RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 041063
(490 letters)
>gnl|CDD|212517 cd09991, HDAC_classI, Class I histone deacetylases. Class I
histone deacetylases (HDACs) are Zn-dependent enzymes
that catalyze hydrolysis of N(6)-acetyl-lysine residues
in histone amino termini to yield a deacetylated histone
(EC 3.5.1.98). Enzymes belonging to this group
participate in regulation of a number of processes
through protein (mostly different histones) modification
(deacetylation). Class I histone deacetylases in general
act via the formation of large multiprotein complexes.
This group includes animal HDAC1, HDAC2, HDAC3, HDAC8,
fungal RPD3, HOS1 and HOS2, plant HDA9, protist,
archaeal and bacterial (AcuC) deacetylases. Members of
this class are involved in cell cycle regulation, DNA
damage response, embryonic development, cytokine
signaling important for immune response and in
posttranslational control of the acetyl coenzyme A
synthetase. In mammals, they are known to be involved in
progression of various tumors. Specific inhibitors of
mammalian histone deacetylases are an emerging class of
promising novel anticancer drugs.
Length = 306
Score = 613 bits (1584), Expect = 0.0
Identities = 221/308 (71%), Positives = 270/308 (87%), Gaps = 2/308 (0%)
Query: 67 FYEPTIGDYYYGQGHPMKPHRIRMAHNLIVHYGLHRRMEVNRPFPAGPSDIRRFHTDEYV 126
FY+P +G+YYYGQGHPMKPHRIRM H+LI+ YGL+++ME+ RP PA ++ +FH+D+Y+
Sbjct: 1 FYDPDVGNYYYGQGHPMKPHRIRMTHSLILSYGLYKKMEIYRPRPATAEELTKFHSDDYI 60
Query: 127 EFLASVSPESSGDPSFSRHLKRFNVGEDCPVFDGLFGFCQASAGGSIGAAVKLNRGDADI 186
+FL SVSP++ F + L+RFNVGEDCPVFDGL+ +CQ AGGSI AAVKLNRG ADI
Sbjct: 61 DFLRSVSPDN--MKEFKKQLERFNVGEDCPVFDGLYEYCQLYAGGSIAAAVKLNRGQADI 118
Query: 187 AVNWAGGLHHAKKSEASGFCYVNDIVLGILELLKVHRRVLYVDIDVHHGDGVEEAFYTTD 246
A+NWAGGLHHAKKSEASGFCYVNDIVL ILELLK H+RVLY+DID+HHGDGVEEAFYTTD
Sbjct: 119 AINWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTD 178
Query: 247 RVMTVSFHKFGDFFPGTGHIKDVGAGQGKFYALNVPLNDGLDDESFRGLFRPIIQKVMEV 306
RVMTVSFHKFG++F ++D+GAG+GK+YA+NVPL DG+DDES+ +F P++ KVMEV
Sbjct: 179 RVMTVSFHKFGEYFFPGTGLRDIGAGKGKYYAVNVPLKDGIDDESYLQIFEPVLSKVMEV 238
Query: 307 YQPDAVVLQCGADSLSGDRLGCFNLSVKGHADCLRFLRSFNVPLMVLGGGGYTIRNVARC 366
+QP AVVLQCGADSL+GDRLGCFNLS+KGHA C++F++SFN+PL+VLGGGGYT+RNVARC
Sbjct: 239 FQPSAVVLQCGADSLAGDRLGCFNLSIKGHAKCVKFVKSFNIPLLVLGGGGYTLRNVARC 298
Query: 367 WCYETAVA 374
W YETAV
Sbjct: 299 WTYETAVL 306
>gnl|CDD|212528 cd10004, RPD3-like, reduced potassium dependency-3 (RPD3)-like.
Proteins of the Rpd3-like family are class I
Zn-dependent Histone deacetylases that catalyze
hydrolysis of an N(6)-acetyl-lysine residue of a histone
to yield a deacetylated histone (EC 3.5.1.98). RPD3 is
the yeast homolog of class I HDACs. The main function of
RPD3-like group members is regulation of a number of
different processes through protein (mostly different
histones) modification (deacetylation). This group
includes fungal RPD3 and acts via the formation of large
multiprotein complexes. Members of this group are
involved in cell cycle regulation, DNA damage response,
embryonic development and cytokine signaling important
for immune response. Histone deacetylation by yeast RPD3
represses genes regulated by the Ash1 and Ume6
DNA-binding proteins. In mammals, they are known to be
involved in progression of various tumors. Specific
inhibitors of mammalian histone deacetylases could be a
therapeutic drug option.
Length = 375
Score = 613 bits (1583), Expect = 0.0
Identities = 244/377 (64%), Positives = 309/377 (81%), Gaps = 2/377 (0%)
Query: 61 KRRVSYFYEPTIGDYYYGQGHPMKPHRIRMAHNLIVHYGLHRRMEVNRPFPAGPSDIRRF 120
K++V+YFY+ +G+Y YG GHPMKPHRIRMAH+L+++YGL+++ME+ R PA +++ +F
Sbjct: 1 KKKVAYFYDSDVGNYAYGPGHPMKPHRIRMAHSLVMNYGLYKKMEIYRAKPATKNEMTQF 60
Query: 121 HTDEYVEFLASVSPESSGDPSFSRHLKRFNVGEDCPVFDGLFGFCQASAGGSIGAAVKLN 180
HTDEY++FL+ V+P++ F + ++NVG+DCPVFDGLF FC SAGGS+ A +LN
Sbjct: 61 HTDEYIDFLSRVTPDNM--EKFQKEQVKYNVGDDCPVFDGLFEFCSISAGGSMEGAARLN 118
Query: 181 RGDADIAVNWAGGLHHAKKSEASGFCYVNDIVLGILELLKVHRRVLYVDIDVHHGDGVEE 240
RG DIAVNWAGGLHHAKKSEASGFCYVNDIVLGILELL+ H+RVLY+DIDVHHGDGVEE
Sbjct: 119 RGKCDIAVNWAGGLHHAKKSEASGFCYVNDIVLGILELLRYHQRVLYIDIDVHHGDGVEE 178
Query: 241 AFYTTDRVMTVSFHKFGDFFPGTGHIKDVGAGQGKFYALNVPLNDGLDDESFRGLFRPII 300
AFYTTDRVMT SFHK+G++FPGTG ++D+G G GK YA+NVPL DG+DDES++ +F P+I
Sbjct: 179 AFYTTDRVMTCSFHKYGEYFPGTGELRDIGIGTGKNYAVNVPLRDGIDDESYKSIFEPVI 238
Query: 301 QKVMEVYQPDAVVLQCGADSLSGDRLGCFNLSVKGHADCLRFLRSFNVPLMVLGGGGYTI 360
+ VME YQP+AVVLQCG DSLSGDRLGCFNLS+KGHA+C+ F++SFN+P++VLGGGGYT+
Sbjct: 239 KHVMEWYQPEAVVLQCGGDSLSGDRLGCFNLSMKGHANCVNFVKSFNLPMLVLGGGGYTM 298
Query: 361 RNVARCWCYETAVAVGVEPDNKLPYNEYYEYFGPDYTLHVEPCNMENLNAHKDMEKIRNT 420
RNVAR W +ET + G E D LPYNEYYEY+GPDY L+V P NMEN N + ++KI
Sbjct: 299 RNVARTWAFETGLLAGEELDKDLPYNEYYEYYGPDYELNVRPSNMENHNTPEYLDKITTA 358
Query: 421 LLEQLSGLIHAPSVPFQ 437
++E L APSV Q
Sbjct: 359 VIENLRNTSFAPSVQMQ 375
>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 = 609 bits (1573), Expect = 0.0
Identities = 227/382 (59%), Positives = 303/382 (79%), Gaps = 4/382 (1%)
Query: 62 RRVSYFYEPTIGDYYYGQGHPMKPHRIRMAHNLIVHYGLHRRMEVNRPFPAGPSDIRRFH 121
+RV+YFY+P +G+++YG GHPMKPHR+ + H+L++HYGL+++M+V +P+ A D+ RFH
Sbjct: 1 KRVAYFYDPDVGNFHYGPGHPMKPHRLALTHSLVLHYGLYKKMQVYKPYRASAHDMCRFH 60
Query: 122 TDEYVEFLASVSPESSGDPSFSRHLKRFNVGEDCPVFDGLFGFCQASAGGSIGAAVKLNR 181
+++Y++FL V+P++ F++ L +FNVG+DCPVF GLF FC G S+ A KLN
Sbjct: 61 SEDYIDFLQRVTPQNI--QGFTKSLNQFNVGDDCPVFPGLFDFCSMYTGASLEGATKLNH 118
Query: 182 GDADIAVNWAGGLHHAKKSEASGFCYVNDIVLGILELLKVHRRVLYVDIDVHHGDGVEEA 241
DIA+NW+GGLHHAKK EASGFCYVNDIV+ ILELLK H RVLY+DID+HHGDGV+EA
Sbjct: 119 KICDIAINWSGGLHHAKKFEASGFCYVNDIVIAILELLKYHPRVLYIDIDIHHGDGVQEA 178
Query: 242 FYTTDRVMTVSFHKFGD-FFPGTGHIKDVGAGQGKFYALNVPLNDGLDDESFRGLFRPII 300
FY TDRVMTVSFHK+G+ FFPGTG + +VGA G++Y++NVPL DG+DD+S+ LF+P+I
Sbjct: 179 FYLTDRVMTVSFHKYGNYFFPGTGDMYEVGAESGRYYSVNVPLKDGIDDQSYLQLFKPVI 238
Query: 301 QKVMEVYQPDAVVLQCGADSLSGDRLGCFNLSVKGHADCLRFLRSFNVPLMVLGGGGYTI 360
Q+V++ YQP +VLQCGADSL DRLGCFNLS+KGH +C+ F++SFN+PL+VLGGGGYT+
Sbjct: 239 QQVIDFYQPTCIVLQCGADSLGCDRLGCFNLSIKGHGECVEFVKSFNIPLLVLGGGGYTV 298
Query: 361 RNVARCWCYETAVAVGVEPDNKLPYNEYYEYFGPDYTLHVE-PCNMENLNAHKDMEKIRN 419
RNVARCW YET++ V E N+LPYNEY+EYF PD+TLH + +EN N+ + +++IR
Sbjct: 299 RNVARCWTYETSLLVDEEISNELPYNEYFEYFAPDFTLHPDVSTRIENQNSKQYLDQIRQ 358
Query: 420 TLLEQLSGLIHAPSVPFQTTPA 441
T+ E L L HAPSV Q P
Sbjct: 359 TVFENLKMLNHAPSVQMQDVPP 380
>gnl|CDD|240251 PTZ00063, PTZ00063, histone deacetylase; Provisional.
Length = 436
Score = 579 bits (1493), Expect = 0.0
Identities = 247/399 (61%), Positives = 307/399 (76%), Gaps = 6/399 (1%)
Query: 61 KRRVSYFYEPTIGDYYYGQGHPMKPHRIRMAHNLIVHYGLHRRMEVNRPFPAGPSDIRRF 120
++RVSYFY+P IG YYYG GHPMKP RIRMAH LI+ Y L++ ME+ RP + ++ F
Sbjct: 3 RKRVSYFYDPDIGSYYYGPGHPMKPQRIRMAHALILSYDLYKHMEIYRPHKSVEPELVLF 62
Query: 121 HTDEYVEFLASVSPESSGDPSFSRHLKRFNVGE--DCPVFDGLFGFCQASAGGSIGAAVK 178
H +EYV+FL+S+SPE+ D F+ LKRFNVGE DCPVFDGLF F Q+ AG SI A K
Sbjct: 63 HDEEYVDFLSSISPENYRD--FTYQLKRFNVGEATDCPVFDGLFEFQQSCAGASIDGAYK 120
Query: 179 LNRGDADIAVNWAGGLHHAKKSEASGFCYVNDIVLGILELLKVHRRVLYVDIDVHHGDGV 238
LN ADI VNW+GGLHHAK+SEASGFCY+NDIVLGILELLK H RV+Y+DIDVHHGDGV
Sbjct: 121 LNNHQADICVNWSGGLHHAKRSEASGFCYINDIVLGILELLKYHARVMYIDIDVHHGDGV 180
Query: 239 EEAFYTTDRVMTVSFHKFGDFFPGTGHIKDVGAGQGKFYALNVPLNDGLDDESFRGLFRP 298
EEAFY T RVMTVSFHKFGDFFPGTG + D+G QGK+Y++NVPLNDG+DD+SF LF+P
Sbjct: 181 EEAFYVTHRVMTVSFHKFGDFFPGTGDVTDIGVAQGKYYSVNVPLNDGIDDDSFVDLFKP 240
Query: 299 IIQKVMEVYQPDAVVLQCGADSLSGDRLGCFNLSVKGHADCLRFLRSFNVPLMVLGGGGY 358
+I K +EVY+P A+VLQCGADSL+GDRLG FNL++KGHA C+ F+RS N+PL+VLGGGGY
Sbjct: 241 VISKCVEVYRPGAIVLQCGADSLTGDRLGRFNLTIKGHAACVEFVRSLNIPLLVLGGGGY 300
Query: 359 TIRNVARCWCYETAVAVG--VEPDNKLPYNEYYEYFGPDYTLHVEPCNMENLNAHKDMEK 416
TIRNVARCW YET V + E +++ N+YY+Y+ PD+ LH++P N+ N N+ + +EK
Sbjct: 301 TIRNVARCWAYETGVILNKHDEMSDQISLNDYYDYYAPDFQLHLQPSNIPNYNSPEHLEK 360
Query: 417 IRNTLLEQLSGLIHAPSVPFQTTPATTQVPEEPEEDMER 455
I+ +LE L L HAP V F P + +ED +
Sbjct: 361 IKVKILENLRYLEHAPGVQFAYVPPDFFDRDIDDEDEKN 399
>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 = 559 bits (1442), Expect = 0.0
Identities = 246/370 (66%), Positives = 316/370 (85%), Gaps = 2/370 (0%)
Query: 59 GKKRRVSYFYEPTIGDYYYGQGHPMKPHRIRMAHNLIVHYGLHRRMEVNRPFPAGPSDIR 118
G K++V Y+Y+ +G+YYYGQGHPMKPHRIRM HNL+++YGL+R+ME+ RP A ++
Sbjct: 3 GTKKKVCYYYDGDVGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKANAEEMT 62
Query: 119 RFHTDEYVEFLASVSPESSGDPSFSRHLKRFNVGEDCPVFDGLFGFCQASAGGSIGAAVK 178
++H+D+Y++FL S+ P++ + +S+ ++RFNVGEDCPVFDGLF FCQ SAGGS+ +AVK
Sbjct: 63 KYHSDDYIKFLRSIRPDNMSE--YSKQMQRFNVGEDCPVFDGLFEFCQLSAGGSVASAVK 120
Query: 179 LNRGDADIAVNWAGGLHHAKKSEASGFCYVNDIVLGILELLKVHRRVLYVDIDVHHGDGV 238
LN+ DIAVNWAGGLHHAKKSEASGFCYVNDIVL ILELLK H+RVLY+DID+HHGDGV
Sbjct: 121 LNKQQTDIAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGV 180
Query: 239 EEAFYTTDRVMTVSFHKFGDFFPGTGHIKDVGAGQGKFYALNVPLNDGLDDESFRGLFRP 298
EEAFYTTDRVMTVSFHK+G++FPGTG ++D+GAG+GK+YA+N PL DG+DDES+ +F+P
Sbjct: 181 EEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNYPLRDGIDDESYEAIFKP 240
Query: 299 IIQKVMEVYQPDAVVLQCGADSLSGDRLGCFNLSVKGHADCLRFLRSFNVPLMVLGGGGY 358
++ KVME++QP AVVLQCGADSLSGDRLGCFNL++KGHA C+ F++SFN+P+++LGGGGY
Sbjct: 241 VMSKVMEMFQPSAVVLQCGADSLSGDRLGCFNLTIKGHAKCVEFVKSFNLPMLMLGGGGY 300
Query: 359 TIRNVARCWCYETAVAVGVEPDNKLPYNEYYEYFGPDYTLHVEPCNMENLNAHKDMEKIR 418
TIRNVARCW YETAVA+ E N+LPYN+Y+EYFGPD+ LH+ P NM N N ++ +EKI+
Sbjct: 301 TIRNVARCWTYETAVALDSEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTNEYLEKIK 360
Query: 419 NTLLEQLSGL 428
L E L L
Sbjct: 361 QRLFENLRML 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 = 548 bits (1414), Expect = 0.0
Identities = 249/368 (67%), Positives = 311/368 (84%), Gaps = 2/368 (0%)
Query: 61 KRRVSYFYEPTIGDYYYGQGHPMKPHRIRMAHNLIVHYGLHRRMEVNRPFPAGPSDIRRF 120
K++V Y+Y+ IG+YYYGQGHPMKPHRIRM HNL+++YGL+R+ME+ RP A ++ ++
Sbjct: 1 KKKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTKY 60
Query: 121 HTDEYVEFLASVSPESSGDPSFSRHLKRFNVGEDCPVFDGLFGFCQASAGGSIGAAVKLN 180
H+DEY++FL S+ P++ + +S+ ++RFNVGEDCPVFDGLF FCQ S GGS+ AVKLN
Sbjct: 61 HSDEYIKFLRSIRPDNMSE--YSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAGAVKLN 118
Query: 181 RGDADIAVNWAGGLHHAKKSEASGFCYVNDIVLGILELLKVHRRVLYVDIDVHHGDGVEE 240
R D+AVNWAGGLHHAKKSEASGFCYVNDIVL ILELLK H+RVLY+DID+HHGDGVEE
Sbjct: 119 RQQTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEE 178
Query: 241 AFYTTDRVMTVSFHKFGDFFPGTGHIKDVGAGQGKFYALNVPLNDGLDDESFRGLFRPII 300
AFYTTDRVMTVSFHK+G++FPGTG ++D+GAG+GK+YA+N P+ DG+DDES+ +F+PII
Sbjct: 179 AFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPII 238
Query: 301 QKVMEVYQPDAVVLQCGADSLSGDRLGCFNLSVKGHADCLRFLRSFNVPLMVLGGGGYTI 360
KVME+YQP AVVLQCGADSLSGDRLGCFNL+VKGHA C+ +++FN+PL++LGGGGYTI
Sbjct: 239 SKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTI 298
Query: 361 RNVARCWCYETAVAVGVEPDNKLPYNEYYEYFGPDYTLHVEPCNMENLNAHKDMEKIRNT 420
RNVARCW YETAVA+ E N+LPYN+Y+EYFGPD+ LH+ P NM N N + MEKI+
Sbjct: 299 RNVARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEYMEKIKQR 358
Query: 421 LLEQLSGL 428
L E L L
Sbjct: 359 LFENLRML 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 = 459 bits (1182), Expect = e-161
Identities = 184/312 (58%), Positives = 239/312 (76%), Gaps = 2/312 (0%)
Query: 64 VSYFYEPTIGDYYYGQGHPMKPHRIRMAHNLIVHYGLHRRMEVNRPFPAGPSDIRRFHTD 123
VSY + + DY++G+ HPMKP R+ + +L++ YGLH+ M+ A ++R+FH
Sbjct: 1 VSYHFNSRVEDYHFGRTHPMKPFRLTLTKHLVMGYGLHKAMDTYEARAATREELRQFHDA 60
Query: 124 EYVEFLASVSPESSGDPSFSRHLKRFNVGEDCPVFDGLFGFCQASAGGSIGAAVKLNRGD 183
+Y++FL+ VSPE++ F + + FN+G+DCPVFDG++ +CQ AG S+ AA KL G
Sbjct: 61 DYLDFLSKVSPENANQLRFDK-AEPFNIGDDCPVFDGMYDYCQLYAGASLDAARKLCSGQ 119
Query: 184 ADIAVNWAGGLHHAKKSEASGFCYVNDIVLGILELLKVHRRVLYVDIDVHHGDGVEEAFY 243
+DIA+NW+GGLHHAKKSEASGFCYVNDIVL IL LL+ RVLY+DIDVHHGDGVEEAFY
Sbjct: 120 SDIAINWSGGLHHAKKSEASGFCYVNDIVLAILNLLRYFPRVLYIDIDVHHGDGVEEAFY 179
Query: 244 TTDRVMTVSFHKF-GDFFPGTGHIKDVGAGQGKFYALNVPLNDGLDDESFRGLFRPIIQK 302
TDRVMT+SFHK+ G+FFPGTG + D G GK +ALNVPL DG+DDE + LF+ II
Sbjct: 180 RTDRVMTLSFHKYNGEFFPGTGDLDDNGGTPGKHFALNVPLEDGIDDEQYNLLFKSIIGP 239
Query: 303 VMEVYQPDAVVLQCGADSLSGDRLGCFNLSVKGHADCLRFLRSFNVPLMVLGGGGYTIRN 362
+E +QP A+VLQCGADSL GDRLG FNL++K H C++F++SF +P++V+GGGGYT RN
Sbjct: 240 TIEKFQPSAIVLQCGADSLGGDRLGQFNLNIKAHGACVKFVKSFGIPMLVVGGGGYTPRN 299
Query: 363 VARCWCYETAVA 374
VAR WCYETAVA
Sbjct: 300 VARAWCYETAVA 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 = 405 bits (1044), Expect = e-139
Identities = 159/348 (45%), Positives = 231/348 (66%), Gaps = 2/348 (0%)
Query: 82 PMKPHRIRMAHNLIVHYGLHRRMEVNRPFPAGPSDIRRFHTDEYVEFLASVSPESSGDPS 141
P P+R M H+LI YGL +++ V +P A ++ FH+DEY++FL S E D
Sbjct: 17 PKVPNRASMVHSLIEAYGLLKQLRVVKPRVATEEELASFHSDEYIQFLKKASNEGDNDEE 76
Query: 142 FSRHLKRFNVGEDCPVFDGLFGFCQASAGGSIGAAVKLNRGDADIAVNWAGGLHHAKKSE 201
S + F +G DCP+F+G++ + A AG ++ AA L G +A+NW GG HHA++ E
Sbjct: 77 PSE-QQEFGLGYDCPIFEGIYDYAAAVAGATLTAAQLLIDGKCKVAINWFGGWHHAQRDE 135
Query: 202 ASGFCYVNDIVLGILELLKVHRRVLYVDIDVHHGDGVEEAFYTTDRVMTVSFHKFGD-FF 260
ASGFCYVNDIVLGIL+L + RVLYVD+D+HHGDGVE+AF T +VMTVS HK+ FF
Sbjct: 136 ASGFCYVNDIVLGILKLREKFDRVLYVDLDLHHGDGVEDAFSFTSKVMTVSLHKYSPGFF 195
Query: 261 PGTGHIKDVGAGQGKFYALNVPLNDGLDDESFRGLFRPIIQKVMEVYQPDAVVLQCGADS 320
PGTG + DVG G+GK+Y +NVPL DG+ DE + +F ++ +++ ++P+AVVLQCGAD+
Sbjct: 196 PGTGDVSDVGLGKGKYYTVNVPLRDGIQDEQYLQIFTAVVPEIVAAFRPEAVVLQCGADT 255
Query: 321 LSGDRLGCFNLSVKGHADCLRFLRSFNVPLMVLGGGGYTIRNVARCWCYETAVAVGVEPD 380
L+GD +G FNL+ G CL+++ + +P ++LGGGGY + N ARCW Y T + +G
Sbjct: 256 LAGDPMGAFNLTPVGIGKCLKYVLGWKLPTLILGGGGYNLANTARCWTYLTGLILGEPLS 315
Query: 381 NKLPYNEYYEYFGPDYTLHVEPCNMENLNAHKDMEKIRNTLLEQLSGL 428
+ +P +E++ +GPDY L + P +LN + +EKI T+ L +
Sbjct: 316 SDIPDHEFFTSYGPDYELEISPSLRPDLNEDQYIEKILETIKGNLKNV 363
>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 = 328 bits (842), Expect = e-110
Identities = 111/307 (36%), Positives = 159/307 (51%), Gaps = 17/307 (5%)
Query: 74 DYYYGQGHPMKPHRIRMAHNLIVHYGLHRRMEVNRPFPAGPSDIRRFHTDEYVEFLASVS 133
D G GHP P R+ L+ GL R+E P PA ++ H+ EYVEFL S
Sbjct: 2 DTGSGLGHPENPERLEAILELLKESGLLDRLEFIAPRPATEEELLLVHSPEYVEFLEEAS 61
Query: 134 PESSGDPSFSRHLKRFNVGEDCPVFDGLFGFCQASAGGSIGAAVKLNRGD-ADIAVNWAG 192
E L R + D PV G + +AGG++ AA + G+ A AV G
Sbjct: 62 LEEEE-------LGRIGLDGDTPVSPGSYEAALLAAGGTLEAADLVLSGENAFAAVRPPG 114
Query: 193 GLHHAKKSEASGFCYVNDIVLGILELLKVH--RRVLYVDIDVHHGDGVEEAFYTTDRVMT 250
HHA++ ASGFC N++ + LLK + +RVL VD+DVHHG+G +E FY RV+T
Sbjct: 115 --HHAERDRASGFCLFNNVAIAARYLLKRYGLKRVLIVDLDVHHGNGTQEIFYDDPRVLT 172
Query: 251 VSFHKFGDFFPGTGHIKDVGAGQGKFYALNVPLNDGLDDESFRGLFRPIIQKVMEVYQPD 310
+S H+ F+PGTG + G G G+ Y LN+PL G DE + F I+ + +QPD
Sbjct: 173 ISIHQDP-FYPGTGFADETGEGAGEGYTLNIPLPPGTGDEEYLAAFEEILLPALREFQPD 231
Query: 311 AVVLQCGADSLSGDRLGCFNLSVKGHADCLRFLRSF----NVPLMVLGGGGYTIRNVARC 366
+++ G D+ +GD LG NL+ +G+A+ R L P++ + GGY + +AR
Sbjct: 232 LILVSAGFDAHAGDPLGGLNLTTEGYAERTRLLLELADAYGGPVVSVLEGGYNLDALARS 291
Query: 367 WCYETAV 373
A
Sbjct: 292 AAAVLAG 298
>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 = 327 bits (839), Expect = e-109
Identities = 110/346 (31%), Positives = 170/346 (49%), Gaps = 21/346 (6%)
Query: 61 KRRVSYFYEPTIGDYYYGQGHPMKPHRIRMAHNLIVHYGLHRRMEVNRPFPAGPSDIRRF 120
+ + Y P ++ GHP P R+R+ L+ GL +E+ P PA ++
Sbjct: 1 MMKTALIYHPEFLEHEPPPGHPENPDRLRLILELLESSGLPDSLELVEPRPATLEELLLV 60
Query: 121 HTDEYVEFLASVSPESSGDPSFSRHLKRFNVGEDCPVFDGLFGFCQASAGGSIGAAVKLN 180
H+ +YVEFL S+S E N+ D PV G + + +AGG++ A +
Sbjct: 61 HSPDYVEFLESLSEEE----------GYGNLDGDTPVSPGTYEAARLAAGGALTAVDAVL 110
Query: 181 RGDADIAVNWAGGLHHAKKSEASGFCYVNDIVLGILELLK-VHRRVLYVDIDVHHGDGVE 239
G+ + HHA + ASGFC N++ + LLK +RV +D DVHHG+G +
Sbjct: 111 EGEDNAFALVRPPGHHAGRDRASGFCLFNNVAIAAKYLLKKGVKRVAIIDFDVHHGNGTQ 170
Query: 240 EAFYTTDRVMTVSFHKFG-DFFPGTGHIKDVGAGQGKFYALNVPLNDGLDDESFRGLFRP 298
E FY D V+TVS H+ G F+PGTG ++G G + +N+PL G D+S+
Sbjct: 171 EIFYDDDDVLTVSLHQDGRPFYPGTGGADEIGEG-KEGNNVNIPLPPGTGDDSYLEALEE 229
Query: 299 IIQKVMEVYQPDAVVLQCGADSLSGDRLGCFNLSVKGHADCLRFLRSF----NVPLMVLG 354
I+ ++E ++PD V++ G D+ GD LG NL+ +G+A R +R P++ +
Sbjct: 230 IVLPLLEEFKPDLVIVSAGFDAHRGDPLGRLNLTEEGYAKIGRAVRKLAEGYGGPVVAVL 289
Query: 355 GGGYTIRNVARCWCYETAVAVG---VEPDNKLPYN-EYYEYFGPDY 396
GGY + +AR A G E + LP + E F DY
Sbjct: 290 EGGYNLDALARSLVAFLAGLAGLVEEELEEPLPEDLELRRAFRADY 335
>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 = 321 bits (824), Expect = e-107
Identities = 118/313 (37%), Positives = 165/313 (52%), Gaps = 17/313 (5%)
Query: 66 YFYEPTIGDYYYGQGHPMKPHRIRMAHNLIVHYGLHRRMEVNRPFPAGPSDIRRFHTDEY 125
+ Y Y +G HP P R+ + +L+ GL +++ P PA ++ FHT +Y
Sbjct: 2 FIYSEEYLRYSFGPNHPFNPPRLSLTKDLLRALGLLPPVDLVPPRPATEEELLLFHTPDY 61
Query: 126 VEFL--ASVSPESSGDPSFSRHLKRFNVG-EDCPVFDGLFGFCQASAGGSIGAAVKLNRG 182
+E + AS E G R +G ED PVF G+ GG++ AA + G
Sbjct: 62 IEAVKEASRGQEPEGRG-------RLGLGTEDNPVFPGMHEAAALVVGGTLLAARLVLEG 114
Query: 183 DADIAVNWAGGLHHAKKSEASGFCYVNDIVLGILELLKVH-RRVLYVDIDVHHGDGVEEA 241
+A A N AGGLHHA + ASGFC ND + I L RV YVDID HHGDGV+ A
Sbjct: 115 EARRAFNPAGGLHHAMRGRASGFCVYNDAAVAIERLRDKGGLRVAYVDIDAHHGDGVQAA 174
Query: 242 FYTTDRVMTVSFHKFGD-FFPGTGHIKDVGAGQGKFYALNVPLNDGLDDESFRGLFRPII 300
FY RV+T+S H+ G FPGTG + ++G G+G YA+N+PL G D+ F F ++
Sbjct: 175 FYDDPRVLTISLHESGRYLFPGTGFVDEIGEGEGYGYAVNIPLPPGTGDDEFLRAFEAVV 234
Query: 301 QKVMEVYQPDAVVLQCGADSLSGDRLGCFNLSVKGHADCLRFLR-----SFNVPLMVLGG 355
++ ++PD +V Q GAD+ +GD L NLS + + +R +R + LGG
Sbjct: 235 PPLLRAFRPDVIVSQHGADAHAGDPLTHLNLSNRAYRAAVRRIRELADEYCGGRWLALGG 294
Query: 356 GGYTIRNVARCWC 368
GGY VAR W
Sbjct: 295 GGYNPDVVARAWA 307
>gnl|CDD|240374 PTZ00346, PTZ00346, histone deacetylase; Provisional.
Length = 429
Score = 305 bits (783), Expect = 1e-99
Identities = 150/310 (48%), Positives = 202/310 (65%), Gaps = 6/310 (1%)
Query: 81 HPMKPHRIRMAHNLIVHYGLHRRMEVNRPFPAGPSDIRRFHTDEYVEFLASVSPESSGDP 140
H MKP+R+ A ++ + P ++ +HTD Y LA++ S
Sbjct: 43 HAMKPYRVLAAMEIVRSLKIDAHCRTVVPPLVKVEELMAYHTDTY---LANLGLHSCRSW 99
Query: 141 SFSRHLKRFNVGEDCPVFDGLFGFCQASAGGSIGAAVKLNRGDADIAVNWAGGLHHAKKS 200
++ + DCP +GL A+A G++ AV LN G D+AV+W GG+HH+K
Sbjct: 100 LWNAETSKVFFSGDCPPVEGLMEHSIATASGTLMGAVLLNSGQVDVAVHWGGGMHHSKCG 159
Query: 201 EASGFCYVNDIVLGILELLKVHRRVLYVDIDVHHGDGVEEAFYTTDRVMTVSFHKFGD-F 259
E SGFCYVNDIVLGILELLK H RVLYVDID+HHGDGV+EAF T+DRV T+S HKFG+ F
Sbjct: 160 ECSGFCYVNDIVLGILELLKCHDRVLYVDIDMHHGDGVDEAFCTSDRVFTLSLHKFGESF 219
Query: 260 FPGTGHIKDVGAGQGKFYALNVPLNDGLDDESFRGLFRPIIQKVMEVYQPDAVVLQCGAD 319
FPGTGH +DVG G+G++Y++N+ + DG+ D + GLF + ++ Y PDA+VLQCGAD
Sbjct: 220 FPGTGHPRDVGYGRGRYYSMNLAVWDGITDFYYLGLFEHALHSIVRRYSPDAIVLQCGAD 279
Query: 320 SLSGDRLGCFNLSVKGHADCLRFLRSFNVPLMVLGGGGYTIRNVARCWCYETAVAVG--V 377
SL+GDRLG NLS GH C++ +R +P++ LGGGGYTIRNVA+ W YET++ G +
Sbjct: 280 SLAGDRLGLLNLSSFGHGQCVQAVRDLGIPMLALGGGGYTIRNVAKLWAYETSILTGHPL 339
Query: 378 EPDNKLPYNE 387
P+ LP E
Sbjct: 340 PPNTVLPVAE 349
>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 = 290 bits (744), Expect = 2e-95
Identities = 119/294 (40%), Positives = 173/294 (58%), Gaps = 26/294 (8%)
Query: 87 RIRMAHNLIVHYGLHR-RMEVNRPFPAGPSDIRRFHTDEYVEFLASVSPESSGDPSFSRH 145
R + H+LI YGL + E+ P A D+ ++H +YV+FL
Sbjct: 21 RSSLVHSLIRAYGLLQHFDEIIEPERATRKDLTKYHDKDYVDFL---------------- 64
Query: 146 LKRFNVGEDCPVFDGLFGFCQASAGGSIGAAVKLNRG-DADIAVNWAGGLHHAKKSEASG 204
LK++ + +DCPVF L + Q AG S+ A L + DIA+NW GG HHA+KS ASG
Sbjct: 65 LKKYGLEDDCPVFPFLSMYVQLVAGSSLALAKHLITQVERDIAINWYGGRHHAQKSRASG 124
Query: 205 FCYVNDIVLGILELLKVH-RRVLYVDIDVHHGDGVEEAFYTTDRVMTVSFHKFGD-FFPG 262
FCYVNDIVL IL L + RRV Y+D+D+HHGDGVE AF+ + V+T S H++ FFPG
Sbjct: 125 FCYVNDIVLAILRLRRARFRRVFYLDLDLHHGDGVESAFFFSKNVLTCSIHRYDPGFFPG 184
Query: 263 TGHIKDVGAGQGKFYALNVPLNDGLDDESFRGLFRPIIQKVMEVYQPDAVVLQCGADSLS 322
TG +K+ LN+PL GL D++ + I++ ++E ++P+ +V+QCG D LS
Sbjct: 185 TGSLKN----SSDKGMLNIPLKRGLSDKTLLRIIDSIVRPLIEKFEPEVIVIQCGCDGLS 240
Query: 323 GDRLGCFNLSVKGHADCLRF-LRSF-NVPLMVLGGGGYTIRNVARCWCYETAVA 374
GD +NL+++G+ + L+ F + P ++LGGGGY AR W Y T++
Sbjct: 241 GDPHKEWNLTIRGYGSVIELLLKEFKDKPTLLLGGGGYNHTEAARAWTYLTSMV 294
>gnl|CDD|212512 cd09301, HDAC, Histone deacetylase (HDAC) classes I, II, IV and
related proteins. The HDAC/HDAC-like family includes
Zn-dependent histone deacetylase classes I, II and IV
(class III HDACs, also called sirtuins, are
NAD-dependent and structurally unrelated, and therefore
not part of this family). Histone deacetylases catalyze
hydrolysis of N(6)-acetyl-lysine residues in histone
amino termini to yield a deacetylated histone (EC
3.5.1.98), as opposed to the acetylation reaction by
some histone acetyltransferases (EC 2.3.1.48).
Deacetylases of this family are involved in signal
transduction through histone and other protein
modification, and can repress/activate transcription of
a number of different genes. They usually act via the
formation of large multiprotein complexes. They are
involved in various cellular processes, including cell
cycle regulation, DNA damage response, embryonic
development, cytokine signaling important for immune
response and post-translational control of the acetyl
coenzyme A synthetase. In mammals, they are known to be
involved in progression of different tumors. Specific
inhibitors of mammalian histone deacetylases are an
emerging class of promising novel anticancer drugs.
Length = 279
Score = 284 bits (729), Expect = 2e-93
Identities = 106/292 (36%), Positives = 147/292 (50%), Gaps = 17/292 (5%)
Query: 87 RIRMAHNLIVHYGLHRRMEVNRPFPAGPSDIRRFHTDEYVEFLASVSPESSGDPSFSRHL 146
RIR + GL ++E+ A + + HT+EY+ L + ++ S
Sbjct: 1 RIRDLIEALKELGLRPKIELIECREATEELLLKVHTEEYLNELKANFAVATITES----- 55
Query: 147 KRFNVGEDCPVFDGLFGFCQASAGGSIGAAVKLNRGDADIAVNWA-GGLHHAKKSEASGF 205
K G + PV F + S GG + AA + +G+ + A G HHA KS A GF
Sbjct: 56 KPVIFGPNFPVQRHYFRGARLSTGGVVEAAELVAKGELERAFAVVGAGGHHAGKSRAWGF 115
Query: 206 CYVNDIVLGILELLKV-HRRVLYVDIDVHHGDGVEEAFYTTDRVMTVSFHKFGDFFPGTG 264
CY ND+VL I L + R+L +D D HHGDG EAFY DRV+ +SFH + + G G
Sbjct: 116 CYFNDVVLAIKFLRERGISRILIIDTDAHHGDGTREAFYDDDRVLHMSFHNYDIYPFGRG 175
Query: 265 HIKDVGAGQGKFYALNVPLNDGLDDESFRGLFRPIIQKVMEVYQPDAVVLQCGADSLSGD 324
+GK Y +NVPL DGL DE + +I KV+E ++P+ VVLQ G D+ GD
Sbjct: 176 --------KGKGYKINVPLEDGLGDEEYLDAVERVISKVLEEFEPEVVVLQFGHDTHEGD 227
Query: 325 RLGCFNLSVKGHADCLRFLRSFN--VPLMVLGGGGYTIRNVARCWCYETAVA 374
RLG FNLS KG ++ F P++++ GGGY AR W
Sbjct: 228 RLGGFNLSEKGFVKLAEIVKEFARGGPILMVLGGGYNPEAAARIWTAIIKEL 279
>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 = 175 bits (447), Expect = 2e-51
Identities = 89/296 (30%), Positives = 138/296 (46%), Gaps = 24/296 (8%)
Query: 81 HPMKPHRIRMAHNLIVHYGLHRRMEVNRPFPAGPSDIRRFHTDEYVEFLASVSPESSGDP 140
HP +P R+ + GL R+ P PA ++ R HT EY+E + G
Sbjct: 1 HPERPERLLAILEALEEEGLLDRLVFVEPRPATEEELLRVHTPEYIERVEETCEA--GGG 58
Query: 141 SFSRHLKRFNVGEDCPVFDGLFGFCQASAGGSIGAAVKLNRGDADIA---VNWAGGLHHA 197
D V G + +AG ++ A + G+A+ A V G HHA
Sbjct: 59 YLD---------PDTYVSPGSYEAALLAAGAALAAVDAVLSGEAENAFALVRPPG--HHA 107
Query: 198 KKSEASGFCYVNDIVLGILELLKVH--RRVLYVDIDVHHGDGVEEAFYTTDRVMTVSFHK 255
+ A GFC N++ + K + +RVL VD DVHHG+G ++ FY V+ S H+
Sbjct: 108 EPDRAMGFCLFNNVAIAARYAQKRYGLKRVLIVDWDVHHGNGTQDIFYDDPSVLYFSIHQ 167
Query: 256 FGDFFPGTGHIKDVGAGQGKFYALNVPLNDGLDDESFRGLFRPIIQKVMEVYQPDAVVLQ 315
+ F+PGTG ++ G G G+ + +NVPL G D + F ++ + +QPD V++
Sbjct: 168 Y-PFYPGTGAAEETGGGAGEGFTINVPLPPGSGDAEYLAAFEEVLLPIAREFQPDLVLVS 226
Query: 316 CGADSLSGDRLGCFNLSVKGHADCLRFLRSF-----NVPLMVLGGGGYTIRNVARC 366
G D+ GD LG NL+ +G+A R L+ L+ + GGY + +A
Sbjct: 227 AGFDAHRGDPLGGMNLTPEGYARLTRLLKELADEHCGGRLVFVLEGGYNLEALAES 282
>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 = 160 bits (406), Expect = 1e-44
Identities = 79/266 (29%), Positives = 124/266 (46%), Gaps = 18/266 (6%)
Query: 67 FYEPTIGDYYYGQGHPMKPHRIRMAHNLIVHYGLHRRMEVNRPFPAGPSDIRRFHTDEYV 126
+ P G HP P R NL+ GL + + P PA ++ R HT EY+
Sbjct: 19 LFLPVGGLLVQPGRHPENPETKRRIKNLLEVSGLSDHLVLITPRPATDEELLRVHTPEYI 78
Query: 127 EFLASVSPESSGDPSFSRHLKRFNVGEDCPVFDGLFGFCQASAGGSIGAAVKLNRGDADI 186
+ + + S G+ G P G + +AGG+I A + G+ D
Sbjct: 79 DRVKAASAAGGGE-----------AGGGTPFGPGSYEIALLAAGGAIAAVDAVLDGEVDN 127
Query: 187 A---VNWAGGLHHAKKSEASGFCYVNDIVLGILELLKVH--RRVLYVDIDVHHGDGVEEA 241
A V G HHA+ + GFC N++ + L V +RV VD DVHHG+G +
Sbjct: 128 AYALVRPPG--HHAEPDQGMGFCLFNNVAIAARHALAVGGVKRVAVVDWDVHHGNGTQAI 185
Query: 242 FYTTDRVMTVSFHKFGDFFPGTGHIKDVGAGQGKFYALNVPLNDGLDDESFRGLFRPIIQ 301
FY V+T+S H+ F P +G +++ G G G+ Y LN+PL G D ++ F I+
Sbjct: 186 FYDDPDVLTISLHQDRCFPPDSGAVEERGEGAGEGYNLNIPLPPGSGDGAYLHAFERIVL 245
Query: 302 KVMEVYQPDAVVLQCGADSLSGDRLG 327
+ ++P+ +++ G D+ + D LG
Sbjct: 246 PALRAFRPELIIVASGFDASAFDPLG 271
>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 = 156 bits (396), Expect = 5e-44
Identities = 94/292 (32%), Positives = 136/292 (46%), Gaps = 33/292 (11%)
Query: 81 HPMKPHRIRMAHNLIVHYGLHRRMEVNRPFPAGPSDIRRFHTDEYVEFLASVSPESSGDP 140
H + + ++ GL ++ P PA D+ R H EY+E L SG+
Sbjct: 1 HRFPMRKYGLLREALLEEGLVLPEDIVEPEPATREDLLRVHDPEYLESL------KSGEL 54
Query: 141 SFSRHLKRFNVGEDCPVFDGLFGFCQASAGGSIGAA-VKLNRGDADIAVNWAGGLHHAKK 199
S ++R P L + + GG+I AA + L G +A+N AGG HHA
Sbjct: 55 S-REEIRRIGF----PWSPELVERTRLAVGGTILAARLALEHG---LAINLAGGTHHAFP 106
Query: 200 SEASGFCYVNDIVLGILELLKVH--RRVLYVDIDVHHGDGVEEAFYTTDRVMTVSFHKFG 257
GFC NDI + LL RRVL VD+DVH G+G F V T S H
Sbjct: 107 DRGEGFCVFNDIAIAARVLLAEGLVRRVLIVDLDVHQGNGTAAIFADDPSVFTFSMHG-E 165
Query: 258 DFFPGTGHIKDVGAGQGKFYALNVPLNDGLDDESFRGLFRPIIQKVMEVYQPDAVVLQCG 317
+P D L+VPL DG D+ + + +++ ++PD V G
Sbjct: 166 KNYPFRKEPSD----------LDVPLPDGTGDDEYLAALEEALPRLLAEFRPDLVFYNAG 215
Query: 318 ADSLSGDRLGCFNLSVKG--HADC--LRFLRSFNVPLMVLGGGGYTIRNVAR 365
D L+GDRLG +LS++G D LRF R+ +P+ ++ GGGY+ R++AR
Sbjct: 216 VDVLAGDRLGRLSLSLEGLRERDRLVLRFARARGIPVAMVLGGGYS-RDIAR 266
>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 = 155 bits (393), Expect = 2e-43
Identities = 85/298 (28%), Positives = 128/298 (42%), Gaps = 43/298 (14%)
Query: 80 GHPMKPHRIRMAHNLIVHYGLHRR--MEVNRPFPAGPSDIRRFHTDEYVEFLASVSPESS 137
HP P R + L R EV P G I H +YV+FL +
Sbjct: 24 PHPENPERAEAILD-----ALKRAGLGEVLPPRDFGLEPILAVHDPDYVDFLETADT--- 75
Query: 138 GDPSFSRHLKRFNVGEDCPVFDGLFGFCQASAGGSIGAAVKLNRGDADIAVNWAGGL--- 194
D P+ +G + A+A ++ AA + G+ A L
Sbjct: 76 ----------------DTPISEGTWEAALAAADTALTAADLVLEGE-----RAAYALCRP 114
Query: 195 --HHAKKSEASGFCYVNDIVLGILELLKVHRRVLYVDIDVHHGDGVEEAFYTTDRVMTVS 252
HHA + A GFCY N+ + L RV +D+DVHHG+G +E FY V+ VS
Sbjct: 115 PGHHAGRDRAGGFCYFNNAAIAAQYLRDRAGRVAILDVDVHHGNGTQEIFYERPDVLYVS 174
Query: 253 FHKFGD---FFPGT-GHIKDVGAGQGKFYALNVPLNDGLDDESFRGLFRPIIQKVMEVYQ 308
H GD F+P G + G G+G+ Y LN+PL G D+ + + + +
Sbjct: 175 IH--GDPRTFYPFFLGFADETGEGEGEGYNLNLPLPPGTGDDDYLAALDEALAAIAA-FG 231
Query: 309 PDAVVLQCGADSLSGDRLGCFNLSVKGHADCLRFLRSFNVPLMVLGGGGYTIRNVARC 366
PDA+V+ G D+ GD L F L+ + +A R + + +P + + GGY + + R
Sbjct: 232 PDALVVSLGFDTHEGDPLSDFKLTTEDYARIGRRIAALGLPTVFVQEGGYNVDALGRN 289
>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 = 130 bits (329), Expect = 5e-34
Identities = 79/317 (24%), Positives = 139/317 (43%), Gaps = 46/317 (14%)
Query: 77 YGQGHPMKPHRIRMAHNLIVHYGLHRRMEVNRPFPAGPSDIRRFHTDEYVEFLASVSPES 136
+ H P R+ + GL R A +I H+ EY++ + S
Sbjct: 3 WDSNHIECPERLEAILERLTQDGLLERCVKIPAREAEEDEILLVHSQEYIDLVKSTETME 62
Query: 137 SGDPSFSRHLKRFNVGEDCPVFDGLFGFCQAS---AGGSIGAAVKLNRGDADIAVNWAGG 193
+ L+ C +D ++ C ++ A + G+ ++L + AG
Sbjct: 63 KEE------LESL-----CSGYDSVY-LCPSTYEAARLAAGSTIEL------VKAVMAGK 104
Query: 194 L-----------HHAKKSEASGFCYVNDIVLGILELLKVHR--RVLYVDIDVHHGDGVEE 240
+ HHA ++EA+G+C N++ + ++ R+L VD DVHHG G ++
Sbjct: 105 IQNGFALIRPPGHHAMRNEANGYCIFNNVAIAAKYAIEKLGLKRILIVDWDVHHGQGTQQ 164
Query: 241 AFYTTDRVMTVSFHKF--GDFFPGTGHIKD-----VGAGQGKFYALNVPLND-GLDDESF 292
FY RV+ S H++ G F+P H+ + +G G G + +NVPLN GL D +
Sbjct: 165 GFYEDPRVLYFSIHRYEHGRFWP---HLFESDYDYIGVGHGYGFNVNVPLNQTGLGDADY 221
Query: 293 RGLFRPIIQKVMEVYQPDAVVLQCGADSLSGDRLGCFNLSVKGHADCLRFLRSFNVP-LM 351
+F I+ + +QP+ V++ G D+ GD G ++ G+A R L L+
Sbjct: 222 LAIFHHILLPLALEFQPELVLVSAGFDASIGDPEGEMAVTPAGYAHLTRLLMGLAGGKLL 281
Query: 352 VLGGGGYTIRNVARCWC 368
++ GGY + ++A
Sbjct: 282 LVLEGGYLLESLAESVS 298
>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 = 119 bits (301), Expect = 5e-30
Identities = 78/309 (25%), Positives = 143/309 (46%), Gaps = 20/309 (6%)
Query: 80 GHPMKPHRIRMAHNLIVHYGLHRRMEVNRPFPAGPSDIRRFHTDEYVEFLASVSPESSGD 139
GHP P RI + GL R A ++ H++E+++ + S+ +
Sbjct: 15 GHPECPQRISRIYERHNDLGLLERCLRLPSRLATEDELLLCHSEEHLDEMKSLEKMKPRE 74
Query: 140 PSFSRHLKRFNVGEDCP-VFDGLFGFCQASAGGSIGAAVKL---NRGDADIAVNWAGGLH 195
+R K ++ P + C A G + V+ +A+ G H
Sbjct: 75 --LNRLGKEYDSIYIHPDSYQ-----CALLAAGCVLQVVEAVLTGESRNGVAIVRPPG-H 126
Query: 196 HAKKSEASGFCYVNDIVLGILELLKVH--RRVLYVDIDVHHGDGVEEAFYTTDRVMTVSF 253
HA++ A GFC+ N++ + K + +R+L VD DVHHG+G + F + V+ +S
Sbjct: 127 HAEQDTACGFCFFNNVAIAARYAQKKYGLKRILIVDWDVHHGNGTQHMFESDPSVLYISL 186
Query: 254 HKF--GDFFPGT--GHIKDVGAGQGKFYALNVPLN-DGLDDESFRGLFRPIIQKVMEVYQ 308
H++ G FFP + G+ VG G+G+ + +N+P N G+ D + F+ ++ + +
Sbjct: 187 HRYDNGSFFPNSPEGNYDVVGKGKGEGFNVNIPWNKGGMGDAEYIAAFQQVVLPIAYEFN 246
Query: 309 PDAVVLQCGADSLSGDRLGCFNLSVKGHADCLRFLRSF-NVPLMVLGGGGYTIRNVARCW 367
P+ V++ G D+ GD LG ++ +G+A L S ++V+ GGY + +++
Sbjct: 247 PELVLVSAGFDAARGDPLGGCKVTPEGYAHMTHMLMSLAGGRVIVILEGGYNLTSISESM 306
Query: 368 CYETAVAVG 376
T +G
Sbjct: 307 SMCTKTLLG 315
>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 = 115 bits (291), Expect = 6e-29
Identities = 93/317 (29%), Positives = 142/317 (44%), Gaps = 24/317 (7%)
Query: 80 GHPMKPHRIRMAHNLIVHYGLHRRMEVNRPFPAGPSDIRRFHTDEY---VEFLASVSPES 136
HP P RI + GL RM A +I H++E+ VE +S E
Sbjct: 2 PHPEDPSRISRIFEKLKEAGLINRMLRIPIREATKEEILLVHSEEHWDRVEATEKMSDEQ 61
Query: 137 SGDPSFSRHLKRFNVGEDCPVFDGLFGFC-QASAGGSIGA--AVKLNRGDADIAVNWAGG 193
D + V D FC + S GG+I A AV R AV G
Sbjct: 62 LKDRTEIFERDSLYVNNDT-------AFCARLSCGGAIEACRAVAEGRVKNAFAVVRPPG 114
Query: 194 LHHAKKSEASGFCYVNDIVLGILELLKVH----RRVLYVDIDVHHGDGVEEAFYTTDRVM 249
HHA+ E+ GFC+ N++ + L + +++L +D D+HHG+G + AFY V+
Sbjct: 115 -HHAEPDESMGFCFFNNVAVAAKWLQTEYPDKIKKILILDWDIHHGNGTQRAFYDDPNVL 173
Query: 250 TVSFHKF--GDFFPGT--GHIKDVGAGQGKFYALNVPLND-GLDDESFRGLFRPIIQKVM 304
+S H+F G F+PGT G + VG G G + +N+P G+ D + F+ I+ +
Sbjct: 174 YISLHRFENGGFYPGTPYGDYESVGEGAGLGFNVNIPWPQGGMGDADYIYAFQRIVMPIA 233
Query: 305 EVYQPDAVVLQCGADSLSGDRLGCFNLSVKGHADCLRFLRSF-NVPLMVLGGGGYTIRNV 363
+ PD V++ G D+ GD LG +++ G+A L S L+V GGY + +
Sbjct: 234 YEFDPDLVIISAGFDAADGDELGQCHVTPAGYAHMTHMLMSLAGGKLVVALEGGYNLDAI 293
Query: 364 ARCWCYETAVAVGVEPD 380
+ V +G P
Sbjct: 294 SDSALAVAKVLLGEAPP 310
>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 = 113 bits (286), Expect = 2e-28
Identities = 73/257 (28%), Positives = 110/257 (42%), Gaps = 22/257 (8%)
Query: 81 HPMKPHRIRMAHNLIVHYGLHRRMEVNRPFPAGPSDIRRFHTDEYVEFLASVSPESSGDP 140
HP P R+ + ++ GL R + PA + R H YV+ L + +PE
Sbjct: 1 HPESPERLEAILDALIASGLDRLLRQLEAPPATREQLLRVHDAAYVDRLEAAAPEE---- 56
Query: 141 SFSRHLKRFNVGEDCPVFDGLFGFCQASAGGSIGAAVKLNRGDAD---IAVNWAGGLHHA 197
+ D + G +AG + A + G+A AV G HHA
Sbjct: 57 ------GLVQLDPDTAMSPGSLEAALRAAGAVVAAVDAVMAGEARNAFCAVRPPG--HHA 108
Query: 198 KKSEASGFCYVNDIVLGILELLKVH--RRVLYVDIDVHHGDGVEEAFYTTDRVMTVSFHK 255
++ +A GFC N++ + L H RV VD DVHHG+G E+ F RV+ S H+
Sbjct: 109 ERDKAMGFCLFNNVAIAAAHALAHHGLERVAIVDFDVHHGNGTEDIFRDDPRVLFCSSHQ 168
Query: 256 FGDFFPGTGHIKDVGAGQGKFYALNVPLNDGLDDESFRGLFRPIIQKVMEVYQPDAVVLQ 315
+PGTG + G G +NVPL G FR ++ ++PD +++
Sbjct: 169 HP-LYPGTGAPDETGHGN----IVNVPLPAGTGGAEFREAVEDRWLPALDAFKPDLILIS 223
Query: 316 CGADSLSGDRLGCFNLS 332
G D+ D L NL+
Sbjct: 224 AGFDAHRDDPLAQLNLT 240
>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 = 112 bits (281), Expect = 2e-28
Identities = 39/237 (16%), Positives = 62/237 (26%), Gaps = 51/237 (21%)
Query: 162 FGFCQASAGGSIGAAVKLNRGDADIAVNWAGGLHHAKKSEASGFCYVNDIVLGILELLKV 221
+ AG + D + V G H+ N + + E +
Sbjct: 8 AEAHELLAGVVVAVLK-----DGKVPVVLGG--DHSI---------ANGAIRAVAE---L 48
Query: 222 HRRVLYVDIDVHHGDGVEEAFY--------------TTDRVMTVSFHKFGDFFPGTGHIK 267
H + +D+D HH EAF V VS G G
Sbjct: 49 HPDLGVIDVDAHHDVRTPEAFGKGNHHTPRHLLCEPLISDVHIVSIGIRGVSNGEAG--- 105
Query: 268 DVGAGQGKFYALNVPLNDGLDDESFRGLFRPIIQKVMEVYQPDAVVLQCGADSLSGD--- 324
GA K + + + D +F I+ + + D V L D L
Sbjct: 106 --GAYARKLGVVYFSMTEV-DKLGLGDVFEEIVSYLG--DKGDNVYLSVDVDGLDPSFAP 160
Query: 325 ---RLGCFNLSVKGHADCLRFLRSFNVPLMVLGGGGYTI----RNVARCWCYETAVA 374
G LS + + N+ + + + AR T
Sbjct: 161 GTGTPGPGGLSYREGLYITERIAKTNLVVGLDIVEVNPLLDETGRTARLAAALTLEL 217
>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 = 112 bits (281), Expect = 4e-27
Identities = 59/173 (34%), Positives = 94/173 (54%), Gaps = 19/173 (10%)
Query: 195 HHAKKSEASGFCYVNDIVLG--ILELLKVHRRVLYVDIDVHHGDGVEEAFYTTDRVMTVS 252
HHA+ S+A GFC+ N + + L+ R++L VD DVHHG+G ++ FY V+ +S
Sbjct: 151 HHAEPSQAMGFCFFNSVAIAAKQLQQKLKLRKILIVDWDVHHGNGTQQIFYEDPNVLYIS 210
Query: 253 FHKF--GDFFPGTGHIKDVGAGQGKFYALNVPLNDGLD----DESFRGLFRPIIQKVMEV 306
H++ G+FFPGTG +VG+G G+ + +N+ + GLD D + FR ++ +
Sbjct: 211 LHRYDDGNFFPGTGAPTEVGSGAGEGFNVNIAWSGGLDPPMGDAEYLAAFRTVVMPIARE 270
Query: 307 YQPDAVVLQCGADSLSG--DRLGCFNLSVKGHADCLRFL-RSFNVPLMVLGGG 356
+ PD V++ G D+ G LG + +S C ++ R LM L GG
Sbjct: 271 FSPDIVLVSAGFDAAEGHPPPLGGYKVSPA----CFGYMTRQ----LMNLAGG 315
>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 = 105 bits (262), Expect = 1e-24
Identities = 61/172 (35%), Positives = 94/172 (54%), Gaps = 17/172 (9%)
Query: 195 HHAKKSEASGFCYVNDIVLG--ILELLKVHRRVLYVDIDVHHGDGVEEAFYTTDRVMTVS 252
HHA++S GFCY N + + +L+ ++L VD DVHHG+G ++AFY+ V+ +S
Sbjct: 154 HHAEESTPMGFCYFNSVAIAAKLLQQRLNVSKILIVDWDVHHGNGTQQAFYSDPNVLYMS 213
Query: 253 FHKF--GDFFPGTGHIKDVGAGQGKFYALNVPLNDGLD----DESFRGLFRPIIQKVMEV 306
H++ G+FFPG+G +VG G G + +N+ GLD D + FR ++ +
Sbjct: 214 LHRYDDGNFFPGSGAPDEVGTGPGVGFNVNMAFTGGLDPPMGDAEYLAAFRTVVMPIASE 273
Query: 307 YQPDAVVLQCGADSLSGD--RLGCFNLSVKGHADCLRFLRSFNVPLMVLGGG 356
+ PD V++ G D++ G LG +NLS K C +L LM L GG
Sbjct: 274 FAPDVVLVSSGFDAVEGHPTPLGGYNLSAK----CFGYLTK---QLMGLAGG 318
>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 = 104 bits (260), Expect = 2e-24
Identities = 59/172 (34%), Positives = 91/172 (52%), Gaps = 17/172 (9%)
Query: 195 HHAKKSEASGFCYVNDIVLGI--LELLKVHRRVLYVDIDVHHGDGVEEAFYTTDRVMTVS 252
HHA S A GFC+ N + + L+ ++L VD DVHHG+G ++ FY V+ +S
Sbjct: 152 HHADHSTAMGFCFFNSVAIACRQLQQQGKASKILIVDWDVHHGNGTQQTFYQDPSVLYIS 211
Query: 253 FHKF--GDFFPGTGHIKDVGAGQGKFYALNVPLNDGLD----DESFRGLFRPIIQKVMEV 306
H+ G+FFPG+G + +VGAG G+ + +NV GLD D + FR ++ +
Sbjct: 212 LHRHDDGNFFPGSGAVDEVGAGSGEGFNVNVAWAGGLDPPMGDPEYLAAFRIVVMPIARE 271
Query: 307 YQPDAVVLQCGADSLSGD--RLGCFNLSVKGHADCLRFLRSFNVPLMVLGGG 356
+ PD V++ G D+ G LG +++S K C ++ LM L GG
Sbjct: 272 FSPDLVLVSAGFDAAEGHPAPLGGYHVSAK----CFGYMTQ---QLMNLAGG 316
>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 = 104 bits (260), Expect = 3e-24
Identities = 57/172 (33%), Positives = 95/172 (55%), Gaps = 17/172 (9%)
Query: 195 HHAKKSEASGFCYVNDIVLG--ILELLKVHRRVLYVDIDVHHGDGVEEAFYTTDRVMTVS 252
HHA++S A GFC+ N + + +L+ ++L VD D+HHG+G ++AFY V+ +S
Sbjct: 154 HHAEESTAMGFCFFNSVAIAAKLLQQKLNVGKILIVDWDIHHGNGTQQAFYNDPNVLYIS 213
Query: 253 FHKF--GDFFPGTGHIKDVGAGQGKFYALNVPLNDGLD----DESFRGLFRPIIQKVMEV 306
H++ G+FFPG+G +VGAG G + +N+ G+D D + FR ++ +
Sbjct: 214 LHRYDDGNFFPGSGAPDEVGAGPGVGFNVNIAWTGGVDPPIGDVEYLTAFRTVVMPIANE 273
Query: 307 YQPDAVVLQCGADSLSGDR--LGCFNLSVKGHADCLRFLRSFNVPLMVLGGG 356
+ PD V++ G D++ G + LG ++++ K C L LM L GG
Sbjct: 274 FSPDVVLVSAGFDAVEGHQSPLGGYSVTAK----CFGHLTK---QLMTLAGG 318
>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 = 103 bits (257), Expect = 5e-24
Identities = 56/155 (36%), Positives = 92/155 (59%), Gaps = 14/155 (9%)
Query: 195 HHAKKSEASGFCYVNDIVLG---ILELLKVHRRVLYVDIDVHHGDGVEEAFYTTDRVMTV 251
HHA++S A GFC+ N + + + + L + + +L VD+DVHHG+G ++AFY ++ +
Sbjct: 152 HHAEESTAMGFCFFNSVAITAKYLRDQLNISK-ILIVDLDVHHGNGTQQAFYADPSILYI 210
Query: 252 SFHKF--GDFFPGTGHIKDVGAGQGKFYALNVPLNDGLD----DESFRGLFRPIIQKVME 305
S H++ G+FFPG+G +VG G G+ Y +N+ GLD D + FR I++ V +
Sbjct: 211 SLHRYDEGNFFPGSGAPNEVGTGLGEGYNINIAWTGGLDPPMGDVEYLEAFRTIVKPVAK 270
Query: 306 VYQPDAVVLQCGADSLSGDR--LGCFNLSVK--GH 336
+ PD V++ G D+L G LG + ++ K GH
Sbjct: 271 EFDPDMVLVSAGFDALEGHTPPLGGYKVTAKCFGH 305
>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 = 92.6 bits (230), Expect = 1e-20
Identities = 79/305 (25%), Positives = 127/305 (41%), Gaps = 30/305 (9%)
Query: 81 HPMKPHRIRMAHNLIVHYGLHRRMEVNRPFPAGPSDIRRFHTDEYVEFLASVSPESSGDP 140
P P R+ ++ GL R + A ++ H+ EYV + S + +
Sbjct: 7 FPECPERLHAIREKLIQEGLLERCVSVQAREASEEELLLVHSPEYVALMKSTQYMTEEE- 65
Query: 141 SFSRHLKRFNVGEDCPVFDGLFGFCQASAGGSIGAAV------KLNRGDADIAVNWAGGL 194
L+ D C A GS+ V ++ G +A+ G
Sbjct: 66 -----LRTLADTYDSVYLHPNSYSCACLAVGSVLQLVDKVLGGEIRNG---LAIVRPPG- 116
Query: 195 HHAKKSEASGFCYVNDIVLGILELLKVHR--RVLYVDIDVHHGDGVEEAFYTTDRVMTVS 252
HHA+ + G+C N++ + + H RVL VD DVHHG G + F V+ S
Sbjct: 117 HHAQHDKMDGYCMFNNVAIAARYAQQKHGVQRVLIVDWDVHHGQGTQFIFEQDPSVLYFS 176
Query: 253 FHKF--GDFFPGTGHIKD-----VGAGQGKFYALNVPLND-GLDDESFRGLFRPIIQKVM 304
H++ G F+P H+K+ VG G+G+ Y +NVP N G+ D + F ++ V
Sbjct: 177 IHRYEQGRFWP---HLKESDSSAVGFGRGEGYNINVPWNQVGMRDADYIAAFLHVLLPVA 233
Query: 305 EVYQPDAVVLQCGADSLSGDRLGCFNLSVKGHADCLRFLRSFNVPLMVLG-GGGYTIRNV 363
+QP V++ G D++ GD G + A L ++L GGY +R++
Sbjct: 234 LEFQPQLVLVAAGFDAVIGDPKGEMAATPACFAHLTHLLMGLAGGKLILSLEGGYNLRSL 293
Query: 364 ARCWC 368
A C
Sbjct: 294 AEGVC 298
>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 = 76.8 bits (189), Expect = 2e-15
Identities = 53/189 (28%), Positives = 89/189 (47%), Gaps = 22/189 (11%)
Query: 195 HHAKKSEASGFCYVNDIVLGILELLKVH--RRVLYVDIDVHHGDGVEEAFYTTDRVMTVS 252
HH++++ A+GFC N++ + K + R+L VD DVHHG G++ F V+ S
Sbjct: 117 HHSQRNAANGFCVFNNVAIAAEYAKKKYGLHRILIVDWDVHHGQGIQYIFEEDPSVLYFS 176
Query: 253 FHKF--GDFFPG--TGHIKDVGAGQGKFYALNVPLND-GLDDESFRGLFRPIIQKVMEVY 307
+H++ F+P VG G+G + +N+P N G+ + + F ++ + +
Sbjct: 177 WHRYEHQRFWPFLRESDYDAVGRGKGLGFNINLPWNKVGMGNADYLAAFFHVLLPLAFEF 236
Query: 308 QPDAVVLQCGADSLSGDRLGCFNLSVKGHADCLRFLRSFNVPLMVLGG--------GGYT 359
P+ V++ G DS GD G + +C L LMVL G GGY
Sbjct: 237 DPELVLVSAGFDSAIGDPEGQMCAT----PECFAHLTHL---LMVLAGGKLCAVLEGGYH 289
Query: 360 IRNVARCWC 368
+ ++A C
Sbjct: 290 LESLAESVC 298
>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 = 52.1 bits (125), Expect = 3e-07
Identities = 20/48 (41%), Positives = 31/48 (64%), Gaps = 2/48 (4%)
Query: 195 HHAKKSEASGFCYVNDIVLGILELLKVH--RRVLYVDIDVHHGDGVEE 240
HH +S SGFC+VN++ +G H RV+ +DID+HHG+G ++
Sbjct: 120 HHCSESTPSGFCWVNNVHVGAAHAYLTHGITRVVILDIDLHHGNGTQD 167
>gnl|CDD|227549 COG5224, HAP2, CCAAT-binding factor, subunit B [Transcription].
Length = 248
Score = 30.2 bits (67), Expect = 2.1
Identities = 8/42 (19%), Positives = 13/42 (30%), Gaps = 3/42 (7%)
Query: 433 SVPFQTTPATTQVPEEPEEDMERRPKPRIWNGEDYESDHDED 474
+VP + T E + + RP ES +
Sbjct: 27 TVPATVSSEVTHTSEGYADSNDSRPSSI---SNSSESPAPIN 65
>gnl|CDD|146273 pfam03546, Treacle, Treacher Collins syndrome protein Treacle.
Length = 519
Score = 30.6 bits (68), Expect = 2.1
Identities = 17/48 (35%), Positives = 21/48 (43%), Gaps = 9/48 (18%)
Query: 431 APSVPFQTTPATTQVPEEPEEDMERRPKPRIWNGEDYESDHDEDDKPP 478
AP P +T PA QV E +ED E + ESD +E P
Sbjct: 352 APVPPGKTGPAVAQVKAEVQEDSE---------SSEEESDSEEAAATP 390
>gnl|CDD|143437 cd07119, ALDH_BADH-GbsA, Bacillus subtilis NAD+-dependent betaine
aldehyde dehydrogenase-like. Included in this CD is the
NAD+-dependent, betaine aldehyde dehydrogenase (BADH,
GbsA, EC=1.2.1.8) of Bacillus subtilis involved in the
synthesis of the osmoprotectant glycine betaine from
choline or glycine betaine aldehyde.
Length = 482
Score = 30.0 bits (68), Expect = 3.5
Identities = 14/27 (51%), Positives = 15/27 (55%), Gaps = 3/27 (11%)
Query: 49 EGASLVSG---PDGKKRRVSYFYEPTI 72
EGA LV G P G + YF EPTI
Sbjct: 338 EGARLVCGGKRPTGDELAKGYFVEPTI 364
>gnl|CDD|99747 cd06454, KBL_like, KBL_like; this family belongs to the pyridoxal
phosphate (PLP)-dependent aspartate aminotransferase
superfamily (fold I). The major groups in this CD
corresponds to serine palmitoyltransferase (SPT),
5-aminolevulinate synthase (ALAS),
8-amino-7-oxononanoate synthase (AONS), and
2-amino-3-ketobutyrate CoA ligase (KBL). SPT is
responsible for the condensation of L-serine with
palmitoyl-CoA to produce 3-ketodihydrospingosine, the
reaction of the first step in sphingolipid biosynthesis.
ALAS is involved in heme biosynthesis; it catalyzes the
synthesis of 5-aminolevulinic acid from glycine and
succinyl-coenzyme A. AONS catalyses the decarboxylative
condensation of l-alanine and pimeloyl-CoA in the first
committed step of biotin biosynthesis. KBL catalyzes the
second reaction step of the metabolic degradation
pathway for threonine converting 2-amino-3-ketobutyrate,
to glycine and acetyl-CoA. The members of this CD are
widely found in all three forms of life.
Length = 349
Score = 28.7 bits (65), Expect = 7.1
Identities = 18/53 (33%), Positives = 27/53 (50%), Gaps = 11/53 (20%)
Query: 215 ILELLKVHRRVLYVDIDVH-------HGDGVEEAFYTTDRV--MTVSFHK-FG 257
+++L K + +L+VD + H HG GVEE TD V + + K FG
Sbjct: 154 LVDLAKKYGAILFVD-EAHSVGVYGPHGRGVEEFGGLTDDVDIIMGTLGKAFG 205
>gnl|CDD|220400 pfam09785, Prp31_C, Prp31 C terminal domain. This is the C
terminal domain of the pre-mRNA processing factor
Prp31. Prp31 is required for U4/U6.U5 tri-snRNP
formation. In humans this protein has been linked to
autosomal dominant retinitis pigmentosa.
Length = 124
Score = 27.7 bits (62), Expect = 7.6
Identities = 6/22 (27%), Positives = 16/22 (72%)
Query: 23 KKRERGGKKKRHKREKSQLSKM 44
K++RGG++ R +E+ ++++
Sbjct: 15 PKKKRGGRRFRKMKERFAMTEL 36
>gnl|CDD|143436 cd07118, ALDH_SNDH, Gluconobacter oxydans L-sorbosone
dehydrogenase-like. Included in this CD is the
L-sorbosone dehydrogenase (SNDH) from Gluconobacter
oxydans UV10. In G. oxydans, D-sorbitol is converted to
2-keto-L-gulonate (a precursor of L-ascorbic acid) in
sequential oxidation steps catalyzed by a FAD-dependent,
L-sorbose dehydrogenase and an NAD(P)+-dependent,
L-sorbosone dehydrogenase.
Length = 454
Score = 28.8 bits (65), Expect = 7.7
Identities = 10/25 (40%), Positives = 14/25 (56%)
Query: 48 TEGASLVSGPDGKKRRVSYFYEPTI 72
EGA+L+ G + FY+PTI
Sbjct: 322 AEGATLLLGGERLASAAGLFYQPTI 346
>gnl|CDD|200509 cd11248, Sema_MET_like, The Sema domain, a protein interacting
module, of MET and RON receptor tyrosine kinases. This
family includes MET and RON receptor tyrosine kinases.
MET is encoded by the c-met protooncogene. MET is the
receptor for hepatocyte growth factor/scatter factor
(HGF/SF). HGF/SF and MET regulates multiple cellular
events and are essential for the development of several
tissues and organs, including the placenta, liver, and
several groups of skeletal muscles. RON receptor
tyrosine kinase is a Macrophage-stimulating protein
(MSP) receptor. Upon binding of MSP, RON is activated
via autophosphorylation within its kinase catalytic
domain, resulting in a variety of effects including
proliferation, tubular morphogenesis, angiogenesis,
cellular motility and invasiveness. By interacting with
downstream signaling molecules, it regulates macrophage
migration, phagocytosis, and nitric oxide production.
MET and RON receptors have been implicated in cancer
development and migration. They are composed of
alpha-beta heterodimers. The extracellular alpha chain
is disulfide linked to the beta chain, which contains an
extracellular ligand-binding region with a Sema domain,
a PSI domain and four IPT repeats, a transmembrane
segment, and an intracellular catalytic tyrosine kinase
domain. The Sema domain is necessary for receptor
dimerization and activation.
Length = 467
Score = 28.5 bits (64), Expect = 7.9
Identities = 29/121 (23%), Positives = 41/121 (33%), Gaps = 16/121 (13%)
Query: 43 KMEEPTEGASLVSGPDGKK------RRVSYFYEPTIGDYYYGQGHPMKPHRI---RMAHN 93
K P+ V+ P G K R YF+ + P PH I R+ +
Sbjct: 119 KNNSPSYCPDCVASPLGTKVTNVESGRTIYFFVANSVNSSLAGSFP--PHSISVRRLKED 176
Query: 94 LIVHYGLHRRMEVNRPFPAG-PSD-IRRFHTDEYVEFLASVSPESSGDPS--FSRHLKRF 149
++V P + FH+ +V FL +V ES PS F L R
Sbjct: 177 GFGFLSDQSYLDVLPSLRDSYPIKYVYSFHSGPFVYFL-TVQRESLTKPSSAFHTRLVRL 235
Query: 150 N 150
Sbjct: 236 C 236
>gnl|CDD|143407 cd07088, ALDH_LactADH-AldA, Escherichia coli lactaldehyde
dehydrogenase AldA-like. Lactaldehyde dehydrogenase
from Escherichia coli (AldA, LactADH, EC=1.2.1.22), an
NAD(+)-dependent enzyme involved in the metabolism of
L-fucose and L-rhamnose, and other similar sequences are
present in this CD.
Length = 468
Score = 28.8 bits (65), Expect = 7.9
Identities = 15/41 (36%), Positives = 23/41 (56%), Gaps = 5/41 (12%)
Query: 37 EKSQLSKMEEPTE-----GASLVSGPDGKKRRVSYFYEPTI 72
++ L K+EE E GA+L++G + YFYEPT+
Sbjct: 320 NEAALDKVEEMVERAVEAGATLLTGGKRPEGEKGYFYEPTV 360
>gnl|CDD|237553 PRK13905, murB, UDP-N-acetylenolpyruvoylglucosamine reductase;
Provisional.
Length = 298
Score = 28.2 bits (64), Expect = 9.1
Identities = 8/20 (40%), Positives = 13/20 (65%)
Query: 337 ADCLRFLRSFNVPLMVLGGG 356
+ L+ L+ N+P+ VLG G
Sbjct: 44 QEFLKLLKENNIPVTVLGNG 63
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
0.320 0.140 0.437
Gapped
Lambda K H
0.267 0.0811 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 25,939,624
Number of extensions: 2579202
Number of successful extensions: 2511
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2415
Number of HSP's successfully gapped: 50
Length of query: 490
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 389
Effective length of database: 6,457,848
Effective search space: 2512102872
Effective search space used: 2512102872
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 61 (27.1 bits)