RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14943
(328 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 = 292 bits (749), Expect = e-100
Identities = 108/193 (55%), Positives = 139/193 (72%), Gaps = 15/193 (7%)
Query: 53 QVILEDLDLWLKFQSHTNEMIVTKNGRRMFPVVKVSIKGLEPDAMYTVLLEFLQIEQKRW 112
V LED +LW KF EMI+TK+GRRMFP +KVS+ GL+P+A+Y+VLL+F+ ++ R+
Sbjct: 1 TVSLEDRELWDKFHELGTEMIITKSGRRMFPTLKVSVSGLDPNALYSVLLDFVPVDDHRY 60
Query: 113 KYVNGEWVPAGKPEQPPMNAMYLHPESPNFGEHWMKDCVSFAKVKLTNH-SNGSGQIMLN 171
K+ NGEWV AGK E P +Y+HP+SP G HWMK VSF KVKLTN+ +G+G I+LN
Sbjct: 61 KFHNGEWVVAGKAEPHPPPRVYIHPDSPATGAHWMKQPVSFDKVKLTNNKLDGNGHIILN 120
Query: 172 SLHKYEPRIHLVKVATE---QQIIKTFPFPETQFIAVTAYQNEEFIAVTAYQNEEVTSLK 228
S+HKY+PR+H+V+V E Q+ ++TF FPETQ FIAVTAYQNEE+T LK
Sbjct: 121 SMHKYQPRLHIVRVDDESPSQRTVRTFSFPETQ-----------FIAVTAYQNEEITKLK 169
Query: 229 IKFNPFAKAFLDA 241
I NPFAK F DA
Sbjct: 170 IDNNPFAKGFRDA 182
Score = 93.5 bits (233), Expect = 5e-23
Identities = 32/59 (54%), Positives = 41/59 (69%), Gaps = 1/59 (1%)
Query: 255 NEWKYVNGEWVPAGKPEQPPMNAMYLHPESPNFGEHWMKDCVSFAKVKLTNH-SNGSGQ 312
+ +K+ NGEWV AGK E P +Y+HP+SP G HWMK VSF KVKLTN+ +G+G
Sbjct: 58 HRYKFHNGEWVVAGKAEPHPPPRVYIHPDSPATGAHWMKQPVSFDKVKLTNNKLDGNGH 116
Score = 42.6 bits (101), Expect = 7e-05
Identities = 15/30 (50%), Positives = 25/30 (83%)
Query: 1 MFPVVKVSIKGLEPDAMYTVLLEFLQIEQK 30
MFP +KVS+ GL+P+A+Y+VLL+F+ ++
Sbjct: 29 MFPTLKVSVSGLDPNALYSVLLDFVPVDDH 58
>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 = 285 bits (732), Expect = 2e-97
Identities = 95/198 (47%), Positives = 133/198 (67%), Gaps = 16/198 (8%)
Query: 51 NPQVILEDLDLWLKFQSHTNEMIVTKNGRRMFPVVKVSIKGLEPDAMYTVLLEFLQIEQK 110
+V LE+ +LW KF EMI+TK+GRRMFP +KV + GL+P+A+Y+VL++ + ++
Sbjct: 1 GIKVSLENRELWKKFHELGTEMIITKSGRRMFPTLKVKVSGLDPNALYSVLMDLVPVDDH 60
Query: 111 RWKYVNGEWVPAGKPEQPPMNAMYLHPESPNFGEHWMKDCVSFAKVKLTNH-SNGSGQIM 169
R+K+ G+WV AGK E +Y+HP+SP G HWMK VSF K+KLTN+ + +G I+
Sbjct: 61 RYKFSGGKWVVAGKAEPHLPPRVYVHPDSPATGAHWMKQPVSFDKLKLTNNTLDNNGHII 120
Query: 170 LNSLHKYEPRIHLVKV----ATEQQIIKTFPFPETQFIAVTAYQNEEFIAVTAYQNEEVT 225
LNS+HKY+PR+H+V+V ++++TF FPET EFIAVTAYQN+E+T
Sbjct: 121 LNSMHKYQPRLHIVEVDDSSPFSWRLVQTFSFPET-----------EFIAVTAYQNQEIT 169
Query: 226 SLKIKFNPFAKAFLDAKE 243
LKI NPFAK F D
Sbjct: 170 QLKIDNNPFAKGFRDNGR 187
Score = 91.1 bits (227), Expect = 6e-22
Identities = 27/57 (47%), Positives = 37/57 (64%), Gaps = 1/57 (1%)
Query: 257 WKYVNGEWVPAGKPEQPPMNAMYLHPESPNFGEHWMKDCVSFAKVKLTNH-SNGSGQ 312
+K+ G+WV AGK E +Y+HP+SP G HWMK VSF K+KLTN+ + +G
Sbjct: 62 YKFSGGKWVVAGKAEPHLPPRVYVHPDSPATGAHWMKQPVSFDKLKLTNNTLDNNGH 118
Score = 43.3 bits (103), Expect = 4e-05
Identities = 12/30 (40%), Positives = 23/30 (76%)
Query: 1 MFPVVKVSIKGLEPDAMYTVLLEFLQIEQK 30
MFP +KV + GL+P+A+Y+VL++ + ++
Sbjct: 31 MFPTLKVKVSGLDPNALYSVLMDLVPVDDH 60
>gnl|CDD|214656 smart00425, TBOX, Domain first found in the mice T locus
(Brachyury) protein.
Length = 190
Score = 261 bits (668), Expect = 9e-88
Identities = 102/201 (50%), Positives = 135/201 (67%), Gaps = 18/201 (8%)
Query: 52 PQVILEDLDLWLKFQSHTNEMIVTKNGRRMFPVVKVSIKGLEPDAMYTVLLEFLQIEQKR 111
+V LED +LW KF EMIVTK+GRRMFP +K + GL+P+A+Y+VL++ + ++ KR
Sbjct: 1 IKVSLEDKELWRKFHELGTEMIVTKSGRRMFPTLKYKVSGLDPNALYSVLMDLVPVDDKR 60
Query: 112 WKYVNGEWVPAGKPEQPPMNAMYLHPESPNFGEHWMKDCVSFAKVKLTNHS---NGSGQI 168
+K+ NG+WV AGK E + +Y+HP+SP G HWMK VSF KVKLTN+ NG QI
Sbjct: 61 YKFNNGKWVVAGKAEPHMPSRVYVHPDSPATGAHWMKQPVSFDKVKLTNNQSDKNGHLQI 120
Query: 169 MLNSLHKYEPRIHLVKVATEQQII----KTFPFPETQFIAVTAYQNEEFIAVTAYQNEEV 224
+LNS+HKY+PR+H+V+V + I KTF FPETQ FIAVTAYQN+++
Sbjct: 121 ILNSMHKYQPRLHIVEVDDISKEILSQFKTFVFPETQ-----------FIAVTAYQNQKI 169
Query: 225 TSLKIKFNPFAKAFLDAKEKT 245
T LKI NPFAK F D +
Sbjct: 170 TKLKIDNNPFAKGFRDQGRRR 190
Score = 83.1 bits (206), Expect = 5e-19
Identities = 28/49 (57%), Positives = 35/49 (71%)
Query: 257 WKYVNGEWVPAGKPEQPPMNAMYLHPESPNFGEHWMKDCVSFAKVKLTN 305
+K+ NG+WV AGK E + +Y+HP+SP G HWMK VSF KVKLTN
Sbjct: 61 YKFNNGKWVVAGKAEPHMPSRVYVHPDSPATGAHWMKQPVSFDKVKLTN 109
Score = 38.8 bits (91), Expect = 0.001
Identities = 14/52 (26%), Positives = 28/52 (53%), Gaps = 7/52 (13%)
Query: 1 MFPVVKVSIKGLEPDAMYTVLLEFLQIEQKSVAMSIEMIKSDSQQYEAYGNP 52
MFP +K + GL+P+A+Y+VL++ V + + K ++ ++ G
Sbjct: 30 MFPTLKYKVSGLDPNALYSVLMDL-------VPVDDKRYKFNNGKWVVAGKA 74
>gnl|CDD|238892 cd01911, proteasome_alpha, proteasome alpha subunit. The 20S
proteasome, multisubunit proteolytic complex, is the
central enzyme of nonlysosomal protein degradation in
both the cytosol and nucleus. It is composed of 28
subunits arranged as four homoheptameric rings that
stack on top of one another forming an elongated
alpha-beta-beta-alpha cylinder with a central cavity.
The proteasome alpha and beta subunits are members of
the N-terminal nucleophile (Ntn)-hydrolase superfamily.
Their N-terminal threonine residues are exposed as a
nucleophile in peptide bond hydrolysis. Mammals have 7
different alpha and 10 different beta proteasome subunit
genes while archaea have one of each.
Length = 209
Score = 29.7 bits (68), Expect = 1.7
Identities = 13/56 (23%), Positives = 31/56 (55%), Gaps = 5/56 (8%)
Query: 69 TNEMIVTKNGRRMFPV---VKVSIKGLEPDAMYTVLLEFLQIEQKRWKYVNGEWVP 121
T++++ + ++F + + ++ GL DA VL+ ++E + ++Y GE +P
Sbjct: 48 TSKLLDPSSVEKIFKIDDHIGCAVAGLTADAR--VLVNRARVEAQNYRYTYGEPIP 101
>gnl|CDD|239718 cd03749, proteasome_alpha_type_1, proteasome_alpha_type_1. The 20S
proteasome, multisubunit proteolytic complex, is the
central enzyme of nonlysosomal protein degradation in
both the cytosol and nucleus. It is composed of 28
subunits arranged as four homoheptameric rings that
stack on top of one another forming an elongated
alpha-beta-beta-alpha cylinder with a central cavity.
The proteasome alpha and beta subunits are members of
the N-terminal nucleophile (Ntn)-hydrolase superfamily.
Their N-terminal threonine residues are exposed as a
nucleophile in peptide bond hydrolysis. Mammals have 7
alpha and 7 beta proteasome subunits while archaea have
one of each.
Length = 211
Score = 28.8 bits (65), Expect = 3.2
Identities = 12/49 (24%), Positives = 26/49 (53%), Gaps = 5/49 (10%)
Query: 79 RRMFPV---VKVSIKGLEPDAMYTVLLEFLQIEQKRWKYVNGEWVPAGK 124
+++F V + ++I GL DA VL +++ E +++V +P +
Sbjct: 56 KKIFKVDDHIGIAIAGLTADA--RVLSRYMRQECLNYRFVYDSPIPVSR 102
>gnl|CDD|218326 pfam04915, DltD_N, DltD N-terminal region. DltD is and integral
membrane protein involved in the biosynthesis of
D-alanyl-lipoteichoic acid. This is important in
controlling the net ionic charge in lipoteichoic acid
(LTA). This family is found in bacteria of the
Bacillus/Clostridium group. DltD binds Dcp and ligates
it with D-alanine. DltD does not ligate acyl carrier
protein (ACP) with D-alanine. It also has thioesterase
activity for mischarged D-alanyl-acyl carrier protein
(ACP). DltD is thought to be responsible for
discriminating between Dcp involved in the
D-alanylation of LTA, and ACP involved in fatty acid
biosynthesis. This family consists of the N-terminal
region of DltD.
Length = 62
Score = 26.8 bits (60), Expect = 3.3
Identities = 5/27 (18%), Positives = 15/27 (55%)
Query: 27 IEQKSVAMSIEMIKSDSQQYEAYGNPQ 53
++Q + ++S + K + +A +P+
Sbjct: 3 VKQAATSLSPNVFKGTLIKQKALSDPK 29
>gnl|CDD|218790 pfam05876, Terminase_GpA, Phage terminase large subunit (GpA).
This family consists of several phage terminase large
subunit proteins as well as related sequences from
several bacterial species. The DNA packaging enzyme of
bacteriophage lambda, terminase, is a heteromultimer
composed of a small subunit, gpNu1, and a large subunit,
gpA, products of the Nu1 and A genes, respectively.
Terminase is involved in the site-specific binding and
cutting of the DNA in the initial stages of packaging.
It is now known that gpA is actively involved in late
stages of packaging, including DNA translocation, and
that this enzyme contains separate functional domains
for its early and late packaging activities.
Length = 552
Score = 28.4 bits (64), Expect = 6.4
Identities = 8/32 (25%), Positives = 12/32 (37%), Gaps = 5/32 (15%)
Query: 108 EQKRWKYVNGEWVPAGKPEQPP-----MNAMY 134
KR G W+ +P +NA+Y
Sbjct: 242 HHKRAMLRAGRWIATAPIRRPRHAGFHLNALY 273
>gnl|CDD|238928 cd01966, Nitrogenase_NifN_1, Nitrogenase_nifN1: A subgroup of the
NifN subunit of the NifEN complex: NifN forms an
alpha2beta2 tetramer with NifE. NifN and nifE are
structurally homologous to nitrogenase MoFe protein beta
and alpha subunits respectively. NifEN participates in
the synthesis of the iron-molybdenum cofactor (FeMoco)
of the MoFe protein. NifB-co (an iron and sulfur
containing precursor of the FeMoco) from NifB is
transferred to the NifEN complex where it is further
processed to FeMoco. The nifEN bound precursor of FeMoco
has been identified as a molybdenum-free, iron- and
sulfur- containing analog of FeMoco. It has been
suggested that this nifEN bound precursor also acts as a
cofactor precursor in nitrogenase systems which require
a cofactor other than FeMoco: i.e. iron-vanadium
cofactor (FeVco) or iron only cofactor (FeFeco).
Length = 417
Score = 28.0 bits (63), Expect = 6.8
Identities = 9/17 (52%), Positives = 10/17 (58%)
Query: 145 HWMKDCVSFAKVKLTNH 161
H + C SFAKV L H
Sbjct: 28 HGAQGCTSFAKVLLVRH 44
Score = 28.0 bits (63), Expect = 6.8
Identities = 9/17 (52%), Positives = 10/17 (58%)
Query: 290 HWMKDCVSFAKVKLTNH 306
H + C SFAKV L H
Sbjct: 28 HGAQGCTSFAKVLLVRH 44
>gnl|CDD|223319 COG0241, HisB, Histidinol phosphatase and related phosphatases
[Amino acid transport and metabolism].
Length = 181
Score = 27.3 bits (61), Expect = 8.9
Identities = 10/44 (22%), Positives = 13/44 (29%), Gaps = 1/44 (2%)
Query: 172 SLHKYEPRIHLVKVATEQQIIKTFPFPETQFIAVTAYQNEEFIA 215
L LV V T Q I F E F + + +
Sbjct: 40 LLKLQRAGYKLV-VVTNQSGIGRGYFTEADFDKLHNKMLKILAS 82
>gnl|CDD|220320 pfam09623, Cas_NE0113, CRISPR-associated protein NE0113
(Cas_NE0113). Members of this minor CRISPR-associated
(Cas) protein family are encoded in cas gene clusters
in Vibrio vulnificus YJ016, Nitrosomonas europaea ATCC
19718, Mannheimia succiniciproducens MBEL55E, and
Verrucomicrobium spinosum.
Length = 225
Score = 27.3 bits (61), Expect = 9.4
Identities = 12/32 (37%), Positives = 18/32 (56%), Gaps = 2/32 (6%)
Query: 52 PQVILEDLDLWLKFQSHTNEMIV--TKNGRRM 81
PQV+ E L L+ +E++V TK+GR
Sbjct: 13 PQVVTETLYALLQQGRPPDEVVVITTKDGRVR 44
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
0.316 0.132 0.399
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: 16,416,680
Number of extensions: 1518929
Number of successful extensions: 1150
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1141
Number of HSP's successfully gapped: 19
Length of query: 328
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 231
Effective length of database: 6,635,264
Effective search space: 1532745984
Effective search space used: 1532745984
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 (21.6 bits)
S2: 59 (26.5 bits)