RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7374
(106 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 = 62.6 bits (153), Expect = 1e-13
Identities = 20/31 (64%), Positives = 26/31 (83%)
Query: 75 VTCHLETKELWDKFNELGTEMIITKTGRKLF 105
+ LE +ELW KF+ELGTEMIITK+GR++F
Sbjct: 2 IKVSLENRELWKKFHELGTEMIITKSGRRMF 32
>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 = 61.5 bits (150), Expect = 3e-13
Identities = 22/30 (73%), Positives = 27/30 (90%)
Query: 76 TCHLETKELWDKFNELGTEMIITKTGRKLF 105
T LE +ELWDKF+ELGTEMIITK+GR++F
Sbjct: 1 TVSLEDRELWDKFHELGTEMIITKSGRRMF 30
>gnl|CDD|214656 smart00425, TBOX, Domain first found in the mice T locus
(Brachyury) protein.
Length = 190
Score = 60.7 bits (148), Expect = 7e-13
Identities = 20/32 (62%), Positives = 26/32 (81%)
Query: 75 VTCHLETKELWDKFNELGTEMIITKTGRKLFQ 106
+ LE KELW KF+ELGTEMI+TK+GR++F
Sbjct: 1 IKVSLEDKELWRKFHELGTEMIVTKSGRRMFP 32
>gnl|CDD|147993 pfam06126, Herpes_LAMP2, Herpesvirus Latent membrane protein 2.
Family of Kaposi's sarcoma-associated herpesvirus (HHV8)
latent membrane protein.
Length = 510
Score = 28.5 bits (63), Expect = 0.64
Identities = 9/45 (20%), Positives = 16/45 (35%)
Query: 32 RSRSPPEISSSTSGGDDASLDVCQTPPLNPLLQERFNSEELRHVT 76
R I S T+ + + C + PLN L + + +
Sbjct: 407 FFRIHSRILSHTTDMALSPVRGCGSEPLNELELQELHRDPPNTFG 451
>gnl|CDD|178165 PLN02550, PLN02550, threonine dehydratase.
Length = 591
Score = 26.4 bits (58), Expect = 3.7
Identities = 14/64 (21%), Positives = 21/64 (32%), Gaps = 6/64 (9%)
Query: 6 TPISSYHNHKRRRGSPIRKSQRDRDDRSRSPPEISSSTSGGDDASLDVCQTPPLNPLLQE 65
T S +H S+ S I ++ D+ S+ P PLL+
Sbjct: 8 TAGSPLRSH------IGSPSKPVVGSTPFSRSRIPAAVDSADETSMAPPPPPSPLPLLKV 61
Query: 66 RFNS 69
NS
Sbjct: 62 SPNS 65
>gnl|CDD|132735 cd06937, NR_LBD_RAR, The ligand binding domain (LBD) of retinoic
acid receptor (RAR), a members of the nuclear receptor
superfamily. The ligand binding domain (LBD) of
retinoic acid receptor (RAR): Retinoic acid receptors
are members of the nuclear receptor (NR) superfamily of
ligand-regulated transcription factors. RARs mediate
the biological effect of retinoids, including both
naturally dietary vitamin A (retinol) metabolites and
active synthetic analogs. Retinoids play key roles in a
wide variety of essential biological processes, such as
vertebrate embryonic morphogenesis and organogenesis,
differentiation and apoptosis, and homeostasis. RARs
function as heterodimers with retinoic X receptors by
binding to specific RAR response elements (RAREs) found
in the promoter regions of retinoid target genes. In
the absence of ligand, the RAR-RXR heterodimer recruits
the corepressor proteins NCoR or AMRT, and associated
factors such as histone deacetylases or
DNA-methyltransferases, leading to an inactive
condensed chromatin structure, preventing
transcription. Upon ligand binding, the corepressors
are released, and coactivator complexes such as histone
acetyltransferase or histone arginine
methyltransferases are recruited to activate
transcription. There are three RAR subtypes (alpha,
beta, gamma), originating from three distinct genes.
For each subtype, several isoforms exist that differ in
their N-terminal region, allowing retinoids to exert
their pleiotropic effects. Like other members of the
nuclear receptor (NR) superfamily of ligand-activated
transcription factors, retinoic acid receptors have a
central well conserved DNA binding domain (DBD), a
variable N-terminal domain, a non-conserved hinge and a
C-terminal ligand binding domain (LBD).
Length = 231
Score = 25.9 bits (57), Expect = 4.1
Identities = 10/15 (66%), Positives = 12/15 (80%)
Query: 83 ELWDKFNELGTEMII 97
LWDKF+EL T+ II
Sbjct: 38 GLWDKFSELSTKCII 52
>gnl|CDD|218926 pfam06178, KdgM, Oligogalacturonate-specific porin protein (KdgM).
This family consists of several bacterial proteins which
are homologous to the oligogalacturonate-specific porin
protein KdgM from Erwinia chrysanthemi. The
phytopathogenic Gram-negative bacteria Erwinia
chrysanthemi secretes pectinases, which are able to
degrade the pectic polymers of plant cell walls, and
uses the degradation products as a carbon source for
growth. KdgM is a major outer membrane protein, whose
synthesis is strongly induced in the presence of pectic
derivatives. KdgM behaves like a voltage-dependent porin
that is slightly selective for anions and that exhibits
fast block in the presence of trigalacturonate. In
contrast to most porins, KdgM seems to be monomeric.
Length = 218
Score = 25.5 bits (56), Expect = 5.1
Identities = 5/23 (21%), Positives = 11/23 (47%), Gaps = 1/23 (4%)
Query: 12 HNHKRRRGSPIRKSQRDRDDRSR 34
++ KR + +D +D+ R
Sbjct: 115 YDFKRYSST-DLDGDKDNNDQYR 136
>gnl|CDD|204177 pfam09245, MA-Mit, Mycoplasma arthritidis-derived mitogen.
Mycoplasma arthritidis-derived mitogen (MA-Mit) adopts a
completely alpha-helical structure consisting of ten
alpha helices. It is a superantigen that can activate
large fractions of T cells bearing particular TCR V-beta
elements. Two MA-Mit molecules form an asymmetric dimer
and cross-link two MHC antigens to form a dimerised
MA-Mit-MHC complex.
Length = 152
Score = 25.4 bits (55), Expect = 6.5
Identities = 12/23 (52%), Positives = 15/23 (65%)
Query: 82 KELWDKFNELGTEMIITKTGRKL 104
+ELWDK +L EM I G+KL
Sbjct: 130 QELWDKAVKLTKEMKIKLKGQKL 152
>gnl|CDD|240474 cd12894, SPRY_PRY_TRIM36, PRY/SPRY domain in tripartite
motif-containing protein 36 (TRIM36). This domain,
consisting of the distinct N-terminal PRY subdomain
followed by the SPRY subdomain, is found at the
C-terminus of TRIM36, a Class I TRIM protein. TRIM36
(also known as Haprin or RNF98) has a ubiquitin ligase
activity and interacts with centromere protein-H, one of
the kinetochore proteins. It has been shown that TRIM36
is potentially associated with chromosome segregation
and that an excess of TRIM36 may cause chromosomal
instability. In Xenopus laevis, TRIM36 is expressed
during early embryogenesis and plays an important role
in the arrangement of somites during their formation.
Length = 202
Score = 25.2 bits (55), Expect = 7.9
Identities = 13/56 (23%), Positives = 20/56 (35%)
Query: 29 RDDRSRSPPEISSSTSGGDDASLDVCQTPPLNPLLQERFNSEELRHVTCHLETKEL 84
RD S + S SG +D D Q L + + + HV ++ L
Sbjct: 91 RDISSPRYDQDSGHDSGSEDTCYDSSQPFTLATIGMGKLFIPKSPHVENEPASRVL 146
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
0.314 0.131 0.386
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: 5,305,440
Number of extensions: 428654
Number of successful extensions: 285
Number of sequences better than 10.0: 1
Number of HSP's gapped: 283
Number of HSP's successfully gapped: 27
Length of query: 106
Length of database: 10,937,602
Length adjustment: 71
Effective length of query: 35
Effective length of database: 7,788,468
Effective search space: 272596380
Effective search space used: 272596380
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: 42 (22.0 bits)
S2: 53 (24.2 bits)