.3
Identities = 20/120 (16%), Positives = 37/120 (30%), Gaps = 12/120 (10%)
Query: 84 MLETASIASGASIAVFLVVILCFSLYVHCQRRKKQAQAASVCCTDGPGSSLQRPRMPFER 143
+E+ S ++ + L + A+ T LQ +P+ R
Sbjct: 106 SVESMSQGLLLNLLLLLGAAALGGRAL--------GFNANGFLTALGIFLLQLLLLPYSR 157
Query: 144 -RPSPADFV---LTRITTEAPRAADTRTSITITGKGDSVSASQLYHQSSPPLPHMSHPPS 199
+ AD L A R ++ K + + S++ P +HPP
Sbjct: 158 KQEYEADEAGARLGGDKDLARAGYKPRAAVKFLAKLAAENLSRVSGGKLYPELLSTHPPL 217
>gnl|CDD|200219 TIGR02927, SucB_Actino, 2-oxoglutarate dehydrogenase, E2 component,
dihydrolipoamide succinyltransferase. This model
represents an Actinobacterial clade of E2 enzyme, a
component of the 2-oxoglutarate dehydrogenase complex
involved in the TCA cycle. These proteins have multiple
domains including the catalytic domain (pfam00198), one
or two biotin domains (pfam00364) and an E3-component
binding domain (pfam02817).
Length = 579
Score = 28.1 bits (62), Expect = 4.3
Identities = 16/71 (22%), Positives = 27/71 (38%), Gaps = 4/71 (5%)
Query: 145 PSPADFVLTRITTEAPRAADTRTSITITGK----GDSVSASQLYHQSSPPLPHMSHPPSC 200
PSPA VL I + + I G+ G + + +++P + P+
Sbjct: 49 PSPAAGVLLEIRAPEDDTVEVGGVLAIIGEPGEAGSEPAPAAPEPEAAPEPEAPAPAPTP 108
Query: 201 TPLPPAPSQPP 211
PAP+ P
Sbjct: 109 AAEAPAPAAPQ 119
>gnl|CDD|221170 pfam11696, DUF3292, Protein of unknown function (DUF3292). This
eukaryotic family of proteins has no known function.
Length = 641
Score = 27.4 bits (61), Expect = 6.6
Identities = 10/43 (23%), Positives = 15/43 (34%), Gaps = 8/43 (18%)
Query: 188 SPPLPHMSHPPSCTPLPPAPSQP----PDDIKADMRSSQVSAT 226
+ PLP PP + L APS P + ++
Sbjct: 402 AAPLP----PPPSSSLRKAPSSPASIDHKQLNLGASEEEIDQA 440
>gnl|CDD|204999 pfam12661, hEGF, Human growth factor-like EGF. hEGF, or human
growth factor-like EGF, domains have six conserved
residues disulfide-bonded into the characteristic
'ababcc' pattern. They are involved in growth and
proliferation of cells, in proteins of the Notch/Delta
pathway, neurogulin and selectins. hEGFs are also found
in mosaic proteins with four-disulfide laminin EGFs
such as aggrecan and perlecan. The core fold of the EGF
domain consists of two small beta-hairpins packed
against each other. Two major structural variants have
been identified based on the structural context of the
C-terminal Cys residue of disulfide 'c' in the
C-terminal hairpin: hEGFs and cEGFs. In hEGFs the
C-terminal thiol resides in the beta-turn, resulting in
shorter loop-lengths between the Cys residues of
disulfide 'c', typically C[8-9]XC. These shorter
loop-lengths are also typical of the four-disulfide EGF
domains, laminin ad integrin. Tandem hEGF domains have
six linking residues between terminal cysteines of
adjacent domains. hEGF domains may or may not bind
calcium in the linker region. hEGF domains with the
consensus motif CXD4X[F,Y]XCXC are hydroxylated
exclusively in the Asp residue.
Length = 13
Score = 24.2 bits (54), Expect = 6.9
Identities = 7/12 (58%), Positives = 8/12 (66%)
Query: 56 CECADGYMGQRC 67
C+C GY G RC
Sbjct: 2 CQCPPGYTGPRC 13
>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1. Members
of this family are necessary for accurate chromosome
transmission during cell division.
Length = 804
Score = 27.4 bits (61), Expect = 7.6
Identities = 8/30 (26%), Positives = 11/30 (36%)
Query: 182 QLYHQSSPPLPHMSHPPSCTPLPPAPSQPP 211
Q + + P + P PP P Q P
Sbjct: 208 QGHPEQVQPQQFLPAPSQAPAQPPLPPQLP 237
>gnl|CDD|214544 smart00181, EGF, Epidermal growth factor-like domain.
Length = 35
Score = 24.4 bits (53), Expect = 9.0
Identities = 14/34 (41%), Positives = 14/34 (41%), Gaps = 6/34 (17%)
Query: 36 YCLNGATCFTVKIGESLLYNCECADGYMGQ-RCE 68
C NG TC Y C C GY G RCE
Sbjct: 7 PCSNG-TCINTPGS----YTCSCPPGYTGDKRCE 35
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
0.319 0.131 0.416
Gapped
Lambda K H
0.267 0.0647 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,136,528
Number of extensions: 969047
Number of successful extensions: 1661
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1614
Number of HSP's successfully gapped: 61
Length of query: 229
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 135
Effective length of database: 6,768,326
Effective search space: 913724010
Effective search space used: 913724010
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: 57 (25.9 bits)