RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1924
(265 letters)
>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 = 272 bits (698), Expect = 1e-91
Identities = 100/119 (84%), Positives = 108/119 (90%)
Query: 25 NVGEDCPVFDGLYEFCQLSAGGSVAAAVKLNKQASEICINWGGGLHHAKKSEASGFCYVN 84
NVGEDCPVFDGLYE+CQL AGGS+AAAVKLN+ ++I INW GGLHHAKKSEASGFCYVN
Sbjct: 82 NVGEDCPVFDGLYEYCQLYAGGSIAAAVKLNRGQADIAINWAGGLHHAKKSEASGFCYVN 141
Query: 85 DIVLGILELLKYHQRVLYIDVDVHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRD 143
DIVL ILELLKYHQRVLYID+D+HHGDGVEEAFYTTDRVMTVSFHK+GEYF LRD
Sbjct: 142 DIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKFGEYFFPGTGLRD 200
Score = 190 bits (485), Expect = 2e-59
Identities = 71/84 (84%), Positives = 78/84 (92%)
Query: 182 NVGEDCPVFDGLYEFCQLSAGGSVAAAVKLNKQASEICINWGGGLHHAKKSEASGFCYVN 241
NVGEDCPVFDGLYE+CQL AGGS+AAAVKLN+ ++I INW GGLHHAKKSEASGFCYVN
Sbjct: 82 NVGEDCPVFDGLYEYCQLYAGGSIAAAVKLNRGQADIAINWAGGLHHAKKSEASGFCYVN 141
Query: 242 DIVLGILELLKYHQRVLYIDVDVH 265
DIVL ILELLKYHQRVLYID+D+H
Sbjct: 142 DIVLAILELLKYHQRVLYIDIDIH 165
>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 = 246 bits (630), Expect = 2e-80
Identities = 98/119 (82%), Positives = 109/119 (91%)
Query: 25 NVGEDCPVFDGLYEFCQLSAGGSVAAAVKLNKQASEICINWGGGLHHAKKSEASGFCYVN 84
NVG+DCPVFDGL+EFC +SAGGS+ A +LN+ +I +NW GGLHHAKKSEASGFCYVN
Sbjct: 88 NVGDDCPVFDGLFEFCSISAGGSMEGAARLNRGKCDIAVNWAGGLHHAKKSEASGFCYVN 147
Query: 85 DIVLGILELLKYHQRVLYIDVDVHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRD 143
DIVLGILELL+YHQRVLYID+DVHHGDGVEEAFYTTDRVMT SFHKYGEYFPGTG+LRD
Sbjct: 148 DIVLGILELLRYHQRVLYIDIDVHHGDGVEEAFYTTDRVMTCSFHKYGEYFPGTGELRD 206
Score = 165 bits (419), Expect = 6e-49
Identities = 65/84 (77%), Positives = 75/84 (89%)
Query: 182 NVGEDCPVFDGLYEFCQLSAGGSVAAAVKLNKQASEICINWGGGLHHAKKSEASGFCYVN 241
NVG+DCPVFDGL+EFC +SAGGS+ A +LN+ +I +NW GGLHHAKKSEASGFCYVN
Sbjct: 88 NVGDDCPVFDGLFEFCSISAGGSMEGAARLNRGKCDIAVNWAGGLHHAKKSEASGFCYVN 147
Query: 242 DIVLGILELLKYHQRVLYIDVDVH 265
DIVLGILELL+YHQRVLYID+DVH
Sbjct: 148 DIVLGILELLRYHQRVLYIDIDVH 171
>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 = 236 bits (604), Expect = 1e-76
Identities = 108/120 (90%), Positives = 116/120 (96%)
Query: 25 NVGEDCPVFDGLYEFCQLSAGGSVAAAVKLNKQASEICINWGGGLHHAKKSEASGFCYVN 84
NVGEDCPVFDGL+EFCQLSAGGSVA+AVKLNKQ ++I +NW GGLHHAKKSEASGFCYVN
Sbjct: 92 NVGEDCPVFDGLFEFCQLSAGGSVASAVKLNKQQTDIAVNWAGGLHHAKKSEASGFCYVN 151
Query: 85 DIVLGILELLKYHQRVLYIDVDVHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDM 144
DIVL ILELLKYHQRVLYID+D+HHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRD+
Sbjct: 152 DIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDI 211
Score = 161 bits (407), Expect = 3e-47
Identities = 73/84 (86%), Positives = 80/84 (95%)
Query: 182 NVGEDCPVFDGLYEFCQLSAGGSVAAAVKLNKQASEICINWGGGLHHAKKSEASGFCYVN 241
NVGEDCPVFDGL+EFCQLSAGGSVA+AVKLNKQ ++I +NW GGLHHAKKSEASGFCYVN
Sbjct: 92 NVGEDCPVFDGLFEFCQLSAGGSVASAVKLNKQQTDIAVNWAGGLHHAKKSEASGFCYVN 151
Query: 242 DIVLGILELLKYHQRVLYIDVDVH 265
DIVL ILELLKYHQRVLYID+D+H
Sbjct: 152 DIVLAILELLKYHQRVLYIDIDIH 175
>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 = 234 bits (600), Expect = 7e-76
Identities = 87/121 (71%), Positives = 101/121 (83%), Gaps = 1/121 (0%)
Query: 25 NVGEDCPVFDGLYEFCQLSAGGSVAAAVKLNKQASEICINWGGGLHHAKKSEASGFCYVN 84
NVG+DCPVF GL++FC + G S+ A KLN + +I INW GGLHHAKK EASGFCYVN
Sbjct: 87 NVGDDCPVFPGLFDFCSMYTGASLEGATKLNHKICDIAINWSGGLHHAKKFEASGFCYVN 146
Query: 85 DIVLGILELLKYHQRVLYIDVDVHHGDGVEEAFYTTDRVMTVSFHKYGEY-FPGTGDLRD 143
DIV+ ILELLKYH RVLYID+D+HHGDGV+EAFY TDRVMTVSFHKYG Y FPGTGD+ +
Sbjct: 147 DIVIAILELLKYHPRVLYIDIDIHHGDGVQEAFYLTDRVMTVSFHKYGNYFFPGTGDMYE 206
Query: 144 M 144
+
Sbjct: 207 V 207
Score = 163 bits (414), Expect = 4e-48
Identities = 58/84 (69%), Positives = 68/84 (80%)
Query: 182 NVGEDCPVFDGLYEFCQLSAGGSVAAAVKLNKQASEICINWGGGLHHAKKSEASGFCYVN 241
NVG+DCPVF GL++FC + G S+ A KLN + +I INW GGLHHAKK EASGFCYVN
Sbjct: 87 NVGDDCPVFPGLFDFCSMYTGASLEGATKLNHKICDIAINWSGGLHHAKKFEASGFCYVN 146
Query: 242 DIVLGILELLKYHQRVLYIDVDVH 265
DIV+ ILELLKYH RVLYID+D+H
Sbjct: 147 DIVIAILELLKYHPRVLYIDIDIH 170
>gnl|CDD|240251 PTZ00063, PTZ00063, histone deacetylase; Provisional.
Length = 436
Score = 228 bits (583), Expect = 9e-73
Identities = 91/122 (74%), Positives = 105/122 (86%), Gaps = 2/122 (1%)
Query: 25 NVGE--DCPVFDGLYEFCQLSAGGSVAAAVKLNKQASEICINWGGGLHHAKKSEASGFCY 82
NVGE DCPVFDGL+EF Q AG S+ A KLN ++IC+NW GGLHHAK+SEASGFCY
Sbjct: 90 NVGEATDCPVFDGLFEFQQSCAGASIDGAYKLNNHQADICVNWSGGLHHAKRSEASGFCY 149
Query: 83 VNDIVLGILELLKYHQRVLYIDVDVHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLR 142
+NDIVLGILELLKYH RV+YID+DVHHGDGVEEAFY T RVMTVSFHK+G++FPGTGD+
Sbjct: 150 INDIVLGILELLKYHARVMYIDIDVHHGDGVEEAFYVTHRVMTVSFHKFGDFFPGTGDVT 209
Query: 143 DM 144
D+
Sbjct: 210 DI 211
Score = 157 bits (398), Expect = 2e-45
Identities = 63/86 (73%), Positives = 72/86 (83%), Gaps = 2/86 (2%)
Query: 182 NVGE--DCPVFDGLYEFCQLSAGGSVAAAVKLNKQASEICINWGGGLHHAKKSEASGFCY 239
NVGE DCPVFDGL+EF Q AG S+ A KLN ++IC+NW GGLHHAK+SEASGFCY
Sbjct: 90 NVGEATDCPVFDGLFEFQQSCAGASIDGAYKLNNHQADICVNWSGGLHHAKRSEASGFCY 149
Query: 240 VNDIVLGILELLKYHQRVLYIDVDVH 265
+NDIVLGILELLKYH RV+YID+DVH
Sbjct: 150 INDIVLGILELLKYHARVMYIDIDVH 175
>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 = 223 bits (571), Expect = 2e-72
Identities = 93/124 (75%), Positives = 104/124 (83%), Gaps = 1/124 (0%)
Query: 23 PVNVGEDCPVFDGLYEFCQLSAGGSVAAAVKLNKQASEICINWGGGLHHAKKSEASGFCY 82
P N+G+DCPVFDG+Y++CQL AG S+ AA KL S+I INW GGLHHAKKSEASGFCY
Sbjct: 84 PFNIGDDCPVFDGMYDYCQLYAGASLDAARKLCSGQSDIAINWSGGLHHAKKSEASGFCY 143
Query: 83 VNDIVLGILELLKYHQRVLYIDVDVHHGDGVEEAFYTTDRVMTVSFHKY-GEYFPGTGDL 141
VNDIVL IL LL+Y RVLYID+DVHHGDGVEEAFY TDRVMT+SFHKY GE+FPGTGDL
Sbjct: 144 VNDIVLAILNLLRYFPRVLYIDIDVHHGDGVEEAFYRTDRVMTLSFHKYNGEFFPGTGDL 203
Query: 142 RDME 145
D
Sbjct: 204 DDNG 207
Score = 154 bits (392), Expect = 2e-45
Identities = 62/86 (72%), Positives = 71/86 (82%)
Query: 180 PVNVGEDCPVFDGLYEFCQLSAGGSVAAAVKLNKQASEICINWGGGLHHAKKSEASGFCY 239
P N+G+DCPVFDG+Y++CQL AG S+ AA KL S+I INW GGLHHAKKSEASGFCY
Sbjct: 84 PFNIGDDCPVFDGMYDYCQLYAGASLDAARKLCSGQSDIAINWSGGLHHAKKSEASGFCY 143
Query: 240 VNDIVLGILELLKYHQRVLYIDVDVH 265
VNDIVL IL LL+Y RVLYID+DVH
Sbjct: 144 VNDIVLAILNLLRYFPRVLYIDIDVH 169
>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 = 215 bits (549), Expect = 2e-68
Identities = 105/120 (87%), Positives = 114/120 (95%)
Query: 25 NVGEDCPVFDGLYEFCQLSAGGSVAAAVKLNKQASEICINWGGGLHHAKKSEASGFCYVN 84
NVGEDCPVFDGL+EFCQLS GGSVA AVKLN+Q +++ +NW GGLHHAKKSEASGFCYVN
Sbjct: 88 NVGEDCPVFDGLFEFCQLSTGGSVAGAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVN 147
Query: 85 DIVLGILELLKYHQRVLYIDVDVHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDM 144
DIVL ILELLKYHQRVLYID+D+HHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRD+
Sbjct: 148 DIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDI 207
Score = 160 bits (406), Expect = 3e-47
Identities = 70/84 (83%), Positives = 78/84 (92%)
Query: 182 NVGEDCPVFDGLYEFCQLSAGGSVAAAVKLNKQASEICINWGGGLHHAKKSEASGFCYVN 241
NVGEDCPVFDGL+EFCQLS GGSVA AVKLN+Q +++ +NW GGLHHAKKSEASGFCYVN
Sbjct: 88 NVGEDCPVFDGLFEFCQLSTGGSVAGAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVN 147
Query: 242 DIVLGILELLKYHQRVLYIDVDVH 265
DIVL ILELLKYHQRVLYID+D+H
Sbjct: 148 DIVLAILELLKYHQRVLYIDIDIH 171
>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 = 180 bits (460), Expect = 4e-55
Identities = 68/121 (56%), Positives = 89/121 (73%), Gaps = 1/121 (0%)
Query: 24 VNVGEDCPVFDGLYEFCQLSAGGSVAAAVKLNKQASEICINWGGGLHHAKKSEASGFCYV 83
+G DCP+F+G+Y++ AG ++ AA L ++ INW GG HHA++ EASGFCYV
Sbjct: 83 FGLGYDCPIFEGIYDYAAAVAGATLTAAQLLIDGKCKVAINWFGGWHHAQRDEASGFCYV 142
Query: 84 NDIVLGILELLKYHQRVLYIDVDVHHGDGVEEAFYTTDRVMTVSFHKYGE-YFPGTGDLR 142
NDIVLGIL+L + RVLY+D+D+HHGDGVE+AF T +VMTVS HKY +FPGTGD+
Sbjct: 143 NDIVLGILKLREKFDRVLYVDLDLHHGDGVEDAFSFTSKVMTVSLHKYSPGFFPGTGDVS 202
Query: 143 D 143
D
Sbjct: 203 D 203
Score = 124 bits (313), Expect = 2e-33
Identities = 44/85 (51%), Positives = 61/85 (71%)
Query: 181 VNVGEDCPVFDGLYEFCQLSAGGSVAAAVKLNKQASEICINWGGGLHHAKKSEASGFCYV 240
+G DCP+F+G+Y++ AG ++ AA L ++ INW GG HHA++ EASGFCYV
Sbjct: 83 FGLGYDCPIFEGIYDYAAAVAGATLTAAQLLIDGKCKVAINWFGGWHHAQRDEASGFCYV 142
Query: 241 NDIVLGILELLKYHQRVLYIDVDVH 265
NDIVLGIL+L + RVLY+D+D+H
Sbjct: 143 NDIVLGILKLREKFDRVLYVDLDLH 167
>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 = 162 bits (413), Expect = 4e-49
Identities = 64/162 (39%), Positives = 80/162 (49%), Gaps = 17/162 (10%)
Query: 21 SFPVNVGEDCPVFDGLYEFCQLSAGGSVAAAVKLNKQASEICINW-GGGLHHAKKSEASG 79
S PV G + PV + +LS GG V AA + K E G G HHA KS A G
Sbjct: 55 SKPVIFGPNFPVQRHYFRGARLSTGGVVEAAELVAKGELERAFAVVGAGGHHAGKSRAWG 114
Query: 80 FCYVNDIVLGILELLKY-HQRVLYIDVDVHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGT 138
FCY ND+VL I L + R+L ID D HHGDG EAFY DRV+ +SFH Y Y G
Sbjct: 115 FCYFNDVVLAIKFLRERGISRILIIDTDAHHGDGTREAFYDDDRVLHMSFHNYDIYPFGR 174
Query: 139 GD-------------LRDMERVEKFNVIESRVM--FTPDFFL 165
G L D E ++ + S+V+ F P+ +
Sbjct: 175 GKGKGYKINVPLEDGLGDEEYLDAVERVISKVLEEFEPEVVV 216
Score = 110 bits (277), Expect = 5e-29
Identities = 39/90 (43%), Positives = 46/90 (51%), Gaps = 2/90 (2%)
Query: 178 SFPVNVGEDCPVFDGLYEFCQLSAGGSVAAAVKLNKQASEICINW-GGGLHHAKKSEASG 236
S PV G + PV + +LS GG V AA + K E G G HHA KS A G
Sbjct: 55 SKPVIFGPNFPVQRHYFRGARLSTGGVVEAAELVAKGELERAFAVVGAGGHHAGKSRAWG 114
Query: 237 FCYVNDIVLGILELLKY-HQRVLYIDVDVH 265
FCY ND+VL I L + R+L ID D H
Sbjct: 115 FCYFNDVVLAIKFLRERGISRILIIDTDAH 144
>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 = 162 bits (413), Expect = 6e-49
Identities = 67/127 (52%), Positives = 83/127 (65%), Gaps = 3/127 (2%)
Query: 29 DCPVFDGLYEFCQLSAGGSVAAAVKLNKQASE-ICINWGGGLHHAKKSEASGFCYVNDIV 87
DCPVF L + QL AG S+A A L Q I INW GG HHA+KS ASGFCYVNDIV
Sbjct: 73 DCPVFPFLSMYVQLVAGSSLALAKHLITQVERDIAINWYGGRHHAQKSRASGFCYVNDIV 132
Query: 88 LGILELLKYH-QRVLYIDVDVHHGDGVEEAFYTTDRVMTVSFHKYGE-YFPGTGDLRDME 145
L IL L + +RV Y+D+D+HHGDGVE AF+ + V+T S H+Y +FPGTG L++
Sbjct: 133 LAILRLRRARFRRVFYLDLDLHHGDGVESAFFFSKNVLTCSIHRYDPGFFPGTGSLKNSS 192
Query: 146 RVEKFNV 152
N+
Sbjct: 193 DKGMLNI 199
Score = 110 bits (277), Expect = 7e-29
Identities = 47/82 (57%), Positives = 55/82 (67%), Gaps = 2/82 (2%)
Query: 186 DCPVFDGLYEFCQLSAGGSVAAAVKLNKQASE-ICINWGGGLHHAKKSEASGFCYVNDIV 244
DCPVF L + QL AG S+A A L Q I INW GG HHA+KS ASGFCYVNDIV
Sbjct: 73 DCPVFPFLSMYVQLVAGSSLALAKHLITQVERDIAINWYGGRHHAQKSRASGFCYVNDIV 132
Query: 245 LGILELLKYH-QRVLYIDVDVH 265
L IL L + +RV Y+D+D+H
Sbjct: 133 LAILRLRRARFRRVFYLDLDLH 154
>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 = 161 bits (409), Expect = 4e-48
Identities = 55/117 (47%), Positives = 71/117 (60%), Gaps = 2/117 (1%)
Query: 27 GEDCPVFDGLYEFCQLSAGGSVAAAVKLNKQASEICINWGGGLHHAKKSEASGFCYVNDI 86
ED PVF G++E L GG++ AA + + + N GGLHHA + ASGFC ND
Sbjct: 84 TEDNPVFPGMHEAAALVVGGTLLAARLVLEGEARRAFNPAGGLHHAMRGRASGFCVYNDA 143
Query: 87 VLGILELL-KYHQRVLYIDVDVHHGDGVEEAFYTTDRVMTVSFHKYGEY-FPGTGDL 141
+ I L K RV Y+D+D HHGDGV+ AFY RV+T+S H+ G Y FPGTG +
Sbjct: 144 AVAIERLRDKGGLRVAYVDIDAHHGDGVQAAFYDDPRVLTISLHESGRYLFPGTGFV 200
Score = 103 bits (260), Expect = 3e-26
Identities = 35/83 (42%), Positives = 46/83 (55%), Gaps = 1/83 (1%)
Query: 184 GEDCPVFDGLYEFCQLSAGGSVAAAVKLNKQASEICINWGGGLHHAKKSEASGFCYVNDI 243
ED PVF G++E L GG++ AA + + + N GGLHHA + ASGFC ND
Sbjct: 84 TEDNPVFPGMHEAAALVVGGTLLAARLVLEGEARRAFNPAGGLHHAMRGRASGFCVYNDA 143
Query: 244 VLGILELL-KYHQRVLYIDVDVH 265
+ I L K RV Y+D+D H
Sbjct: 144 AVAIERLRDKGGLRVAYVDIDAH 166
>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 = 159 bits (405), Expect = 3e-47
Identities = 48/118 (40%), Positives = 65/118 (55%), Gaps = 2/118 (1%)
Query: 25 NVGEDCPVFDGLYEFCQLSAGGSVAAAVKLNKQASEICINWGGGLHHAKKSEASGFCYVN 84
N+ D PV G YE +L+AGG++ A + + HHA + ASGFC N
Sbjct: 80 NLDGDTPVSPGTYEAARLAAGGALTAVDAVLEGEDNAFALVRPPGHHAGRDRASGFCLFN 139
Query: 85 DIVLGILELLK-YHQRVLYIDVDVHHGDGVEEAFYTTDRVMTVSFHKYGEY-FPGTGD 140
++ + LLK +RV ID DVHHG+G +E FY D V+TVS H+ G +PGTG
Sbjct: 140 NVAIAAKYLLKKGVKRVAIIDFDVHHGNGTQEIFYDDDDVLTVSLHQDGRPFYPGTGG 197
Score = 112 bits (281), Expect = 4e-29
Identities = 42/153 (27%), Positives = 66/153 (43%), Gaps = 13/153 (8%)
Query: 126 VSFHKYGEYFP-GTGDLRD-MERVEKFNVIESRVMFTPDFF--LQILIVN-PFFLY---- 176
H+ P LR +E +E + +S + P ++L+V+ P ++
Sbjct: 12 FLEHEPPPGHPENPDRLRLILELLESSGLPDSLELVEPRPATLEELLLVHSPDYVEFLES 71
Query: 177 ---PSFPVNVGEDCPVFDGLYEFCQLSAGGSVAAAVKLNKQASEICINWGGGLHHAKKSE 233
N+ D PV G YE +L+AGG++ A + + HHA +
Sbjct: 72 LSEEEGYGNLDGDTPVSPGTYEAARLAAGGALTAVDAVLEGEDNAFALVRPPGHHAGRDR 131
Query: 234 ASGFCYVNDIVLGILELLK-YHQRVLYIDVDVH 265
ASGFC N++ + LLK +RV ID DVH
Sbjct: 132 ASGFCLFNNVAIAAKYLLKKGVKRVAIIDFDVH 164
>gnl|CDD|240374 PTZ00346, PTZ00346, histone deacetylase; Provisional.
Length = 429
Score = 159 bits (403), Expect = 3e-46
Identities = 71/117 (60%), Positives = 90/117 (76%), Gaps = 1/117 (0%)
Query: 29 DCPVFDGLYEFCQLSAGGSVAAAVKLNKQASEICINWGGGLHHAKKSEASGFCYVNDIVL 88
DCP +GL E +A G++ AV LN ++ ++WGGG+HH+K E SGFCYVNDIVL
Sbjct: 113 DCPPVEGLMEHSIATASGTLMGAVLLNSGQVDVAVHWGGGMHHSKCGECSGFCYVNDIVL 172
Query: 89 GILELLKYHQRVLYIDVDVHHGDGVEEAFYTTDRVMTVSFHKYGE-YFPGTGDLRDM 144
GILELLK H RVLY+D+D+HHGDGV+EAF T+DRV T+S HK+GE +FPGTG RD+
Sbjct: 173 GILELLKCHDRVLYVDIDMHHGDGVDEAFCTSDRVFTLSLHKFGESFFPGTGHPRDV 229
Score = 107 bits (267), Expect = 1e-26
Identities = 46/80 (57%), Positives = 59/80 (73%)
Query: 186 DCPVFDGLYEFCQLSAGGSVAAAVKLNKQASEICINWGGGLHHAKKSEASGFCYVNDIVL 245
DCP +GL E +A G++ AV LN ++ ++WGGG+HH+K E SGFCYVNDIVL
Sbjct: 113 DCPPVEGLMEHSIATASGTLMGAVLLNSGQVDVAVHWGGGMHHSKCGECSGFCYVNDIVL 172
Query: 246 GILELLKYHQRVLYIDVDVH 265
GILELLK H RVLY+D+D+H
Sbjct: 173 GILELLKCHDRVLYVDIDMH 192
>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 = 150 bits (380), Expect = 7e-44
Identities = 48/120 (40%), Positives = 72/120 (60%), Gaps = 6/120 (5%)
Query: 27 GEDCPVFDGLYEFCQLSAGGSVAAAVK-LNKQASEICINWGGGLHHAKKSEASGFCYVND 85
D PV G YE L+AGG++ AA L+ + + + G HHA++ ASGFC N+
Sbjct: 73 DGDTPVSPGSYEAALLAAGGTLEAADLVLSGENAFAAVRPPG--HHAERDRASGFCLFNN 130
Query: 86 IVLGILELLKYH--QRVLYIDVDVHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRD 143
+ + LLK + +RVL +D+DVHHG+G +E FY RV+T+S H+ ++PGTG +
Sbjct: 131 VAIAARYLLKRYGLKRVLIVDLDVHHGNGTQEIFYDDPRVLTISIHQDP-FYPGTGFADE 189
Score = 101 bits (253), Expect = 3e-25
Identities = 33/85 (38%), Positives = 49/85 (57%), Gaps = 5/85 (5%)
Query: 184 GEDCPVFDGLYEFCQLSAGGSVAAAVK-LNKQASEICINWGGGLHHAKKSEASGFCYVND 242
D PV G YE L+AGG++ AA L+ + + + G HHA++ ASGFC N+
Sbjct: 73 DGDTPVSPGSYEAALLAAGGTLEAADLVLSGENAFAAVRPPG--HHAERDRASGFCLFNN 130
Query: 243 IVLGILELLKYH--QRVLYIDVDVH 265
+ + LLK + +RVL +D+DVH
Sbjct: 131 VAIAARYLLKRYGLKRVLIVDLDVH 155
>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 = 92.2 bits (230), Expect = 4e-22
Identities = 39/103 (37%), Positives = 50/103 (48%), Gaps = 8/103 (7%)
Query: 31 PVFDGLYEFCQLSAGGSVAAAVKLNKQASE--ICINWGGGLHHAKKSEASGFCYVNDIVL 88
P L E +L+ GG++ AA + A E + IN GG HHA GFC NDI +
Sbjct: 65 PWSPELVERTRLAVGGTILAA----RLALEHGLAINLAGGTHHAFPDRGEGFCVFNDIAI 120
Query: 89 GILELLKYH--QRVLYIDVDVHHGDGVEEAFYTTDRVMTVSFH 129
LL +RVL +D+DVH G+G F V T S H
Sbjct: 121 AARVLLAEGLVRRVLIVDLDVHQGNGTAAIFADDPSVFTFSMH 163
Score = 72.5 bits (179), Expect = 4e-15
Identities = 32/82 (39%), Positives = 42/82 (51%), Gaps = 8/82 (9%)
Query: 188 PVFDGLYEFCQLSAGGSVAAAVKLNKQASE--ICINWGGGLHHAKKSEASGFCYVNDIVL 245
P L E +L+ GG++ AA + A E + IN GG HHA GFC NDI +
Sbjct: 65 PWSPELVERTRLAVGGTILAA----RLALEHGLAINLAGGTHHAFPDRGEGFCVFNDIAI 120
Query: 246 GILELLKYH--QRVLYIDVDVH 265
LL +RVL +D+DVH
Sbjct: 121 AARVLLAEGLVRRVLIVDLDVH 142
>gnl|CDD|212518 cd09992, HDAC_classII, Histone deacetylases and histone-like
deacetylases, classII. Class II histone deacetylases
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. This group includes animal
HDAC4,5,6,7,8,9,10, fungal HOS3 and HDA1, plant HDA5 and
HDA15 as well as other eukaryotes, archaeal and
bacterial histone-like deacetylases. Eukaryotic
deacetylases mostly use histones (H2, H3, H4) as
substrates for deacetylation; however, non-histone
substrates are known (for example, tubulin). Substrates
for prokaryotic histone-like deacetylases are not known.
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. Interaction partners of class II deacetylases
include 14-3-3 proteins, MEF2 family of transcriptional
factors, CtBP, calmodulin (CaM), SMRT, N-CoR, BCL6,
HP1alpha and SUMO. Histone deacetylases play a role in
the regulation of cell cycle, cell differentiation and
survival. Class II mammalian HDACs are differentially
inhibited by structurally diverse compounds with known
antitumor activities, thus presenting them as potential
drug targets for human diseases resulting from aberrant
acetylation.
Length = 291
Score = 87.9 bits (219), Expect = 2e-20
Identities = 42/122 (34%), Positives = 61/122 (50%), Gaps = 12/122 (9%)
Query: 29 DCPVFDGLYEFCQLSAGGSVAAAVKLNKQASEICINWGGGL-----HHAKKSEASGFCYV 83
D V G YE L+AG ++AA + S N L HHA+ A GFC
Sbjct: 63 DTYVSPGSYEAALLAAGAALAAVDAV---LSGEAEN-AFALVRPPGHHAEPDRAMGFCLF 118
Query: 84 NDIVLGILELLKYH--QRVLYIDVDVHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDL 141
N++ + K + +RVL +D DVHHG+G ++ FY V+ S H+Y ++PGTG
Sbjct: 119 NNVAIAARYAQKRYGLKRVLIVDWDVHHGNGTQDIFYDDPSVLYFSIHQYP-FYPGTGAA 177
Query: 142 RD 143
+
Sbjct: 178 EE 179
Score = 46.3 bits (111), Expect = 6e-06
Identities = 29/87 (33%), Positives = 40/87 (45%), Gaps = 11/87 (12%)
Query: 186 DCPVFDGLYEFCQLSAGGSVAAAVKLNKQASEICINWGGGL-----HHAKKSEASGFCYV 240
D V G YE L+AG ++AA + S N L HHA+ A GFC
Sbjct: 63 DTYVSPGSYEAALLAAGAALAAVDAV---LSGEAEN-AFALVRPPGHHAEPDRAMGFCLF 118
Query: 241 NDIVLGILELLKYH--QRVLYIDVDVH 265
N++ + K + +RVL +D DVH
Sbjct: 119 NNVAIAARYAQKRYGLKRVLIVDWDVH 145
>gnl|CDD|212521 cd09996, HDAC_classII_1, Histone deacetylases and histone-like
deacetylases, classII. This subfamily includes
bacterial as well as eukaryotic 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. Included in this
family is a bacterial HDAC-like amidohydrolase
(Bordetella/Alcaligenes species FB18817, denoted as
FB188 HDAH) shown to be most similar in sequence and
function to class II HDAC6 domain 3 or b (HDAC6b). FB188
HDAH is able to remove the acetyl moiety from acetylated
histones, and can be inhibited by common HDAC inhibitors
such as SAHA (suberoylanilide hydroxamic acid) as well
as class II-specific but not class I specific
inhibitors.
Length = 359
Score = 87.2 bits (217), Expect = 7e-20
Identities = 40/127 (31%), Positives = 61/127 (48%), Gaps = 15/127 (11%)
Query: 26 VGEDCPVFDGLYEFCQLSAGGSVAA--AVKLNKQASEICINWGGGL-----HHAKKSEAS 78
G P G YE L+AGG++AA AV L+ + L HHA+ +
Sbjct: 92 AGGGTPFGPGSYEIALLAAGGAIAAVDAV-LDGEVDN-----AYALVRPPGHHAEPDQGM 145
Query: 79 GFCYVNDIVLGILELLKYH--QRVLYIDVDVHHGDGVEEAFYTTDRVMTVSFHKYGEYFP 136
GFC N++ + L +RV +D DVHHG+G + FY V+T+S H+ + P
Sbjct: 146 GFCLFNNVAIAARHALAVGGVKRVAVVDWDVHHGNGTQAIFYDDPDVLTISLHQDRCFPP 205
Query: 137 GTGDLRD 143
+G + +
Sbjct: 206 DSGAVEE 212
Score = 47.9 bits (115), Expect = 2e-06
Identities = 29/92 (31%), Positives = 41/92 (44%), Gaps = 15/92 (16%)
Query: 183 VGEDCPVFDGLYEFCQLSAGGSVAA--AVKLNKQASEICINWGGGL-----HHAKKSEAS 235
G P G YE L+AGG++AA AV L+ + L HHA+ +
Sbjct: 92 AGGGTPFGPGSYEIALLAAGGAIAAVDAV-LDGEVDN-----AYALVRPPGHHAEPDQGM 145
Query: 236 GFCYVNDIVLGILELLKYH--QRVLYIDVDVH 265
GFC N++ + L +RV +D DVH
Sbjct: 146 GFCLFNNVAIAARHALAVGGVKRVAVVDWDVH 177
>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 = 82.2 bits (204), Expect = 2e-18
Identities = 36/120 (30%), Positives = 53/120 (44%), Gaps = 19/120 (15%)
Query: 29 DCPVFDGLYEFCQLSAGGSVAAAVKLNKQASEICINWGGGL---------HHAKKSEASG 79
D P+ +G +E +A ++ AA + + G HHA + A G
Sbjct: 76 DTPISEGTWEAALAAADTALTAADLVLE---------GERAAYALCRPPGHHAGRDRAGG 126
Query: 80 FCYVNDIVLGILELLKYHQRVLYIDVDVHHGDGVEEAFYTTDRVMTVSFHKYGE-YFPGT 138
FCY N+ + L RV +DVDVHHG+G +E FY V+ VS H ++P
Sbjct: 127 FCYFNNAAIAAQYLRDRAGRVAILDVDVHHGNGTQEIFYERPDVLYVSIHGDPRTFYPFF 186
Score = 49.8 bits (120), Expect = 4e-07
Identities = 25/89 (28%), Positives = 37/89 (41%), Gaps = 18/89 (20%)
Query: 186 DCPVFDGLYEFCQLSAGGSVAAAVKLNKQASEICINWGGGL---------HHAKKSEASG 236
D P+ +G +E +A ++ AA + + G HHA + A G
Sbjct: 76 DTPISEGTWEAALAAADTALTAADLVLE---------GERAAYALCRPPGHHAGRDRAGG 126
Query: 237 FCYVNDIVLGILELLKYHQRVLYIDVDVH 265
FCY N+ + L RV +DVDVH
Sbjct: 127 FCYFNNAAIAAQYLRDRAGRVAILDVDVH 155
>gnl|CDD|212541 cd11599, HDAC_classII_2, Histone deacetylases and histone-like
deacetylases, classII. This subfamily includes
eukaryotic as well as bacterial 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. In D. discoideum,
where four homologs (HdaA, HdaB, HdaC, HdaD) have been
identified, HDAC activity is important for regulating
the timing of gene expression during development. Also,
inhibition of HDAC activity by trichostatin A is shown
to cause hyperacetylation of the histone and a delay in
cell aggregation and differentiation.
Length = 288
Score = 78.7 bits (195), Expect = 4e-17
Identities = 29/79 (36%), Positives = 45/79 (56%), Gaps = 3/79 (3%)
Query: 70 HHAKKSEASGFCYVNDIVLGILELLKYH--QRVLYIDVDVHHGDGVEEAFYTTDRVMTVS 127
HHA++ +A GFC N++ + L +H +RV +D DVHHG+G E+ F RV+ S
Sbjct: 106 HHAERDKAMGFCLFNNVAIAAAHALAHHGLERVAIVDFDVHHGNGTEDIFRDDPRVLFCS 165
Query: 128 FHKYGEYFPGTGDLRDMER 146
H++ +PGTG +
Sbjct: 166 SHQH-PLYPGTGAPDETGH 183
Score = 45.6 bits (109), Expect = 9e-06
Identities = 16/41 (39%), Positives = 25/41 (60%), Gaps = 2/41 (4%)
Query: 227 HHAKKSEASGFCYVNDIVLGILELLKYH--QRVLYIDVDVH 265
HHA++ +A GFC N++ + L +H +RV +D DVH
Sbjct: 106 HHAERDKAMGFCLFNNVAIAAAHALAHHGLERVAIVDFDVH 146
>gnl|CDD|212544 cd11681, HDAC_classIIa, Histone deacetylases, class IIa. Class IIa
histone deacetylases are Zn-dependent enzymes that
catalyze hydrolysis of N(6)-acetyl-lysine residues of
histones (EC 3.5.1.98) to yield deacetylated histones.
This subclass includes animal HDAC4, HDAC5, HDAC7, and
HDCA9. 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. Class IIa histone deacetylases are
signal-dependent co-repressors, they have N-terminal
regulatory domain with two or three conserved serine
residues, phosphorylation of these residues is important
for ability to shuttle between the nucleus and cytoplasm
and act as transcriptional co-repressors. HDAC9 is
involved in regulation of gene expression and dendritic
growth in developing cortical neurons. It also plays a
role in hematopoiesis. HDAC7 is involved in regulation
of myocyte migration and differentiation. HDAC5 is
involved in integration of chronic drug (cocaine)
addiction and depression with changes in chromatin
structure and gene expression. HDAC4 participates in
regulation of chondrocyte hypertrophy and
skeletogenesis.
Length = 377
Score = 78.2 bits (193), Expect = 1e-16
Identities = 30/75 (40%), Positives = 47/75 (62%), Gaps = 4/75 (5%)
Query: 70 HHAKKSEASGFCYVNDIVLG--ILELLKYHQRVLYIDVDVHHGDGVEEAFYTTDRVMTVS 127
HHA+ S+A GFC+ N + + L+ +++L +D DVHHG+G ++ FY V+ +S
Sbjct: 151 HHAEPSQAMGFCFFNSVAIAAKQLQQKLKLRKILIVDWDVHHGNGTQQIFYEDPNVLYIS 210
Query: 128 FHKY--GEYFPGTGD 140
H+Y G +FPGTG
Sbjct: 211 LHRYDDGNFFPGTGA 225
Score = 40.8 bits (96), Expect = 4e-04
Identities = 15/41 (36%), Positives = 25/41 (60%), Gaps = 2/41 (4%)
Query: 227 HHAKKSEASGFCYVNDIVLG--ILELLKYHQRVLYIDVDVH 265
HHA+ S+A GFC+ N + + L+ +++L +D DVH
Sbjct: 151 HHAEPSQAMGFCFFNSVAIAAKQLQQKLKLRKILIVDWDVH 191
>gnl|CDD|212527 cd10003, HDAC6-dom2, Histone deacetylase 6, domain 2. Histone
deacetylase 6 is a class IIb Zn-dependent 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. HDACs usually act via association with DNA
binding proteins to target specific chromatin regions.
HDAC6 is the only histone deacetylase with internal
duplication of two catalytic domains which appear to
function independently of each other, and also has a
C-terminal ubiquitin-binding domain. It is located in
the cytoplasm and associates with microtubule motor
complex, functioning as the tubulin deacetylase and
regulating microtubule-dependent cell motility. Known
interaction partners of HDAC6 are alpha tubulin and
ubiquitin-like modifier FAT10 (also known as Ubiquitin D
or UBD).
Length = 350
Score = 72.0 bits (177), Expect = 1e-14
Identities = 35/108 (32%), Positives = 57/108 (52%), Gaps = 8/108 (7%)
Query: 40 CQLSAGGSVAAAVKL---NKQASEICINWGGGLHHAKKSEASGFCYVNDIVLGI-LELLK 95
C L A G V V+ + + + I G HHA++ A GFC+ N++ + K
Sbjct: 94 CALLAAGCVLQVVEAVLTGESRNGVAIVRPPG-HHAEQDTACGFCFFNNVAIAARYAQKK 152
Query: 96 YH-QRVLYIDVDVHHGDGVEEAFYTTDRVMTVSFHKY--GEYFPGTGD 140
Y +R+L +D DVHHG+G + F + V+ +S H+Y G +FP + +
Sbjct: 153 YGLKRILIVDWDVHHGNGTQHMFESDPSVLYISLHRYDNGSFFPNSPE 200
Score = 42.7 bits (101), Expect = 1e-04
Identities = 24/74 (32%), Positives = 37/74 (50%), Gaps = 6/74 (8%)
Query: 197 CQLSAGGSVAAAVKL---NKQASEICINWGGGLHHAKKSEASGFCYVNDIVLGI-LELLK 252
C L A G V V+ + + + I G HHA++ A GFC+ N++ + K
Sbjct: 94 CALLAAGCVLQVVEAVLTGESRNGVAIVRPPG-HHAEQDTACGFCFFNNVAIAARYAQKK 152
Query: 253 YH-QRVLYIDVDVH 265
Y +R+L +D DVH
Sbjct: 153 YGLKRILIVDWDVH 166
>gnl|CDD|212530 cd10006, HDAC4, Histone deacetylase 4. Histone deacetylase 4 is a
class IIa Zn-dependent enzyme 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. Class IIa histone deacetylases are
signal-dependent co-repressors, having N-terminal
regulatory domain with two or three conserved serine
residues; phosphorylation of these residues is important
for ability to shuttle between the nucleus and cytoplasm
and act as transcriptional co-repressors. HDAC4
participates in regulation of chondrocyte hypertrophy
and skeletogenesis. However, biological substrates for
HDAC4 have not been identified; only low lysine
deacetylation activity has been demonstrated and active
site mutant has enhanced activity toward acetylated
lysines. HDAC4 does not bind DNA directly, but through
transcription factors MEF2C (myocyte enhancer factor-2C)
and MEF2D. Other known interaction partners of the
protein are 14-3-3 proteins, SMRT and N-CoR
co-repressors, BCL6, HP1, SUMO-1 ubiquitin-like protein,
and ANKRA2. It appears to interact in a multiprotein
complex with RbAp48 and HDAC3. Furthermore, HDAC4 is
required for TGFbeta1-induced myofibroblastic
differentiation.
Length = 409
Score = 70.5 bits (172), Expect = 6e-14
Identities = 30/74 (40%), Positives = 48/74 (64%), Gaps = 4/74 (5%)
Query: 70 HHAKKSEASGFCYVNDIVLG--ILELLKYHQRVLYIDVDVHHGDGVEEAFYTTDRVMTVS 127
HHA++S GFCY N + + +L+ ++L +D DVHHG+G ++AFY+ V+ +S
Sbjct: 154 HHAEESTPMGFCYFNSVAIAAKLLQQRLNVSKILIVDWDVHHGNGTQQAFYSDPNVLYMS 213
Query: 128 FHKY--GEYFPGTG 139
H+Y G +FPG+G
Sbjct: 214 LHRYDDGNFFPGSG 227
Score = 33.9 bits (77), Expect = 0.085
Identities = 15/41 (36%), Positives = 24/41 (58%), Gaps = 2/41 (4%)
Query: 227 HHAKKSEASGFCYVNDIVLG--ILELLKYHQRVLYIDVDVH 265
HHA++S GFCY N + + +L+ ++L +D DVH
Sbjct: 154 HHAEESTPMGFCYFNSVAIAAKLLQQRLNVSKILIVDWDVH 194
>gnl|CDD|212531 cd10007, HDAC5, Histone deacetylase 5. Histone deacetylase 5 is a
class IIa Zn-dependent enzyme 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. Class IIa histone deacetylases are
signal-dependent co-repressors, having N-terminal
regulatory domain with two or three conserved serine
residues; phosphorylation of these residues is important
for ability to shuttle between the nucleus and cytoplasm
and act as transcriptional co-repressors. HDAC5 is
involved in integration of chronic drug (cocaine)
addiction and depression with changes in chromatin
structure and gene expression; cocaine regulates HDAC5
function to antagonize the rewarding impact of cocaine,
possibly by blocking drug-stimulated gene expression
that supports drug-induced behavioral change. It is also
involved in regulation of angiogenesis and cell cycle as
well as immune system development. HDAC5 and HDAC9 have
been found to be significantly up-regulated in high-risk
medulloblastoma compared with low-risk and may
potentially be novel drug targets.
Length = 420
Score = 70.4 bits (172), Expect = 7e-14
Identities = 30/75 (40%), Positives = 49/75 (65%), Gaps = 6/75 (8%)
Query: 70 HHAKKSEASGFCYVNDIVLGILELLKYH---QRVLYIDVDVHHGDGVEEAFYTTDRVMTV 126
HHA++S A GFC+ N + + +LL+ ++L +D D+HHG+G ++AFY V+ +
Sbjct: 154 HHAEESTAMGFCFFNSVAIAA-KLLQQKLNVGKILIVDWDIHHGNGTQQAFYNDPNVLYI 212
Query: 127 SFHKY--GEYFPGTG 139
S H+Y G +FPG+G
Sbjct: 213 SLHRYDDGNFFPGSG 227
Score = 33.4 bits (76), Expect = 0.097
Identities = 15/42 (35%), Positives = 26/42 (61%), Gaps = 4/42 (9%)
Query: 227 HHAKKSEASGFCYVNDIVLGILELLKYH---QRVLYIDVDVH 265
HHA++S A GFC+ N + + +LL+ ++L +D D+H
Sbjct: 154 HHAEESTAMGFCFFNSVAIAA-KLLQQKLNVGKILIVDWDIH 194
>gnl|CDD|212542 cd11600, HDAC_Clr3, Class II Histone deacetylase Clr3 and similar
proteins. Clr3 is a class II Histone deacetylase
Zn-dependent enzyme that catalyzes hydrolysis of an
N(6)-acetyl-lysine residue of a histone to yield a
deacetylated histone (EC 3.5.1.98). Clr3 is the homolog
of the class-II HDAC HdaI in S. cerevisiae, and is
essential for silencing in heterochromatin regions, such
as centromeric regions, ribosomal DNA, the mating-type
region and telomeric loci. Clr3 has also been implicated
in the regulation of stress-related genes; the histone
acetyltransferase, Gcn5, in S. cerevisiae,
preferentially acetylates global histone H3K14 while
Clr3 preferentially deacetylates H3K14ac, and therefore,
interplay between Gcn5 and Clr3 is crucial for the
regulation of many stress-response genes.
Length = 313
Score = 69.3 bits (170), Expect = 1e-13
Identities = 43/128 (33%), Positives = 68/128 (53%), Gaps = 16/128 (12%)
Query: 39 FC-QLSAGGSVAA--AVKLNKQASEICINWGGGLHHAKKSEASGFCYVNDIVLGILELLK 95
FC +LS GG++ A AV + + + G HHA+ E+ GFC+ N++ + L
Sbjct: 82 FCARLSCGGAIEACRAVAEGRVKNAFAVVRPPG-HHAEPDESMGFCFFNNVAVAAKWLQT 140
Query: 96 -YH---QRVLYIDVDVHHGDGVEEAFYTTDRVMTVSFHKY--GEYFPGTGDLRDMERV-- 147
Y +++L +D D+HHG+G + AFY V+ +S H++ G ++PGT D E V
Sbjct: 141 EYPDKIKKILILDWDIHHGNGTQRAFYDDPNVLYISLHRFENGGFYPGT-PYGDYESVGE 199
Query: 148 ---EKFNV 152
FNV
Sbjct: 200 GAGLGFNV 207
Score = 35.0 bits (81), Expect = 0.027
Identities = 24/77 (31%), Positives = 41/77 (53%), Gaps = 8/77 (10%)
Query: 196 FC-QLSAGGSVAA--AVKLNKQASEICINWGGGLHHAKKSEASGFCYVNDIVLGILELLK 252
FC +LS GG++ A AV + + + G HHA+ E+ GFC+ N++ + L
Sbjct: 82 FCARLSCGGAIEACRAVAEGRVKNAFAVVRPPG-HHAEPDESMGFCFFNNVAVAAKWLQT 140
Query: 253 -YH---QRVLYIDVDVH 265
Y +++L +D D+H
Sbjct: 141 EYPDKIKKILILDWDIH 157
>gnl|CDD|212533 cd10009, HDAC9, Histone deacetylase 9. Histone deacetylase 9 is a
class IIa Zn-dependent enzyme 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. Class IIa histone deacetylases are
signal-dependent co-repressors, they have N-terminal
regulatory domain with two or three conserved serine
residues, phosphorylation of these residues is important
for ability to shuttle between the nucleus and cytoplasm
and act as transcriptional co-repressors. HDAC9 is
involved in regulation of gene expression and dendritic
growth in developing cortical neurons. It also plays a
role in hematopoiesis. Its deregulated expression may be
associated with some human cancers. HDAC5 and HDAC9 have
been found to be significantly up-regulated in high-risk
medulloblastoma compared with low-risk and may
potentially be novel drug targets.
Length = 379
Score = 69.3 bits (169), Expect = 1e-13
Identities = 30/78 (38%), Positives = 49/78 (62%), Gaps = 12/78 (15%)
Query: 70 HHAKKSEASGFCYVNDIVLGILELLKYHQ------RVLYIDVDVHHGDGVEEAFYTTDRV 123
HHA++S A GFC+ N + + KY + ++L +D+DVHHG+G ++AFY +
Sbjct: 152 HHAEESTAMGFCFFNSVAI----TAKYLRDQLNISKILIVDLDVHHGNGTQQAFYADPSI 207
Query: 124 MTVSFHKY--GEYFPGTG 139
+ +S H+Y G +FPG+G
Sbjct: 208 LYISLHRYDEGNFFPGSG 225
Score = 33.5 bits (76), Expect = 0.10
Identities = 16/45 (35%), Positives = 26/45 (57%), Gaps = 10/45 (22%)
Query: 227 HHAKKSEASGFCYVNDIVLGILELLKYHQ------RVLYIDVDVH 265
HHA++S A GFC+ N + + KY + ++L +D+DVH
Sbjct: 152 HHAEESTAMGFCFFNSVAI----TAKYLRDQLNISKILIVDLDVH 192
>gnl|CDD|212526 cd10002, HDAC10_HDAC6-dom1, Histone deacetylase 6, domain 1 and
histone deacetylase 10. Histone deacetylases 6 and 10
are class IIb Zn-dependent enzymes that catalyze
hydrolysis of N(6)-acetyl-lysine 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.
HDACs usually act via association with DNA binding
proteins to target specific chromatin regions. HDAC6 is
the only histone deacetylase with internal duplication
of two catalytic domains which appear to function
independently of each other, and also has a C-terminal
ubiquitin-binding domain. It is located in the cytoplasm
and associates with microtubule motor complex,
functioning as the tubulin deacetylase and regulating
microtubule-dependent cell motility. HDAC10 has an
N-terminal deacetylase domain and a C-terminal
pseudo-repeat that shares significant similarity with
its catalytic domain. It is located in the nucleus and
cytoplasm, and is involved in regulation of
melanogenesis. It transcriptionally down-regulates
thioredoxin-interacting protein (TXNIP), leading to
altered reactive oxygen species (ROS) signaling in human
gastric cancer cells. Known interaction partners of
HDAC6 are alpha tubulin (substrate) and ubiquitin-like
modifier FAT10 (also known as Ubiquitin D or UBD) while
interaction partners of HDAC10 are Pax3, KAP1, hsc70 and
HDAC3 proteins.
Length = 336
Score = 68.9 bits (169), Expect = 1e-13
Identities = 35/107 (32%), Positives = 59/107 (55%), Gaps = 7/107 (6%)
Query: 37 YEFCQLSAGGSV--AAAVKLNKQASEICINWGGGLHHAKKSEASGFCYVNDIVLGILELL 94
YE +L+AG ++ AV K + + G HHA ++EA+G+C N++ + +
Sbjct: 83 YEAARLAAGSTIELVKAVMAGKIQNGFALIRPPG-HHAMRNEANGYCIFNNVAIAAKYAI 141
Query: 95 KYH--QRVLYIDVDVHHGDGVEEAFYTTDRVMTVSFHKY--GEYFPG 137
+ +R+L +D DVHHG G ++ FY RV+ S H+Y G ++P
Sbjct: 142 EKLGLKRILIVDWDVHHGQGTQQGFYEDPRVLYFSIHRYEHGRFWPH 188
Score = 39.6 bits (93), Expect = 0.001
Identities = 23/76 (30%), Positives = 41/76 (53%), Gaps = 5/76 (6%)
Query: 194 YEFCQLSAGGSV--AAAVKLNKQASEICINWGGGLHHAKKSEASGFCYVNDIVLGILELL 251
YE +L+AG ++ AV K + + G HHA ++EA+G+C N++ + +
Sbjct: 83 YEAARLAAGSTIELVKAVMAGKIQNGFALIRPPG-HHAMRNEANGYCIFNNVAIAAKYAI 141
Query: 252 KYH--QRVLYIDVDVH 265
+ +R+L +D DVH
Sbjct: 142 EKLGLKRILIVDWDVH 157
>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 = 66.2 bits (162), Expect = 4e-13
Identities = 32/160 (20%), Positives = 47/160 (29%), Gaps = 49/160 (30%)
Query: 38 EFCQLSAGGSVAAAVKLNKQASEICINWGGGLHHAKKSEASGFCYVNDIVLGILELLKYH 97
E +L AG VA ++ + GG H+ N + + EL H
Sbjct: 9 EAHELLAGVVVAVLKD-----GKVPVVLGG--DHSI---------ANGAIRAVAEL---H 49
Query: 98 QRVLYIDVDVHHGDGVEEAFY--------------TTDRVMTVSFHKYGEYFPGTG---- 139
+ IDVD HH EAF V VS G G
Sbjct: 50 PDLGVIDVDAHHDVRTPEAFGKGNHHTPRHLLCEPLISDVHIVSIGIRGVSNGEAGGAYA 109
Query: 140 -----------DLRDMERVEKFNVIESRVMFTPDF-FLQI 167
++ + + F I S + D +L +
Sbjct: 110 RKLGVVYFSMTEVDKLGLGDVFEEIVSYLGDKGDNVYLSV 149
Score = 38.1 bits (89), Expect = 0.002
Identities = 18/71 (25%), Positives = 26/71 (36%), Gaps = 19/71 (26%)
Query: 195 EFCQLSAGGSVAAAVKLNKQASEICINWGGGLHHAKKSEASGFCYVNDIVLGILELLKYH 254
E +L AG VA ++ + GG H+ N + + EL H
Sbjct: 9 EAHELLAGVVVAVLKD-----GKVPVVLGG--DHSI---------ANGAIRAVAEL---H 49
Query: 255 QRVLYIDVDVH 265
+ IDVD H
Sbjct: 50 PDLGVIDVDAH 60
>gnl|CDD|212532 cd10008, HDAC7, Histone deacetylase 7. Histone deacetylase 7 is a
class IIa Zn-dependent enzyme 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. Class IIa histone deacetylases are
signal-dependent co-repressors, having N-terminal
regulatory domain with two or three conserved serine
residues; phosphorylation of these residues is important
for ability to shuttle between the nucleus and cytoplasm
and act as transcriptional co-repressors. HDAC7 is
involved in regulation of myocyte migration and
differentiation. Known interaction partners of class IIa
HDAC7 are myocyte enhancer factors - MEF2A, -2C, and
-2D, 14-3-3 proteins, SMRT and N-CoR co-repressors,
HDAC3, ETA (endothelin receptor). This enzyme is also
involved in the development of the immune system as well
as brain and heart development. Multiple alternatively
spliced transcript variants encoding several isoforms
have been found for this gene.
Length = 378
Score = 67.7 bits (165), Expect = 5e-13
Identities = 28/74 (37%), Positives = 44/74 (59%), Gaps = 4/74 (5%)
Query: 70 HHAKKSEASGFCYVNDIVLGI--LELLKYHQRVLYIDVDVHHGDGVEEAFYTTDRVMTVS 127
HHA S A GFC+ N + + L+ ++L +D DVHHG+G ++ FY V+ +S
Sbjct: 152 HHADHSTAMGFCFFNSVAIACRQLQQQGKASKILIVDWDVHHGNGTQQTFYQDPSVLYIS 211
Query: 128 FHKY--GEYFPGTG 139
H++ G +FPG+G
Sbjct: 212 LHRHDDGNFFPGSG 225
Score = 34.6 bits (79), Expect = 0.040
Identities = 15/41 (36%), Positives = 22/41 (53%), Gaps = 2/41 (4%)
Query: 227 HHAKKSEASGFCYVNDIVLGI--LELLKYHQRVLYIDVDVH 265
HHA S A GFC+ N + + L+ ++L +D DVH
Sbjct: 152 HHADHSTAMGFCFFNSVAIACRQLQQQGKASKILIVDWDVH 192
>gnl|CDD|212546 cd11683, HDAC10, Histone deacetylase 10. Histone deacetylases 10
are class IIb Zn-dependent enzymes that catalyze
hydrolysis of N(6)-acetyl-lysine 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.
HDACs usually act via association with DNA binding
proteins to target specific chromatin regions. HDAC10
has an N-terminal deacetylase domain and a C-terminal
pseudo-repeat that shares significant similarity with
its catalytic domain. It is located in the nucleus and
cytoplasm, and is involved in regulation of
melanogenesis. It transcriptionally down-regulates
thioredoxin-interacting protein (TXNIP), leading to
altered reactive oxygen species (ROS) signaling in human
gastric cancer cells. Known interaction partners of
HDAC10 are Pax3, KAP1, hsc70 and HDAC3 proteins.
Length = 337
Score = 56.0 bits (135), Expect = 4e-09
Identities = 23/71 (32%), Positives = 41/71 (57%), Gaps = 4/71 (5%)
Query: 70 HHAKKSEASGFCYVNDIVLGILELLKYH--QRVLYIDVDVHHGDGVEEAFYTTDRVMTVS 127
HH++++ A+GFC N++ + K + R+L +D DVHHG G++ F V+ S
Sbjct: 117 HHSQRNAANGFCVFNNVAIAAEYAKKKYGLHRILIVDWDVHHGQGIQYIFEEDPSVLYFS 176
Query: 128 FHKY--GEYFP 136
+H+Y ++P
Sbjct: 177 WHRYEHQRFWP 187
Score = 37.1 bits (86), Expect = 0.007
Identities = 14/41 (34%), Positives = 25/41 (60%), Gaps = 2/41 (4%)
Query: 227 HHAKKSEASGFCYVNDIVLGILELLKYH--QRVLYIDVDVH 265
HH++++ A+GFC N++ + K + R+L +D DVH
Sbjct: 117 HHSQRNAANGFCVFNNVAIAAEYAKKKYGLHRILIVDWDVH 157
>gnl|CDD|212545 cd11682, HDAC6-dom1, Histone deacetylase 6, domain 1. Histone
deacetylases 6 are class IIb Zn-dependent enzymes that
catalyze hydrolysis of N(6)-acetyl-lysine 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.
HDACs usually act via association with DNA binding
proteins to target specific chromatin regions. HDAC6 is
the only histone deacetylase with internal duplication
of two catalytic domains which appear to function
independently of each other, and also has a C-terminal
ubiquitin-binding domain. It is located in the cytoplasm
and associates with microtubule motor complex,
functioning as the tubulin deacetylase and regulating
microtubule-dependent cell motility. Known interaction
partners of HDAC6 are alpha tubulin (substrate) and
ubiquitin-like modifier FAT10 (also known as Ubiquitin D
or UBD).
Length = 337
Score = 52.2 bits (125), Expect = 7e-08
Identities = 35/105 (33%), Positives = 48/105 (45%), Gaps = 10/105 (9%)
Query: 40 CQLSAGGSVAAAVKLNKQASEIC----INWGGGLHHAKKSEASGFCYVNDIVLGILELLK 95
C A GSV V EI I G HHA+ + G+C N++ + +
Sbjct: 85 CACLAVGSVLQLVD-KVLGGEIRNGLAIVRPPG-HHAQHDKMDGYCMFNNVAIAARYAQQ 142
Query: 96 YH--QRVLYIDVDVHHGDGVEEAFYTTDRVMTVSFHKY--GEYFP 136
H QRVL +D DVHHG G + F V+ S H+Y G ++P
Sbjct: 143 KHGVQRVLIVDWDVHHGQGTQFIFEQDPSVLYFSIHRYEQGRFWP 187
Score = 34.4 bits (79), Expect = 0.050
Identities = 25/75 (33%), Positives = 33/75 (44%), Gaps = 8/75 (10%)
Query: 197 CQLSAGGSVAAAVKLNKQASEIC----INWGGGLHHAKKSEASGFCYVNDIVLGILELLK 252
C A GSV V EI I G HHA+ + G+C N++ + +
Sbjct: 85 CACLAVGSVLQLVD-KVLGGEIRNGLAIVRPPG-HHAQHDKMDGYCMFNNVAIAARYAQQ 142
Query: 253 YH--QRVLYIDVDVH 265
H QRVL +D DVH
Sbjct: 143 KHGVQRVLIVDWDVH 157
>gnl|CDD|212522 cd09998, HDAC_Hos3, Class II histone deacetylases Hos3 and related
proteins. Fungal histone deacetylase Hos3 from
Saccharomyces cerevisiae is a Zn-dependent enzyme
belonging to HDAC class II. It 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. Hos3 deacetylase is homodimer, in vitro it
shows specificity to H4, H3 and H2A.
Length = 353
Score = 49.8 bits (119), Expect = 5e-07
Identities = 19/48 (39%), Positives = 31/48 (64%), Gaps = 2/48 (4%)
Query: 70 HHAKKSEASGFCYVNDIVLGILELLKYH--QRVLYIDVDVHHGDGVEE 115
HH +S SGFC+VN++ +G H RV+ +D+D+HHG+G ++
Sbjct: 120 HHCSESTPSGFCWVNNVHVGAAHAYLTHGITRVVILDIDLHHGNGTQD 167
Score = 38.6 bits (90), Expect = 0.002
Identities = 16/41 (39%), Positives = 25/41 (60%), Gaps = 2/41 (4%)
Query: 227 HHAKKSEASGFCYVNDIVLGILELLKYH--QRVLYIDVDVH 265
HH +S SGFC+VN++ +G H RV+ +D+D+H
Sbjct: 120 HHCSESTPSGFCWVNNVHVGAAHAYLTHGITRVVILDIDLH 160
>gnl|CDD|236972 PRK11761, cysM, cysteine synthase B; Provisional.
Length = 296
Score = 31.4 bits (72), Expect = 0.40
Identities = 9/19 (47%), Positives = 17/19 (89%)
Query: 39 FCQLSAGGSVAAAVKLNKQ 57
FC +S+GG+VAAA+++ ++
Sbjct: 253 FCGVSSGGAVAAALRIARE 271
Score = 31.4 bits (72), Expect = 0.40
Identities = 9/19 (47%), Positives = 17/19 (89%)
Query: 196 FCQLSAGGSVAAAVKLNKQ 214
FC +S+GG+VAAA+++ ++
Sbjct: 253 FCGVSSGGAVAAALRIARE 271
>gnl|CDD|99747 cd06454, KBL_like, KBL_like; this family belongs to the pyridoxal
phosphate (PLP)-dependent aspartate aminotransferase
superfamily (fold I). The major groups in this CD
corresponds to serine palmitoyltransferase (SPT),
5-aminolevulinate synthase (ALAS),
8-amino-7-oxononanoate synthase (AONS), and
2-amino-3-ketobutyrate CoA ligase (KBL). SPT is
responsible for the condensation of L-serine with
palmitoyl-CoA to produce 3-ketodihydrospingosine, the
reaction of the first step in sphingolipid biosynthesis.
ALAS is involved in heme biosynthesis; it catalyzes the
synthesis of 5-aminolevulinic acid from glycine and
succinyl-coenzyme A. AONS catalyses the decarboxylative
condensation of l-alanine and pimeloyl-CoA in the first
committed step of biotin biosynthesis. KBL catalyzes the
second reaction step of the metabolic degradation
pathway for threonine converting 2-amino-3-ketobutyrate,
to glycine and acetyl-CoA. The members of this CD are
widely found in all three forms of life.
Length = 349
Score = 30.6 bits (70), Expect = 0.69
Identities = 21/70 (30%), Positives = 33/70 (47%), Gaps = 14/70 (20%)
Query: 90 ILELLKYHQRVLYIDVDVH-------HGDGVEEAFYTTDRV--MTVSFHK----YGEYFP 136
+++L K + +L++D + H HG GVEE TD V + + K G Y
Sbjct: 154 LVDLAKKYGAILFVD-EAHSVGVYGPHGRGVEEFGGLTDDVDIIMGTLGKAFGAVGGYIA 212
Query: 137 GTGDLRDMER 146
G+ +L D R
Sbjct: 213 GSKELIDYLR 222
>gnl|CDD|187581 cd05273, GME-like_SDR_e, Arabidopsis thaliana
GDP-mannose-3',5'-epimerase (GME)-like, extended (e)
SDRs. This subgroup of NDP-sugar epimerase/dehydratases
are extended SDRs; they have the characteristic active
site tetrad, and an NAD-binding motif: TGXXGXX[AG],
which is a close match to the canonical NAD-binding
motif. Members include Arabidopsis thaliana
GDP-mannose-3',5'-epimerase (GME) which catalyzes the
epimerization of two positions of GDP-alpha-D-mannose to
form GDP-beta-L-galactose. 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 = 328
Score = 29.0 bits (65), Expect = 2.7
Identities = 16/62 (25%), Positives = 22/62 (35%), Gaps = 12/62 (19%)
Query: 39 FCQLSAGGSVAAA-----VKLNKQASEICINWGGGLHHAKKSEASGFCYVNDIVLGILEL 93
G A A V K I WG GL + F Y++D V G+ L
Sbjct: 181 RGTWDGGREKAPAAMCRKVATAKDGDRFEI-WGDGL------QTRSFTYIDDCVEGLRRL 233
Query: 94 LK 95
++
Sbjct: 234 ME 235
Score = 29.0 bits (65), Expect = 2.7
Identities = 16/62 (25%), Positives = 22/62 (35%), Gaps = 12/62 (19%)
Query: 196 FCQLSAGGSVAAA-----VKLNKQASEICINWGGGLHHAKKSEASGFCYVNDIVLGILEL 250
G A A V K I WG GL + F Y++D V G+ L
Sbjct: 181 RGTWDGGREKAPAAMCRKVATAKDGDRFEI-WGDGL------QTRSFTYIDDCVEGLRRL 233
Query: 251 LK 252
++
Sbjct: 234 ME 235
>gnl|CDD|233286 TIGR01136, cysKM, cysteine synthase. This model discriminates
cysteine synthases (EC 2.5.1.47) (both CysK and CysM)
from cystathionine beta-synthase, a protein found
primarily in eukaryotes and carrying a C-terminal CBS
domain lacking from this protein. Bacterial proteins
lacking the CBS domain but otherwise showing
resemblamnce to cystathionine beta-synthases and
considerable phylogenetic distance from known cysteine
synthases were excluded from the seed and score below
the trusted cutoff [Amino acid biosynthesis, Serine
family].
Length = 299
Score = 28.4 bits (64), Expect = 4.3
Identities = 9/21 (42%), Positives = 14/21 (66%)
Query: 39 FCQLSAGGSVAAAVKLNKQAS 59
+S+G +VAAA+KL K+
Sbjct: 256 LVGISSGAAVAAALKLAKRLE 276
Score = 28.4 bits (64), Expect = 4.3
Identities = 9/21 (42%), Positives = 14/21 (66%)
Query: 196 FCQLSAGGSVAAAVKLNKQAS 216
+S+G +VAAA+KL K+
Sbjct: 256 LVGISSGAAVAAALKLAKRLE 276
>gnl|CDD|107284 cd06289, PBP1_MalI_like, Ligand-binding domain of MalI, a
transcription regulator of the maltose system of
Escherichia coli and its close homologs from other
bacteria. This group includes the ligand-binding domain
of MalI, a transcription regulator of the maltose system
of Escherichia coli and its close homologs from other
bacteria. They are members of the LacI-GalR family of
repressor proteins which are composed of two functional
domains: an N-terminal HTH (helix-turn-helix) domain,
which is responsible for the DNA-binding specificity,
and a C-terminal ligand-binding domain, which is
homologous to the sugar-binding domain of ABC-type
transport systems that contain the type I periplasmic
binding protein-like fold. As also observed in the
periplasmic binding proteins, the C-terminal domain of
the bacterial transcription repressor undergoes a
conformational change upon ligand binding which in turn
changes the DNA binding affinity of the repressor.
Length = 268
Score = 28.3 bits (64), Expect = 4.5
Identities = 23/100 (23%), Positives = 30/100 (30%), Gaps = 19/100 (19%)
Query: 30 CPVFDGLYEFCQLSAGGSVAAAVKLNKQASEI-CINWGGGLHHAKKSEASGFCYVNDIV- 87
P L S G A +L I C+ ND+V
Sbjct: 148 LPFDSELVVEGPPSRQGGAEAVAQLLDLPPRPTAI----------------VCF-NDLVA 190
Query: 88 LGILELLKYHQRVLYIDVDVHHGDGVEEAFYTTDRVMTVS 127
G + L+ D+ V D V EA T + TVS
Sbjct: 191 FGAMSGLRRAGLTPGRDIAVVGFDDVAEAALATPALTTVS 230
>gnl|CDD|187643 cd08939, KDSR-like_SDR_c, 3-ketodihydrosphingosine reductase (KDSR)
and related proteins, classical (c) SDR. These proteins
include members identified as KDSR, ribitol type
dehydrogenase, and others. The group shows strong
conservation of the active site tetrad and glycine rich
NAD-binding motif of the classical SDRs. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes 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 (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) 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. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. 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. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 239
Score = 27.2 bits (61), Expect = 7.9
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 98 QRVLYIDVDVHHGDGVEEAF 117
Q+V YI D+ + VE+AF
Sbjct: 54 QKVSYISADLSDYEEVEQAF 73
>gnl|CDD|200381 TIGR04130, FnlA, UDP-N-acetylglucosamine
4,6-dehydratase/5-epimerase. The FnlA enzyme is the
first step in the biosynthesis of UDP-FucNAc from
UDP-GlcNAc in E. coli (along with FnlB and FnlC). The
proteins identified by this model include FnlA homologs
in the O-antigen clusters of O4, O25, O26, O29 (Shigella
D11), O118, O145 and O172 serotype strains, all of which
produce O-antigens containing FucNAc (or the further
modified FucNAm). A homolog from Pseudomonas aerugiosa
serotype O11, WbjB, also involved in the biosynthesis of
UDP-FucNAc has been characterized and is now believed to
carry out both the initial 4,6-dehydratase reaction and
the subsequent epimerization of the resulting methyl
group at C-5. A phylogenetic tree of related sequences
shows a distinct clade of enzymes involved in the
biosynthesis of UDP-QuiNAc (Qui=qinovosamine). This
clade appears to be descendant from the common ancestor
of the Pseudomonas and E. coli fucose-biosynthesis
enzymes. It has been hypothesized that the first step in
the biosynthesis of these two compounds may be the same,
and thus that these enzymes all have the same function.
At present, lacking sufficient confirmation of this, the
current model trusted cutoff only covers the tree
segment surrounding the E. coli genes. The clades
containing the Pseudomonas and QuiNAc biosynthesis
enzymes score above the noise cutoff. Immediately below
the noise cutoff are enzymes involved in the
biosynthesis of UDP-RhaNAc (Rha=rhamnose), which again
may or may not produce the same product.
Length = 337
Score = 27.2 bits (60), Expect = 9.9
Identities = 17/81 (20%), Positives = 38/81 (46%), Gaps = 3/81 (3%)
Query: 83 VNDIVLGILELLKYHQRVLYIDVDVHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLR 142
+ + + + ELL H+ + I + HG+ + EA + + + ++ G+Y+ DLR
Sbjct: 231 IETLAIALKELLNAHEHPVNI-IGTRHGEKLYEALLSREEM--IAAIDMGDYYRVPPDLR 287
Query: 143 DMERVEKFNVIESRVMFTPDF 163
D+ + + R+ D+
Sbjct: 288 DLNYGKYVEHGDRRISEVEDY 308
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
0.326 0.144 0.454
Gapped
Lambda K H
0.267 0.0779 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,854,373
Number of extensions: 1321440
Number of successful extensions: 1458
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1400
Number of HSP's successfully gapped: 75
Length of query: 265
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 170
Effective length of database: 6,723,972
Effective search space: 1143075240
Effective search space used: 1143075240
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 58 (26.0 bits)