RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 014167
(429 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 = 637 bits (1644), Expect = 0.0
Identities = 239/381 (62%), Positives = 305/381 (80%), Gaps = 3/381 (0%)
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 TDRVMTVSFHKFGDLFFPGTGDVKEIGEREGKFYAINVPLKDGIDDTSFTRLFKTIISKV 245
TDRVMTVSFHK+G+ FFPGTGD+ E+G G++Y++NVPLKDGIDD S+ +LFK +I +V
Sbjct: 182 TDRVMTVSFHKYGNYFFPGTGDMYEVGAESGRYYSVNVPLKDGIDDQSYLQLFKPVIQQV 241
Query: 246 VETYAPGAIVLQCGADSLAGDRLGCFNLSIDGHAECVRFVKKFNLPLLVTGGGGYTKENV 305
++ Y P IVLQCGADSL DRLGCFNLSI GH ECV FVK FN+PLLV GGGGYT NV
Sbjct: 242 IDFYQPTCIVLQCGADSLGCDRLGCFNLSIKGHGECVEFVKSFNIPLLVLGGGGYTVRNV 301
Query: 306 ARCWTVETGILLDTELPNEIPENEYIKYFAPECSLRIPN--GHIENLNSKSYLSTIKMQV 363
ARCWT ET +L+D E+ NE+P NEY +YFAP+ +L P+ IEN NSK YL I+ V
Sbjct: 302 ARCWTYETSLLVDEEISNELPYNEYFEYFAPDFTLH-PDVSTRIENQNSKQYLDQIRQTV 360
Query: 364 LENLRSIQHAPSVQMQEVPPD 384
ENL+ + HAPSVQMQ+VPPD
Sbjct: 361 FENLKMLNHAPSVQMQDVPPD 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 = 596 bits (1538), Expect = 0.0
Identities = 208/307 (67%), Positives = 254/307 (82%), Gaps = 1/307 (0%)
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 NWAGGLHHAKKCEASGFCYINDLVLGILELLKYHARVLYIDIDVHHGDGVEEAFYFTDRV 189
NWAGGLHHAKK EASGFCY+ND+VL ILELLKYH RVLYIDID+HHGDGVEEAFY TDRV
Sbjct: 121 NWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRV 180
Query: 190 MTVSFHKFGDLFFPGTGDVKEIGEREGKFYAINVPLKDGIDDTSFTRLFKTIISKVVETY 249
MTVSFHKFG+ +F +++IG +GK+YA+NVPLKDGIDD S+ ++F+ ++SKV+E +
Sbjct: 181 MTVSFHKFGE-YFFPGTGLRDIGAGKGKYYAVNVPLKDGIDDESYLQIFEPVLSKVMEVF 239
Query: 250 APGAIVLQCGADSLAGDRLGCFNLSIDGHAECVRFVKKFNLPLLVTGGGGYTKENVARCW 309
P A+VLQCGADSLAGDRLGCFNLSI GHA+CV+FVK FN+PLLV GGGGYT NVARCW
Sbjct: 240 QPSAVVLQCGADSLAGDRLGCFNLSIKGHAKCVKFVKSFNIPLLVLGGGGYTLRNVARCW 299
Query: 310 TVETGIL 316
T ET +L
Sbjct: 300 TYETAVL 306
>gnl|CDD|240251 PTZ00063, PTZ00063, histone deacetylase; Provisional.
Length = 436
Score = 592 bits (1529), Expect = 0.0
Identities = 252/403 (62%), Positives = 306/403 (75%), Gaps = 6/403 (1%)
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 YFTDRVMTVSFHKFGDLFFPGTGDVKEIGEREGKFYAINVPLKDGIDDTSFTRLFKTIIS 243
Y T RVMTVSFHKFGD FFPGTGDV +IG +GK+Y++NVPL DGIDD SF LFK +IS
Sbjct: 185 YVTHRVMTVSFHKFGD-FFPGTGDVTDIGVAQGKYYSVNVPLNDGIDDDSFVDLFKPVIS 243
Query: 244 KVVETYAPGAIVLQCGADSLAGDRLGCFNLSIDGHAECVRFVKKFNLPLLVTGGGGYTKE 303
K VE Y PGAIVLQCGADSL GDRLG FNL+I GHA CV FV+ N+PLLV GGGGYT
Sbjct: 244 KCVEVYRPGAIVLQCGADSLTGDRLGRFNLTIKGHAACVEFVRSLNIPLLVLGGGGYTIR 303
Query: 304 NVARCWTVETGILLD--TELPNEIPENEYIKYFAPECSLRIPNGHIENLNSKSYLSTIKM 361
NVARCW ETG++L+ E+ ++I N+Y Y+AP+ L + +I N NS +L IK+
Sbjct: 304 NVARCWAYETGVILNKHDEMSDQISLNDYYDYYAPDFQLHLQPSNIPNYNSPEHLEKIKV 363
Query: 362 QVLENLRSIQHAPSVQMQEVPPDFYIPEFD-EDEQNPDERMDQ 403
++LENLR ++HAP VQ VPPDF+ + D EDE+N E D+
Sbjct: 364 KILENLRYLEHAPGVQFAYVPPDFFDRDIDDEDEKNQYELSDE 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 = 566 bits (1461), Expect = 0.0
Identities = 234/376 (62%), Positives = 290/376 (77%), Gaps = 1/376 (0%)
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 YFTDRVMTVSFHKFGDLFFPGTGDVKEIGEREGKFYAINVPLKDGIDDTSFTRLFKTIIS 243
Y TDRVMT SFHK+G+ +FPGTG++++IG GK YA+NVPL+DGIDD S+ +F+ +I
Sbjct: 181 YTTDRVMTCSFHKYGE-YFPGTGELRDIGIGTGKNYAVNVPLRDGIDDESYKSIFEPVIK 239
Query: 244 KVVETYAPGAIVLQCGADSLAGDRLGCFNLSIDGHAECVRFVKKFNLPLLVTGGGGYTKE 303
V+E Y P A+VLQCG DSL+GDRLGCFNLS+ GHA CV FVK FNLP+LV GGGGYT
Sbjct: 240 HVMEWYQPEAVVLQCGGDSLSGDRLGCFNLSMKGHANCVNFVKSFNLPMLVLGGGGYTMR 299
Query: 304 NVARCWTVETGILLDTELPNEIPENEYIKYFAPECSLRIPNGHIENLNSKSYLSTIKMQV 363
NVAR W ETG+L EL ++P NEY +Y+ P+ L + ++EN N+ YL I V
Sbjct: 300 NVARTWAFETGLLAGEELDKDLPYNEYYEYYGPDYELNVRPSNMENHNTPEYLDKITTAV 359
Query: 364 LENLRSIQHAPSVQMQ 379
+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 = 511 bits (1317), Expect = 0.0
Identities = 230/368 (62%), Positives = 298/368 (80%), Gaps = 1/368 (0%)
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 FYFTDRVMTVSFHKFGDLFFPGTGDVKEIGEREGKFYAINVPLKDGIDDTSFTRLFKTII 242
FY TDRVMTVSFHK+G+ +FPGTGD+++IG +GK+YA+N PL+DGIDD S+ +FK ++
Sbjct: 184 FYTTDRVMTVSFHKYGE-YFPGTGDLRDIGAGKGKYYAVNYPLRDGIDDESYEAIFKPVM 242
Query: 243 SKVVETYAPGAIVLQCGADSLAGDRLGCFNLSIDGHAECVRFVKKFNLPLLVTGGGGYTK 302
SKV+E + P A+VLQCGADSL+GDRLGCFNL+I GHA+CV FVK FNLP+L+ GGGGYT
Sbjct: 243 SKVMEMFQPSAVVLQCGADSLSGDRLGCFNLTIKGHAKCVEFVKSFNLPMLMLGGGGYTI 302
Query: 303 ENVARCWTVETGILLDTELPNEIPENEYIKYFAPECSLRIPNGHIENLNSKSYLSTIKMQ 362
NVARCWT ET + LD+E+PNE+P N+Y +YF P+ L I ++ N N+ YL IK +
Sbjct: 303 RNVARCWTYETAVALDSEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTNEYLEKIKQR 362
Query: 363 VLENLRSI 370
+ 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 = 497 bits (1281), Expect = e-176
Identities = 226/367 (61%), Positives = 294/367 (80%), Gaps = 1/367 (0%)
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 YFTDRVMTVSFHKFGDLFFPGTGDVKEIGEREGKFYAINVPLKDGIDDTSFTRLFKTIIS 243
Y TDRVMTVSFHK+G+ +FPGTGD+++IG +GK+YA+N P++DGIDD S+ ++FK IIS
Sbjct: 181 YTTDRVMTVSFHKYGE-YFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIIS 239
Query: 244 KVVETYAPGAIVLQCGADSLAGDRLGCFNLSIDGHAECVRFVKKFNLPLLVTGGGGYTKE 303
KV+E Y P A+VLQCGADSL+GDRLGCFNL++ GHA+CV VK FNLPLL+ GGGGYT
Sbjct: 240 KVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTIR 299
Query: 304 NVARCWTVETGILLDTELPNEIPENEYIKYFAPECSLRIPNGHIENLNSKSYLSTIKMQV 363
NVARCWT ET + LD E+PNE+P N+Y +YF P+ L I ++ N N+ Y+ IK ++
Sbjct: 300 NVARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEYMEKIKQRL 359
Query: 364 LENLRSI 370
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 = 481 bits (1241), Expect = e-171
Identities = 182/311 (58%), Positives = 229/311 (73%), Gaps = 1/311 (0%)
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 TDRVMTVSFHKFGDLFFPGTGDVKEIGEREGKFYAINVPLKDGIDDTSFTRLFKTIISKV 245
TDRVMT+SFHK+ FFPGTGD+ + G GK +A+NVPL+DGIDD + LFK+II
Sbjct: 181 TDRVMTLSFHKYNGEFFPGTGDLDDNGGTPGKHFALNVPLEDGIDDEQYNLLFKSIIGPT 240
Query: 246 VETYAPGAIVLQCGADSLAGDRLGCFNLSIDGHAECVRFVKKFNLPLLVTGGGGYTKENV 305
+E + P AIVLQCGADSL GDRLG FNL+I H CV+FVK F +P+LV GGGGYT NV
Sbjct: 241 IEKFQPSAIVLQCGADSLGGDRLGQFNLNIKAHGACVKFVKSFGIPMLVVGGGGYTPRNV 300
Query: 306 ARCWTVETGIL 316
AR W ET +
Sbjct: 301 ARAWCYETAVA 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 = 403 bits (1038), Expect = e-139
Identities = 156/351 (44%), Positives = 230/351 (65%), Gaps = 3/351 (0%)
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 CEASGFCYINDLVLGILELLKYHARVLYIDIDVHHGDGVEEAFYFTDRVMTVSFHKFGDL 200
EASGFCY+ND+VLGIL+L + RVLY+D+D+HHGDGVE+AF FT +VMTVS HK+
Sbjct: 134 DEASGFCYVNDIVLGILKLREKFDRVLYVDLDLHHGDGVEDAFSFTSKVMTVSLHKYSPG 193
Query: 201 FFPGTGDVKEIGEREGKFYAINVPLKDGIDDTSFTRLFKTIISKVVETYAPGAIVLQCGA 260
FFPGTGDV ++G +GK+Y +NVPL+DGI D + ++F ++ ++V + P A+VLQCGA
Sbjct: 194 FFPGTGDVSDVGLGKGKYYTVNVPLRDGIQDEQYLQIFTAVVPEIVAAFRPEAVVLQCGA 253
Query: 261 DSLAGDRLGCFNLSIDGHAECVRFVKKFNLPLLVTGGGGYTKENVARCWTVETGILLDTE 320
D+LAGD +G FNL+ G +C+++V + LP L+ GGGGY N ARCWT TG++L
Sbjct: 254 DTLAGDPMGAFNLTPVGIGKCLKYVLGWKLPTLILGGGGYNLANTARCWTYLTGLILGEP 313
Query: 321 LPNEIPENEYIKYFAPECSLRIPNGHIENLNSKSYLSTIKMQVLENLRSIQ 371
L ++IP++E+ + P+ L I +LN Y+ I + NL+++
Sbjct: 314 LSSDIPDHEFFTSYGPDYELEISPSLRPDLNEDQYIEKILETIKGNLKNVV 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 = 325 bits (834), Expect = e-109
Identities = 110/340 (32%), Positives = 159/340 (46%), Gaps = 18/340 (5%)
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 FTDRVMTVSFHKFGDLFFPGTGDVKEIGEREGKFYAINVPLKDGIDDTSFTRLFKTIISK 244
D V+TVS H+ G F+PGTG EIGE + +N+PL G D S+ + I+
Sbjct: 175 DDDDVLTVSLHQDGRPFYPGTGGADEIGE-GKEGNNVNIPLPPGTGDDSYLEALEEIVLP 233
Query: 245 VVETYAPGAIVLQCGADSLAGDRLGCFNLSIDGHAECVRFVKKFNL----PLLVTGGGGY 300
++E + P +++ G D+ GD LG NL+ +G+A+ R V+K P++ GGY
Sbjct: 234 LLEEFKPDLVIVSAGFDAHRGDPLGRLNLTEEGYAKIGRAVRKLAEGYGGPVVAVLEGGY 293
Query: 301 TKENVARCWTVETGILLD---TELPNEIPEN-EYIKYFAP 336
+ +AR L EL +PE+ E + F
Sbjct: 294 NLDALARSLVAFLAGLAGLVEEELEEPLPEDLELRRAFRA 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 = 324 bits (832), Expect = e-109
Identities = 125/309 (40%), Positives = 163/309 (52%), Gaps = 10/309 (3%)
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 DRVMTVSFHKFGDLFFPGTGDVKEIGEREGKFYAINVPLKDGIDDTSFTRLFKTIISKVV 246
RV+T+S H+ G FPGTG V EIGE EG YA+N+PL G D F R F+ ++ ++
Sbjct: 179 PRVLTISLHESGRYLFPGTGFVDEIGEGEGYGYAVNIPLPPGTGDDEFLRAFEAVVPPLL 238
Query: 247 ETYAPGAIVLQCGADSLAGDRLGCFNLSIDGHAECVRFVK-----KFNLPLLVTGGGGYT 301
+ P IV Q GAD+ AGD L NLS + VR ++ L GGGGY
Sbjct: 239 RAFRPDVIVSQHGADAHAGDPLTHLNLSNRAYRAAVRRIRELADEYCGGRWLALGGGGYN 298
Query: 302 KENVARCWT 310
+ VAR W
Sbjct: 299 PDVVARAWA 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 = 314 bits (808), Expect = e-106
Identities = 106/306 (34%), Positives = 155/306 (50%), Gaps = 16/306 (5%)
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--ARVLYIDIDVHHGDGVEEAFYFTDRVMTVSFH 195
A++ ASGFC N++ + LLK + RVL +D+DVHHG+G +E FY RV+T+S H
Sbjct: 117 AERDRASGFCLFNNVAIAARYLLKRYGLKRVLIVDLDVHHGNGTQEIFYDDPRVLTISIH 176
Query: 196 KFGDLFFPGTGDVKEIGEREGKFYAINVPLKDGIDDTSFTRLFKTIISKVVETYAPGAIV 255
+ F+PGTG E GE G+ Y +N+PL G D + F+ I+ + + P I+
Sbjct: 177 QDP--FYPGTGFADETGEGAGEGYTLNIPLPPGTGDEEYLAAFEEILLPALREFQPDLIL 234
Query: 256 LQCGADSLAGDRLGCFNLSIDGHAECVRFVKKF----NLPLLVTGGGGYTKENVARCWTV 311
+ G D+ AGD LG NL+ +G+AE R + + P++ GGY + +AR
Sbjct: 235 VSAGFDAHAGDPLGGLNLTTEGYAERTRLLLELADAYGGPVVSVLEGGYNLDALARSAAA 294
Query: 312 ETGILL 317
LL
Sbjct: 295 VLAGLL 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 = 287 bits (736), Expect = 5e-95
Identities = 119/292 (40%), Positives = 169/292 (57%), Gaps = 23/292 (7%)
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-RVLYIDIDVHHGDGVEEAFYFTDRVMTVSFHKFGDLFFPGTG 206
Y+ND+VL IL L + RV Y+D+D+HHGDGVE AF+F+ V+T S H++ FFPGTG
Sbjct: 127 YVNDIVLAILRLRRARFRRVFYLDLDLHHGDGVESAFFFSKNVLTCSIHRYDPGFFPGTG 186
Query: 207 DVKEIGEREGKFYAINVPLKDGIDDTSFTRLFKTIISKVVETYAPGAIVLQCGADSLAGD 266
+K +N+PLK G+ D + R+ +I+ ++E + P IV+QCG D L+GD
Sbjct: 187 SLKN----SSDKGMLNIPLKRGLSDKTLLRIIDSIVRPLIEKFEPEVIVIQCGCDGLSGD 242
Query: 267 RLGCFNLSIDGHAECVRFVKKF--NLPLLVTGGGGYTKENVARCWTVETGIL 316
+NL+I G+ + + K + P L+ GGGGY AR WT T ++
Sbjct: 243 PHKEWNLTIRGYGSVIELLLKEFKDKPTLLLGGGGYNHTEAARAWTYLTSMV 294
>gnl|CDD|240374 PTZ00346, PTZ00346, histone deacetylase; Provisional.
Length = 429
Score = 290 bits (742), Expect = 3e-94
Identities = 145/312 (46%), Positives = 191/312 (61%), Gaps = 1/312 (0%)
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 WAGGLHHAKKCEASGFCYINDLVLGILELLKYHARVLYIDIDVHHGDGVEEAFYFTDRVM 190
W GG+HH+K E SGFCY+ND+VLGILELLK H RVLY+DID+HHGDGV+EAF +DRV
Sbjct: 149 WGGGMHHSKCGECSGFCYVNDIVLGILELLKCHDRVLYVDIDMHHGDGVDEAFCTSDRVF 208
Query: 191 TVSFHKFGDLFFPGTGDVKEIGEREGKFYAINVPLKDGIDDTSFTRLFKTIISKVVETYA 250
T+S HKFG+ FFPGTG +++G G++Y++N+ + DGI D + LF+ + +V Y+
Sbjct: 209 TLSLHKFGESFFPGTGHPRDVGYGRGRYYSMNLAVWDGITDFYYLGLFEHALHSIVRRYS 268
Query: 251 PGAIVLQCGADSLAGDRLGCFNLSIDGHAECVRFVKKFNLPLLVTGGGGYTKENVARCWT 310
P AIVLQCGADSLAGDRLG NLS GH +CV+ V+ +P+L GGGGYT NVA+ W
Sbjct: 269 PDAIVLQCGADSLAGDRLGLLNLSSFGHGQCVQAVRDLGIPMLALGGGGYTIRNVAKLWA 328
Query: 311 VETGILLDTELP 322
ET IL LP
Sbjct: 329 YETSILTGHPLP 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 = 259 bits (664), Expect = 2e-84
Identities = 104/291 (35%), Positives = 142/291 (48%), Gaps = 16/291 (5%)
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-HARVLYIDIDVHHGDGVEEAFYFTDRVMTVSFHKFGDLFFPGTGD 207
ND+VL I L + +R+L ID D HHGDG EAFY DRV+ +SFH + F
Sbjct: 118 FNDVVLAIKFLRERGISRILIIDTDAHHGDGTREAFYDDDRVLHMSFHNYDIYPF----- 172
Query: 208 VKEIGEREGKFYAINVPLKDGIDDTSFTRLFKTIISKVVETYAPGAIVLQCGADSLAGDR 267
G +GK Y INVPL+DG+ D + + +ISKV+E + P +VLQ G D+ GDR
Sbjct: 173 ----GRGKGKGYKINVPLEDGLGDEEYLDAVERVISKVLEEFEPEVVVLQFGHDTHEGDR 228
Query: 268 LGCFNLSIDGHAECVRFVKKFN--LPLLVTGGGGYTKENVARCWTVETGIL 316
LG FNLS G + VK+F P+L+ GGGY E AR WT L
Sbjct: 229 LGGFNLSEKGFVKLAEIVKEFARGGPILMVLGGGYNPEAAARIWTAIIKEL 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 = 157 bits (399), Expect = 5e-45
Identities = 84/287 (29%), Positives = 126/287 (43%), Gaps = 31/287 (10%)
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--RVLYIDIDVHHGDGVEEAFYFTDRVMTVSFHKFGDL 200
GFC ND+ + LL RVL +D+DVH G+G F V T S H G+
Sbjct: 109 GEGFCVFNDIAIAARVLLAEGLVRRVLIVDLDVHQGNGTAAIFADDPSVFTFSMH--GEK 166
Query: 201 FFPGTGDVKEIGEREGKFYAINVPLKDGIDDTSFTRLFKTIISKVVETYAPGAIVLQCGA 260
+P KE + ++VPL DG D + + + +++ + P + G
Sbjct: 167 NYPF---RKEPSD-------LDVPLPDGTGDDEYLAALEEALPRLLAEFRPDLVFYNAGV 216
Query: 261 DSLAGDRLGCFNLSIDGHAE----CVRFVKKFNLPLLVTGGGGYTKE 303
D LAGDRLG +LS++G E +RF + +P+ + GGGY+++
Sbjct: 217 DVLAGDRLGRLSLSLEGLRERDRLVLRFARARGIPVAMVLGGGYSRD 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 = 150 bits (381), Expect = 2e-42
Identities = 82/297 (27%), Positives = 131/297 (44%), Gaps = 27/297 (9%)
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--ARVLYIDIDVHHGDGVEEAFYFTDRVMTVSFHK 196
+ A GFC N++ + K + RVL +D DVHHG+G ++ FY V+ S H+
Sbjct: 108 EPDRAMGFCLFNNVAIAARYAQKRYGLKRVLIVDWDVHHGNGTQDIFYDDPSVLYFSIHQ 167
Query: 197 FGDLFFPGTGDVKEIGEREGKFYAINVPLKDGIDDTSFTRLFKTIISKVVETYAPGAIVL 256
+ F+PGTG +E G G+ + INVPL G D + F+ ++ + + P +++
Sbjct: 168 YP--FYPGTGAAEETGGGAGEGFTINVPLPPGSGDAEYLAAFEEVLLPIAREFQPDLVLV 225
Query: 257 QCGADSLAGDRLGCFNLSIDGHAECVRFVKKF-----NLPLLVTGGGGYTKENVARC 308
G D+ GD LG NL+ +G+A R +K+ L+ GGY E +A
Sbjct: 226 SAGFDAHRGDPLGGMNLTPEGYARLTRLLKELADEHCGGRLVFVLEGGYNLEALAES 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 = 142 bits (360), Expect = 4e-39
Identities = 77/268 (28%), Positives = 113/268 (42%), Gaps = 30/268 (11%)
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 YHARVLYIDIDVHHGDGVEEAFYFTDRVMTVSFHKFGDLFFPGT-GDVKEIGEREGKFYA 220
RV +D+DVHHG+G +E FY V+ VS H F+P G E GE EG+ Y
Sbjct: 143 RAGRVAILDVDVHHGNGTQEIFYERPDVLYVSIHGDPRTFYPFFLGFADETGEGEGEGYN 202
Query: 221 INVPLKDGIDDTSFTRLFKTIISKVVETYAPGAIVLQCGADSLAGDRLGCFNLSIDGHAE 280
+N+PL G D + ++ + + P A+V+ G D+ GD L F L+ + +A
Sbjct: 203 LNLPLPPGTGDDDYLAALDEALAA-IAAFGPDALVVSLGFDTHEGDPLSDFKLTTEDYAR 261
Query: 281 CVRFVKKFNLPLLVTGGGGYTKENVARC 308
R + LP + GGY + + R
Sbjct: 262 IGRRIAALGLPTVFVQEGGYNVDALGRN 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 = 119 bits (302), Expect = 2e-30
Identities = 89/347 (25%), Positives = 143/347 (41%), Gaps = 35/347 (10%)
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 GVEEAFYFTDRVMTVSFHKFGDLFFPGTGDVKEIGEREGKFYAINVPLKDGIDDTSFTRL 237
G + FY V+T+S H+ F P +G V+E GE G+ Y +N+PL G D ++
Sbjct: 181 GTQAIFYDDPDVLTISLHQDR-CFPPDSGAVEERGEGAGEGYNLNIPLPPGSGDGAYLHA 239
Query: 238 FKTIISKVVETYAPGAIVLQCGADSLAGDRLGCFNLSIDGHAECVRFVKKFNLP-----L 292
F+ I+ + + P I++ G D+ A D LG L+ DG R ++ L
Sbjct: 240 FERIVLPALRAFRPELIIVASGFDASAFDPLGRMMLTSDGFRALTRKLRDLADELCGGRL 299
Query: 293 LVTGGGGYTKENVARCW--TVETGILLDTELPNEIPENEYIKYFAPE 337
++ GGY++ V C +E L P Y + +
Sbjct: 300 VMVHEGGYSEAYVPFCGLAVLEE--LSGVRTGIADPLLYYPEAQGGQ 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 = 113 bits (284), Expect = 3e-28
Identities = 85/328 (25%), Positives = 140/328 (42%), Gaps = 28/328 (8%)
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---ILELLKYHARVLYIDIDVHHGDGVEEAFYFTDRVMTVS 193
HA + EA+G+C N++ + +E L R+L +D DVHHG G ++ FY RV+ S
Sbjct: 118 HAMRNEANGYCIFNNVAIAAKYAIEKLGLK-RILIVDWDVHHGQGTQQGFYEDPRVLYFS 176
Query: 194 FHKFGD-LFFPG--TGDVKEIGEREGKFYAINVPLKD-GIDDTSFTRLFKTIISKVVETY 249
H++ F+P D IG G + +NVPL G+ D + +F I+ + +
Sbjct: 177 IHRYEHGRFWPHLFESDYDYIGVGHGYGFNVNVPLNQTGLGDADYLAIFHHILLPLALEF 236
Query: 250 APGAIVLQCGADSLAGDRLGCFNLSIDGHAECVRFVKKFNLP-LLVTGGGGYTKENVARC 308
P +++ G D+ GD G ++ G+A R + LL+ GGY E++A
Sbjct: 237 QPELVLVSAGFDASIGDPEGEMAVTPAGYAHLTRLLMGLAGGKLLLVLEGGYLLESLAES 296
Query: 309 --WTVETGILLDTELPN---EIPENEYI 331
T+ LL LP IP +
Sbjct: 297 VSMTLRG--LLGDPLPPLAPPIPIRSVL 322
>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 = 105 bits (264), Expect = 1e-25
Identities = 70/271 (25%), Positives = 124/271 (45%), Gaps = 18/271 (6%)
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---RVLYIDIDVHHGDGVEEAFYFTDRVMTV 192
HA+ E+ GFC+ N++ + L Y ++L +D D+HHG+G + AFY V+ +
Sbjct: 116 HAEPDESMGFCFFNNVAVAAKWLQTEYPDKIKKILILDWDIHHGNGTQRAFYDDPNVLYI 175
Query: 193 SFHKF-GDLFFPGT--GDVKEIGEREGKFYAINVPLKD-GIDDTSFTRLFKTIISKVVET 248
S H+F F+PGT GD + +GE G + +N+P G+ D + F+ I+ +
Sbjct: 176 SLHRFENGGFYPGTPYGDYESVGEGAGLGFNVNIPWPQGGMGDADYIYAFQRIVMPIAYE 235
Query: 249 YAPGAIVLQCGADSLAGDRLGCFNLSIDGHA 279
+ P +++ G D+ GD LG +++ G+A
Sbjct: 236 FDPDLVIISAGFDAADGDELGQCHVTPAGYA 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 = 99.7 bits (249), Expect = 3e-23
Identities = 74/313 (23%), Positives = 141/313 (45%), Gaps = 19/313 (6%)
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-RVLYIDIDVHHGDGVEEAFYFTDRVMTVSF 194
HA++ A GFC+ N++ + KY R+L +D DVHHG+G + F V+ +S
Sbjct: 127 HAEQDTACGFCFFNNVAIAARYAQKKYGLKRILIVDWDVHHGNGTQHMFESDPSVLYISL 186
Query: 195 HKFGD-LFFPGT--GDVKEIGEREGKFYAINVPL-KDGIDDTSFTRLFKTIISKVVETYA 250
H++ + FFP + G+ +G+ +G+ + +N+P K G+ D + F+ ++ + +
Sbjct: 187 HRYDNGSFFPNSPEGNYDVVGKGKGEGFNVNIPWNKGGMGDAEYIAAFQQVVLPIAYEFN 246
Query: 251 PGAIVLQCGADSLAGDRLGCFNLSIDGHAECVRFVKKF-NLPLLVTGGGGYTKENVARCW 309
P +++ G D+ GD LG ++ +G+A + ++V GGY +++
Sbjct: 247 PELVLVSAGFDAARGDPLGGCKVTPEGYAHMTHMLMSLAGGRVIVILEGGYNLTSISESM 306
Query: 310 TVETGILLDTELP 322
++ T LL P
Sbjct: 307 SMCTKTLLGDPPP 319
>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 = 96.3 bits (240), Expect = 4e-23
Identities = 40/238 (16%), Positives = 62/238 (26%), Gaps = 52/238 (21%)
Query: 103 FEFCQIYAGGTIDAARRLNNQLCDIAINWAGGLHHAKKCEASGFCYINDLVLGILELLKY 162
E ++ AG + + + + G H+ N + + EL
Sbjct: 8 AEAHELLAGVVVAVLKD-----GKVPVVLGG--DHSI---------ANGAIRAVAEL--- 48
Query: 163 HARVLYIDIDVHHGDGVEEAFYF--------------TDRVMTVSFHKFGDLFFPGTGDV 208
H + ID+D HH EAF V VS G
Sbjct: 49 HPDLGVIDVDAHHDVRTPEAFGKGNHHTPRHLLCEPLISDVHIVSIGIRGVSNGE----- 103
Query: 209 KEIGEREGKFYAINVPLKDGIDDTSFTRLFKTIISKVVETYAPGAIVLQCGADSLAGD-- 266
G K + + + D +F+ I+S + + L D L
Sbjct: 104 -AGGAYARKLGVVYFSMTEV-DKLGLGDVFEEIVSYL--GDKGDNVYLSVDVDGLDPSFA 159
Query: 267 ----RLGCFNLSIDGHAECVRFVKKFNLPLLVTGGGGYT----KENVARCWTVETGIL 316
G LS + K NL + + AR T L
Sbjct: 160 PGTGTPGPGGLSYREGLYITERIAKTNLVVGLDIVEVNPLLDETGRTARLAAALTLEL 217
>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 = 97.6 bits (244), Expect = 6e-23
Identities = 70/258 (27%), Positives = 105/258 (40%), Gaps = 25/258 (9%)
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--RVLYIDIDVHHGDGVEEAFYFTDRVMTVSFHK 196
++ +A GFC N++ + L +H RV +D DVHHG+G E+ F RV+ S H+
Sbjct: 109 ERDKAMGFCLFNNVAIAAAHALAHHGLERVAIVDFDVHHGNGTEDIFRDDPRVLFCSSHQ 168
Query: 197 FGDLFFPGTGDVKEIGEREGKFYAINVPLKDGIDDTSFTRLFKTIISKVVETYAPGAIVL 256
+PGTG E G +NVPL G F + ++ + P I++
Sbjct: 169 HP--LYPGTGAPDETGHG----NIVNVPLPAGTGGAEFREAVEDRWLPALDAFKPDLILI 222
Query: 257 QCGADSLAGDRLGCFNLS 274
G D+ D L NL+
Sbjct: 223 SAGFDAHRDDPLAQLNLT 240
>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 = 97.0 bits (242), Expect = 4e-22
Identities = 74/286 (25%), Positives = 119/286 (41%), Gaps = 44/286 (15%)
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 GDGVEEAFYFTDRVMTVSFHKFGD-LFFPGTGDVKEIGEREGKFYAINVPLKDGID---- 230
G+G ++ FY V+ +S H++ D FFPGTG E+G G+ + +N+ G+D
Sbjct: 193 GNGTQQIFYEDPNVLYISLHRYDDGNFFPGTGAPTEVGSGAGEGFNVNIAWSGGLDPPMG 252
Query: 231 DTSFTRLFKTIISKVVETYAPGAIVLQCGADSLAG--DRLGCFNLS 274
D + F+T++ + ++P +++ G D+ G LG + +S
Sbjct: 253 DAEYLAAFRTVVMPIAREFSPDIVLVSAGFDAAEGHPPPLGGYKVS 298
>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 = 95.9 bits (238), Expect = 1e-21
Identities = 79/277 (28%), Positives = 128/277 (46%), Gaps = 44/277 (15%)
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--ILELLKYHARVLYIDIDVHHGDGVEEAFYFTDRVMTVSFHKF 197
+ GFCY N + + +L+ +++L +D DVHHG+G ++AFY V+ +S H++
Sbjct: 158 ESTPMGFCYFNSVAIAAKLLQQRLNVSKILIVDWDVHHGNGTQQAFYSDPNVLYMSLHRY 217
Query: 198 GD-LFFPGTGDVKEIGEREGKFYAINVPLKDGID----DTSFTRLFKTIISKVVETYAPG 252
D FFPG+G E+G G + +N+ G+D D + F+T++ + +AP
Sbjct: 218 DDGNFFPGSGAPDEVGTGPGVGFNVNMAFTGGLDPPMGDAEYLAAFRTVVMPIASEFAPD 277
Query: 253 AIVLQCGADSLAGD--RLGCFNLSIDGHAECVRFVKK 287
+++ G D++ G LG +NLS A+C ++ K
Sbjct: 278 VVLVSSGFDAVEGHPTPLGGYNLS----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 = 91.6 bits (227), Expect = 4e-20
Identities = 44/149 (29%), Positives = 85/149 (57%), Gaps = 11/149 (7%)
Query: 136 HHAKKCEASGFCYINDLVLGILELLKYH---ARVLYIDIDVHHGDGVEEAFYFTDRVMTV 192
HHA++ A GFC+ N + + +LL+ ++L +D D+HHG+G ++AFY V+ +
Sbjct: 154 HHAEESTAMGFCFFNSVAIAA-KLLQQKLNVGKILIVDWDIHHGNGTQQAFYNDPNVLYI 212
Query: 193 SFHKFGD-LFFPGTGDVKEIGEREGKFYAINVPLKDGID----DTSFTRLFKTIISKVVE 247
S H++ D FFPG+G E+G G + +N+ G+D D + F+T++ +
Sbjct: 213 SLHRYDDGNFFPGSGAPDEVGAGPGVGFNVNIAWTGGVDPPIGDVEYLTAFRTVVMPIAN 272
Query: 248 TYAPGAIVLQCGADSLAGDR--LGCFNLS 274
++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 = 5e-20
Identities = 45/137 (32%), Positives = 78/137 (56%), Gaps = 7/137 (5%)
Query: 136 HHAKKCEASGFCYINDLVLGILELLKYH--ARVLYIDIDVHHGDGVEEAFYFTDRVMTVS 193
HHA++ A GFC+ N + + L +++L +D+DVHHG+G ++AFY ++ +S
Sbjct: 152 HHAEESTAMGFCFFNSVAITAKYLRDQLNISKILIVDLDVHHGNGTQQAFYADPSILYIS 211
Query: 194 FHKFGD-LFFPGTGDVKEIGEREGKFYAINVPLKDGID----DTSFTRLFKTIISKVVET 248
H++ + FFPG+G E+G G+ Y IN+ G+D D + F+TI+ V +
Sbjct: 212 LHRYDEGNFFPGSGAPNEVGTGLGEGYNINIAWTGGLDPPMGDVEYLEAFRTIVKPVAKE 271
Query: 249 YAPGAIVLQCGADSLAG 265
+ 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 = 3e-19
Identities = 42/137 (30%), Positives = 73/137 (53%), Gaps = 7/137 (5%)
Query: 136 HHAKKCEASGFCYINDLVLGI--LELLKYHARVLYIDIDVHHGDGVEEAFYFTDRVMTVS 193
HHA A GFC+ N + + L+ +++L +D DVHHG+G ++ FY V+ +S
Sbjct: 152 HHADHSTAMGFCFFNSVAIACRQLQQQGKASKILIVDWDVHHGNGTQQTFYQDPSVLYIS 211
Query: 194 FHKFGD-LFFPGTGDVKEIGEREGKFYAINVPLKDGID----DTSFTRLFKTIISKVVET 248
H+ D FFPG+G V E+G G+ + +NV G+D D + F+ ++ +
Sbjct: 212 LHRHDDGNFFPGSGAVDEVGAGSGEGFNVNVAWAGGLDPPMGDPEYLAAFRIVVMPIARE 271
Query: 249 YAPGAIVLQCGADSLAG 265
++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 = 76.4 bits (188), Expect = 2e-15
Identities = 83/315 (26%), Positives = 143/315 (45%), Gaps = 35/315 (11%)
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--RVLYIDIDVHHGDGVEEAFYFTDRVMTVSFHKF-GD 199
A+GFC N++ + K + R+L +D DVHHG G++ F V+ S+H++
Sbjct: 124 ANGFCVFNNVAIAAEYAKKKYGLHRILIVDWDVHHGQGIQYIFEEDPSVLYFSWHRYEHQ 183
Query: 200 LFFPG--TGDVKEIGEREGKFYAINVPL-KDGIDDTSFTRLFKTIISKVVETYAPGAIVL 256
F+P D +G +G + IN+P K G+ + + F ++ + + P +++
Sbjct: 184 RFWPFLRESDYDAVGRGKGLGFNINLPWNKVGMGNADYLAAFFHVLLPLAFEFDPELVLV 243
Query: 257 QCGADSLAGDRLGCFNLSIDGHAECVRFVKKFNLPLLVTGG-------GGYTKENVAR-- 307
G DS GD G + EC + + L GG GGY E++A
Sbjct: 244 SAGFDSAIGDPEGQMCAT----PECFAHLTHLLMVL--AGGKLCAVLEGGYHLESLAESV 297
Query: 308 CWTVETGILLDTELP 322
C TV+T LL LP
Sbjct: 298 CMTVQT--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 = 74.9 bits (184), Expect = 8e-15
Identities = 65/256 (25%), Positives = 110/256 (42%), Gaps = 14/256 (5%)
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--RVLYIDIDVHHGDGVEEAFYFTDRVMTVSFHKF 197
+ G+C N++ + + H RVL +D DVHHG G + F V+ S H++
Sbjct: 121 HDKMDGYCMFNNVAIAARYAQQKHGVQRVLIVDWDVHHGQGTQFIFEQDPSVLYFSIHRY 180
Query: 198 GD-LFFP--GTGDVKEIGEREGKFYAINVPL-KDGIDDTSFTRLFKTIISKVVETYAPGA 253
F+P D +G G+ Y INVP + G+ D + F ++ V + P
Sbjct: 181 EQGRFWPHLKESDSSAVGFGRGEGYNINVPWNQVGMRDADYIAAFLHVLLPVALEFQPQL 240
Query: 254 IVLQCGADSLAGDRLG 269
+++ G D++ GD G
Sbjct: 241 VLVAAGFDAVIGDPKG 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 = 46.3 bits (110), Expect = 2e-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 = 0.14
Identities = 13/53 (24%), Positives = 23/53 (43%), Gaps = 4/53 (7%)
Query: 374 PSVQMQEVPPDFYI-PEFDEDEQNPDERMDQHTQDKQIQRDDEFYEGDNDNDH 425
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 = 0.85
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 = 1.7
Identities = 17/58 (29%), Positives = 25/58 (43%), Gaps = 8/58 (13%)
Query: 279 AECVRFVKKFNLPLLVTGGGGYTKENVARCWTVETGILLDTELPNEI----PENEYIK 332
A VR + LP+LV GGG ++ + G++LD N I PE+
Sbjct: 14 AAIVRLANENGLPVLVRGGG----SSLLGDAVLTGGVVLDLSRLNGILEIDPEDGTAT 67
>gnl|CDD|183384 PRK11924, PRK11924, RNA polymerase sigma factor; Provisional.
Length = 179
Score = 29.9 bits (68), Expect = 1.7
Identities = 19/81 (23%), Positives = 29/81 (35%), Gaps = 10/81 (12%)
Query: 337 ECSLRIPNGHIENLNSKS----YLSTIKMQVL-ENLRSIQHAPSVQMQEVPPDFYIPEFD 391
E LR + N K +L TI V + LR + +V + PEF
Sbjct: 46 EAFLRAWR-KADLFNGKGSARTWLLTIARNVCYDLLRRRRREKAVLSDDALE----PEFA 100
Query: 392 EDEQNPDERMDQHTQDKQIQR 412
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 = 1.8
Identities = 14/36 (38%), Positives = 18/36 (50%), Gaps = 1/36 (2%)
Query: 358 TIKMQVLENLRSIQHAP-SVQMQEVPPDFYIPEFDE 392
TI V+E LR + P V + PD IP+F E
Sbjct: 43 TIGPLVVEALRPLTELPLDVHLMVEEPDRIIPDFAE 78
>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 = 2.4
Identities = 15/68 (22%), Positives = 27/68 (39%), Gaps = 6/68 (8%)
Query: 349 NLNSKSYLSTIK---MQVLENLRSIQHAPSVQMQEVPPDFYIPEFDEDEQNPD---ERMD 402
N S ++S K +V+ LR+ +V + PD + E+ +N D +
Sbjct: 101 NSYSFDFVSLFKPESQEVIYELRAKLRKDNVGLPTSNPDLAVIVLPEEFKNKDIWNSEIA 160
Query: 403 QHTQDKQI 410
T+ Q
Sbjct: 161 GLTRPNQD 168
>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 = 2.4
Identities = 11/27 (40%), Positives = 16/27 (59%), Gaps = 1/27 (3%)
Query: 172 DVHHGDGVEEAFYFTDRV-MTVSFHKF 197
++H GD VEE +DR + + FH F
Sbjct: 167 EIHPGDAVEEKLSLSDRFGLWLGFHPF 193
>gnl|CDD|181604 PRK08990, PRK08990, flagellar motor protein PomA; Reviewed.
Length = 254
Score = 28.9 bits (65), Expect = 5.5
Identities = 14/38 (36%), Positives = 17/38 (44%), Gaps = 1/38 (2%)
Query: 171 IDVHHGDGVEEAFYFTDRVMTVSFHKFGDLFFPGTGDV 208
+D H GD V A D +T H+ G F GDV
Sbjct: 113 VDGHDGDVVRAALE-KDIALTEERHETGIGIFRAFGDV 149
>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
>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 = 9.4
Identities = 26/113 (23%), Positives = 38/113 (33%), Gaps = 27/113 (23%)
Query: 156 ILELLKYHARVLYIDIDVHHGDGVEEAFYFTDRVMTVSFHKFGDLFFPGTGDVKEIGERE 215
I L K + V EA D V+T G + +E ER
Sbjct: 48 IAILAKKLVEEAGAPVKVEATTDRREALEGADFVITQ--------IRVGGLEAREKDER- 98
Query: 216 GKFYAINVPLKDGID--DTS----FTRLFKTI-----ISKVVETYAPGAIVLQ 257
+PLK G+ +T+ +TI I+K +E P A +L
Sbjct: 99 -------IPLKHGLYGQETNGPGGIFYGLRTIPVILDIAKDMEKVCPNAWMLN 144
>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 = 27.9 bits (63), Expect = 9.7
Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 11/53 (20%)
Query: 156 ILELLKYHARVLYIDIDVH-------HGDGVEEAFYFTDRV--MTVSFHK-FG 198
+++L K + +L++D + H HG GVEE TD V + + K FG
Sbjct: 154 LVDLAKKYGAILFVD-EAHSVGVYGPHGRGVEEFGGLTDDVDIIMGTLGKAFG 205
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: 22,660,882
Number of extensions: 2244356
Number of successful extensions: 2029
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1943
Number of HSP's successfully gapped: 55
Length of query: 429
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 329
Effective length of database: 6,502,202
Effective search space: 2139224458
Effective search space used: 2139224458
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: 60 (26.8 bits)