RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7373
(95 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 = 130 bits (329), Expect = 4e-40
Identities = 47/92 (51%), Positives = 63/92 (68%), Gaps = 6/92 (6%)
Query: 2 TVLYPDSPFTGDQLRKQVVSFEKVKLTNNEMDKHGHLVLNSMHKYQPRIHLVKRHESTIN 61
++PDSP TG KQ VSF+K+KLTNN +D +GH++LNSMHKYQPR+H+V+ +S
Sbjct: 83 VYVHPDSPATGAHWMKQPVSFDKLKLTNNTLDNNGHIILNSMHKYQPRLHIVEVDDS--- 139
Query: 62 HPITDLEAEEYKTFIYPESIFTAVTAYQNQLI 93
+ +TF +PE+ F AVTAYQNQ I
Sbjct: 140 ---SPFSWRLVQTFSFPETEFIAVTAYQNQEI 168
>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 = 126 bits (318), Expect = 2e-38
Identities = 46/92 (50%), Positives = 64/92 (69%), Gaps = 7/92 (7%)
Query: 2 TVLYPDSPFTGDQLRKQVVSFEKVKLTNNEMDKHGHLVLNSMHKYQPRIHLVKRHESTIN 61
++PDSP TG KQ VSF+KVKLTNN++D +GH++LNSMHKYQPR+H+V+ + + +
Sbjct: 81 VYIHPDSPATGAHWMKQPVSFDKVKLTNNKLDGNGHIILNSMHKYQPRLHIVRVDDESPS 140
Query: 62 HPITDLEAEEYKTFIYPESIFTAVTAYQNQLI 93
+TF +PE+ F AVTAYQN+ I
Sbjct: 141 QRT-------VRTFSFPETQFIAVTAYQNEEI 165
>gnl|CDD|214656 smart00425, TBOX, Domain first found in the mice T locus
(Brachyury) protein.
Length = 190
Score = 113 bits (284), Expect = 2e-33
Identities = 50/94 (53%), Positives = 66/94 (70%), Gaps = 8/94 (8%)
Query: 2 TVLYPDSPFTGDQLRKQVVSFEKVKLTNNEMDKHGHL--VLNSMHKYQPRIHLVKRHEST 59
++PDSP TG KQ VSF+KVKLTNN+ DK+GHL +LNSMHKYQPR+H+V+ + +
Sbjct: 82 VYVHPDSPATGAHWMKQPVSFDKVKLTNNQSDKNGHLQIILNSMHKYQPRLHIVEVDDIS 141
Query: 60 INHPITDLEAEEYKTFIYPESIFTAVTAYQNQLI 93
++KTF++PE+ F AVTAYQNQ I
Sbjct: 142 KEIL------SQFKTFVFPETQFIAVTAYQNQKI 169
>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 = 29.2 bits (66), Expect = 0.14
Identities = 15/52 (28%), Positives = 24/52 (46%), Gaps = 5/52 (9%)
Query: 26 KLTNNEMDKHGHLVLNSMHK-----YQPRIHLVKRHESTINHPITDLEAEEY 72
KL ++ + + LV YQ R+ L + H+ + ITDL E+Y
Sbjct: 29 KLESDYLKEEDVLVAIGTRHKSYGSYQGRVFLRRAHDLDASLVITDLRLEDY 80
>gnl|CDD|180685 PRK06767, PRK06767, methionine gamma-lyase; Provisional.
Length = 386
Score = 26.0 bits (57), Expect = 3.6
Identities = 17/67 (25%), Positives = 27/67 (40%), Gaps = 8/67 (11%)
Query: 1 STVLYPDSPFTGDQLRKQ--VVSFEKVKLTNNEMDKHGHLVLNSMHKYQPRIHLVKRHES 58
V YP+ Q+++ V+SF +K E +N +H + L E+
Sbjct: 282 EGVWYPEGELASRQMKRGGGVISFS-IKGGKEETQA----FINDLHFITIAVSL-GDTET 335
Query: 59 TINHPIT 65
I HP T
Sbjct: 336 LIQHPAT 342
>gnl|CDD|234958 PRK01544, PRK01544, bifunctional N5-glutamine
S-adenosyl-L-methionine-dependent methyltransferase/tRNA
(m7G46) methyltransferase; Reviewed.
Length = 506
Score = 26.0 bits (57), Expect = 4.0
Identities = 11/40 (27%), Positives = 25/40 (62%)
Query: 3 VLYPDSPFTGDQLRKQVVSFEKVKLTNNEMDKHGHLVLNS 42
+L+PD Q +K++ + E++K+ +++ +G+LV S
Sbjct: 423 ILFPDPWIKNKQKKKRIFNKERLKILQDKLKDNGNLVFAS 462
>gnl|CDD|211327 cd02553, PseudoU_synth_RsuA, Pseudouridine synthase, Escherichia
coli RsuA like. This group is comprised of eukaryotic
and bacterial proteins similar to Escherichia coli
RsuA. Pseudouridine synthases catalyze the
isomerization of specific uridines in an RNA molecule
to pseudouridines (5-ribosyluracil, psi). No cofactors
are required. E.coli RsuA makes psi516 in 16S RNA. Psi
at this position is not generally conserved in other
organisms.
Length = 167
Score = 25.6 bits (57), Expect = 4.2
Identities = 8/27 (29%), Positives = 16/27 (59%)
Query: 47 QPRIHLVKRHESTINHPITDLEAEEYK 73
P+ H+ K +E T+ P+T+ + E +
Sbjct: 64 SPKKHVPKTYEVTLAGPLTEDDIEAFA 90
>gnl|CDD|173674 cd05583, STKc_MSK_N, N-terminal catalytic domain of the Protein
Serine/Threonine Kinase, Mitogen and stress-activated
kinase. Serine/Threonine Kinases (STKs), Mitogen and
stress-activated kinase (MSK) subfamily, N-terminal
catalytic (c) domain. STKs catalyze the transfer of the
gamma-phosphoryl group from ATP to serine/threonine
residues on protein substrates. The MSK subfamily is
part of a larger superfamily that includes the catalytic
domains of other protein STKs, protein tyrosine kinases,
RIO kinases, aminoglycoside phosphotransferase, choline
kinase, and phosphoinositide 3-kinase. MSKs contain an
N-terminal kinase domain (NTD) from the AGC family and a
C-terminal kinase domain (CTD) from the CAMK family,
similar to 90 kDa ribosomal protein S6 kinases (RSKs).
MSKs are activated by two major signaling cascades, the
Ras-MAPK and p38 stress kinase pathways, in response to
various stimuli such as growth factors, hormones,
neurotransmitters, cellular stress, and pro-inflammatory
cytokines. This triggers phosphorylation in the
activation loop (A-loop) of the CTD of MSK. The active
CTD phosphorylates the hydrophobic motif (HM) in the
C-terminal extension of NTD, which facilitates the
phosphorylation of the A-loop and activates the NTD,
which in turn phosphorylates downstream targets. MSKs
are predominantly nuclear proteins. They are widely
expressed in many tissues including heart, brain, lung,
liver, kidney, and pancreas. There are two isoforms of
MSK, called MSK1 and MSK2.
Length = 288
Score = 25.5 bits (56), Expect = 4.7
Identities = 10/28 (35%), Positives = 16/28 (57%)
Query: 13 DQLRKQVVSFEKVKLTNNEMDKHGHLVL 40
D L + + + +KL N +D GH+VL
Sbjct: 119 DHLHQLGIIYRDIKLENILLDSEGHVVL 146
>gnl|CDD|236897 PRK11303, PRK11303, DNA-binding transcriptional regulator FruR;
Provisional.
Length = 328
Score = 25.2 bits (56), Expect = 6.2
Identities = 5/23 (21%), Positives = 12/23 (52%), Gaps = 3/23 (13%)
Query: 37 HLVLNSM---HKYQPRIHLVKRH 56
L L ++ K +P + ++R+
Sbjct: 302 ELALAALDEPRKPKPGLTRIRRN 324
>gnl|CDD|182098 PRK09828, PRK09828, putative fimbrial outer membrane usher protein;
Provisional.
Length = 865
Score = 25.1 bits (55), Expect = 7.9
Identities = 9/42 (21%), Positives = 19/42 (45%), Gaps = 9/42 (21%)
Query: 29 NNEMDKHGHLVLNSMHKYQPRIHLVKRHESTINHPITDLEAE 70
N+ +D+ G+ V +++ Y E+ + I LE +
Sbjct: 717 NSTIDRWGYGVTSALSPY---------RENRVALDINTLEND 749
>gnl|CDD|215104 PLN00207, PLN00207, polyribonucleotide nucleotidyltransferase;
Provisional.
Length = 891
Score = 24.9 bits (54), Expect = 9.1
Identities = 10/32 (31%), Positives = 14/32 (43%)
Query: 30 NEMDKHGHLVLNSMHKYQPRIHLVKRHESTIN 61
EM K + KY P IH++K +N
Sbjct: 666 AEMSKCSPPPSKRLSKYAPLIHIMKVKPEKVN 697
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
0.318 0.133 0.382
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: 4,709,588
Number of extensions: 363662
Number of successful extensions: 286
Number of sequences better than 10.0: 1
Number of HSP's gapped: 282
Number of HSP's successfully gapped: 16
Length of query: 95
Length of database: 10,937,602
Length adjustment: 62
Effective length of query: 33
Effective length of database: 8,187,654
Effective search space: 270192582
Effective search space used: 270192582
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (24.2 bits)