RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 013038
(451 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 = 624 bits (1612), Expect = 0.0
Identities = 239/403 (59%), Positives = 305/403 (75%), Gaps = 25/403 (6%)
Query: 6 KISYFYDGDVGSVYFGPNHPMKPHRLCMTHHLVLSYDLHKKMEIYRPHKAYPVELAQFHS 65
+++YFYD DVG+ ++GP HPMKPHRL +TH LVL Y L+KKM++Y+P++A ++ +FHS
Sbjct: 2 RVAYFYDPDVGNFHYGPGHPMKPHRLALTHSLVLHYGLYKKMQVYKPYRASAHDMCRFHS 61
Query: 66 ADYVEFLHRITPDTQHLFRQELTKYNLGEDCPVFENLFEFCQIYAGGTIDAARRLNNQLC 125
DY++FL R+TP F + L ++N+G+DCPVF LF+FC +Y G +++ A +LN+++C
Sbjct: 62 EDYIDFLQRVTPQNIQGFTKSLNQFNVGDDCPVFPGLFDFCSMYTGASLEGATKLNHKIC 121
Query: 126 DIAINWAGGLHHAKKCEASGFCYINDLVLGILELLKYHARVLYIDIDVHHGDGVEEAFYF 185
DIAINW+GGLHHAKK EASGFCY+ND+V+ ILELLKYH RVLYIDID+HHGDGV+EAFY
Sbjct: 122 DIAINWSGGLHHAKKFEASGFCYVNDIVIAILELLKYHPRVLYIDIDIHHGDGVQEAFYL 181
Query: 186 TDRLLQTCRYNLTKYLILVTYPDVKVMTVSFHKFGDLFFPGTGDVKEIGEREGKFYAINV 245
TDR VMTVSFHK+G+ FFPGTGD+ E+G G++Y++NV
Sbjct: 182 TDR----------------------VMTVSFHKYGNYFFPGTGDMYEVGAESGRYYSVNV 219
Query: 246 PLKDGIDDTSFTRLFKTIISKVVETYAPGAIVLQCGADSLAGDRLGCFNLSIDGHAECVR 305
PLKDGIDD S+ +LFK +I +V++ Y P IVLQCGADSL DRLGCFNLSI GH ECV
Sbjct: 220 PLKDGIDDQSYLQLFKPVIQQVIDFYQPTCIVLQCGADSLGCDRLGCFNLSIKGHGECVE 279
Query: 306 FVKKFNLPLLVTGGGGYTKENVARCWTVETGILLDTELPNEIPENEYIKYFAPECSLRIP 365
FVK FN+PLLV GGGGYT NVARCWT ET +L+D E+ NE+P NEY +YFAP+ +L P
Sbjct: 280 FVKSFNIPLLVLGGGGYTVRNVARCWTYETSLLVDEEISNELPYNEYFEYFAPDFTLH-P 338
Query: 366 N--GHIENLNSKSYLSTIKMQVLENLRSIQHAPSVQMQEVPPD 406
+ IEN NSK YL I+ V ENL+ + HAPSVQMQ+VPPD
Sbjct: 339 DVSTRIENQNSKQYLDQIRQTVFENLKMLNHAPSVQMQDVPPD 381
>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 = 583 bits (1505), Expect = 0.0
Identities = 208/329 (63%), Positives = 254/329 (77%), Gaps = 23/329 (6%)
Query: 10 FYDGDVGSVYFGPNHPMKPHRLCMTHHLVLSYDLHKKMEIYRPHKAYPVELAQFHSADYV 69
FYD DVG+ Y+G HPMKPHR+ MTH L+LSY L+KKMEIYRP A EL +FHS DY+
Sbjct: 1 FYDPDVGNYYYGQGHPMKPHRIRMTHSLILSYGLYKKMEIYRPRPATAEELTKFHSDDYI 60
Query: 70 EFLHRITPDTQHLFRQELTKYNLGEDCPVFENLFEFCQIYAGGTIDAARRLNNQLCDIAI 129
+FL ++PD F+++L ++N+GEDCPVF+ L+E+CQ+YAGG+I AA +LN DIAI
Sbjct: 61 DFLRSVSPDNMKEFKKQLERFNVGEDCPVFDGLYEYCQLYAGGSIAAAVKLNRGQADIAI 120
Query: 130 NWAGGLHHAKKCEASGFCYINDLVLGILELLKYHARVLYIDIDVHHGDGVEEAFYFTDRL 189
NWAGGLHHAKK EASGFCY+ND+VL ILELLKYH RVLYIDID+HHGDGVEEAFY TDR
Sbjct: 121 NWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDR- 179
Query: 190 LQTCRYNLTKYLILVTYPDVKVMTVSFHKFGDLFFPGTGDVKEIGEREGKFYAINVPLKD 249
VMTVSFHKFG+ +F +++IG +GK+YA+NVPLKD
Sbjct: 180 ---------------------VMTVSFHKFGE-YFFPGTGLRDIGAGKGKYYAVNVPLKD 217
Query: 250 GIDDTSFTRLFKTIISKVVETYAPGAIVLQCGADSLAGDRLGCFNLSIDGHAECVRFVKK 309
GIDD S+ ++F+ ++SKV+E + P A+VLQCGADSLAGDRLGCFNLSI GHA+CV+FVK
Sbjct: 218 GIDDESYLQIFEPVLSKVMEVFQPSAVVLQCGADSLAGDRLGCFNLSIKGHAKCVKFVKS 277
Query: 310 FNLPLLVTGGGGYTKENVARCWTVETGIL 338
FN+PLLV GGGGYT NVARCWT ET +L
Sbjct: 278 FNIPLLVLGGGGYTLRNVARCWTYETAVL 306
>gnl|CDD|240251 PTZ00063, PTZ00063, histone deacetylase; Provisional.
Length = 436
Score = 581 bits (1499), Expect = 0.0
Identities = 252/425 (59%), Positives = 306/425 (72%), Gaps = 28/425 (6%)
Query: 6 KISYFYDGDVGSVYFGPNHPMKPHRLCMTHHLVLSYDLHKKMEIYRPHKAYPVELAQFHS 65
++SYFYD D+GS Y+GP HPMKP R+ M H L+LSYDL+K MEIYRPHK+ EL FH
Sbjct: 5 RVSYFYDPDIGSYYYGPGHPMKPQRIRMAHALILSYDLYKHMEIYRPHKSVEPELVLFHD 64
Query: 66 ADYVEFLHRITPDTQHLFRQELTKYNLGE--DCPVFENLFEFCQIYAGGTIDAARRLNNQ 123
+YV+FL I+P+ F +L ++N+GE DCPVF+ LFEF Q AG +ID A +LNN
Sbjct: 65 EEYVDFLSSISPENYRDFTYQLKRFNVGEATDCPVFDGLFEFQQSCAGASIDGAYKLNNH 124
Query: 124 LCDIAINWAGGLHHAKKCEASGFCYINDLVLGILELLKYHARVLYIDIDVHHGDGVEEAF 183
DI +NW+GGLHHAK+ EASGFCYIND+VLGILELLKYHARV+YIDIDVHHGDGVEEAF
Sbjct: 125 QADICVNWSGGLHHAKRSEASGFCYINDIVLGILELLKYHARVMYIDIDVHHGDGVEEAF 184
Query: 184 YFTDRLLQTCRYNLTKYLILVTYPDVKVMTVSFHKFGDLFFPGTGDVKEIGEREGKFYAI 243
Y T R VMTVSFHKFGD FFPGTGDV +IG +GK+Y++
Sbjct: 185 YVTHR----------------------VMTVSFHKFGD-FFPGTGDVTDIGVAQGKYYSV 221
Query: 244 NVPLKDGIDDTSFTRLFKTIISKVVETYAPGAIVLQCGADSLAGDRLGCFNLSIDGHAEC 303
NVPL DGIDD SF LFK +ISK VE Y PGAIVLQCGADSL GDRLG FNL+I GHA C
Sbjct: 222 NVPLNDGIDDDSFVDLFKPVISKCVEVYRPGAIVLQCGADSLTGDRLGRFNLTIKGHAAC 281
Query: 304 VRFVKKFNLPLLVTGGGGYTKENVARCWTVETGILLD--TELPNEIPENEYIKYFAPECS 361
V FV+ N+PLLV GGGGYT NVARCW ETG++L+ E+ ++I N+Y Y+AP+
Sbjct: 282 VEFVRSLNIPLLVLGGGGYTIRNVARCWAYETGVILNKHDEMSDQISLNDYYDYYAPDFQ 341
Query: 362 LRIPNGHIENLNSKSYLSTIKMQVLENLRSIQHAPSVQMQEVPPDFYIPEFD-EDEQNPD 420
L + +I N NS +L IK+++LENLR ++HAP VQ VPPDF+ + D EDE+N
Sbjct: 342 LHLQPSNIPNYNSPEHLEKIKVKILENLRYLEHAPGVQFAYVPPDFFDRDIDDEDEKNQY 401
Query: 421 ERMDQ 425
E D+
Sbjct: 402 ELSDE 406
>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 = 554 bits (1429), Expect = 0.0
Identities = 234/398 (58%), Positives = 290/398 (72%), Gaps = 23/398 (5%)
Query: 4 KDKISYFYDGDVGSVYFGPNHPMKPHRLCMTHHLVLSYDLHKKMEIYRPHKAYPVELAQF 63
K K++YFYD DVG+ +GP HPMKPHR+ M H LV++Y L+KKMEIYR A E+ QF
Sbjct: 1 KKKVAYFYDSDVGNYAYGPGHPMKPHRIRMAHSLVMNYGLYKKMEIYRAKPATKNEMTQF 60
Query: 64 HSADYVEFLHRITPDTQHLFRQELTKYNLGEDCPVFENLFEFCQIYAGGTIDAARRLNNQ 123
H+ +Y++FL R+TPD F++E KYN+G+DCPVF+ LFEFC I AGG+++ A RLN
Sbjct: 61 HTDEYIDFLSRVTPDNMEKFQKEQVKYNVGDDCPVFDGLFEFCSISAGGSMEGAARLNRG 120
Query: 124 LCDIAINWAGGLHHAKKCEASGFCYINDLVLGILELLKYHARVLYIDIDVHHGDGVEEAF 183
CDIA+NWAGGLHHAKK EASGFCY+ND+VLGILELL+YH RVLYIDIDVHHGDGVEEAF
Sbjct: 121 KCDIAVNWAGGLHHAKKSEASGFCYVNDIVLGILELLRYHQRVLYIDIDVHHGDGVEEAF 180
Query: 184 YFTDRLLQTCRYNLTKYLILVTYPDVKVMTVSFHKFGDLFFPGTGDVKEIGEREGKFYAI 243
Y TDR VMT SFHK+G+ +FPGTG++++IG GK YA+
Sbjct: 181 YTTDR----------------------VMTCSFHKYGE-YFPGTGELRDIGIGTGKNYAV 217
Query: 244 NVPLKDGIDDTSFTRLFKTIISKVVETYAPGAIVLQCGADSLAGDRLGCFNLSIDGHAEC 303
NVPL+DGIDD S+ +F+ +I V+E Y P A+VLQCG DSL+GDRLGCFNLS+ GHA C
Sbjct: 218 NVPLRDGIDDESYKSIFEPVIKHVMEWYQPEAVVLQCGGDSLSGDRLGCFNLSMKGHANC 277
Query: 304 VRFVKKFNLPLLVTGGGGYTKENVARCWTVETGILLDTELPNEIPENEYIKYFAPECSLR 363
V FVK FNLP+LV GGGGYT NVAR W ETG+L EL ++P NEY +Y+ P+ L
Sbjct: 278 VNFVKSFNLPMLVLGGGGYTMRNVARTWAFETGLLAGEELDKDLPYNEYYEYYGPDYELN 337
Query: 364 IPNGHIENLNSKSYLSTIKMQVLENLRSIQHAPSVQMQ 401
+ ++EN N+ YL I V+ENLR+ APSVQMQ
Sbjct: 338 VRPSNMENHNTPEYLDKITTAVIENLRNTSFAPSVQMQ 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 = 498 bits (1284), Expect = e-177
Identities = 230/390 (58%), Positives = 298/390 (76%), Gaps = 23/390 (5%)
Query: 3 SKDKISYFYDGDVGSVYFGPNHPMKPHRLCMTHHLVLSYDLHKKMEIYRPHKAYPVELAQ 62
+K K+ Y+YDGDVG+ Y+G HPMKPHR+ MTH+L+L+Y L++KMEIYRPHKA E+ +
Sbjct: 4 TKKKVCYYYDGDVGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKANAEEMTK 63
Query: 63 FHSADYVEFLHRITPDTQHLFRQELTKYNLGEDCPVFENLFEFCQIYAGGTIDAARRLNN 122
+HS DY++FL I PD + +++ ++N+GEDCPVF+ LFEFCQ+ AGG++ +A +LN
Sbjct: 64 YHSDDYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSAGGSVASAVKLNK 123
Query: 123 QLCDIAINWAGGLHHAKKCEASGFCYINDLVLGILELLKYHARVLYIDIDVHHGDGVEEA 182
Q DIA+NWAGGLHHAKK EASGFCY+ND+VL ILELLKYH RVLYIDID+HHGDGVEEA
Sbjct: 124 QQTDIAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEA 183
Query: 183 FYFTDRLLQTCRYNLTKYLILVTYPDVKVMTVSFHKFGDLFFPGTGDVKEIGEREGKFYA 242
FY TDR VMTVSFHK+G+ +FPGTGD+++IG +GK+YA
Sbjct: 184 FYTTDR----------------------VMTVSFHKYGE-YFPGTGDLRDIGAGKGKYYA 220
Query: 243 INVPLKDGIDDTSFTRLFKTIISKVVETYAPGAIVLQCGADSLAGDRLGCFNLSIDGHAE 302
+N PL+DGIDD S+ +FK ++SKV+E + P A+VLQCGADSL+GDRLGCFNL+I GHA+
Sbjct: 221 VNYPLRDGIDDESYEAIFKPVMSKVMEMFQPSAVVLQCGADSLSGDRLGCFNLTIKGHAK 280
Query: 303 CVRFVKKFNLPLLVTGGGGYTKENVARCWTVETGILLDTELPNEIPENEYIKYFAPECSL 362
CV FVK FNLP+L+ GGGGYT NVARCWT ET + LD+E+PNE+P N+Y +YF P+ L
Sbjct: 281 CVEFVKSFNLPMLMLGGGGYTIRNVARCWTYETAVALDSEIPNELPYNDYFEYFGPDFKL 340
Query: 363 RIPNGHIENLNSKSYLSTIKMQVLENLRSI 392
I ++ N N+ YL IK ++ ENLR +
Sbjct: 341 HISPSNMTNQNTNEYLEKIKQRLFENLRML 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 = 484 bits (1248), Expect = e-171
Identities = 218/389 (56%), Positives = 287/389 (73%), Gaps = 23/389 (5%)
Query: 4 KDKISYFYDGDVGSVYFGPNHPMKPHRLCMTHHLVLSYDLHKKMEIYRPHKAYPVELAQF 63
K K+ Y+YDGD+G+ Y+G HPMKPHR+ MTH+L+L+Y L++KMEIYRPHKA E+ ++
Sbjct: 1 KKKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTKY 60
Query: 64 HSADYVEFLHRITPDTQHLFRQELTKYNLGEDCPVFENLFEFCQIYAGGTIDAARRLNNQ 123
HS +Y++FL I PD + +++ ++N+GEDCPVF+ LFEFCQ+ GG++ A +LN Q
Sbjct: 61 HSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAGAVKLNRQ 120
Query: 124 LCDIAINWAGGLHHAKKCEASGFCYINDLVLGILELLKYHARVLYIDIDVHHGDGVEEAF 183
D+A+NWAGGLHHAKK EASGFCY+ND+VL ILELLKYH RVLYIDID+HHGDGVEEAF
Sbjct: 121 QTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAF 180
Query: 184 YFTDRLLQTCRYNLTKYLILVTYPDVKVMTVSFHKFGDLFFPGTGDVKEIGEREGKFYAI 243
Y TDR++ + +Y FPGTGD+++IG +GK+YA+
Sbjct: 181 YTTDRVMTVSFHKYGEY-----------------------FPGTGDLRDIGAGKGKYYAV 217
Query: 244 NVPLKDGIDDTSFTRLFKTIISKVVETYAPGAIVLQCGADSLAGDRLGCFNLSIDGHAEC 303
N P++DGIDD S+ ++FK IISKV+E Y P A+VLQCGADSL+GDRLGCFNL++ GHA+C
Sbjct: 218 NFPMRDGIDDESYGQIFKPIISKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKC 277
Query: 304 VRFVKKFNLPLLVTGGGGYTKENVARCWTVETGILLDTELPNEIPENEYIKYFAPECSLR 363
V VK FNLPLL+ GGGGYT NVARCWT ET + LD E+PNE+P N+Y +YF P+ L
Sbjct: 278 VEVVKTFNLPLLMLGGGGYTIRNVARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLH 337
Query: 364 IPNGHIENLNSKSYLSTIKMQVLENLRSI 392
I ++ N N+ Y+ IK ++ ENLR +
Sbjct: 338 ISPSNMTNQNTPEYMEKIKQRLFENLRML 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 = 470 bits (1211), Expect = e-166
Identities = 182/333 (54%), Positives = 229/333 (68%), Gaps = 23/333 (6%)
Query: 7 ISYFYDGDVGSVYFGPNHPMKPHRLCMTHHLVLSYDLHKKMEIYRPHKAYPVELAQFHSA 66
+SY ++ V +FG HPMKP RL +T HLV+ Y LHK M+ Y A EL QFH A
Sbjct: 1 VSYHFNSRVEDYHFGRTHPMKPFRLTLTKHLVMGYGLHKAMDTYEARAATREELRQFHDA 60
Query: 67 DYVEFLHRITPDTQ-HLFRQELTKYNLGEDCPVFENLFEFCQIYAGGTIDAARRLNNQLC 125
DY++FL +++P+ L + +N+G+DCPVF+ ++++CQ+YAG ++DAAR+L +
Sbjct: 61 DYLDFLSKVSPENANQLRFDKAEPFNIGDDCPVFDGMYDYCQLYAGASLDAARKLCSGQS 120
Query: 126 DIAINWAGGLHHAKKCEASGFCYINDLVLGILELLKYHARVLYIDIDVHHGDGVEEAFYF 185
DIAINW+GGLHHAKK EASGFCY+ND+VL IL LL+Y RVLYIDIDVHHGDGVEEAFY
Sbjct: 121 DIAINWSGGLHHAKKSEASGFCYVNDIVLAILNLLRYFPRVLYIDIDVHHGDGVEEAFYR 180
Query: 186 TDRLLQTCRYNLTKYLILVTYPDVKVMTVSFHKFGDLFFPGTGDVKEIGEREGKFYAINV 245
TDR VMT+SFHK+ FFPGTGD+ + G GK +A+NV
Sbjct: 181 TDR----------------------VMTLSFHKYNGEFFPGTGDLDDNGGTPGKHFALNV 218
Query: 246 PLKDGIDDTSFTRLFKTIISKVVETYAPGAIVLQCGADSLAGDRLGCFNLSIDGHAECVR 305
PL+DGIDD + LFK+II +E + P AIVLQCGADSL GDRLG FNL+I H CV+
Sbjct: 219 PLEDGIDDEQYNLLFKSIIGPTIEKFQPSAIVLQCGADSLGGDRLGQFNLNIKAHGACVK 278
Query: 306 FVKKFNLPLLVTGGGGYTKENVARCWTVETGIL 338
FVK F +P+LV GGGGYT NVAR W ET +
Sbjct: 279 FVKSFGIPMLVVGGGGYTPRNVARAWCYETAVA 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 = 390 bits (1005), Expect = e-134
Identities = 157/373 (42%), Positives = 230/373 (61%), Gaps = 25/373 (6%)
Query: 23 NHPMKPHRLCMTHHLVLSYDLHKKMEIYRPHKAYPVELAQFHSADYVEFLHRITP--DTQ 80
P P+R M H L+ +Y L K++ + +P A ELA FHS +Y++FL + + D
Sbjct: 15 RLPKVPNRASMVHSLIEAYGLLKQLRVVKPRVATEEELASFHSDEYIQFLKKASNEGDND 74
Query: 81 HLFRQELTKYNLGEDCPVFENLFEFCQIYAGGTIDAARRLNNQLCDIAINWAGGLHHAKK 140
E ++ LG DCP+FE ++++ AG T+ AA+ L + C +AINW GG HHA++
Sbjct: 75 EEP-SEQQEFGLGYDCPIFEGIYDYAAAVAGATLTAAQLLIDGKCKVAINWFGGWHHAQR 133
Query: 141 CEASGFCYINDLVLGILELLKYHARVLYIDIDVHHGDGVEEAFYFTDRLLQTCRYNLTKY 200
EASGFCY+ND+VLGIL+L + RVLY+D+D+HHGDGVE+AF FT
Sbjct: 134 DEASGFCYVNDIVLGILKLREKFDRVLYVDLDLHHGDGVEDAFSFTS------------- 180
Query: 201 LILVTYPDVKVMTVSFHKFGDLFFPGTGDVKEIGEREGKFYAINVPLKDGIDDTSFTRLF 260
KVMTVS HK+ FFPGTGDV ++G +GK+Y +NVPL+DGI D + ++F
Sbjct: 181 ---------KVMTVSLHKYSPGFFPGTGDVSDVGLGKGKYYTVNVPLRDGIQDEQYLQIF 231
Query: 261 KTIISKVVETYAPGAIVLQCGADSLAGDRLGCFNLSIDGHAECVRFVKKFNLPLLVTGGG 320
++ ++V + P A+VLQCGAD+LAGD +G FNL+ G +C+++V + LP L+ GGG
Sbjct: 232 TAVVPEIVAAFRPEAVVLQCGADTLAGDPMGAFNLTPVGIGKCLKYVLGWKLPTLILGGG 291
Query: 321 GYTKENVARCWTVETGILLDTELPNEIPENEYIKYFAPECSLRIPNGHIENLNSKSYLST 380
GY N ARCWT TG++L L ++IP++E+ + P+ L I +LN Y+
Sbjct: 292 GYNLANTARCWTYLTGLILGEPLSSDIPDHEFFTSYGPDYELEISPSLRPDLNEDQYIEK 351
Query: 381 IKMQVLENLRSIQ 393
I + NL+++
Sbjct: 352 ILETIKGNLKNVV 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 = 313 bits (805), Expect = e-104
Identities = 110/362 (30%), Positives = 159/362 (43%), Gaps = 40/362 (11%)
Query: 6 KISYFYDGDVGSVYFGPNHPMKPHRLCMTHHLVLSYDLHKKMEIYRPHKAYPVELAQFHS 65
K + Y + P HP P RL + L+ S L +E+ P A EL HS
Sbjct: 3 KTALIYHPEFLEHEPPPGHPENPDRLRLILELLESSGLPDSLELVEPRPATLEELLLVHS 62
Query: 66 ADYVEFLHRITPDTQHLFRQELTKYNLGEDCPVFENLFEFCQIYAGGTIDAARRLNNQLC 125
DYVEFL ++ + NL D PV +E ++ AGG + A +
Sbjct: 63 PDYVEFLESLSEEEG--------YGNLDGDTPVSPGTYEAARLAAGGALTAVDAVLEGED 114
Query: 126 DIAINWAGGLHHAKKCEASGFCYINDLVLGILELLK-YHARVLYIDIDVHHGDGVEEAFY 184
+ HHA + ASGFC N++ + LLK RV ID DVHHG+G +E FY
Sbjct: 115 NAFALVRPPGHHAGRDRASGFCLFNNVAIAAKYLLKKGVKRVAIIDFDVHHGNGTQEIFY 174
Query: 185 FTDRLLQTCRYNLTKYLILVTYPDVKVMTVSFHKFGDLFFPGTGDVKEIGEREGKFYAIN 244
D V+TVS H+ G F+PGTG EIGE + +N
Sbjct: 175 DDDD----------------------VLTVSLHQDGRPFYPGTGGADEIGE-GKEGNNVN 211
Query: 245 VPLKDGIDDTSFTRLFKTIISKVVETYAPGAIVLQCGADSLAGDRLGCFNLSIDGHAECV 304
+PL G D S+ + I+ ++E + P +++ G D+ GD LG NL+ +G+A+
Sbjct: 212 IPLPPGTGDDSYLEALEEIVLPLLEEFKPDLVIVSAGFDAHRGDPLGRLNLTEEGYAKIG 271
Query: 305 RFVKKFNL----PLLVTGGGGYTKENVARCWTVETGILLD---TELPNEIPEN-EYIKYF 356
R V+K P++ GGY + +AR L EL +PE+ E + F
Sbjct: 272 RAVRKLAEGYGGPVVAVLEGGYNLDALARSLVAFLAGLAGLVEEELEEPLPEDLELRRAF 331
Query: 357 AP 358
Sbjct: 332 RA 333
>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 = 312 bits (802), Expect = e-104
Identities = 125/331 (37%), Positives = 163/331 (49%), Gaps = 32/331 (9%)
Query: 9 YFYDGDVGSVYFGPNHPMKPHRLCMTHHLVLSYDLHKKMEIYRPHKAYPVELAQFHSADY 68
+ Y + FGPNHP P RL +T L+ + L +++ P A EL FH+ DY
Sbjct: 2 FIYSEEYLRYSFGPNHPFNPPRLSLTKDLLRALGLLPPVDLVPPRPATEEELLLFHTPDY 61
Query: 69 VEFLHRITPDTQHLFRQELTKYNLG-EDCPVFENLFEFCQIYAGGTIDAARRLNNQLCDI 127
+E + + + R + LG ED PVF + E + GGT+ AAR +
Sbjct: 62 IEAVKEASRGQEPEGRG---RLGLGTEDNPVFPGMHEAAALVVGGTLLAARLVLEGEARR 118
Query: 128 AINWAGGLHHAKKCEASGFCYINDLVLGILELL-KYHARVLYIDIDVHHGDGVEEAFYFT 186
A N AGGLHHA + ASGFC ND + I L K RV Y+DID HHGDGV+ AFY
Sbjct: 119 AFNPAGGLHHAMRGRASGFCVYNDAAVAIERLRDKGGLRVAYVDIDAHHGDGVQAAFYDD 178
Query: 187 DRLLQTCRYNLTKYLILVTYPDVKVMTVSFHKFGDLFFPGTGDVKEIGEREGKFYAINVP 246
R V+T+S H+ G FPGTG V EIGE EG YA+N+P
Sbjct: 179 PR----------------------VLTISLHESGRYLFPGTGFVDEIGEGEGYGYAVNIP 216
Query: 247 LKDGIDDTSFTRLFKTIISKVVETYAPGAIVLQCGADSLAGDRLGCFNLSIDGHAECVRF 306
L G D F R F+ ++ ++ + P IV Q GAD+ AGD L NLS + VR
Sbjct: 217 LPPGTGDDEFLRAFEAVVPPLLRAFRPDVIVSQHGADAHAGDPLTHLNLSNRAYRAAVRR 276
Query: 307 VK-----KFNLPLLVTGGGGYTKENVARCWT 332
++ L GGGGY + VAR W
Sbjct: 277 IRELADEYCGGRWLALGGGGYNPDVVARAWA 307
>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 = 303 bits (778), Expect = e-101
Identities = 106/328 (32%), Positives = 155/328 (47%), Gaps = 38/328 (11%)
Query: 19 YFGPNHPMKPHRLCMTHHLVLSYDLHKKMEIYRPHKAYPVELAQFHSADYVEFLHRITPD 78
G HP P RL L+ L ++E P A EL HS +YVEFL + +
Sbjct: 4 GSGLGHPENPERLEAILELLKESGLLDRLEFIAPRPATEEELLLVHSPEYVEFLEEASLE 63
Query: 79 TQHLFRQELTKYNLGEDCPVFENLFEFCQIYAGGTIDAARR-LNNQLCDIAINWAGGLHH 137
+EL + L D PV +E + AGGT++AA L+ + A+ G HH
Sbjct: 64 -----EEELGRIGLDGDTPVSPGSYEAALLAAGGTLEAADLVLSGENAFAAVRPPG--HH 116
Query: 138 AKKCEASGFCYINDLVLGILELLKYH--ARVLYIDIDVHHGDGVEEAFYFTDRLLQTCRY 195
A++ ASGFC N++ + LLK + RVL +D+DVHHG+G +E FY R
Sbjct: 117 AERDRASGFCLFNNVAIAARYLLKRYGLKRVLIVDLDVHHGNGTQEIFYDDPR------- 169
Query: 196 NLTKYLILVTYPDVKVMTVSFHKFGDLFFPGTGDVKEIGEREGKFYAINVPLKDGIDDTS 255
V+T+S H+ F+PGTG E GE G+ Y +N+PL G D
Sbjct: 170 ---------------VLTISIHQDP--FYPGTGFADETGEGAGEGYTLNIPLPPGTGDEE 212
Query: 256 FTRLFKTIISKVVETYAPGAIVLQCGADSLAGDRLGCFNLSIDGHAECVRFVKKF----N 311
+ F+ I+ + + P I++ G D+ AGD LG NL+ +G+AE R + +
Sbjct: 213 YLAAFEEILLPALREFQPDLILVSAGFDAHAGDPLGGLNLTTEGYAERTRLLLELADAYG 272
Query: 312 LPLLVTGGGGYTKENVARCWTVETGILL 339
P++ GGY + +AR LL
Sbjct: 273 GPVVSVLEGGYNLDALARSAAAVLAGLL 300
>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 = 274 bits (702), Expect = 1e-89
Identities = 119/314 (37%), Positives = 169/314 (53%), Gaps = 45/314 (14%)
Query: 30 RLCMTHHLVLSYDLHK-KMEIYRPHKAYPVELAQFHSADYVEFLHRITPDTQHLFRQELT 88
R + H L+ +Y L + EI P +A +L ++H DYV+FL L
Sbjct: 21 RSSLVHSLIRAYGLLQHFDEIIEPERATRKDLTKYHDKDYVDFL--------------LK 66
Query: 89 KYNLGEDCPVFENLFEFCQIYAGGTIDAARRLNNQL-CDIAINWAGGLHHAKKCEASGFC 147
KY L +DCPVF L + Q+ AG ++ A+ L Q+ DIAINW GG HHA+K ASGFC
Sbjct: 67 KYGLEDDCPVFPFLSMYVQLVAGSSLALAKHLITQVERDIAINWYGGRHHAQKSRASGFC 126
Query: 148 YINDLVLGILELLKYHA-RVLYIDIDVHHGDGVEEAFYFTDRLLQTCRYNLTKYLILVTY 206
Y+ND+VL IL L + RV Y+D+D+HHGDGVE AF+F+
Sbjct: 127 YVNDIVLAILRLRRARFRRVFYLDLDLHHGDGVESAFFFSKN------------------ 168
Query: 207 PDVKVMTVSFHKFGDLFFPGTGDVKEIGEREGKFYAINVPLKDGIDDTSFTRLFKTIISK 266
V+T S H++ FFPGTG +K +N+PLK G+ D + R+ +I+
Sbjct: 169 ----VLTCSIHRYDPGFFPGTGSLKN----SSDKGMLNIPLKRGLSDKTLLRIIDSIVRP 220
Query: 267 VVETYAPGAIVLQCGADSLAGDRLGCFNLSIDGHAECVRFVKKF--NLPLLVTGGGGYTK 324
++E + P IV+QCG D L+GD +NL+I G+ + + K + P L+ GGGGY
Sbjct: 221 LIEKFEPEVIVIQCGCDGLSGDPHKEWNLTIRGYGSVIELLLKEFKDKPTLLLGGGGYNH 280
Query: 325 ENVARCWTVETGIL 338
AR WT T ++
Sbjct: 281 TEAARAWTYLTSMV 294
>gnl|CDD|240374 PTZ00346, PTZ00346, histone deacetylase; Provisional.
Length = 429
Score = 278 bits (711), Expect = 3e-89
Identities = 145/334 (43%), Positives = 191/334 (57%), Gaps = 23/334 (6%)
Query: 11 YDGDVGSVYFGPNHPMKPHRLCMTHHLVLSYDLHKKMEIYRPHKAYPVELAQFHSADYVE 70
Y D+ F P H MKP+R+ +V S + P EL +H+ Y+
Sbjct: 30 YASDMNISAFVPQHAMKPYRVLAAMEIVRSLKIDAHCRTVVPPLVKVEELMAYHTDTYLA 89
Query: 71 FLHRITPDTQHLFRQELTKYNLGEDCPVFENLFEFCQIYAGGTIDAARRLNNQLCDIAIN 130
L + L+ E +K DCP E L E A GT+ A LN+ D+A++
Sbjct: 90 NLG-LHSCRSWLWNAETSKVFFSGDCPPVEGLMEHSIATASGTLMGAVLLNSGQVDVAVH 148
Query: 131 WAGGLHHAKKCEASGFCYINDLVLGILELLKYHARVLYIDIDVHHGDGVEEAFYFTDRLL 190
W GG+HH+K E SGFCY+ND+VLGILELLK H RVLY+DID+HHGDGV+EAF +DR
Sbjct: 149 WGGGMHHSKCGECSGFCYVNDIVLGILELLKCHDRVLYVDIDMHHGDGVDEAFCTSDR-- 206
Query: 191 QTCRYNLTKYLILVTYPDVKVMTVSFHKFGDLFFPGTGDVKEIGEREGKFYAINVPLKDG 250
V T+S HKFG+ FFPGTG +++G G++Y++N+ + DG
Sbjct: 207 --------------------VFTLSLHKFGESFFPGTGHPRDVGYGRGRYYSMNLAVWDG 246
Query: 251 IDDTSFTRLFKTIISKVVETYAPGAIVLQCGADSLAGDRLGCFNLSIDGHAECVRFVKKF 310
I D + LF+ + +V Y+P AIVLQCGADSLAGDRLG NLS GH +CV+ V+
Sbjct: 247 ITDFYYLGLFEHALHSIVRRYSPDAIVLQCGADSLAGDRLGLLNLSSFGHGQCVQAVRDL 306
Query: 311 NLPLLVTGGGGYTKENVARCWTVETGILLDTELP 344
+P+L GGGGYT NVA+ W ET IL LP
Sbjct: 307 GIPMLALGGGGYTIRNVAKLWAYETSILTGHPLP 340
>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 = 247 bits (633), Expect = 1e-79
Identities = 104/313 (33%), Positives = 142/313 (45%), Gaps = 38/313 (12%)
Query: 30 RLCMTHHLVLSYDLHKKMEIYRPHKAYPVELAQFHSADYVEFLHRITPDTQHLFRQELTK 89
R+ + L K+E+ +A L + H+ +Y+ L E
Sbjct: 1 RIRDLIEALKELGLRPKIELIECREATEELLLKVHTEEYLNELKANFAVATIT---ESKP 57
Query: 90 YNLGEDCPVFENLFEFCQIYAGGTIDAARRLNNQLCDIAINWA-GGLHHAKKCEASGFCY 148
G + PV + F ++ GG ++AA + + A G HHA K A GFCY
Sbjct: 58 VIFGPNFPVQRHYFRGARLSTGGVVEAAELVAKGELERAFAVVGAGGHHAGKSRAWGFCY 117
Query: 149 INDLVLGILELLKY-HARVLYIDIDVHHGDGVEEAFYFTDRLLQTCRYNLTKYLILVTYP 207
ND+VL I L + +R+L ID D HHGDG EAFY DR
Sbjct: 118 FNDVVLAIKFLRERGISRILIIDTDAHHGDGTREAFYDDDR------------------- 158
Query: 208 DVKVMTVSFHKFGDLFFPGTGDVKEIGEREGKFYAINVPLKDGIDDTSFTRLFKTIISKV 267
V+ +SFH + F G +GK Y INVPL+DG+ D + + +ISKV
Sbjct: 159 ---VLHMSFHNYDIYPF---------GRGKGKGYKINVPLEDGLGDEEYLDAVERVISKV 206
Query: 268 VETYAPGAIVLQCGADSLAGDRLGCFNLSIDGHAECVRFVKKFN--LPLLVTGGGGYTKE 325
+E + P +VLQ G D+ GDRLG FNLS G + VK+F P+L+ GGGY E
Sbjct: 207 LEEFEPEVVVLQFGHDTHEGDRLGGFNLSEKGFVKLAEIVKEFARGGPILMVLGGGYNPE 266
Query: 326 NVARCWTVETGIL 338
AR WT L
Sbjct: 267 AAARIWTAIIKEL 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 = 148 bits (375), Expect = 2e-41
Identities = 86/309 (27%), Positives = 128/309 (41%), Gaps = 53/309 (17%)
Query: 24 HPMKPHRLCMTHHLVLSYDLHKKMEIYRPHKAYPVELAQFHSADYVEFLHRITPDTQHLF 83
H + + +L L +I P A +L + H +Y+E L + +
Sbjct: 1 HRFPMRKYGLLREALLEEGLVLPEDIVEPEPATREDLLRVHDPEYLESLKSGELSREEIR 60
Query: 84 RQELTKYNLGEDCPVFENLFEFCQIYAGGTIDAARR-LNNQLCDIAINWAGGLHHAKKCE 142
R P L E ++ GGTI AAR L +AIN AGG HHA
Sbjct: 61 RIGF---------PWSPELVERTRLAVGGTILAARLALE---HGLAINLAGGTHHAFPDR 108
Query: 143 ASGFCYINDLVLGILELLKYHA--RVLYIDIDVHHGDGVEEAFYFTDRLLQTCRYNLTKY 200
GFC ND+ + LL RVL +D+DVH G+G F D
Sbjct: 109 GEGFCVFNDIAIAARVLLAEGLVRRVLIVDLDVHQGNGTAA--IFAD------------- 153
Query: 201 LILVTYPDVKVMTVSFHKFGDLFFPGTGDVKEIGEREGKFYAINVPLKDGIDDTSFTRLF 260
D V T S H G+ +P KE + ++VPL DG D +
Sbjct: 154 -------DPSVFTFSMH--GEKNYPF---RKEPSD-------LDVPLPDGTGDDEYLAAL 194
Query: 261 KTIISKVVETYAPGAIVLQCGADSLAGDRLGCFNLSIDGHAE----CVRFVKKFNLPLLV 316
+ + +++ + P + G D LAGDRLG +LS++G E +RF + +P+ +
Sbjct: 195 EEALPRLLAEFRPDLVFYNAGVDVLAGDRLGRLSLSLEGLRERDRLVLRFARARGIPVAM 254
Query: 317 TGGGGYTKE 325
GGGY+++
Sbjct: 255 VLGGGYSRD 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 = 138 bits (350), Expect = 1e-37
Identities = 82/319 (25%), Positives = 131/319 (41%), Gaps = 49/319 (15%)
Query: 24 HPMKPHRLCMTHHLVLSYDLHKKMEIYRPHKAYPVELAQFHSADYVEFLHRITPDTQHLF 83
HP +P RL + L ++ P A EL + H+ +Y+E +
Sbjct: 1 HPERPERLLAILEALEEEGLLDRLVFVEPRPATEEELLRVHTPEYIERVEETCEAGGGY- 59
Query: 84 RQELTKYNLGEDCPVFENLFEFCQIYAGGTIDAARRLNNQLCDIAINWA-----GGLHHA 138
L D V +E + AG + A + + + A +A G HHA
Sbjct: 60 --------LDPDTYVSPGSYEAALLAAGAALAAVDAVLSGEAENA--FALVRPPG--HHA 107
Query: 139 KKCEASGFCYINDLVLGILELLKYH--ARVLYIDIDVHHGDGVEEAFYFTDRLLQTCRYN 196
+ A GFC N++ + K + RVL +D DVHHG+G ++ FY
Sbjct: 108 EPDRAMGFCLFNNVAIAARYAQKRYGLKRVLIVDWDVHHGNGTQDIFYDDPS-------- 159
Query: 197 LTKYLILVTYPDVKVMTVSFHKFGDLFFPGTGDVKEIGEREGKFYAINVPLKDGIDDTSF 256
V+ S H++ F+PGTG +E G G+ + INVPL G D +
Sbjct: 160 --------------VLYFSIHQYP--FYPGTGAAEETGGGAGEGFTINVPLPPGSGDAEY 203
Query: 257 TRLFKTIISKVVETYAPGAIVLQCGADSLAGDRLGCFNLSIDGHAECVRFVKKF-----N 311
F+ ++ + + P +++ G D+ GD LG NL+ +G+A R +K+
Sbjct: 204 LAAFEEVLLPIAREFQPDLVLVSAGFDAHRGDPLGGMNLTPEGYARLTRLLKELADEHCG 263
Query: 312 LPLLVTGGGGYTKENVARC 330
L+ GGY E +A
Sbjct: 264 GRLVFVLEGGYNLEALAES 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 = 131 bits (331), Expect = 8e-35
Identities = 80/290 (27%), Positives = 117/290 (40%), Gaps = 52/290 (17%)
Query: 48 EIYRPHKAYPVE-LAQFHSADYVEFLHRITPDTQHLFRQELTKYNLGEDCPVFENLFEFC 106
P + + +E + H DYV+FL DT D P+ E +E
Sbjct: 45 GEVLPPRDFGLEPILAVHDPDYVDFLETA--DT---------------DTPISEGTWEAA 87
Query: 107 QIYAGGTIDAARRLNNQLCDIAINWAGGL-----HHAKKCEASGFCYINDLVLGILELLK 161
A + AA + A L HHA + A GFCY N+ + L
Sbjct: 88 LAAADTALTAADLVLE-----GERAAYALCRPPGHHAGRDRAGGFCYFNNAAIAAQYLRD 142
Query: 162 YHARVLYIDIDVHHGDGVEEAFYFTDRLLQTCRYNLTKYLILVTYPDVKVMTVSFHKFGD 221
RV +D+DVHHG+G +E FY +R PD V+ VS H
Sbjct: 143 RAGRVAILDVDVHHGNGTQEIFY--ER------------------PD--VLYVSIHGDPR 180
Query: 222 LFFPGT-GDVKEIGEREGKFYAINVPLKDGIDDTSFTRLFKTIISKVVETYAPGAIVLQC 280
F+P G E GE EG+ Y +N+PL G D + ++ + + P A+V+
Sbjct: 181 TFYPFFLGFADETGEGEGEGYNLNLPLPPGTGDDDYLAALDEALAA-IAAFGPDALVVSL 239
Query: 281 GADSLAGDRLGCFNLSIDGHAECVRFVKKFNLPLLVTGGGGYTKENVARC 330
G D+ GD L F L+ + +A R + LP + GGY + + R
Sbjct: 240 GFDTHEGDPLSDFKLTTEDYARIGRRIAALGLPTVFVQEGGYNVDALGRN 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 (276), Expect = 1e-26
Identities = 92/369 (24%), Positives = 146/369 (39%), Gaps = 57/369 (15%)
Query: 7 ISYFYDGDVGSVYFGPNHPMKPHRLCMTHHLVLSYDLHKKMEIYRPHKAYPVELAQFHSA 66
+ F V G HP P +L+ L + + P A EL + H+
Sbjct: 17 GALFLPVGGLLVQPGR-HPENPETKRRIKNLLEVSGLSDHLVLITPRPATDEELLRVHTP 75
Query: 67 DYVEFLHRITPDTQHLFRQELTKYNLGEDC---PVFENLFEFCQIYAGGTIDAARR-LNN 122
+Y++ R+ + + GE P +E + AGG I A L+
Sbjct: 76 EYID---RV---------KAASAAGGGEAGGGTPFGPGSYEIALLAAGGAIAAVDAVLDG 123
Query: 123 QLCDIA---INWAGGLHHAKKCEASGFCYINDLVLGILELLKYH--ARVLYIDIDVHHGD 177
++ D A + G HHA+ + GFC N++ + L RV +D DVHHG+
Sbjct: 124 EV-DNAYALVRPPG--HHAEPDQGMGFCLFNNVAIAARHALAVGGVKRVAVVDWDVHHGN 180
Query: 178 GVEEAFYFTDRLLQTCRYNLTKYLILVTYPDVKVMTVSFHKFGDLFFPGTGDVKEIGERE 237
G + FY D PD V+T+S H+ F P +G V+E GE
Sbjct: 181 GTQAIFY--DD------------------PD--VLTISLHQDR-CFPPDSGAVEERGEGA 217
Query: 238 GKFYAINVPLKDGIDDTSFTRLFKTIISKVVETYAPGAIVLQCGADSLAGDRLGCFNLSI 297
G+ Y +N+PL G D ++ F+ I+ + + P I++ G D+ A D LG L+
Sbjct: 218 GEGYNLNIPLPPGSGDGAYLHAFERIVLPALRAFRPELIIVASGFDASAFDPLGRMMLTS 277
Query: 298 DGHAECVRFVKKFNLP-----LLVTGGGGYTKENVARCW--TVETGILLDTELPNEIPEN 350
DG R ++ L++ GGY++ V C +E L P
Sbjct: 278 DGFRALTRKLRDLADELCGGRLVMVHEGGYSEAYVPFCGLAVLEE--LSGVRTGIADPLL 335
Query: 351 EYIKYFAPE 359
Y + +
Sbjct: 336 YYPEAQGGQ 344
>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 = 103 bits (260), Expect = 1e-24
Identities = 85/350 (24%), Positives = 141/350 (40%), Gaps = 50/350 (14%)
Query: 22 PNHPMKPHRLCMTHHLVLSYDLHKKMEIYRPHKAYPVELAQFHSADYVEFLHRITPDTQH 81
NH P RL + L ++ +A E+ HS +Y++ + +
Sbjct: 5 SNHIECPERLEAILERLTQDGLLERCVKIPAREAEEDEILLVHSQEYIDLVKSTETMEKE 64
Query: 82 LFRQELTKYNLGEDCPVFENLFEFCQIYAGGTIDA-----ARRLNNQLCDIAINWAGGLH 136
+ Y+ CP + +E ++ AG TI+ A ++ N I G H
Sbjct: 65 ELESLCSGYDSVYLCP---STYEAARLAAGSTIELVKAVMAGKIQNGFA--LIRPPG--H 117
Query: 137 HAKKCEASGFCYINDLVLG---ILELLKYHARVLYIDIDVHHGDGVEEAFYFTDRLLQTC 193
HA + EA+G+C N++ + +E L R+L +D DVHHG G ++ F
Sbjct: 118 HAMRNEANGYCIFNNVAIAAKYAIEKLGLK-RILIVDWDVHHGQGTQQGF---------- 166
Query: 194 RYNLTKYLILVTYPDVKVMTVSFHKFGD-LFFPG--TGDVKEIGEREGKFYAINVPLKD- 249
Y D +V+ S H++ F+P D IG G + +NVPL
Sbjct: 167 ------------YEDPRVLYFSIHRYEHGRFWPHLFESDYDYIGVGHGYGFNVNVPLNQT 214
Query: 250 GIDDTSFTRLFKTIISKVVETYAPGAIVLQCGADSLAGDRLGCFNLSIDGHAECVRFVKK 309
G+ D + +F I+ + + P +++ G D+ GD G ++ G+A R +
Sbjct: 215 GLGDADYLAIFHHILLPLALEFQPELVLVSAGFDASIGDPEGEMAVTPAGYAHLTRLLMG 274
Query: 310 FNLP-LLVTGGGGYTKENVARC--WTVETGILLDTELPN---EIPENEYI 353
LL+ GGY E++A T+ LL LP IP +
Sbjct: 275 LAGGKLLLVLEGGYLLESLAESVSMTLRG--LLGDPLPPLAPPIPIRSVL 322
>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 = 96.7 bits (241), Expect = 4e-23
Identities = 43/247 (17%), Positives = 68/247 (27%), Gaps = 48/247 (19%)
Query: 103 FEFCQIYAGGTIDAARRLNNQLCDIAINWAGGLHHAKKCEASGFCYINDLVLGILELLKY 162
E ++ AG + + + + G H+ N + + EL
Sbjct: 8 AEAHELLAGVVVAVLKD-----GKVPVVLGG--DHSI---------ANGAIRAVAEL--- 48
Query: 163 HARVLYIDIDVHHGDGVEEAFYFTDRLLQTCRYNLTKYLILVTYPDVK-VMTVSFHKFGD 221
H + ID+D HH EAF + N L+ P + V VS G
Sbjct: 49 HPDLGVIDVDAHHDVRTPEAFG---------KGNHHTPRHLLCEPLISDVHIVSIGIRGV 99
Query: 222 LFFPGTGDVKEIGEREGKFYAINVPLKDGIDDTSFTRLFKTIISKVVETYAPGAIVLQCG 281
G K + + + D +F+ I+S + + L
Sbjct: 100 SNGE------AGGAYARKLGVVYFSMTEV-DKLGLGDVFEEIVSYL--GDKGDNVYLSVD 150
Query: 282 ADSLAGD------RLGCFNLSIDGHAECVRFVKKFNLPLLVTGGGGYT----KENVARCW 331
D L G LS + K NL + + AR
Sbjct: 151 VDGLDPSFAPGTGTPGPGGLSYREGLYITERIAKTNLVVGLDIVEVNPLLDETGRTARLA 210
Query: 332 TVETGIL 338
T L
Sbjct: 211 AALTLEL 217
>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 = 94.7 bits (236), Expect = 1e-21
Identities = 71/293 (24%), Positives = 125/293 (42%), Gaps = 40/293 (13%)
Query: 22 PNHPMKPHRLCMTHHLVLSYDLHKKMEIYRPHKAYPVELAQFHSADYVEFLHRITPDTQH 81
HP P R+ + L +M +A E+ HS ++ + + T
Sbjct: 1 DPHPEDPSRISRIFEKLKEAGLINRMLRIPIREATKEEILLVHSEEHWDRV-EATEKMSD 59
Query: 82 LFRQELTKYNLGEDCPVFENLFEFCQIYAGGTIDAAR-----RLNNQLCDIAINWAGGLH 136
++ T+ + V + ++ GG I+A R R+ N A+ G H
Sbjct: 60 EQLKDRTEIFERDSLYVNNDTAFCARLSCGGAIEACRAVAEGRVKNA---FAVVRPPG-H 115
Query: 137 HAKKCEASGFCYINDLVLGILELLK-YHA---RVLYIDIDVHHGDGVEEAFYFTDRLLQT 192
HA+ E+ GFC+ N++ + L Y ++L +D D+HHG+G + AFY
Sbjct: 116 HAEPDESMGFCFFNNVAVAAKWLQTEYPDKIKKILILDWDIHHGNGTQRAFYD------- 168
Query: 193 CRYNLTKYLILVTYPDVKVMTVSFHKF-GDLFFPGT--GDVKEIGEREGKFYAINVPLKD 249
D V+ +S H+F F+PGT GD + +GE G + +N+P
Sbjct: 169 ---------------DPNVLYISLHRFENGGFYPGTPYGDYESVGEGAGLGFNVNIPWPQ 213
Query: 250 -GIDDTSFTRLFKTIISKVVETYAPGAIVLQCGADSLAGDRLGCFNLSIDGHA 301
G+ D + F+ I+ + + P +++ G D+ GD LG +++ G+A
Sbjct: 214 GGMGDADYIYAFQRIVMPIAYEFDPDLVIISAGFDAADGDELGQCHVTPAGYA 266
>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 = 89.3 bits (222), Expect = 2e-19
Identities = 75/335 (22%), Positives = 142/335 (42%), Gaps = 41/335 (12%)
Query: 22 PNHPMKPHRLCMTHHLVLSYDLHKKMEIYRPHKAYPVELAQFHSADYV---EFLHRITPD 78
P HP P R+ + L ++ A EL HS +++ + L ++ P
Sbjct: 14 PGHPECPQRISRIYERHNDLGLLERCLRLPSRLATEDELLLCHSEEHLDEMKSLEKMKP- 72
Query: 79 TQHLFRQELTKYNLGEDCPVFENLFEFCQIYAGGTIDAARRL--NNQLCDIAINWAGGLH 136
+ L R +Y+ P + ++ + AG + + +AI G H
Sbjct: 73 -RELNRLGK-EYDSIYIHP---DSYQCALLAAGCVLQVVEAVLTGESRNGVAIVRPPG-H 126
Query: 137 HAKKCEASGFCYINDLVLGI-LELLKYHA-RVLYIDIDVHHGDGVEEAFYFTDRLLQTCR 194
HA++ A GFC+ N++ + KY R+L +D DVHHG+G + F
Sbjct: 127 HAEQDTACGFCFFNNVAIAARYAQKKYGLKRILIVDWDVHHGNGTQHMF----------- 175
Query: 195 YNLTKYLILVTYPDVKVMTVSFHKFGD-LFFPGT--GDVKEIGEREGKFYAINVPL-KDG 250
D V+ +S H++ + FFP + G+ +G+ +G+ + +N+P K G
Sbjct: 176 -----------ESDPSVLYISLHRYDNGSFFPNSPEGNYDVVGKGKGEGFNVNIPWNKGG 224
Query: 251 IDDTSFTRLFKTIISKVVETYAPGAIVLQCGADSLAGDRLGCFNLSIDGHAECVRFVKKF 310
+ D + F+ ++ + + P +++ G D+ GD LG ++ +G+A +
Sbjct: 225 MGDAEYIAAFQQVVLPIAYEFNPELVLVSAGFDAARGDPLGGCKVTPEGYAHMTHMLMSL 284
Query: 311 -NLPLLVTGGGGYTKENVARCWTVETGILLDTELP 344
++V GGY +++ ++ T LL P
Sbjct: 285 AGGRVIVILEGGYNLTSISESMSMCTKTLLGDPPP 319
>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 = 88.6 bits (220), Expect = 3e-19
Identities = 75/308 (24%), Positives = 120/308 (38%), Gaps = 66/308 (21%)
Query: 23 NHPMKPHRLCMTHHLVLSYDLHKKMEIYRPHKAYPVELAQFHSADYVEFLHRITPDTQHL 82
+HP RL + L + E R KA EL HS + T L
Sbjct: 23 SHPEHGGRLQSIWSRLQETGLVNRCERLRGRKATLEELQLVHSEVHTLLY-----GTNPL 77
Query: 83 FRQELTKYNLGEDCPVFENLFEFCQIYAGG-------------TIDAARRLNNQLCDIAI 129
R +L L F ++ GG T +AAR + D+A
Sbjct: 78 SRLKLDPTKLAGL-----PQKSFVRLPCGGIGVDSDTVWNELHTSNAARMAVGCVIDLAF 132
Query: 130 NWAGGL------------HHAKKCEASGFCYINDLVLG--ILELLKYHARVLYIDIDVHH 175
A G HHA+ +A GFC+ N + + L+ ++L +D DVHH
Sbjct: 133 KVATGELKNGFAVVRPPGHHAEPSQAMGFCFFNSVAIAAKQLQQKLKLRKILIVDWDVHH 192
Query: 176 GDGVEEAFYFTDRLLQTCRYNLTKYLILVTYPDVKVMTVSFHKFGD-LFFPGTGDVKEIG 234
G+G ++ F Y D V+ +S H++ D FFPGTG E+G
Sbjct: 193 GNGTQQIF----------------------YEDPNVLYISLHRYDDGNFFPGTGAPTEVG 230
Query: 235 EREGKFYAINVPLKDGID----DTSFTRLFKTIISKVVETYAPGAIVLQCGADSLAG--D 288
G+ + +N+ G+D D + F+T++ + ++P +++ G D+ G
Sbjct: 231 SGAGEGFNVNIAWSGGLDPPMGDAEYLAAFRTVVMPIAREFSPDIVLVSAGFDAAEGHPP 290
Query: 289 RLGCFNLS 296
LG + +S
Sbjct: 291 PLGGYKVS 298
>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 = 85.6 bits (213), Expect = 1e-18
Identities = 70/280 (25%), Positives = 105/280 (37%), Gaps = 47/280 (16%)
Query: 24 HPMKPHRLCMTHHLVLSYDLHKKMEIYRPHKAYPVELAQFHSADYVEFLHRITPDTQHLF 83
HP P RL +++ L + + A +L + H A YV+ L P+ +
Sbjct: 1 HPESPERLEAILDALIASGLDRLLRQLEAPPATREQLLRVHDAAYVDRLEAAAPEEGLVQ 60
Query: 84 RQELTKYNLGEDCPVFENLFEFCQIYAGGTIDA-----ARRLNNQLCDIAINWAGGLHHA 138
L D + E AG + A A N C A+ G HHA
Sbjct: 61 --------LDPDTAMSPGSLEAALRAAGAVVAAVDAVMAGEARNAFC--AVRPPG--HHA 108
Query: 139 KKCEASGFCYINDLVLGILELLKYHA--RVLYIDIDVHHGDGVEEAFYFTDRLLQTCRYN 196
++ +A GFC N++ + L +H RV +D DVHHG+G E+ F R
Sbjct: 109 ERDKAMGFCLFNNVAIAAAHALAHHGLERVAIVDFDVHHGNGTEDIFRDDPR-------- 160
Query: 197 LTKYLILVTYPDVKVMTVSFHKFGDLFFPGTGDVKEIGEREGKFYAINVPLKDGIDDTSF 256
V+ S H+ +PGTG E G +NVPL G F
Sbjct: 161 --------------VLFCSSHQHP--LYPGTGAPDETGHG----NIVNVPLPAGTGGAEF 200
Query: 257 TRLFKTIISKVVETYAPGAIVLQCGADSLAGDRLGCFNLS 296
+ ++ + P I++ G D+ D L NL+
Sbjct: 201 REAVEDRWLPALDAFKPDLILISAGFDAHRDDPLAQLNLT 240
>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 = 87.0 bits (215), Expect = 2e-18
Identities = 80/299 (26%), Positives = 129/299 (43%), Gaps = 66/299 (22%)
Query: 43 LHKKMEIYRPHKAYPVELAQFHSADYVEFLHRITPDTQHLFRQEL-TKYNLGEDCPVFEN 101
L K E R KA EL HS H + T L RQ+L +K LG VF
Sbjct: 46 LRGKCECIRGRKATLEELQTVHSE-----AHTLLYGTNPLNRQKLDSKKLLGSLASVFVR 100
Query: 102 L----------FEFCQIYAGGTIDAARRLNNQLCDIAINWAGGL------------HHAK 139
L + ++++ G AAR + ++ A G HHA+
Sbjct: 101 LPCGGVGVDSDTIWNEVHSSG---AARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAE 157
Query: 140 KCEASGFCYINDLVLG--ILELLKYHARVLYIDIDVHHGDGVEEAFYFTDRLLQTCRYNL 197
+ GFCY N + + +L+ +++L +D DVHHG+G ++AF
Sbjct: 158 ESTPMGFCYFNSVAIAAKLLQQRLNVSKILIVDWDVHHGNGTQQAF-------------- 203
Query: 198 TKYLILVTYPDVKVMTVSFHKFGD-LFFPGTGDVKEIGEREGKFYAINVPLKDGID---- 252
Y D V+ +S H++ D FFPG+G E+G G + +N+ G+D
Sbjct: 204 --------YSDPNVLYMSLHRYDDGNFFPGSGAPDEVGTGPGVGFNVNMAFTGGLDPPMG 255
Query: 253 DTSFTRLFKTIISKVVETYAPGAIVLQCGADSLAGD--RLGCFNLSIDGHAECVRFVKK 309
D + F+T++ + +AP +++ G D++ G LG +NLS A+C ++ K
Sbjct: 256 DAEYLAAFRTVVMPIASEFAPDVVLVSSGFDAVEGHPTPLGGYNLS----AKCFGYLTK 310
>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 = 82.3 bits (203), Expect = 5e-17
Identities = 45/171 (26%), Positives = 86/171 (50%), Gaps = 33/171 (19%)
Query: 136 HHAKKCEASGFCYINDLVLGILELLKYH---ARVLYIDIDVHHGDGVEEAFYFTDRLLQT 192
HHA++ A GFC+ N + + +LL+ ++L +D D+HHG+G ++AF
Sbjct: 154 HHAEESTAMGFCFFNSVAIAA-KLLQQKLNVGKILIVDWDIHHGNGTQQAF--------- 203
Query: 193 CRYNLTKYLILVTYPDVKVMTVSFHKFGD-LFFPGTGDVKEIGEREGKFYAINVPLKDGI 251
Y D V+ +S H++ D FFPG+G E+G G + +N+ G+
Sbjct: 204 -------------YNDPNVLYISLHRYDDGNFFPGSGAPDEVGAGPGVGFNVNIAWTGGV 250
Query: 252 D----DTSFTRLFKTIISKVVETYAPGAIVLQCGADSLAGDR--LGCFNLS 296
D D + F+T++ + ++P +++ G D++ G + LG ++++
Sbjct: 251 DPPIGDVEYLTAFRTVVMPIANEFSPDVVLVSAGFDAVEGHQSPLGGYSVT 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 = 82.0 bits (202), Expect = 6e-17
Identities = 46/159 (28%), Positives = 79/159 (49%), Gaps = 29/159 (18%)
Query: 136 HHAKKCEASGFCYINDLVLGILELLKYH--ARVLYIDIDVHHGDGVEEAFYFTDRLLQTC 193
HHA++ A GFC+ N + + L +++L +D+DVHHG+G ++AF
Sbjct: 152 HHAEESTAMGFCFFNSVAITAKYLRDQLNISKILIVDLDVHHGNGTQQAF---------- 201
Query: 194 RYNLTKYLILVTYPDVKVMTVSFHKFGD-LFFPGTGDVKEIGEREGKFYAINVPLKDGID 252
Y D ++ +S H++ + FFPG+G E+G G+ Y IN+ G+D
Sbjct: 202 ------------YADPSILYISLHRYDEGNFFPGSGAPNEVGTGLGEGYNINIAWTGGLD 249
Query: 253 ----DTSFTRLFKTIISKVVETYAPGAIVLQCGADSLAG 287
D + F+TI+ V + + P +++ G D+L G
Sbjct: 250 PPMGDVEYLEAFRTIVKPVAKEFDPDMVLVSAGFDALEG 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 = 79.7 bits (196), Expect = 3e-16
Identities = 43/159 (27%), Positives = 74/159 (46%), Gaps = 29/159 (18%)
Query: 136 HHAKKCEASGFCYINDLVLGI--LELLKYHARVLYIDIDVHHGDGVEEAFYFTDRLLQTC 193
HHA A GFC+ N + + L+ +++L +D DVHHG+G ++ F
Sbjct: 152 HHADHSTAMGFCFFNSVAIACRQLQQQGKASKILIVDWDVHHGNGTQQTF---------- 201
Query: 194 RYNLTKYLILVTYPDVKVMTVSFHKFGD-LFFPGTGDVKEIGEREGKFYAINVPLKDGID 252
Y D V+ +S H+ D FFPG+G V E+G G+ + +NV G+D
Sbjct: 202 ------------YQDPSVLYISLHRHDDGNFFPGSGAVDEVGAGSGEGFNVNVAWAGGLD 249
Query: 253 ----DTSFTRLFKTIISKVVETYAPGAIVLQCGADSLAG 287
D + F+ ++ + ++P +++ G D+ G
Sbjct: 250 PPMGDPEYLAAFRIVVMPIAREFSPDLVLVSAGFDAAEG 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 = 68.4 bits (167), Expect = 1e-12
Identities = 84/337 (24%), Positives = 146/337 (43%), Gaps = 57/337 (16%)
Query: 28 PHRLCMTHHLVLSYDLHKKMEIYRPHKAYPVELAQFHSADYVEFLHRITPDTQHLFRQEL 87
P RL ++ + Y L ++ +A E+ HS +Y+ + +TQ + ++EL
Sbjct: 11 PERLTASYERLRQYGLVQRCLRLPAREASEEEILLVHSPEYLSLVR----ETQVMNKEEL 66
Query: 88 TKYNLGEDCPVF-ENLFEFCQIYAGGT---IDAARRLNNQLCD-IAINWAGGLHHAKKCE 142
+ D F N F ++ AG T +DA L ++ + +A+ G HH+++
Sbjct: 67 MAISGKYDAVYFHPNTFHCARLAAGATLQLVDAV--LTGEVQNGMALVRPPG-HHSQRNA 123
Query: 143 ASGFCYINDLVLGILELLKYHA--RVLYIDIDVHHGDGVEEAFYFTDRLLQTCRYNLTKY 200
A+GFC N++ + K + R+L +D DVHHG G++ + F +
Sbjct: 124 ANGFCVFNNVAIAAEYAKKKYGLHRILIVDWDVHHGQGIQ--YIFEE------------- 168
Query: 201 LILVTYPDVKVMTVSFHKF-GDLFFPG--TGDVKEIGEREGKFYAINVPL-KDGIDDTSF 256
D V+ S+H++ F+P D +G +G + IN+P K G+ + +
Sbjct: 169 -------DPSVLYFSWHRYEHQRFWPFLRESDYDAVGRGKGLGFNINLPWNKVGMGNADY 221
Query: 257 TRLFKTIISKVVETYAPGAIVLQCGADSLAGDRLGCFNLSIDGHAECVRFVKKFNLPLLV 316
F ++ + + P +++ G DS GD G + EC + + L
Sbjct: 222 LAAFFHVLLPLAFEFDPELVLVSAGFDSAIGDPEGQMCAT----PECFAHLTHLLMVL-- 275
Query: 317 TGG-------GGYTKENVAR--CWTVETGILLDTELP 344
GG GGY E++A C TV+T LL LP
Sbjct: 276 AGGKLCAVLEGGYHLESLAESVCMTVQT--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 = 2e-12
Identities = 67/278 (24%), Positives = 112/278 (40%), Gaps = 36/278 (12%)
Query: 23 NHPMKPHRLCMTHHLVLSYDLHKKMEIYRPHKAYPVELAQFHSADYVEFLHRITPDTQHL 82
+ P P RL ++ L ++ + +A EL HS +YV + TQ++
Sbjct: 6 SFPECPERLHAIREKLIQEGLLERCVSVQAREASEEELLLVHSPEYVALMK----STQYM 61
Query: 83 FRQELTKYNLGEDCPVFENLFEFCQIYAGGTI--DAARRLNNQLCD-IAINWAGGLHHAK 139
+EL D C A G++ + L ++ + +AI G HHA+
Sbjct: 62 TEEELRTLADTYDSVYLHPNSYSCACLAVGSVLQLVDKVLGGEIRNGLAIVRPPG-HHAQ 120
Query: 140 KCEASGFCYINDLVLGILELLKYHA--RVLYIDIDVHHGDGVEEAFYFTDRLLQTCRYNL 197
+ G+C N++ + + H RVL +D DVHHG G + F F
Sbjct: 121 HDKMDGYCMFNNVAIAARYAQQKHGVQRVLIVDWDVHHGQGTQ--FIFEQ---------- 168
Query: 198 TKYLILVTYPDVKVMTVSFHKFGD-LFFP--GTGDVKEIGEREGKFYAINVPL-KDGIDD 253
D V+ S H++ F+P D +G G+ Y INVP + G+ D
Sbjct: 169 ----------DPSVLYFSIHRYEQGRFWPHLKESDSSAVGFGRGEGYNINVPWNQVGMRD 218
Query: 254 TSFTRLFKTIISKVVETYAPGAIVLQCGADSLAGDRLG 291
+ F ++ V + P +++ G D++ GD G
Sbjct: 219 ADYIAAFLHVLLPVALEFQPQLVLVAAGFDAVIGDPKG 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 = 1e-05
Identities = 18/48 (37%), Positives = 30/48 (62%), Gaps = 2/48 (4%)
Query: 136 HHAKKCEASGFCYINDLVLGILELLKYHA--RVLYIDIDVHHGDGVEE 181
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 = 0.13
Identities = 13/53 (24%), Positives = 23/53 (43%), Gaps = 4/53 (7%)
Query: 396 PSVQMQEVPPDFYI-PEFDEDEQNPDERMDQHTQDKQIQRDDEFYEGDNDNDH 447
PSVQ P D Y+ P E+E++ E + + +R ++ + H
Sbjct: 134 PSVQQVPRPQDLYVLPPLPEEEKHSSEEESEKEWE---ERMNQKQALQEEFFH 183
>gnl|CDD|240649 cd12172, PGDH_like_2, Putative D-3-Phosphoglycerate Dehydrogenases,
NAD-binding and catalytic domains. Phosphoglycerate
dehydrogenases (PGDHs) catalyze the initial step in the
biosynthesis of L-serine from D-3-phosphoglycerate.
PGDHs come in 3 distinct structural forms, with this
first group being related to 2-hydroxy acid
dehydrogenases, sharing structural similarity to formate
and glycerate dehydrogenases of the D-specific
2-hydroxyacid dehydrogenase superfamily, which also
include groups such as L-alanine dehydrogenase and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. Many, not all, members of this family are
dimeric.
Length = 306
Score = 31.3 bits (72), Expect = 0.87
Identities = 16/48 (33%), Positives = 26/48 (54%), Gaps = 3/48 (6%)
Query: 38 VLSYDLHKKMEIYRPHKAYPVELAQ-FHSADYVEFLH-RITPDTQHLF 83
VL+YD + E + H V L + +D++ LH +TP+T+HL
Sbjct: 168 VLAYDPYPDEEFAKEHGVEFVSLEELLKESDFI-SLHLPLTPETRHLI 214
>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 = 29.5 bits (67), Expect = 1.6
Identities = 17/58 (29%), Positives = 25/58 (43%), Gaps = 8/58 (13%)
Query: 301 AECVRFVKKFNLPLLVTGGGGYTKENVARCWTVETGILLDTELPNEI----PENEYIK 354
A VR + LP+LV GGG ++ + G++LD N I PE+
Sbjct: 14 AAIVRLANENGLPVLVRGGG----SSLLGDAVLTGGVVLDLSRLNGILEIDPEDGTAT 67
>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 = 1.7
Identities = 14/36 (38%), Positives = 18/36 (50%), Gaps = 1/36 (2%)
Query: 380 TIKMQVLENLRSIQHAP-SVQMQEVPPDFYIPEFDE 414
TI V+E LR + P V + PD IP+F E
Sbjct: 43 TIGPLVVEALRPLTELPLDVHLMVEEPDRIIPDFAE 78
>gnl|CDD|183384 PRK11924, PRK11924, RNA polymerase sigma factor; Provisional.
Length = 179
Score = 29.9 bits (68), Expect = 1.9
Identities = 19/81 (23%), Positives = 29/81 (35%), Gaps = 10/81 (12%)
Query: 359 ECSLRIPNGHIENLNSKS----YLSTIKMQVL-ENLRSIQHAPSVQMQEVPPDFYIPEFD 413
E LR + N K +L TI V + LR + +V + PEF
Sbjct: 46 EAFLRAWR-KADLFNGKGSARTWLLTIARNVCYDLLRRRRREKAVLSDDALE----PEFA 100
Query: 414 EDEQNPDERMDQHTQDKQIQR 434
E + P+ + +I R
Sbjct: 101 ETAETPEAALLAKDDLARIDR 121
>gnl|CDD|215145 PLN02258, PLN02258, 9-cis-epoxycarotenoid dioxygenase NCED.
Length = 590
Score = 30.4 bits (69), Expect = 2.4
Identities = 16/39 (41%), Positives = 21/39 (53%), Gaps = 2/39 (5%)
Query: 154 LGILELLKYHARVLYIDIDVHHGDGVEEA--FYFTDRLL 190
GI L+ ++AR L+ +D G GV A YF RLL
Sbjct: 213 SGIARLMLFYARGLFGLVDASRGTGVANAGLVYFNGRLL 251
>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 = 2.5
Identities = 15/68 (22%), Positives = 27/68 (39%), Gaps = 6/68 (8%)
Query: 371 NLNSKSYLSTIK---MQVLENLRSIQHAPSVQMQEVPPDFYIPEFDEDEQNPD---ERMD 424
N S ++S K +V+ LR+ +V + PD + E+ +N D +
Sbjct: 101 NSYSFDFVSLFKPESQEVIYELRAKLRKDNVGLPTSNPDLAVIVLPEEFKNKDIWNSEIA 160
Query: 425 QHTQDKQI 432
T+ Q
Sbjct: 161 GLTRPNQD 168
>gnl|CDD|238976 cd02018, TPP_PFOR, Thiamine pyrophosphate (TPP family), Pyruvate
ferredoxin/flavodoxin oxidoreductase (PFOR) subfamily,
TPP-binding module; PFOR catalyzes the oxidative
decarboxylation of pyruvate to form acetyl-CoA, a
crucial step in many metabolic pathways. Archaea,
anaerobic bacteria and eukaryotes that lack mitochondria
(and therefore pyruvate dehydrogenase) use PFOR to
oxidatively decarboxylate pyruvate, with ferredoxin or
flavodoxin as the electron acceptor. PFORs can be
homodimeric, heterodimeric, or heterotetrameric,
depending on the organism. These enzymes are dependent
on TPP and a divalent metal cation as cofactors.
Length = 237
Score = 28.6 bits (64), Expect = 6.2
Identities = 12/51 (23%), Positives = 21/51 (41%), Gaps = 3/51 (5%)
Query: 58 VELAQFHSADYVEFLHRITPDTQHLFRQELTKYNLGEDCPVFENLFEFCQI 108
V +A H YV R++P + F + + + D P F + + C
Sbjct: 159 VLIAATHGCVYVA---RLSPALKKHFLKVVKEAISRTDGPTFIHAYTPCIT 206
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
0.322 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: 23,756,695
Number of extensions: 2352672
Number of successful extensions: 2112
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2013
Number of HSP's successfully gapped: 52
Length of query: 451
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 351
Effective length of database: 6,502,202
Effective search space: 2282272902
Effective search space used: 2282272902
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 (21.9 bits)
S2: 61 (27.2 bits)