RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8530
(68 letters)
>gnl|CDD|212519 cd09993, HDAC_classIV, Histone deacetylase class IV also known as
histone deacetylase 11. Class IV histone deacetylases
(HDAC11; EC 3.5.1.98) are predicted Zn-dependent
enzymes. This class includes animal HDAC11, plant HDA2
and related bacterial deacetylases. Enzymes in this
subfamily participate in regulation of a number of
different processes through protein modification
(deacetylation). They catalyze hydrolysis of
N(6)-acetyl-lysine of histones (or other proteins) to
yield a deacetylated proteins. Histone deacetylases
often act as members of large multi-protein complexes
such as mSin3A or SMRT/N-CoR. Human HDAC11 does not
associate with them but can interact with HDAC6 in vivo.
It has been suggested that HDAC11 and HDAC6 may use
non-histone proteins as their substrates and play a role
other than to directly modulate chromatin structure. In
normal tissues, expression of HDAC11 is limited to
kidney, heart, brain, skeletal muscle and testis,
suggesting that its function might be tissue-specific.
In mammals, HDAC11 proteins are known to be involved in
progression of various tumors. HDAC11 plays an essential
role in regulating OX40 ligand (OX40L) expression in
Hodgkin lymphoma (HL); selective inhibition of HDAC11
expression significantly up-regulates OX40L and induces
apoptosis in HL cell lines. Thus, inhibition of HDAC11
could be a therapeutic drug option for antitumor immune
response in HL patients.
Length = 275
Score = 61.7 bits (151), Expect = 2e-13
Identities = 21/60 (35%), Positives = 29/60 (48%), Gaps = 9/60 (15%)
Query: 10 VDMLED----HL-----GIIRRDELVFMKARERRVPIVMLTSGGYLKQTARIIADSILNL 60
VD+L L G+ RD LV AR R +P+ M+ GGY + AR++A L
Sbjct: 216 VDVLAGDRLGRLSLSLEGLRERDRLVLRFARARGIPVAMVLGGGYSRDIARLVARHAQTL 275
>gnl|CDD|212512 cd09301, HDAC, Histone deacetylase (HDAC) classes I, II, IV and
related proteins. The HDAC/HDAC-like family includes
Zn-dependent histone deacetylase classes I, II and IV
(class III HDACs, also called sirtuins, are
NAD-dependent and structurally unrelated, and therefore
not part of this family). Histone deacetylases catalyze
hydrolysis of N(6)-acetyl-lysine residues in histone
amino termini to yield a deacetylated histone (EC
3.5.1.98), as opposed to the acetylation reaction by
some histone acetyltransferases (EC 2.3.1.48).
Deacetylases of this family are involved in signal
transduction through histone and other protein
modification, and can repress/activate transcription of
a number of different genes. They usually act via the
formation of large multiprotein complexes. They are
involved in various cellular processes, including cell
cycle regulation, DNA damage response, embryonic
development, cytokine signaling important for immune
response and post-translational control of the acetyl
coenzyme A synthetase. In mammals, they are known to be
involved in progression of different tumors. Specific
inhibitors of mammalian histone deacetylases are an
emerging class of promising novel anticancer drugs.
Length = 279
Score = 35.1 bits (81), Expect = 7e-04
Identities = 16/44 (36%), Positives = 22/44 (50%), Gaps = 3/44 (6%)
Query: 18 GIIRRDELVFMKARERRVPIVMLTSGGY-LKQTARIIADSILNL 60
G ++ E+V AR PI+M+ GGY + ARI I L
Sbjct: 238 GFVKLAEIVKEFAR--GGPILMVLGGGYNPEAAARIWTAIIKEL 279
>gnl|CDD|240148 cd05017, SIS_PGI_PMI_1, The members of this protein family
contain the SIS (Sugar ISomerase) domain and have both
the phosphoglucose isomerase (PGI) and the
phosphomannose isomerase (PMI) functions. These
functions catalyze the reversible reactions of glucose
6-phosphate to fructose 6-phosphate, and mannose
6-phosphate to fructose 6-phosphate, respectively at an
equal rate. This protein contains two SIS domains. This
alignment is based on the first SIS domain.
Length = 119
Score = 30.7 bits (70), Expect = 0.019
Identities = 12/26 (46%), Positives = 16/26 (61%)
Query: 26 VFMKARERRVPIVMLTSGGYLKQTAR 51
+A+ER IV +TSGG L + AR
Sbjct: 62 AVEQAKERGAKIVAITSGGKLLEMAR 87
>gnl|CDD|216151 pfam00850, Hist_deacetyl, Histone deacetylase domain. Histones can
be reversibly acetylated on several lysine residues.
Regulation of transcription is caused in part by this
mechanism. Histone deacetylases catalyze the removal of
the acetyl group. Histone deacetylases are related to
other proteins.
Length = 300
Score = 29.5 bits (67), Expect = 0.073
Identities = 11/42 (26%), Positives = 16/42 (38%)
Query: 18 GIIRRDELVFMKARERRVPIVMLTSGGYLKQTARIIADSILN 59
G R L+ A P+V + GGY A ++L
Sbjct: 256 GYAERTRLLLELADAYGGPVVSVLEGGYNLDALARSAAAVLA 297
>gnl|CDD|181536 PRK08674, PRK08674, bifunctional phosphoglucose/phosphomannose
isomerase; Validated.
Length = 337
Score = 29.2 bits (66), Expect = 0.10
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 26 VFMKARERRVPIVMLTSGGYLKQTAR 51
+A +R I+ +TSGG LK+ A+
Sbjct: 97 AVEQALKRGAKIIAITSGGKLKEMAK 122
>gnl|CDD|181883 PRK09468, ompR, osmolarity response regulator; Provisional.
Length = 239
Score = 26.9 bits (60), Expect = 0.63
Identities = 14/35 (40%), Positives = 20/35 (57%), Gaps = 7/35 (20%)
Query: 12 ML--EDHLGIIRRDELVFMKARERRVPIVMLTSGG 44
ML ED L I RR ++++ PI+MLT+ G
Sbjct: 58 MLPGEDGLSICRR-----LRSQNNPTPIIMLTAKG 87
>gnl|CDD|216301 pfam01105, EMP24_GP25L, emp24/gp25L/p24 family/GOLD. Members of
this family are implicated in bringing cargo forward
from the ER and binding to coat proteins by their
cytoplasmic domains. This domain corresponds closely to
the beta-strand rich GOLD domain described in. The GOLD
domain is always found combined with lipid- or
membrane-association domains.
Length = 178
Score = 26.1 bits (58), Expect = 1.1
Identities = 10/29 (34%), Positives = 18/29 (62%), Gaps = 1/29 (3%)
Query: 6 MGDQVDMLEDHLGIIRRDELVFMKARERR 34
+ +++ LED L I+R E +++ RE R
Sbjct: 112 LEEELKKLEDQLNDIKR-EQKYLREREAR 139
>gnl|CDD|236122 PRK07877, PRK07877, hypothetical protein; Provisional.
Length = 722
Score = 26.5 bits (59), Expect = 1.1
Identities = 8/14 (57%), Positives = 11/14 (78%)
Query: 29 KARERRVPIVMLTS 42
AR RR+P++M TS
Sbjct: 216 AARARRIPVLMATS 229
>gnl|CDD|216041 pfam00648, Peptidase_C2, Calpain family cysteine protease.
Length = 302
Score = 25.9 bits (57), Expect = 1.6
Identities = 10/27 (37%), Positives = 16/27 (59%)
Query: 7 GDQVDMLEDHLGIIRRDELVFMKARER 33
G+ VD++ D + ELVF+ + ER
Sbjct: 103 GEWVDVVVDDRLPTKDGELVFVHSAER 129
>gnl|CDD|226402 COG3885, COG3885, Uncharacterized conserved protein [Function
unknown].
Length = 261
Score = 25.9 bits (57), Expect = 1.7
Identities = 13/50 (26%), Positives = 21/50 (42%), Gaps = 6/50 (12%)
Query: 12 MLEDHLGIIRRDELVFMKARERRVPIVMLTSGGYLKQTARIIADSILNLA 61
L+D++ +I + L + R + PI Y R +AD I A
Sbjct: 51 RLDDYIAVIYSEYLSGLPYRTKHHPI----RKEYK--NDRELADKIYEEA 94
>gnl|CDD|233259 TIGR01070, mutS1, DNA mismatch repair protein MutS. [DNA
metabolism, DNA replication, recombination, and repair].
Length = 840
Score = 25.1 bits (55), Expect = 3.5
Identities = 14/53 (26%), Positives = 25/53 (47%), Gaps = 7/53 (13%)
Query: 11 DMLEDHLGIIRRDELVFMKARERRVPIVMLTSGGYLKQTARIIA--DSILNLA 61
+LE I+ ++ +F + RE + L++ AR +A D + NLA
Sbjct: 497 KVLEAEGKILALEKELFEELRELLKKYL-----EALQEAARALAELDVLANLA 544
>gnl|CDD|217163 pfam02646, RmuC, RmuC family. This family contains several
bacterial RmuC DNA recombination proteins. The function
of the RMUC protein is unknown but it is suspected that
it is either a structural protein that protects DNA
against nuclease action, or is itself involved in DNA
cleavage at the regions of DNA secondary structures.
Length = 301
Score = 24.6 bits (54), Expect = 4.4
Identities = 8/20 (40%), Positives = 12/20 (60%)
Query: 19 IIRRDELVFMKARERRVPIV 38
IR D + +ARE+ V +V
Sbjct: 187 AIRADPELDQEAREKNVVLV 206
>gnl|CDD|234723 PRK00311, panB, 3-methyl-2-oxobutanoate hydroxymethyltransferase;
Reviewed.
Length = 264
Score = 24.3 bits (54), Expect = 4.9
Identities = 11/36 (30%), Positives = 16/36 (44%), Gaps = 6/36 (16%)
Query: 27 FMKARERRVPIVMLTSGGYLKQTARII----ADSIL 58
K ++ IVMLT+ Y A++ D IL
Sbjct: 7 LQKMKQEGEKIVMLTAYDYP--FAKLFDEAGVDVIL 40
>gnl|CDD|119342 cd06557, KPHMT-like, Ketopantoate hydroxymethyltransferase
(KPHMT) is the first enzyme in the pantothenate
biosynthesis pathway. Ketopantoate
hydroxymethyltransferase (KPHMT) catalyzes the first
committed step in the biosynthesis of pantothenate
(vitamin B5), which is a precursor to coenzyme A and is
required for penicillin biosynthesis.
Length = 254
Score = 24.3 bits (54), Expect = 5.0
Identities = 12/36 (33%), Positives = 17/36 (47%), Gaps = 6/36 (16%)
Query: 27 FMKARERRVPIVMLTSGGYLKQTARII----ADSIL 58
K ++ IVMLT+ Y TA++ D IL
Sbjct: 4 LQKMKKAGEKIVMLTA--YDYPTAKLADEAGVDVIL 37
>gnl|CDD|183678 PRK12681, cysB, transcriptional regulator CysB; Reviewed.
Length = 324
Score = 23.7 bits (52), Expect = 8.3
Identities = 9/11 (81%), Positives = 9/11 (81%)
Query: 9 QVDMLEDHLGI 19
QV MLED LGI
Sbjct: 36 QVRMLEDELGI 46
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
0.328 0.142 0.410
Gapped
Lambda K H
0.267 0.0742 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,643,107
Number of extensions: 288829
Number of successful extensions: 432
Number of sequences better than 10.0: 1
Number of HSP's gapped: 432
Number of HSP's successfully gapped: 25
Length of query: 68
Length of database: 10,937,602
Length adjustment: 39
Effective length of query: 29
Effective length of database: 9,207,796
Effective search space: 267026084
Effective search space used: 267026084
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 (21.7 bits)
S2: 53 (24.2 bits)