RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 019524
(339 letters)
>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 = 354 bits (911), Expect = e-123
Identities = 109/267 (40%), Positives = 144/267 (53%), Gaps = 9/267 (3%)
Query: 54 HPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIE 113
H F K+G + + L EG + IVEP A++EDLL VH YL+SL+S + E
Sbjct: 1 HRFPMRKYGLLREALLEEGLVLPEDIVEPEPATREDLLRVHDPEYLESLKSG---ELSRE 57
Query: 114 VPPVALFPNCLVQRKVLYPFRKQVGGTILAAKLAKERGWAINVGGGFHHCSADEGGGFCA 173
FP +++ R VGGTILAA+LA E G AIN+ GG HH D G GFC
Sbjct: 58 EIRRIGFPWSP---ELVERTRLAVGGTILAARLALEHGLAINLAGGTHHAFPDRGEGFCV 114
Query: 174 YADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRVYILDMFNPGIYPRDYEA 233
+ DI++ + + RV+I+DLD HQGNG F+ D V+ M YP
Sbjct: 115 FNDIAIAARVLLAEGLVRRVLIVDLDVHQGNGTAAIFADDPSVFTFSMHGEKNYPFR--- 171
Query: 234 RRFIDQKVEVVSGTTTNEYLKKLDEALEVAGHTFDPELVIYNAGTDILEGDPLGMLKISP 293
+ D V + GT +EYL L+EAL F P+LV YNAG D+L GD LG L +S
Sbjct: 172 KEPSDLDVPLPDGTGDDEYLAALEEALPRLLAEFRPDLVFYNAGVDVLAGDRLGRLSLSL 231
Query: 294 DGIAARDEKTFRFARSRNIPIVMLTSG 320
+G+ RD RFAR+R IP+ M+ G
Sbjct: 232 EGLRERDRLVLRFARARGIPVAMVLGG 258
>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 = 222 bits (568), Expect = 5e-71
Identities = 79/278 (28%), Positives = 124/278 (44%), Gaps = 14/278 (5%)
Query: 53 LHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIII 112
HP + + I + L G LD+ + P A++E+LL+VHS Y++ L+ +
Sbjct: 8 GHPENPERLEAILELLKESGLLDRLEFIAPRPATEEELLLVHSPEYVEFLEEA--SLEEE 65
Query: 113 EVPPVALFPNCLVQRKVLYPFRKQVGGTILAAKLA---KERGWAINVGGGFHHCSADEGG 169
E+ + L + V GGT+ AA L + A+ G HH D
Sbjct: 66 ELGRIGLDGDTPVSPGSYEAALLAAGGTLEAADLVLSGENAFAAVRPPG--HHAERDRAS 123
Query: 170 GFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRVYILDMFNPGIYP- 228
GFC + ++++ Y + + RV+I+DLD H GNG ++ F D RV + + YP
Sbjct: 124 GFCLFNNVAIAARYLLKRYGLKRVLIVDLDVHHGNGTQEIFYDDPRVLTISIHQDPFYPG 183
Query: 229 ------RDYEARRFIDQKVEVVSGTTTNEYLKKLDEALEVAGHTFDPELVIYNAGTDILE 282
A + + GT EYL +E L A F P+L++ +AG D
Sbjct: 184 TGFADETGEGAGEGYTLNIPLPPGTGDEEYLAAFEEILLPALREFQPDLILVSAGFDAHA 243
Query: 283 GDPLGMLKISPDGIAARDEKTFRFARSRNIPIVMLTSG 320
GDPLG L ++ +G A R A + P+V + G
Sbjct: 244 GDPLGGLNLTTEGYAERTRLLLELADAYGGPVVSVLEG 281
>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 = 216 bits (552), Expect = 6e-69
Identities = 92/276 (33%), Positives = 129/276 (46%), Gaps = 8/276 (2%)
Query: 60 KWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVAL 119
+ + + L G K ++E EA++E LL VH+E YL L+++ V+ I E PV
Sbjct: 1 RIRDLIEALKELGLRPKIELIECREATEELLLKVHTEEYLNELKANFAVATITESKPVIF 60
Query: 120 FPNCLVQRKVLYPFRKQVGGTILAAKLA----KERGWAINVGGGFHHCSADEGGGFCAYA 175
PN VQR R GG + AA+L ER +A+ VG G HH GFC +
Sbjct: 61 GPNFPVQRHYFRGARLSTGGVVEAAELVAKGELERAFAV-VGAGGHHAGKSRAWGFCYFN 119
Query: 176 DISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRVYILDMFNPGIYPRDYEARR 235
D+ L I + + ISR++IID DAH G+G + F D RV + N IYP +
Sbjct: 120 DVVLAIKFLR-ERGISRILIIDTDAHHGDGTREAFYDDDRVLHMSFHNYDIYPFGRGKGK 178
Query: 236 FIDQKVEVVSGTTTNEYLKKLDEALEVAGHTFDPELVIYNAGTDILEGDPLGMLKISPDG 295
V + G EYL ++ + F+PE+V+ G D EGD LG +S G
Sbjct: 179 GYKINVPLEDGLGDEEYLDAVERVISKVLEEFEPEVVVLQFGHDTHEGDRLGGFNLSEKG 238
Query: 296 IAARDEKTFRFARSRNIPIVMLTSGPITSEKVLALW 331
E FAR PI+M+ G E +W
Sbjct: 239 FVKLAEIVKEFARGG--PILMVLGGGYNPEAAARIW 272
>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 = 165 bits (420), Expect = 2e-48
Identities = 81/299 (27%), Positives = 120/299 (40%), Gaps = 24/299 (8%)
Query: 32 IFKLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLL 91
+ K LIY P++ HP + + I + L S G D +VEP A+ E+LL
Sbjct: 1 MMKTALIYHPEFLEHEPP--PGHPENPDRLRLILELLESSGLPDSLELVEPRPATLEELL 58
Query: 92 VVHSESYLKSLQS-SPNVSIIIEVPPVALFPNCLVQRKVLYPFRKQVGGTILAAKLAKE- 149
+VHS Y++ L+S S + P + L GG + A E
Sbjct: 59 LVHSPDYVEFLESLSEEEGYGNLDGDTPVSPG-TYEAARLA-----AGGALTAVDAVLEG 112
Query: 150 -RGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEK 208
V HH D GFC + ++++ Y + + RV IID D H GNG ++
Sbjct: 113 EDNAFALVRPPGHHAGRDRASGFCLFNNVAIAAKYLLKK-GVKRVAIIDFDVHHGNGTQE 171
Query: 209 DFSSDSRVYILDMFNPGIYPRDYEARRFIDQKVEVVSGTTTN----------EYLKKLDE 258
F D V + + Y D+ E G N YL+ L+E
Sbjct: 172 IFYDDDDVLTVSLH--QDGRPFYPGTGGADEIGEGKEGNNVNIPLPPGTGDDSYLEALEE 229
Query: 259 ALEVAGHTFDPELVIYNAGTDILEGDPLGMLKISPDGIAARDEKTFRFARSRNIPIVML 317
+ F P+LVI +AG D GDPLG L ++ +G A + A P+V +
Sbjct: 230 IVLPLLEEFKPDLVIVSAGFDAHRGDPLGRLNLTEEGYAKIGRAVRKLAEGYGGPVVAV 288
>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 = 125 bits (317), Expect = 1e-33
Identities = 76/294 (25%), Positives = 119/294 (40%), Gaps = 55/294 (18%)
Query: 37 LIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSE 96
IYS +Y G HPF+ + L + G L +V P A++E+LL+ H+
Sbjct: 2 FIYSEEYLRYSFG--PNHPFNPPRLSLTKDLLRALGLLPPVDLVPPRPATEEELLLFHTP 59
Query: 97 SYLKSLQSSPNVSIIIEVPPVAL-------FPNC-----LVQRKVLYPFRKQVGGTILAA 144
Y+++++ + + L FP LV VGGT+LAA
Sbjct: 60 DYIEAVKEASRGQEPEGRGRLGLGTEDNPVFPGMHEAAALV-----------VGGTLLAA 108
Query: 145 KL--AKERGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQ 202
+L E A N GG HH GFC Y D ++ I RV +D+DAH
Sbjct: 109 RLVLEGEARRAFNPAGGLHHAMRGRASGFCVYNDAAVAIERL-RDKGGLRVAYVDIDAHH 167
Query: 203 GNGHEKDFSSDSRVYILDMFNPGIYPRDYEARR-------FIDQK-----------VEVV 244
G+G + F D RV + + +E+ R F+D+ + +
Sbjct: 168 GDGVQAAFYDDPRVLTISL---------HESGRYLFPGTGFVDEIGEGEGYGYAVNIPLP 218
Query: 245 SGTTTNEYLKKLDEALEVAGHTFDPELVIYNAGTDILEGDPLGMLKISPDGIAA 298
GT +E+L+ + + F P++++ G D GDPL L +S A
Sbjct: 219 PGTGDDEFLRAFEAVVPPLLRAFRPDVIVSQHGADAHAGDPLTHLNLSNRAYRA 272
>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 = 117 bits (294), Expect = 5e-30
Identities = 73/252 (28%), Positives = 115/252 (45%), Gaps = 31/252 (12%)
Query: 68 LSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVA--------- 118
+ + G L + +V+P A++E+L HS+ Y++ L+ + N E P
Sbjct: 30 IEAYGLLKQLRVVKPRVATEEELASFHSDEYIQFLKKASNEGDNDEEPSEQQEFGLGYDC 89
Query: 119 -LFPNCLVQRKVLYPFRKQVGG-TILAAKL--AKERGWAINVGGGFHHCSADEGGGFCAY 174
+F +Y + V G T+ AA+L + AIN GG+HH DE GFC
Sbjct: 90 PIFEG-------IYDYAAAVAGATLTAAQLLIDGKCKVAINWFGGWHHAQRDEASGFCYV 142
Query: 175 ADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRVYILDM--FNPGIYP---- 228
DI L I ++ RV+ +DLD H G+G E FS S+V + + ++PG +P
Sbjct: 143 NDIVLGILK--LREKFDRVLYVDLDLHHGDGVEDAFSFTSKVMTVSLHKYSPGFFPGTGD 200
Query: 229 -RDY-EAR-RFIDQKVEVVSGTTTNEYLKKLDEALEVAGHTFDPELVIYNAGTDILEGDP 285
D + ++ V + G +YL+ + F PE V+ G D L GDP
Sbjct: 201 VSDVGLGKGKYYTVNVPLRDGIQDEQYLQIFTAVVPEIVAAFRPEAVVLQCGADTLAGDP 260
Query: 286 LGMLKISPDGIA 297
+G ++P GI
Sbjct: 261 MGAFNLTPVGIG 272
>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 = 112 bits (282), Expect = 9e-29
Identities = 99/329 (30%), Positives = 134/329 (40%), Gaps = 61/329 (18%)
Query: 38 IYSPDYDISFLGIEKLHPFDSSKWGRIC---QFLSSEGFLDKNCIVEPLEASKEDLLVVH 94
Y PD + G + HP K RI + S G K I P A+ E+L H
Sbjct: 1 FYDPDVGNYYYG--QGHP---MKPHRIRMTHSLILSYGLYKKMEIYRPRPATAEELTKFH 55
Query: 95 SESYLKSLQSSP--------------NVSIIIEVPPVALFPNCLVQRKVLYPF-RKQVGG 139
S+ Y+ L+S NV E PV F LY + + GG
Sbjct: 56 SDDYIDFLRSVSPDNMKEFKKQLERFNVG---EDCPV--FDG-------LYEYCQLYAGG 103
Query: 140 TILAA-KLAK-ERGWAINVGGGFHHCSADEGGGFCAYADISLCI-----HYAFVQLNISR 192
+I AA KL + + AIN GG HH E GFC DI L I ++ R
Sbjct: 104 SIAAAVKLNRGQADIAINWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQ-------R 156
Query: 193 VMIIDLDAHQGNGHEKDFSSDSRVYIL------DMFNPGIYPRDYEAR--RFIDQKVEVV 244
V+ ID+D H G+G E+ F + RV + + F PG RD A ++ V +
Sbjct: 157 VLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKFGEYFFPGTGLRDIGAGKGKYYAVNVPLK 216
Query: 245 SGTTTNEYLKKLDEALEVAGHTFDPELVIYNAGTDILEGDPLGMLKISPDGIAARDEKTF 304
G YL+ + L F P V+ G D L GD LG +S G A K
Sbjct: 217 DGIDDESYLQIFEPVLSKVMEVFQPSAVVLQCGADSLAGDRLGCFNLSIKGHA----KCV 272
Query: 305 RFARSRNIPIVMLTSGPITSEKVLALWSI 333
+F +S NIP+++L G T V W+
Sbjct: 273 KFVKSFNIPLLVLGGGGYTLRNVARCWTY 301
>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 = 105 bits (264), Expect = 3e-26
Identities = 73/257 (28%), Positives = 104/257 (40%), Gaps = 38/257 (14%)
Query: 63 RICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVALFPN 122
I + L EG LD+ VEP A++E+LL VH+ Y++ ++ E L P+
Sbjct: 10 AILEALEEEGLLDRLVFVEPRPATEEELLRVHTPEYIERVEE------TCEAGGGYLDPD 63
Query: 123 CLVQRKVLYPFRKQVGGTILAAKLAKERGWAINVGGGF-------HHCSADEGGGFCAYA 175
V G + A G A N F HH D GFC +
Sbjct: 64 TYVSPGSYEAALLAAGAALAAVDAV-LSGEAEN---AFALVRPPGHHAEPDRAMGFCLFN 119
Query: 176 DISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRVYILDMFNPGIYPRDYEARR 235
++++ YA + + RV+I+D D H GNG + F D V + YP A
Sbjct: 120 NVAIAARYAQKRYGLKRVLIVDWDVHHGNGTQDIFYDDPSVLYFSIHQYPFYPGTGAAE- 178
Query: 236 FIDQKVEVVS----GTTTN----------EYLKKLDEALEVAGHTFDPELVIYNAGTDIL 281
E G T N EYL +E L F P+LV+ +AG D
Sbjct: 179 ------ETGGGAGEGFTINVPLPPGSGDAEYLAAFEEVLLPIAREFQPDLVLVSAGFDAH 232
Query: 282 EGDPLGMLKISPDGIAA 298
GDPLG + ++P+G A
Sbjct: 233 RGDPLGGMNLTPEGYAR 249
>gnl|CDD|240374 PTZ00346, PTZ00346, histone deacetylase; Provisional.
Length = 429
Score = 94.7 bits (235), Expect = 1e-21
Identities = 87/310 (28%), Positives = 139/310 (44%), Gaps = 27/310 (8%)
Query: 39 YSPDYDIS-FLGIEKLHPFDSSKWGRICQFLSSEGFLDKNC--IVEPLEASKEDLLVVHS 95
Y+ D +IS F+ + P+ I + L +D +C +V PL E+L+ H+
Sbjct: 30 YASDMNISAFVPQHAMKPYRVLAAMEIVRSLK----IDAHCRTVVPPL-VKVEELMAYHT 84
Query: 96 ESYLKSLQSSPNVSII--IEVPPVALFPNCLVQRKVLYPFRKQVGGTILAAKL--AKERG 151
++YL +L S + E V +C ++ GT++ A L + +
Sbjct: 85 DTYLANLGLHSCRSWLWNAETSKVFFSGDCPPVEGLMEHSIATASGTLMGAVLLNSGQVD 144
Query: 152 WAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFS 211
A++ GGG HH E GFC DI L I ++ + RV+ +D+D H G+G ++ F
Sbjct: 145 VAVHWGGGMHHSKCGECSGFCYVNDIVLGI-LELLKCH-DRVLYVDIDMHHGDGVDEAFC 202
Query: 212 SDSRVYILDM------FNPGI-YPRD--YEARRFIDQKVEVVSGTTTNEYLKKLDEALEV 262
+ RV+ L + F PG +PRD Y R+ + V G T YL + AL
Sbjct: 203 TSDRVFTLSLHKFGESFFPGTGHPRDVGYGRGRYYSMNLAVWDGITDFYYLGLFEHALHS 262
Query: 263 AGHTFDPELVIYNAGTDILEGDPLGMLKISPDGIAARDEKTFRFARSRNIPIVMLTSGPI 322
+ P+ ++ G D L GD LG+L +S G + + R IP++ L G
Sbjct: 263 IVRRYSPDAIVLQCGADSLAGDRLGLLNLSSFGHG----QCVQAVRDLGIPMLALGGGGY 318
Query: 323 TSEKVLALWS 332
T V LW+
Sbjct: 319 TIRNVAKLWA 328
>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 = 85.6 bits (212), Expect = 5e-19
Identities = 77/278 (27%), Positives = 108/278 (38%), Gaps = 41/278 (14%)
Query: 79 IVEPLEASKEDLLVVHSESYLKSL-QSSP---NVSIIIEVPPVALFPNCLVQRKVLYPFR 134
E A++E+L H YL L + SP N + P + +C V +Y +
Sbjct: 43 TYEARAATREELRQFHDADYLDFLSKVSPENANQLRFDKAEPFNIGDDCPVFDG-MYDYC 101
Query: 135 KQVGGTILAA--KL-AKERGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNI- 190
+ G L A KL + + AIN GG HH E GFC DI L I LN+
Sbjct: 102 QLYAGASLDAARKLCSGQSDIAINWSGGLHHAKKSEASGFCYVNDIVLAI------LNLL 155
Query: 191 ---SRVMIIDLDAHQGNGHEKDFSSDSRVYILDM------FNPG--------IYPRDYEA 233
RV+ ID+D H G+G E+ F RV L F PG P + A
Sbjct: 156 RYFPRVLYIDIDVHHGDGVEEAFYRTDRVMTLSFHKYNGEFFPGTGDLDDNGGTPGKHFA 215
Query: 234 RRFIDQKVEVVSGTTTNEYLKKLDEALEVAGHTFDPELVIYNAGTDILEGDPLGMLKISP 293
V + G +Y + F P ++ G D L GD LG ++
Sbjct: 216 -----LNVPLEDGIDDEQYNLLFKSIIGPTIEKFQPSAIVLQCGADSLGGDRLGQFNLN- 269
Query: 294 DGIAARDEKTFRFARSRNIPIVMLTSGPITSEKVLALW 331
I A +F +S IP++++ G T V W
Sbjct: 270 --IKAHGA-CVKFVKSFGIPMLVVGGGGYTPRNVARAW 304
>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 = 85.0 bits (211), Expect = 8e-19
Identities = 58/232 (25%), Positives = 88/232 (37%), Gaps = 38/232 (16%)
Query: 74 LDKNC--IVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVALFPNCLVQRKVLY 131
L ++ I+EP A+++DL H + Y+ L L +C
Sbjct: 34 LLQHFDEIIEPERATRKDLTKYHDKDYVDFLLKK-----------YGLEDDC-------P 75
Query: 132 PF-------RKQVGGTILAAKLAK---ERGWAINVGGGFHHCSADEGGGFCAYADISLCI 181
F + G ++ AK ER AIN GG HH GFC DI L I
Sbjct: 76 VFPFLSMYVQLVAGSSLALAKHLITQVERDIAINWYGGRHHAQKSRASGFCYVNDIVLAI 135
Query: 182 HYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRVYILD--MFNPGIYP----RDYEARR 235
+ RV +DLD H G+G E F V ++PG +P + +
Sbjct: 136 L-RLRRARFRRVFYLDLDLHHGDGVESAFFFSKNVLTCSIHRYDPGFFPGTGSLKNSSDK 194
Query: 236 FIDQKVEVVSGTTTNEYLKKLDEALEVAGHTFDPELVIYNAGTDILEGDPLG 287
+ + G + L+ +D + F+PE+++ G D L GDP
Sbjct: 195 G-MLNIPLKRGLSDKTLLRIIDSIVRPLIEKFEPEVIVIQCGCDGLSGDPHK 245
>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 = 85.5 bits (212), Expect = 1e-18
Identities = 68/273 (24%), Positives = 112/273 (41%), Gaps = 36/273 (13%)
Query: 51 EKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSI 110
+ HP + RI + + G L++ + A++++LL+ HSE +L ++S +
Sbjct: 13 DPGHPECPQRISRIYERHNDLGLLERCLRLPSRLATEDELLLCHSEEHLDEMKSLEKMK- 71
Query: 111 IIEVPPVALFP-----NCLVQRKVLYPFRKQVGGTILAAKLAKERGWAINVGGGF----- 160
P L + + Y G +L A G + N G
Sbjct: 72 -----PRELNRLGKEYDSIYIHPDSYQCALLAAGCVLQVVEAVLTGESRN-GVAIVRPPG 125
Query: 161 HHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRVYILD 220
HH D GFC + ++++ YA + + R++I+D D H GNG + F SD V +
Sbjct: 126 HHAEQDTACGFCFFNNVAIAARYAQKKYGLKRILIVDWDVHHGNGTQHMFESDPSVLYIS 185
Query: 221 MF---NPGIYPRDYEARRFIDQKVEVVSGTTTN-------------EYLKKLDEALEVAG 264
+ N +P E V G N EY+ + +
Sbjct: 186 LHRYDNGSFFPNSPEGNY---DVVGKGKGEGFNVNIPWNKGGMGDAEYIAAFQQVVLPIA 242
Query: 265 HTFDPELVIYNAGTDILEGDPLGMLKISPDGIA 297
+ F+PELV+ +AG D GDPLG K++P+G A
Sbjct: 243 YEFNPELVLVSAGFDAARGDPLGGCKVTPEGYA 275
>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 = 85.5 bits (211), Expect = 1e-18
Identities = 86/312 (27%), Positives = 132/312 (42%), Gaps = 19/312 (6%)
Query: 34 KLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVV 93
K + Y D D+ + HP + L + G K I P +A+ E++
Sbjct: 5 KKKVCYYYDGDVGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKANAEEMTKY 64
Query: 94 HSESYLKSLQS--SPNVS-IIIEVPPVALFPNCLVQRKVLYPFRKQVGGTILAA-KLAKE 149
HS+ Y+K L+S N+S ++ + +C V + + GG++ +A KL K+
Sbjct: 65 HSDDYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSAGGSVASAVKLNKQ 124
Query: 150 R-GWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEK 208
+ A+N GG HH E GFC DI L I ++ + RV+ ID+D H G+G E+
Sbjct: 125 QTDIAVNWAGGLHHAKKSEASGFCYVNDIVLAI-LELLKYH-QRVLYIDIDIHHGDGVEE 182
Query: 209 DFSSDSRVYILDMFNPGIY-P-----RDYEA--RRFIDQKVEVVSGTTTNEYLKKLDEAL 260
F + RV + G Y P RD A ++ + G Y +
Sbjct: 183 AFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNYPLRDGIDDESYEAIFKPVM 242
Query: 261 EVAGHTFDPELVIYNAGTDILEGDPLGMLKISPDGIAARDEKTFRFARSRNIPIVMLTSG 320
F P V+ G D L GD LG ++ G A K F +S N+P++ML G
Sbjct: 243 SKVMEMFQPSAVVLQCGADSLSGDRLGCFNLTIKGHA----KCVEFVKSFNLPMLMLGGG 298
Query: 321 PITSEKVLALWS 332
T V W+
Sbjct: 299 GYTIRNVARCWT 310
>gnl|CDD|212545 cd11682, HDAC6-dom1, Histone deacetylase 6, domain 1. Histone
deacetylases 6 are class IIb Zn-dependent enzymes that
catalyze hydrolysis of N(6)-acetyl-lysine of a histone
to yield a deacetylated histone (EC 3.5.1.98). Histone
acetylation/deacetylation process is important for
mediation of transcriptional regulation of many genes.
HDACs usually act via association with DNA binding
proteins to target specific chromatin regions. HDAC6 is
the only histone deacetylase with internal duplication
of two catalytic domains which appear to function
independently of each other, and also has a C-terminal
ubiquitin-binding domain. It is located in the cytoplasm
and associates with microtubule motor complex,
functioning as the tubulin deacetylase and regulating
microtubule-dependent cell motility. Known interaction
partners of HDAC6 are alpha tubulin (substrate) and
ubiquitin-like modifier FAT10 (also known as Ubiquitin D
or UBD).
Length = 337
Score = 84.9 bits (210), Expect = 1e-18
Identities = 71/261 (27%), Positives = 104/261 (39%), Gaps = 46/261 (17%)
Query: 68 LSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVS------IIIEVPPVALFP 121
L EG L++ V+ EAS+E+LL+VHS Y+ ++S+ ++ + V L P
Sbjct: 21 LIQEGLLERCVSVQAREASEEELLLVHSPEYVALMKSTQYMTEEELRTLADTYDSVYLHP 80
Query: 122 N-----CLVQRKVLYPFRKQVGGTILAAKLAKERGWAINVGGGFHHCSADEGGGFCAYAD 176
N CL VL K +GG I G AI G HH D+ G+C + +
Sbjct: 81 NSYSCACLAVGSVLQLVDKVLGGEI-------RNGLAIVRPPG-HHAQHDKMDGYCMFNN 132
Query: 177 ISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRVYILDMFNPGIYPRDYEARRF 236
+++ YA + + RV+I+D D H G G + F D V + YE RF
Sbjct: 133 VAIAARYAQQKHGVQRVLIVDWDVHHGQGTQFIFEQDPSVLYFSIHR-------YEQGRF 185
Query: 237 IDQKVEVVSGTTTNE--------------------YLKKLDEALEVAGHTFDPELVIYNA 276
E S Y+ L F P+LV+ A
Sbjct: 186 WPHLKESDSSAVGFGRGEGYNINVPWNQVGMRDADYIAAFLHVLLPVALEFQPQLVLVAA 245
Query: 277 GTDILEGDPLGMLKISPDGIA 297
G D + GDP G + +P A
Sbjct: 246 GFDAVIGDPKGEMAATPACFA 266
>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 = 83.8 bits (208), Expect = 4e-18
Identities = 61/257 (23%), Positives = 101/257 (39%), Gaps = 43/257 (16%)
Query: 63 RICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYL---KSLQSSPNVSIIIEVPPVAL 119
RI L G D ++ P A+ E+LL VH+ Y+ K+ ++ E
Sbjct: 42 RIKNLLEVSGLSDHLVLITPRPATDEELLRVHTPEYIDRVKAASAAGGG----EAGGGTP 97
Query: 120 FPN------CLVQRKVLYPFRKQVGGTILAAKLAKE----RGWAINVGGGFHHCSADEGG 169
F L GG I A + +A+ G HH D+G
Sbjct: 98 FGPGSYEIALL-----------AAGGAIAAVDAVLDGEVDNAYALVRPPG-HHAEPDQGM 145
Query: 170 GFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRVYILDMFNPGIYPR 229
GFC + ++++ +A + RV ++D D H GNG + F D V + + +P
Sbjct: 146 GFCLFNNVAIAARHALAVGGVKRVAVVDWDVHHGNGTQAIFYDDPDVLTISLHQDRCFPP 205
Query: 230 DYEARRFIDQK-----------VEVVSGTTTNEYLKKLDEALEVAGHTFDPELVIYNAGT 278
D ++++ + + G+ YL + + A F PEL+I +G
Sbjct: 206 DSG---AVEERGEGAGEGYNLNIPLPPGSGDGAYLHAFERIVLPALRAFRPELIIVASGF 262
Query: 279 DILEGDPLGMLKISPDG 295
D DPLG + ++ DG
Sbjct: 263 DASAFDPLGRMMLTSDG 279
>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 = 82.4 bits (204), Expect = 8e-18
Identities = 75/270 (27%), Positives = 121/270 (44%), Gaps = 32/270 (11%)
Query: 54 HPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSI--I 111
HP D S+ RI + L G +++ + EA+KE++L+VHSE + ++++ +S +
Sbjct: 3 HPEDPSRISRIFEKLKEAGLINRMLRIPIREATKEEILLVHSEEHWDRVEATEKMSDEQL 62
Query: 112 IEVPPVALFPNCLVQRKVLYPFRKQVGGTILAAKLAKERGWAINVGGGF-------HHCS 164
+ + + V + R GG I A + A G V F HH
Sbjct: 63 KDRTEIFERDSLYVNNDTAFCARLSCGGAIEACR-AVAEG---RVKNAFAVVRPPGHHAE 118
Query: 165 ADEGGGFCAYADISLCIHYAFVQLN----ISRVMIIDLDAHQGNGHEKDFSSDSRV-YI- 218
DE GFC + ++ + ++Q I +++I+D D H GNG ++ F D V YI
Sbjct: 119 PDESMGFCFFNNV--AVAAKWLQTEYPDKIKKILILDWDIHHGNGTQRAFYDDPNVLYIS 176
Query: 219 LDMF-NPGIYP-RDYEARRFIDQ------KVEV---VSGTTTNEYLKKLDEALEVAGHTF 267
L F N G YP Y + + V + G +Y+ + + F
Sbjct: 177 LHRFENGGFYPGTPYGDYESVGEGAGLGFNVNIPWPQGGMGDADYIYAFQRIVMPIAYEF 236
Query: 268 DPELVIYNAGTDILEGDPLGMLKISPDGIA 297
DP+LVI +AG D +GD LG ++P G A
Sbjct: 237 DPDLVIISAGFDAADGDELGQCHVTPAGYA 266
>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 = 82.8 bits (204), Expect = 1e-17
Identities = 82/312 (26%), Positives = 129/312 (41%), Gaps = 19/312 (6%)
Query: 34 KLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVV 93
K + Y D DI + HP + L + G K I P +A+ E++
Sbjct: 1 KKKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTKY 60
Query: 94 HSESYLKSLQS--SPNVS-IIIEVPPVALFPNCLVQRKVLYPFRKQVGGTILAA-KLAKE 149
HS+ Y+K L+S N+S ++ + +C V + + GG++ A KL ++
Sbjct: 61 HSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAGAVKLNRQ 120
Query: 150 R-GWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEK 208
+ A+N GG HH E GFC DI L I ++ + RV+ ID+D H G+G E+
Sbjct: 121 QTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAI-LELLKYH-QRVLYIDIDIHHGDGVEE 178
Query: 209 DFSSDSRVYI---LDMFN--PGIYP-RDYEA--RRFIDQKVEVVSGTTTNEYLKKLDEAL 260
F + RV PG RD A ++ + G Y + +
Sbjct: 179 AFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPII 238
Query: 261 EVAGHTFDPELVIYNAGTDILEGDPLGMLKISPDGIAARDEKTFRFARSRNIPIVMLTSG 320
+ P V+ G D L GD LG ++ G A K ++ N+P++ML G
Sbjct: 239 SKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHA----KCVEVVKTFNLPLLMLGGG 294
Query: 321 PITSEKVLALWS 332
T V W+
Sbjct: 295 GYTIRNVARCWT 306
>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 = 80.8 bits (200), Expect = 4e-17
Identities = 66/259 (25%), Positives = 113/259 (43%), Gaps = 32/259 (12%)
Query: 63 RICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVALFPN 122
I + L+ +G L++ + EA ++++L+VHS+ Y+ ++S+ + + + +
Sbjct: 16 AILERLTQDGLLERCVKIPAREAEEDEILLVHSQEYIDLVKSTETMEKEELESLCSGYDS 75
Query: 123 CLVQRKVLYPFRKQVGGTILAAKLAKERGWAINVGGGF-------HHCSADEGGGFCAYA 175
+ R G TI K + GF HH +E G+C +
Sbjct: 76 VYLCPSTYEAARLAAGSTIELVKAVMAGK----IQNGFALIRPPGHHAMRNEANGYCIFN 131
Query: 176 DISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRV-------YILDMFNPGIYP 228
++++ YA +L + R++I+D D H G G ++ F D RV Y F P ++
Sbjct: 132 NVAIAAKYAIEKLGLKRILIVDWDVHHGQGTQQGFYEDPRVLYFSIHRYEHGRFWPHLFE 191
Query: 229 RDYEARRFIDQK------VEV---VSGTTTNEYLKK-LDEALEVAGHTFDPELVIYNAGT 278
DY+ I V V +G +YL L +A F PELV+ +AG
Sbjct: 192 SDYDY---IGVGHGYGFNVNVPLNQTGLGDADYLAIFHHILLPLA-LEFQPELVLVSAGF 247
Query: 279 DILEGDPLGMLKISPDGIA 297
D GDP G + ++P G A
Sbjct: 248 DASIGDPEGEMAVTPAGYA 266
>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 = 78.7 bits (195), Expect = 1e-16
Identities = 62/237 (26%), Positives = 100/237 (42%), Gaps = 27/237 (11%)
Query: 68 LSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVALFPNCLVQR 127
L + G +E A++E LL VH +Y+ L+++ E V L P+ +
Sbjct: 15 LIASGLDRLLRQLEAPPATREQLLRVHDAAYVDRLEAA-----APEEGLVQLDPDTAMSP 69
Query: 128 KVLYPFRKQVGGTILA--AKLAKERGWAINVGGGF-------HHCSADEGGGFCAYADIS 178
L + G + A A +A G A N F HH D+ GFC + +++
Sbjct: 70 GSLEAALRAAGAVVAAVDAVMA---GEARNA---FCAVRPPGHHAERDKAMGFCLFNNVA 123
Query: 179 LCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRVYILDMFNPGIYP-----RDYEA 233
+ +A + RV I+D D H GNG E F D RV +YP +
Sbjct: 124 IAAAHALAHHGLERVAIVDFDVHHGNGTEDIFRDDPRVLFCSSHQHPLYPGTGAPDETGH 183
Query: 234 RRFIDQKVEVVSGTTTNEYLKKLDEALEVAGHTFDPELVIYNAGTDILEGDPLGMLK 290
++ V + +GT E+ + +++ A F P+L++ +AG D DPL L
Sbjct: 184 GNIVN--VPLPAGTGGAEFREAVEDRWLPALDAFKPDLILISAGFDAHRDDPLAQLN 238
>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 = 74.9 bits (184), Expect = 3e-15
Identities = 67/243 (27%), Positives = 105/243 (43%), Gaps = 21/243 (8%)
Query: 74 LDKNCIVEPL-EASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVALFPNCLVQRKVLYP 132
L + C+ P EAS+E++L+VHS YL ++ + ++ + + +
Sbjct: 26 LVQRCLRLPAREASEEEILLVHSPEYLSLVRETQVMNKEELMAISGKYDAVYFHPNTFHC 85
Query: 133 FRKQVGGT--ILAAKLAKE--RGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQL 188
R G T ++ A L E G A+ G HH + GFC + ++++ YA +
Sbjct: 86 ARLAAGATLQLVDAVLTGEVQNGMALVRPPG-HHSQRNAANGFCVFNNVAIAAEYAKKKY 144
Query: 189 NISRVMIIDLDAHQGNGHEKDFSSDSRV-------YILDMFNPGIYPRDYEA------RR 235
+ R++I+D D H G G + F D V Y F P + DY+A
Sbjct: 145 GLHRILIVDWDVHHGQGIQYIFEEDPSVLYFSWHRYEHQRFWPFLRESDYDAVGRGKGLG 204
Query: 236 F-IDQKVEVVSGTTTNEYLKKLDEALEVAGHTFDPELVIYNAGTDILEGDPLGMLKISPD 294
F I+ V G +YL L FDPELV+ +AG D GDP G + +P+
Sbjct: 205 FNINLPWNKV-GMGNADYLAAFFHVLLPLAFEFDPELVLVSAGFDSAIGDPEGQMCATPE 263
Query: 295 GIA 297
A
Sbjct: 264 CFA 266
>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 = 72.0 bits (176), Expect = 5e-14
Identities = 80/304 (26%), Positives = 126/304 (41%), Gaps = 57/304 (18%)
Query: 54 HPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIE 113
HP + + I L G L+K ++ +AS E++ +VHSE + SL N +
Sbjct: 24 HPEHAGRIQSIWSRLQETGLLNKCERIQGRKASLEEIQLVHSEHH--SLLYGTNPLDGQK 81
Query: 114 VPPVALFPNCLVQRKVLYP--------------------FRKQVGGTI-LAAKLAK---E 149
+ P L + + P R VG I LA+K+A +
Sbjct: 82 LDPRILLGDDSQKFFSSLPCGGLGVDSDTIWNELHSSGAARMAVGCVIELASKVASGELK 141
Query: 150 RGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKD 209
G+A+ G HH GFC + +++ Y QLNIS+++I+DLD H GNG ++
Sbjct: 142 NGFAVVRPPG-HHAEESTAMGFCFFNSVAITAKYLRDQLNISKILIVDLDVHHGNGTQQA 200
Query: 210 FSSD-SRVYI-LDMFNPG-IYPRDYEARRFIDQKVEVVSGTTTN---------------- 250
F +D S +YI L ++ G +P EV +G
Sbjct: 201 FYADPSILYISLHRYDEGNFFPGSGAPN-------EVGTGLGEGYNINIAWTGGLDPPMG 253
Query: 251 --EYLKKLDEALEVAGHTFDPELVIYNAGTDILEGD--PLGMLKISPDGIAARDEKTFRF 306
EYL+ ++ FDP++V+ +AG D LEG PLG K++ ++
Sbjct: 254 DVEYLEAFRTIVKPVAKEFDPDMVLVSAGFDALEGHTPPLGGYKVTAKCFGHLTKQLMTL 313
Query: 307 ARSR 310
A R
Sbjct: 314 ADGR 317
>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 = 71.3 bits (175), Expect = 7e-14
Identities = 80/287 (27%), Positives = 112/287 (39%), Gaps = 44/287 (15%)
Query: 72 GFLDKNCIVEPLEASKEDLLVVHSESYLKSLQS-SPNVSIIIEVPPVALFPNCLVQRKV- 129
G K + +P AS D+ HSE Y+ LQ +P + F L Q V
Sbjct: 38 GLYKKMQVYKPYRASAHDMCRFHSEDYIDFLQRVTPQ--------NIQGFTKSLNQFNVG 89
Query: 130 --------LYPFRKQVGGTIL--AAKL-AKERGWAINVGGGFHHCSADEGGGFCAYADIS 178
L+ F G L A KL K AIN GG HH E GFC DI
Sbjct: 90 DDCPVFPGLFDFCSMYTGASLEGATKLNHKICDIAINWSGGLHHAKKFEASGFCYVNDIV 149
Query: 179 LCIHYAFVQLNI----SRVMIIDLDAHQGNGHEKDFSSDSRVYIL------DMFNPG--- 225
+ I L + RV+ ID+D H G+G ++ F RV + + F PG
Sbjct: 150 IAI------LELLKYHPRVLYIDIDIHHGDGVQEAFYLTDRVMTVSFHKYGNYFFPGTGD 203
Query: 226 IYPRDYEARRFIDQKVEVVSGTTTNEYLKKLDEALEVAGHTFDPELVIYNAGTDILEGDP 285
+Y E+ R+ V + G YL+ ++ + P ++ G D L D
Sbjct: 204 MYEVGAESGRYYSVNVPLKDGIDDQSYLQLFKPVIQQVIDFYQPTCIVLQCGADSLGCDR 263
Query: 286 LGMLKISPDGIAARDEKTFRFARSRNIPIVMLTSGPITSEKVLALWS 332
LG +S G F +S NIP+++L G T V W+
Sbjct: 264 LGCFNLSIKGHGE----CVEFVKSFNIPLLVLGGGGYTVRNVARCWT 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 = 71.4 bits (175), Expect = 8e-14
Identities = 62/207 (29%), Positives = 88/207 (42%), Gaps = 20/207 (9%)
Query: 138 GGTI-LAAKLAKER-GWAINVGGGFHHCSADEGGGFCAYADISLCI--HYAFVQLNISRV 193
GG++ AA+L + + A+N GG HH E GFC DI L I + Q RV
Sbjct: 108 GGSMEGAARLNRGKCDIAVNWAGGLHHAKKSEASGFCYVNDIVLGILELLRYHQ----RV 163
Query: 194 MIIDLDAHQGNGHEKDFSSDSRVYILDMFNPGIY-PRDYEAR-------RFIDQKVEVVS 245
+ ID+D H G+G E+ F + RV G Y P E R + V +
Sbjct: 164 LYIDIDVHHGDGVEEAFYTTDRVMTCSFHKYGEYFPGTGELRDIGIGTGKNYAVNVPLRD 223
Query: 246 GTTTNEYLKKLDEALEVAGHTFDPELVIYNAGTDILEGDPLGMLKISPDGIAARDEKTFR 305
G Y + ++ + PE V+ G D L GD LG +S G A
Sbjct: 224 GIDDESYKSIFEPVIKHVMEWYQPEAVVLQCGGDSLSGDRLGCFNLSMKGHAN----CVN 279
Query: 306 FARSRNIPIVMLTSGPITSEKVLALWS 332
F +S N+P+++L G T V W+
Sbjct: 280 FVKSFNLPMLVLGGGGYTMRNVARTWA 306
>gnl|CDD|240251 PTZ00063, PTZ00063, histone deacetylase; Provisional.
Length = 436
Score = 69.5 bits (170), Expect = 4e-13
Identities = 74/274 (27%), Positives = 115/274 (41%), Gaps = 31/274 (11%)
Query: 79 IVEPLEASKEDLLVVHSESYLKSLQS-SP----NVSIIIEVPPVALFPNCLVQRKVLYPF 133
I P ++ + +L++ H E Y+ L S SP + + ++ V +C V L+ F
Sbjct: 48 IYRPHKSVEPELVLFHDEEYVDFLSSISPENYRDFTYQLKRFNVGEATDCPVFDG-LFEF 106
Query: 134 RKQ-VGGTILAA-KLAKERG-WAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNI 190
++ G +I A KL + +N GG HH E GFC DI L I L +
Sbjct: 107 QQSCAGASIDGAYKLNNHQADICVNWSGGLHHAKRSEASGFCYINDIVLGI------LEL 160
Query: 191 ----SRVMIIDLDAHQGNGHEKDFSSDSRVYILDM-----FNPG---IYPRDYEARRFID 238
+RVM ID+D H G+G E+ F RV + F PG + ++
Sbjct: 161 LKYHARVMYIDIDVHHGDGVEEAFYVTHRVMTVSFHKFGDFFPGTGDVTDIGVAQGKYYS 220
Query: 239 QKVEVVSGTTTNEYLKKLDEALEVAGHTFDPELVIYNAGTDILEGDPLGMLKISPDGIAA 298
V + G + ++ + + P ++ G D L GD LG ++ G AA
Sbjct: 221 VNVPLNDGIDDDSFVDLFKPVISKCVEVYRPGAIVLQCGADSLTGDRLGRFNLTIKGHAA 280
Query: 299 RDEKTFRFARSRNIPIVMLTSGPITSEKVLALWS 332
F RS NIP+++L G T V W+
Sbjct: 281 ----CVEFVRSLNIPLLVLGGGGYTIRNVARCWA 310
>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 = 67.9 bits (167), Expect = 6e-13
Identities = 62/287 (21%), Positives = 104/287 (36%), Gaps = 58/287 (20%)
Query: 37 LIYSPDYDI-----SFLGIEKLHPFDS-SKWGRICQFLSSEGFLDKNCIVEPLEASKEDL 90
++YS D+ + + + ++ + I L G + ++ P + E +
Sbjct: 2 IVYSEDHLLHHPKTELSRGKLVPHPENPERAEAILDALKRAGLGE---VLPPRDFGLEPI 58
Query: 91 LVVHSESYLKSLQSSPNVSIIIEVPPVALFPNCLVQRKVLYPFRKQVGGTILAAKLAKE- 149
L VH Y+ L++ + + + AA L E
Sbjct: 59 LAVHDPDYVDFLET--------------ADTDTPISEGTWEAALAAADTALTAADLVLEG 104
Query: 150 RGWAINVG---GGFHHCSADEGGGFC-----AYADISLCIHYAFVQLNISRVMIIDLDAH 201
A + G HH D GGFC A A Y + RV I+D+D H
Sbjct: 105 ERAAYALCRPPG--HHAGRDRAGGFCYFNNAAIA-----AQYL--RDRAGRVAILDVDVH 155
Query: 202 QGNGHEKDFSSDSRVYILDM------FNPGI--YPRD---YEARRFIDQKVEVV--SGTT 248
GNG ++ F V + + F P + + E + + + GT
Sbjct: 156 HGNGTQEIFYERPDVLYVSIHGDPRTFYPFFLGFADETGEGEGEGY---NLNLPLPPGTG 212
Query: 249 TNEYLKKLDEALEVAGHTFDPELVIYNAGTDILEGDPLGMLKISPDG 295
++YL LDEAL F P+ ++ + G D EGDPL K++ +
Sbjct: 213 DDDYLAALDEALAAI-AAFGPDALVVSLGFDTHEGDPLSDFKLTTED 258
>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 = 55.8 bits (134), Expect = 1e-08
Identities = 49/183 (26%), Positives = 76/183 (41%), Gaps = 39/183 (21%)
Query: 134 RKQVGGTI-LAAKLAK---ERGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLN 189
R VG I LA K+A + G+A+ G HH GFC + +++ +LN
Sbjct: 124 RMAVGCLIELAFKVAAGELKNGFAVIRPPG-HHAEESTAMGFCFFNSVAIAAKLLQQKLN 182
Query: 190 ISRVMIIDLDAHQGNGHEKDFSSDSRVYILDM-------FNPGIYPRDYEARRFIDQKVE 242
+ +++I+D D H GNG ++ F +D V + + F PG D +V
Sbjct: 183 VGKILIVDWDIHHGNGTQQAFYNDPNVLYISLHRYDDGNFFPGSGAPD---------EVG 233
Query: 243 VVSGTTTN----------------EYLKKLDEALEVAGHTFDPELVIYNAGTDILEG--D 284
G N EYL + + F P++V+ +AG D +EG
Sbjct: 234 AGPGVGFNVNIAWTGGVDPPIGDVEYLTAFRTVVMPIANEFSPDVVLVSAGFDAVEGHQS 293
Query: 285 PLG 287
PLG
Sbjct: 294 PLG 296
>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 = 55.0 bits (133), Expect = 2e-08
Identities = 68/287 (23%), Positives = 110/287 (38%), Gaps = 72/287 (25%)
Query: 59 SKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVA 118
S W R L G +++ + +A+ E+L +VHSE + ++P + ++ +A
Sbjct: 33 SIWSR----LQETGLVNRCERLRGRKATLEELQLVHSEVHTLLYGTNPLSRLKLDPTKLA 88
Query: 119 LFPNCLVQRKVLY---------------------PFRKQVGGTI-LAAKLAK---ERGWA 153
P Q+ + R VG I LA K+A + G+A
Sbjct: 89 GLP----QKSFVRLPCGGIGVDSDTVWNELHTSNAARMAVGCVIDLAFKVATGELKNGFA 144
Query: 154 INVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSD 213
+ G HH + GFC + +++ +L + +++I+D D H GNG ++ F D
Sbjct: 145 VVRPPG-HHAEPSQAMGFCFFNSVAIAAKQLQQKLKLRKILIVDWDVHHGNGTQQIFYED 203
Query: 214 SRVYILDM-------FNPGIYPRDYEARRFIDQKVEVVSGT----TTN------------ 250
V + + F PG EV SG N
Sbjct: 204 PNVLYISLHRYDDGNFFPGTGAPT-----------EVGSGAGEGFNVNIAWSGGLDPPMG 252
Query: 251 --EYLKKLDEALEVAGHTFDPELVIYNAGTDILEGDP--LGMLKISP 293
EYL + F P++V+ +AG D EG P LG K+SP
Sbjct: 253 DAEYLAAFRTVVMPIAREFSPDIVLVSAGFDAAEGHPPPLGGYKVSP 299
>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 = 53.9 bits (129), Expect = 4e-08
Identities = 38/150 (25%), Positives = 63/150 (42%), Gaps = 20/150 (13%)
Query: 161 HHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRVYILD 220
HH GFC + +++ +LN+S+++I+D D H GNG ++ F SD V +
Sbjct: 154 HHAEESTPMGFCYFNSVAIAAKLLQQRLNVSKILIVDWDVHHGNGTQQAFYSDPNVLYMS 213
Query: 221 M-------FNPGIYPRD---------YEARRFIDQKVEVVSGTTTNEYLKKLDEALEVAG 264
+ F PG D + ++ G EYL +
Sbjct: 214 LHRYDDGNFFPGSGAPDEVGTGPGVGFNVNMAFTGGLDPPMGDA--EYLAAFRTVVMPIA 271
Query: 265 HTFDPELVIYNAGTDILEGD--PLGMLKIS 292
F P++V+ ++G D +EG PLG +S
Sbjct: 272 SEFAPDVVLVSSGFDAVEGHPTPLGGYNLS 301
>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 = 52.8 bits (127), Expect = 8e-08
Identities = 18/45 (40%), Positives = 28/45 (62%)
Query: 161 HHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNG 205
HHCS GFC ++ + +A++ I+RV+I+D+D H GNG
Sbjct: 120 HHCSESTPSGFCWVNNVHVGAAHAYLTHGITRVVILDIDLHHGNG 164
>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 = 52.7 bits (126), Expect = 9e-08
Identities = 49/181 (27%), Positives = 71/181 (39%), Gaps = 38/181 (20%)
Query: 140 TILAAKLAK---ERGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMII 196
T LA K+A + G+A+ G HH GFC + +++ Q S+++I+
Sbjct: 129 TDLAFKVASRELKNGFAVVRPPG-HHADHSTAMGFCFFNSVAIACRQLQQQGKASKILIV 187
Query: 197 DLDAHQGNGHEKDFSSDSRVYILDM-------FNPGIYPRDYEARRFIDQKVEVVSGTTT 249
D D H GNG ++ F D V + + F PG D +V SG
Sbjct: 188 DWDVHHGNGTQQTFYQDPSVLYISLHRHDDGNFFPGSGAVD---------EVGAGSGEGF 238
Query: 250 N----------------EYLKKLDEALEVAGHTFDPELVIYNAGTDILEGD--PLGMLKI 291
N EYL + F P+LV+ +AG D EG PLG +
Sbjct: 239 NVNVAWAGGLDPPMGDPEYLAAFRIVVMPIAREFSPDLVLVSAGFDAAEGHPAPLGGYHV 298
Query: 292 S 292
S
Sbjct: 299 S 299
>gnl|CDD|238860 cd01822, Lysophospholipase_L1_like, Lysophospholipase L1-like
subgroup of SGNH-hydrolases. The best characterized
member in this family is TesA, an E. coli periplasmic
protein with thioesterase, esterase, arylesterase,
protease and lysophospholipase activity.
Length = 177
Score = 30.6 bits (70), Expect = 0.66
Identities = 23/75 (30%), Positives = 32/75 (42%), Gaps = 12/75 (16%)
Query: 244 VSGTTTNEYLKKLDEALEVAGHTFDPELVIYN-AGTDILEGDPLGMLKISPDGIAARDEK 302
VSG TT L +L L P+LVI G D L G I PD A +
Sbjct: 44 VSGDTTAGGLARLPALLA----QHKPDLVILELGGNDGLRG-------IPPDQTRANLRQ 92
Query: 303 TFRFARSRNIPIVML 317
A++R P++++
Sbjct: 93 MIETAQARGAPVLLV 107
>gnl|CDD|227889 COG5602, SIN3, Histone deacetylase complex, SIN3 component
[Chromatin structure and dynamics].
Length = 1163
Score = 31.8 bits (72), Expect = 0.66
Identities = 19/61 (31%), Positives = 28/61 (45%), Gaps = 5/61 (8%)
Query: 1 MSSSSSPSVTTDAETLKRNRILSSKLYFDIPIFKLPLI-YSPDYDISFLGIEKLHPFDSS 59
MSS D E LK N L+F + IF++ +I Y ++ L I+ L SS
Sbjct: 742 MSSYLES----DKERLKANLKTIVSLFFLLCIFRIIIIVYERLLNVKGLNIDGLKADRSS 797
Query: 60 K 60
+
Sbjct: 798 R 798
>gnl|CDD|161785 TIGR00239, 2oxo_dh_E1, 2-oxoglutarate dehydrogenase, E1 component.
The 2-oxoglutarate dehydrogenase complex consists of
this thiamine pyrophosphate-binding subunit (E1),
dihydrolipoamide succinyltransferase (E2), and lipoamide
dehydrogenase (E3). The E1 ortholog from Corynebacterium
glutamicum is unusual in having an N-terminal extension
that resembles the dihydrolipoamide succinyltransferase
(E2) component of 2-oxoglutarate dehydrogenase [Energy
metabolism, TCA cycle].
Length = 929
Score = 31.8 bits (72), Expect = 0.68
Identities = 14/45 (31%), Positives = 25/45 (55%), Gaps = 3/45 (6%)
Query: 12 DAETLKRNRILSSKLYFDIPIFKLPLIYSPDYDISFLGIEKLHPF 56
D E +KR + S K+Y+D+ + D++ + IE+L+PF
Sbjct: 809 DPEGVKRLVLCSGKVYYDLHEQRRKN---GQKDVAIVRIEQLYPF 850
>gnl|CDD|238141 cd00229, SGNH_hydrolase, SGNH_hydrolase, or GDSL_hydrolase, is a
diverse family of lipases and esterases. The tertiary
fold of the enzyme is substantially different from that
of the alpha/beta hydrolase family and unique among all
known hydrolases; its active site closely resembles the
typical Ser-His-Asp(Glu) triad from other serine
hydrolases, but may lack the carboxlic acid.
Length = 187
Score = 29.3 bits (65), Expect = 2.2
Identities = 27/100 (27%), Positives = 36/100 (36%), Gaps = 12/100 (12%)
Query: 227 YPRDYEARRFIDQKVEV----VSGTTTNEYLKKLDEALEVAGHTFDPELVIYNAGT-DIL 281
Y VEV VSG TT + L++L L + P+LVI GT D+
Sbjct: 22 SLLLYLLLLAGGPGVEVINLGVSGATTADALRRLGLRLALLKD--KPDLVIIELGTNDLG 79
Query: 282 EGDPLGMLKISPDGIAARDEKTFRFARSRNIPIVMLTSGP 321
G S D A E+ R R ++ P
Sbjct: 80 RG-----GDTSIDEFKANLEELLDALRERAPGAKVILITP 114
>gnl|CDD|239110 cd02619, Peptidase_C1, C1 Peptidase family (MEROPS database
nomenclature), also referred to as the papain family;
composed of two subfamilies of cysteine peptidases
(CPs), C1A (papain) and C1B (bleomycin hydrolase).
Papain-like enzymes are mostly endopeptidases with some
exceptions like cathepsins B, C, H and X, which are
exopeptidases. Papain-like CPs have different functions
in various organisms. Plant CPs are used to mobilize
storage proteins in seeds while mammalian CPs are
primarily lysosomal enzymes responsible for protein
degradation in the lysosome. Papain-like CPs are
synthesized as inactive proenzymes with N-terminal
propeptide regions, which are removed upon activation.
Bleomycin hydrolase (BH) is a CP that detoxifies
bleomycin by hydrolysis of an amide group. It acts as a
carboxypeptidase on its C-terminus to convert itself
into an aminopeptidase and peptide ligase. BH is found
in all tissues in mammals as well as in many other
eukaryotes. It forms a hexameric ring barrel structure
with the active sites imbedded in the central channel.
Some members of the C1 family are proteins classified as
non-peptidase homologs which lack peptidase activity or
have missing active site residues.
Length = 223
Score = 29.0 bits (65), Expect = 2.8
Identities = 12/75 (16%), Positives = 22/75 (29%), Gaps = 6/75 (8%)
Query: 172 CAYADISLCIH---YAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRVYILDMFNPGIYP 228
+ + I +V L+ + I D G D + + GI P
Sbjct: 27 AYALESAYRIKGGEDEYVDLSPQYLYICANDECLGINGSCDGGGPLSALLKLVALKGIPP 86
Query: 229 RD---YEARRFIDQK 240
+ Y A ++
Sbjct: 87 EEDYPYGAESDGEEP 101
>gnl|CDD|220524 pfam10021, DUF2263, Uncharacterized protein conserved in bacteria
(DUF2263). This domain, found in various hypothetical
bacterial and eukaryotic proteins, has no known
function.
Length = 149
Score = 28.5 bits (64), Expect = 2.8
Identities = 13/41 (31%), Positives = 17/41 (41%), Gaps = 6/41 (14%)
Query: 2 SSSSSPSVTTDAETLKRNRILSSKLYFDIPIFKLPLIYSPD 42
SS + E + +R S LY D +IYSPD
Sbjct: 108 RSSLYFCLIKYPEFYEFHRAQKSPLYPD------YMIYSPD 142
>gnl|CDD|187631 cd05373, SDR_c10, classical (c) SDR, subgroup 10. This subgroup
resembles the classical SDRs, but has an incomplete
match to the canonical glycine rich NAD-binding motif
and lacks the typical active site tetrad (instead of the
critical active site Tyr, it has Phe, but contains the
nearby Lys). SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet), an NAD(P)(H)-binding
region, and a structurally diverse C-terminal region.
Classical SDRs are typically about 250 residues long,
while extended SDRs are approximately 350 residues.
Sequence identity between different SDR enzymes are
typically in the 15-30% range, but the enzymes share the
Rossmann fold NAD-binding motif and characteristic
NAD-binding and catalytic sequence patterns. These
enzymes catalyze a wide range of activities including
the metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 238
Score = 28.5 bits (64), Expect = 3.9
Identities = 18/88 (20%), Positives = 30/88 (34%), Gaps = 30/88 (34%)
Query: 233 ARRFIDQKVEVVSGTTTNEYLKKL-DEALEVAGH-----------------TFD------ 268
ARRF + V L+ L + + AG FD
Sbjct: 16 ARRFAAEGFSVALAARREAKLEALLVDIIRDAGGSAKAVPTDARDEDEVIALFDLIEEEI 75
Query: 269 --PELVIYNAGTDILEGDPLGMLKISPD 294
E+++YNAG ++ +L+ +P
Sbjct: 76 GPLEVLVYNAGANV----WFPILETTPR 99
>gnl|CDD|218127 pfam04522, DUF585, Protein of unknown function (DUF585). This
region represents the N terminus of bromovirus 2a
protein, and is always found N terminal to a predicted
RNA-dependent RNA polymerase region (pfam00978).
Length = 248
Score = 28.7 bits (64), Expect = 4.1
Identities = 10/30 (33%), Positives = 16/30 (53%), Gaps = 2/30 (6%)
Query: 55 PFDSSKWGRICQFLSS--EGFLDKNCIVEP 82
PFD ++WG C +++ EGF + I
Sbjct: 73 PFDQARWGSCCLNVTNLAEGFTGRRLIPLA 102
>gnl|CDD|178207 PLN02597, PLN02597, phosphoenolpyruvate carboxykinase [ATP].
Length = 555
Score = 29.0 bits (65), Expect = 4.4
Identities = 22/77 (28%), Positives = 31/77 (40%), Gaps = 23/77 (29%)
Query: 210 FSSDSRVYILDMF---NPGIYPRDYEARRFIDQKVEVVSGTT------TNEYLKKLDEAL 260
+S +V++ D F +P E R KV +VS N ++ E L
Sbjct: 117 LNSLDKVFVNDQFLNWDP-------ENRI----KVRIVSARAYHSLFMHNMCIRPTPEEL 165
Query: 261 EVAGHTFDPELVIYNAG 277
E G P+ IYNAG
Sbjct: 166 EDFG---TPDFTIYNAG 179
>gnl|CDD|238866 cd01828, sialate_O-acetylesterase_like2,
sialate_O-acetylesterase_like subfamily of the
SGNH-hydrolases, a diverse family of lipases and
esterases. The tertiary fold of the enzyme is
substantially different from that of the alpha/beta
hydrolase family and unique among all known hydrolases;
its active site closely resembles the Ser-His-Asp(Glu)
triad found in other serine hydrolases.
Length = 169
Score = 28.0 bits (63), Expect = 5.2
Identities = 22/87 (25%), Positives = 34/87 (39%), Gaps = 15/87 (17%)
Query: 244 VSGTTTNEYLKKLDEALEVAGHTFDPELVIYNAGT-DILEGDPLGMLKISPDGIAARDEK 302
+SG TT L +LDE + + P+ + G D+ +G S + I A
Sbjct: 29 ISGDTTRGLLARLDEDVALQ-----PKAIFIMIGINDLAQG-------TSDEDIVANYRT 76
Query: 303 TFRFAR--SRNIPIVMLTSGPITSEKV 327
R NI IV+ + P+ K
Sbjct: 77 ILEKLRKHFPNIKIVVQSILPVGELKS 103
>gnl|CDD|170182 PRK09965, PRK09965, 3-phenylpropionate dioxygenase ferredoxin
subunit; Provisional.
Length = 106
Score = 27.0 bits (60), Expect = 5.8
Identities = 10/22 (45%), Positives = 14/22 (63%), Gaps = 1/22 (4%)
Query: 70 SEGFLDKNCIVE-PLEASKEDL 90
SEG+L+ + VE PL A+ L
Sbjct: 50 SEGYLEDDATVECPLHAASFCL 71
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.321 0.139 0.414
Gapped
Lambda K H
0.267 0.0776 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,728,404
Number of extensions: 1759958
Number of successful extensions: 1706
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1649
Number of HSP's successfully gapped: 75
Length of query: 339
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 241
Effective length of database: 6,590,910
Effective search space: 1588409310
Effective search space used: 1588409310
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: 59 (26.4 bits)