RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7364
(73 letters)
>gnl|CDD|238106 cd00182, TBOX, T-box DNA binding domain of the T-box family of
transcriptional regulators. The T-box family is an
ancient group that appears to play a critical role in
development in all animal species. These genes were
uncovered on the basis of similarity to the DNA binding
domain of murine Brachyury (T) gene product, the
defining feature of the family. Common features shared
by T-box family members are DNA-binding and
transcriptional regulatory activity, a role in
development and conserved expression patterns, most of
the known genes in all species being expressed in
mesoderm or mesoderm precursors.
Length = 188
Score = 113 bits (286), Expect = 6e-34
Identities = 38/68 (55%), Positives = 49/68 (72%), Gaps = 4/68 (5%)
Query: 1 MHRYQPRIHLIKWRDQGTPITDLELEQYRTYVFPESVFTAVTAYQNQLITKLKIDSNPFA 60
MH+YQPR+H+++ D L +T+ FPE+ F AVTAYQNQ IT+LKID+NPFA
Sbjct: 124 MHKYQPRLHIVEVDDSSPFSWRL----VQTFSFPETEFIAVTAYQNQEITQLKIDNNPFA 179
Query: 61 KGFRDSSR 68
KGFRD+ R
Sbjct: 180 KGFRDNGR 187
>gnl|CDD|216184 pfam00907, T-box, T-box. The T-box encodes a 180 amino acid domain
that binds to DNA. Genes encoding T-box proteins are
found in a wide range of animals, but not in other
kingdoms such as plants. Family members are all thought
to bind to the DNA consensus sequence TCACACCT. they are
found exclusively in the nucleus, and perform
DNA-binding and transcriptional activation/repression
roles. They are generally required for development of
the specific tissues they are expressed in, and
mutations in T-box genes are implicated in human
conditions such as DiGeorge syndrome and X-linked cleft
palate, which feature malformations.
Length = 182
Score = 105 bits (263), Expect = 1e-30
Identities = 38/66 (57%), Positives = 49/66 (74%), Gaps = 5/66 (7%)
Query: 1 MHRYQPRIHLIKWRDQGTPITDLELEQYRTYVFPESVFTAVTAYQNQLITKLKIDSNPFA 60
MH+YQPR+H+++ D +P RT+ FPE+ F AVTAYQN+ ITKLKID+NPFA
Sbjct: 122 MHKYQPRLHIVR-VDDESPSQRT----VRTFSFPETQFIAVTAYQNEEITKLKIDNNPFA 176
Query: 61 KGFRDS 66
KGFRD+
Sbjct: 177 KGFRDA 182
>gnl|CDD|214656 smart00425, TBOX, Domain first found in the mice T locus
(Brachyury) protein.
Length = 190
Score = 101 bits (253), Expect = 6e-29
Identities = 42/68 (61%), Positives = 52/68 (76%), Gaps = 4/68 (5%)
Query: 1 MHRYQPRIHLIKWRDQGTPITDLELEQYRTYVFPESVFTAVTAYQNQLITKLKIDSNPFA 60
MH+YQPR+H+++ D I L Q++T+VFPE+ F AVTAYQNQ ITKLKID+NPFA
Sbjct: 125 MHKYQPRLHIVEVDDISKEI----LSQFKTFVFPETQFIAVTAYQNQKITKLKIDNNPFA 180
Query: 61 KGFRDSSR 68
KGFRD R
Sbjct: 181 KGFRDQGR 188
>gnl|CDD|143285 cd05877, Ig_LP_like, Immunoglobulin (Ig)-like domain of human
cartilage link protein (LP). Ig_LP_like:
immunoglobulin (Ig)-like domain similar to that that
found in human cartilage link protein (LP). In
cartilage, chondroitin-keratan sulfate proteoglycan
(CSPG), aggrecan, forms cartilage link protein
stabilized aggregates with hyaluronan (HA). These
aggregates contribute to the tissue's load bearing
properties. Aggregates having other CSPGs substituting
for aggrecan may contribute to the structural integrity
of many different tissues. Members of the vertebrate
HPLN (hyaluronan/HA and proteoglycan binding link)
protein family are physically linked adjacent to CSPG
genes.
Length = 106
Score = 27.3 bits (61), Expect = 0.38
Identities = 13/31 (41%), Positives = 15/31 (48%), Gaps = 2/31 (6%)
Query: 3 RYQPRIHLIKW--RDQGTPITDLELEQYRTY 31
YQ R+ L + D ITDL LE Y Y
Sbjct: 53 SYQGRVFLRRAHDLDASLVITDLRLEDYGRY 83
>gnl|CDD|185439 PTZ00091, PTZ00091, 40S ribosomal protein S5; Provisional.
Length = 193
Score = 25.5 bits (56), Expect = 2.3
Identities = 13/36 (36%), Positives = 16/36 (44%), Gaps = 2/36 (5%)
Query: 12 KWRDQGTPITDLELEQYRTYVFPESVFTAVTA--YQ 45
KW ++DL L+ Y SVF TA YQ
Sbjct: 11 KWSYDDVQVSDLSLKDYIAVTTKASVFVPHTAGRYQ 46
>gnl|CDD|183733 PRK12769, PRK12769, putative oxidoreductase Fe-S binding subunit;
Reviewed.
Length = 654
Score = 25.5 bits (56), Expect = 2.4
Identities = 8/20 (40%), Positives = 13/20 (65%)
Query: 2 HRYQPRIHLIKWRDQGTPIT 21
H + PRI +IK + Q + +T
Sbjct: 36 HHFHPRITVIKHQQQRSAVT 55
>gnl|CDD|217143 pfam02614, UxaC, Glucuronate isomerase. This is a family of
Glucuronate isomerases also known as D-glucuronate
isomerase, uronic isomerase, uronate isomerase, or
uronic acid isomerase, EC:5.3.1.12. This enzyme
catalyzes the reactions: D-glucuronate <=>
D-fructuronate and D-galacturonate <=> D-tagaturonate.
It is not however clear where the experimental evidence
for this functional assignment came from and thus this
family has no literature reference.
Length = 469
Score = 25.3 bits (56), Expect = 3.1
Identities = 6/18 (33%), Positives = 12/18 (66%)
Query: 16 QGTPITDLELEQYRTYVF 33
G P+T E+E+++T +
Sbjct: 262 SGEPLTPEEIEKFKTAML 279
>gnl|CDD|119430 cd05170, PIKKc_SMG1, Suppressor of morphogenetic effect on
genitalia-1 (SMG-1), catalytic domain; The SMG-1
catalytic domain subfamily is part of a larger
superfamily that includes the catalytic domains of other
kinases such as the typical serine/threonine/tyrosine
protein kinases (PKs), aminoglycoside
phosphotransferase, choline kinase, and RIO kinases.
SMG-1 is a member of the phosphoinositide
3-kinase-related protein kinase (PIKK) subfamily. PIKKs
have intrinsic serine/threonine kinase activity and are
distinguished from other PKs by their unique catalytic
domain, similar to that of lipid PI3K, and their large
molecular weight (240-470 kDa). In addition to its
catalytic domain, SMG-1 contains a FATC (FRAP, ATM and
TRRAP, C-terminal) domain at the C-terminus. SMG-1 plays
a critical role in the mRNA surveillance mechanism known
as non-sense mediated mRNA decay (NMD). NMD protects the
cells from the accumulation of aberrant mRNAs with
premature termination codons (PTCs) generated by genome
mutations and by errors during transcription and
splicing. SMG-1 phosphorylates Upf1, another central
component of NMD, at the C-terminus upon recognition of
PTCs. The phosphorylation/dephosphorylation cycle of
Upf1 is essential for promoting NMD.
Length = 307
Score = 24.7 bits (54), Expect = 5.0
Identities = 13/43 (30%), Positives = 19/43 (44%), Gaps = 4/43 (9%)
Query: 6 PRIHLIKWRDQGTPITDLELEQYRTYVFPESVFTAVTAYQNQL 48
PR LI+W D TP+ L Y+ + E+V A +
Sbjct: 80 PRSGLIQWVDGATPLFGL----YKRWQQREAVLQAQKSQVGYQ 118
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
0.323 0.137 0.416
Gapped
Lambda K H
0.267 0.0751 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,693,810
Number of extensions: 264891
Number of successful extensions: 211
Number of sequences better than 10.0: 1
Number of HSP's gapped: 208
Number of HSP's successfully gapped: 9
Length of query: 73
Length of database: 10,937,602
Length adjustment: 43
Effective length of query: 30
Effective length of database: 9,030,380
Effective search space: 270911400
Effective search space used: 270911400
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (24.2 bits)