RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10341
(213 letters)
>gnl|CDD|212529 cd10005, HDAC3, Histone deacetylase 3 (HDAC3). HDAC3 is a
Zn-dependent class I histone deacetylase that catalyzes
hydrolysis of N(6)-acetyl-lysine residue of a histone to
yield a deacetylated histone (EC 3.5.1.98). Histone
acetylation/deacetylation process is important for
mediation of transcriptional regulation of many genes.
In order to target specific chromatin regions, HDAC3 can
interact with DNA-binding proteins (transcriptional
factors) either directly or after forming complexes with
a number of other proteins, as observed for the
SMPT/N-CoR complex which recruits human HDAC3 to
specific chromatin loci and activates deacetylation.
Human HDAC3 is also involved in deacetylation of
non-histone substrates such as RelA, SPY and p53
factors. This protein can also down-regulate p53
function and subsequently modulate cell growth and
apoptosis. This gene is therefore regarded as a
potential tumor suppressor gene. HDAC3 plays a role in
various physiological processes, including subcellular
protein localization, cell cycle progression, cell
differentiation, apoptosis and survival. HDAC3 has been
found to be overexpressed in some tumors including
leukemia, lung carcinoma, colon cancer and maxillary
carcinoma. Thus, inhibitors precisely targeting HDAC3
(in some cases together with retinoic acid or
hyperthermia) could be a therapeutic drug option.
Length = 381
Score = 199 bits (507), Expect = 8e-63
Identities = 77/123 (62%), Positives = 100/123 (81%)
Query: 36 LGGGGLGQFSLTTKGHGECVKFVRDLNVPLLVLGGGGYTLRNVARCWTYETSLLVNEEIS 95
LG LG F+L+ KGHGECV+FV+ N+PLLVLGGGGYT+RNVARCWTYETSLLV+EEIS
Sbjct: 259 LGCDRLGCFNLSIKGHGECVEFVKSFNIPLLVLGGGGYTVRNVARCWTYETSLLVDEEIS 318
Query: 96 NDIPDSLYKDFFQPDYNLHPEFVHKHDNANSKQYLELITKTVYDNLKMVAFSPSVQMQDM 155
N++P + Y ++F PD+ LHP+ + +N NSKQYL+ I +TV++NLKM+ +PSVQMQD+
Sbjct: 319 NELPYNEYFEYFAPDFTLHPDVSTRIENQNSKQYLDQIRQTVFENLKMLNHAPSVQMQDV 378
Query: 156 IGD 158
D
Sbjct: 379 PPD 381
>gnl|CDD|240251 PTZ00063, PTZ00063, histone deacetylase; Provisional.
Length = 436
Score = 140 bits (354), Expect = 1e-39
Identities = 65/146 (44%), Positives = 94/146 (64%), Gaps = 7/146 (4%)
Query: 36 LGGGGLGQFSLTTKGHGECVKFVRDLNVPLLVLGGGGYTLRNVARCWTYETSLLVN--EE 93
L G LG+F+LT KGH CV+FVR LN+PLLVLGGGGYT+RNVARCW YET +++N +E
Sbjct: 263 LTGDRLGRFNLTIKGHAACVEFVRSLNIPLLVLGGGGYTIRNVARCWAYETGVILNKHDE 322
Query: 94 ISNDIPDSLYKDFFQPDYNLH--PEFVHKHDNANSKQYLELITKTVYDNLKMVAFSPSVQ 151
+S+ I + Y D++ PD+ LH P + N NS ++LE I + +NL+ + +P VQ
Sbjct: 323 MSDQISLNDYYDYYAPDFQLHLQPSNI---PNYNSPEHLEKIKVKILENLRYLEHAPGVQ 379
Query: 152 MQDMIGDVFTRDIGAVLDEMDPDIKN 177
+ D F RDI ++ ++ +
Sbjct: 380 FAYVPPDFFDRDIDDEDEKNQYELSD 405
>gnl|CDD|212528 cd10004, RPD3-like, reduced potassium dependency-3 (RPD3)-like.
Proteins of the Rpd3-like family are class I
Zn-dependent Histone deacetylases that catalyze
hydrolysis of an N(6)-acetyl-lysine residue of a histone
to yield a deacetylated histone (EC 3.5.1.98). RPD3 is
the yeast homolog of class I HDACs. The main function of
RPD3-like group members is regulation of a number of
different processes through protein (mostly different
histones) modification (deacetylation). This group
includes fungal RPD3 and acts via the formation of large
multiprotein complexes. Members of this group are
involved in cell cycle regulation, DNA damage response,
embryonic development and cytokine signaling important
for immune response. Histone deacetylation by yeast RPD3
represses genes regulated by the Ash1 and Ume6
DNA-binding proteins. In mammals, they are known to be
involved in progression of various tumors. Specific
inhibitors of mammalian histone deacetylases could be a
therapeutic drug option.
Length = 375
Score = 134 bits (339), Expect = 6e-38
Identities = 59/118 (50%), Positives = 81/118 (68%), Gaps = 1/118 (0%)
Query: 36 LGGGGLGQFSLTTKGHGECVKFVRDLNVPLLVLGGGGYTLRNVARCWTYETSLLVNEEIS 95
L G LG F+L+ KGH CV FV+ N+P+LVLGGGGYT+RNVAR W +ET LL EE+
Sbjct: 259 LSGDRLGCFNLSMKGHANCVNFVKSFNLPMLVLGGGGYTMRNVARTWAFETGLLAGEELD 318
Query: 96 NDIPDSLYKDFFQPDYNLHPEFVHKHDNANSKQYLELITKTVYDNLKMVAFSPSVQMQ 153
D+P + Y +++ PDY L+ +N N+ +YL+ IT V +NL+ +F+PSVQMQ
Sbjct: 319 KDLPYNEYYEYYGPDYELNVR-PSNMENHNTPEYLDKITTAVIENLRNTSFAPSVQMQ 375
>gnl|CDD|212534 cd10010, HDAC1, Histone deacetylase 1 (HDAC1). Histone deacetylase
1 (HDAC1) is a Zn-dependent class I enzyme that
catalyzes hydrolysis of N(6)-acetyl-lysine residue of a
histone to yield a deacetylated histone (EC 3.5.1.98).
Histone acetylation/deacetylation process is important
for mediation of transcriptional regulation of many
genes. HDAC1 is involved in regulation through
association with DNA binding proteins to target specific
chromatin regions. In particular, HDAC1 appears to play
a major role in pre-implantation embryogenesis in
establishing a repressive chromatin state. Its
interaction with retinoblastoma tumor-suppressor protein
is essential in the control of cell proliferation and
differentiation. Together with metastasis-associated
protein-2 (MTA2), it deacetylates p53, thereby
modulating its effect on cell growth and apoptosis. It
participates in DNA-damage response, along with HDAC2;
together, they promote DNA non-homologous end-joining.
HDAC1 is also involved in tumorogenesis; its
overexpression modulates cancer progression. Specific
inhibitors of HDAC1 are currently used in cancer
therapy.
Length = 371
Score = 120 bits (302), Expect = 1e-32
Identities = 54/109 (49%), Positives = 80/109 (73%), Gaps = 1/109 (0%)
Query: 36 LGGGGLGQFSLTTKGHGECVKFVRDLNVPLLVLGGGGYTLRNVARCWTYETSLLVNEEIS 95
L G LG F+LT KGH +CV+FV+ N+P+L+LGGGGYT+RNVARCWTYET++ ++ EI
Sbjct: 263 LSGDRLGCFNLTIKGHAKCVEFVKSFNLPMLMLGGGGYTIRNVARCWTYETAVALDSEIP 322
Query: 96 NDIPDSLYKDFFQPDYNLHPEFVHKHDNANSKQYLELITKTVYDNLKMV 144
N++P + Y ++F PD+ LH N N+ +YLE I + +++NL+M+
Sbjct: 323 NELPYNDYFEYFGPDFKLHIS-PSNMTNQNTNEYLEKIKQRLFENLRML 370
>gnl|CDD|212535 cd10011, HDAC2, Histone deacetylase 2 (HDAC2). Histone deacetylase
2 (HDAC2) is a Zn-dependent class I enzyme that
catalyzes hydrolysis of N(6)-acetyl-lysine residue of a
histone to yield a deacetylated histone (EC 3.5.1.98).
Histone acetylation/deacetylation process is important
for mediation of transcriptional regulation of many
genes. HDAC2 is involved in regulation through
association with DNA binding proteins to target specific
chromatin regions. It forms transcriptional repressor
complexes by associating with several proteins,
including the mammalian zinc-finger transcription factor
YY1, thus playing an important role in transcriptional
regulation, cell cycle progression and developmental
events. Additionally, a few non-histone HDAC2 substrates
have been found. HDAC2 plays a role in embryonic
development and cytokine signaling important for immune
response, and is over-expressed in several solid tumors
including oral, prostate, ovarian, endometrial and
gastric cancer. It participates in DNA-damage response,
along with HDAC1; together, they can promote DNA
non-homologous end-joining. HDAC2 is considered an
important cancer prognostic marker. Inhibitors
specifically targeting HDAC2 could be a therapeutic drug
option.
Length = 366
Score = 117 bits (293), Expect = 2e-31
Identities = 53/109 (48%), Positives = 79/109 (72%), Gaps = 1/109 (0%)
Query: 36 LGGGGLGQFSLTTKGHGECVKFVRDLNVPLLVLGGGGYTLRNVARCWTYETSLLVNEEIS 95
L G LG F+LT KGH +CV+ V+ N+PLL+LGGGGYT+RNVARCWTYET++ ++ EI
Sbjct: 259 LSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTIRNVARCWTYETAVALDCEIP 318
Query: 96 NDIPDSLYKDFFQPDYNLHPEFVHKHDNANSKQYLELITKTVYDNLKMV 144
N++P + Y ++F PD+ LH N N+ +Y+E I + +++NL+M+
Sbjct: 319 NELPYNDYFEYFGPDFKLHIS-PSNMTNQNTPEYMEKIKQRLFENLRML 366
>gnl|CDD|212524 cd10000, HDAC8, Histone deacetylase 8 (HDAC8). HDAC8 is a
Zn-dependent class I histone deacetylase that catalyzes
hydrolysis of an N(6)-acetyl-lysine residue of a histone
to yield a deacetylated histone (EC 3.5.1.98). Histone
acetylation/deacetylation process is important for
mediation of transcriptional regulation of many genes.
Histone deacetylases usually act via association with
DNA binding proteins to target specific chromatin
regions. HDAC8 is found in human cytoskeleton-bound
protein fraction and insoluble cell pellets. It plays a
crucial role in intramembraneous bone formation;
germline deletion of HDAC8 is detrimental to skull bone
formation. HDAC8 is possibly associated with the smooth
muscle actin cytockeleton and may regulate the
contractive capacity of smooth muscle cells. HDAC8 is
also involved in the metabolic control of the estrogen
receptor related receptor (ERR)-alpha/peroxisome
proliferator activated receptor (PPAR) gamma coactivator
1 alpha (PGC1-alpha) transcriptional complex as well as
in the development of neuroblastoma and T-cell lymphoma.
HDAC8-selective small-molecule inhibitors could be a
therapeutic drug option for these diseases.
Length = 364
Score = 108 bits (272), Expect = 3e-28
Identities = 52/116 (44%), Positives = 68/116 (58%), Gaps = 11/116 (9%)
Query: 35 VLGGGGLGQFSLTTKGHGECVKFVRDLNVPLLVLGGGGYTLRNVARCWTYETSLLVNEEI 94
L G +G F+LT G G+C+K+V +P L+LGGGGY L N ARCWTY T L++ E +
Sbjct: 255 TLAGDPMGAFNLTPVGIGKCLKYVLGWKLPTLILGGGGYNLANTARCWTYLTGLILGEPL 314
Query: 95 SNDIPDSLYKDFFQ---PDYNLH--PEFVHKHDNANSKQYLELITKTVYDNLKMVA 145
S+DIPD +FF PDY L P + N QY+E I +T+ NLK V
Sbjct: 315 SSDIPDH---EFFTSYGPDYELEISPS---LRPDLNEDQYIEKILETIKGNLKNVV 364
>gnl|CDD|212517 cd09991, HDAC_classI, Class I histone deacetylases. Class I
histone deacetylases (HDACs) are Zn-dependent enzymes
that catalyze hydrolysis of N(6)-acetyl-lysine residues
in histone amino termini to yield a deacetylated histone
(EC 3.5.1.98). Enzymes belonging to this group
participate in regulation of a number of processes
through protein (mostly different histones) modification
(deacetylation). Class I histone deacetylases in general
act via the formation of large multiprotein complexes.
This group includes animal HDAC1, HDAC2, HDAC3, HDAC8,
fungal RPD3, HOS1 and HOS2, plant HDA9, protist,
archaeal and bacterial (AcuC) deacetylases. Members of
this class are involved in cell cycle regulation, DNA
damage response, embryonic development, cytokine
signaling important for immune response and in
posttranslational control of the acetyl coenzyme A
synthetase. In mammals, they are known to be involved in
progression of various tumors. Specific inhibitors of
mammalian histone deacetylases are an emerging class of
promising novel anticancer drugs.
Length = 306
Score = 107 bits (269), Expect = 3e-28
Identities = 39/54 (72%), Positives = 46/54 (85%)
Query: 36 LGGGGLGQFSLTTKGHGECVKFVRDLNVPLLVLGGGGYTLRNVARCWTYETSLL 89
L G LG F+L+ KGH +CVKFV+ N+PLLVLGGGGYTLRNVARCWTYET++L
Sbjct: 253 LAGDRLGCFNLSIKGHAKCVKFVKSFNIPLLVLGGGGYTLRNVARCWTYETAVL 306
>gnl|CDD|212540 cd11598, HDAC_Hos2, Class I histone deacetylases including ScHos2
and SpPhd1. This subfamily includes Class I histone
deacetylase (HDAC) Hos2 from Saccharomyces cerevisiae as
well as a histone deacetylase Phd1 from
Schizosaccharomyces pombe. Hos2 binds to the coding
regions of genes during gene activation, specifically it
deacetylates the lysines in H3 and H4 histone tails. It
is preferentially associated with genes of high activity
genome-wide and is shown to be necessary for efficient
transcription. Thus, Hos2 is directly required for gene
activation in contrast to other class I histone
deacetylases. Protein encoded by phd1 is inhibited by
trichostatin A (TSA), a specific inhibitor of histone
deacetylase, and is involved in the meiotic cell cycle
in S. pombe. Class 1 HDACs are Zn-dependent enzymes that
catalyze hydrolysis of N(6)-acetyl-lysine residues in
histone amino termini to yield a deacetylated histone
(EC 3.5.1.98).
Length = 311
Score = 96.4 bits (240), Expect = 5e-24
Identities = 34/54 (62%), Positives = 41/54 (75%)
Query: 36 LGGGGLGQFSLTTKGHGECVKFVRDLNVPLLVLGGGGYTLRNVARCWTYETSLL 89
LGG LGQF+L K HG CVKFV+ +P+LV+GGGGYT RNVAR W YET++
Sbjct: 258 LGGDRLGQFNLNIKAHGACVKFVKSFGIPMLVVGGGGYTPRNVARAWCYETAVA 311
>gnl|CDD|240374 PTZ00346, PTZ00346, histone deacetylase; Provisional.
Length = 429
Score = 78.9 bits (194), Expect = 3e-17
Identities = 33/54 (61%), Positives = 43/54 (79%)
Query: 36 LGGGGLGQFSLTTKGHGECVKFVRDLNVPLLVLGGGGYTLRNVARCWTYETSLL 89
L G LG +L++ GHG+CV+ VRDL +P+L LGGGGYT+RNVA+ W YETS+L
Sbjct: 281 LAGDRLGLLNLSSFGHGQCVQAVRDLGIPMLALGGGGYTIRNVAKLWAYETSIL 334
>gnl|CDD|223201 COG0123, AcuC, Deacetylases, including yeast histone deacetylase
and acetoin utilization protein [Chromatin structure and
dynamics / Secondary metabolites biosynthesis,
transport, and catabolism].
Length = 340
Score = 60.1 bits (146), Expect = 7e-11
Identities = 24/79 (30%), Positives = 39/79 (49%), Gaps = 8/79 (10%)
Query: 41 LGQFSLTTKGHGECVKFVRDL----NVPLLVLGGGGYTLRNVARCWTYETSLL---VNEE 93
LG+ +LT +G+ + + VR L P++ + GGY L +AR + L V EE
Sbjct: 257 LGRLNLTEEGYAKIGRAVRKLAEGYGGPVVAVLEGGYNLDALARSLVAFLAGLAGLVEEE 316
Query: 94 ISNDIP-DSLYKDFFQPDY 111
+ +P D + F+ DY
Sbjct: 317 LEEPLPEDLELRRAFRADY 335
>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 = 58.4 bits (142), Expect = 2e-10
Identities = 16/53 (30%), Positives = 27/53 (50%), Gaps = 4/53 (7%)
Query: 41 LGQFSLTTKGHGECVKFVRDL----NVPLLVLGGGGYTLRNVARCWTYETSLL 89
LG +LTT+G+ E + + +L P++ + GGY L +AR + L
Sbjct: 247 LGGLNLTTEGYAERTRLLLELADAYGGPVVSVLEGGYNLDALARSAAAVLAGL 299
>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 = 56.7 bits (137), Expect = 8e-10
Identities = 19/54 (35%), Positives = 28/54 (51%), Gaps = 2/54 (3%)
Query: 38 GGGLGQFSLTTKGHGECVKFVRDLN--VPLLVLGGGGYTLRNVARCWTYETSLL 89
G LG F+L+ KG + + V++ P+L++ GGGY AR WT L
Sbjct: 226 GDRLGGFNLSEKGFVKLAEIVKEFARGGPILMVLGGGYNPEAAARIWTAIIKEL 279
>gnl|CDD|212520 cd09994, HDAC_AcuC_like, Class I histone deacetylase AcuC (Acetoin
utilization protein)-like enzymes. AcuC (Acetoin
utilization protein) is a class I deacetylase found only
in bacteria and is involved in post-translational
control of the acetyl-coenzyme A synthetase (AcsA).
Deacetylase AcuC works in coordination with deacetylase
SrtN (class III), possibly to maintain AcsA in active
(deacetylated) form and let the cell grow under low
concentration of acetate. B. subtilis AcuC is a member
of operon acuABC; this operon is repressed by the
presence of glucose and does not show induction by
acetoin; acetoin is a bacterial fermentation product
that can be converted to acetate via the butanediol
cycle in absence of other carbon sources. Inactivation
of AcuC leads to slower growth and lower cell yield
under low-acetate conditions in Bacillus subtilis. In
general, Class I histone deacetylases (HDACs) are
Zn-dependent enzymes that catalyze hydrolysis of
N(6)-acetyl-lysine residues in histone amino termini to
yield a deacetylated histone (EC 3.5.1.98). Enzymes
belonging to this group participate in regulation of a
number of processes through protein (mostly different
histones) modification (deacetylation). Class I histone
deacetylases in general act via the formation of large
multiprotein complexes. Members of this class are
involved in cell cycle regulation, DNA damage response,
embryonic development, cytokine signaling important for
immune response and in posttranslational control of the
acetyl coenzyme A synthetase.
Length = 313
Score = 55.6 bits (135), Expect = 2e-09
Identities = 16/48 (33%), Positives = 23/48 (47%), Gaps = 5/48 (10%)
Query: 41 LGQFSLTTKGHGECVKFVRDL-----NVPLLVLGGGGYTLRNVARCWT 83
L +L+ + + V+ +R+L L LGGGGY VAR W
Sbjct: 260 LTHLNLSNRAYRAAVRRIRELADEYCGGRWLALGGGGYNPDVVARAWA 307
>gnl|CDD|212543 cd11680, HDAC_Hos1, Class I histone deacetylases Hos1 and related
proteins. Saccharomyces cerevisiae Hos1 is responsible
for Smc3 deacetylation. Smc3 is an important player
during the establishment of sister chromatid cohesion.
Hos1 belongs to the class I histone deacetylases
(HDACs). HDACs are Zn-dependent enzymes that catalyze
hydrolysis of N(6)-acetyl-lysine residues in histone
amino termini to yield a deacetylated histone (EC
3.5.1.98). Enzymes belonging to this group participate
in regulation of a number of processes through protein
(mostly different histones) modification
(deacetylation). Class I histone deacetylases in general
act via the formation of large multiprotein complexes.
Other class I HDACs are animal HDAC1, HDAC2, HDAC3,
HDAC8, fungal RPD3 and HOS2, plant HDA9, protist,
archaeal and bacterial (AcuC) deacetylases. Members of
this class are involved in cell cycle regulation, DNA
damage response, embryonic development, cytokine
signaling important for immune response and in
posttranslational control of the acetyl coenzyme A
synthetase.
Length = 294
Score = 53.8 bits (130), Expect = 9e-09
Identities = 22/63 (34%), Positives = 35/63 (55%), Gaps = 7/63 (11%)
Query: 34 LVLGGGGL-----GQFSLTTKGHGECVKFVRD--LNVPLLVLGGGGYTLRNVARCWTYET 86
+ G GL +++LT +G+G ++ + + P L+LGGGGY AR WTY T
Sbjct: 232 IQCGCDGLSGDPHKEWNLTIRGYGSVIELLLKEFKDKPTLLLGGGGYNHTEAARAWTYLT 291
Query: 87 SLL 89
S++
Sbjct: 292 SMV 294
>gnl|CDD|212513 cd09987, Arginase_HDAC, Arginase-like and histone-like hydrolases.
Arginase-like/histone-like hydrolase superfamily
includes metal-dependent enzymes that belong to
Arginase-like amidino hydrolase family and
histone/histone-like deacetylase class I, II, IV family,
respectively. These enzymes catalyze hydrolysis of amide
bond. Arginases are known to be involved in control of
cellular levels of arginine and ornithine, in histidine
and arginine degradation and in clavulanic acid
biosynthesis. Deacetylases play a role in signal
transduction through histone and/or other protein
modification and can repress/activate transcription of a
number of different genes. They participate in different
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. Mammalian histone deacetyases 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 = 217
Score = 36.2 bits (84), Expect = 0.006
Identities = 9/55 (16%), Positives = 16/55 (29%), Gaps = 4/55 (7%)
Query: 37 GGGGLGQFSLTTKGHGECVKFVRDLNVPLLVLGGGGYTL----RNVARCWTYETS 87
G G G L+ + + + N+ + + L AR T
Sbjct: 161 GTGTPGPGGLSYREGLYITERIAKTNLVVGLDIVEVNPLLDETGRTARLAAALTL 215
>gnl|CDD|212525 cd10001, HDAC_classII_APAH, Histone deacetylase class IIa. This
subfamily includes bacterial acetylpolyamine
amidohydrolase (APAH) as well as other Class II histone
deacetylase (HDAC) and related proteins. Deacetylases of
class II are Zn-dependent enzymes that catalyze
hydrolysis of N(6)-acetyl-lysine residues of histones
(EC 3.5.1.98) and possibly other proteins to yield
deacetylated histones/other proteins. Mycoplana ramosa
APAH exhibits broad substrate specificity and catalyzes
the deacetylation of polyamines such as putrescine,
spermidine, and spermine by cleavage of a non-peptide
amide bond.
Length = 298
Score = 32.9 bits (76), Expect = 0.094
Identities = 11/42 (26%), Positives = 20/42 (47%)
Query: 40 GLGQFSLTTKGHGECVKFVRDLNVPLLVLGGGGYTLRNVARC 81
L F LTT+ + + + L +P + + GGY + + R
Sbjct: 248 PLSDFKLTTEDYARIGRRIAALGLPTVFVQEGGYNVDALGRN 289
Score = 30.2 bits (69), Expect = 0.77
Identities = 11/35 (31%), Positives = 17/35 (48%), Gaps = 1/35 (2%)
Query: 6 HDRLGQFSLTTKGHGECVKFVRDLNVP-LLVLGGG 39
D L F LTT+ + + + L +P + V GG
Sbjct: 246 GDPLSDFKLTTEDYARIGRRIAALGLPTVFVQEGG 280
>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 = 31.3 bits (72), Expect = 0.28
Identities = 23/74 (31%), Positives = 34/74 (45%), Gaps = 29/74 (39%)
Query: 7 DRLGQFSLTTKGHGECVKFVRDLNVPLLVLGGGGLGQFSLTTKGHGECVKFVRDLNVPLL 66
DRLG+ SL+ +G E RD LVL +F R +P+
Sbjct: 222 DRLGRLSLSLEGLRE-----RDR----LVL-------------------RFARARGIPVA 253
Query: 67 VLGGGGYTLRNVAR 80
++ GGGY+ R++AR
Sbjct: 254 MVLGGGYS-RDIAR 266
>gnl|CDD|237777 PRK14652, PRK14652, UDP-N-acetylenolpyruvoylglucosamine reductase;
Provisional.
Length = 302
Score = 30.6 bits (69), Expect = 0.50
Identities = 26/86 (30%), Positives = 34/86 (39%), Gaps = 11/86 (12%)
Query: 23 VKFVRDLNVPLLVLGGGG------LGQFSLTTKGHGECVKFVRDLNVPLLVLGGGGYTLR 76
++ VR+L VPL +LGGG G + + + D LVLG G R
Sbjct: 52 LRAVRELGVPLSILGGGANTLVADAGVRGVVLRLPQDFPGESTDGGR--LVLGAGAPISR 109
Query: 77 NVARCWTYETSLLVNEEISNDIPDSL 102
AR LV E IP +L
Sbjct: 110 LPARA---HAHGLVGMEFLAGIPGTL 132
>gnl|CDD|234053 TIGR02903, spore_lon_C, ATP-dependent protease, Lon family.
Members of this protein family resemble the widely
distributed ATP-dependent protease La, also called Lon
and LonA. It resembles even more closely LonB, which is
a LonA paralog found in genomes if and only if the
species is capable of endospore formation (as in
Bacillus subtilis, Clostridium tetani, and select other
members of the Firmicutes) and expressed specifically in
the forespore compartment. Members of this family are
restricted to a subset of spore-forming species, and are
very likely to participate in the program of endospore
formation. We propose the designation LonC [Protein
fate, Degradation of proteins, peptides, and
glycopeptides, Cellular processes, Sporulation and
germination].
Length = 615
Score = 30.9 bits (70), Expect = 0.52
Identities = 19/48 (39%), Positives = 30/48 (62%), Gaps = 7/48 (14%)
Query: 157 GDVFTRDIGAVLDEMDPDIKNPQLE--EDKRVDPANEFYDGDNDQDAP 202
G +F +IG E+DP ++N L+ EDKRV+ ++ +YD D D + P
Sbjct: 267 GVLFIDEIG----ELDPLLQNKLLKVLEDKRVEFSSSYYDPD-DPNVP 309
>gnl|CDD|182141 PRK09913, PRK09913, putative fructose-like phosphotransferase
system subunit EIIA; Provisional.
Length = 148
Score = 28.7 bits (64), Expect = 1.5
Identities = 7/25 (28%), Positives = 16/25 (64%)
Query: 113 LHPEFVHKHDNANSKQYLELITKTV 137
+H +F+H+ ++ Q L L+ +T+
Sbjct: 122 IHQDFIHQLKQGDTDQVLALLNQTL 146
>gnl|CDD|176958 CHL00015, ndhE, NADH dehydrogenase subunit 4L.
Length = 101
Score = 27.7 bits (62), Expect = 2.1
Identities = 13/38 (34%), Positives = 20/38 (52%), Gaps = 2/38 (5%)
Query: 130 LELITKTVYDNLKMVAFSPSVQMQDMIGDVFTRDIGAV 167
LELI V N+ V FS + + GD+F+ + A+
Sbjct: 34 LELILNAV--NINFVTFSDFFDSRQLKGDIFSIFVIAI 69
>gnl|CDD|233194 TIGR00930, 2a30, K-Cl cotransporter. [Transport and binding
proteins, Other].
Length = 953
Score = 28.5 bits (64), Expect = 3.4
Identities = 20/92 (21%), Positives = 35/92 (38%), Gaps = 12/92 (13%)
Query: 129 YLELITKTVYDNLKMVAFSPSVQMQDMIGD-----VFTRD--IGAVLDEMDPDIK-NPQL 180
YL L TK V+ K+ F + + + I A + + DI PQ
Sbjct: 780 YL-LTTKKVWKKCKIRIFVGAQKDDRSEQEKKDMATLLYKFRIDAEVIVVLMDINAKPQT 838
Query: 181 EEDKRVDPANE---FYDGDNDQDAPDTEMSWG 209
E + + + + D++A D +M+W
Sbjct: 839 ESMEAFEEMIRPFRLHKTEKDREAKDPKMTWT 870
>gnl|CDD|129966 TIGR00888, guaA_Nterm, GMP synthase (glutamine-hydrolyzing),
N-terminal domain or A subunit. This protein of purine
de novo biosynthesis is well-conserved. However, it
appears to split into two separate polypeptide chains
in most of the Archaea. This N-terminal region would be
the smaller subunit [Purines, pyrimidines, nucleosides,
and nucleotides, Purine ribonucleotide biosynthesis].
Length = 188
Score = 27.3 bits (61), Expect = 4.4
Identities = 10/41 (24%), Positives = 20/41 (48%), Gaps = 3/41 (7%)
Query: 26 VRDLNVPLLVLGGGGLGQFSLTTKGHGECVKFVRDLNVPLL 66
+R+ N ++L GG S+ + + + +L VP+L
Sbjct: 37 IREKNPKGIILSGG---PSSVYAENAPRADEKIFELGVPVL 74
>gnl|CDD|183743 PRK12785, fliL, flagellar basal body-associated protein FliL;
Reviewed.
Length = 166
Score = 27.3 bits (61), Expect = 4.9
Identities = 12/21 (57%), Positives = 15/21 (71%)
Query: 33 LLVLGGGGLGQFSLTTKGHGE 53
+L+LGGGG G F + GHGE
Sbjct: 34 VLLLGGGGGGFFFFFSHGHGE 54
>gnl|CDD|99794 cd06197, FNR_like_2, FAD/NAD(P) binding domain of ferredoxin
reductase-like proteins. Ferredoxin reductase (FNR) was
intially identified as a chloroplast reductase activity,
catalyzing the electron transfer from reduced
iron-sulfur protein ferredoxin to NADP+ as the final
step in the electron transport mechanism of photosystem
I. FNR transfers electrons from reduced ferredoxin to
FAD (forming FADH2 via a semiquinone intermediate) and
then transfers a hydride ion to convert NADP+ to NADPH.
FNR has since been shown to utilize a variety of
electron acceptors and donors and have a variety of
physiological functions in a variety of organisms
including nitrogen assimilation, dinitrogen fixation,
steroid hydroxylation, fatty acid metabolism, oxygenase
activity, and methane assimilation. FNR has an
NAD(P)-binding sub-domain of the alpha/beta class and a
discrete (usually N-terminal) flavin sub-domain which
varies in orientation with respect to the NAD(P)
binding domain. The N-terminal moeity may contain a
flavin prosthetic group (as in flavoenzymes) or use
flavin as a substrate. Because flavins such as FAD can
exist in oxidized, semiquinone (one-electron reduced),
or fully reduced hydroquinone forms, FNR can interact
with one and two electron carriers. FNR has a strong
preference for NADP(H) vs NAD(H).
Length = 220
Score = 27.4 bits (61), Expect = 5.3
Identities = 17/69 (24%), Positives = 29/69 (42%), Gaps = 14/69 (20%)
Query: 2 WTLS-----HDRLGQFSLTTKGHGECVKFVRDLN-------VPLLVLGGGGLGQFSLTTK 49
+T+S +F +T + G F+ + + + VLG G G+F+L+
Sbjct: 63 FTVSSAPPHDPATDEFEITVRKKGPVTGFLFQVARRLREQGLEVPVLGVG--GEFTLSLP 120
Query: 50 GHGECVKFV 58
G G K V
Sbjct: 121 GEGAERKMV 129
Score = 27.0 bits (60), Expect = 7.7
Identities = 11/46 (23%), Positives = 19/46 (41%), Gaps = 8/46 (17%)
Query: 42 GQFSLTTKGHGECVKFVRDLN-------VPLLVLG-GGGYTLRNVA 79
+F +T + G F+ + + + VLG GG +TL
Sbjct: 76 DEFEITVRKKGPVTGFLFQVARRLREQGLEVPVLGVGGEFTLSLPG 121
>gnl|CDD|182105 PRK09840, PRK09840, catecholate siderophore receptor Fiu;
Provisional.
Length = 761
Score = 27.8 bits (62), Expect = 5.3
Identities = 11/34 (32%), Positives = 14/34 (41%), Gaps = 1/34 (2%)
Query: 173 PDIKNPQLEEDKRVDPANEFYDGDNDQDAPDTEM 206
P L +VD N FY D+D D T+
Sbjct: 277 PSAGRAALNHAGKVDTHN-FYGTDSDYDDSTTDT 309
>gnl|CDD|221109 pfam11428, DUF3196, Protein of unknown function (DUF3196). This
proteins is the product of the gene MPN330 and is
thought to involved in a cellular function that has yet
to be characterized. The proteins has 11 helices and a
novel fold. No function is currently known for this
protein.
Length = 286
Score = 27.1 bits (60), Expect = 6.5
Identities = 14/60 (23%), Positives = 26/60 (43%), Gaps = 8/60 (13%)
Query: 90 VNEEISNDIPDSLYKDFF--QPDYNLHP------EFVHKHDNANSKQYLELITKTVYDNL 141
E +N+I D+L +F PD+N++ ++V Y + I K + D +
Sbjct: 221 SLLEFANEIIDALLVYYFPLHPDHNVNLLAKKIIQYVKNIVENEVVNYKDEIIKLIVDTI 280
>gnl|CDD|235724 PRK06178, PRK06178, acyl-CoA synthetase; Validated.
Length = 567
Score = 27.3 bits (61), Expect = 6.9
Identities = 8/27 (29%), Positives = 14/27 (51%)
Query: 4 LSHDRLGQFSLTTKGHGECVKFVRDLN 30
+ H R ++ L++ V FV+ LN
Sbjct: 314 MDHPRFAEYDLSSLRQVRVVSFVKKLN 340
>gnl|CDD|179614 PRK03633, PRK03633, putative MFS family transporter protein;
Provisional.
Length = 381
Score = 26.9 bits (60), Expect = 8.9
Identities = 10/22 (45%), Positives = 12/22 (54%)
Query: 65 LLVLGGGGYTLRNVARCWTYET 86
L +LG G+TL VA W E
Sbjct: 292 LFILGAAGFTLYPVAMAWACEK 313
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 0.139 0.427
Gapped
Lambda K H
0.267 0.0624 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,034,576
Number of extensions: 1041275
Number of successful extensions: 1011
Number of sequences better than 10.0: 1
Number of HSP's gapped: 996
Number of HSP's successfully gapped: 51
Length of query: 213
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 120
Effective length of database: 6,812,680
Effective search space: 817521600
Effective search space used: 817521600
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: 57 (26.0 bits)