RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 017484
(371 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 = 524 bits (1351), Expect = 0.0
Identities = 197/297 (66%), Positives = 242/297 (81%), Gaps = 3/297 (1%)
Query: 32 YNLGEDCPVFENLFEFCQIYAGGTIDAARRLNNQLCDIAINWAGGLHHAKKCEASGFCYI 91
+N+G+DCPVF LF+FC +Y G +++ A +LN+++CDIAINW+GGLHHAKK EASGFCY+
Sbjct: 86 FNVGDDCPVFPGLFDFCSMYTGASLEGATKLNHKICDIAINWSGGLHHAKKFEASGFCYV 145
Query: 92 NDLVLGILELLKYHARVLYIDIDVHHGDGVEEAFYFTDRVMTVSFHKFGDLFFPGTGDVK 151
ND+V+ ILELLKYH RVLYIDID+HHGDGV+EAFY TDRVMTVSFHK+G+ FFPGTGD+
Sbjct: 146 NDIVIAILELLKYHPRVLYIDIDIHHGDGVQEAFYLTDRVMTVSFHKYGNYFFPGTGDMY 205
Query: 152 EIGEREGKFYAINVPLKDGIDDTSFTRLFKTIISKVVETYAPGAIVLQCGADSLAGDRLG 211
E+G G++Y++NVPLKDGIDD S+ +LFK +I +V++ Y P IVLQCGADSL DRLG
Sbjct: 206 EVGAESGRYYSVNVPLKDGIDDQSYLQLFKPVIQQVIDFYQPTCIVLQCGADSLGCDRLG 265
Query: 212 CFNLSIDGHAECVRFVKKFNLPLLVTGGGGYTKENVARCWTVETGILLDTELPNEIPENE 271
CFNLSI GH ECV FVK FN+PLLV GGGGYT NVARCWT ET +L+D E+ NE+P NE
Sbjct: 266 CFNLSIKGHGECVEFVKSFNIPLLVLGGGGYTVRNVARCWTYETSLLVDEEISNELPYNE 325
Query: 272 YIKYFAPECSLRIPN--GHIENLNSKSYLSTIKMQVLENLRSIQHAPSVQMQEVPPD 326
Y +YFAP+ +L P+ IEN NSK YL I+ V ENL+ + HAPSVQMQ+VPPD
Sbjct: 326 YFEYFAPDFTLH-PDVSTRIENQNSKQYLDQIRQTVFENLKMLNHAPSVQMQDVPPD 381
>gnl|CDD|240251 PTZ00063, PTZ00063, histone deacetylase; Provisional.
Length = 436
Score = 497 bits (1281), Expect = e-176
Identities = 222/403 (55%), Positives = 268/403 (66%), Gaps = 64/403 (15%)
Query: 6 KISYFYDGDVGSVYFGPNHPM------------------------KPHRL---------- 31
++SYFYD D+GS Y+GP HPM +PH+
Sbjct: 5 RVSYFYDPDIGSYYYGPGHPMKPQRIRMAHALILSYDLYKHMEIYRPHKSVEPELVLFHD 64
Query: 32 ------------------------YNLGE--DCPVFENLFEFCQIYAGGTIDAARRLNNQ 65
+N+GE DCPVF+ LFEF Q AG +ID A +LNN
Sbjct: 65 EEYVDFLSSISPENYRDFTYQLKRFNVGEATDCPVFDGLFEFQQSCAGASIDGAYKLNNH 124
Query: 66 LCDIAINWAGGLHHAKKCEASGFCYINDLVLGILELLKYHARVLYIDIDVHHGDGVEEAF 125
DI +NW+GGLHHAK+ EASGFCYIND+VLGILELLKYHARV+YIDIDVHHGDGVEEAF
Sbjct: 125 QADICVNWSGGLHHAKRSEASGFCYINDIVLGILELLKYHARVMYIDIDVHHGDGVEEAF 184
Query: 126 YFTDRVMTVSFHKFGDLFFPGTGDVKEIGEREGKFYAINVPLKDGIDDTSFTRLFKTIIS 185
Y T RVMTVSFHKFGD FFPGTGDV +IG +GK+Y++NVPL DGIDD SF LFK +IS
Sbjct: 185 YVTHRVMTVSFHKFGD-FFPGTGDVTDIGVAQGKYYSVNVPLNDGIDDDSFVDLFKPVIS 243
Query: 186 KVVETYAPGAIVLQCGADSLAGDRLGCFNLSIDGHAECVRFVKKFNLPLLVTGGGGYTKE 245
K VE Y PGAIVLQCGADSL GDRLG FNL+I GHA CV FV+ N+PLLV GGGGYT
Sbjct: 244 KCVEVYRPGAIVLQCGADSLTGDRLGRFNLTIKGHAACVEFVRSLNIPLLVLGGGGYTIR 303
Query: 246 NVARCWTVETGILLD--TELPNEIPENEYIKYFAPECSLRIPNGHIENLNSKSYLSTIKM 303
NVARCW ETG++L+ E+ ++I N+Y Y+AP+ L + +I N NS +L IK+
Sbjct: 304 NVARCWAYETGVILNKHDEMSDQISLNDYYDYYAPDFQLHLQPSNIPNYNSPEHLEKIKV 363
Query: 304 QVLENLRSIQHAPSVQMQEVPPDFYIPEFD-EDEQNPDERMDQ 345
++LENLR ++HAP VQ VPPDF+ + D EDE+N E D+
Sbjct: 364 KILENLRYLEHAPGVQFAYVPPDFFDRDIDDEDEKNQYELSDE 406
>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 = 484 bits (1247), Expect = e-173
Identities = 179/307 (58%), Positives = 212/307 (69%), Gaps = 59/307 (19%)
Query: 10 FYDGDVGSVYFGPNHPMKPHRL---------YNL-------------------------- 34
FYD DVG+ Y+G HPMKPHR+ Y L
Sbjct: 1 FYDPDVGNYYYGQGHPMKPHRIRMTHSLILSYGLYKKMEIYRPRPATAEELTKFHSDDYI 60
Query: 35 -----------------------GEDCPVFENLFEFCQIYAGGTIDAARRLNNQLCDIAI 71
GEDCPVF+ L+E+CQ+YAGG+I AA +LN DIAI
Sbjct: 61 DFLRSVSPDNMKEFKKQLERFNVGEDCPVFDGLYEYCQLYAGGSIAAAVKLNRGQADIAI 120
Query: 72 NWAGGLHHAKKCEASGFCYINDLVLGILELLKYHARVLYIDIDVHHGDGVEEAFYFTDRV 131
NWAGGLHHAKK EASGFCY+ND+VL ILELLKYH RVLYIDID+HHGDGVEEAFY TDRV
Sbjct: 121 NWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRV 180
Query: 132 MTVSFHKFGDLFFPGTGDVKEIGEREGKFYAINVPLKDGIDDTSFTRLFKTIISKVVETY 191
MTVSFHKFG+ +F +++IG +GK+YA+NVPLKDGIDD S+ ++F+ ++SKV+E +
Sbjct: 181 MTVSFHKFGE-YFFPGTGLRDIGAGKGKYYAVNVPLKDGIDDESYLQIFEPVLSKVMEVF 239
Query: 192 APGAIVLQCGADSLAGDRLGCFNLSIDGHAECVRFVKKFNLPLLVTGGGGYTKENVARCW 251
P A+VLQCGADSLAGDRLGCFNLSI GHA+CV+FVK FN+PLLV GGGGYT NVARCW
Sbjct: 240 QPSAVVLQCGADSLAGDRLGCFNLSIKGHAKCVKFVKSFNIPLLVLGGGGYTLRNVARCW 299
Query: 252 TVETGIL 258
T ET +L
Sbjct: 300 TYETAVL 306
>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 = 455 bits (1173), Expect = e-161
Identities = 200/376 (53%), Positives = 246/376 (65%), Gaps = 59/376 (15%)
Query: 4 KDKISYFYDGDVGSVYFGPNHPMKPHRL---------YNLGEDCPVF------------- 41
K K++YFYD DVG+ +GP HPMKPHR+ Y L + ++
Sbjct: 1 KKKVAYFYDSDVGNYAYGPGHPMKPHRIRMAHSLVMNYGLYKKMEIYRAKPATKNEMTQF 60
Query: 42 ------------------------------------ENLFEFCQIYAGGTIDAARRLNNQ 65
+ LFEFC I AGG+++ A RLN
Sbjct: 61 HTDEYIDFLSRVTPDNMEKFQKEQVKYNVGDDCPVFDGLFEFCSISAGGSMEGAARLNRG 120
Query: 66 LCDIAINWAGGLHHAKKCEASGFCYINDLVLGILELLKYHARVLYIDIDVHHGDGVEEAF 125
CDIA+NWAGGLHHAKK EASGFCY+ND+VLGILELL+YH RVLYIDIDVHHGDGVEEAF
Sbjct: 121 KCDIAVNWAGGLHHAKKSEASGFCYVNDIVLGILELLRYHQRVLYIDIDVHHGDGVEEAF 180
Query: 126 YFTDRVMTVSFHKFGDLFFPGTGDVKEIGEREGKFYAINVPLKDGIDDTSFTRLFKTIIS 185
Y TDRVMT SFHK+G+ +FPGTG++++IG GK YA+NVPL+DGIDD S+ +F+ +I
Sbjct: 181 YTTDRVMTCSFHKYGE-YFPGTGELRDIGIGTGKNYAVNVPLRDGIDDESYKSIFEPVIK 239
Query: 186 KVVETYAPGAIVLQCGADSLAGDRLGCFNLSIDGHAECVRFVKKFNLPLLVTGGGGYTKE 245
V+E Y P A+VLQCG DSL+GDRLGCFNLS+ GHA CV FVK FNLP+LV GGGGYT
Sbjct: 240 HVMEWYQPEAVVLQCGGDSLSGDRLGCFNLSMKGHANCVNFVKSFNLPMLVLGGGGYTMR 299
Query: 246 NVARCWTVETGILLDTELPNEIPENEYIKYFAPECSLRIPNGHIENLNSKSYLSTIKMQV 305
NVAR W ETG+L EL ++P NEY +Y+ P+ L + ++EN N+ YL I V
Sbjct: 300 NVARTWAFETGLLAGEELDKDLPYNEYYEYYGPDYELNVRPSNMENHNTPEYLDKITTAV 359
Query: 306 LENLRSIQHAPSVQMQ 321
+ENLR+ APSVQMQ
Sbjct: 360 IENLRNTSFAPSVQMQ 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 = 417 bits (1074), Expect = e-146
Identities = 201/368 (54%), Positives = 255/368 (69%), Gaps = 59/368 (16%)
Query: 3 SKDKISYFYDGDVGSVYFGPNHPM------------------------KPHRL------- 31
+K K+ Y+YDGDVG+ Y+G HPM +PH+
Sbjct: 4 TKKKVCYYYDGDVGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKANAEEMTK 63
Query: 32 ---------------------------YNLGEDCPVFENLFEFCQIYAGGTIDAARRLNN 64
+N+GEDCPVF+ LFEFCQ+ AGG++ +A +LN
Sbjct: 64 YHSDDYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSAGGSVASAVKLNK 123
Query: 65 QLCDIAINWAGGLHHAKKCEASGFCYINDLVLGILELLKYHARVLYIDIDVHHGDGVEEA 124
Q DIA+NWAGGLHHAKK EASGFCY+ND+VL ILELLKYH RVLYIDID+HHGDGVEEA
Sbjct: 124 QQTDIAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEA 183
Query: 125 FYFTDRVMTVSFHKFGDLFFPGTGDVKEIGEREGKFYAINVPLKDGIDDTSFTRLFKTII 184
FY TDRVMTVSFHK+G+ +FPGTGD+++IG +GK+YA+N PL+DGIDD S+ +FK ++
Sbjct: 184 FYTTDRVMTVSFHKYGE-YFPGTGDLRDIGAGKGKYYAVNYPLRDGIDDESYEAIFKPVM 242
Query: 185 SKVVETYAPGAIVLQCGADSLAGDRLGCFNLSIDGHAECVRFVKKFNLPLLVTGGGGYTK 244
SKV+E + P A+VLQCGADSL+GDRLGCFNL+I GHA+CV FVK FNLP+L+ GGGGYT
Sbjct: 243 SKVMEMFQPSAVVLQCGADSLSGDRLGCFNLTIKGHAKCVEFVKSFNLPMLMLGGGGYTI 302
Query: 245 ENVARCWTVETGILLDTELPNEIPENEYIKYFAPECSLRIPNGHIENLNSKSYLSTIKMQ 304
NVARCWT ET + LD+E+PNE+P N+Y +YF P+ L I ++ N N+ YL IK +
Sbjct: 303 RNVARCWTYETAVALDSEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTNEYLEKIKQR 362
Query: 305 VLENLRSI 312
+ ENLR +
Sbjct: 363 LFENLRML 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 = 404 bits (1040), Expect = e-141
Identities = 198/367 (53%), Positives = 251/367 (68%), Gaps = 59/367 (16%)
Query: 4 KDKISYFYDGDVGSVYFGPNHPM------------------------KPHRL-------- 31
K K+ Y+YDGD+G+ Y+G HPM +PH+
Sbjct: 1 KKKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTKY 60
Query: 32 --------------------------YNLGEDCPVFENLFEFCQIYAGGTIDAARRLNNQ 65
+N+GEDCPVF+ LFEFCQ+ GG++ A +LN Q
Sbjct: 61 HSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAGAVKLNRQ 120
Query: 66 LCDIAINWAGGLHHAKKCEASGFCYINDLVLGILELLKYHARVLYIDIDVHHGDGVEEAF 125
D+A+NWAGGLHHAKK EASGFCY+ND+VL ILELLKYH RVLYIDID+HHGDGVEEAF
Sbjct: 121 QTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAF 180
Query: 126 YFTDRVMTVSFHKFGDLFFPGTGDVKEIGEREGKFYAINVPLKDGIDDTSFTRLFKTIIS 185
Y TDRVMTVSFHK+G+ +FPGTGD+++IG +GK+YA+N P++DGIDD S+ ++FK IIS
Sbjct: 181 YTTDRVMTVSFHKYGE-YFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIIS 239
Query: 186 KVVETYAPGAIVLQCGADSLAGDRLGCFNLSIDGHAECVRFVKKFNLPLLVTGGGGYTKE 245
KV+E Y P A+VLQCGADSL+GDRLGCFNL++ GHA+CV VK FNLPLL+ GGGGYT
Sbjct: 240 KVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTIR 299
Query: 246 NVARCWTVETGILLDTELPNEIPENEYIKYFAPECSLRIPNGHIENLNSKSYLSTIKMQV 305
NVARCWT ET + LD E+PNE+P N+Y +YF P+ L I ++ N N+ Y+ IK ++
Sbjct: 300 NVARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEYMEKIKQRL 359
Query: 306 LENLRSI 312
ENLR +
Sbjct: 360 FENLRML 366
>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 = 388 bits (998), Expect = e-135
Identities = 147/227 (64%), Positives = 180/227 (79%)
Query: 32 YNLGEDCPVFENLFEFCQIYAGGTIDAARRLNNQLCDIAINWAGGLHHAKKCEASGFCYI 91
+N+G+DCPVF+ ++++CQ+YAG ++DAAR+L + DIAINW+GGLHHAKK EASGFCY+
Sbjct: 85 FNIGDDCPVFDGMYDYCQLYAGASLDAARKLCSGQSDIAINWSGGLHHAKKSEASGFCYV 144
Query: 92 NDLVLGILELLKYHARVLYIDIDVHHGDGVEEAFYFTDRVMTVSFHKFGDLFFPGTGDVK 151
ND+VL IL LL+Y RVLYIDIDVHHGDGVEEAFY TDRVMT+SFHK+ FFPGTGD+
Sbjct: 145 NDIVLAILNLLRYFPRVLYIDIDVHHGDGVEEAFYRTDRVMTLSFHKYNGEFFPGTGDLD 204
Query: 152 EIGEREGKFYAINVPLKDGIDDTSFTRLFKTIISKVVETYAPGAIVLQCGADSLAGDRLG 211
+ G GK +A+NVPL+DGIDD + LFK+II +E + P AIVLQCGADSL GDRLG
Sbjct: 205 DNGGTPGKHFALNVPLEDGIDDEQYNLLFKSIIGPTIEKFQPSAIVLQCGADSLGGDRLG 264
Query: 212 CFNLSIDGHAECVRFVKKFNLPLLVTGGGGYTKENVARCWTVETGIL 258
FNL+I H CV+FVK F +P+LV GGGGYT NVAR W ET +
Sbjct: 265 QFNLNIKAHGACVKFVKSFGIPMLVVGGGGYTPRNVARAWCYETAVA 311
>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 = 360 bits (927), Expect = e-124
Identities = 134/290 (46%), Positives = 196/290 (67%)
Query: 24 HPMKPHRLYNLGEDCPVFENLFEFCQIYAGGTIDAARRLNNQLCDIAINWAGGLHHAKKC 83
+ + LG DCP+FE ++++ AG T+ AA+ L + C +AINW GG HHA++
Sbjct: 75 EEPSEQQEFGLGYDCPIFEGIYDYAAAVAGATLTAAQLLIDGKCKVAINWFGGWHHAQRD 134
Query: 84 EASGFCYINDLVLGILELLKYHARVLYIDIDVHHGDGVEEAFYFTDRVMTVSFHKFGDLF 143
EASGFCY+ND+VLGIL+L + RVLY+D+D+HHGDGVE+AF FT +VMTVS HK+ F
Sbjct: 135 EASGFCYVNDIVLGILKLREKFDRVLYVDLDLHHGDGVEDAFSFTSKVMTVSLHKYSPGF 194
Query: 144 FPGTGDVKEIGEREGKFYAINVPLKDGIDDTSFTRLFKTIISKVVETYAPGAIVLQCGAD 203
FPGTGDV ++G +GK+Y +NVPL+DGI D + ++F ++ ++V + P A+VLQCGAD
Sbjct: 195 FPGTGDVSDVGLGKGKYYTVNVPLRDGIQDEQYLQIFTAVVPEIVAAFRPEAVVLQCGAD 254
Query: 204 SLAGDRLGCFNLSIDGHAECVRFVKKFNLPLLVTGGGGYTKENVARCWTVETGILLDTEL 263
+LAGD +G FNL+ G +C+++V + LP L+ GGGGY N ARCWT TG++L L
Sbjct: 255 TLAGDPMGAFNLTPVGIGKCLKYVLGWKLPTLILGGGGYNLANTARCWTYLTGLILGEPL 314
Query: 264 PNEIPENEYIKYFAPECSLRIPNGHIENLNSKSYLSTIKMQVLENLRSIQ 313
++IP++E+ + P+ L I +LN Y+ I + NL+++
Sbjct: 315 SSDIPDHEFFTSYGPDYELEISPSLRPDLNEDQYIEKILETIKGNLKNVV 364
>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 = 276 bits (708), Expect = 5e-91
Identities = 94/332 (28%), Positives = 136/332 (40%), Gaps = 60/332 (18%)
Query: 6 KISYFYDGDVGSVYFGPNHPMKPHRL---------------------------------- 31
K + Y + P HP P RL
Sbjct: 3 KTALIYHPEFLEHEPPPGHPENPDRLRLILELLESSGLPDSLELVEPRPATLEELLLVHS 62
Query: 32 ----------------YNLGEDCPVFENLFEFCQIYAGGTIDAARRLNNQLCDIAINWAG 75
NL D PV +E ++ AGG + A + +
Sbjct: 63 PDYVEFLESLSEEEGYGNLDGDTPVSPGTYEAARLAAGGALTAVDAVLEGEDNAFALVRP 122
Query: 76 GLHHAKKCEASGFCYINDLVLGILELLK-YHARVLYIDIDVHHGDGVEEAFYFTDRVMTV 134
HHA + ASGFC N++ + LLK RV ID DVHHG+G +E FY D V+TV
Sbjct: 123 PGHHAGRDRASGFCLFNNVAIAAKYLLKKGVKRVAIIDFDVHHGNGTQEIFYDDDDVLTV 182
Query: 135 SFHKFGDLFFPGTGDVKEIGEREGKFYAINVPLKDGIDDTSFTRLFKTIISKVVETYAPG 194
S H+ G F+PGTG EIGE + +N+PL G D S+ + I+ ++E + P
Sbjct: 183 SLHQDGRPFYPGTGGADEIGE-GKEGNNVNIPLPPGTGDDSYLEALEEIVLPLLEEFKPD 241
Query: 195 AIVLQCGADSLAGDRLGCFNLSIDGHAECVRFVKKFNL----PLLVTGGGGYTKENVARC 250
+++ G D+ GD LG NL+ +G+A+ R V+K P++ GGY + +AR
Sbjct: 242 LVIVSAGFDAHRGDPLGRLNLTEEGYAKIGRAVRKLAEGYGGPVVAVLEGGYNLDALARS 301
Query: 251 WTVETGILLD---TELPNEIPEN-EYIKYFAP 278
L EL +PE+ E + F
Sbjct: 302 LVAFLAGLAGLVEEELEEPLPEDLELRRAFRA 333
>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 = 272 bits (699), Expect = 3e-90
Identities = 84/238 (35%), Positives = 125/238 (52%), Gaps = 11/238 (4%)
Query: 29 HRLYNLGEDCPVFENLFEFCQIYAGGTIDAARR-LNNQLCDIAINWAGGLHHAKKCEASG 87
L D PV +E + AGGT++AA L+ + A+ G HHA++ ASG
Sbjct: 67 LGRIGLDGDTPVSPGSYEAALLAAGGTLEAADLVLSGENAFAAVRPPG--HHAERDRASG 124
Query: 88 FCYINDLVLGILELLKYH--ARVLYIDIDVHHGDGVEEAFYFTDRVMTVSFHKFGDLFFP 145
FC N++ + LLK + RVL +D+DVHHG+G +E FY RV+T+S H+ F+P
Sbjct: 125 FCLFNNVAIAARYLLKRYGLKRVLIVDLDVHHGNGTQEIFYDDPRVLTISIHQDP--FYP 182
Query: 146 GTGDVKEIGEREGKFYAINVPLKDGIDDTSFTRLFKTIISKVVETYAPGAIVLQCGADSL 205
GTG E GE G+ Y +N+PL G D + F+ I+ + + P I++ G D+
Sbjct: 183 GTGFADETGEGAGEGYTLNIPLPPGTGDEEYLAAFEEILLPALREFQPDLILVSAGFDAH 242
Query: 206 AGDRLGCFNLSIDGHAECVRFVKKF----NLPLLVTGGGGYTKENVARCWTVETGILL 259
AGD LG NL+ +G+AE R + + P++ GGY + +AR LL
Sbjct: 243 AGDPLGGLNLTTEGYAERTRLLLELADAYGGPVVSVLEGGYNLDALARSAAAVLAGLL 300
>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 = 271 bits (696), Expect = 2e-89
Identities = 102/228 (44%), Positives = 126/228 (55%), Gaps = 7/228 (3%)
Query: 32 YNLG-EDCPVFENLFEFCQIYAGGTIDAARRLNNQLCDIAINWAGGLHHAKKCEASGFCY 90
LG ED PVF + E + GGT+ AAR + A N AGGLHHA + ASGFC
Sbjct: 80 LGLGTEDNPVFPGMHEAAALVVGGTLLAARLVLEGEARRAFNPAGGLHHAMRGRASGFCV 139
Query: 91 INDLVLGILELL-KYHARVLYIDIDVHHGDGVEEAFYFTDRVMTVSFHKFGDLFFPGTGD 149
ND + I L K RV Y+DID HHGDGV+ AFY RV+T+S H+ G FPGTG
Sbjct: 140 YNDAAVAIERLRDKGGLRVAYVDIDAHHGDGVQAAFYDDPRVLTISLHESGRYLFPGTGF 199
Query: 150 VKEIGEREGKFYAINVPLKDGIDDTSFTRLFKTIISKVVETYAPGAIVLQCGADSLAGDR 209
V EIGE EG YA+N+PL G D F R F+ ++ ++ + P IV Q GAD+ AGD
Sbjct: 200 VDEIGEGEGYGYAVNIPLPPGTGDDEFLRAFEAVVPPLLRAFRPDVIVSQHGADAHAGDP 259
Query: 210 LGCFNLSIDGHAECVRFVK-----KFNLPLLVTGGGGYTKENVARCWT 252
L NLS + VR ++ L GGGGY + VAR W
Sbjct: 260 LTHLNLSNRAYRAAVRRIRELADEYCGGRWLALGGGGYNPDVVARAWA 307
Score = 32.1 bits (74), Expect = 0.35
Identities = 10/23 (43%), Positives = 12/23 (52%)
Query: 9 YFYDGDVGSVYFGPNHPMKPHRL 31
+ Y + FGPNHP P RL
Sbjct: 2 FIYSEEYLRYSFGPNHPFNPPRL 24
>gnl|CDD|240374 PTZ00346, PTZ00346, histone deacetylase; Provisional.
Length = 429
Score = 273 bits (699), Expect = 1e-88
Identities = 125/228 (54%), Positives = 160/228 (70%)
Query: 37 DCPVFENLFEFCQIYAGGTIDAARRLNNQLCDIAINWAGGLHHAKKCEASGFCYINDLVL 96
DCP E L E A GT+ A LN+ D+A++W GG+HH+K E SGFCY+ND+VL
Sbjct: 113 DCPPVEGLMEHSIATASGTLMGAVLLNSGQVDVAVHWGGGMHHSKCGECSGFCYVNDIVL 172
Query: 97 GILELLKYHARVLYIDIDVHHGDGVEEAFYFTDRVMTVSFHKFGDLFFPGTGDVKEIGER 156
GILELLK H RVLY+DID+HHGDGV+EAF +DRV T+S HKFG+ FFPGTG +++G
Sbjct: 173 GILELLKCHDRVLYVDIDMHHGDGVDEAFCTSDRVFTLSLHKFGESFFPGTGHPRDVGYG 232
Query: 157 EGKFYAINVPLKDGIDDTSFTRLFKTIISKVVETYAPGAIVLQCGADSLAGDRLGCFNLS 216
G++Y++N+ + DGI D + LF+ + +V Y+P AIVLQCGADSLAGDRLG NLS
Sbjct: 233 RGRYYSMNLAVWDGITDFYYLGLFEHALHSIVRRYSPDAIVLQCGADSLAGDRLGLLNLS 292
Query: 217 IDGHAECVRFVKKFNLPLLVTGGGGYTKENVARCWTVETGILLDTELP 264
GH +CV+ V+ +P+L GGGGYT NVA+ W ET IL LP
Sbjct: 293 SFGHGQCVQAVRDLGIPMLALGGGGYTIRNVAKLWAYETSILTGHPLP 340
>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 = 261 bits (668), Expect = 1e-85
Identities = 101/231 (43%), Positives = 142/231 (61%), Gaps = 8/231 (3%)
Query: 32 YNLGEDCPVFENLFEFCQIYAGGTIDAARRLNNQL-CDIAINWAGGLHHAKKCEASGFCY 90
Y L +DCPVF L + Q+ AG ++ A+ L Q+ DIAINW GG HHA+K ASGFCY
Sbjct: 68 YGLEDDCPVFPFLSMYVQLVAGSSLALAKHLITQVERDIAINWYGGRHHAQKSRASGFCY 127
Query: 91 INDLVLGILELLKYHA-RVLYIDIDVHHGDGVEEAFYFTDRVMTVSFHKFGDLFFPGTGD 149
+ND+VL IL L + RV Y+D+D+HHGDGVE AF+F+ V+T S H++ FFPGTG
Sbjct: 128 VNDIVLAILRLRRARFRRVFYLDLDLHHGDGVESAFFFSKNVLTCSIHRYDPGFFPGTGS 187
Query: 150 VKEIGEREGKFYAINVPLKDGIDDTSFTRLFKTIISKVVETYAPGAIVLQCGADSLAGDR 209
+K +N+PLK G+ D + R+ +I+ ++E + P IV+QCG D L+GD
Sbjct: 188 LKN----SSDKGMLNIPLKRGLSDKTLLRIIDSIVRPLIEKFEPEVIVIQCGCDGLSGDP 243
Query: 210 LGCFNLSIDGHAECVRFVKKF--NLPLLVTGGGGYTKENVARCWTVETGIL 258
+NL+I G+ + + K + P L+ GGGGY AR WT T ++
Sbjct: 244 HKEWNLTIRGYGSVIELLLKEFKDKPTLLLGGGGYNHTEAARAWTYLTSMV 294
>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 = 231 bits (590), Expect = 4e-74
Identities = 94/230 (40%), Positives = 123/230 (53%), Gaps = 13/230 (5%)
Query: 33 NLGEDCPVFENLFEFCQIYAGGTIDAARRLNNQLCDIAINWA-GGLHHAKKCEASGFCYI 91
G + PV + F ++ GG ++AA + + A G HHA K A GFCY
Sbjct: 59 IFGPNFPVQRHYFRGARLSTGGVVEAAELVAKGELERAFAVVGAGGHHAGKSRAWGFCYF 118
Query: 92 NDLVLGILELLKY-HARVLYIDIDVHHGDGVEEAFYFTDRVMTVSFHKFGDLFFPGTGDV 150
ND+VL I L + +R+L ID D HHGDG EAFY DRV+ +SFH + F
Sbjct: 119 NDVVLAIKFLRERGISRILIIDTDAHHGDGTREAFYDDDRVLHMSFHNYDIYPF------ 172
Query: 151 KEIGEREGKFYAINVPLKDGIDDTSFTRLFKTIISKVVETYAPGAIVLQCGADSLAGDRL 210
G +GK Y INVPL+DG+ D + + +ISKV+E + P +VLQ G D+ GDRL
Sbjct: 173 ---GRGKGKGYKINVPLEDGLGDEEYLDAVERVISKVLEEFEPEVVVLQFGHDTHEGDRL 229
Query: 211 GCFNLSIDGHAECVRFVKKFN--LPLLVTGGGGYTKENVARCWTVETGIL 258
G FNLS G + VK+F P+L+ GGGY E AR WT L
Sbjct: 230 GGFNLSEKGFVKLAEIVKEFARGGPILMVLGGGYNPEAAARIWTAIIKEL 279
>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 = 140 bits (356), Expect = 2e-39
Identities = 72/214 (33%), Positives = 104/214 (48%), Gaps = 22/214 (10%)
Query: 39 PVFENLFEFCQIYAGGTIDAARR-LNNQLCDIAINWAGGLHHAKKCEASGFCYINDLVLG 97
P L E ++ GGTI AAR L +AIN AGG HHA GFC ND+ +
Sbjct: 65 PWSPELVERTRLAVGGTILAARLALE---HGLAINLAGGTHHAFPDRGEGFCVFNDIAIA 121
Query: 98 ILELLKYHA--RVLYIDIDVHHGDGVEEAFYFTDRVMTVSFHKFGDLFFPGTGDVKEIGE 155
LL RVL +D+DVH G+G F V T S H G+ +P KE +
Sbjct: 122 ARVLLAEGLVRRVLIVDLDVHQGNGTAAIFADDPSVFTFSMH--GEKNYPF---RKEPSD 176
Query: 156 REGKFYAINVPLKDGIDDTSFTRLFKTIISKVVETYAPGAIVLQCGADSLAGDRLGCFNL 215
++VPL DG D + + + +++ + P + G D LAGDRLG +L
Sbjct: 177 -------LDVPLPDGTGDDEYLAALEEALPRLLAEFRPDLVFYNAGVDVLAGDRLGRLSL 229
Query: 216 SIDGHAE----CVRFVKKFNLPLLVTGGGGYTKE 245
S++G E +RF + +P+ + GGGY+++
Sbjct: 230 SLEGLRERDRLVLRFARARGIPVAMVLGGGYSRD 263
>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 = 136 bits (344), Expect = 2e-37
Identities = 65/211 (30%), Positives = 103/211 (48%), Gaps = 18/211 (8%)
Query: 52 AGGTIDAARRLNNQLCDIAINWA-----GGLHHAKKCEASGFCYINDLVLGILELLKYH- 105
AG + A + + + A +A G HHA+ A GFC N++ + K +
Sbjct: 78 AGAALAAVDAVLSGEAENA--FALVRPPG--HHAEPDRAMGFCLFNNVAIAARYAQKRYG 133
Query: 106 -ARVLYIDIDVHHGDGVEEAFYFTDRVMTVSFHKFGDLFFPGTGDVKEIGEREGKFYAIN 164
RVL +D DVHHG+G ++ FY V+ S H++ F+PGTG +E G G+ + IN
Sbjct: 134 LKRVLIVDWDVHHGNGTQDIFYDDPSVLYFSIHQYP--FYPGTGAAEETGGGAGEGFTIN 191
Query: 165 VPLKDGIDDTSFTRLFKTIISKVVETYAPGAIVLQCGADSLAGDRLGCFNLSIDGHAECV 224
VPL G D + F+ ++ + + P +++ G D+ GD LG NL+ +G+A
Sbjct: 192 VPLPPGSGDAEYLAAFEEVLLPIAREFQPDLVLVSAGFDAHRGDPLGGMNLTPEGYARLT 251
Query: 225 RFVKKF-----NLPLLVTGGGGYTKENVARC 250
R +K+ L+ GGY E +A
Sbjct: 252 RLLKELADEHCGGRLVFVLEGGYNLEALAES 282
>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 = 134 bits (340), Expect = 7e-37
Identities = 67/220 (30%), Positives = 98/220 (44%), Gaps = 12/220 (5%)
Query: 37 DCPVFENLFEFCQIYAGGTIDAARRLNNQLCDIAINWAGGL-----HHAKKCEASGFCYI 91
D P+ E +E A + AA + A L HHA + A GFCY
Sbjct: 76 DTPISEGTWEAALAAADTALTAADLVLE-----GERAAYALCRPPGHHAGRDRAGGFCYF 130
Query: 92 NDLVLGILELLKYHARVLYIDIDVHHGDGVEEAFYFTDRVMTVSFHKFGDLFFPGT-GDV 150
N+ + L RV +D+DVHHG+G +E FY V+ VS H F+P G
Sbjct: 131 NNAAIAAQYLRDRAGRVAILDVDVHHGNGTQEIFYERPDVLYVSIHGDPRTFYPFFLGFA 190
Query: 151 KEIGEREGKFYAINVPLKDGIDDTSFTRLFKTIISKVVETYAPGAIVLQCGADSLAGDRL 210
E GE EG+ Y +N+PL G D + ++ + + P A+V+ G D+ GD L
Sbjct: 191 DETGEGEGEGYNLNLPLPPGTGDDDYLAALDEALAA-IAAFGPDALVVSLGFDTHEGDPL 249
Query: 211 GCFNLSIDGHAECVRFVKKFNLPLLVTGGGGYTKENVARC 250
F L+ + +A R + LP + GGY + + R
Sbjct: 250 SDFKLTTEDYARIGRRIAALGLPTVFVQEGGYNVDALGRN 289
>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 = 109 bits (274), Expect = 7e-27
Identities = 73/259 (28%), Positives = 114/259 (44%), Gaps = 19/259 (7%)
Query: 34 LGEDCPVFENLFEFCQIYAGGTIDAARR-LNNQLCDIA---INWAGGLHHAKKCEASGFC 89
G P +E + AGG I A L+ ++ D A + G HHA+ + GFC
Sbjct: 92 AGGGTPFGPGSYEIALLAAGGAIAAVDAVLDGEV-DNAYALVRPPG--HHAEPDQGMGFC 148
Query: 90 YINDLVLGILELLKYH--ARVLYIDIDVHHGDGVEEAFYFTDRVMTVSFHKFGDLFFPGT 147
N++ + L RV +D DVHHG+G + FY V+T+S H+ F P +
Sbjct: 149 LFNNVAIAARHALAVGGVKRVAVVDWDVHHGNGTQAIFYDDPDVLTISLHQDR-CFPPDS 207
Query: 148 GDVKEIGEREGKFYAINVPLKDGIDDTSFTRLFKTIISKVVETYAPGAIVLQCGADSLAG 207
G V+E GE G+ Y +N+PL G D ++ F+ I+ + + P I++ G D+ A
Sbjct: 208 GAVEERGEGAGEGYNLNIPLPPGSGDGAYLHAFERIVLPALRAFRPELIIVASGFDASAF 267
Query: 208 DRLGCFNLSIDGHAECVRFVKKFNLP-----LLVTGGGGYTKENVARCW--TVETGILLD 260
D LG L+ DG R ++ L++ GGY++ V C +E L
Sbjct: 268 DPLGRMMLTSDGFRALTRKLRDLADELCGGRLVMVHEGGYSEAYVPFCGLAVLEE--LSG 325
Query: 261 TELPNEIPENEYIKYFAPE 279
P Y + +
Sbjct: 326 VRTGIADPLLYYPEAQGGQ 344
>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 = 97.1 bits (242), Expect = 1e-23
Identities = 40/238 (16%), Positives = 62/238 (26%), Gaps = 52/238 (21%)
Query: 45 FEFCQIYAGGTIDAARRLNNQLCDIAINWAGGLHHAKKCEASGFCYINDLVLGILELLKY 104
E ++ AG + + + + G H+ N + + EL
Sbjct: 8 AEAHELLAGVVVAVLKD-----GKVPVVLGG--DHSI---------ANGAIRAVAEL--- 48
Query: 105 HARVLYIDIDVHHGDGVEEAFYF--------------TDRVMTVSFHKFGDLFFPGTGDV 150
H + ID+D HH EAF V VS G
Sbjct: 49 HPDLGVIDVDAHHDVRTPEAFGKGNHHTPRHLLCEPLISDVHIVSIGIRGVSNGE----- 103
Query: 151 KEIGEREGKFYAINVPLKDGIDDTSFTRLFKTIISKVVETYAPGAIVLQCGADSLAGD-- 208
G K + + + D +F+ I+S + + L D L
Sbjct: 104 -AGGAYARKLGVVYFSMTEV-DKLGLGDVFEEIVSYL--GDKGDNVYLSVDVDGLDPSFA 159
Query: 209 ----RLGCFNLSIDGHAECVRFVKKFNLPLLVTGGGGYT----KENVARCWTVETGIL 258
G LS + K NL + + AR T L
Sbjct: 160 PGTGTPGPGGLSYREGLYITERIAKTNLVVGLDIVEVNPLLDETGRTARLAAALTLEL 217
>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 = 96.6 bits (241), Expect = 2e-22
Identities = 71/250 (28%), Positives = 114/250 (45%), Gaps = 25/250 (10%)
Query: 42 ENLFEFCQIYAGGTIDA-----ARRLNNQLCDIAINWAGGLHHAKKCEASGFCYINDLVL 96
+ +E ++ AG TI+ A ++ N I G HHA + EA+G+C N++ +
Sbjct: 80 PSTYEAARLAAGSTIELVKAVMAGKIQNGFA--LIRPPG--HHAMRNEANGYCIFNNVAI 135
Query: 97 G---ILELLKYHARVLYIDIDVHHGDGVEEAFYFTDRVMTVSFHKFGD-LFFPG--TGDV 150
+E L R+L +D DVHHG G ++ FY RV+ S H++ F+P D
Sbjct: 136 AAKYAIEKLGLK-RILIVDWDVHHGQGTQQGFYEDPRVLYFSIHRYEHGRFWPHLFESDY 194
Query: 151 KEIGEREGKFYAINVPLKD-GIDDTSFTRLFKTIISKVVETYAPGAIVLQCGADSLAGDR 209
IG G + +NVPL G+ D + +F I+ + + P +++ G D+ GD
Sbjct: 195 DYIGVGHGYGFNVNVPLNQTGLGDADYLAIFHHILLPLALEFQPELVLVSAGFDASIGDP 254
Query: 210 LGCFNLSIDGHAECVRFVKKFNLP-LLVTGGGGYTKENVARC--WTVETGILLDTELPN- 265
G ++ G+A R + LL+ GGY E++A T+ LL LP
Sbjct: 255 EGEMAVTPAGYAHLTRLLMGLAGGKLLLVLEGGYLLESLAESVSMTLRG--LLGDPLPPL 312
Query: 266 --EIPENEYI 273
IP +
Sbjct: 313 APPIPIRSVL 322
>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 = 96.6 bits (241), Expect = 2e-22
Identities = 45/148 (30%), Positives = 80/148 (54%), Gaps = 9/148 (6%)
Query: 78 HHAKKCEASGFCYINDLVLG--ILELLKYHARVLYIDIDVHHGDGVEEAFYFTDRVMTVS 135
HHA+ +A GFC+ N + + L+ ++L +D DVHHG+G ++ FY V+ +S
Sbjct: 151 HHAEPSQAMGFCFFNSVAIAAKQLQQKLKLRKILIVDWDVHHGNGTQQIFYEDPNVLYIS 210
Query: 136 FHKFGD-LFFPGTGDVKEIGEREGKFYAINVPLKDGID----DTSFTRLFKTIISKVVET 190
H++ D FFPGTG E+G G+ + +N+ G+D D + F+T++ +
Sbjct: 211 LHRYDDGNFFPGTGAPTEVGSGAGEGFNVNIAWSGGLDPPMGDAEYLAAFRTVVMPIARE 270
Query: 191 YAPGAIVLQCGADSLAG--DRLGCFNLS 216
++P +++ G D+ G LG + +S
Sbjct: 271 FSPDIVLVSAGFDAAEGHPPPLGGYKVS 298
>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 = 95.5 bits (238), Expect = 3e-22
Identities = 48/152 (31%), Positives = 83/152 (54%), Gaps = 8/152 (5%)
Query: 78 HHAKKCEASGFCYINDLVLGILELLK-YHA---RVLYIDIDVHHGDGVEEAFYFTDRVMT 133
HHA+ E+ GFC+ N++ + L Y ++L +D D+HHG+G + AFY V+
Sbjct: 115 HHAEPDESMGFCFFNNVAVAAKWLQTEYPDKIKKILILDWDIHHGNGTQRAFYDDPNVLY 174
Query: 134 VSFHKF-GDLFFPGT--GDVKEIGEREGKFYAINVPLKD-GIDDTSFTRLFKTIISKVVE 189
+S H+F F+PGT GD + +GE G + +N+P G+ D + F+ I+ +
Sbjct: 175 ISLHRFENGGFYPGTPYGDYESVGEGAGLGFNVNIPWPQGGMGDADYIYAFQRIVMPIAY 234
Query: 190 TYAPGAIVLQCGADSLAGDRLGCFNLSIDGHA 221
+ P +++ G D+ GD LG +++ G+A
Sbjct: 235 EFDPDLVIISAGFDAADGDELGQCHVTPAGYA 266
>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 = 94.3 bits (234), Expect = 2e-21
Identities = 51/161 (31%), Positives = 89/161 (55%), Gaps = 13/161 (8%)
Query: 78 HHAKKCEASGFCYINDLVLG--ILELLKYHARVLYIDIDVHHGDGVEEAFYFTDRVMTVS 135
HHA++ GFCY N + + +L+ +++L +D DVHHG+G ++AFY V+ +S
Sbjct: 154 HHAEESTPMGFCYFNSVAIAAKLLQQRLNVSKILIVDWDVHHGNGTQQAFYSDPNVLYMS 213
Query: 136 FHKFGD-LFFPGTGDVKEIGEREGKFYAINVPLKDGID----DTSFTRLFKTIISKVVET 190
H++ D FFPG+G E+G G + +N+ G+D D + F+T++ +
Sbjct: 214 LHRYDDGNFFPGSGAPDEVGTGPGVGFNVNMAFTGGLDPPMGDAEYLAAFRTVVMPIASE 273
Query: 191 YAPGAIVLQCGADSLAGD--RLGCFNLSIDGHAECVRFVKK 229
+AP +++ G D++ G LG +NLS A+C ++ K
Sbjct: 274 FAPDVVLVSSGFDAVEGHPTPLGGYNLS----AKCFGYLTK 310
>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 = 93.2 bits (232), Expect = 3e-21
Identities = 64/256 (25%), Positives = 120/256 (46%), Gaps = 19/256 (7%)
Query: 24 HPMKPHRLYNLGED------CPVFENLFEFCQIYAGGTIDAARRL--NNQLCDIAINWAG 75
MKP L LG++ P + ++ + AG + + +AI
Sbjct: 68 EKMKPRELNRLGKEYDSIYIHP---DSYQCALLAAGCVLQVVEAVLTGESRNGVAIVRPP 124
Query: 76 GLHHAKKCEASGFCYINDLVLGI-LELLKYHA-RVLYIDIDVHHGDGVEEAFYFTDRVMT 133
G HHA++ A GFC+ N++ + KY R+L +D DVHHG+G + F V+
Sbjct: 125 G-HHAEQDTACGFCFFNNVAIAARYAQKKYGLKRILIVDWDVHHGNGTQHMFESDPSVLY 183
Query: 134 VSFHKFGD-LFFPGT--GDVKEIGEREGKFYAINVPL-KDGIDDTSFTRLFKTIISKVVE 189
+S H++ + FFP + G+ +G+ +G+ + +N+P K G+ D + F+ ++ +
Sbjct: 184 ISLHRYDNGSFFPNSPEGNYDVVGKGKGEGFNVNIPWNKGGMGDAEYIAAFQQVVLPIAY 243
Query: 190 TYAPGAIVLQCGADSLAGDRLGCFNLSIDGHAECVRFVKKF-NLPLLVTGGGGYTKENVA 248
+ P +++ G D+ GD LG ++ +G+A + ++V GGY +++
Sbjct: 244 EFNPELVLVSAGFDAARGDPLGGCKVTPEGYAHMTHMLMSLAGGRVIVILEGGYNLTSIS 303
Query: 249 RCWTVETGILLDTELP 264
++ T LL P
Sbjct: 304 ESMSMCTKTLLGDPPP 319
>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 = 92.2 bits (230), Expect = 3e-21
Identities = 45/141 (31%), Positives = 67/141 (47%), Gaps = 8/141 (5%)
Query: 78 HHAKKCEASGFCYINDLVLGILELLKYHA--RVLYIDIDVHHGDGVEEAFYFTDRVMTVS 135
HHA++ +A GFC N++ + L +H RV +D DVHHG+G E+ F RV+ S
Sbjct: 106 HHAERDKAMGFCLFNNVAIAAAHALAHHGLERVAIVDFDVHHGNGTEDIFRDDPRVLFCS 165
Query: 136 FHKFGDLFFPGTGDVKEIGEREGKFYAINVPLKDGIDDTSFTRLFKTIISKVVETYAPGA 195
H+ +PGTG E G +NVPL G F + ++ + P
Sbjct: 166 SHQHP--LYPGTGAPDETGHG----NIVNVPLPAGTGGAEFREAVEDRWLPALDAFKPDL 219
Query: 196 IVLQCGADSLAGDRLGCFNLS 216
I++ G D+ D L NL+
Sbjct: 220 ILISAGFDAHRDDPLAQLNLT 240
>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 = 92.0 bits (228), Expect = 2e-20
Identities = 44/149 (29%), Positives = 85/149 (57%), Gaps = 11/149 (7%)
Query: 78 HHAKKCEASGFCYINDLVLGILELLKYH---ARVLYIDIDVHHGDGVEEAFYFTDRVMTV 134
HHA++ A GFC+ N + + +LL+ ++L +D D+HHG+G ++AFY V+ +
Sbjct: 154 HHAEESTAMGFCFFNSVAIAA-KLLQQKLNVGKILIVDWDIHHGNGTQQAFYNDPNVLYI 212
Query: 135 SFHKFGD-LFFPGTGDVKEIGEREGKFYAINVPLKDGID----DTSFTRLFKTIISKVVE 189
S H++ D FFPG+G E+G G + +N+ G+D D + F+T++ +
Sbjct: 213 SLHRYDDGNFFPGSGAPDEVGAGPGVGFNVNIAWTGGVDPPIGDVEYLTAFRTVVMPIAN 272
Query: 190 TYAPGAIVLQCGADSLAGDR--LGCFNLS 216
++P +++ G D++ G + LG ++++
Sbjct: 273 EFSPDVVLVSAGFDAVEGHQSPLGGYSVT 301
>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 = 90.8 bits (225), Expect = 3e-20
Identities = 45/137 (32%), Positives = 78/137 (56%), Gaps = 7/137 (5%)
Query: 78 HHAKKCEASGFCYINDLVLGILELLKYH--ARVLYIDIDVHHGDGVEEAFYFTDRVMTVS 135
HHA++ A GFC+ N + + L +++L +D+DVHHG+G ++AFY ++ +S
Sbjct: 152 HHAEESTAMGFCFFNSVAITAKYLRDQLNISKILIVDLDVHHGNGTQQAFYADPSILYIS 211
Query: 136 FHKFGD-LFFPGTGDVKEIGEREGKFYAINVPLKDGID----DTSFTRLFKTIISKVVET 190
H++ + FFPG+G E+G G+ Y IN+ G+D D + F+TI+ V +
Sbjct: 212 LHRYDEGNFFPGSGAPNEVGTGLGEGYNINIAWTGGLDPPMGDVEYLEAFRTIVKPVAKE 271
Query: 191 YAPGAIVLQCGADSLAG 207
+ P +++ G D+L G
Sbjct: 272 FDPDMVLVSAGFDALEG 288
>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 = 88.5 bits (219), Expect = 2e-19
Identities = 42/137 (30%), Positives = 73/137 (53%), Gaps = 7/137 (5%)
Query: 78 HHAKKCEASGFCYINDLVLGI--LELLKYHARVLYIDIDVHHGDGVEEAFYFTDRVMTVS 135
HHA A GFC+ N + + L+ +++L +D DVHHG+G ++ FY V+ +S
Sbjct: 152 HHADHSTAMGFCFFNSVAIACRQLQQQGKASKILIVDWDVHHGNGTQQTFYQDPSVLYIS 211
Query: 136 FHKFGD-LFFPGTGDVKEIGEREGKFYAINVPLKDGID----DTSFTRLFKTIISKVVET 190
H+ D FFPG+G V E+G G+ + +NV G+D D + F+ ++ +
Sbjct: 212 LHRHDDGNFFPGSGAVDEVGAGSGEGFNVNVAWAGGLDPPMGDPEYLAAFRIVVMPIARE 271
Query: 191 YAPGAIVLQCGADSLAG 207
++P +++ G D+ G
Sbjct: 272 FSPDLVLVSAGFDAAEG 288
>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 = 68.0 bits (166), Expect = 1e-12
Identities = 57/202 (28%), Positives = 94/202 (46%), Gaps = 23/202 (11%)
Query: 78 HHAKKCEASGFCYINDLVLGILELLKYHA--RVLYIDIDVHHGDGVEEAFYFTDRVMTVS 135
HH+++ A+GFC N++ + K + R+L +D DVHHG G++ F V+ S
Sbjct: 117 HHSQRNAANGFCVFNNVAIAAEYAKKKYGLHRILIVDWDVHHGQGIQYIFEEDPSVLYFS 176
Query: 136 FHKF-GDLFFPG--TGDVKEIGEREGKFYAINVPL-KDGIDDTSFTRLFKTIISKVVETY 191
+H++ F+P D +G +G + IN+P K G+ + + F ++ + +
Sbjct: 177 WHRYEHQRFWPFLRESDYDAVGRGKGLGFNINLPWNKVGMGNADYLAAFFHVLLPLAFEF 236
Query: 192 APGAIVLQCGADSLAGDRLGCFNLSIDGHAECVRFVKKFNLPLLVTGG-------GGYTK 244
P +++ G DS GD G + EC + + L GG GGY
Sbjct: 237 DPELVLVSAGFDSAIGDPEGQMCAT----PECFAHLTHLLMVL--AGGKLCAVLEGGYHL 290
Query: 245 ENVAR--CWTVETGILLDTELP 264
E++A C TV+T LL LP
Sbjct: 291 ESLAESVCMTVQT--LLGDPLP 310
>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 = 67.6 bits (165), Expect = 1e-12
Identities = 45/159 (28%), Positives = 76/159 (47%), Gaps = 8/159 (5%)
Query: 60 RRLNNQLCD-IAINWAGGLHHAKKCEASGFCYINDLVLGILELLKYHA--RVLYIDIDVH 116
+ L ++ + +AI G HHA+ + G+C N++ + + H RVL +D DVH
Sbjct: 99 KVLGGEIRNGLAIVRPPG-HHAQHDKMDGYCMFNNVAIAARYAQQKHGVQRVLIVDWDVH 157
Query: 117 HGDGVEEAFYFTDRVMTVSFHKFGD-LFFP--GTGDVKEIGEREGKFYAINVPL-KDGID 172
HG G + F V+ S H++ F+P D +G G+ Y INVP + G+
Sbjct: 158 HGQGTQFIFEQDPSVLYFSIHRYEQGRFWPHLKESDSSAVGFGRGEGYNINVPWNQVGMR 217
Query: 173 DTSFTRLFKTIISKVVETYAPGAIVLQCGADSLAGDRLG 211
D + F ++ V + P +++ G D++ GD G
Sbjct: 218 DADYIAAFLHVLLPVALEFQPQLVLVAAGFDAVIGDPKG 256
>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 = 46.7 bits (111), Expect = 9e-06
Identities = 18/48 (37%), Positives = 30/48 (62%), Gaps = 2/48 (4%)
Query: 78 HHAKKCEASGFCYINDLVLGILELLKYHA--RVLYIDIDVHHGDGVEE 123
HH + SGFC++N++ +G H RV+ +DID+HHG+G ++
Sbjct: 120 HHCSESTPSGFCWVNNVHVGAAHAYLTHGITRVVILDIDLHHGNGTQD 167
>gnl|CDD|233044 TIGR00600, rad2, DNA excision repair protein (rad2). All proteins
in this family for which functions are known are flap
endonucleases that generate the 3' incision next to DNA
damage as part of nucleotide excision repair. This
family is related to many other flap endonuclease
families including the fen1 family. This family is based
on the phylogenomic analysis of JA Eisen (1999, Ph.D.
Thesis, Stanford University) [DNA metabolism, DNA
replication, recombination, and repair].
Length = 1034
Score = 34.5 bits (79), Expect = 0.11
Identities = 13/53 (24%), Positives = 23/53 (43%), Gaps = 4/53 (7%)
Query: 316 PSVQMQEVPPDFYI-PEFDEDEQNPDERMDQHTQDKQIQRDDEFYEGDNDNDH 367
PSVQ P D Y+ P E+E++ E + + +R ++ + H
Sbjct: 134 PSVQQVPRPQDLYVLPPLPEEEKHSSEEESEKEWE---ERMNQKQALQEEFFH 183
>gnl|CDD|183384 PRK11924, PRK11924, RNA polymerase sigma factor; Provisional.
Length = 179
Score = 30.3 bits (69), Expect = 1.1
Identities = 19/81 (23%), Positives = 29/81 (35%), Gaps = 10/81 (12%)
Query: 279 ECSLRIPNGHIENLNSKS----YLSTIKMQVL-ENLRSIQHAPSVQMQEVPPDFYIPEFD 333
E LR + N K +L TI V + LR + +V + PEF
Sbjct: 46 EAFLRAWR-KADLFNGKGSARTWLLTIARNVCYDLLRRRRREKAVLSDDALE----PEFA 100
Query: 334 EDEQNPDERMDQHTQDKQIQR 354
E + P+ + +I R
Sbjct: 101 ETAETPEAALLAKDDLARIDR 121
>gnl|CDD|216142 pfam00834, Ribul_P_3_epim, Ribulose-phosphate 3 epimerase family.
This enzyme catalyzes the conversion of D-ribulose
5-phosphate into D-xylulose 5-phosphate.
Length = 201
Score = 30.0 bits (68), Expect = 1.4
Identities = 14/36 (38%), Positives = 18/36 (50%), Gaps = 1/36 (2%)
Query: 300 TIKMQVLENLRSIQHAP-SVQMQEVPPDFYIPEFDE 334
TI V+E LR + P V + PD IP+F E
Sbjct: 43 TIGPLVVEALRPLTELPLDVHLMVEEPDRIIPDFAE 78
>gnl|CDD|218685 pfam05673, DUF815, Protein of unknown function (DUF815). This
family consists of several bacterial proteins of unknown
function.
Length = 248
Score = 29.8 bits (68), Expect = 2.0
Identities = 11/27 (40%), Positives = 16/27 (59%), Gaps = 1/27 (3%)
Query: 114 DVHHGDGVEEAFYFTDRV-MTVSFHKF 139
++H GD VEE +DR + + FH F
Sbjct: 167 EIHPGDAVEEKLSLSDRFGLWLGFHPF 193
>gnl|CDD|216574 pfam01565, FAD_binding_4, FAD binding domain. This family consists
of various enzymes that use FAD as a co-factor, most of
the enzymes are similar to oxygen oxidoreductase. One of
the enzymes Vanillyl-alcohol oxidase (VAO) has a solved
structure, the alignment includes the FAD binding site,
called the PP-loop, between residues 99-110. The FAD
molecule is covalently bound in the known structure,
however the residue that links to the FAD is not in the
alignment. VAO catalyzes the oxidation of a wide variety
of substrates, ranging form aromatic amines to
4-alkylphenols. Other members of this family include
D-lactate dehydrogenase, this enzyme catalyzes the
conversion of D-lactate to pyruvate using FAD as a
co-factor; mitomycin radical oxidase, this enzyme
oxidises the reduced form of mitomycins and is involved
in mitomycin resistance. This family includes MurB an
UDP-N-acetylenolpyruvoylglucosamine reductase enzyme
EC:1.1.1.158. This enzyme is involved in the
biosynthesis of peptidoglycan.
Length = 139
Score = 29.1 bits (66), Expect = 2.0
Identities = 17/58 (29%), Positives = 25/58 (43%), Gaps = 8/58 (13%)
Query: 221 AECVRFVKKFNLPLLVTGGGGYTKENVARCWTVETGILLDTELPNEI----PENEYIK 274
A VR + LP+LV GGG ++ + G++LD N I PE+
Sbjct: 14 AAIVRLANENGLPVLVRGGG----SSLLGDAVLTGGVVLDLSRLNGILEIDPEDGTAT 67
>gnl|CDD|219599 pfam07832, Bse634I, Cfr10I/Bse634I restriction endonuclease.
Cfr10I and Bse634I are two Type II restriction
endonucleases. They exhibit a conserved tetrameric
architecture that is of functional importance, wherein
two dimers are arranged 'back-to-back' with their
putative DNA-binding clefts facing opposite directions.
These clefts are formed between two monomers that
interact, mainly via hydrophobic interactions supported
by a few hydrogen bonds, to form a U-shaped dimer. Each
monomer is folded to form a compact alpha-beta
structure, whose core is made up of a five-stranded
mixed beta-sheet.The monomer may be split into separate
N-terminal and C-terminal subdomains at a hinge located
in helix alpha3.
Length = 281
Score = 29.8 bits (67), Expect = 2.1
Identities = 15/68 (22%), Positives = 27/68 (39%), Gaps = 6/68 (8%)
Query: 291 NLNSKSYLSTIK---MQVLENLRSIQHAPSVQMQEVPPDFYIPEFDEDEQNPD---ERMD 344
N S ++S K +V+ LR+ +V + PD + E+ +N D +
Sbjct: 101 NSYSFDFVSLFKPESQEVIYELRAKLRKDNVGLPTSNPDLAVIVLPEEFKNKDIWNSEIA 160
Query: 345 QHTQDKQI 352
T+ Q
Sbjct: 161 GLTRPNQD 168
>gnl|CDD|181604 PRK08990, PRK08990, flagellar motor protein PomA; Reviewed.
Length = 254
Score = 28.5 bits (64), Expect = 5.5
Identities = 14/38 (36%), Positives = 17/38 (44%), Gaps = 1/38 (2%)
Query: 113 IDVHHGDGVEEAFYFTDRVMTVSFHKFGDLFFPGTGDV 150
+D H GD V A D +T H+ G F GDV
Sbjct: 113 VDGHDGDVVRAALE-KDIALTEERHETGIGIFRAFGDV 149
>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 = 28.3 bits (64), Expect = 7.2
Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 11/53 (20%)
Query: 98 ILELLKYHARVLYIDIDVH-------HGDGVEEAFYFTDRV--MTVSFHK-FG 140
+++L K + +L++D + H HG GVEE TD V + + K FG
Sbjct: 154 LVDLAKKYGAILFVD-EAHSVGVYGPHGRGVEEFGGLTDDVDIIMGTLGKAFG 205
>gnl|CDD|224403 COG1486, CelF, Alpha-galactosidases/6-phospho-beta-glucosidases,
family 4 of glycosyl hydrolases [Carbohydrate transport
and metabolism].
Length = 442
Score = 28.4 bits (64), Expect = 7.5
Identities = 26/113 (23%), Positives = 38/113 (33%), Gaps = 27/113 (23%)
Query: 98 ILELLKYHARVLYIDIDVHHGDGVEEAFYFTDRVMTVSFHKFGDLFFPGTGDVKEIGERE 157
I L K + V EA D V+T G + +E ER
Sbjct: 48 IAILAKKLVEEAGAPVKVEATTDRREALEGADFVITQ--------IRVGGLEAREKDER- 98
Query: 158 GKFYAINVPLKDGID--DTS----FTRLFKTI-----ISKVVETYAPGAIVLQ 199
+PLK G+ +T+ +TI I+K +E P A +L
Sbjct: 99 -------IPLKHGLYGQETNGPGGIFYGLRTIPVILDIAKDMEKVCPNAWMLN 144
>gnl|CDD|215145 PLN02258, PLN02258, 9-cis-epoxycarotenoid dioxygenase NCED.
Length = 590
Score = 28.1 bits (63), Expect = 8.7
Identities = 21/65 (32%), Positives = 33/65 (50%), Gaps = 9/65 (13%)
Query: 96 LGILELLKYHARVLYIDIDVHHGDGVEEA--FYFTDRVMTVSFHKFGDLFF----PGTGD 149
GI L+ ++AR L+ +D G GV A YF R++ +S DL + G GD
Sbjct: 213 SGIARLMLFYARGLFGLVDASRGTGVANAGLVYFNGRLLAMSED---DLPYQVRITGDGD 269
Query: 150 VKEIG 154
++ +G
Sbjct: 270 LETVG 274
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
0.321 0.141 0.437
Gapped
Lambda K H
0.267 0.0776 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 19,623,934
Number of extensions: 1940243
Number of successful extensions: 1735
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1666
Number of HSP's successfully gapped: 58
Length of query: 371
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 273
Effective length of database: 6,590,910
Effective search space: 1799318430
Effective search space used: 1799318430
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 60 (26.8 bits)