RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10342
(285 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 = 439 bits (1131), Expect = e-156
Identities = 172/223 (77%), Positives = 194/223 (86%)
Query: 4 KTVSYFYNPDVGNFHYGAKHPMKPHRLSVINSLILGYGLHKKMQIYRPYKASYHDMCRFH 63
K V+YFY+PDVGNFHYG HPMKPHRL++ +SL+L YGL+KKMQ+Y+PY+AS HDMCRFH
Sbjct: 1 KRVAYFYDPDVGNFHYGPGHPMKPHRLALTHSLVLHYGLYKKMQVYKPYRASAHDMCRFH 60
Query: 64 SAEYIDFLHTVSPDKIHEHTKFLCQFASGEDCPIFHGLYDFCSMYTGASLEGAIQLNNNC 123
S +YIDFL V+P I TK L QF G+DCP+F GL+DFCSMYTGASLEGA +LN+
Sbjct: 61 SEDYIDFLQRVTPQNIQGFTKSLNQFNVGDDCPVFPGLFDFCSMYTGASLEGATKLNHKI 120
Query: 124 CDIAINWSGGLHHAKKSEASGFCYVNDIVIAILELLKYHPRVLYIDIDVHHGDGVQDAFY 183
CDIAINWSGGLHHAKK EASGFCYVNDIVIAILELLKYHPRVLYIDID+HHGDGVQ+AFY
Sbjct: 121 CDIAINWSGGLHHAKKFEASGFCYVNDIVIAILELLKYHPRVLYIDIDIHHGDGVQEAFY 180
Query: 184 LTDRVMTVSFHKYGGGFFPCSGDMYEIGAEGGRYYSVNVRNRD 226
LTDRVMTVSFHKYG FFP +GDMYE+GAE GRYYSVNV +D
Sbjct: 181 LTDRVMTVSFHKYGNYFFPGTGDMYEVGAESGRYYSVNVPLKD 223
>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 = 383 bits (985), Expect = e-135
Identities = 141/218 (64%), Positives = 175/218 (80%), Gaps = 1/218 (0%)
Query: 9 FYNPDVGNFHYGAKHPMKPHRLSVINSLILGYGLHKKMQIYRPYKASYHDMCRFHSAEYI 68
FY+PDVGN++YG HPMKPHR+ + +SLIL YGL+KKM+IYRP A+ ++ +FHS +YI
Sbjct: 1 FYDPDVGNYYYGQGHPMKPHRIRMTHSLILSYGLYKKMEIYRPRPATAEELTKFHSDDYI 60
Query: 69 DFLHTVSPDKIHEHTKFLCQFASGEDCPIFHGLYDFCSMYTGASLEGAIQLNNNCCDIAI 128
DFL +VSPD + E K L +F GEDCP+F GLY++C +Y G S+ A++LN DIAI
Sbjct: 61 DFLRSVSPDNMKEFKKQLERFNVGEDCPVFDGLYEYCQLYAGGSIAAAVKLNRGQADIAI 120
Query: 129 NWSGGLHHAKKSEASGFCYVNDIVIAILELLKYHPRVLYIDIDVHHGDGVQDAFYLTDRV 188
NW+GGLHHAKKSEASGFCYVNDIV+AILELLKYH RVLYIDID+HHGDGV++AFY TDRV
Sbjct: 121 NWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRV 180
Query: 189 MTVSFHKYGGGFFPCSGDMYEIGAEGGRYYSVNVRNRD 226
MTVSFHK+G FFP + +IGA G+YY+VNV +D
Sbjct: 181 MTVSFHKFGEYFFP-GTGLRDIGAGKGKYYAVNVPLKD 217
>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 = 335 bits (861), Expect = e-115
Identities = 139/245 (56%), Positives = 185/245 (75%), Gaps = 1/245 (0%)
Query: 3 NKTVSYFYNPDVGNFHYGAKHPMKPHRLSVINSLILGYGLHKKMQIYRPYKASYHDMCRF 62
K V+YFY+ DVGN+ YG HPMKPHR+ + +SL++ YGL+KKM+IYR A+ ++M +F
Sbjct: 1 KKKVAYFYDSDVGNYAYGPGHPMKPHRIRMAHSLVMNYGLYKKMEIYRAKPATKNEMTQF 60
Query: 63 HSAEYIDFLHTVSPDKIHEHTKFLCQFASGEDCPIFHGLYDFCSMYTGASLEGAIQLNNN 122
H+ EYIDFL V+PD + + K ++ G+DCP+F GL++FCS+ G S+EGA +LN
Sbjct: 61 HTDEYIDFLSRVTPDNMEKFQKEQVKYNVGDDCPVFDGLFEFCSISAGGSMEGAARLNRG 120
Query: 123 CCDIAINWSGGLHHAKKSEASGFCYVNDIVIAILELLKYHPRVLYIDIDVHHGDGVQDAF 182
CDIA+NW+GGLHHAKKSEASGFCYVNDIV+ ILELL+YH RVLYIDIDVHHGDGV++AF
Sbjct: 121 KCDIAVNWAGGLHHAKKSEASGFCYVNDIVLGILELLRYHQRVLYIDIDVHHGDGVEEAF 180
Query: 183 YLTDRVMTVSFHKYGGGFFPCSGDMYEIGAEGGRYYSVNVRNRDLSPHSSHKRMFRERVH 242
Y TDRVMT SFHKY G +FP +G++ +IG G+ Y+VNV RD S+K +F +
Sbjct: 181 YTTDRVMTCSFHKY-GEYFPGTGELRDIGIGTGKNYAVNVPLRDGIDDESYKSIFEPVIK 239
Query: 243 SLLPF 247
++ +
Sbjct: 240 HVMEW 244
>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 = 325 bits (835), Expect = e-112
Identities = 125/218 (57%), Positives = 163/218 (74%), Gaps = 1/218 (0%)
Query: 6 VSYFYNPDVGNFHYGAKHPMKPHRLSVINSLILGYGLHKKMQIYRPYKASYHDMCRFHSA 65
VSY +N V ++H+G HPMKP RL++ L++GYGLHK M Y A+ ++ +FH A
Sbjct: 1 VSYHFNSRVEDYHFGRTHPMKPFRLTLTKHLVMGYGLHKAMDTYEARAATREELRQFHDA 60
Query: 66 EYIDFLHTVSPDKIHEHTK-FLCQFASGEDCPIFHGLYDFCSMYTGASLEGAIQLNNNCC 124
+Y+DFL VSP+ ++ F G+DCP+F G+YD+C +Y GASL+ A +L +
Sbjct: 61 DYLDFLSKVSPENANQLRFDKAEPFNIGDDCPVFDGMYDYCQLYAGASLDAARKLCSGQS 120
Query: 125 DIAINWSGGLHHAKKSEASGFCYVNDIVIAILELLKYHPRVLYIDIDVHHGDGVQDAFYL 184
DIAINWSGGLHHAKKSEASGFCYVNDIV+AIL LL+Y PRVLYIDIDVHHGDGV++AFY
Sbjct: 121 DIAINWSGGLHHAKKSEASGFCYVNDIVLAILNLLRYFPRVLYIDIDVHHGDGVEEAFYR 180
Query: 185 TDRVMTVSFHKYGGGFFPCSGDMYEIGAEGGRYYSVNV 222
TDRVMT+SFHKY G FFP +GD+ + G G+++++NV
Sbjct: 181 TDRVMTLSFHKYNGEFFPGTGDLDDNGGTPGKHFALNV 218
>gnl|CDD|240251 PTZ00063, PTZ00063, histone deacetylase; Provisional.
Length = 436
Score = 315 bits (808), Expect = e-106
Identities = 132/224 (58%), Positives = 173/224 (77%), Gaps = 3/224 (1%)
Query: 1 MSNKTVSYFYNPDVGNFHYGAKHPMKPHRLSVINSLILGYGLHKKMQIYRPYKASYHDMC 60
K VSYFY+PD+G+++YG HPMKP R+ + ++LIL Y L+K M+IYRP+K+ ++
Sbjct: 1 SMRKRVSYFYDPDIGSYYYGPGHPMKPQRIRMAHALILSYDLYKHMEIYRPHKSVEPELV 60
Query: 61 RFHSAEYIDFLHTVSPDKIHEHTKFLCQFASGE--DCPIFHGLYDFCSMYTGASLEGAIQ 118
FH EY+DFL ++SP+ + T L +F GE DCP+F GL++F GAS++GA +
Sbjct: 61 LFHDEEYVDFLSSISPENYRDFTYQLKRFNVGEATDCPVFDGLFEFQQSCAGASIDGAYK 120
Query: 119 LNNNCCDIAINWSGGLHHAKKSEASGFCYVNDIVIAILELLKYHPRVLYIDIDVHHGDGV 178
LNN+ DI +NWSGGLHHAK+SEASGFCY+NDIV+ ILELLKYH RV+YIDIDVHHGDGV
Sbjct: 121 LNNHQADICVNWSGGLHHAKRSEASGFCYINDIVLGILELLKYHARVMYIDIDVHHGDGV 180
Query: 179 QDAFYLTDRVMTVSFHKYGGGFFPCSGDMYEIGAEGGRYYSVNV 222
++AFY+T RVMTVSFHK+ G FFP +GD+ +IG G+YYSVNV
Sbjct: 181 EEAFYVTHRVMTVSFHKF-GDFFPGTGDVTDIGVAQGKYYSVNV 223
>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 = 304 bits (780), Expect = e-103
Identities = 138/237 (58%), Positives = 187/237 (78%), Gaps = 1/237 (0%)
Query: 2 SNKTVSYFYNPDVGNFHYGAKHPMKPHRLSVINSLILGYGLHKKMQIYRPYKASYHDMCR 61
+ K V Y+Y+ DVGN++YG HPMKPHR+ + ++L+L YGL++KM+IYRP+KA+ +M +
Sbjct: 4 TKKKVCYYYDGDVGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKANAEEMTK 63
Query: 62 FHSAEYIDFLHTVSPDKIHEHTKFLCQFASGEDCPIFHGLYDFCSMYTGASLEGAIQLNN 121
+HS +YI FL ++ PD + E++K + +F GEDCP+F GL++FC + G S+ A++LN
Sbjct: 64 YHSDDYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSAGGSVASAVKLNK 123
Query: 122 NCCDIAINWSGGLHHAKKSEASGFCYVNDIVIAILELLKYHPRVLYIDIDVHHGDGVQDA 181
DIA+NW+GGLHHAKKSEASGFCYVNDIV+AILELLKYH RVLYIDID+HHGDGV++A
Sbjct: 124 QQTDIAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEA 183
Query: 182 FYLTDRVMTVSFHKYGGGFFPCSGDMYEIGAEGGRYYSVNVRNRDLSPHSSHKRMFR 238
FY TDRVMTVSFHKY G +FP +GD+ +IGA G+YY+VN RD S++ +F+
Sbjct: 184 FYTTDRVMTVSFHKY-GEYFPGTGDLRDIGAGKGKYYAVNYPLRDGIDDESYEAIFK 239
>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 = 295 bits (755), Expect = 4e-99
Identities = 139/242 (57%), Positives = 190/242 (78%), Gaps = 1/242 (0%)
Query: 4 KTVSYFYNPDVGNFHYGAKHPMKPHRLSVINSLILGYGLHKKMQIYRPYKASYHDMCRFH 63
K V Y+Y+ D+GN++YG HPMKPHR+ + ++L+L YGL++KM+IYRP+KA+ +M ++H
Sbjct: 2 KKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTKYH 61
Query: 64 SAEYIDFLHTVSPDKIHEHTKFLCQFASGEDCPIFHGLYDFCSMYTGASLEGAIQLNNNC 123
S EYI FL ++ PD + E++K + +F GEDCP+F GL++FC + TG S+ GA++LN
Sbjct: 62 SDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAGAVKLNRQQ 121
Query: 124 CDIAINWSGGLHHAKKSEASGFCYVNDIVIAILELLKYHPRVLYIDIDVHHGDGVQDAFY 183
D+A+NW+GGLHHAKKSEASGFCYVNDIV+AILELLKYH RVLYIDID+HHGDGV++AFY
Sbjct: 122 TDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFY 181
Query: 184 LTDRVMTVSFHKYGGGFFPCSGDMYEIGAEGGRYYSVNVRNRDLSPHSSHKRMFRERVHS 243
TDRVMTVSFHKYG FP +GD+ +IGA G+YY+VN RD S+ ++F+ +
Sbjct: 182 TTDRVMTVSFHKYGEY-FPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIISK 240
Query: 244 LL 245
++
Sbjct: 241 VM 242
>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 = 256 bits (656), Expect = 3e-84
Identities = 103/205 (50%), Positives = 140/205 (68%), Gaps = 3/205 (1%)
Query: 24 PMKPHRLSVINSLILGYGLHKKMQIYRPYKASYHDMCRFHSAEYIDFLHTVSP--DKIHE 81
P P+R S+++SLI YGL K++++ +P A+ ++ FHS EYI FL S D E
Sbjct: 17 PKVPNRASMVHSLIEAYGLLKQLRVVKPRVATEEELASFHSDEYIQFLKKASNEGDNDEE 76
Query: 82 HTKFLCQFASGEDCPIFHGLYDFCSMYTGASLEGAIQLNNNCCDIAINWSGGLHHAKKSE 141
++ +F G DCPIF G+YD+ + GA+L A L + C +AINW GG HHA++ E
Sbjct: 77 PSEQQ-EFGLGYDCPIFEGIYDYAAAVAGATLTAAQLLIDGKCKVAINWFGGWHHAQRDE 135
Query: 142 ASGFCYVNDIVIAILELLKYHPRVLYIDIDVHHGDGVQDAFYLTDRVMTVSFHKYGGGFF 201
ASGFCYVNDIV+ IL+L + RVLY+D+D+HHGDGV+DAF T +VMTVS HKY GFF
Sbjct: 136 ASGFCYVNDIVLGILKLREKFDRVLYVDLDLHHGDGVEDAFSFTSKVMTVSLHKYSPGFF 195
Query: 202 PCSGDMYEIGAEGGRYYSVNVRNRD 226
P +GD+ ++G G+YY+VNV RD
Sbjct: 196 PGTGDVSDVGLGKGKYYTVNVPLRD 220
>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 = 229 bits (586), Expect = 5e-74
Identities = 71/233 (30%), Positives = 107/233 (45%), Gaps = 13/233 (5%)
Query: 3 NKTVSYFYNPDVGNFHYGAKHPMKPHRLSVINSLILGYGLHKKMQIYRPYKASYHDMCRF 62
+ Y+P+ HP P RL +I L+ GL +++ P A+ ++
Sbjct: 1 MMKTALIYHPEFLEHEPPPGHPENPDRLRLILELLESSGLPDSLELVEPRPATLEELLLV 60
Query: 63 HSAEYIDFLHTVSPDKIHEHTKFLCQFASGEDCPIFHGLYDFCSMYTGASLEGAIQLNNN 122
HS +Y++FL ++S ++ D P+ G Y+ + G +L +
Sbjct: 61 HSPDYVEFLESLSEEEG--------YGNLDGDTPVSPGTYEAARLAAGGALTAVDAVLEG 112
Query: 123 CCDIAINWSGGLHHAKKSEASGFCYVNDIVIAILELLK-YHPRVLYIDIDVHHGDGVQDA 181
+ HHA + ASGFC N++ IA LLK RV ID DVHHG+G Q+
Sbjct: 113 EDNAFALVRPPGHHAGRDRASGFCLFNNVAIAAKYLLKKGVKRVAIIDFDVHHGNGTQEI 172
Query: 182 FYLTDRVMTVSFHKYGGGFFPCSGDMYEIGAEGGRYYSVNVRNRDLSPHSSHK 234
FY D V+TVS H+ G F+P +G EIG EG +VN+ L P +
Sbjct: 173 FYDDDDVLTVSLHQDGRPFYPGTGGADEIG-EGKEGNNVNIP---LPPGTGDD 221
>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 = 220 bits (563), Expect = 7e-71
Identities = 79/216 (36%), Positives = 115/216 (53%), Gaps = 3/216 (1%)
Query: 8 YFYNPDVGNFHYGAKHPMKPHRLSVINSLILGYGLHKKMQIYRPYKASYHDMCRFHSAEY 67
+ Y+ + + +G HP P RLS+ L+ GL + + P A+ ++ FH+ +Y
Sbjct: 2 FIYSEEYLRYSFGPNHPFNPPRLSLTKDLLRALGLLPPVDLVPPRPATEEELLLFHTPDY 61
Query: 68 IDFLHTVSPDKIHEHTKFLCQFASGEDCPIFHGLYDFCSMYTGASLEGAIQLNNNCCDIA 127
I+ + S + E L ED P+F G+++ ++ G +L A + A
Sbjct: 62 IEAVKEASRGQEPEGRGRLGL--GTEDNPVFPGMHEAAALVVGGTLLAARLVLEGEARRA 119
Query: 128 INWSGGLHHAKKSEASGFCYVNDIVIAILELL-KYHPRVLYIDIDVHHGDGVQDAFYLTD 186
N +GGLHHA + ASGFC ND +AI L K RV Y+DID HHGDGVQ AFY
Sbjct: 120 FNPAGGLHHAMRGRASGFCVYNDAAVAIERLRDKGGLRVAYVDIDAHHGDGVQAAFYDDP 179
Query: 187 RVMTVSFHKYGGGFFPCSGDMYEIGAEGGRYYSVNV 222
RV+T+S H+ G FP +G + EIG G Y+VN+
Sbjct: 180 RVLTISLHESGRYLFPGTGFVDEIGEGEGYGYAVNI 215
>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 = 201 bits (513), Expect = 2e-63
Identities = 74/250 (29%), Positives = 114/250 (45%), Gaps = 24/250 (9%)
Query: 17 FHYGAKHPMKPHRLSVINSLILGYGLHKKMQIYRPYKASYHDMCRFHSAEYIDFL-HTVS 75
G HP P RL I L+ GL +++ P A+ ++ HS EY++FL
Sbjct: 3 TGSGLGHPENPERLEAILELLKESGLLDRLEFIAPRPATEEELLLVHSPEYVEFLEEASL 62
Query: 76 PDKIHEHTKFLCQFASGEDCPIFHGLYDFCSMYTGASLEGAIQ-LNNNCCDIAINWSGGL 134
++ D P+ G Y+ + G +LE A L+ A+ G
Sbjct: 63 EEEELGRIGL------DGDTPVSPGSYEAALLAAGGTLEAADLVLSGENAFAAVRPPG-- 114
Query: 135 HHAKKSEASGFCYVNDIVIAILELLKYHP--RVLYIDIDVHHGDGVQDAFYLTDRVMTVS 192
HHA++ ASGFC N++ IA LLK + RVL +D+DVHHG+G Q+ FY RV+T+S
Sbjct: 115 HHAERDRASGFCLFNNVAIAARYLLKRYGLKRVLIVDLDVHHGNGTQEIFYDDPRVLTIS 174
Query: 193 FHKYGGGFFPCSGDMYEIGAEGGRYYSVNVRNRDLSPHSSHKRMFRERVHSLLPFVF--- 249
H+ F+P +G E G G Y++N+ L P + + +L
Sbjct: 175 IHQD--PFYPGTGFADETGEGAGEGYTLNI---PLPPGTGD-EEYLAAFEEILLPALREF 228
Query: 250 ---VVFFSSG 256
++ S+G
Sbjct: 229 QPDLILVSAG 238
>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 = 181 bits (462), Expect = 6e-56
Identities = 80/197 (40%), Positives = 114/197 (57%), Gaps = 21/197 (10%)
Query: 29 RLSVINSLILGYGLHK-KMQIYRPYKASYHDMCRFHSAEYIDFLHTVSPDKIHEHTKFLC 87
R S+++SLI YGL + +I P +A+ D+ ++H +Y+DFL L
Sbjct: 21 RSSLVHSLIRAYGLLQHFDEIIEPERATRKDLTKYHDKDYVDFL--------------LK 66
Query: 88 QFASGEDCPIFHGLYDFCSMYTGASLEGAIQLNNNC-CDIAINWSGGLHHAKKSEASGFC 146
++ +DCP+F L + + G+SL A L DIAINW GG HHA+KS ASGFC
Sbjct: 67 KYGLEDDCPVFPFLSMYVQLVAGSSLALAKHLITQVERDIAINWYGGRHHAQKSRASGFC 126
Query: 147 YVNDIVIAILELLKYH-PRVLYIDIDVHHGDGVQDAFYLTDRVMTVSFHKYGGGFFPCSG 205
YVNDIV+AIL L + RV Y+D+D+HHGDGV+ AF+ + V+T S H+Y GFFP +G
Sbjct: 127 YVNDIVLAILRLRRARFRRVFYLDLDLHHGDGVESAFFFSKNVLTCSIHRYDPGFFPGTG 186
Query: 206 DMYEIGAEGGRYYSVNV 222
+ +N+
Sbjct: 187 SL----KNSSDKGMLNI 199
>gnl|CDD|240374 PTZ00346, PTZ00346, histone deacetylase; Provisional.
Length = 429
Score = 164 bits (415), Expect = 1e-47
Identities = 89/236 (37%), Positives = 131/236 (55%), Gaps = 1/236 (0%)
Query: 10 YNPDVGNFHYGAKHPMKPHRLSVINSLILGYGLHKKMQIYRPYKASYHDMCRFHSAEYID 69
Y D+ + +H MKP+R+ ++ + + P ++ +H+ Y+
Sbjct: 30 YASDMNISAFVPQHAMKPYRVLAAMEIVRSLKIDAHCRTVVPPLVKVEELMAYHTDTYLA 89
Query: 70 FLHTVSPDKIHEHTKFLCQFASGEDCPIFHGLYDFCSMYTGASLEGAIQLNNNCCDIAIN 129
L S + + F SG DCP GL + +L GA+ LN+ D+A++
Sbjct: 90 NLGLHSCRSWLWNAETSKVFFSG-DCPPVEGLMEHSIATASGTLMGAVLLNSGQVDVAVH 148
Query: 130 WSGGLHHAKKSEASGFCYVNDIVIAILELLKYHPRVLYIDIDVHHGDGVQDAFYLTDRVM 189
W GG+HH+K E SGFCYVNDIV+ ILELLK H RVLY+DID+HHGDGV +AF +DRV
Sbjct: 149 WGGGMHHSKCGECSGFCYVNDIVLGILELLKCHDRVLYVDIDMHHGDGVDEAFCTSDRVF 208
Query: 190 TVSFHKYGGGFFPCSGDMYEIGAEGGRYYSVNVRNRDLSPHSSHKRMFRERVHSLL 245
T+S HK+G FFP +G ++G GRYYS+N+ D + +F +HS++
Sbjct: 209 TLSLHKFGESFFPGTGHPRDVGYGRGRYYSMNLAVWDGITDFYYLGLFEHALHSIV 264
>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 = 159 bits (404), Expect = 2e-47
Identities = 65/231 (28%), Positives = 99/231 (42%), Gaps = 18/231 (7%)
Query: 29 RLSVINSLILGYGLHKKMQIYRPYKASYHDMCRFHSAEYIDFLHTVSPDKIHEHTKFLCQ 88
R+ + + GL K+++ +A+ + + H+ EY++ L +K
Sbjct: 1 RIRDLIEALKELGLRPKIELIECREATEELLLKVHTEEYLNELKANFAVATITESK---P 57
Query: 89 FASGEDCPIFHGLYDFCSMYTGASLEGAIQLNNNCCDIAINW-SGGLHHAKKSEASGFCY 147
G + P+ + + TG +E A + + A G HHA KS A GFCY
Sbjct: 58 VIFGPNFPVQRHYFRGARLSTGGVVEAAELVAKGELERAFAVVGAGGHHAGKSRAWGFCY 117
Query: 148 VNDIVIAILELLKY-HPRVLYIDIDVHHGDGVQDAFYLTDRVMTVSFHKYGGGFFPCSGD 206
ND+V+AI L + R+L ID D HHGDG ++AFY DRV+ +SFH Y F
Sbjct: 118 FNDVVLAIKFLRERGISRILIIDTDAHHGDGTREAFYDDDRVLHMSFHNYDIYPF----- 172
Query: 207 MYEIGAEGGRYYSVNVRNRDLSPHSSHKRMFRERV----HSLLPFVFVVFF 253
G G+ Y +NV D + + P V V+ F
Sbjct: 173 ----GRGKGKGYKINVPLEDGLGDEEYLDAVERVISKVLEEFEPEVVVLQF 219
>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 = 118 bits (298), Expect = 1e-31
Identities = 60/205 (29%), Positives = 91/205 (44%), Gaps = 18/205 (8%)
Query: 23 HPMKPHRLSVINSLILGYGLHKKMQIYRPYKASYHDMCRFHSAEYIDFLHTVSPDKIHEH 82
HP +P RL I + GL ++ P A+ ++ R H+ EYI+ +
Sbjct: 1 HPERPERLLAILEALEEEGLLDRLVFVEPRPATEEELLRVHTPEYIERVEETCEAGGGY- 59
Query: 83 TKFLCQFASGEDCPIFHGLYDFCSMYTGASLEGAIQLNNNCCDIA---INWSGGLHHAKK 139
D + G Y+ + GA+L + + + A + G HHA+
Sbjct: 60 --------LDPDTYVSPGSYEAALLAAGAALAAVDAVLSGEAENAFALVRPPG--HHAEP 109
Query: 140 SEASGFCYVNDIVIAILELLKYH--PRVLYIDIDVHHGDGVQDAFYLTDRVMTVSFHKYG 197
A GFC N++ IA K + RVL +D DVHHG+G QD FY V+ S H+Y
Sbjct: 110 DRAMGFCLFNNVAIAARYAQKRYGLKRVLIVDWDVHHGNGTQDIFYDDPSVLYFSIHQY- 168
Query: 198 GGFFPCSGDMYEIGAEGGRYYSVNV 222
F+P +G E G G +++NV
Sbjct: 169 -PFYPGTGAAEETGGGAGEGFTINV 192
>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 = 113 bits (286), Expect = 2e-29
Identities = 62/222 (27%), Positives = 92/222 (41%), Gaps = 23/222 (10%)
Query: 9 FYNPDVGNFHYGAKHPMKPHRLSVINSLILGYGLHKKMQIYRPYKASYHDMCRFHSAEYI 68
+ P G +HP P I +L+ GL + + P A+ ++ R H+ EYI
Sbjct: 19 LFLPVGGLLVQPGRHPENPETKRRIKNLLEVSGLSDHLVLITPRPATDEELLRVHTPEYI 78
Query: 69 DFLHTVSPDKIHEHTKFLCQFASGEDC---PIFHGLYDFCSMYTGASLEGAIQLNNNCCD 125
D K GE P G Y+ + G ++ + + D
Sbjct: 79 D------------RVKAASAAGGGEAGGGTPFGPGSYEIALLAAGGAIAAVDAVLDGEVD 126
Query: 126 IA---INWSGGLHHAKKSEASGFCYVNDIVIAILELLKYHP--RVLYIDIDVHHGDGVQD 180
A + G HHA+ + GFC N++ IA L RV +D DVHHG+G Q
Sbjct: 127 NAYALVRPPG--HHAEPDQGMGFCLFNNVAIAARHALAVGGVKRVAVVDWDVHHGNGTQA 184
Query: 181 AFYLTDRVMTVSFHKYGGGFFPCSGDMYEIGAEGGRYYSVNV 222
FY V+T+S H+ F P SG + E G G Y++N+
Sbjct: 185 IFYDDPDVLTISLHQ-DRCFPPDSGAVEERGEGAGEGYNLNI 225
>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 = 101 bits (254), Expect = 3e-25
Identities = 63/226 (27%), Positives = 95/226 (42%), Gaps = 29/226 (12%)
Query: 23 HPMKPHRLSVINSLILGYGLHKKMQIYRPYKASYHDMCRFHSAEYIDFLHTVSPDKIHEH 82
HP P RL I ++ GL + ++ A+ + R H A Y+D L +P++
Sbjct: 1 HPESPERLEAILDALIASGLDRLLRQLEAPPATREQLLRVHDAAYVDRLEAAAPEEGLVQ 60
Query: 83 TKFLCQFASGEDCPIFHGLYDFCSMYTGASLEG-----AIQLNNNCCDIAINWSGGLHHA 137
D + G + GA + A + N C A+ G HHA
Sbjct: 61 L--------DPDTAMSPGSLEAALRAAGAVVAAVDAVMAGEARNAFC--AVRPPG--HHA 108
Query: 138 KKSEASGFCYVNDIVIAILELLKYHP--RVLYIDIDVHHGDGVQDAFYLTDRVMTVSFHK 195
++ +A GFC N++ IA L +H RV +D DVHHG+G +D F RV+ S H+
Sbjct: 109 ERDKAMGFCLFNNVAIAAAHALAHHGLERVAIVDFDVHHGNGTEDIFRDDPRVLFCSSHQ 168
Query: 196 YGGGFFPCSGDMYEIGAEGGRYYSVNVRNRDLSPHSSHKRMFRERV 241
+ +P +G E G N+ N L + FRE V
Sbjct: 169 H--PLYPGTGAPDETGHG-------NIVNVPLPAGTG-GAEFREAV 204
>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 = 98.4 bits (246), Expect = 4e-24
Identities = 51/166 (30%), Positives = 67/166 (40%), Gaps = 28/166 (16%)
Query: 63 HSAEYIDFLHTVSPDKIHEHTKFLCQFASGEDCPIFHGLYDFCSMYTGASLEGAIQLNNN 122
H +Y+DFL T D PI G ++ +L A L
Sbjct: 62 HDPDYVDFLETADTD-----------------TPISEGTWEAALAAADTALTAA-DLVLE 103
Query: 123 CCDIAINWSGGL-----HHAKKSEASGFCYVNDIVIAILELLKYHPRVLYIDIDVHHGDG 177
A L HHA + A GFCY N+ IA L RV +D+DVHHG+G
Sbjct: 104 GERAAY----ALCRPPGHHAGRDRAGGFCYFNNAAIAAQYLRDRAGRVAILDVDVHHGNG 159
Query: 178 VQDAFYLTDRVMTVSFHKYGGGFFP-CSGDMYEIGAEGGRYYSVNV 222
Q+ FY V+ VS H F+P G E G G Y++N+
Sbjct: 160 TQEIFYERPDVLYVSIHGDPRTFYPFFLGFADETGEGEGEGYNLNL 205
>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 = 97.0 bits (242), Expect = 2e-23
Identities = 64/209 (30%), Positives = 94/209 (44%), Gaps = 15/209 (7%)
Query: 23 HPMKPHRLSVINSLILGYGLHKKMQIYRPYKASYHDMCRFHSAEYIDFLHTVSPDKIHEH 82
H P RL I + GL ++ +A ++ HS EYID + + + E
Sbjct: 7 HIECPERLEAILERLTQDGLLERCVKIPAREAEEDEILLVHSQEYIDLVKSTETMEKEE- 65
Query: 83 TKFLCQFASGEDCPIFHG-LYDFCSMYTGASLE--GAIQLNNNCCDIAINWSGGLHHAKK 139
L SG D Y+ + G+++E A+ A+ G HHA +
Sbjct: 66 ---LESLCSGYDSVYLCPSTYEAARLAAGSTIELVKAVMAGKIQNGFALIRPPG-HHAMR 121
Query: 140 SEASGFCYVNDIVIA---ILELLKYHPRVLYIDIDVHHGDGVQDAFYLTDRVMTVSFHKY 196
+EA+G+C N++ IA +E L R+L +D DVHHG G Q FY RV+ S H+Y
Sbjct: 122 NEANGYCIFNNVAIAAKYAIEKLGLK-RILIVDWDVHHGQGTQQGFYEDPRVLYFSIHRY 180
Query: 197 -GGGFFP--CSGDMYEIGAEGGRYYSVNV 222
G F+P D IG G ++VNV
Sbjct: 181 EHGRFWPHLFESDYDYIGVGHGYGFNVNV 209
>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 = 96.6 bits (241), Expect = 3e-23
Identities = 61/210 (29%), Positives = 96/210 (45%), Gaps = 17/210 (8%)
Query: 23 HPMKPHRLSVINSLILGYGLHKKMQIYRPYKASYHDMCRFHSAEYIDF---LHTVSPDKI 79
HP P R+S I GL ++ A+ ++ HS E++D L + P ++
Sbjct: 16 HPECPQRISRIYERHNDLGLLERCLRLPSRLATEDELLLCHSEEHLDEMKSLEKMKPREL 75
Query: 80 HEHTKFLCQFASGEDCPIFHGLYDFCSMYTGASLEG--AIQLNNNCCDIAINWSGGLHHA 137
+ ++ S P Y + G L+ A+ + +AI G HHA
Sbjct: 76 NRLG---KEYDSIYIHP---DSYQCALLAAGCVLQVVEAVLTGESRNGVAIVRPPG-HHA 128
Query: 138 KKSEASGFCYVNDIVIAI-LELLKYHP-RVLYIDIDVHHGDGVQDAFYLTDRVMTVSFHK 195
++ A GFC+ N++ IA KY R+L +D DVHHG+G Q F V+ +S H+
Sbjct: 129 EQDTACGFCFFNNVAIAARYAQKKYGLKRILIVDWDVHHGNGTQHMFESDPSVLYISLHR 188
Query: 196 Y-GGGFFPCS--GDMYEIGAEGGRYYSVNV 222
Y G FFP S G+ +G G ++VN+
Sbjct: 189 YDNGSFFPNSPEGNYDVVGKGKGEGFNVNI 218
>gnl|CDD|212542 cd11600, HDAC_Clr3, Class II Histone deacetylase Clr3 and similar
proteins. Clr3 is a class II Histone deacetylase
Zn-dependent enzyme that catalyzes hydrolysis of an
N(6)-acetyl-lysine residue of a histone to yield a
deacetylated histone (EC 3.5.1.98). Clr3 is the homolog
of the class-II HDAC HdaI in S. cerevisiae, and is
essential for silencing in heterochromatin regions, such
as centromeric regions, ribosomal DNA, the mating-type
region and telomeric loci. Clr3 has also been implicated
in the regulation of stress-related genes; the histone
acetyltransferase, Gcn5, in S. cerevisiae,
preferentially acetylates global histone H3K14 while
Clr3 preferentially deacetylates H3K14ac, and therefore,
interplay between Gcn5 and Clr3 is crucial for the
regulation of many stress-response genes.
Length = 313
Score = 95.1 bits (237), Expect = 8e-23
Identities = 59/219 (26%), Positives = 100/219 (45%), Gaps = 31/219 (14%)
Query: 23 HPMKPHRLSVINSLILGYGLHKKMQIYRPYKASYHDMCRFHSAEYIDF---LHTVSPDKI 79
HP P R+S I + GL +M +A+ ++ HS E+ D +S +++
Sbjct: 3 HPEDPSRISRIFEKLKEAGLINRMLRIPIREATKEEILLVHSEEHWDRVEATEKMSDEQL 62
Query: 80 HEHTKFLCQFASGEDCPIFHGLYDFCSMYTGA---SLEGAIQLNNNCCD------IAINW 130
+ T+ + LY + S GAI+ + A+
Sbjct: 63 KDRTEIFER----------DSLY-VNNDTAFCARLSCGGAIEACRAVAEGRVKNAFAVVR 111
Query: 131 SGGLHHAKKSEASGFCYVNDIVIAILELLKYHP----RVLYIDIDVHHGDGVQDAFYLTD 186
G HHA+ E+ GFC+ N++ +A L +P ++L +D D+HHG+G Q AFY
Sbjct: 112 PPG-HHAEPDESMGFCFFNNVAVAAKWLQTEYPDKIKKILILDWDIHHGNGTQRAFYDDP 170
Query: 187 RVMTVSFHKY-GGGFFPCS--GDMYEIGAEGGRYYSVNV 222
V+ +S H++ GGF+P + GD +G G ++VN+
Sbjct: 171 NVLYISLHRFENGGFYPGTPYGDYESVGEGAGLGFNVNI 209
>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 = 94.7 bits (236), Expect = 3e-22
Identities = 37/91 (40%), Positives = 55/91 (60%), Gaps = 3/91 (3%)
Query: 135 HHAKKSEASGFCYVNDIVIA--ILELLKYHPRVLYIDIDVHHGDGVQDAFYLTDRVMTVS 192
HHA+ S+A GFC+ N + IA L+ ++L +D DVHHG+G Q FY V+ +S
Sbjct: 151 HHAEPSQAMGFCFFNSVAIAAKQLQQKLKLRKILIVDWDVHHGNGTQQIFYEDPNVLYIS 210
Query: 193 FHKY-GGGFFPCSGDMYEIGAEGGRYYSVNV 222
H+Y G FFP +G E+G+ G ++VN+
Sbjct: 211 LHRYDDGNFFPGTGAPTEVGSGAGEGFNVNI 241
>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 = 87.9 bits (219), Expect = 2e-20
Identities = 51/185 (27%), Positives = 73/185 (39%), Gaps = 21/185 (11%)
Query: 23 HPMKPHRLSVINSLILGYGLHKKMQIYRPYKASYHDMCRFHSAEYIDFLHTVSPDKIHEH 82
H + ++ +L GL I P A+ D+ R H EY++ L + +
Sbjct: 1 HRFPMRKYGLLREALLEEGLVLPEDIVEPEPATREDLLRVHDPEYLESLKSGELSREEIR 60
Query: 83 TKFLCQFASGEDCPIFHGLYDFCSMYTGASLEG---AIQLNNNCCDIAINWSGGLHHAKK 139
P L + + G ++ A++ +AIN +GG HHA
Sbjct: 61 RIGF---------PWSPELVERTRLAVGGTILAARLALE-----HGLAINLAGGTHHAFP 106
Query: 140 SEASGFCYVNDIVIAILELLKYHP--RVLYIDIDVHHGDGVQDAFYLTDRVMTVSFHKYG 197
GFC NDI IA LL RVL +D+DVH G+G F V T S H G
Sbjct: 107 DRGEGFCVFNDIAIAARVLLAEGLVRRVLIVDLDVHQGNGTAAIFADDPSVFTFSMH--G 164
Query: 198 GGFFP 202
+P
Sbjct: 165 EKNYP 169
>gnl|CDD|212531 cd10007, HDAC5, Histone deacetylase 5. Histone deacetylase 5 is a
class IIa Zn-dependent enzyme that catalyzes hydrolysis
of an N(6)-acetyl-lysine residue of a histone to yield a
deacetylated histone (EC 3.5.1.98). Histone
acetylation/deacetylation process is important for
mediation of transcriptional regulation of many genes.
Histone deacetylases usually act via association with
DNA binding proteins to target specific chromatin
regions. Class IIa histone deacetylases are
signal-dependent co-repressors, having N-terminal
regulatory domain with two or three conserved serine
residues; phosphorylation of these residues is important
for ability to shuttle between the nucleus and cytoplasm
and act as transcriptional co-repressors. HDAC5 is
involved in integration of chronic drug (cocaine)
addiction and depression with changes in chromatin
structure and gene expression; cocaine regulates HDAC5
function to antagonize the rewarding impact of cocaine,
possibly by blocking drug-stimulated gene expression
that supports drug-induced behavioral change. It is also
involved in regulation of angiogenesis and cell cycle as
well as immune system development. HDAC5 and HDAC9 have
been found to be significantly up-regulated in high-risk
medulloblastoma compared with low-risk and may
potentially be novel drug targets.
Length = 420
Score = 82.3 bits (203), Expect = 9e-18
Identities = 40/92 (43%), Positives = 58/92 (63%), Gaps = 5/92 (5%)
Query: 135 HHAKKSEASGFCYVNDIVIAILELLKYH---PRVLYIDIDVHHGDGVQDAFYLTDRVMTV 191
HHA++S A GFC+ N + IA +LL+ ++L +D D+HHG+G Q AFY V+ +
Sbjct: 154 HHAEESTAMGFCFFNSVAIAA-KLLQQKLNVGKILIVDWDIHHGNGTQQAFYNDPNVLYI 212
Query: 192 SFHKY-GGGFFPCSGDMYEIGAEGGRYYSVNV 222
S H+Y G FFP SG E+GA G ++VN+
Sbjct: 213 SLHRYDDGNFFPGSGAPDEVGAGPGVGFNVNI 244
>gnl|CDD|212532 cd10008, HDAC7, Histone deacetylase 7. Histone deacetylase 7 is a
class IIa Zn-dependent enzyme that catalyzes hydrolysis
of an N(6)-acetyl-lysine residue of a histone to yield a
deacetylated histone (EC 3.5.1.98). Histone
acetylation/deacetylation process is important for
mediation of transcriptional regulation of many genes.
Histone deacetylases usually act via association with
DNA binding proteins to target specific chromatin
regions. Class IIa histone deacetylases are
signal-dependent co-repressors, having N-terminal
regulatory domain with two or three conserved serine
residues; phosphorylation of these residues is important
for ability to shuttle between the nucleus and cytoplasm
and act as transcriptional co-repressors. HDAC7 is
involved in regulation of myocyte migration and
differentiation. Known interaction partners of class IIa
HDAC7 are myocyte enhancer factors - MEF2A, -2C, and
-2D, 14-3-3 proteins, SMRT and N-CoR co-repressors,
HDAC3, ETA (endothelin receptor). This enzyme is also
involved in the development of the immune system as well
as brain and heart development. Multiple alternatively
spliced transcript variants encoding several isoforms
have been found for this gene.
Length = 378
Score = 79.3 bits (195), Expect = 7e-17
Identities = 39/91 (42%), Positives = 54/91 (59%), Gaps = 3/91 (3%)
Query: 135 HHAKKSEASGFCYVNDIVIAI--LELLKYHPRVLYIDIDVHHGDGVQDAFYLTDRVMTVS 192
HHA S A GFC+ N + IA L+ ++L +D DVHHG+G Q FY V+ +S
Sbjct: 152 HHADHSTAMGFCFFNSVAIACRQLQQQGKASKILIVDWDVHHGNGTQQTFYQDPSVLYIS 211
Query: 193 FHKY-GGGFFPCSGDMYEIGAEGGRYYSVNV 222
H++ G FFP SG + E+GA G ++VNV
Sbjct: 212 LHRHDDGNFFPGSGAVDEVGAGSGEGFNVNV 242
>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 = 78.1 bits (192), Expect = 2e-16
Identities = 37/91 (40%), Positives = 54/91 (59%), Gaps = 3/91 (3%)
Query: 135 HHAKKSEASGFCYVNDIVIAILELLKYH--PRVLYIDIDVHHGDGVQDAFYLTDRVMTVS 192
HHA++S A GFC+ N + I L ++L +D+DVHHG+G Q AFY ++ +S
Sbjct: 152 HHAEESTAMGFCFFNSVAITAKYLRDQLNISKILIVDLDVHHGNGTQQAFYADPSILYIS 211
Query: 193 FHKYG-GGFFPCSGDMYEIGAEGGRYYSVNV 222
H+Y G FFP SG E+G G Y++N+
Sbjct: 212 LHRYDEGNFFPGSGAPNEVGTGLGEGYNINI 242
>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 = 77.4 bits (190), Expect = 4e-16
Identities = 39/91 (42%), Positives = 55/91 (60%), Gaps = 3/91 (3%)
Query: 135 HHAKKSEASGFCYVNDIVIA--ILELLKYHPRVLYIDIDVHHGDGVQDAFYLTDRVMTVS 192
HHA++S GFCY N + IA +L+ ++L +D DVHHG+G Q AFY V+ +S
Sbjct: 154 HHAEESTPMGFCYFNSVAIAAKLLQQRLNVSKILIVDWDVHHGNGTQQAFYSDPNVLYMS 213
Query: 193 FHKY-GGGFFPCSGDMYEIGAEGGRYYSVNV 222
H+Y G FFP SG E+G G ++VN+
Sbjct: 214 LHRYDDGNFFPGSGAPDEVGTGPGVGFNVNM 244
>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 = 76.4 bits (188), Expect = 5e-16
Identities = 58/210 (27%), Positives = 87/210 (41%), Gaps = 13/210 (6%)
Query: 21 AKHPMKPHRLSVINSLILGYGLHKKMQIYRPYKASYHDMCRFHSAEYIDFLHTVSPDKIH 80
P P RL I ++ GL ++ + +AS ++ HS EY+ + +
Sbjct: 5 ESFPECPERLHAIREKLIQEGLLERCVSVQAREASEEELLLVHSPEYVALMKSTQYMTEE 64
Query: 81 EHTKFLCQFASGEDCPIFH-GLYDFCSMYTGASLE--GAIQLNNNCCDIAINWSGGLHHA 137
E L A D H Y + G+ L+ + +AI G HHA
Sbjct: 65 E----LRTLADTYDSVYLHPNSYSCACLAVGSVLQLVDKVLGGEIRNGLAIVRPPG-HHA 119
Query: 138 KKSEASGFCYVNDIVIAILELLKYH--PRVLYIDIDVHHGDGVQDAFYLTDRVMTVSFHK 195
+ + G+C N++ IA + H RVL +D DVHHG G Q F V+ S H+
Sbjct: 120 QHDKMDGYCMFNNVAIAARYAQQKHGVQRVLIVDWDVHHGQGTQFIFEQDPSVLYFSIHR 179
Query: 196 Y-GGGFFP--CSGDMYEIGAEGGRYYSVNV 222
Y G F+P D +G G Y++NV
Sbjct: 180 YEQGRFWPHLKESDSSAVGFGRGEGYNINV 209
>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 = 67.2 bits (164), Expect = 8e-13
Identities = 63/244 (25%), Positives = 107/244 (43%), Gaps = 22/244 (9%)
Query: 27 PHRLSVINSLILGYGLHKKMQIYRPYKASYHDMCRFHSAEYIDFLHTVSPDKIHEHTKFL 86
P RL+ + YGL ++ +AS ++ HS EY+ + E
Sbjct: 11 PERLTASYERLRQYGLVQRCLRLPAREASEEEILLVHSPEYLSLVRETQVMNKEELMAIS 70
Query: 87 CQFASGEDCPIFH-GLYDFCSMYTGASLE--GAIQLNNNCCDIAINWSGGLHHAKKSEAS 143
++ D FH + + GA+L+ A+ +A+ G HH++++ A+
Sbjct: 71 GKY----DAVYFHPNTFHCARLAAGATLQLVDAVLTGEVQNGMALVRPPG-HHSQRNAAN 125
Query: 144 GFCYVNDIVIAILELLKYH--PRVLYIDIDVHHGDGVQDAFYLTDRVMTVSFHKY-GGGF 200
GFC N++ IA K + R+L +D DVHHG G+Q F V+ S+H+Y F
Sbjct: 126 GFCVFNNVAIAAEYAKKKYGLHRILIVDWDVHHGQGIQYIFEEDPSVLYFSWHRYEHQRF 185
Query: 201 FPC--SGDMYEIGAEGGRYYSVNVR-NRDLSPHSSHKRMFRERVHSLLPFVF-----VVF 252
+P D +G G +++N+ N+ ++ + F H LLP F +V
Sbjct: 186 WPFLRESDYDAVGRGKGLGFNINLPWNKVGMGNADYLAAF---FHVLLPLAFEFDPELVL 242
Query: 253 FSSG 256
S+G
Sbjct: 243 VSAG 246
>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 = 56.2 bits (136), Expect = 2e-09
Identities = 29/148 (19%), Positives = 43/148 (29%), Gaps = 35/148 (23%)
Query: 124 CDIAINWSGGLHHAKKSEASGFCYVNDIVIAILELLKYHPRVLYIDIDVHHGDGVQDAFY 183
+ + G H+ N + A+ EL HP + ID+D HH +AF
Sbjct: 25 GKVPVVLGG--DHSI---------ANGAIRAVAEL---HPDLGVIDVDAHHDVRTPEAFG 70
Query: 184 --------------LTDRVMTVSFHKYGGGFFPCSGDMYEIGAEGGRYYSVNVRNRDLSP 229
L V VS G GA + V ++
Sbjct: 71 KGNHHTPRHLLCEPLISDVHIVSIGIRGVSNGE------AGGAYARKLGVVYFSMTEVDK 124
Query: 230 HSSHKRMFRERVHSLLPFVFVVFFSSGL 257
+F E V L V+ S +
Sbjct: 125 -LGLGDVFEEIVSYLGDKGDNVYLSVDV 151
>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 = 53.2 bits (128), Expect = 4e-08
Identities = 21/48 (43%), Positives = 30/48 (62%), Gaps = 2/48 (4%)
Query: 135 HHAKKSEASGFCYVNDIVIAILELLKYH--PRVLYIDIDVHHGDGVQD 180
HH +S SGFC+VN++ + H RV+ +DID+HHG+G QD
Sbjct: 120 HHCSESTPSGFCWVNNVHVGAAHAYLTHGITRVVILDIDLHHGNGTQD 167
>gnl|CDD|184936 PRK14973, PRK14973, DNA topoisomerase I; Provisional.
Length = 936
Score = 31.4 bits (71), Expect = 0.63
Identities = 12/39 (30%), Positives = 17/39 (43%), Gaps = 2/39 (5%)
Query: 58 DMCRFHSAEYIDFLHTVSPDKIHEHTKFLCQFASGEDCP 96
D C H Y+ +SP+ I H K +C+ G P
Sbjct: 828 DFCSVH-PAYLALKTGISPETICRHAKLVCE-KLGRPVP 864
>gnl|CDD|222264 pfam13614, AAA_31, AAA domain. This family includes a wide variety
of AAA domains including some that have lost essential
nucleotide binding residues in the P-loop.
Length = 145
Score = 29.9 bits (68), Expect = 0.84
Identities = 17/71 (23%), Positives = 29/71 (40%), Gaps = 14/71 (19%)
Query: 157 ELLKYHPRVLYIDIDVHHGD----------GVQDAFYLTDRVMTVSFHKYGG----GFFP 202
L + P+VLY+D++ + GD G+ D Y R+ ++ GG
Sbjct: 24 SLAEEGPKVLYLDLEEYSGDLALFLGLEPKGLSDLLYYLKRLDSMLIQAMGGLDYLAPPR 83
Query: 203 CSGDMYEIGAE 213
D+ E+ E
Sbjct: 84 NPEDLREVSPE 94
>gnl|CDD|130314 TIGR01247, drrB, daunorubicin resistance ABC transporter membrane
protein. This model describes daunorubicin resistance
ABC transporter, membrane associated protein in bacteria
and archaea. The protein associated with effux of the
drug, daunorubicin. This transport system belong to the
larger ATP-Binding Cassette (ABC) transporter
superfamily. The characteristic feature of these
transporter is the obligatory coupling of ATP hydrolysis
to substrate translocation. The minimal configuration of
bacterial ABC transport system: an ATPase or ATP binding
subunit; An integral membrane protein; a hydrophilic
polypetpide, which likely functions as substrate binding
protein. In eukaryotes proteins of similar function
include p-gyco proteins, multidrug resistance protein
etc [Transport and binding proteins, Other].
Length = 236
Score = 30.1 bits (68), Expect = 0.92
Identities = 14/36 (38%), Positives = 19/36 (52%), Gaps = 4/36 (11%)
Query: 234 KRMFRER---VHSLL-PFVFVVFFSSGLGKLFRFSS 265
KR R R V S+L P ++++FF G FRF
Sbjct: 4 KRFIRSRSRIVGSILNPLLWLIFFGKGWSGAFRFPM 39
>gnl|CDD|99747 cd06454, KBL_like, KBL_like; this family belongs to the pyridoxal
phosphate (PLP)-dependent aspartate aminotransferase
superfamily (fold I). The major groups in this CD
corresponds to serine palmitoyltransferase (SPT),
5-aminolevulinate synthase (ALAS),
8-amino-7-oxononanoate synthase (AONS), and
2-amino-3-ketobutyrate CoA ligase (KBL). SPT is
responsible for the condensation of L-serine with
palmitoyl-CoA to produce 3-ketodihydrospingosine, the
reaction of the first step in sphingolipid biosynthesis.
ALAS is involved in heme biosynthesis; it catalyzes the
synthesis of 5-aminolevulinic acid from glycine and
succinyl-coenzyme A. AONS catalyses the decarboxylative
condensation of l-alanine and pimeloyl-CoA in the first
committed step of biotin biosynthesis. KBL catalyzes the
second reaction step of the metabolic degradation
pathway for threonine converting 2-amino-3-ketobutyrate,
to glycine and acetyl-CoA. The members of this CD are
widely found in all three forms of life.
Length = 349
Score = 30.2 bits (69), Expect = 1.3
Identities = 18/68 (26%), Positives = 35/68 (51%), Gaps = 13/68 (19%)
Query: 154 AILELLKYHPRVLYIDIDVH-------HGDGVQDAFYLTDRV--MTVSFHK-YG--GGFF 201
+++L K + +L++D + H HG GV++ LTD V + + K +G GG+
Sbjct: 153 ELVDLAKKYGAILFVD-EAHSVGVYGPHGRGVEEFGGLTDDVDIIMGTLGKAFGAVGGYI 211
Query: 202 PCSGDMYE 209
S ++ +
Sbjct: 212 AGSKELID 219
>gnl|CDD|181604 PRK08990, PRK08990, flagellar motor protein PomA; Reviewed.
Length = 254
Score = 28.9 bits (65), Expect = 2.6
Identities = 14/38 (36%), Positives = 19/38 (50%), Gaps = 1/38 (2%)
Query: 170 IDVHHGDGVQDAFYLTDRVMTVSFHKYGGGFFPCSGDM 207
+D H GD V+ A D +T H+ G G F GD+
Sbjct: 113 VDGHDGDVVRAAL-EKDIALTEERHETGIGIFRAFGDV 149
>gnl|CDD|192395 pfam09821, ABC_transp, ABC nitrate/sulfonate/bicarbonate family
transporter, ATPase subunit. Members of this family are
found in various prokaryotic ABC transporters,
predominantly involved in nitrate, sulfonate and
bicarbonate translocation.
Length = 120
Score = 27.9 bits (63), Expect = 2.6
Identities = 10/45 (22%), Positives = 20/45 (44%), Gaps = 9/45 (20%)
Query: 204 SGDMYEIGAEGGRYYSVNVRNRDLSPHSSHKRMFRERVHSLLPFV 248
GD+ E+ G R+ ++ R K +F E++ + +P
Sbjct: 31 GGDI-ELTPLGRRFAEADIDER--------KELFAEQLLAHVPLA 66
>gnl|CDD|218685 pfam05673, DUF815, Protein of unknown function (DUF815). This
family consists of several bacterial proteins of unknown
function.
Length = 248
Score = 28.6 bits (65), Expect = 2.9
Identities = 12/39 (30%), Positives = 19/39 (48%), Gaps = 8/39 (20%)
Query: 171 DVHHGDGVQDAFYLTDRV-MTVSFHKYGGGFFPCSGDMY 208
++H GD V++ L+DR + + FH P D Y
Sbjct: 167 EIHPGDAVEEKLSLSDRFGLWLGFH-------PFDQDEY 198
>gnl|CDD|238215 cd00361, arom_aa_hydroxylase, Biopterin-dependent aromatic amino
acid hydroxylase; a family of non-heme,
iron(II)-dependent enzymes that includes prokaryotic and
eukaryotic phenylalanine-4-hydroxylase (PheOH),
eukaryotic tyrosine hydroxylase (TyrOH) and eukaryotic
tryptophan hydroxylase (TrpOH). PheOH converts
L-phenylalanine to L-tyrosine, an important step in
phenylalanine catabolism and neurotransmitter
biosynthesis, and is linked to a severe variant of
phenylketonuria in humans. TyrOH and TrpOH are involved
in the biosynthesis of catecholamine and serotonin,
respectively. The eukaryotic enzymes are all
homotetramers.
Length = 221
Score = 28.3 bits (64), Expect = 3.9
Identities = 8/25 (32%), Positives = 11/25 (44%), Gaps = 4/25 (16%)
Query: 61 RFHSAEYI----DFLHTVSPDKIHE 81
F +YI + +T PD HE
Sbjct: 84 VFPVTQYIRHPEEPDYTPEPDIFHE 108
>gnl|CDD|217595 pfam03514, GRAS, GRAS family transcription factor. Sequence
analysis of the products of the GRAS (GAI, RGA, SCR)
gene family indicates that they share a variable
amino-terminus and a highly conserved carboxyl-terminus
that contains five recognisable motifs. Proteins in the
GRAS family are transcription factors that seem to be
involved in development and other processes. Mutation of
the SCARECROW (SCR) gene results in a radial pattern
defect, loss of a ground tissue layer, in the root. The
PAT1 protein is involved in phytochrome A signal
transduction.
Length = 372
Score = 28.4 bits (64), Expect = 4.2
Identities = 10/22 (45%), Positives = 12/22 (54%)
Query: 154 AILELLKYHPRVLYIDIDVHHG 175
AILE + RV ID D+ G
Sbjct: 101 AILEAFEGEERVHIIDFDIGQG 122
>gnl|CDD|132082 TIGR03037, anthran_nbaC, 3-hydroxyanthranilate 3,4-dioxygenase.
Members of this protein family, from both bacteria and
eukaryotes, are the enzyme 3-hydroxyanthranilate
3,4-dioxygenase. This enzyme acts on the tryptophan
metabolite 3-hydroxyanthranilate and produces
2-amino-3-carboxymuconate semialdehyde, which can
rearrange spontaneously to quinolinic acid and feed into
nicotinamide biosynthesis, or undergo further enzymatic
degradation.
Length = 159
Score = 27.4 bits (61), Expect = 5.3
Identities = 13/37 (35%), Positives = 17/37 (45%), Gaps = 3/37 (8%)
Query: 200 FFPCSGDMYEIGAEGGRYYSVNVRNRD---LSPHSSH 233
F+ G+MY E G+ V +R D L PH H
Sbjct: 52 FYQLKGEMYLKVTEEGKREDVPIREGDIFLLPPHVPH 88
>gnl|CDD|216704 pfam01793, Glyco_transf_15, Glycolipid 2-alpha-mannosyltransferase.
This is a family of alpha-1,2 mannosyl-transferases
involved in N-linked and O-linked glycosylation of
proteins. Some of the enzymes in this family have been
shown to be involved in O- and N-linked glycan
modifications in the Golgi.
Length = 273
Score = 27.8 bits (63), Expect = 6.6
Identities = 7/12 (58%), Positives = 8/12 (66%)
Query: 53 KASYHDMCRFHS 64
SY MCRF+S
Sbjct: 98 SESYRHMCRFNS 109
>gnl|CDD|185765 cd09242, BRO1_ScBro1_like, Protein-interacting, N-terminal,
Bro1-like domain of Saccharomyces cerevisiae Bro1 and
related proteins. This family contains the N-terminal,
Bro1-like domain of Saccharomyces cerevisiae Bro1 and
related proteins. It belongs to the BRO1_Alix_like
superfamily which also includes the Bro1-like domains of
mammalian Alix (apoptosis-linked gene-2 interacting
protein X), His-Domain type N23 protein tyrosine
phosphatase (HD-PTP, also known as PTPN23), RhoA-binding
proteins Rhophilin-1 and -2, Brox, Saccharomyces
cerevisiae Rim20 (also known as PalA), Ustilago maydis
Rim23 (also known as PalC), and related domains. Alix,
HD-PTP, Brox, Bro1, Rim20, and Rim23, interact with the
ESCRT (Endosomal Sorting Complexes Required for
Transport) system. Bro1 participates in endosomal
trafficking. Bro1-like domains are boomerang-shaped, and
part of the domain is a tetratricopeptide repeat
(TPR)-like structure. Bro1-like domains bind components
of the ESCRT-III complex: Snf7 in the case of Bro1. Snf7
binds to a conserved hydrophobic patch on the middle of
the concave side of the Bro1 domain. RIM20, and some
other members of the BRO1_Alix_like superfamily
including Alix, also have a V-shaped (V) domain. In the
case of Alix, the V-domain contains a binding site for
the retroviral late assembly (L) domain YPXnL motif,
which is partially conserved in the superfamily. The
Alix V-domain is also a dimerization domain. The
C-terminal portion (V-domain and proline rich-region) of
Bro1 interacts with Doa4, a protease that
deubiquitinates integral membrane proteins sorted into
the lumenal vesicles of late-endosomal multivesicular
bodies. It interacts with a YPxL motif in the Doa4
catalytic domain to stimulate its deubiquitination
activity.
Length = 348
Score = 27.6 bits (62), Expect = 8.6
Identities = 12/38 (31%), Positives = 18/38 (47%), Gaps = 3/38 (7%)
Query: 52 YKASYHDM-CRFHSAEYI--DFLHTVSPDKIHEHTKFL 86
K + ++ +YI +FLH S D E+ KFL
Sbjct: 132 LKEAITNLQQAAGCFQYINENFLHAPSVDLQQENVKFL 169
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
0.327 0.141 0.453
Gapped
Lambda K H
0.267 0.0721 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,611,218
Number of extensions: 1392956
Number of successful extensions: 1620
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1562
Number of HSP's successfully gapped: 55
Length of query: 285
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 189
Effective length of database: 6,679,618
Effective search space: 1262447802
Effective search space used: 1262447802
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 58 (26.1 bits)