RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8281
(178 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 = 39.9 bits (94), Expect = 1e-05
Identities = 18/36 (50%), Positives = 26/36 (72%), Gaps = 1/36 (2%)
Query: 96 NECES-SPCLNGGSCSDHVGRFSCTCGHGYTGQRCQ 130
+EC S +PC NGG+C + VG + C+C GYTG+ C+
Sbjct: 3 DECASGNPCQNGGTCVNTVGSYRCSCPPGYTGRNCE 38
Score = 34.5 bits (80), Expect = 0.001
Identities = 13/31 (41%), Positives = 17/31 (54%)
Query: 137 DPNPCSHHHYCVDKGNTFACECPKGYQGPNC 167
NPC + CV+ ++ C CP GY G NC
Sbjct: 7 SGNPCQNGGTCVNTVGSYRCSCPPGYTGRNC 37
Score = 33.0 bits (76), Expect = 0.006
Identities = 18/38 (47%), Positives = 25/38 (65%), Gaps = 2/38 (5%)
Query: 57 NLDDCAS-SPCG-HGICVDQTDGYRCYCQPGYSGEQCQ 92
++D+CAS +PC G CV+ YRC C PGY+G C+
Sbjct: 1 DIDECASGNPCQNGGTCVNTVGSYRCSCPPGYTGRNCE 38
Score = 28.8 bits (65), Expect = 0.22
Identities = 19/39 (48%), Positives = 25/39 (64%), Gaps = 4/39 (10%)
Query: 18 DPCESG-PCQNGGSCAASNLTAQQFKCLCPPGFSGSLCQ 55
D C SG PCQNGG+C T ++C CPPG++G C+
Sbjct: 3 DECASGNPCQNGGTC---VNTVGSYRCSCPPGYTGRNCE 38
>gnl|CDD|214542 smart00179, EGF_CA, Calcium-binding EGF-like domain.
Length = 39
Score = 34.9 bits (81), Expect = 0.001
Identities = 18/37 (48%), Positives = 25/37 (67%), Gaps = 2/37 (5%)
Query: 96 NECES-SPCLNGGSCSDHVGRFSCTCGHGYT-GQRCQ 130
+EC S +PC NGG+C + VG + C C GYT G+ C+
Sbjct: 3 DECASGNPCQNGGTCVNTVGSYRCECPPGYTDGRNCE 39
Score = 30.3 bits (69), Expect = 0.054
Identities = 14/33 (42%), Positives = 19/33 (57%), Gaps = 1/33 (3%)
Query: 137 DPNPCSHHHYCVDKGNTFACECPKGYQ-GPNCD 168
NPC + CV+ ++ CECP GY G NC+
Sbjct: 7 SGNPCQNGGTCVNTVGSYRCECPPGYTDGRNCE 39
Score = 28.4 bits (64), Expect = 0.24
Identities = 18/39 (46%), Positives = 26/39 (66%), Gaps = 3/39 (7%)
Query: 57 NLDDCAS-SPCGHG-ICVDQTDGYRCYCQPGYS-GEQCQ 92
++D+CAS +PC +G CV+ YRC C PGY+ G C+
Sbjct: 1 DIDECASGNPCQNGGTCVNTVGSYRCECPPGYTDGRNCE 39
>gnl|CDD|222213 pfam13546, DDE_5, DDE superfamily endonuclease. This family of
proteins are related to pfam00665 and are probably
endonucleases of the DDE superfamily. Transposase
proteins are necessary for efficient DNA transposition.
This domain is a member of the DDE superfamily, which
contain three carboxylate residues that are believed to
be responsible for coordinating metal ions needed for
catalysis. The catalytic activity of this enzyme
involves DNA cleavage at a specific site followed by a
strand transfer reaction.
Length = 272
Score = 33.9 bits (78), Expect = 0.026
Identities = 11/50 (22%), Positives = 15/50 (30%), Gaps = 2/50 (4%)
Query: 100 SSPCLNGGSCSDHVGRFSCTCGHGYTGQRCQIKVDLCDPNPCSHHHYCVD 149
+ G S VGR C + C + V L H +D
Sbjct: 90 ETGIPKKGKKSPGVGRQYCGTAGPGKRENCIVGVFLAYVG--DGGHCLLD 137
>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 = 0.049
Identities = 14/30 (46%), Positives = 17/30 (56%)
Query: 137 DPNPCSHHHYCVDKGNTFACECPKGYQGPN 166
NPCS+ CVD + CECP+GY G
Sbjct: 3 PNNPCSNGGTCVDTPGGYTCECPEGYTGKR 32
Score = 29.3 bits (66), Expect = 0.12
Identities = 15/27 (55%), Positives = 19/27 (70%)
Query: 102 PCLNGGSCSDHVGRFSCTCGHGYTGQR 128
PC NGG+C D G ++C C GYTG+R
Sbjct: 6 PCSNGGTCVDTPGGYTCECPEGYTGKR 32
>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 = 30.1 bits (68), Expect = 0.067
Identities = 15/30 (50%), Positives = 19/30 (63%)
Query: 99 ESSPCLNGGSCSDHVGRFSCTCGHGYTGQR 128
S+PC NGG+C + G + C C GYTG R
Sbjct: 4 ASNPCSNGGTCVNTPGSYRCVCPPGYTGDR 33
Score = 30.1 bits (68), Expect = 0.069
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 137 DPNPCSHHHYCVDKGNTFACECPKGYQGPN 166
NPCS+ CV+ ++ C CP GY G
Sbjct: 4 ASNPCSNGGTCVNTPGSYRCVCPPGYTGDR 33
Score = 26.3 bits (58), Expect = 1.5
Identities = 15/29 (51%), Positives = 20/29 (68%), Gaps = 1/29 (3%)
Query: 62 ASSPCGH-GICVDQTDGYRCYCQPGYSGE 89
AS+PC + G CV+ YRC C PGY+G+
Sbjct: 4 ASNPCSNGGTCVNTPGSYRCVCPPGYTGD 32
Score = 24.4 bits (53), Expect = 7.9
Identities = 14/32 (43%), Positives = 20/32 (62%), Gaps = 3/32 (9%)
Query: 21 ESGPCQNGGSCAASNLTAQQFKCLCPPGFSGS 52
S PC NGG+C T ++C+CPPG++G
Sbjct: 4 ASNPCSNGGTC---VNTPGSYRCVCPPGYTGD 32
>gnl|CDD|214544 smart00181, EGF, Epidermal growth factor-like domain.
Length = 35
Score = 29.4 bits (66), Expect = 0.13
Identities = 11/26 (42%), Positives = 15/26 (57%)
Query: 63 SSPCGHGICVDQTDGYRCYCQPGYSG 88
PC +G C++ Y C C PGY+G
Sbjct: 5 GGPCSNGTCINTPGSYTCSCPPGYTG 30
Score = 25.2 bits (55), Expect = 4.2
Identities = 10/28 (35%), Positives = 15/28 (53%), Gaps = 1/28 (3%)
Query: 137 DPNPCSHHHYCVDKGNTFACECPKGYQG 164
PCS+ C++ ++ C CP GY G
Sbjct: 4 SGGPCSNGT-CINTPGSYTCSCPPGYTG 30
>gnl|CDD|165214 PHA02887, PHA02887, EGF-like protein; Provisional.
Length = 126
Score = 31.1 bits (70), Expect = 0.14
Identities = 14/44 (31%), Positives = 22/44 (50%), Gaps = 5/44 (11%)
Query: 89 EQCQYEYNE-CESSPCLNGGSCSDHVGRFSCTCGHGYTGQRCQI 131
E+C+ ++N+ C + C+N + C C GYTG RC
Sbjct: 84 EKCKNDFNDFCINGECMNIIDLDEKF----CICNKGYTGIRCDE 123
>gnl|CDD|165381 PHA03099, PHA03099, epidermal growth factor-like protein
(EGF-like protein); Provisional.
Length = 139
Score = 30.4 bits (68), Expect = 0.25
Identities = 13/30 (43%), Positives = 17/30 (56%), Gaps = 2/30 (6%)
Query: 66 CGHGICVD--QTDGYRCYCQPGYSGEQCQY 93
C HG C+ DG C C GY+G +CQ+
Sbjct: 53 CLHGDCIHARDIDGMYCRCSHGYTGIRCQH 82
Score = 28.1 bits (62), Expect = 1.9
Identities = 10/13 (76%), Positives = 10/13 (76%)
Query: 118 CTCGHGYTGQRCQ 130
C C HGYTG RCQ
Sbjct: 69 CRCSHGYTGIRCQ 81
>gnl|CDD|233277 TIGR01116, ATPase-IIA1_Ca, sarco/endoplasmic reticulum
calcium-translocating P-type ATPase. This model
describes the P-type ATPase responsible for
translocating calcium ions across the endoplasmic
reticulum membrane of eukaryotes , and is of particular
importance in the sarcoplasmic reticulum of skeletal and
cardiac muscle in vertebrates. These pumps transfer Ca2+
from the cytoplasm to the lumen of the endoplasmic
reticulum. In humans and mice, at least, there are
multiple isoforms of the SERCA pump with overlapping but
not redundant functions. Defects in SERCA isoforms are
associated with diseases in humans. The calcium P-type
ATPases have been characterized as Type IIA based on a
phylogenetic analysis which distinguishes this group
from the Type IIB PMCA calcium pump modelled by
TIGR01517. A separate analysis divides Type IIA into
sub-types, SERCA and PMR1 the latter of which is
modelled by TIGR01522 [Transport and binding proteins,
Cations and iron carrying compounds].
Length = 917
Score = 28.6 bits (64), Expect = 1.8
Identities = 17/49 (34%), Positives = 22/49 (44%), Gaps = 8/49 (16%)
Query: 109 CSDHVGRFSCTCGHGYTGQRCQIKVDLCDPNPCSHHHYCVDKGNTFACE 157
CSD G + T Q KV DP+ S + +CV G T+A E
Sbjct: 293 CSDKTGTLT-------TNQMSVCKVVALDPSSSSLNEFCVT-GTTYAPE 333
>gnl|CDD|184363 PRK13879, PRK13879, conjugal transfer protein TrbJ; Provisional.
Length = 253
Score = 27.8 bits (62), Expect = 3.0
Identities = 8/12 (66%), Positives = 8/12 (66%)
Query: 100 SSPCLNGGSCSD 111
SSPC NG CS
Sbjct: 121 SSPCFNGAGCSP 132
>gnl|CDD|221435 pfam12132, DUF3587, Protein of unknown function (DUF3587). This
protein is found in viruses. Proteins in this family are
typically between 209 and 248 amino acids in length.
Length = 201
Score = 26.9 bits (60), Expect = 5.7
Identities = 13/43 (30%), Positives = 18/43 (41%), Gaps = 7/43 (16%)
Query: 109 CSDHVGRF-SCTCGHGYTGQRCQIKVDLCDPNPCSH---HHYC 147
CSD+ R+ SC C + V + C + HHYC
Sbjct: 131 CSDY--RYASCPCHLLNDDGDPEAFVKPS-VDECPYGHFHHYC 170
>gnl|CDD|227662 COG5368, COG5368, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 451
Score = 27.1 bits (60), Expect = 6.0
Identities = 12/29 (41%), Positives = 14/29 (48%)
Query: 134 DLCDPNPCSHHHYCVDKGNTFACECPKGY 162
D + NPC Y D AC+ PKGY
Sbjct: 277 DYANYNPCGFRGYGEDLWGLSACDGPKGY 305
>gnl|CDD|185716 cd08039, Adenylation_DNA_ligase_Fungal, Adenylation domain of
uncharacterized fungal ATP-dependent DNA ligase-like
proteins. ATP-dependent polynucleotide ligases catalyze
phosphodiester bond formation using nicked nucleic acid
substrates with the high energy nucleotide of ATP as a
cofactor in a three step reaction mechanism. DNA ligases
play a vital role in the diverse processes of DNA
replication, recombination and repair. ATP-dependent
ligases are present in many organisms such as viruses,
bacteriophages, eukarya, archaea and bacteria. This
group is composed of uncharacterized fungal proteins
with similarity to ATP-dependent DNA ligases. ATP
dependent DNA ligases have a highly modular architecture
consisting of a unique arrangement of two or more
discrete domains including a DNA-binding domain, an
adenylation (nucleotidyltransferase (NTase)) domain, and
an oligonucleotide/oligosaccharide binding (OB)-fold
domain. The adenylation domain binds ATP and contains
many of the active-site residues. The adenylation and
C-terminal OB-fold domains comprise a catalytic core
unit that is common to most members of the ATP-dependent
DNA ligase family. The catalytic core unit contains six
conserved sequence motifs (I, III, IIIa, IV, V and VI)
that define this family of related
nucleotidyltransferases. This model characterizes the
adenylation domain of this group of uncharacterized
fungal proteins. It is not known whether these proteins
also contain an OB-fold domain.
Length = 235
Score = 26.6 bits (59), Expect = 7.4
Identities = 7/18 (38%), Positives = 10/18 (55%)
Query: 124 YTGQRCQIKVDLCDPNPC 141
Y G+ CQI +DL +
Sbjct: 30 YDGEYCQIHIDLSKDSSP 47
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
0.322 0.141 0.513
Gapped
Lambda K H
0.267 0.0665 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,119,920
Number of extensions: 642295
Number of successful extensions: 508
Number of sequences better than 10.0: 1
Number of HSP's gapped: 489
Number of HSP's successfully gapped: 89
Length of query: 178
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 87
Effective length of database: 6,901,388
Effective search space: 600420756
Effective search space used: 600420756
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 (21.9 bits)
S2: 56 (25.5 bits)