RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9084
(103 letters)
>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 = 92.3 bits (230), Expect = 4e-25
Identities = 45/141 (31%), Positives = 61/141 (43%), Gaps = 55/141 (39%)
Query: 15 RRMFPTFQVRLFNLDPDAEYMLMMDFVPVDDKRYRY------------------------ 50
RRMFPT +V + LDP+A Y +++DFVPVDD RY++
Sbjct: 27 RRMFPTLKVSVSGLDPNALYSVLLDFVPVDDHRYKFHNGEWVVAGKAEPHPPPRVYIHPD 86
Query: 51 -------------AFHR---------QIGSLV--SL----PRFHVVLLSPESNSASATSP 82
+F + G ++ S+ PR H+V + ES S
Sbjct: 87 SPATGAHWMKQPVSFDKVKLTNNKLDGNGHIILNSMHKYQPRLHIVRVDDESPSQRT--- 143
Query: 83 FKTFLFPETMFTAVTAYQNHR 103
+TF FPET F AVTAYQN
Sbjct: 144 VRTFSFPETQFIAVTAYQNEE 164
>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 = 92.7 bits (231), Expect = 4e-25
Identities = 46/141 (32%), Positives = 58/141 (41%), Gaps = 54/141 (38%)
Query: 15 RRMFPTFQVRLFNLDPDAEYMLMMDFVPVDDKRY-------------------RYAFH-- 53
RRMFPT +V++ LDP+A Y ++MD VPVDD RY R H
Sbjct: 29 RRMFPTLKVKVSGLDPNALYSVLMDLVPVDDHRYKFSGGKWVVAGKAEPHLPPRVYVHPD 88
Query: 54 ---------RQIGS------------------LVSL----PRFHVVLLSPESNSASATSP 82
+Q S L S+ PR H+V + S +
Sbjct: 89 SPATGAHWMKQPVSFDKLKLTNNTLDNNGHIILNSMHKYQPRLHIVEVDDSSPFS--WRL 146
Query: 83 FKTFLFPETMFTAVTAYQNHR 103
+TF FPET F AVTAYQN
Sbjct: 147 VQTFSFPETEFIAVTAYQNQE 167
>gnl|CDD|214656 smart00425, TBOX, Domain first found in the mice T locus
(Brachyury) protein.
Length = 190
Score = 81.9 bits (203), Expect = 5e-21
Identities = 43/141 (30%), Positives = 62/141 (43%), Gaps = 52/141 (36%)
Query: 15 RRMFPTFQVRLFNLDPDAEYMLMMDFVPVDDKRYRY------------------------ 50
RRMFPT + ++ LDP+A Y ++MD VPVDDKRY++
Sbjct: 28 RRMFPTLKYKVSGLDPNALYSVLMDLVPVDDKRYKFNNGKWVVAGKAEPHMPSRVYVHPD 87
Query: 51 -------------AFHR------------QIGSLV-SLPRFHVVLLSPESNSAS--ATSP 82
+F + + ++ S+ ++ L E + S S
Sbjct: 88 SPATGAHWMKQPVSFDKVKLTNNQSDKNGHLQIILNSMHKYQPRLHIVEVDDISKEILSQ 147
Query: 83 FKTFLFPETMFTAVTAYQNHR 103
FKTF+FPET F AVTAYQN +
Sbjct: 148 FKTFVFPETQFIAVTAYQNQK 168
>gnl|CDD|187547 cd05236, FAR-N_SDR_e, fatty acyl CoA reductases (FARs), extended
(e) SDRs. SDRs are Rossmann-fold NAD(P)H-binding
proteins, many of which may function as fatty acyl CoA
reductases (FAR), acting on medium and long chain fatty
acids, and have been reported to be involved in diverse
processes such as biosynthesis of insect pheromones,
plant cuticular wax production, and mammalian wax
biosynthesis. In Arabidopsis thaliana, proteins with
this particular architecture have also been identified
as the MALE STERILITY 2 (MS2) gene product, which is
implicated in male gametogenesis. Mutations in MS2
inhibit the synthesis of exine (sporopollenin),
rendering plants unable to reduce pollen wall fatty
acids to corresponding alcohols. This N-terminal domain
shares the catalytic triad (but not the upstream Asn)
and characteristic NADP-binding motif of the extended
SDR family. Extended SDRs are distinct from classical
SDRs. In addition to the Rossmann fold (alpha/beta
folding pattern with a central beta-sheet) core region
typical of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 320
Score = 30.0 bits (68), Expect = 0.14
Identities = 9/29 (31%), Positives = 14/29 (48%), Gaps = 4/29 (13%)
Query: 17 MFPTFQVRLFNLDPDAEYMLMMDFVPVDD 45
+ +R N DP+A + D +PVD
Sbjct: 246 AYGKGILRTMNADPNA----VADIIPVDV 270
>gnl|CDD|216711 pfam01802, Herpes_V23, Herpesvirus VP23 like capsid protein. This
family consist of various capsid proteins from members
of the herpesviridae. The capsid protein VP23 in herpes
simplex virus forms a triplex together with VP19C these
fit between and link together adjacent capsomers as
formed by VP5 and VP26. VP3 along with the scaffolding
proteins helps to form normal capsids by defining the
curvature of the shell and size of the particle.
Length = 296
Score = 29.5 bits (67), Expect = 0.21
Identities = 7/26 (26%), Positives = 14/26 (53%), Gaps = 1/26 (3%)
Query: 54 RQIGSLVSL-PRFHVVLLSPESNSAS 78
+Q+G + +L P V S ++ A+
Sbjct: 268 QQLGDIFNLGPLLRVCDFSGDNKVAT 293
>gnl|CDD|183854 PRK13042, PRK13042, superantigen-like protein; Reviewed.
Length = 291
Score = 26.1 bits (57), Expect = 3.4
Identities = 13/40 (32%), Positives = 20/40 (50%), Gaps = 1/40 (2%)
Query: 23 VRLFNLDPDAEYMLMMDFVPVDDKRYRYAFHRQIGSLVSL 62
+R N+ PD ++ + V DDK+Y HR + V L
Sbjct: 131 IRFMNVVPDY-FIYKIALVGKDDKKYGEGVHRNVDVFVVL 169
>gnl|CDD|213280 cd05912, OSB_CoA_lg, O-succinylbenzoate-CoA ligase (also known as
O-succinylbenzoate-CoA synthase, OSB-CoA synthetase, or
MenE). O-succinylbenzoic acid-CoA synthase catalyzes
the coenzyme A (CoA)- and ATP-dependent conversion of
o-succinylbenzoic acid to o-succinylbenzoyl-CoA. The
reaction is the fourth step of the biosynthesis pathway
of menaquinone (vitamin K2). In certain bacteria,
menaquinone is used during fumarate reduction in
anaerobic respiration. In cyanobacteria, the product of
the menaquinone pathway is phylloquinone
(2-methyl-3-phytyl-1,4-naphthoquinone), a molecule used
exclusively as an electron transfer cofactor in
Photosystem 1. In green sulfur bacteria and
heliobacteria, menaquinones are used as loosely bound
secondary electron acceptors in the photosynthetic
reaction center.
Length = 407
Score = 26.0 bits (58), Expect = 4.3
Identities = 7/21 (33%), Positives = 8/21 (38%)
Query: 47 RYRYAFHRQIGSLVSLPRFHV 67
L+SLP FHV
Sbjct: 110 AENLGLTPDDNWLLSLPLFHV 130
>gnl|CDD|153077 cd07930, bacterial_phosphagen_kinase, Phosphagen (guanidino)
kinases found in bacteria. Phosphagen (guanidino)
kinases are enzymes that transphosphorylate a high
energy phosphoguanidino compound, such as
phosphocreatine (PCr) or phosphoarginine, which is used
as an energy-storage and -transport metabolite, to ADP,
thereby creating ATP. This subfamily is specific to
bacteria and lacks an N-terminal domain, which otherwise
forms part of the substrate binding site. Most of the
catalytic residues are found in the larger C-terminal
domain, however, which appears conserved in these
bacterial proteins. Their functions have not been
characterized.
Length = 232
Score = 25.2 bits (56), Expect = 6.6
Identities = 12/45 (26%), Positives = 19/45 (42%), Gaps = 6/45 (13%)
Query: 22 QVRLFNLDPDAEYMLMMDFVPVDD---KRYRYAFHRQIGSLVSLP 63
Q L L + Y +DD ++ YAF ++G L + P
Sbjct: 105 QCLLPGLQLEEAYERADK---IDDLLEEKLDYAFDEKLGYLTACP 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
0.327 0.138 0.447
Gapped
Lambda K H
0.267 0.0771 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,417,843
Number of extensions: 454766
Number of successful extensions: 482
Number of sequences better than 10.0: 1
Number of HSP's gapped: 480
Number of HSP's successfully gapped: 18
Length of query: 103
Length of database: 10,937,602
Length adjustment: 69
Effective length of query: 34
Effective length of database: 7,877,176
Effective search space: 267823984
Effective search space used: 267823984
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 53 (24.1 bits)