RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 008057
(579 letters)
>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 = 416 bits (1073), Expect = e-144
Identities = 137/307 (44%), Positives = 190/307 (61%), Gaps = 20/307 (6%)
Query: 34 HPENPNRIKAIWNKLQAAGIPQRCVVLNAKEAKDKNLLSVHTENHVNLIKNISSKQFDSR 93
HPE P R+ AI L+ G+ R V + + A ++ LL VHT ++ ++
Sbjct: 1 HPERPERLLAILEALEEEGLLDRLVFVEPRPATEEELLRVHTPEYIERVEETCEA----- 55
Query: 94 RDRIASKLNSIYLNEGSSEAAYLAAGSVIEVAERVAEGELNSAFAIVRPPGHHAEPDEAM 153
Y++ GS EAA LAAG+ + + V GE +AFA+VRPPGHHAEPD AM
Sbjct: 56 --GGGYLDPDTYVSPGSYEAALLAAGAALAAVDAVLSGEAENAFALVRPPGHHAEPDRAM 113
Query: 154 GFCLYNNVAVAASFLLNERPELGINKILIVDWDVHHGNSTQKMFWKDPRVLFFSVHRHEF 213
GFCL+NNVA+AA + G+ ++LIVDWDVHHGN TQ +F+ DP VL+FS+H++
Sbjct: 114 GFCLFNNVAIAARYAQK---RYGLKRVLIVDWDVHHGNGTQDIFYDDPSVLYFSIHQYP- 169
Query: 214 GTFYPANDDGFYTMIGEGPGLGYNINVPWENGRCGDADYLAVWDHILLPVAKDFGPDIII 273
FYP G G G G G+ INVP G GDA+YLA ++ +LLP+A++F PD+++
Sbjct: 170 --FYPG--TGAAEETGGGAGEGFTINVPLPPG-SGDAEYLAAFEEVLLPIAREFQPDLVL 224
Query: 274 ISAGFDAAAGDPLGGCRVTPYGYSVMLKKLMDFA----QGKIVLALEGGYNLGSISNSVL 329
+SAGFDA GDPLGG +TP GY+ + + L + A G++V LEGGYNL +++ SVL
Sbjct: 225 VSAGFDAHRGDPLGGMNLTPEGYARLTRLLKELADEHCGGRLVFVLEGGYNLEALAESVL 284
Query: 330 ACMNVLL 336
A + LL
Sbjct: 285 AVLEALL 291
>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 = 417 bits (1075), Expect = e-143
Identities = 155/354 (43%), Positives = 225/354 (63%), Gaps = 4/354 (1%)
Query: 19 YDERMCKHNTPDGDYHPENPNRIKAIWNKLQAAGIPQRCVVLNAKEAKDKNLLSVHTENH 78
YD+RM H+ HPE P RI I+ + G+ +RC+ L ++ A + LL H+E H
Sbjct: 1 YDQRMMNHHNLWDPGHPECPQRISRIYERHNDLGLLERCLRLPSRLATEDELLLCHSEEH 60
Query: 79 VNLIKNISSKQFDSRRDRIASKLNSIYLNEGSSEAAYLAAGSVIEVAERVAEGELNSAFA 138
++ +K++ + +R+ + +SIY++ S + A LAAG V++V E V GE + A
Sbjct: 61 LDEMKSLEKMK-PRELNRLGKEYDSIYIHPDSYQCALLAAGCVLQVVEAVLTGESRNGVA 119
Query: 139 IVRPPGHHAEPDEAMGFCLYNNVAVAASFLLNERPELGINKILIVDWDVHHGNSTQKMFW 198
IVRPPGHHAE D A GFC +NNVA+AA + + G+ +ILIVDWDVHHGN TQ MF
Sbjct: 120 IVRPPGHHAEQDTACGFCFFNNVAIAARYAQKK---YGLKRILIVDWDVHHGNGTQHMFE 176
Query: 199 KDPRVLFFSVHRHEFGTFYPANDDGFYTMIGEGPGLGYNINVPWENGRCGDADYLAVWDH 258
DP VL+ S+HR++ G+F+P + +G Y ++G+G G G+N+N+PW G GDA+Y+A +
Sbjct: 177 SDPSVLYISLHRYDNGSFFPNSPEGNYDVVGKGKGEGFNVNIPWNKGGMGDAEYIAAFQQ 236
Query: 259 ILLPVAKDFGPDIIIISAGFDAAAGDPLGGCRVTPYGYSVMLKKLMDFAQGKIVLALEGG 318
++LP+A +F P+++++SAGFDAA GDPLGGC+VTP GY+ M LM A G++++ LEGG
Sbjct: 237 VVLPIAYEFNPELVLVSAGFDAARGDPLGGCKVTPEGYAHMTHMLMSLAGGRVIVILEGG 296
Query: 319 YNLGSISNSVLACMNVLLEDKPVAGSSEAYPFESTWRVIQAVRKKLSAFWPTLA 372
YNL SIS S+ C LL D P P S + I V + +W +L
Sbjct: 297 YNLTSISESMSMCTKTLLGDPPPVLDLPRPPCSSALKSINNVLQVHQKYWKSLR 350
>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 = 397 bits (1021), Expect = e-135
Identities = 158/311 (50%), Positives = 211/311 (67%), Gaps = 4/311 (1%)
Query: 32 DYHPENPNRIKAIWNKLQAAGIPQRCVVLNAKEAKDKNLLSVHTENHVNLIKNISSKQFD 91
D HPE+P+RI I+ KL+ AG+ R + + +EA + +L VH+E H + ++ +
Sbjct: 1 DPHPEDPSRISRIFEKLKEAGLINRMLRIPIREATKEEILLVHSEEHWDRVEATEKMSDE 60
Query: 92 SRRDR--IASKLNSIYLNEGSSEAAYLAAGSVIEVAERVAEGELNSAFAIVRPPGHHAEP 149
+DR I + S+Y+N ++ A L+ G IE VAEG + +AFA+VRPPGHHAEP
Sbjct: 61 QLKDRTEIFERD-SLYVNNDTAFCARLSCGGAIEACRAVAEGRVKNAFAVVRPPGHHAEP 119
Query: 150 DEAMGFCLYNNVAVAASFLLNERPELGINKILIVDWDVHHGNSTQKMFWKDPRVLFFSVH 209
DE+MGFC +NNVAVAA +L E P+ I KILI+DWD+HHGN TQ+ F+ DP VL+ S+H
Sbjct: 120 DESMGFCFFNNVAVAAKWLQTEYPDK-IKKILILDWDIHHGNGTQRAFYDDPNVLYISLH 178
Query: 210 RHEFGTFYPANDDGFYTMIGEGPGLGYNINVPWENGRCGDADYLAVWDHILLPVAKDFGP 269
R E G FYP G Y +GEG GLG+N+N+PW G GDADY+ + I++P+A +F P
Sbjct: 179 RFENGGFYPGTPYGDYESVGEGAGLGFNVNIPWPQGGMGDADYIYAFQRIVMPIAYEFDP 238
Query: 270 DIIIISAGFDAAAGDPLGGCRVTPYGYSVMLKKLMDFAQGKIVLALEGGYNLGSISNSVL 329
D++IISAGFDAA GD LG C VTP GY+ M LM A GK+V+ALEGGYNL +IS+S L
Sbjct: 239 DLVIISAGFDAADGDELGQCHVTPAGYAHMTHMLMSLAGGKLVVALEGGYNLDAISDSAL 298
Query: 330 ACMNVLLEDKP 340
A VLL + P
Sbjct: 299 AVAKVLLGEAP 309
>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 = 375 bits (964), Expect = e-126
Identities = 158/379 (41%), Positives = 231/379 (60%), Gaps = 31/379 (8%)
Query: 16 GLLYDERMCKHNTPDGD--YHPENPNRIKAIWNKLQAAGIPQRCVVLNAKEAKDKNLLSV 73
GL YD M KH G+ HPE+ R+++IW++LQ G+ RC L ++A + L V
Sbjct: 4 GLAYDPLMLKHQCICGNNSSHPEHGGRLQSIWSRLQETGLVNRCERLRGRKATLEELQLV 63
Query: 74 HTENHVNL--IKNISSKQFDSRRDRIASKLNSIYL-------------NEG-SSEAAYLA 117
H+E H L +S + D + + + + L NE +S AA +A
Sbjct: 64 HSEVHTLLYGTNPLSRLKLDPTKLAGLPQKSFVRLPCGGIGVDSDTVWNELHTSNAARMA 123
Query: 118 AGSVIEVAERVAEGELNSAFAIVRPPGHHAEPDEAMGFCLYNNVAVAASFLLNERPELGI 177
G VI++A +VA GEL + FA+VRPPGHHAEP +AMGFC +N+VA+AA L + +L +
Sbjct: 124 VGCVIDLAFKVATGELKNGFAVVRPPGHHAEPSQAMGFCFFNSVAIAAKQL---QQKLKL 180
Query: 178 NKILIVDWDVHHGNSTQKMFWKDPRVLFFSVHRHEFGTFYPANDDGFYTMIGEGPGLGYN 237
KILIVDWDVHHGN TQ++F++DP VL+ S+HR++ G F+P G T +G G G G+N
Sbjct: 181 RKILIVDWDVHHGNGTQQIFYEDPNVLYISLHRYDDGNFFPGT--GAPTEVGSGAGEGFN 238
Query: 238 INVPWENG---RCGDADYLAVWDHILLPVAKDFGPDIIIISAGFDAAAGDP--LGGCRVT 292
+N+ W G GDA+YLA + +++P+A++F PDI+++SAGFDAA G P LGG +V+
Sbjct: 239 VNIAWSGGLDPPMGDAEYLAAFRTVVMPIAREFSPDIVLVSAGFDAAEGHPPPLGGYKVS 298
Query: 293 PYGYSVMLKKLMDFAQGKIVLALEGGYNLGSISNSVLACMNVLLEDKPVAGSSEAY---P 349
P + M ++LM+ A GK+VLALEGGY+L +I ++ AC+ LL D+ S E P
Sbjct: 299 PACFGYMTRQLMNLAGGKVVLALEGGYDLTAICDASEACVRALLGDELDPLSEEELERRP 358
Query: 350 FESTWRVIQAVRKKLSAFW 368
+ ++ V S +W
Sbjct: 359 NPNAVTSLEKVIAIQSPYW 377
>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 = 370 bits (953), Expect = e-125
Identities = 141/314 (44%), Positives = 194/314 (61%), Gaps = 17/314 (5%)
Query: 26 HNTPDGDYHPENPNRIKAIWNKLQAAGIPQRCVVLNAKEAKDKNLLSVHTENHVNLIKNI 85
H+T G HPENP R++AI L+ +G+ R + + A ++ LL VH+ +V ++
Sbjct: 1 HDTGSGLGHPENPERLEAILELLKESGLLDRLEFIAPRPATEEELLLVHSPEYVEFLEEA 60
Query: 86 SSKQFDSRRDRIASKLNSIYLNEGSSEAAYLAAGSVIEVAERVAEGELNSAFAIVRPPGH 145
S ++ + R ++ GS EAA LAAG +E A+ V GE +AFA VRPPGH
Sbjct: 61 SLEEEELGR---IGLDGDTPVSPGSYEAALLAAGGTLEAADLVLSGE--NAFAAVRPPGH 115
Query: 146 HAEPDEAMGFCLYNNVAVAASFLLNERPELGINKILIVDWDVHHGNSTQKMFWKDPRVLF 205
HAE D A GFCL+NNVA+AA +LL G+ ++LIVD DVHHGN TQ++F+ DPRVL
Sbjct: 116 HAERDRASGFCLFNNVAIAARYLLKR---YGLKRVLIVDLDVHHGNGTQEIFYDDPRVLT 172
Query: 206 FSVHRHEFGTFYPANDDGFYTMIGEGPGLGYNINVPWENGRCGDADYLAVWDHILLPVAK 265
S+H+ F YP GF GEG G GY +N+P G GD +YLA ++ ILLP +
Sbjct: 173 ISIHQDPF---YP--GTGFADETGEGAGEGYTLNIPLPPG-TGDEEYLAAFEEILLPALR 226
Query: 266 DFGPDIIIISAGFDAAAGDPLGGCRVTPYGYSVMLKKLMDFA---QGKIVLALEGGYNLG 322
+F PD+I++SAGFDA AGDPLGG +T GY+ + L++ A G +V LEGGYNL
Sbjct: 227 EFQPDLILVSAGFDAHAGDPLGGLNLTTEGYAERTRLLLELADAYGGPVVSVLEGGYNLD 286
Query: 323 SISNSVLACMNVLL 336
+++ S A + LL
Sbjct: 287 ALARSAAAVLAGLL 300
>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 = 349 bits (897), Expect = e-116
Identities = 143/337 (42%), Positives = 214/337 (63%), Gaps = 7/337 (2%)
Query: 29 PDGDYHPENPNRIKAIWNKLQAAGIPQRCVVLNAKEAKDKNLLSVHTENHVNLIKNISSK 88
H E P R++AI +L G+ +RCV + A+EA++ +L VH++ +++L+K+ +
Sbjct: 2 NWDSNHIECPERLEAILERLTQDGLLERCVKIPAREAEEDEILLVHSQEYIDLVKSTETM 61
Query: 89 QFDSRRDRIASKLNSIYLNEGSSEAAYLAAGSVIEVAERVAEGELNSAFAIVRPPGHHAE 148
+ + + S +S+YL + EAA LAAGS IE+ + V G++ + FA++RPPGHHA
Sbjct: 62 E-KEELESLCSGYDSVYLCPSTYEAARLAAGSTIELVKAVMAGKIQNGFALIRPPGHHAM 120
Query: 149 PDEAMGFCLYNNVAVAASFLLNERPELGINKILIVDWDVHHGNSTQKMFWKDPRVLFFSV 208
+EA G+C++NNVA+AA + + + LG+ +ILIVDWDVHHG TQ+ F++DPRVL+FS+
Sbjct: 121 RNEANGYCIFNNVAIAAKYAIEK---LGLKRILIVDWDVHHGQGTQQGFYEDPRVLYFSI 177
Query: 209 HRHEFGTFYPANDDGFYTMIGEGPGLGYNINVPWENGRCGDADYLAVWDHILLPVAKDFG 268
HR+E G F+P + Y IG G G G+N+NVP GDADYLA++ HILLP+A +F
Sbjct: 178 HRYEHGRFWPHLFESDYDYIGVGHGYGFNVNVPLNQTGLGDADYLAIFHHILLPLALEFQ 237
Query: 269 PDIIIISAGFDAAAGDPLGGCRVTPYGYSVMLKKLMDFAQGKIVLALEGGYNLGSISNSV 328
P+++++SAGFDA+ GDP G VTP GY+ + + LM A GK++L LEGGY L S++ SV
Sbjct: 238 PELVLVSAGFDASIGDPEGEMAVTPAGYAHLTRLLMGLAGGKLLLVLEGGYLLESLAESV 297
Query: 329 LACMNVLLEDKP---VAGSSEAYPFESTWRVIQAVRK 362
+ LL D E+ I +
Sbjct: 298 SMTLRGLLGDPLPPLAPPIPIRSVLETILNAIAHLSP 334
>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 = 312 bits (802), Expect = e-102
Identities = 144/338 (42%), Positives = 209/338 (61%), Gaps = 6/338 (1%)
Query: 32 DYHPENPNRIKAIWNKLQAAGIPQRCVVLNAKEAKDKNLLSVHTENHVNLIKNISSKQFD 91
+ PE P R+ AI KL G+ +RCV + A+EA ++ LL VH+ +V L+K+ +
Sbjct: 5 ESFPECPERLHAIREKLIQEGLLERCVSVQAREASEEELLLVHSPEYVALMKSTQYMTEE 64
Query: 92 SRRDRIASKLNSIYLNEGSSEAAYLAAGSVIEVAERVAEGELNSAFAIVRPPGHHAEPDE 151
R +A +S+YL+ S A LA GSV+++ ++V GE+ + AIVRPPGHHA+ D+
Sbjct: 65 ELRT-LADTYDSVYLHPNSYSCACLAVGSVLQLVDKVLGGEIRNGLAIVRPPGHHAQHDK 123
Query: 152 AMGFCLYNNVAVAASFLLNERPELGINKILIVDWDVHHGNSTQKMFWKDPRVLFFSVHRH 211
G+C++NNVA+AA + + + G+ ++LIVDWDVHHG TQ +F +DP VL+FS+HR+
Sbjct: 124 MDGYCMFNNVAIAARY---AQQKHGVQRVLIVDWDVHHGQGTQFIFEQDPSVLYFSIHRY 180
Query: 212 EFGTFYPANDDGFYTMIGEGPGLGYNINVPWENGRCGDADYLAVWDHILLPVAKDFGPDI 271
E G F+P + + +G G G GYNINVPW DADY+A + H+LLPVA +F P +
Sbjct: 181 EQGRFWPHLKESDSSAVGFGRGEGYNINVPWNQVGMRDADYIAAFLHVLLPVALEFQPQL 240
Query: 272 IIISAGFDAAAGDPLGGCRVTPYGYSVMLKKLMDFAQGKIVLALEGGYNLGSISNSVLAC 331
++++AGFDA GDP G TP ++ + LM A GK++L+LEGGYNL S++ V A
Sbjct: 241 VLVAAGFDAVIGDPKGEMAATPACFAHLTHLLMGLAGGKLILSLEGGYNLRSLAEGVCAS 300
Query: 332 MNVLLEDK-PVAGSSEAYPFESTWRVIQAVRKKLSAFW 368
+ LL D P+ S A P S + L FW
Sbjct: 301 LKALLGDPCPMLESPGA-PCRSALASVSCTISALEPFW 337
>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 = 309 bits (793), Expect = e-100
Identities = 136/375 (36%), Positives = 195/375 (52%), Gaps = 45/375 (12%)
Query: 15 VGLLYDERMCKHNTPDGDY-------------HPENPNRIKAIWNKLQAAGIPQRCVVLN 61
G ++DER H+T G HPENP + I N L+ +G+ V++
Sbjct: 1 TGFVWDERYLWHDTGTGALFLPVGGLLVQPGRHPENPETKRRIKNLLEVSGLSDHLVLIT 60
Query: 62 AKEAKDKNLLSVHTENHVNLIKNISSKQFDSRRDRIASKLNSIYLNEGSSEAAYLAAGSV 121
+ A D+ LL VHT +++ +K S + GS E A LAAG
Sbjct: 61 PRPATDEELLRVHTPEYIDRVKAAS----AAGGGEAGGGT---PFGPGSYEIALLAAGGA 113
Query: 122 IEVAERVAEGELNSAFAIVRPPGHHAEPDEAMGFCLYNNVAVAASFLLNERPELGINKIL 181
I + V +GE+++A+A+VRPPGHHAEPD+ MGFCL+NNVA+AA L G+ ++
Sbjct: 114 IAAVDAVLDGEVDNAYALVRPPGHHAEPDQGMGFCLFNNVAIAARHALA---VGGVKRVA 170
Query: 182 IVDWDVHHGNSTQKMFWKDPRVLFFSVHRHEFGTFYPANDDGFYTMIGEGPGLGYNINVP 241
+VDWDVHHGN TQ +F+ DP VL S+H+ +P D G GEG G GYN+N+P
Sbjct: 171 VVDWDVHHGNGTQAIFYDDPDVLTISLHQDR---CFPP-DSGAVEERGEGAGEGYNLNIP 226
Query: 242 WENGRCGDADYLAVWDHILLPVAKDFGPDIIIISAGFDAAAGDPLGGCRVTPYGYSVMLK 301
G GD YL ++ I+LP + F P++II+++GFDA+A DPLG +T G+ + +
Sbjct: 227 LPPG-SGDGAYLHAFERIVLPALRAFRPELIIVASGFDASAFDPLGRMMLTSDGFRALTR 285
Query: 302 KLMDFA----QGKIVLALEGGYNLGSISNSVLACMNVLLE-----DKPVAGSSEAY---- 348
KL D A G++V+ EGGY+ + LA + L P+ EA
Sbjct: 286 KLRDLADELCGGRLVMVHEGGYSEAYVPFCGLAVLEELSGVRTGIADPLLYYPEAQGGQE 345
Query: 349 --PFESTWRVIQAVR 361
P + I A
Sbjct: 346 LQPHQR--AAIDAAA 358
>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 = 300 bits (769), Expect = 2e-97
Identities = 127/348 (36%), Positives = 196/348 (56%), Gaps = 22/348 (6%)
Query: 12 KRRVGLLYDERMCKHNTPDGDYHPENPNRIKAIWNKLQAAGIPQRCVVLNAKEAKDKNLL 71
+ L+Y +H HPENP+R++ I L+++G+P ++ + A + LL
Sbjct: 1 MMKTALIYHPEFLEH--EPPPGHPENPDRLRLILELLESSGLPDSLELVEPRPATLEELL 58
Query: 72 SVHTENHVNLIKNISSKQFDSRRDRIASKLNSIYLNEGSSEAAYLAAGSVIEVAERVAEG 131
VH+ ++V ++++S ++ D ++ G+ EAA LAAG + + V EG
Sbjct: 59 LVHSPDYVEFLESLSEEEGYGNLD------GDTPVSPGTYEAARLAAGGALTAVDAVLEG 112
Query: 132 ELNSAFAIVRPPGHHAEPDEAMGFCLYNNVAVAASFLLNERPELGINKILIVDWDVHHGN 191
E ++AFA+VRPPGHHA D A GFCL+NNVA+AA +LL + G+ ++ I+D+DVHHGN
Sbjct: 113 E-DNAFALVRPPGHHAGRDRASGFCLFNNVAIAAKYLLKK----GVKRVAIIDFDVHHGN 167
Query: 192 STQKMFWKDPRVLFFSVHRHEFGTFYPANDDGFYTMIGEGPGLGYNINVPWENGRCGDAD 251
TQ++F+ D VL S+H+ FYP G IGEG G N+N+P G GD
Sbjct: 168 GTQEIFYDDDDVLTVSLHQDG-RPFYPGT--GGADEIGEG-KEGNNVNIPLPPG-TGDDS 222
Query: 252 YLAVWDHILLPVAKDFGPDIIIISAGFDAAAGDPLGGCRVTPYGYSVMLKKLMDFAQ--- 308
YL + I+LP+ ++F PD++I+SAGFDA GDPLG +T GY+ + + + A+
Sbjct: 223 YLEALEEIVLPLLEEFKPDLVIVSAGFDAHRGDPLGRLNLTEEGYAKIGRAVRKLAEGYG 282
Query: 309 GKIVLALEGGYNLGSISNSVLACMNVLL-EDKPVAGSSEAYPFESTWR 355
G +V LEGGYNL +++ S++A + L + E
Sbjct: 283 GPVVAVLEGGYNLDALARSLVAFLAGLAGLVEEELEEPLPEDLELRRA 330
>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 = 294 bits (753), Expect = 1e-94
Identities = 155/380 (40%), Positives = 230/380 (60%), Gaps = 32/380 (8%)
Query: 16 GLLYDERMCKHNTPDGD--YHPENPNRIKAIWNKLQAAGIPQRCVVLNAKEAKDKNLLSV 73
GL+YD M KH GD HPE+ RI++IW++LQ G+ +C L ++A + L SV
Sbjct: 4 GLVYDSVMLKHQCSCGDNSNHPEHAGRIQSIWSRLQERGLRSQCECLRGRKASLEELQSV 63
Query: 74 HTENHVNL--IKNISSKQFDSRR------DRIASKL---------NSIYLNEGSSEAAYL 116
H+E HV L +S + D+ + R+ L ++I+ SS AA
Sbjct: 64 HSERHVLLYGTNPLSRLKLDNGKLAGLLAQRMFVMLPCGGVGVDTDTIWNELHSSNAARW 123
Query: 117 AAGSVIEVAERVAEGELNSAFAIVRPPGHHAEPDEAMGFCLYNNVAVAASFLLNERPELG 176
AAGSV ++A +VA EL + FA+VRPPGHHA+ AMGFC +N+VA+A L +
Sbjct: 124 AAGSVTDLAFKVASRELKNGFAVVRPPGHHADHSTAMGFCFFNSVAIACRQLQQQGK--- 180
Query: 177 INKILIVDWDVHHGNSTQKMFWKDPRVLFFSVHRHEFGTFYPANDDGFYTMIGEGPGLGY 236
+KILIVDWDVHHGN TQ+ F++DP VL+ S+HRH+ G F+P + G +G G G G+
Sbjct: 181 ASKILIVDWDVHHGNGTQQTFYQDPSVLYISLHRHDDGNFFPGS--GAVDEVGAGSGEGF 238
Query: 237 NINVPWENG---RCGDADYLAVWDHILLPVAKDFGPDIIIISAGFDAAAGD--PLGGCRV 291
N+NV W G GD +YLA + +++P+A++F PD++++SAGFDAA G PLGG V
Sbjct: 239 NVNVAWAGGLDPPMGDPEYLAAFRIVVMPIAREFSPDLVLVSAGFDAAEGHPAPLGGYHV 298
Query: 292 TPYGYSVMLKKLMDFAQGKIVLALEGGYNLGSISNSVLACMNVLLEDKPVAGSSEAY--- 348
+ + M ++LM+ A G +VLALEGG++L +I ++ AC+ LL ++ S E++
Sbjct: 299 SAKCFGYMTQQLMNLAGGAVVLALEGGHDLTAICDASEACVAALLGNEVDPLSEESWKQK 358
Query: 349 PFESTWRVIQAVRKKLSAFW 368
P + R ++AV + S +W
Sbjct: 359 PNLNAIRSLEAVIRVHSKYW 378
>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 = 291 bits (746), Expect = 5e-93
Identities = 137/349 (39%), Positives = 218/349 (62%), Gaps = 29/349 (8%)
Query: 16 GLLYDERMCKHNTPDGD--YHPENPNRIKAIWNKLQAAGIPQRCVVLNAKEAKDKNLLSV 73
GL+YD M KH G+ HPE+ RI+++W++LQ G+ +C + ++A + +V
Sbjct: 6 GLVYDTFMLKHQCTCGNTNVHPEHAGRIQSVWSRLQETGLLGKCERVRGRKATLDEIQTV 65
Query: 74 HTENHVNLIKN--ISSKQFDSRR--DRIASKL-------------NSIYLNEGSSEAAYL 116
H+E+H L ++ ++ DS++ ++ K+ ++++ SS A +
Sbjct: 66 HSEHHTLLYGTSPLNRQKLDSKKLLGPLSQKMYAVLPCGGIGVDSDTVWNEMHSSSAVRM 125
Query: 117 AAGSVIEVAERVAEGELNSAFAIVRPPGHHAEPDEAMGFCLYNNVAVAASFLLNERPELG 176
A G +IE+A +VA GEL + FA++RPPGHHAE AMGFC +N+VA+AA L + +L
Sbjct: 126 AVGCLIELAFKVAAGELKNGFAVIRPPGHHAEESTAMGFCFFNSVAIAAKLL---QQKLN 182
Query: 177 INKILIVDWDVHHGNSTQKMFWKDPRVLFFSVHRHEFGTFYPANDDGFYTMIGEGPGLGY 236
+ KILIVDWD+HHGN TQ+ F+ DP VL+ S+HR++ G F+P + G +G GPG+G+
Sbjct: 183 VGKILIVDWDIHHGNGTQQAFYNDPNVLYISLHRYDDGNFFPGS--GAPDEVGAGPGVGF 240
Query: 237 NINVPWENG---RCGDADYLAVWDHILLPVAKDFGPDIIIISAGFDAAAG--DPLGGCRV 291
N+N+ W G GD +YL + +++P+A +F PD++++SAGFDA G PLGG V
Sbjct: 241 NVNIAWTGGVDPPIGDVEYLTAFRTVVMPIANEFSPDVVLVSAGFDAVEGHQSPLGGYSV 300
Query: 292 TPYGYSVMLKKLMDFAQGKIVLALEGGYNLGSISNSVLACMNVLLEDKP 340
T + + K+LM A G++VLALEGG++L +I ++ AC++ LL +
Sbjct: 301 TAKCFGHLTKQLMTLAGGRVVLALEGGHDLTAICDASEACVSALLGMEL 349
>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 = 285 bits (732), Expect = 4e-92
Identities = 136/335 (40%), Positives = 208/335 (62%), Gaps = 8/335 (2%)
Query: 36 ENPNRIKAIWNKLQAAGIPQRCVVLNAKEAKDKNLLSVHTENHVNLIKNISSKQFDSRRD 95
E P R+ A + +L+ G+ QRC+ L A+EA ++ +L VH+ +++L++
Sbjct: 9 EVPERLTASYERLRQYGLVQRCLRLPAREASEEEILLVHSPEYLSLVRETQVMN-KEELM 67
Query: 96 RIASKLNSIYLNEGSSEAAYLAAGSVIEVAERVAEGELNSAFAIVRPPGHHAEPDEAMGF 155
I+ K +++Y + + A LAAG+ +++ + V GE+ + A+VRPPGHH++ + A GF
Sbjct: 68 AISGKYDAVYFHPNTFHCARLAAGATLQLVDAVLTGEVQNGMALVRPPGHHSQRNAANGF 127
Query: 156 CLYNNVAVAASFLLNERPELGINKILIVDWDVHHGNSTQKMFWKDPRVLFFSVHRHEFGT 215
C++NNVA+AA + + + G+++ILIVDWDVHHG Q +F +DP VL+FS HR+E
Sbjct: 128 CVFNNVAIAAEY---AKKKYGLHRILIVDWDVHHGQGIQYIFEEDPSVLYFSWHRYEHQR 184
Query: 216 FYPANDDGFYTMIGEGPGLGYNINVPWENGRCGDADYLAVWDHILLPVAKDFGPDIIIIS 275
F+P + Y +G G GLG+NIN+PW G+ADYLA + H+LLP+A +F P+++++S
Sbjct: 185 FWPFLRESDYDAVGRGKGLGFNINLPWNKVGMGNADYLAAFFHVLLPLAFEFDPELVLVS 244
Query: 276 AGFDAAAGDPLGGCRVTPYGYSVMLKKLMDFAQGKIVLALEGGYNLGSISNSVLACMNV- 334
AGFD+A GDP G TP ++ + LM A GK+ LEGGY+L S++ SV CM V
Sbjct: 245 AGFDSAIGDPEGQMCATPECFAHLTHLLMVLAGGKLCAVLEGGYHLESLAESV--CMTVQ 302
Query: 335 -LLEDKPVAGSSEAYPFESTWRVIQAVRKKLSAFW 368
LL D S E P +S IQ VR + +W
Sbjct: 303 TLLGDPLPRLSGEMTPCQSALESIQNVRAAQAPYW 337
>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 = 282 bits (723), Expect = 3e-91
Identities = 123/307 (40%), Positives = 175/307 (57%), Gaps = 23/307 (7%)
Query: 34 HPENPNRIKAIWNKLQAAGIPQRCVVLNAKEAKDKNLLSVHTENHVNLIKNISSKQFDSR 93
HPE+P R++AI + L A+G+ + L A A + LL VH +V+ ++ + ++ +
Sbjct: 1 HPESPERLEAILDALIASGLDRLLRQLEAPPATREQLLRVHDAAYVDRLEAAAPEEGLVQ 60
Query: 94 RDRIASKLNSIYLNEGSSEAAYLAAGSVIEVAERVAEGELNSAFAIVRPPGHHAEPDEAM 153
D ++ GS EAA AAG+V+ + V GE +AF VRPPGHHAE D+AM
Sbjct: 61 LD------PDTAMSPGSLEAALRAAGAVVAAVDAVMAGEARNAFCAVRPPGHHAERDKAM 114
Query: 154 GFCLYNNVAVAASFLLNERPELGINKILIVDWDVHHGNSTQKMFWKDPRVLFFSVHRHEF 213
GFCL+NNVA+AA+ L G+ ++ IVD+DVHHGN T+ +F DPRVLF S H+H
Sbjct: 115 GFCLFNNVAIAAAHALAHH---GLERVAIVDFDVHHGNGTEDIFRDDPRVLFCSSHQHP- 170
Query: 214 GTFYPANDDGFYTMIGEGPGLGYNINVPWENGRCGDADYLAVWDHILLPVAKDFGPDIII 273
YP T + G G +NVP G G A++ + LP F PD+I+
Sbjct: 171 --LYP------GTGAPDETGHGNIVNVPLPAG-TGGAEFREAVEDRWLPALDAFKPDLIL 221
Query: 274 ISAGFDAAAGDPLGGCRVTPYGYSVMLKKLMDFA----QGKIVLALEGGYNLGSISNSVL 329
ISAGFDA DPL +T Y+ + ++LMD A G+IV LEGGY+L +++ SV
Sbjct: 222 ISAGFDAHRDDPLAQLNLTEEDYAWITEQLMDVADRYCDGRIVSVLEGGYDLSALARSVA 281
Query: 330 ACMNVLL 336
A + L+
Sbjct: 282 AHVRALM 288
>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 = 284 bits (728), Expect = 1e-90
Identities = 156/415 (37%), Positives = 244/415 (58%), Gaps = 38/415 (9%)
Query: 16 GLLYDERMCKHNTPDGD--YHPENPNRIKAIWNKLQAAGIPQRCVVLNAKEAKDKNLLSV 73
GL+YD M KH G+ HPE+ RI++IW++LQ G+ +C + ++A + L +V
Sbjct: 7 GLVYDTLMLKHQCTCGNSNSHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTV 66
Query: 74 HTENHVNL--IKNISSKQFDSRRDR--------------IASKLNSIYLNEGSSEAAYLA 117
H+E H L ++ ++ DS++ + ++I+ SS AA LA
Sbjct: 67 HSEAHTLLYGTNPLNRQKLDSKKLLGSLASVFVRLPCGGVGVDSDTIWNEVHSSGAARLA 126
Query: 118 AGSVIEVAERVAEGELNSAFAIVRPPGHHAEPDEAMGFCLYNNVAVAASFLLNERPELGI 177
G V+E+ +VA GEL + FA+VRPPGHHAE MGFC +N+VA+AA LL +R L +
Sbjct: 127 VGCVVELVFKVATGELKNGFAVVRPPGHHAEESTPMGFCYFNSVAIAAK-LLQQR--LNV 183
Query: 178 NKILIVDWDVHHGNSTQKMFWKDPRVLFFSVHRHEFGTFYPANDDGFYTMIGEGPGLGYN 237
+KILIVDWDVHHGN TQ+ F+ DP VL+ S+HR++ G F+P + G +G GPG+G+N
Sbjct: 184 SKILIVDWDVHHGNGTQQAFYSDPNVLYMSLHRYDDGNFFPGS--GAPDEVGTGPGVGFN 241
Query: 238 INVPWENG---RCGDADYLAVWDHILLPVAKDFGPDIIIISAGFDAAAGD--PLGGCRVT 292
+N+ + G GDA+YLA + +++P+A +F PD++++S+GFDA G PLGG ++
Sbjct: 242 VNMAFTGGLDPPMGDAEYLAAFRTVVMPIASEFAPDVVLVSSGFDAVEGHPTPLGGYNLS 301
Query: 293 PYGYSVMLKKLMDFAQGKIVLALEGGYNLGSISNSVLACMNVLLEDK--PVAGSS-EAYP 349
+ + K+LM A G+IVLALEGG++L +I ++ AC++ LL ++ P+ + P
Sbjct: 302 AKCFGYLTKQLMGLAGGRIVLALEGGHDLTAICDASEACVSALLGNELDPLPEKVLQQRP 361
Query: 350 FESTWRVIQAVRKKLSAFWPTLADELPTKLTSLKAPPAHMISSSDSEDEDTKVET 404
+ R ++ V + S +W L T SL I + E+E+ + T
Sbjct: 362 NANAVRSMEKVMEIHSKYWRCLQRTTSTAGYSL-------IEAQTCENEEAETVT 409
>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 = 281 bits (719), Expect = 1e-89
Identities = 150/353 (42%), Positives = 216/353 (61%), Gaps = 31/353 (8%)
Query: 16 GLLYDERMCKHNTPDGDY--HPENPNRIKAIWNKLQAAGIPQRCVVLNAKEAKDKNLLSV 73
G+ YD M KH G+ HPE+ RI++IW++LQ G+ +C + ++A + + V
Sbjct: 4 GIAYDPLMLKHQCVCGNSTTHPEHAGRIQSIWSRLQETGLLNKCERIQGRKASLEEIQLV 63
Query: 74 HTENHV----------------NLIKNISSKQFDSRR-DRIASKLNSIYLNEGSSEAAYL 116
H+E+H L+ + S K F S + ++I+ SS AA +
Sbjct: 64 HSEHHSLLYGTNPLDGQKLDPRILLGDDSQKFFSSLPCGGLGVDSDTIWNELHSSGAARM 123
Query: 117 AAGSVIEVAERVAEGELNSAFAIVRPPGHHAEPDEAMGFCLYNNVAVAASFLLNERPELG 176
A G VIE+A +VA GEL + FA+VRPPGHHAE AMGFC +N+VA+ A +L R +L
Sbjct: 124 AVGCVIELASKVASGELKNGFAVVRPPGHHAEESTAMGFCFFNSVAITAKYL---RDQLN 180
Query: 177 INKILIVDWDVHHGNSTQKMFWKDPRVLFFSVHRHEFGTFYPANDDGFYTMIGEGPGLGY 236
I+KILIVD DVHHGN TQ+ F+ DP +L+ S+HR++ G F+P + G +G G G GY
Sbjct: 181 ISKILIVDLDVHHGNGTQQAFYADPSILYISLHRYDEGNFFPGS--GAPNEVGTGLGEGY 238
Query: 237 NINVPWENG---RCGDADYLAVWDHILLPVAKDFGPDIIIISAGFDAAAGD--PLGGCRV 291
NIN+ W G GD +YL + I+ PVAK+F PD++++SAGFDA G PLGG +V
Sbjct: 239 NINIAWTGGLDPPMGDVEYLEAFRTIVKPVAKEFDPDMVLVSAGFDALEGHTPPLGGYKV 298
Query: 292 TPYGYSVMLKKLMDFAQGKIVLALEGGYNLGSISNSVLACMNVLL--EDKPVA 342
T + + K+LM A G++VLALEGG++L +I ++ AC+N LL E +P+A
Sbjct: 299 TAKCFGHLTKQLMTLADGRVVLALEGGHDLTAICDASEACVNALLGNELEPLA 351
>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 = 271 bits (695), Expect = 6e-87
Identities = 115/326 (35%), Positives = 174/326 (53%), Gaps = 35/326 (10%)
Query: 17 LLYDERMCKHNTPDGD------YHPENPNRIKAIWNKLQAAGIPQRCVVLNAKEAKDKNL 70
++Y E H+ HPENP R +AI + L+ AG+ VL ++ + +
Sbjct: 2 IVYSEDHLLHHPKTELSRGKLVPHPENPERAEAILDALKRAGLG---EVLPPRDFGLEPI 58
Query: 71 LSVHTENHVNLIKNISSKQFDSRRDRIASKLNSIYLNEGSSEAAYLAAGSVIEVAERVAE 130
L+VH ++V+ ++ D+ ++EG+ EAA AA + + A+ V E
Sbjct: 59 LAVHDPDYVDFLET-----ADT----------DTPISEGTWEAALAAADTALTAADLVLE 103
Query: 131 GELNSAFAIVRPPGHHAEPDEAMGFCLYNNVAVAASFLLNERPELGINKILIVDWDVHHG 190
GE +A+A+ RPPGHHA D A GFC +NN A+AA +L + ++ I+D DVHHG
Sbjct: 104 GE-RAAYALCRPPGHHAGRDRAGGFCYFNNAAIAAQYLRDRAG-----RVAILDVDVHHG 157
Query: 191 NSTQKMFWKDPRVLFFSVHRHEFGTFYPANDDGFYTMIGEGPGLGYNINVPWENGRCGDA 250
N TQ++F++ P VL+ S+H TFYP GF GEG G GYN+N+P G GD
Sbjct: 158 NGTQEIFYERPDVLYVSIHGD-PRTFYPFF-LGFADETGEGEGEGYNLNLPLPPG-TGDD 214
Query: 251 DYLAVWDHILLPVAKDFGPDIIIISAGFDAAAGDPLGGCRVTPYGYSVMLKKLMDFAQGK 310
DYLA D L +A FGPD +++S GFD GDPL ++T Y+ + +++
Sbjct: 215 DYLAALDEALAAIA-AFGPDALVVSLGFDTHEGDPLSDFKLTTEDYARIGRRIAA-LGLP 272
Query: 311 IVLALEGGYNLGSISNSVLACMNVLL 336
V EGGYN+ ++ + +A +
Sbjct: 273 TVFVQEGGYNVDALGRNAVAFLAGFE 298
>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 = 4e-66
Identities = 101/297 (34%), Positives = 158/297 (53%), Gaps = 19/297 (6%)
Query: 40 RIKAIWNKLQAAGIPQRCVVLNAKEAKDKNLLSVHTENHVNLIKNISSKQFDSRRDRIAS 99
RI+ + L+ G+ + ++ +EA ++ LL VHTE ++N +K + + +
Sbjct: 1 RIRDLIEALKELGLRPKIELIECREATEELLLKVHTEEYLNELKANFAVATITESKPVIF 60
Query: 100 KLNSIYLNEGSSEAAYLAAGSVIEVAERVAEGELNSAFAIVRPPGHHAEPDEAMGFCLYN 159
N + A L+ G V+E AE VA+GEL AFA+V GHHA A GFC +N
Sbjct: 61 GPN-FPVQRHYFRGARLSTGGVVEAAELVAKGELERAFAVVGAGGHHAGKSRAWGFCYFN 119
Query: 160 NVAVAASFLLNERPELGINKILIVDWDVHHGNSTQKMFWKDPRVLFFSVHRHEFGTFYPA 219
+V +A FL E GI++ILI+D D HHG+ T++ F+ D RVL S H
Sbjct: 120 DVVLAIKFLR----ERGISRILIIDTDAHHGDGTREAFYDDDRVLHMSFHN--------- 166
Query: 220 NDDGFYTMIGEGPGLGYNINVPWENGRCGDADYLAVWDHILLPVAKDFGPDIIIISAGFD 279
D + G G G GY INVP E+G GD +YL + ++ V ++F P+++++ G D
Sbjct: 167 YDIYPF---GRGKGKGYKINVPLEDG-LGDEEYLDAVERVISKVLEEFEPEVVVLQFGHD 222
Query: 280 AAAGDPLGGCRVTPYGYSVMLKKLMDFAQGK-IVLALEGGYNLGSISNSVLACMNVL 335
GD LGG ++ G+ + + + +FA+G I++ L GGYN + + A + L
Sbjct: 223 THEGDRLGGFNLSEKGFVKLAEIVKEFARGGPILMVLGGGYNPEAAARIWTAIIKEL 279
>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 = 208 bits (531), Expect = 2e-62
Identities = 103/314 (32%), Positives = 158/314 (50%), Gaps = 25/314 (7%)
Query: 17 LLYDERMCKHNTPDGDYHPENPNRIKAIWNKLQAAGIPQRCVVLNAKEAKDKNLLSVHTE 76
+Y E +++ G HP NP R+ + L+A G+ ++ + A ++ LL HT
Sbjct: 2 FIYSEEYLRYSF--GPNHPFNPPRLSLTKDLLRALGLLPPVDLVPPRPATEEELLLFHTP 59
Query: 77 NHVNLIKNISSKQFDSRRDR--IASKLNSIYLNEGSSEAAYLAAGSVIEVAERVAEGELN 134
+++ +K S Q R R + ++ N ++ G EAA L G + A V EGE
Sbjct: 60 DYIEAVKEASRGQEPEGRGRLGLGTEDNPVF--PGMHEAAALVVGGTLLAARLVLEGEAR 117
Query: 135 SAFAIVRPPG--HHAEPDEAMGFCLYNNVAVAASFLLNERPELGINKILIVDWDVHHGNS 192
AF P G HHA A GFC+YN+ AVA L ++ G ++ VD D HHG+
Sbjct: 118 RAFN---PAGGLHHAMRGRASGFCVYNDAAVAIERLRDK----GGLRVAYVDIDAHHGDG 170
Query: 193 TQKMFWKDPRVLFFSVHRHEFG-TFYPANDDGFYTMIGEGPGLGYNINVPWENGRCGDAD 251
Q F+ DPRVL S+H E G +P GF IGEG G GY +N+P G GD +
Sbjct: 171 VQAAFYDDPRVLTISLH--ESGRYLFPGT--GFVDEIGEGEGYGYAVNIPLPPG-TGDDE 225
Query: 252 YLAVWDHILLPVAKDFGPDIIIISAGFDAAAGDPLGGCRVTPYGYSVMLKKLMD----FA 307
+L ++ ++ P+ + F PD+I+ G DA AGDPL ++ Y ++++ + +
Sbjct: 226 FLRAFEAVVPPLLRAFRPDVIVSQHGADAHAGDPLTHLNLSNRAYRAAVRRIRELADEYC 285
Query: 308 QGKIVLALEGGYNL 321
G+ + GGYN
Sbjct: 286 GGRWLALGGGGYNP 299
>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 = 146 bits (370), Expect = 6e-39
Identities = 84/295 (28%), Positives = 149/295 (50%), Gaps = 16/295 (5%)
Query: 35 PENPNRIKAIWNKLQAAGIPQRCVVLNAKEAKDKNLLSVHTENHVNLIKNISSKQFDSRR 94
P+ PNR + + ++A G+ ++ V+ + A ++ L S H++ ++ +K S++ +
Sbjct: 17 PKVPNRASMVHSLIEAYGLLKQLRVVKPRVATEEELASFHSDEYIQFLKKASNEGDNDEE 76
Query: 95 DRIASKLNSIY---LNEGSSEAAYLAAGSVIEVAERVAEGELNSAFAIVRPPG-HHAEPD 150
+ Y + EG + A AG+ + A+ + +G+ AI G HHA+ D
Sbjct: 77 PSEQQEFGLGYDCPIFEGIYDYAAAVAGATLTAAQLLIDGK--CKVAINWFGGWHHAQRD 134
Query: 151 EAMGFCLYNNVAVAASFLLNERPELGINKILIVDWDVHHGNSTQKMFWKDPRVLFFSVHR 210
EA GFC Y N V L E+ +++L VD D+HHG+ + F +V+ S+H+
Sbjct: 135 EASGFC-YVNDIVLGILKLREK----FDRVLYVDLDLHHGDGVEDAFSFTSKVMTVSLHK 189
Query: 211 HEFGTFYPANDDGFYTMIGEGPGLGYNINVPWENGRCGDADYLAVWDHILLPVAKDFGPD 270
+ G F+P G + +G G G Y +NVP +G D YL ++ ++ + F P+
Sbjct: 190 YSPG-FFPGT--GDVSDVGLGKGKYYTVNVPLRDG-IQDEQYLQIFTAVVPEIVAAFRPE 245
Query: 271 IIIISAGFDAAAGDPLGGCRVTPYGYSVMLKKLMDFAQGKIVLALEGGYNLGSIS 325
+++ G D AGDP+G +TP G LK ++ + ++L GGYNL + +
Sbjct: 246 AVVLQCGADTLAGDPMGAFNLTPVGIGKCLKYVLGWKLPTLILG-GGGYNLANTA 299
>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 = 125 bits (317), Expect = 2e-32
Identities = 80/295 (27%), Positives = 126/295 (42%), Gaps = 42/295 (14%)
Query: 34 HPENPNRIKAIWNKLQAAGIPQRCVVLNAKEAKDKNLLSVHTENHVNLIKNISSKQFDSR 93
H + + L G+ ++ + A ++LL VH ++ ++ S +
Sbjct: 1 HRFPMRKYGLLREALLEEGLVLPEDIVEPEPATREDLLRVHDPEYLE---SLKSGELSRE 57
Query: 94 RDRIASKLNSIYLNEGSSEAAYLAAGSVIEVAERVAEGELNSAFAIVRPPG--HHAEPDE 151
R + E LA G I A L AI G HHA PD
Sbjct: 58 EIR-RIGFP---WSPELVERTRLAVGGTILAARLA----LEHGLAI-NLAGGTHHAFPDR 108
Query: 152 AMGFCLYNNVAVAASFLLNERPELGINKILIVDWDVHHGNSTQKMFWKDPRVLFFSVH-R 210
GFC++N++A+AA LL E + ++LIVD DVH GN T +F DP V FS+H
Sbjct: 109 GEGFCVFNDIAIAARVLLAEG---LVRRVLIVDLDVHQGNGTAAIFADDPSVFTFSMHGE 165
Query: 211 HEFGTFYPANDDGFYTMIGEGPGLGYNINVPWENGRCGDADYLAVWDHILLPVAKDFGPD 270
+ +D ++VP +G GD +YLA + L + +F PD
Sbjct: 166 KNYPFRKEPSD----------------LDVPLPDG-TGDDEYLAALEEALPRLLAEFRPD 208
Query: 271 IIIISAGFDAAAGDPLGGCRVTPYGYSVMLKKLM--DFAQGK---IVLALEGGYN 320
++ +AG D AGD LG ++ G + + + FA+ + + + L GGY+
Sbjct: 209 LVFYNAGVDVLAGDRLGRLSLSLEG--LRERDRLVLRFARARGIPVAMVLGGGYS 261
>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 = 125 bits (315), Expect = 5e-32
Identities = 73/289 (25%), Positives = 129/289 (44%), Gaps = 28/289 (9%)
Query: 35 PENPNRIKAIWNKLQAAGIPQRCV-VLNAKEAKDKNLLSVHTENHVNLIKNISSKQFDSR 93
P N R + + ++A G+ Q ++ + A K+L H +++V+ + + D
Sbjct: 16 PSNKGRSSLVHSLIRAYGLLQHFDEIIEPERATRKDLTKYHDKDYVDFLLKKYGLEDDC- 74
Query: 94 RDRIASKLNSIYLNEGSSEAAYLAAGSVIEVAERVAEGELNSAFAIVRPPG-HHAEPDEA 152
+ S L AGS + +A+ + ++ AI G HHA+ A
Sbjct: 75 -----------PVFPFLSMYVQLVAGSSLALAKHLIT-QVERDIAINWYGGRHHAQKSRA 122
Query: 153 MGFCLYNNVAVAASFLLNERPELGINKILIVDWDVHHGNSTQKMFWKDPRVLFFSVHRHE 212
GFC N++ +A + ++ +D D+HHG+ + F+ VL S+HR++
Sbjct: 123 SGFCYVNDIVLA----ILRLRRARFRRVFYLDLDLHHGDGVESAFFFSKNVLTCSIHRYD 178
Query: 213 FGTFYPANDDGFYTMIGEGPGLGYNINVPWENGRCGDADYLAVWDHILLPVAKDFGPDII 272
G F+P T + +N+P + G D L + D I+ P+ + F P++I
Sbjct: 179 PG-FFPG------TGSLKNSSDKGMLNIPLKRG-LSDKTLLRIIDSIVRPLIEKFEPEVI 230
Query: 273 IISAGFDAAAGDPLGGCRVTPYGYSVMLKKLMDFAQGKIVLAL-EGGYN 320
+I G D +GDP +T GY +++ L+ + K L L GGYN
Sbjct: 231 VIQCGCDGLSGDPHKEWNLTIRGYGSVIELLLKEFKDKPTLLLGGGGYN 279
>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 = 120 bits (304), Expect = 2e-30
Identities = 80/300 (26%), Positives = 147/300 (49%), Gaps = 20/300 (6%)
Query: 27 NTPDGDYHPENPNRIKAIWNKLQAAGIPQRCVVLNAKEAKDKNLLSVHTENHVNLIKNIS 86
N G HP P+RI+ + + + G+ ++ + + A + L H++++++ ++++S
Sbjct: 8 NYYYGQGHPMKPHRIRMTHSLILSYGLYKKMEIYRPRPATAEELTKFHSDDYIDFLRSVS 67
Query: 87 SKQFDSRRDRIASKLNSIY---LNEGSSEAAYLAAGSVIEVAERVAEGELNSAFAIVRPP 143
+ ++ + N + +G E L AG I A ++ G+ + A +
Sbjct: 68 PDNMKEFKKQLE-RFNVGEDCPVFDGLYEYCQLYAGGSIAAAVKLNRGQADIA---INWA 123
Query: 144 G--HHAEPDEAMGFCLYNNVAVAASFLLNERPELGINKILIVDWDVHHGNSTQKMFWKDP 201
G HHA+ EA GFC N++ +A LL ++L +D D+HHG+ ++ F+
Sbjct: 124 GGLHHAKKSEASGFCYVNDIVLAILELLKYHQ-----RVLYIDIDIHHGDGVEEAFYTTD 178
Query: 202 RVLFFSVHRHEFGTFYPANDDGFYTMIGEGPGLGYNINVPWENGRCGDADYLAVWDHILL 261
RV+ S H+ FG ++ IG G G Y +NVP ++G D YL +++ +L
Sbjct: 179 RVMTVSFHK--FGEYFFPGTGLRD--IGAGKGKYYAVNVPLKDG-IDDESYLQIFEPVLS 233
Query: 262 PVAKDFGPDIIIISAGFDAAAGDPLGGCRVTPYGYSVMLKKLMDFAQGKIVLALEGGYNL 321
V + F P +++ G D+ AGD LG ++ G++ +K + F +VL GGY L
Sbjct: 234 KVMEVFQPSAVVLQCGADSLAGDRLGCFNLSIKGHAKCVKFVKSFNIPLLVLG-GGGYTL 292
>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 = 112 bits (283), Expect = 1e-27
Identities = 81/311 (26%), Positives = 145/311 (46%), Gaps = 18/311 (5%)
Query: 19 YDERMCKHNTPDGDYHPENPNRIKAIWNKLQAAGIPQRCVVLNAKEAKDKNLLSVHTENH 78
++ R+ ++ G HP P R+ + + G+ + A+ A + L H ++
Sbjct: 5 FNSRVEDYHF--GRTHPMKPFRLTLTKHLVMGYGLHKAMDTYEARAATREELRQFHDADY 62
Query: 79 VNLIKNISSKQFDSRRDRIASKLN---SIYLNEGSSEAAYLAAGSVIEVAERVAEGELNS 135
++ + +S + + R A N + +G + L AG+ ++ A ++ G+ S
Sbjct: 63 LDFLSKVSPENANQLRFDKAEPFNIGDDCPVFDGMYDYCQLYAGASLDAARKLCSGQ--S 120
Query: 136 AFAIVRPPG-HHAEPDEAMGFCLYNNVAVAASFLLNERPELGINKILIVDWDVHHGNSTQ 194
AI G HHA+ EA GFC N++ +A LL P ++L +D DVHHG+ +
Sbjct: 121 DIAINWSGGLHHAKKSEASGFCYVNDIVLAILNLLRYFP-----RVLYIDIDVHHGDGVE 175
Query: 195 KMFWKDPRVLFFSVHRHEFGTFYPANDDGFYTMIGEGPGLGYNINVPWENGRCGDADYLA 254
+ F++ RV+ S H++ G F+P D G PG + +NVP E+G D Y
Sbjct: 176 EAFYRTDRVMTLSFHKYN-GEFFPGTGD--LDDNGGTPGKHFALNVPLEDG-IDDEQYNL 231
Query: 255 VWDHILLPVAKDFGPDIIIISAGFDAAAGDPLGGCRVTPYGYSVMLKKLMDFAQGKIVLA 314
++ I+ P + F P I++ G D+ GD LG + + +K + F +V+
Sbjct: 232 LFKSIIGPTIEKFQPSAIVLQCGADSLGGDRLGQFNLNIKAHGACVKFVKSFGIPMLVVG 291
Query: 315 LEGGYNLGSIS 325
GGY +++
Sbjct: 292 -GGGYTPRNVA 301
>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 = 114 bits (286), Expect = 1e-27
Identities = 82/319 (25%), Positives = 155/319 (48%), Gaps = 22/319 (6%)
Query: 12 KRRVGLLYDERMCKHNTPDGDYHPENPNRIKAIWNKLQAAGIPQRCVVLNAKEAKDKNLL 71
K++V YD + N G HP P+RI+ + + G+ ++ + AK A +
Sbjct: 1 KKKVAYFYDSDV--GNYAYGPGHPMKPHRIRMAHSLVMNYGLYKKMEIYRAKPATKNEMT 58
Query: 72 SVHTENHVNLIKNISSKQFDSRRDRIASKLN---SIYLNEGSSEAAYLAAGSVIEVAERV 128
HT+ +++ + ++ + + + K N + +G E ++AG +E A R+
Sbjct: 59 QFHTDEYIDFLSRVTPDNMEKFQ-KEQVKYNVGDDCPVFDGLFEFCSISAGGSMEGAARL 117
Query: 129 AEGELNSAFAIVRPPG--HHAEPDEAMGFCLYNNVAVAASFLLNERPELGINKILIVDWD 186
G+ + A V G HHA+ EA GFC N++ + LL ++L +D D
Sbjct: 118 NRGKCDIA---VNWAGGLHHAKKSEASGFCYVNDIVLGILELLRYHQ-----RVLYIDID 169
Query: 187 VHHGNSTQKMFWKDPRVLFFSVHRHEFGTFYPANDDGFYTMIGEGPGLGYNINVPWENGR 246
VHHG+ ++ F+ RV+ S H+ +G ++P G IG G G Y +NVP +G
Sbjct: 170 VHHGDGVEEAFYTTDRVMTCSFHK--YGEYFPGT--GELRDIGIGTGKNYAVNVPLRDG- 224
Query: 247 CGDADYLAVWDHILLPVAKDFGPDIIIISAGFDAAAGDPLGGCRVTPYGYSVMLKKLMDF 306
D Y ++++ ++ V + + P+ +++ G D+ +GD LG ++ G++ + + F
Sbjct: 225 IDDESYKSIFEPVIKHVMEWYQPEAVVLQCGGDSLSGDRLGCFNLSMKGHANCVNFVKSF 284
Query: 307 AQGKIVLALEGGYNLGSIS 325
+VL GGY + +++
Sbjct: 285 NLPMLVLG-GGGYTMRNVA 302
>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 = 102 bits (256), Expect = 9e-24
Identities = 81/318 (25%), Positives = 152/318 (47%), Gaps = 20/318 (6%)
Query: 12 KRRVGLLYDERMCKHNTPDGDYHPENPNRIKAIWNKLQAAGIPQRCVVLNAKEAKDKNLL 71
K++V YD + + G HP P+RI+ N L G+ ++ + +A + +
Sbjct: 5 KKKVCYYYDGDVGNYYYGQG--HPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKANAEEMT 62
Query: 72 SVHTENHVNLIKNISSKQFDSRRDRIASKLN---SIYLNEGSSEAAYLAAGSVIEVAERV 128
H+++++ +++I S + + N + +G E L+AG VA V
Sbjct: 63 KYHSDDYIKFLRSIRPDNM-SEYSKQMQRFNVGEDCPVFDGLFEFCQLSAGG--SVASAV 119
Query: 129 AEGELNSAFAIVRPPG-HHAEPDEAMGFCLYNNVAVAASFLLNERPELGINKILIVDWDV 187
+ + A+ G HHA+ EA GFC N++ +A LL ++L +D D+
Sbjct: 120 KLNKQQTDIAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYH-----QRVLYIDIDI 174
Query: 188 HHGNSTQKMFWKDPRVLFFSVHRHEFGTFYPANDDGFYTMIGEGPGLGYNINVPWENGRC 247
HHG+ ++ F+ RV+ +V H++G ++P D IG G G Y +N P +G
Sbjct: 175 HHGDGVEEAFYTTDRVM--TVSFHKYGEYFPGTGD--LRDIGAGKGKYYAVNYPLRDG-I 229
Query: 248 GDADYLAVWDHILLPVAKDFGPDIIIISAGFDAAAGDPLGGCRVTPYGYSVMLKKLMDFA 307
D Y A++ ++ V + F P +++ G D+ +GD LG +T G++ ++ + F
Sbjct: 230 DDESYEAIFKPVMSKVMEMFQPSAVVLQCGADSLSGDRLGCFNLTIKGHAKCVEFVKSFN 289
Query: 308 QGKIVLALEGGYNLGSIS 325
++L GGY + +++
Sbjct: 290 LPMLMLG-GGGYTIRNVA 306
>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 = 98.3 bits (245), Expect = 3e-22
Identities = 77/288 (26%), Positives = 116/288 (40%), Gaps = 73/288 (25%)
Query: 102 NSIYLNEGSSEAAYLAAGSVIEVAERVAEGEL---NSAFAIVRPPGHHAEPDEAMGFCLY 158
+YL S +A A G+V E + V + E AF +RPPGHH GFC
Sbjct: 74 GDLYLCPESLDAIQGALGAVCEAVDSVFKPESPGTKRAFVAIRPPGHHCSESTPSGFCWV 133
Query: 159 NNVAVAA--SFLLNERPELGINKILIVDWDVHHGNSTQ---------------------- 194
NNV V A ++L + GI +++I+D D+HHGN TQ
Sbjct: 134 NNVHVGAAHAYLTH-----GITRVVILDIDLHHGNGTQDIAWRINAEANKQALESSSYDD 188
Query: 195 --KMFWKDPRVLFFSVHRHEFGTFYPANDDGFYTMIG------EGPGLGYNI-NV---PW 242
R+ + S+H +P +DG + +G G I NV PW
Sbjct: 189 FKPAGAPGLRIFYSSLHDIN---SFPC-EDGDPAKVKDASVSIDGA-HGQWIWNVHLQPW 243
Query: 243 ENGRCGDADYLAVWD---HILLPVAKDF------GPD---IIIISAGFDAAAGDPLG--- 287
+ D+ ++ IL A +F ++ ISAGFDA+ +
Sbjct: 244 TT----EEDFWELYYPKYRILFEKAAEFLRLTTAATPFKTLVFISAGFDASEHEYESMQR 299
Query: 288 -GCRVTPYGYSVMLKKLMDFAQ----GKIVLALEGGYNLGSISNSVLA 330
G V Y + + FA G+++ LEGGY+ ++ + VLA
Sbjct: 300 HGVNVPTSFYYRFARDAVRFADAHAHGRLISVLEGGYSDRALCSGVLA 347
>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 = 95.2 bits (237), Expect = 4e-21
Identities = 77/320 (24%), Positives = 146/320 (45%), Gaps = 25/320 (7%)
Query: 13 RRVGLLYDERMCKHNTPDGDYHPENPNRIKAIWNKLQAAGIPQRCVVLNAKEAKDKNLLS 72
+RV YD + N G HP P+R+ + + G+ ++ V A ++
Sbjct: 1 KRVAYFYDPDV--GNFHYGPGHPMKPHRLALTHSLVLHYGLYKKMQVYKPYRASAHDMCR 58
Query: 73 VHTENHVNLIKNISSKQFDSRRDRIASKLNSIYLNE------GSSEAAYLAAGSVIEVAE 126
H+E++++ ++ ++ + LN + + G + + G+ +E A
Sbjct: 59 FHSEDYIDFLQRVTPQNIQG----FTKSLNQFNVGDDCPVFPGLFDFCSMYTGASLEGAT 114
Query: 127 RVAEGELNSAFAIVRPPG-HHAEPDEAMGFCLYNNVAVAASFLLNERPELGINKILIVDW 185
++ AI G HHA+ EA GFC N++ +A LL P ++L +D
Sbjct: 115 KLNHKI--CDIAINWSGGLHHAKKFEASGFCYVNDIVIAILELLKYHP-----RVLYIDI 167
Query: 186 DVHHGNSTQKMFWKDPRVLFFSVHRHEFGTFYPANDDGFYTMIGEGPGLGYNINVPWENG 245
D+HHG+ Q+ F+ RV+ S H++ F+P D + +G G Y++NVP ++G
Sbjct: 168 DIHHGDGVQEAFYLTDRVMTVSFHKYG-NYFFPGTGDMY--EVGAESGRYYSVNVPLKDG 224
Query: 246 RCGDADYLAVWDHILLPVAKDFGPDIIIISAGFDAAAGDPLGGCRVTPYGYSVMLKKLMD 305
D YL ++ ++ V + P I++ G D+ D LG ++ G+ ++ +
Sbjct: 225 -IDDQSYLQLFKPVIQQVIDFYQPTCIVLQCGADSLGCDRLGCFNLSIKGHGECVEFVKS 283
Query: 306 FAQGKIVLALEGGYNLGSIS 325
F +VL GGY + +++
Sbjct: 284 FNIPLLVLG-GGGYTVRNVA 302
>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 = 88.6 bits (219), Expect = 6e-19
Identities = 78/319 (24%), Positives = 150/319 (47%), Gaps = 22/319 (6%)
Query: 12 KRRVGLLYDERMCKHNTPDGDYHPENPNRIKAIWNKLQAAGIPQRCVVLNAKEAKDKNLL 71
K++V YD + + G HP P+RI+ N L G+ ++ + +A + +
Sbjct: 1 KKKVCYYYDGDIGNYYYGQG--HPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMT 58
Query: 72 SVHTENHVNLIKNISSKQFDSRRDRIASKLN---SIYLNEGSSEAAYLAAGSVIEVAERV 128
H++ ++ +++I S + + N + +G E L+ G + A ++
Sbjct: 59 KYHSDEYIKFLRSIRPDNM-SEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAGAVKL 117
Query: 129 AEGELNSAFAIVRPPG--HHAEPDEAMGFCLYNNVAVAASFLLNERPELGINKILIVDWD 186
+ + A V G HHA+ EA GFC N++ +A LL ++L +D D
Sbjct: 118 NRQQTDMA---VNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYH-----QRVLYIDID 169
Query: 187 VHHGNSTQKMFWKDPRVLFFSVHRHEFGTFYPANDDGFYTMIGEGPGLGYNINVPWENGR 246
+HHG+ ++ F+ RV+ +V H++G ++P D IG G G Y +N P +G
Sbjct: 170 IHHGDGVEEAFYTTDRVM--TVSFHKYGEYFPGTGD--LRDIGAGKGKYYAVNFPMRDG- 224
Query: 247 CGDADYLAVWDHILLPVAKDFGPDIIIISAGFDAAAGDPLGGCRVTPYGYSVMLKKLMDF 306
D Y ++ I+ V + + P +++ G D+ +GD LG +T G++ ++ + F
Sbjct: 225 IDDESYGQIFKPIISKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTF 284
Query: 307 AQGKIVLALEGGYNLGSIS 325
++L GGY + +++
Sbjct: 285 NLPLLMLG-GGGYTIRNVA 302
>gnl|CDD|240251 PTZ00063, PTZ00063, histone deacetylase; Provisional.
Length = 436
Score = 87.6 bits (217), Expect = 2e-18
Identities = 84/332 (25%), Positives = 151/332 (45%), Gaps = 42/332 (12%)
Query: 10 TIKRRVGLLYDERMCKHNTPD-GDY-----HPENPNRIKAIWNKLQAAGIPQRCVVLNAK 63
++++RV YD PD G Y HP P RI+ + + + + +
Sbjct: 1 SMRKRVSYFYD--------PDIGSYYYGPGHPMKPQRIRMAHALILSYDLYKHMEIYRPH 52
Query: 64 EAKDKNLLSVHTENHVNLIKNISSKQFDSRRDRIASKLNSIYLNE--------GSSEAAY 115
++ + L+ H E +V+ + +IS ++ RD +L + E G E
Sbjct: 53 KSVEPELVLFHDEEYVDFLSSISP---ENYRD-FTYQLKRFNVGEATDCPVFDGLFEFQQ 108
Query: 116 LAAGSVIEVAERVAEGELNSAFAIVRPPG--HHAEPDEAMGFCLYNNVAVAASFLLNERP 173
AG+ I+ A ++ + A V G HHA+ EA GFC N++ + LL
Sbjct: 109 SCAGASIDGAYKLNN---HQADICVNWSGGLHHAKRSEASGFCYINDIVLGILELLKYHA 165
Query: 174 ELGINKILIVDWDVHHGNSTQKMFWKDPRVLFFSVHRHEFGTFYPANDDGFYTMIGEGPG 233
+++ +D DVHHG+ ++ F+ RV+ S H+ FG F+P D T IG G
Sbjct: 166 -----RVMYIDIDVHHGDGVEEAFYVTHRVMTVSFHK--FGDFFPGTGD--VTDIGVAQG 216
Query: 234 LGYNINVPWENGRCGDADYLAVWDHILLPVAKDFGPDIIIISAGFDAAAGDPLGGCRVTP 293
Y++NVP +G D ++ ++ ++ + + P I++ G D+ GD LG +T
Sbjct: 217 KYYSVNVPLNDG-IDDDSFVDLFKPVISKCVEVYRPGAIVLQCGADSLTGDRLGRFNLTI 275
Query: 294 YGYSVMLKKLMDFAQGKIVLALEGGYNLGSIS 325
G++ ++ + +VL GGY + +++
Sbjct: 276 KGHAACVEFVRSLNIPLLVLG-GGGYTIRNVA 306
>gnl|CDD|240374 PTZ00346, PTZ00346, histone deacetylase; Provisional.
Length = 429
Score = 84.7 bits (209), Expect = 2e-17
Identities = 55/175 (31%), Positives = 93/175 (53%), Gaps = 13/175 (7%)
Query: 145 HHAEPDEAMGFCLYNNVAVAASFLLNERPELGINKILIVDWDVHHGNSTQKMFWKDPRVL 204
HH++ E GFC N++ + LL +++L VD D+HHG+ + F RV
Sbjct: 154 HHSKCGECSGFCYVNDIVLGILELLKCH-----DRVLYVDIDMHHGDGVDEAFCTSDRV- 207
Query: 205 FFSVHRHEFG-TFYPANDDGFYTMIGEGPGLGYNINVPWENGRCGDADYLAVWDHILLPV 263
F++ H+FG +F+P G +G G G Y++N+ +G D YL +++H L +
Sbjct: 208 -FTLSLHKFGESFFPGT--GHPRDVGYGRGRYYSMNLAVWDG-ITDFYYLGLFEHALHSI 263
Query: 264 AKDFGPDIIIISAGFDAAAGDPLGGCRVTPYGYSVMLKKLMDFAQGKIVLALEGG 318
+ + PD I++ G D+ AGD LG ++ +G+ ++ + D G +LAL GG
Sbjct: 264 VRRYSPDAIVLQCGADSLAGDRLGLLNLSSFGHGQCVQAVRDL--GIPMLALGGG 316
>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 = 47.8 bits (114), Expect = 4e-06
Identities = 21/164 (12%), Positives = 39/164 (23%), Gaps = 34/164 (20%)
Query: 178 NKILIVDWDVHHGNSTQKMFWK--------------DPRVLFFSVHRHEFGTFYPANDDG 223
+ ++D D HH T + F K V S+
Sbjct: 50 PDLGVIDVDAHHDVRTPEAFGKGNHHTPRHLLCEPLISDVHIVSIGIRGVSNGEAG---- 105
Query: 224 FYTMIGEGPGLGYNINVPWENGRCGDADYLAVWDHILLPVAKDFGPDIIIISAGFDAAAG 283
G + V++ I+ + D + +S D
Sbjct: 106 -----GAYARKLGVVYFSMTEVD--KLGLGDVFEEIVSYL--GDKGDNVYLSVDVDGLDP 156
Query: 284 DPLGGC-RVTPYGYSV-----MLKKLMDFAQGKIVLALEGGYNL 321
G P G S + +++ + L + L
Sbjct: 157 SFAPGTGTPGPGGLSYREGLYITERIAKT-NLVVGLDIVEVNPL 199
>gnl|CDD|225254 COG2379, GckA, Putative glycerate kinase [Carbohydrate transport
and metabolism].
Length = 422
Score = 33.8 bits (78), Expect = 0.26
Identities = 21/64 (32%), Positives = 28/64 (43%), Gaps = 11/64 (17%)
Query: 249 DAD-YLAVWDHILLPVAKDFGPDIII--------ISAGFDAAAGDPLGGCRVTPYGYSVM 299
AD Y A+ H LPV G I+I ++ F+ PL G VTPYGY
Sbjct: 20 AADPYRALAAH--LPVLPPKGRTIVIGAGKASAEMARAFEEHWKGPLAGVVVTPYGYGGP 77
Query: 300 LKKL 303
++
Sbjct: 78 CPRI 81
>gnl|CDD|131356 TIGR02303, HpaG-C-term, 4-hydroxyphenylacetate degradation
bifunctional isomerase/decarboxylase, C-terminal
subunit. This model represents one of two
subunits/domains of the bifunctional
isomerase/decarboxylase involved in
4-hydroxyphenylacetate degradation. In E. coli and some
other species this enzyme is encoded by a single
polypeptide containing both this domain and the closely
related N-terminal domain (TIGR02305). In other species
such as Pasteurella multocida these domains are found as
two separate proteins (usually as tandem genes).
Together, these domains carry out the decarboxylation of
5-oxopent-3-ene-1,2,5-tricarboxylic acid (OPET) to
2-hydroxy-2,4-diene-1,7-dioate (HHDD) and the subsequent
isomerization to 2-oxohept-3-ene-1,7-dioate (OHED).
Length = 245
Score = 31.3 bits (71), Expect = 1.1
Identities = 12/39 (30%), Positives = 20/39 (51%), Gaps = 5/39 (12%)
Query: 478 PPKE--ILWKTFPHHLFFGHDSSHTWGPGGVAFLNPECD 514
PP+E + K ++ GH T+ P V F++ EC+
Sbjct: 63 PPEEPLVFLK--GNNTLTGHKGV-TYRPKDVRFMHYECE 98
>gnl|CDD|223159 COG0081, RplA, Ribosomal protein L1 [Translation, ribosomal
structure and biogenesis].
Length = 228
Score = 30.7 bits (70), Expect = 1.9
Identities = 13/31 (41%), Positives = 17/31 (54%)
Query: 61 NAKEAKDKNLLSVHTENHVNLIKNISSKQFD 91
A+EAK V E+ + LIKN +K FD
Sbjct: 83 KAEEAKAAGADYVGGEDLIELIKNGRAKDFD 113
>gnl|CDD|222296 pfam13660, DUF4147, Domain of unknown function (DUF4147). This
domain is frequently found at the N-terminus of proteins
carrying the glycerate kinase-like domain MOFRL,
pfam05161.
Length = 227
Score = 30.1 bits (69), Expect = 2.8
Identities = 14/42 (33%), Positives = 22/42 (52%), Gaps = 9/42 (21%)
Query: 271 IIIISAG---------FDAAAGDPLGGCRVTPYGYSVMLKKL 303
I+++ AG + A GD L G VT YG++V L ++
Sbjct: 37 IVVVGAGKAAAAMAAAAEEALGDRLEGLVVTRYGHAVPLPRI 78
>gnl|CDD|236272 PRK08475, PRK08475, F0F1 ATP synthase subunit B; Validated.
Length = 167
Score = 29.6 bits (67), Expect = 3.2
Identities = 14/55 (25%), Positives = 25/55 (45%), Gaps = 4/55 (7%)
Query: 82 IKNISSKQFDSRRDRIASKLNSIYLNEGSSEAAYLAAGSVIEVAERVAEGELNSA 136
+KN + SR ++I+ +L I S+ A +E A+ AE + +A
Sbjct: 47 LKNF----YKSRINKISKRLEEIQEKLKESKEKKEDALKKLEEAKEKAELIVETA 97
>gnl|CDD|106970 PHA00661, PHA00661, hypothetical protein.
Length = 734
Score = 30.3 bits (68), Expect = 3.2
Identities = 23/82 (28%), Positives = 31/82 (37%), Gaps = 6/82 (7%)
Query: 245 GRCGDADY---LAVWDHILLPVAKDFGPDIIIISAGFDAAAGDPLGGCRVTPYGYSVMLK 301
GR DA Y LA+ + + K GP F A D R+ P+ YSV
Sbjct: 21 GRIDDAKYQSGLAICRNF---IVKPQGPAENRAGFRFVRAVKDSAKKVRLIPFTYSVTQT 77
Query: 302 KLMDFAQGKIVLALEGGYNLGS 323
+++F G GG L
Sbjct: 78 YVLEFGAGYFRFHTNGGTLLNG 99
>gnl|CDD|176118 cd08427, PBP2_LTTR_like_2, The C-terminal substrate binding domain
of an uncharacterized LysR-type transcriptional
regulator, contains the type 2 periplasmic binding fold.
LysR-transcriptional regulators comprise the largest
family of prokaryotic transcription factor. Homologs of
some of LTTRs with similar domain organizations are also
found in the archaea and eukaryotic organisms. The LTTRs
are composed of two functional domains joined by a
linker helix involved in oligomerization: an N-terminal
HTH (helix-turn-helix) domain, which is responsible for
the DNA-binding specificity, and a C-terminal
substrate-binding domain, which is structurally
homologous to the type 2 periplasmic binding proteins.
As also observed in the periplasmic binding proteins,
the C-terminal domain of the bacterial transcriptional
repressor undergoes a conformational change upon
substrate binding which in turn changes the DNA binding
affinity of the repressor. The genes controlled by the
LTTRs have diverse functional roles including amino acid
biosynthesis, CO2 fixation, antibiotic resistance,
degradation of aromatic compounds, nodule formation of
nitrogen-fixing bacteria, and synthesis of virulence
factors, to a name a few. This substrate-binding domain
shows significant homology to the type 2 periplasmic
binding proteins (PBP2), which are responsible for the
uptake of a variety of substrates such as phosphate,
sulfate, polysaccharides, lysine/arginine/ornithine, and
histidine. The PBP2 bind their ligand in the cleft
between these domains in a manner resembling a Venus
flytrap. After binding their specific ligand with high
affinity, they can interact with a cognate membrane
transport complex comprised of two integral membrane
domains and two cytoplasmically located ATPase domains.
This interaction triggers the ligand translocation
across the cytoplasmic membrane energized by ATP
hydrolysis.
Length = 195
Score = 29.1 bits (66), Expect = 5.4
Identities = 11/32 (34%), Positives = 17/32 (53%), Gaps = 1/32 (3%)
Query: 115 YLAAGSVIEVAERVAEGELNSAFAIVRPPGHH 146
++ G E+ RV GEL++A +V PP
Sbjct: 32 HIVPGLSAELLARVDAGELDAAI-VVEPPFPL 62
>gnl|CDD|182863 PRK10954, PRK10954, periplasmic protein disulfide isomerase I;
Provisional.
Length = 207
Score = 28.9 bits (65), Expect = 5.6
Identities = 14/40 (35%), Positives = 17/40 (42%), Gaps = 11/40 (27%)
Query: 338 DKPVAGSSEA-----------YPFESTWRVIQAVRKKLSA 366
DKPVAG + Y FE + V V+KKL
Sbjct: 32 DKPVAGEPQVLEFFSFYCPHCYQFEEVYHVSDNVKKKLPE 71
>gnl|CDD|176520 cd08578, GDPD_NUC-2_fungi, Putative glycerophosphodiester
phosphodiesterase domain of ankyrin repeat protein NUC-2
and similar proteins. This subfamily corresponds to a
putative glycerophosphodiester phosphodiesterase domain
(GDPD) present in Neurospora crassa ankyrin repeat
protein NUC-2 and its Saccharomyces cerevisiae
counterpart, Phosphate system positive regulatory
protein PHO81. Some uncharecaterized NUC-2 sequence
homologs are also included in this family. NUC-2 plays
an important role in the phosphate-regulated signal
transduction pathway in Neurospora crassa. It shows high
similarity to a cyclin-dependent kinase inhibitory
protein PHO81, which is part of the phosphate regulatory
cascade in S. cerevisiae. Both NUC-2 and PHO81 have
multi-domain architecture, including an SPX N-terminal
domain following by several ankyrin repeats and a
putative C-terminal GDPD domain with unknown function.
Although the putative GDPD domain displays sequence
homology to that of bacterial glycerophosphodiester
phosphodiesterases (GP-GDEs, EC 3.1.4.46), the residues
essential for interactions with the substrates and
calcium ions in bacterial GP-GDEs are not conserved in
members of this family, which suggests the function of
putative GDPD domains in these proteins might be
distinct from those in typical bacterial GP-GDEs.
Length = 300
Score = 29.2 bits (66), Expect = 5.6
Identities = 15/45 (33%), Positives = 23/45 (51%), Gaps = 3/45 (6%)
Query: 525 RITLEQFNDVLLQENVYSDDVSSPLFDTNDLNSVANKKAVSLEAL 569
+T EQ +L DD++S + D DL + + + VSLE L
Sbjct: 63 DLTAEQLESILDY---SLDDLNSEISDMVDLKRLLSSRVVSLETL 104
>gnl|CDD|237060 PRK12326, PRK12326, preprotein translocase subunit SecA; Reviewed.
Length = 764
Score = 29.5 bits (67), Expect = 5.8
Identities = 15/40 (37%), Positives = 21/40 (52%), Gaps = 12/40 (30%)
Query: 47 KLQAAGIPQRCVVLNAK----------EAKDKNLLSVHTE 76
+L+AAG+P VVLNAK EA ++V T+
Sbjct: 446 RLRAAGVP--AVVLNAKNDAEEARIIAEAGKYGAVTVSTQ 483
>gnl|CDD|132863 cd07224, Pat_like, Patatin-like phospholipase. Patatin-like
phospholipase. This family consists of various patatin
glycoproteins from plants. The patatin protein accounts
for up to 40% of the total soluble protein in potato
tubers. Patatin is a storage protein, but it also has
the enzymatic activity of lipid acyl hydrolase,
catalysing the cleavage of fatty acids from membrane
lipids. Members of this family have been found also in
vertebrates.
Length = 233
Score = 28.8 bits (65), Expect = 6.1
Identities = 11/27 (40%), Positives = 17/27 (62%), Gaps = 2/27 (7%)
Query: 319 YNLGSISNSVLACMNVLLEDKPVAGSS 345
Y+LG +S +L V+ E P+AG+S
Sbjct: 13 YHLGVLS--LLIEAGVINETTPLAGAS 37
>gnl|CDD|225932 COG3397, COG3397, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 308
Score = 29.1 bits (65), Expect = 6.6
Identities = 10/46 (21%), Positives = 13/46 (28%), Gaps = 6/46 (13%)
Query: 212 EFGTFYPANDDGFYTMIGEGPGLGYNINVPWENGRCGDADYLAVWD 257
E F G + G + +P R G AVW
Sbjct: 152 ELAPFCSITGVG----LEPGKNYRHECTIP--QDRTGYHVIYAVWQ 191
>gnl|CDD|237535 PRK13868, PRK13868, type IV secretion system single-stranded DNA
binding protein VirE2; Provisional.
Length = 556
Score = 29.1 bits (65), Expect = 7.8
Identities = 19/60 (31%), Positives = 30/60 (50%), Gaps = 5/60 (8%)
Query: 92 SRRDRIASKLNSIYLNEGSSEAAYLAAGSVIEVAERVAEGELNSAFAIVRPPGHHAEPDE 151
+ + ++ +L+ L+ SS + G+ EV E EL+S FA + PGH PDE
Sbjct: 62 THTEDLSPRLDEGMLDSQSSHDSGSVHGNQSEV-----ENELSSLFANMALPGHDRRPDE 116
>gnl|CDD|233029 TIGR00574, dnl1, DNA ligase I, ATP-dependent (dnl1). All proteins
in this family with known functions are ATP-dependent
DNA ligases. Functions include DNA repair, DNA
replication, and DNA recombination (or any process
requiring ligation of two single-stranded DNA sections).
This family is based on the phylogenomic analysis of JA
Eisen (1999, Ph.D. Thesis, Stanford University) [DNA
metabolism, DNA replication, recombination, and repair].
Length = 514
Score = 28.8 bits (65), Expect = 10.0
Identities = 25/102 (24%), Positives = 37/102 (36%), Gaps = 7/102 (6%)
Query: 83 KNISSKQFDSRRDRIASKLNSIYLNEGSSEAAYLAAGSVIEVAER--VAEGELNSAFAIV 140
K I+ + +D+ L S+ EA YL +I R +AE + A A
Sbjct: 65 KFIARLSGEGSQDKKIKLLKSLLKRATPLEAKYLI--RLILGDLRIGIAEKTILDALAKA 122
Query: 141 RPPGHHAEPDEAMGFCLYNNVAVAASFLLNERPELGINKILI 182
+ PD F L N++ A LL E + I
Sbjct: 123 F---LLSPPDVERAFNLTNDLGKVAKILLEEGLRGLDKDLSI 161
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
0.318 0.136 0.418
Gapped
Lambda K H
0.267 0.0867 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 29,801,955
Number of extensions: 2936033
Number of successful extensions: 2533
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2406
Number of HSP's successfully gapped: 53
Length of query: 579
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 477
Effective length of database: 6,413,494
Effective search space: 3059236638
Effective search space used: 3059236638
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 (21.7 bits)
S2: 62 (27.4 bits)