RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 048339
(386 letters)
>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 = 477 bits (1231), Expect = e-169
Identities = 153/343 (44%), Positives = 203/343 (59%), Gaps = 7/343 (2%)
Query: 19 VFWDDGMLNHDTGKGLFDTGFDPGFLEVLEKHPENSDRIKNIVSILKRGPISPYISWHSG 78
WD+ L HDTG G G L +HPEN + + I ++L+ +S ++ +
Sbjct: 3 FVWDERYLWHDTGTGALFL-PVGGLLVQPGRHPENPETKRRIKNLLEVSGLSDHLVLITP 61
Query: 79 IPAQIPQLLSFHTPDYINELVEADKAGGKMVCDGTVLNPGSWGAALLAVGTTLSAMKHVL 138
PA +LL HTP+YI+ + A AGG GT PGS+ ALLA G ++A+ VL
Sbjct: 62 RPATDEELLRVHTPEYIDRVKAASAAGGGEAGGGTPFGPGSYEIALLAAGGAIAAVDAVL 121
Query: 139 DGHGKIAYALVRPPGHHAQPTMADGYCFLNNAGLAVQLALNS-GCGKVVVIDIDVHYGNG 197
DG AYALVRPPGHHA+P G+C NN +A + AL G +V V+D DVH+GNG
Sbjct: 122 DGEVDNAYALVRPPGHHAEPDQGMGFCLFNNVAIAARHALAVGGVKRVAVVDWDVHHGNG 181
Query: 198 TAEGFYRSNKVLTISLHMNHGSWGPSHPQNGTVDELGEGEGFGYNLNIPLPNGTGDRGYV 257
T FY VLTISLH + P +G V+E GEG G GYNLNIPLP G+GD Y+
Sbjct: 182 TQAIFYDDPDVLTISLHQDR----CFPPDSGAVEERGEGAGEGYNLNIPLPPGSGDGAYL 237
Query: 258 HAMTELVVPAIQKFEPNMIVLVVGQDSSAFDPNGRQCLTMDGYREMGRIVRSLADRYSGG 317
HA +V+PA++ F P +I++ G D+SAFDP GR LT DG+R + R +R LAD GG
Sbjct: 238 HAFERIVLPALRAFRPELIIVASGFDASAFDPLGRMMLTSDGFRALTRKLRDLADELCGG 297
Query: 318 RLLIVQEGGYHVTYSAYCLHATLEGVLNLPLALLSDPIAYYPE 360
RL++V EGGY Y +C A LE + + ++DP+ YYPE
Sbjct: 298 RLVMVHEGGYSEAYVPFCGLAVLEELSGVRTG-IADPLLYYPE 339
>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 = 300 bits (770), Expect = e-100
Identities = 128/302 (42%), Positives = 183/302 (60%), Gaps = 13/302 (4%)
Query: 48 EKHPENSDRIKNIVSILKRGPISPYISWHSGIPAQIPQLLSFHTPDYINELVEADKAGGK 107
HPEN +R++ I+ +LK + + + + PA +LL H+P+Y+ L EA +
Sbjct: 7 LGHPENPERLEAILELLKESGLLDRLEFIAPRPATEEELLLVHSPEYVEFLEEASLEEEE 66
Query: 108 MVCDG----TVLNPGSWGAALLAVGTTLSAMKHVLDGHGKIAYALVRPPGHHAQPTMADG 163
+ G T ++PGS+ AALLA G TL A VL G + A+A VRPPGHHA+ A G
Sbjct: 67 LGRIGLDGDTPVSPGSYEAALLAAGGTLEAADLVLSG--ENAFAAVRPPGHHAERDRASG 124
Query: 164 YCFLNNAGLAVQLALNS-GCGKVVVIDIDVHYGNGTAEGFYRSNKVLTISLHMNHGSWGP 222
+C NN +A + L G +V+++D+DVH+GNGT E FY +VLTIS+H + P
Sbjct: 125 FCLFNNVAIAARYLLKRYGLKRVLIVDLDVHHGNGTQEIFYDDPRVLTISIHQD-----P 179
Query: 223 SHPQNGTVDELGEGEGFGYNLNIPLPNGTGDRGYVHAMTELVVPAIQKFEPNMIVLVVGQ 282
+P G DE GEG G GY LNIPLP GTGD Y+ A E+++PA+++F+P++I++ G
Sbjct: 180 FYPGTGFADETGEGAGEGYTLNIPLPPGTGDEEYLAAFEEILLPALREFQPDLILVSAGF 239
Query: 283 DSSAFDPNGRQCLTMDGYREMGRIVRSLADRYSGGRLLIVQEGGYHVTYSAYCLHATLEG 342
D+ A DP G LT +GY E R++ LAD Y GG ++ V EGGY++ A A L G
Sbjct: 240 DAHAGDPLGGLNLTTEGYAERTRLLLELADAY-GGPVVSVLEGGYNLDALARSAAAVLAG 298
Query: 343 VL 344
+L
Sbjct: 299 LL 300
>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 = 297 bits (764), Expect = e-100
Identities = 117/296 (39%), Positives = 177/296 (59%), Gaps = 6/296 (2%)
Query: 50 HPENSDRIKNIVSILKRGPISPYISWHSGIPAQIPQLLSFHTPDYINELVEADKAGGKMV 109
HPE +R+ I+ L+ + + + PA +LL HTP+YI + E +AGG +
Sbjct: 1 HPERPERLLAILEALEEEGLLDRLVFVEPRPATEEELLRVHTPEYIERVEETCEAGGGYL 60
Query: 110 CDGTVLNPGSWGAALLAVGTTLSAMKHVLDGHGKIAYALVRPPGHHAQPTMADGYCFLNN 169
T ++PGS+ AALLA G L+A+ VL G + A+ALVRPPGHHA+P A G+C NN
Sbjct: 61 DPDTYVSPGSYEAALLAAGAALAAVDAVLSGEAENAFALVRPPGHHAEPDRAMGFCLFNN 120
Query: 170 AGLAVQLALN-SGCGKVVVIDIDVHYGNGTAEGFYRSNKVLTISLHMNHGSWGPSHPQNG 228
+A + A G +V+++D DVH+GNGT + FY VL S+H P +P G
Sbjct: 121 VAIAARYAQKRYGLKRVLIVDWDVHHGNGTQDIFYDDPSVLYFSIHQ-----YPFYPGTG 175
Query: 229 TVDELGEGEGFGYNLNIPLPNGTGDRGYVHAMTELVVPAIQKFEPNMIVLVVGQDSSAFD 288
+E G G G G+ +N+PLP G+GD Y+ A E+++P ++F+P+++++ G D+ D
Sbjct: 176 AAEETGGGAGEGFTINVPLPPGSGDAEYLAAFEEVLLPIAREFQPDLVLVSAGFDAHRGD 235
Query: 289 PNGRQCLTMDGYREMGRIVRSLADRYSGGRLLIVQEGGYHVTYSAYCLHATLEGVL 344
P G LT +GY + R+++ LAD + GGRL+ V EGGY++ A + A LE +L
Sbjct: 236 PLGGMNLTPEGYARLTRLLKELADEHCGGRLVFVLEGGYNLEALAESVLAVLEALL 291
>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 = 273 bits (699), Expect = 2e-89
Identities = 131/322 (40%), Positives = 189/322 (58%), Gaps = 9/322 (2%)
Query: 39 FDPGFLEV--LEKHPENSDRIKNIVSILKRGPISPYISWHSGIPAQIPQLLSFHTPDYIN 96
+ P FLE HPEN DR++ I+ +L+ + + PA + +LL H+PDY+
Sbjct: 8 YHPEFLEHEPPPGHPENPDRLRLILELLESSGLPDSLELVEPRPATLEELLLVHSPDYVE 67
Query: 97 ELVEADKAGGK-MVCDGTVLNPGSWGAALLAVGTTLSAMKHVLDGHGKIAYALVRPPGHH 155
L + G + T ++PG++ AA LA G L+A+ VL+G A+ALVRPPGHH
Sbjct: 68 FLESLSEEEGYGNLDGDTPVSPGTYEAARLAAGGALTAVDAVLEGEDN-AFALVRPPGHH 126
Query: 156 AQPTMADGYCFLNNAGLAVQLALNSGCGKVVVIDIDVHYGNGTAEGFYRSNKVLTISLHM 215
A A G+C NN +A + L G +V +ID DVH+GNGT E FY + VLT+SL
Sbjct: 127 AGRDRASGFCLFNNVAIAAKYLLKKGVKRVAIIDFDVHHGNGTQEIFYDDDDVLTVSL-- 184
Query: 216 NHGSWGPSHPQNGTVDELGEGEGFGYNLNIPLPNGTGDRGYVHAMTELVVPAIQKFEPNM 275
H P +P G DE+GEG G N+NIPLP GTGD Y+ A+ E+V+P +++F+P++
Sbjct: 185 -HQDGRPFYPGTGGADEIGEG-KEGNNVNIPLPPGTGDDSYLEALEEIVLPLLEEFKPDL 242
Query: 276 IVLVVGQDSSAFDPNGRQCLTMDGYREMGRIVRSLADRYSGGRLLIVQEGGYHVTYSAYC 335
+++ G D+ DP GR LT +GY ++GR VR LA+ Y GG ++ V EGGY++ A
Sbjct: 243 VIVSAGFDAHRGDPLGRLNLTEEGYAKIGRAVRKLAEGY-GGPVVAVLEGGYNLDALARS 301
Query: 336 LHATLEGVLNLPLALLSDPIAY 357
L A L G+ L L +P+
Sbjct: 302 LVAFLAGLAGLVEEELEEPLPE 323
>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 = 250 bits (640), Expect = 4e-81
Identities = 116/299 (38%), Positives = 159/299 (53%), Gaps = 33/299 (11%)
Query: 50 HPENSDRIKNIVSILKRGPISPYISWHSGIPAQIPQLLSFHTPDYINELVEADKAGGKMV 109
HPEN +R + I+ LKR + + + +L+ H PDY++ L AD
Sbjct: 25 HPENPERAEAILDALKRAGLGEVLP---PRDFGLEPILAVHDPDYVDFLETADT------ 75
Query: 110 CDGTVLNPGSWGAALLAVGTTLSAMKHVLDGHGKIAYALVRPPGHHAQPTMADGYCFLNN 169
T ++ G+W AAL A T L+A VL+G + AYAL RPPGHHA A G+C+ NN
Sbjct: 76 --DTPISEGTWEAALAAADTALTAADLVLEGE-RAAYALCRPPGHHAGRDRAGGFCYFNN 132
Query: 170 AGLAVQLALNSGCGKVVVIDIDVHYGNGTAEGFYRSNKVLTISLHMNHGSWGPSHPQN-- 227
A +A Q + G+V ++D+DVH+GNGT E FY VL +S+H P+
Sbjct: 133 AAIAAQYLRDRA-GRVAILDVDVHHGNGTQEIFYERPDVLYVSIH--------GDPRTFY 183
Query: 228 ----GTVDELGEGEGFGYNLNIPLPNGTGDRGYVHAMTELVVPAIQKFEPNMIVLVVGQD 283
G DE GEGEG GYNLN+PLP GTGD Y+ A+ E + AI F P+ +V+ +G D
Sbjct: 184 PFFLGFADETGEGEGEGYNLNLPLPPGTGDDDYLAALDE-ALAAIAAFGPDALVVSLGFD 242
Query: 284 SSAFDPNGRQCLTMDGYREMGRIVRSLADRYSGGRLLIVQEGGYHVTYSAYCLHATLEG 342
+ DP LT + Y +GR + +L G + VQEGGY+V A L G
Sbjct: 243 THEGDPLSDFKLTTEDYARIGRRIAAL-----GLPTVFVQEGGYNVDALGRNAVAFLAG 296
>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 = 230 bits (589), Expect = 3e-73
Identities = 113/292 (38%), Positives = 153/292 (52%), Gaps = 17/292 (5%)
Query: 48 EKHPENSDRIKNIVSILKRGPISPYISWHSGIPAQIPQLLSFHTPDYINELVEADKAGGK 107
HP N R+ +L+ + P + PA +LL FHTPDYI + EA +
Sbjct: 15 PNHPFNPPRLSLTKDLLRALGLLPPVDLVPPRPATEEELLLFHTPDYIEAVKEASRGQEP 74
Query: 108 MVC----DGTVLNP---GSWGAALLAVGTTLSAMKHVLDGHGKIAYALVRPPG--HHAQP 158
GT NP G AA L VG TL A + VL+G + A+ P G HHA
Sbjct: 75 EGRGRLGLGTEDNPVFPGMHEAAALVVGGTLLAARLVLEGEARRAFN---PAGGLHHAMR 131
Query: 159 TMADGYCFLNNAGLAVQLALNSGCGKVVVIDIDVHYGNGTAEGFYRSNKVLTISLHMNHG 218
A G+C N+A +A++ + G +V +DID H+G+G FY +VLTISLH +
Sbjct: 132 GRASGFCVYNDAAVAIERLRDKGGLRVAYVDIDAHHGDGVQAAFYDDPRVLTISLHESGR 191
Query: 219 S-WGPSHPQNGTVDELGEGEGFGYNLNIPLPNGTGDRGYVHAMTELVVPAIQKFEPNMIV 277
+ P G VDE+GEGEG+GY +NIPLP GTGD ++ A +V P ++ F P++IV
Sbjct: 192 YLF----PGTGFVDEIGEGEGYGYAVNIPLPPGTGDDEFLRAFEAVVPPLLRAFRPDVIV 247
Query: 278 LVVGQDSSAFDPNGRQCLTMDGYREMGRIVRSLADRYSGGRLLIVQEGGYHV 329
G D+ A DP L+ YR R +R LAD Y GGR L + GGY+
Sbjct: 248 SQHGADAHAGDPLTHLNLSNRAYRAAVRRIRELADEYCGGRWLALGGGGYNP 299
>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 = 202 bits (517), Expect = 3e-62
Identities = 107/324 (33%), Positives = 173/324 (53%), Gaps = 28/324 (8%)
Query: 48 EKHPENSDRIKNIVSILKRG-------PISPYISWHSGIPAQIPQLLSFHTPDYINELVE 100
H E +R++ I+ L + I A+ ++L H+ +YI+ +
Sbjct: 5 SNHIECPERLEAILERLTQDGLLERCVKIPAR-------EAEEDEILLVHSQEYIDLVKS 57
Query: 101 A---DKAGGKMVCDG---TVLNPGSWGAALLAVGTTLSAMKHVLDGHGKIAYALVRPPGH 154
+K + +C G L P ++ AA LA G+T+ +K V+ G + +AL+RPPGH
Sbjct: 58 TETMEKEELESLCSGYDSVYLCPSTYEAARLAAGSTIELVKAVMAGKIQNGFALIRPPGH 117
Query: 155 HAQPTMADGYCFLNNAGLAVQLALNS-GCGKVVVIDIDVHYGNGTAEGFYRSNKVLTISL 213
HA A+GYC NN +A + A+ G +++++D DVH+G GT +GFY +VL S+
Sbjct: 118 HAMRNEANGYCIFNNVAIAAKYAIEKLGLKRILIVDWDVHHGQGTQQGFYEDPRVLYFSI 177
Query: 214 HM-NHGSWGPSHPQNGTVDELGEGEGFGYNLNIPLPN-GTGDRGYVHAMTELVVPAIQKF 271
H HG + P ++ D +G G G+G+N+N+PL G GD Y+ +++P +F
Sbjct: 178 HRYEHGRFWPHLFES-DYDYIGVGHGYGFNVNVPLNQTGLGDADYLAIFHHILLPLALEF 236
Query: 272 EPNMIVLVVGQDSSAFDPNGRQCLTMDGYREMGRIVRSLADRYSGGRLLIVQEGGYHVTY 331
+P ++++ G D+S DP G +T GY + R++ LA GG+LL+V EGGY +
Sbjct: 237 QPELVLVSAGFDASIGDPEGEMAVTPAGYAHLTRLLMGLA----GGKLLLVLEGGYLLES 292
Query: 332 SAYCLHATLEGVLNLPLALLSDPI 355
A + TL G+L PL L+ PI
Sbjct: 293 LAESVSMTLRGLLGDPLPPLAPPI 316
>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 = 195 bits (497), Expect = 8e-60
Identities = 100/282 (35%), Positives = 149/282 (52%), Gaps = 13/282 (4%)
Query: 50 HPENSDRIKNIVSILKRGPISPYISWHSGIPAQIPQLLSFHTPDYINELVEADKAGGKMV 109
HPE+ +R++ I+ L + + PA QLL H Y++ L A G +
Sbjct: 1 HPESPERLEAILDALIASGLDRLLRQLEAPPATREQLLRVHDAAYVDRLEAAAPEEGLVQ 60
Query: 110 CDG-TVLNPGSWGAALLAVGTTLSAMKHVLDGHGKIAYALVRPPGHHAQPTMADGYCFLN 168
D T ++PGS AAL A G ++A+ V+ G + A+ VRPPGHHA+ A G+C N
Sbjct: 61 LDPDTAMSPGSLEAALRAAGAVVAAVDAVMAGEARNAFCAVRPPGHHAERDKAMGFCLFN 120
Query: 169 NAGLAVQLALNS-GCGKVVVIDIDVHYGNGTAEGFYRSNKVLTISLHMNHGSWGPSHPQN 227
N +A AL G +V ++D DVH+GNGT + F +VL S H + P +P
Sbjct: 121 NVAIAAAHALAHHGLERVAIVDFDVHHGNGTEDIFRDDPRVLFCSSHQH-----PLYPGT 175
Query: 228 GTVDELGEGEGFGYN-LNIPLPNGTGDRGYVHAMTELVVPAIQKFEPNMIVLVVGQDSSA 286
G DE G G N +N+PLP GTG + A+ + +PA+ F+P++I++ G D+
Sbjct: 176 GAPDETGHG-----NIVNVPLPAGTGGAEFREAVEDRWLPALDAFKPDLILISAGFDAHR 230
Query: 287 FDPNGRQCLTMDGYREMGRIVRSLADRYSGGRLLIVQEGGYH 328
DP + LT + Y + + +ADRY GR++ V EGGY
Sbjct: 231 DDPLAQLNLTEEDYAWITEQLMDVADRYCDGRIVSVLEGGYD 272
>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 = 186 bits (473), Expect = 1e-55
Identities = 111/343 (32%), Positives = 178/343 (51%), Gaps = 28/343 (8%)
Query: 21 WDDGMLNHDTGKGLFDTGFDPGFLEVLEKHPENSDRIKNIVSILKRGPISPYISWHSGIP 80
+D M+NH L+D G HPE RI I +
Sbjct: 1 YDQRMMNH---HNLWDPG-----------HPECPQRISRIYERHNDLGLLERCLRLPSRL 46
Query: 81 AQIPQLLSFHTPDYINELVEADKAG----GKMVC--DGTVLNPGSWGAALLAVGTTLSAM 134
A +LL H+ ++++E+ +K ++ D ++P S+ ALLA G L +
Sbjct: 47 ATEDELLLCHSEEHLDEMKSLEKMKPRELNRLGKEYDSIYIHPDSYQCALLAAGCVLQVV 106
Query: 135 KHVLDGHGKIAYALVRPPGHHAQPTMADGYCFLNNAGLAVQLALN-SGCGKVVVIDIDVH 193
+ VL G + A+VRPPGHHA+ A G+CF NN +A + A G +++++D DVH
Sbjct: 107 EAVLTGESRNGVAIVRPPGHHAEQDTACGFCFFNNVAIAARYAQKKYGLKRILIVDWDVH 166
Query: 194 YGNGTAEGFYRSNKVLTISLH-MNHGSWGPSHPQNGTVDELGEGEGFGYNLNIPL-PNGT 251
+GNGT F VL ISLH ++GS+ P+ P+ G D +G+G+G G+N+NIP G
Sbjct: 167 HGNGTQHMFESDPSVLYISLHRYDNGSFFPNSPE-GNYDVVGKGKGEGFNVNIPWNKGGM 225
Query: 252 GDRGYVHAMTELVVPAIQKFEPNMIVLVVGQDSSAFDPNGRQCLTMDGYREMGRIVRSLA 311
GD Y+ A ++V+P +F P ++++ G D++ DP G +T +GY M ++ SLA
Sbjct: 226 GDAEYIAAFQQVVLPIAYEFNPELVLVSAGFDAARGDPLGGCKVTPEGYAHMTHMLMSLA 285
Query: 312 DRYSGGRLLIVQEGGYHVTYSAYCLHATLEGVLNLPLALLSDP 354
GGR++++ EGGY++T + + + +L P +L P
Sbjct: 286 ----GGRVIVILEGGYNLTSISESMSMCTKTLLGDPPPVLDLP 324
>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 = 162 bits (413), Expect = 3e-47
Identities = 96/296 (32%), Positives = 153/296 (51%), Gaps = 24/296 (8%)
Query: 50 HPENSDRIKNIVSILKRGPISPYIS--WHSGI-PAQIPQLLSFHTPDYINELVEA----- 101
HPE+ RI I LK + I+ I A ++L H+ ++ + +
Sbjct: 3 HPEDPSRISRIFEKLKE---AGLINRMLRIPIREATKEEILLVHSEEHWDRVEATEKMSD 59
Query: 102 ---DKAGGKMVCDGTVLNPGSWGAALLAVGTTLSAMKHVLDGHGKIAYALVRPPGHHAQP 158
D +N + A L+ G + A + V +G K A+A+VRPPGHHA+P
Sbjct: 60 EQLKDRTEIFERDSLYVNNDTAFCARLSCGGAIEACRAVAEGRVKNAFAVVRPPGHHAEP 119
Query: 159 TMADGYCFLNNAGLAVQLALNSG---CGKVVVIDIDVHYGNGTAEGFYRSNKVLTISLH- 214
+ G+CF NN +A + K++++D D+H+GNGT FY VL ISLH
Sbjct: 120 DESMGFCFFNNVAVAAKWLQTEYPDKIKKILILDWDIHHGNGTQRAFYDDPNVLYISLHR 179
Query: 215 MNHGSWGPSHPQNGTVDELGEGEGFGYNLNIPLPN-GTGDRGYVHAMTELVVPAIQKFEP 273
+G + P P G + +GEG G G+N+NIP P G GD Y++A +V+P +F+P
Sbjct: 180 FENGGFYPGTPY-GDYESVGEGAGLGFNVNIPWPQGGMGDADYIYAFQRIVMPIAYEFDP 238
Query: 274 NMIVLVVGQDSSAFDPNGRQCLTMDGYREMGRIVRSLADRYSGGRLLIVQEGGYHV 329
+++++ G D++ D G+ +T GY M ++ SLA GG+L++ EGGY++
Sbjct: 239 DLVIISAGFDAADGDELGQCHVTPAGYAHMTHMLMSLA----GGKLVVALEGGYNL 290
>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 = 160 bits (407), Expect = 9e-47
Identities = 86/286 (30%), Positives = 138/286 (48%), Gaps = 21/286 (7%)
Query: 56 RIKNIVSILKRGPISPYISWHSGIPAQIPQLLSFHTPDYINELVEADKAGGKMVCDGTVL 115
RI++++ LK + P I A LL HT +Y+NEL +
Sbjct: 1 RIRDLIEALKELGLRPKIELIECREATEELLLKVHTEEYLNELKANFAVATITESKPVIF 60
Query: 116 NPGSW------GAALLAVGTTLSAMKHVLDGHGKIAYALVRPPGHHAQPTMADGYCFLNN 169
P A L+ G + A + V G + A+A+V GHHA + A G+C+ N+
Sbjct: 61 GPNFPVQRHYFRGARLSTGGVVEAAELVAKGELERAFAVVGAGGHHAGKSRAWGFCYFND 120
Query: 170 AGLAVQLALNSGCGKVVVIDIDVHYGNGTAEGFYRSNKVLTISLHMNHGSWGPSHPQNGT 229
LA++ G ++++ID D H+G+GT E FY ++VL +S H P
Sbjct: 121 VVLAIKFLRERGISRILIIDTDAHHGDGTREAFYDDDRVLHMSFHNYD--IYP------- 171
Query: 230 VDELGEGEGFGYNLNIPLPNGTGDRGYVHAMTELVVPAIQKFEPNMIVLVVGQDSSAFDP 289
G G+G GY +N+PL +G GD Y+ A+ ++ +++FEP ++VL G D+ D
Sbjct: 172 ---FGRGKGKGYKINVPLEDGLGDEEYLDAVERVISKVLEEFEPEVVVLQFGHDTHEGDR 228
Query: 290 NGRQCLTMDGYREMGRIVRSLADRYSGGRLLIVQEGGYHVTYSAYC 335
G L+ G+ ++ IV+ A GG +L+V GGY+ +A
Sbjct: 229 LGGFNLSEKGFVKLAEIVKEFAR---GGPILMVLGGGYNPEAAARI 271
>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 = 158 bits (403), Expect = 1e-45
Identities = 78/268 (29%), Positives = 129/268 (48%), Gaps = 26/268 (9%)
Query: 80 PAQIPQLLSFHTPDYINELVEADKAGGKMVC----------DGTVLNPGSWGAALLAVGT 129
PA +L FH+ DYI+ L K D V G + L G
Sbjct: 45 PATAEELTKFHSDDYIDFLRSVSPDNMKEFKKQLERFNVGEDCPVF-DGLYEYCQLYAGG 103
Query: 130 TLSAMKHVLDGHGKIAYALVRPPG--HHAQPTMADGYCFLNNAGLAVQLALNSGCGKVVV 187
+++A + G IA + G HHA+ + A G+C++N+ LA+ L L +V+
Sbjct: 104 SIAAAVKLNRGQADIA---INWAGGLHHAKKSEASGFCYVNDIVLAI-LELLKYHQRVLY 159
Query: 188 IDIDVHYGNGTAEGFYRSNKVLTISLHMNHGSWGPSHPQNGTVDELGEGEGFGYNLNIPL 247
IDID+H+G+G E FY +++V+T+S H +G + ++G G+G Y +N+PL
Sbjct: 160 IDIDIHHGDGVEEAFYTTDRVMTVSFH----KFGEYFFPGTGLRDIGAGKGKYYAVNVPL 215
Query: 248 PNGTGDRGYVHAMTELVVPAIQKFEPNMIVLVVGQDSSAFDPNGRQCLTMDGYREMGRIV 307
+G D Y+ ++ ++ F+P+ +VL G DS A D G L++ G+ + + V
Sbjct: 216 KDGIDDESYLQIFEPVLSKVMEVFQPSAVVLQCGADSLAGDRLGCFNLSIKGHAKCVKFV 275
Query: 308 RSLADRYSGGRLLIVQEGGYHVTYSAYC 335
+S LL++ GGY + A C
Sbjct: 276 KSF-----NIPLLVLGGGGYTLRNVARC 298
>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 = 150 bits (379), Expect = 4e-42
Identities = 97/308 (31%), Positives = 151/308 (49%), Gaps = 23/308 (7%)
Query: 85 QLLSFHTPDYINELVEA----DKAGGKMVC---DGTVLNPGSWGAALLAVGTTLSAMKHV 137
+LL H+P+Y+ L+++ + + + D L+P S+ A LAVG+ L + V
Sbjct: 42 ELLLVHSPEYV-ALMKSTQYMTEEELRTLADTYDSVYLHPNSYSCACLAVGSVLQLVDKV 100
Query: 138 LDGHGKIAYALVRPPGHHAQPTMADGYCFLNNAGLAVQLA-LNSGCGKVVVIDIDVHYGN 196
L G + A+VRPPGHHAQ DGYC NN +A + A G +V+++D DVH+G
Sbjct: 101 LGGEIRNGLAIVRPPGHHAQHDKMDGYCMFNNVAIAARYAQQKHGVQRVLIVDWDVHHGQ 160
Query: 197 GTAEGFYRSNKVLTISLH-MNHGSWGPSHPQNGTVDELGEGEGFGYNLNIPLPN-GTGDR 254
GT F + VL S+H G + P H + +G G G GYN+N+P G D
Sbjct: 161 GTQFIFEQDPSVLYFSIHRYEQGRFWP-HLKESDSSAVGFGRGEGYNINVPWNQVGMRDA 219
Query: 255 GYVHAMTELVVPAIQKFEPNMIVLVVGQDSSAFDPNGRQCLTMDGYREMGRIVRSLADRY 314
Y+ A +++P +F+P ++++ G D+ DP G T + + ++ LA
Sbjct: 220 DYIAAFLHVLLPVALEFQPQLVLVAAGFDAVIGDPKGEMAATPACFAHLTHLLMGLA--- 276
Query: 315 SGGRLLIVQEGGYHVTYSAYCLHATLEGVLNLPLALLSDPIAYYPEDEAFPVKVIESIKQ 374
GG+L++ EGGY+ L + EGV ALL DP A + S+
Sbjct: 277 -GGKLILSLEGGYN-------LRSLAEGVCASLKALLGDPCPMLESPGAPCRSALASVSC 328
Query: 375 YQNDVIPF 382
+ + PF
Sbjct: 329 TISALEPF 336
>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 = 149 bits (379), Expect = 1e-41
Identities = 107/345 (31%), Positives = 158/345 (45%), Gaps = 47/345 (13%)
Query: 50 HPENSDRIKNIVSILKRGPISPYISWHSGIPAQIPQLLSFHTPDYI-------------- 95
HPE+ R+++I S L+ + G A + +L H+ +
Sbjct: 24 HPEHGGRLQSIWSRLQETGLVNRCERLRGRKATLEELQLVHSEVHTLLYGTNPLSRLKLD 83
Query: 96 -NELVEADKA-------GGKMVCDGTVLNPG-SWGAALLAVGTTLSAMKHVLDGHGKIAY 146
+L + GG V TV N + AA +AVG + V G K +
Sbjct: 84 PTKLAGLPQKSFVRLPCGGIGVDSDTVWNELHTSNAARMAVGCVIDLAFKVATGELKNGF 143
Query: 147 ALVRPPGHHAQPTMADGYCFLNNAGLAV-QLALNSGCGKVVVIDIDVHYGNGTAEGFYRS 205
A+VRPPGHHA+P+ A G+CF N+ +A QL K++++D DVH+GNGT + FY
Sbjct: 144 AVVRPPGHHAEPSQAMGFCFFNSVAIAAKQLQQKLKLRKILIVDWDVHHGNGTQQIFYED 203
Query: 206 NKVLTISLHMNHGSWGPSHPQNGTVDELGEGEGFGYNLNIPLPNGT----GDRGYVHAMT 261
VL ISLH + G P G E+G G G G+N+NI G GD Y+ A
Sbjct: 204 PNVLYISLH-RYDD-GNFFPGTGAPTEVGSGAGEGFNVNIAWSGGLDPPMGDAEYLAAFR 261
Query: 262 ELVVPAIQKFEPNMIVLVVGQDSSAFDPNGRQCLTMDGYRE----MGRIVRSLADRYSGG 317
+V+P ++F P+ IVLV S+ FD + GY+ G + R L +GG
Sbjct: 262 TVVMPIAREFSPD-IVLV----SAGFDAAEGHPPPLGGYKVSPACFGYMTRQLM-NLAGG 315
Query: 318 RLLIVQEGGYHVTYSAYCLHATLEGVLNLPLALLSDPIAYYPEDE 362
++++ EGGY +T A + ALL D + E+E
Sbjct: 316 KVVLALEGGYDLTAICDASEACVR-------ALLGDELDPLSEEE 353
>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 = 146 bits (371), Expect = 8e-41
Identities = 94/307 (30%), Positives = 156/307 (50%), Gaps = 21/307 (6%)
Query: 85 QLLSFHTPDYINELVEADKAGGKMVC------DGTVLNPGSWGAALLAVGTTLSAMKHVL 138
++L H+P+Y++ + E + + D +P ++ A LA G TL + VL
Sbjct: 42 EILLVHSPEYLSLVRETQVMNKEELMAISGKYDAVYFHPNTFHCARLAAGATLQLVDAVL 101
Query: 139 DGHGKIAYALVRPPGHHAQPTMADGYCFLNNAGLAVQLA-LNSGCGKVVVIDIDVHYGNG 197
G + ALVRPPGHH+Q A+G+C NN +A + A G +++++D DVH+G G
Sbjct: 102 TGEVQNGMALVRPPGHHSQRNAANGFCVFNNVAIAAEYAKKKYGLHRILIVDWDVHHGQG 161
Query: 198 TAEGFYRSNKVLTISLH-MNHGSWGPSHPQNGTVDELGEGEGFGYNLNIPLPN-GTGDRG 255
F VL S H H + P ++ D +G G+G G+N+N+P G G+
Sbjct: 162 IQYIFEEDPSVLYFSWHRYEHQRFWPFLRES-DYDAVGRGKGLGFNINLPWNKVGMGNAD 220
Query: 256 YVHAMTELVVPAIQKFEPNMIVLVVGQDSSAFDPNGRQCLTMDGYREMGRIVRSLADRYS 315
Y+ A +++P +F+P ++++ G DS+ DP G+ C T + + + ++ LA
Sbjct: 221 YLAAFFHVLLPLAFEFDPELVLVSAGFDSAIGDPEGQMCATPECFAHLTHLLMVLA---- 276
Query: 316 GGRLLIVQEGGYHVTYSAYCLHATLEGVLNLPLALLSDPIAYYPEDEAFPVKVIESIKQY 375
GG+L V EGGYH+ A + T++ +L PL LS + P A +ESI+
Sbjct: 277 GGKLCAVLEGGYHLESLAESVCMTVQTLLGDPLPRLSGEMT--PCQSA-----LESIQNV 329
Query: 376 QNDVIPF 382
+ P+
Sbjct: 330 RAAQAPY 336
>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 = 135 bits (342), Expect = 2e-36
Identities = 100/327 (30%), Positives = 157/327 (48%), Gaps = 41/327 (12%)
Query: 49 KHPENSDRIKNIVSILKRGPISPYISWHSGIPAQIPQLLSFHTPDYI-----NELVEADK 103
HPE++ RI++I S L+ + G A + +L S H+ ++ N L
Sbjct: 23 NHPEHAGRIQSIWSRLQERGLRSQCECLRGRKASLEELQSVHSERHVLLYGTNPLSRLKL 82
Query: 104 AGGKMV------------CDG------TVLNP-GSWGAALLAVGTTLSAMKHVLDGHGKI 144
GK+ C G T+ N S AA A G+ V K
Sbjct: 83 DNGKLAGLLAQRMFVMLPCGGVGVDTDTIWNELHSSNAARWAAGSVTDLAFKVASRELKN 142
Query: 145 AYALVRPPGHHAQPTMADGYCFLNNAGLAV-QLALNSGCGKVVVIDIDVHYGNGTAEGFY 203
+A+VRPPGHHA + A G+CF N+ +A QL K++++D DVH+GNGT + FY
Sbjct: 143 GFAVVRPPGHHADHSTAMGFCFFNSVAIACRQLQQQGKASKILIVDWDVHHGNGTQQTFY 202
Query: 204 RSNKVLTISLHMNHGSWGPSHPQNGTVDELGEGEGFGYNLNIPLPNG----TGDRGYVHA 259
+ VL ISLH + G P +G VDE+G G G G+N+N+ G GD Y+ A
Sbjct: 203 QDPSVLYISLHRHDD--GNFFPGSGAVDEVGAGSGEGFNVNVAWAGGLDPPMGDPEYLAA 260
Query: 260 MTELVVPAIQKFEPNMIVLVVGQDSSAFDPN--GRQCLTMDGYREMGRIVRSLADRYSGG 317
+V+P ++F P+++++ G D++ P G ++ + M + + +LA GG
Sbjct: 261 FRIVVMPIAREFSPDLVLVSAGFDAAEGHPAPLGGYHVSAKCFGYMTQQLMNLA----GG 316
Query: 318 RLLIVQEGGYHVTY----SAYCLHATL 340
+++ EGG+ +T S C+ A L
Sbjct: 317 AVVLALEGGHDLTAICDASEACVAALL 343
>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 = 132 bits (332), Expect = 1e-34
Identities = 88/260 (33%), Positives = 133/260 (51%), Gaps = 19/260 (7%)
Query: 105 GGKMVCDGTVLNP-GSWGAALLAVGTTLSAMKHVLDGHGKIAYALVRPPGHHAQPTMADG 163
GG V TV N S A +AVG + V G K +A++RPPGHHA+ + A G
Sbjct: 104 GGIGVDSDTVWNEMHSSSAVRMAVGCLIELAFKVAAGELKNGFAVIRPPGHHAEESTAMG 163
Query: 164 YCFLNNAGLAVQLALNS-GCGKVVVIDIDVHYGNGTAEGFYRSNKVLTISLHMNHGSWGP 222
+CF N+ +A +L GK++++D D+H+GNGT + FY VL ISLH G
Sbjct: 164 FCFFNSVAIAAKLLQQKLNVGKILIVDWDIHHGNGTQQAFYNDPNVLYISLHRYDD--GN 221
Query: 223 SHPQNGTVDELGEGEGFGYNLNIPLPNGT----GDRGYVHAMTELVVPAIQKFEPNMIVL 278
P +G DE+G G G G+N+NI G GD Y+ A +V+P +F P+++++
Sbjct: 222 FFPGSGAPDEVGAGPGVGFNVNIAWTGGVDPPIGDVEYLTAFRTVVMPIANEFSPDVVLV 281
Query: 279 VVGQDS--SAFDPNGRQCLTMDGYREMGRIVRSLADRYSGGRLLIVQEGGYHVT----YS 332
G D+ P G +T + + + + +LA GGR+++ EGG+ +T S
Sbjct: 282 SAGFDAVEGHQSPLGGYSVTAKCFGHLTKQLMTLA----GGRVVLALEGGHDLTAICDAS 337
Query: 333 AYCLHATLEGVLN-LPLALL 351
C+ A L L L +L
Sbjct: 338 EACVSALLGMELTPLDNTVL 357
>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 = 128 bits (324), Expect = 2e-34
Identities = 76/260 (29%), Positives = 124/260 (47%), Gaps = 23/260 (8%)
Query: 80 PAQIPQLLSFHTPDYINELVEADKAGGKMVCDGTVLNPGSWGAALLAVGTTLSAMKHVLD 139
A L +H DY++ L+ K G + D V P L G++L+ KH++
Sbjct: 46 RATRKDLTKYHDKDYVDFLL--KKYG--LEDDCPVF-PFLSMYVQLVAGSSLALAKHLIT 100
Query: 140 GHGK---IAYALVRPPGHHAQPTMADGYCFLNNAGLAVQLALNSGCGKVVVIDIDVHYGN 196
+ I + R HHAQ + A G+C++N+ LA+ + +V +D+D+H+G+
Sbjct: 101 QVERDIAINWYGGR---HHAQKSRASGFCYVNDIVLAILRLRRARFRRVFYLDLDLHHGD 157
Query: 197 GTAEGFYRSNKVLTISLHMNHGSWGPS-HPQNGTVDELGEGEGFGYNLNIPLPNGTGDRG 255
G F+ S VLT S+H + P P G++ + LNIPL G D+
Sbjct: 158 GVESAFFFSKNVLTCSIHR----YDPGFFPGTGSLKNSSD----KGMLNIPLKRGLSDKT 209
Query: 256 YVHAMTELVVPAIQKFEPNMIVLVVGQDSSAFDPNGRQCLTMDGYREMGRIVRSLADRYS 315
+ + +V P I+KFEP +IV+ G D + DP+ LT+ GY G ++ L +
Sbjct: 210 LLRIIDSIVRPLIEKFEPEVIVIQCGCDGLSGDPHKEWNLTIRGY---GSVIELLLKEFK 266
Query: 316 GGRLLIVQEGGYHVTYSAYC 335
L++ GGY+ T +A
Sbjct: 267 DKPTLLLGGGGYNHTEAARA 286
>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 = 129 bits (326), Expect = 4e-34
Identities = 89/297 (29%), Positives = 140/297 (47%), Gaps = 30/297 (10%)
Query: 80 PAQIPQLLSFHTPDYINELVEADKAG-GKMVCDGTV---------LNPGSWGAALLAVGT 129
A +L SFH+ +YI L +A G + G + A G
Sbjct: 46 VATEEELASFHSDEYIQFLKKASNEGDNDEEPSEQQEFGLGYDCPIFEGIYDYAAAVAGA 105
Query: 130 TLSAMKHVLDGHGKIAYALVRPPG--HHAQPTMADGYCFLNNAGLAVQLALNSGCGKVVV 187
TL+A + ++DG K+A + G HHAQ A G+C++N+ L + L L +V+
Sbjct: 106 TLTAAQLLIDGKCKVA---INWFGGWHHAQRDEASGFCYVNDIVLGI-LKLREKFDRVLY 161
Query: 188 IDIDVHYGNGTAEGFYRSNKVLTISLHMNHGSWGPSHPQNGTVDELGEGEGFGYNLNIPL 247
+D+D+H+G+G + F ++KV+T+SLH + P G V ++G G+G Y +N+PL
Sbjct: 162 VDLDLHHGDGVEDAFSFTSKVMTVSLHKYSPGFFPG---TGDVSDVGLGKGKYYTVNVPL 218
Query: 248 PNGTGDRGYVHAMTELVVPAIQKFEPNMIVLVVGQDSSAFDPNGRQCLTMDGYREMGRIV 307
+G D Y+ T +V + F P +VL G D+ A DP G LT G G+ +
Sbjct: 219 RDGIQDEQYLQIFTAVVPEIVAAFRPEAVVLQCGADTLAGDPMGAFNLTPVGI---GKCL 275
Query: 308 RSLADRYSGGRLLIVQEGGYHVTYSAYCLHATLEGVLNLPLALLSDPIAYYPEDEAF 364
+ + LI+ GGY++ +A C +L P LS I P+ E F
Sbjct: 276 KYVLG--WKLPTLILGGGGYNLANTARCWTYLTGLILGEP---LSSDI---PDHEFF 324
>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 = 129 bits (325), Expect = 6e-34
Identities = 91/266 (34%), Positives = 142/266 (53%), Gaps = 23/266 (8%)
Query: 105 GGKMVCDGTVLNP-GSWGAALLAVGTTLSAMKHVLDGHGKIAYALVRPPGHHAQPTMADG 163
GG V T+ N S GAA +AVG + V G K +A+VRPPGHHA+ + A G
Sbjct: 102 GGLGVDSDTIWNELHSSGAARMAVGCVIELASKVASGELKNGFAVVRPPGHHAEESTAMG 161
Query: 164 YCFLNNAGLAVQ-LALNSGCGKVVVIDIDVHYGNGTAEGFYRSNKVLTISLH-MNHGSWG 221
+CF N+ + + L K++++D+DVH+GNGT + FY +L ISLH + G++
Sbjct: 162 FCFFNSVAITAKYLRDQLNISKILIVDLDVHHGNGTQQAFYADPSILYISLHRYDEGNF- 220
Query: 222 PSHPQNGTVDELGEGEGFGYNLNIPLPNG----TGDRGYVHAMTELVVPAIQKFEPNMIV 277
P +G +E+G G G GYN+NI G GD Y+ A +V P ++F+P+M++
Sbjct: 221 --FPGSGAPNEVGTGLGEGYNINIAWTGGLDPPMGDVEYLEAFRTIVKPVAKEFDPDMVL 278
Query: 278 LVVGQDS-SAFDPN-GRQCLTMDGYREMGRIVRSLADRYSGGRLLIVQEGGYHVTYSAYC 335
+ G D+ P G +T + + + + +LAD GR+++ EGG+ +T A C
Sbjct: 279 VSAGFDALEGHTPPLGGYKVTAKCFGHLTKQLMTLAD----GRVVLALEGGHDLT--AIC 332
Query: 336 LHATLEGVLNLPLALLSDPIAYYPED 361
+ E +N ALL + + ED
Sbjct: 333 DAS--EACVN---ALLGNELEPLAED 353
>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 = 129 bits (325), Expect = 1e-33
Identities = 104/338 (30%), Positives = 163/338 (48%), Gaps = 43/338 (12%)
Query: 50 HPENSDRIKNIVSILKRGPISPYISWHSGIPAQIPQLLSFHTPDYI---------NELVE 100
HPE++ RI++I S L+ + G A + +L + H+ + + ++
Sbjct: 27 HPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHTLLYGTNPLNRQKLD 86
Query: 101 ADKAGG-------KMVCDG------TVLNP-GSWGAALLAVGTTLSAMKHVLDGHGKIAY 146
+ K G ++ C G T+ N S GAA LAVG + + V G K +
Sbjct: 87 SKKLLGSLASVFVRLPCGGVGVDSDTIWNEVHSSGAARLAVGCVVELVFKVATGELKNGF 146
Query: 147 ALVRPPGHHAQPTMADGYCFLNNAGLAVQLALNS-GCGKVVVIDIDVHYGNGTAEGFYRS 205
A+VRPPGHHA+ + G+C+ N+ +A +L K++++D DVH+GNGT + FY
Sbjct: 147 AVVRPPGHHAEESTPMGFCYFNSVAIAAKLLQQRLNVSKILIVDWDVHHGNGTQQAFYSD 206
Query: 206 NKVLTISLHMNHGSWGPSHPQNGTVDELGEGEGFGYNLNIPLPNG----TGDRGYVHAMT 261
VL +SLH G P +G DE+G G G G+N+N+ G GD Y+ A
Sbjct: 207 PNVLYMSLHRYDD--GNFFPGSGAPDEVGTGPGVGFNVNMAFTGGLDPPMGDAEYLAAFR 264
Query: 262 ELVVPAIQKFEPNMIVLVVGQDSSAFDPNGRQCLTMDGYREMGRIVRSLADR---YSGGR 318
+V+P +F P+ +VLV SS FD + GY + L + +GGR
Sbjct: 265 TVVMPIASEFAPD-VVLV----SSGFDAVEGHPTPLGGYNLSAKCFGYLTKQLMGLAGGR 319
Query: 319 LLIVQEGGYHVT----YSAYCLHATLEGVLN-LPLALL 351
+++ EGG+ +T S C+ A L L+ LP +L
Sbjct: 320 IVLALEGGHDLTAICDASEACVSALLGNELDPLPEKVL 357
>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 = 123 bits (311), Expect = 1e-32
Identities = 81/288 (28%), Positives = 123/288 (42%), Gaps = 36/288 (12%)
Query: 50 HPENSDRIKNIVSILKRGPISPYISWHSGIPAQIPQLLSFHTPDYINEL------VEADK 103
H + + L + PA LL H P+Y+ L E +
Sbjct: 1 HRFPMRKYGLLREALLEEGLVLPEDIVEPEPATREDLLRVHDPEYLESLKSGELSREEIR 60
Query: 104 AGGKMVCDGTVLNPGSWGAALLAVGTTLSAMKHVLDGHGKIAYALVRPPG--HHAQPTMA 161
G ++ LAVG T+ A + L+ HG +A L G HHA P
Sbjct: 61 RIGFPWSPE-LVER-----TRLAVGGTILAARLALE-HG-LAINLA---GGTHHAFPDRG 109
Query: 162 DGYCFLNNAGLAVQLALNSG-CGKVVVIDIDVHYGNGTAEGFYRSNKVLTISLHMNHGSW 220
+G+C N+ +A ++ L G +V+++D+DVH GNGTA F V T S+H
Sbjct: 110 EGFCVFNDIAIAARVLLAEGLVRRVLIVDLDVHQGNGTAAIFADDPSVFTFSMHGEK--N 167
Query: 221 GPSHPQNGTVDELGEGEGFGYNLNIPLPNGTGDRGYVHAMTELVVPAIQKFEPNMIVLVV 280
P + +D +PLP+GTGD Y+ A+ E + + +F P+++
Sbjct: 168 YPFRKEPSDLD-------------VPLPDGTGDDEYLAALEEALPRLLAEFRPDLVFYNA 214
Query: 281 GQDSSAFDPNGRQCLTMDGYREMGRIVRSLADRYSGGRLLIVQEGGYH 328
G D A D GR L+++G RE R+V A G + +V GGY
Sbjct: 215 GVDVLAGDRLGRLSLSLEGLRERDRLVLRFARAR-GIPVAMVLGGGYS 261
>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 = 124 bits (312), Expect = 1e-32
Identities = 83/260 (31%), Positives = 128/260 (49%), Gaps = 24/260 (9%)
Query: 80 PAQIPQLLSFHTPDYINEL----------VEADKAGGKMVCDGTVLNPGSWGAALLAVGT 129
A +L FH DY++ L + DKA + D + G + L G
Sbjct: 48 AATREELRQFHDADYLDFLSKVSPENANQLRFDKAEPFNIGDDCPVFDGMYDYCQLYAGA 107
Query: 130 TLSAMKHVLDGHGKIAYALVRPPG--HHAQPTMADGYCFLNNAGLAVQLALNSGCGKVVV 187
+L A + + G IA G HHA+ + A G+C++N+ LA+ L L +V+
Sbjct: 108 SLDAARKLCSGQSDIAINW---SGGLHHAKKSEASGFCYVNDIVLAI-LNLLRYFPRVLY 163
Query: 188 IDIDVHYGNGTAEGFYRSNKVLTISLHMNHGSWGPSHPQNGTVDELGEGEGFGYNLNIPL 247
IDIDVH+G+G E FYR+++V+T+S H +G + P G +D+ G G + LN+PL
Sbjct: 164 IDIDVHHGDGVEEAFYRTDRVMTLSFHKYNGEF---FPGTGDLDDNGGTPGKHFALNVPL 220
Query: 248 PNGTGDRGYVHAMTELVVPAIQKFEPNMIVLVVGQDSSAFDPNGRQCLTMDGYREMGRIV 307
+G D Y ++ P I+KF+P+ IVL G DS D G+ L + + + V
Sbjct: 221 EDGIDDEQYNLLFKSIIGPTIEKFQPSAIVLQCGADSLGGDRLGQFNLNIKAHGACVKFV 280
Query: 308 RSLADRYSGGRLLIVQEGGY 327
+S G +L+V GGY
Sbjct: 281 KSF-----GIPMLVVGGGGY 295
>gnl|CDD|240251 PTZ00063, PTZ00063, histone deacetylase; Provisional.
Length = 436
Score = 104 bits (262), Expect = 7e-25
Identities = 63/182 (34%), Positives = 98/182 (53%), Gaps = 10/182 (5%)
Query: 154 HHAQPTMADGYCFLNNAGLAVQLALNSGCGKVVVIDIDVHYGNGTAEGFYRSNKVLTISL 213
HHA+ + A G+C++N+ L + L L +V+ IDIDVH+G+G E FY +++V+T+S
Sbjct: 137 HHAKRSEASGFCYINDIVLGI-LELLKYHARVMYIDIDVHHGDGVEEAFYVTHRVMTVSF 195
Query: 214 HMNHGSWGPSHPQNGTVDELGEGEGFGYNLNIPLPNGTGDRGYVHAMTELVVPAIQKFEP 273
H +G P G V ++G +G Y++N+PL +G D +V ++ ++ + P
Sbjct: 196 H----KFGDFFPGTGDVTDIGVAQGKYYSVNVPLNDGIDDDSFVDLFKPVISKCVEVYRP 251
Query: 274 NMIVLVVGQDSSAFDPNGRQCLTMDGYREMGRIVRSLADRYSGGRLLIVQEGGYHVTYSA 333
IVL G DS D GR LT+ G+ VRSL LL++ GGY + A
Sbjct: 252 GAIVLQCGADSLTGDRLGRFNLTIKGHAACVEFVRSL-----NIPLLVLGGGGYTIRNVA 306
Query: 334 YC 335
C
Sbjct: 307 RC 308
>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 = 103 bits (259), Expect = 9e-25
Identities = 60/182 (32%), Positives = 96/182 (52%), Gaps = 9/182 (4%)
Query: 154 HHAQPTMADGYCFLNNAGLAVQLALNSGCGKVVVIDIDVHYGNGTAEGFYRSNKVLTISL 213
HHA+ A G+C++N+ +A+ L L +V+ IDID+H+G+G E FY +++V+T+S
Sbjct: 132 HHAKKFEASGFCYVNDIVIAI-LELLKYHPRVLYIDIDIHHGDGVQEAFYLTDRVMTVSF 190
Query: 214 HMNHGSWGPSHPQNGTVDELGEGEGFGYNLNIPLPNGTGDRGYVHAMTELVVPAIQKFEP 273
H + P G + E+G G Y++N+PL +G D+ Y+ ++ I ++P
Sbjct: 191 HKYGNYF---FPGTGDMYEVGAESGRYYSVNVPLKDGIDDQSYLQLFKPVIQQVIDFYQP 247
Query: 274 NMIVLVVGQDSSAFDPNGRQCLTMDGYREMGRIVRSLADRYSGGRLLIVQEGGYHVTYSA 333
IVL G DS D G L++ G+ E V+S LL++ GGY V A
Sbjct: 248 TCIVLQCGADSLGCDRLGCFNLSIKGHGECVEFVKSF-----NIPLLVLGGGGYTVRNVA 302
Query: 334 YC 335
C
Sbjct: 303 RC 304
>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 = 99.0 bits (246), Expect = 4e-23
Identities = 59/182 (32%), Positives = 99/182 (54%), Gaps = 10/182 (5%)
Query: 154 HHAQPTMADGYCFLNNAGLAVQLALNSGCGKVVVIDIDVHYGNGTAEGFYRSNKVLTISL 213
HHA+ + A G+C++N+ LA+ L L +V+ IDID+H+G+G E FY +++V+T+S
Sbjct: 137 HHAKKSEASGFCYVNDIVLAI-LELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSF 195
Query: 214 HMNHGSWGPSHPQNGTVDELGEGEGFGYNLNIPLPNGTGDRGYVHAMTELVVPAIQKFEP 273
H +G P G + ++G G+G Y +N PL +G D Y ++ ++ F+P
Sbjct: 196 H----KYGEYFPGTGDLRDIGAGKGKYYAVNYPLRDGIDDESYEAIFKPVMSKVMEMFQP 251
Query: 274 NMIVLVVGQDSSAFDPNGRQCLTMDGYREMGRIVRSLADRYSGGRLLIVQEGGYHVTYSA 333
+ +VL G DS + D G LT+ G+ + V+S +L++ GGY + A
Sbjct: 252 SAVVLQCGADSLSGDRLGCFNLTIKGHAKCVEFVKSF-----NLPMLMLGGGGYTIRNVA 306
Query: 334 YC 335
C
Sbjct: 307 RC 308
>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 = 98.3 bits (245), Expect = 8e-23
Identities = 56/176 (31%), Positives = 93/176 (52%), Gaps = 10/176 (5%)
Query: 154 HHAQPTMADGYCFLNNAGLAVQLALNSGCGKVVVIDIDVHYGNGTAEGFYRSNKVLTISL 213
HHA+ + A G+C++N+ L + L L +V+ IDIDVH+G+G E FY +++V+T S
Sbjct: 133 HHAKKSEASGFCYVNDIVLGI-LELLRYHQRVLYIDIDVHHGDGVEEAFYTTDRVMTCSF 191
Query: 214 HMNHGSWGPSHPQNGTVDELGEGEGFGYNLNIPLPNGTGDRGYVHAMTELVVPAIQKFEP 273
H +G P G + ++G G G Y +N+PL +G D Y ++ ++ ++P
Sbjct: 192 H----KYGEYFPGTGELRDIGIGTGKNYAVNVPLRDGIDDESYKSIFEPVIKHVMEWYQP 247
Query: 274 NMIVLVVGQDSSAFDPNGRQCLTMDGYREMGRIVRSLADRYSGGRLLIVQEGGYHV 329
+VL G DS + D G L+M G+ V+S +L++ GGY +
Sbjct: 248 EAVVLQCGGDSLSGDRLGCFNLSMKGHANCVNFVKSF-----NLPMLVLGGGGYTM 298
>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 = 93.6 bits (232), Expect = 3e-21
Identities = 56/182 (30%), Positives = 99/182 (54%), Gaps = 10/182 (5%)
Query: 154 HHAQPTMADGYCFLNNAGLAVQLALNSGCGKVVVIDIDVHYGNGTAEGFYRSNKVLTISL 213
HHA+ + A G+C++N+ LA+ L L +V+ IDID+H+G+G E FY +++V+T+S
Sbjct: 133 HHAKKSEASGFCYVNDIVLAI-LELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVS- 190
Query: 214 HMNHGSWGPSHPQNGTVDELGEGEGFGYNLNIPLPNGTGDRGYVHAMTELVVPAIQKFEP 273
+G P G + ++G G+G Y +N P+ +G D Y ++ ++ ++P
Sbjct: 191 ---FHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIISKVMEMYQP 247
Query: 274 NMIVLVVGQDSSAFDPNGRQCLTMDGYREMGRIVRSLADRYSGGRLLIVQEGGYHVTYSA 333
+ +VL G DS + D G LT+ G+ + +V++ LL++ GGY + A
Sbjct: 248 SAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTF-----NLPLLMLGGGGYTIRNVA 302
Query: 334 YC 335
C
Sbjct: 303 RC 304
>gnl|CDD|240374 PTZ00346, PTZ00346, histone deacetylase; Provisional.
Length = 429
Score = 80.1 bits (197), Expect = 2e-16
Identities = 64/207 (30%), Positives = 107/207 (51%), Gaps = 17/207 (8%)
Query: 126 AVGTTLSAMKHVLDGHGKIAYALVRPPG-HHAQPTMADGYCFLNNAGLAVQLALNSGCGK 184
A GT + A VL G++ A+ G HH++ G+C++N+ L + L L +
Sbjct: 128 ASGTLMGA---VLLNSGQVDVAVHWGGGMHHSKCGECSGFCYVNDIVLGI-LELLKCHDR 183
Query: 185 VVVIDIDVHYGNGTAEGFYRSNKVLTISLHMNHGSW--GPSHPQNGTVDELGEGEGFGYN 242
V+ +DID+H+G+G E F S++V T+SLH S+ G HP+ ++G G G Y+
Sbjct: 184 VLYVDIDMHHGDGVDEAFCTSDRVFTLSLHKFGESFFPGTGHPR-----DVGYGRGRYYS 238
Query: 243 LNIPLPNGTGDRGYVHAMTELVVPAIQKFEPNMIVLVVGQDSSAFDPNGRQCLTMDGYRE 302
+N+ + +G D Y+ + ++++ P+ IVL G DS A D G L+ G+ +
Sbjct: 239 MNLAVWDGITDFYYLGLFEHALHSIVRRYSPDAIVLQCGADSLAGDRLGLLNLSSFGHGQ 298
Query: 303 MGRIVRSLADRYSGGRLLIVQEGGYHV 329
+ VR L G +L + GGY +
Sbjct: 299 CVQAVRDL-----GIPMLALGGGGYTI 320
>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 = 74.4 bits (183), Expect = 8e-15
Identities = 35/96 (36%), Positives = 51/96 (53%), Gaps = 4/96 (4%)
Query: 115 LNPGSWGAALLAVGTTLSAMKHVLDGHG---KIAYALVRPPGHHAQPTMADGYCFLNNAG 171
L P S A A+G A+ V K A+ +RPPGHH + G+C++NN
Sbjct: 78 LCPESLDAIQGALGAVCEAVDSVFKPESPGTKRAFVAIRPPGHHCSESTPSGFCWVNNVH 137
Query: 172 LAVQLA-LNSGCGKVVVIDIDVHYGNGTAEGFYRSN 206
+ A L G +VV++DID+H+GNGT + +R N
Sbjct: 138 VGAAHAYLTHGITRVVILDIDLHHGNGTQDIAWRIN 173
Score = 28.6 bits (64), Expect = 6.5
Identities = 12/28 (42%), Positives = 15/28 (53%)
Query: 300 YREMGRIVRSLADRYSGGRLLIVQEGGY 327
Y R AD ++ GRL+ V EGGY
Sbjct: 309 YYRFARDAVRFADAHAHGRLISVLEGGY 336
>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 = 41.2 bits (97), Expect = 3e-04
Identities = 38/191 (19%), Positives = 56/191 (29%), Gaps = 47/191 (24%)
Query: 140 GHGKIAYALVRPPGHHAQPTMADGYCFLNNAGLAVQLALNSGCGKVVVIDIDVHYGNGTA 199
GK+ L G H+ N A AV + VID+D H+ T
Sbjct: 23 KDGKVPVVLG---GDHSI---------ANGAIRAVAELH----PDLGVIDVDAHHDVRTP 66
Query: 200 EGFYRSNK--------------VLTISLHMNHGSWGPSHPQNGTVDELGEGEGFGYNLNI 245
E F + N V +S+ + S G + G +
Sbjct: 67 EAFGKGNHHTPRHLLCEPLISDVHIVSIGIRGVSNGEAG---------GAYARKLGVVYF 117
Query: 246 PLPNGTGDRGYVHAMTELVVPAIQKFEPNMIVLVVGQDS--SAFDPNGRQCLTMDG--YR 301
+ G E+V + + + L V D +F P G G YR
Sbjct: 118 SMTEVD-KLGLGDVFEEIVSYL--GDKGDNVYLSVDVDGLDPSFAP-GTGTPGPGGLSYR 173
Query: 302 EMGRIVRSLAD 312
E I +A
Sbjct: 174 EGLYITERIAK 184
>gnl|CDD|217042 pfam02449, Glyco_hydro_42, Beta-galactosidase. This group of
beta-galactosidase enzymes belong to the glycosyl
hydrolase 42 family. The enzyme catalyzes the hydrolysis
of terminal, non-reducing terminal beta-D-galactosidase
residues.
Length = 376
Score = 36.1 bits (84), Expect = 0.028
Identities = 24/71 (33%), Positives = 29/71 (40%), Gaps = 9/71 (12%)
Query: 277 VLVVGQDSSAFDPNGRQ--CLTMDGYRE-MGRIVRSLADRYSGGRLLIV----QEGGYHV 329
+L V D R C + YRE RIV +LA+RY LI E G HV
Sbjct: 83 ILPVDADGRRRGFGSRHHYCPSSPVYREYAARIVEALAERYGDHPALIGWHIDNEYGCHV 142
Query: 330 T--YSAYCLHA 338
+ Y C A
Sbjct: 143 SECYCETCQQA 153
>gnl|CDD|107281 cd06286, PBP1_CcpB_like, Ligand-binding domain of a novel
transcription factor implicated in catabolite repression
in Bacillus and Clostridium species. This group
includes the ligand-binding domain of a novel
transcription factor implicated in catabolite repression
in Bacillus and Clostridium species. CcpB is 30%
identical in sequence to CcpA which functions as the
major transcriptional regulator of carbon catabolite
repression/regulation (CCR), a process in which enzymes
necessary for the metabolism of alternative sugars are
inhibited in the presence of glucose. Like CcpA, the
DNA-binding protein CcpB exerts its
catabolite-repressing effect by a mechanism dependent on
the presence of HPr(Ser-P), the small phosphocarrier
proteins of the phosphoenolpyruvate-sugar
phosphotransferase system, but with a less significant
degree.
Length = 260
Score = 32.1 bits (74), Expect = 0.36
Identities = 12/44 (27%), Positives = 20/44 (45%), Gaps = 1/44 (2%)
Query: 133 AMKHVLD-GHGKIAYALVRPPGHHAQPTMADGYCFLNNAGLAVQ 175
A+K+++ G+ KIAY + R ++Q L GL
Sbjct: 105 ALKYLIQKGYRKIAYCIGRKKSLNSQSRKKAYKDALEEYGLTPD 148
>gnl|CDD|220020 pfam08797, HIRAN, HIRAN domain. The HIRAN domain (HIP116, Rad5p
N-terminal) is found in the N-terminal regions of the
SWI2/SNF2 proteins typified by HIP116 and Rad5p. The
HIRAN domain is found as a standalone protein in several
bacteria and prophages, or fused to other catalytic
domains, such as a nuclease of the restriction
endonuclease fold and TDP1-like DNA phosphoesterases, in
the eukaryotes. It has been predicted that this domain
functions as a DNA-binding domain that probably
recognises features associated with damaged DNA or
stalled replication forks.
Length = 95
Score = 28.9 bits (65), Expect = 1.3
Identities = 8/45 (17%), Positives = 21/45 (46%)
Query: 267 AIQKFEPNMIVLVVGQDSSAFDPNGRQCLTMDGYREMGRIVRSLA 311
+ + V++V + + +D N + + + E+G + R +A
Sbjct: 17 GTRYLKVGEEVVLVREPDNPYDKNAIRVYNVGRFSEIGYLPREVA 61
>gnl|CDD|176198 cd08236, sugar_DH, NAD(P)-dependent sugar dehydrogenases. This
group contains proteins identified as sorbitol
dehydrogenases and other sugar dehydrogenases of the
medium-chain dehydrogenase/reductase family (MDR), which
includes zinc-dependent alcohol dehydrogenase and
related proteins. Sorbitol and aldose reductase are
NAD(+) binding proteins of the polyol pathway, which
interconverts glucose and fructose. Sorbitol
dehydrogenase is tetrameric and has a single catalytic
zinc per subunit. NAD(P)(H)-dependent oxidoreductases
are the major enzymes in the interconversion of alcohols
and aldehydes, or ketones. Related proteins include
threonine dehydrogenase, formaldehyde dehydrogenase, and
butanediol dehydrogenase. The medium chain alcohol
dehydrogenase family (MDR) has a NAD(P)(H)-binding
domain in a Rossmann fold of a beta-alpha form. The
N-terminal region typically has an all-beta catalytic
domain. These proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and have 2 tightly bound zinc atoms per subunit. Horse
liver alcohol dehydrogenase is a dimeric enzyme and each
subunit has two domains. The NAD binding domain is in a
Rossmann fold and the catalytic domain contains a zinc
ion to which substrates bind. There is a cleft between
the domains that closes upon formation of the ternary
complex.
Length = 343
Score = 29.9 bits (68), Expect = 2.3
Identities = 8/20 (40%), Positives = 12/20 (60%)
Query: 172 LAVQLALNSGCGKVVVIDID 191
LA+Q G +V+ +DID
Sbjct: 174 LAIQWLKILGAKRVIAVDID 193
>gnl|CDD|149544 pfam08527, PAD_M, Protein-arginine deiminase (PAD) middle domain.
This family represents the central non-catalytic domain
of protein-arginine deiminase. This domain has an
immunoglobulin-like fold.
Length = 159
Score = 28.0 bits (63), Expect = 5.7
Identities = 11/28 (39%), Positives = 16/28 (57%), Gaps = 1/28 (3%)
Query: 128 GTTLSAMKHVLDGHGKIAYALVRPPGHH 155
G +LS +HVL G K++Y + R G
Sbjct: 105 GKSLSDYEHVL-GPQKLSYEVPRLGGER 131
>gnl|CDD|223768 COG0696, GpmI, Phosphoglyceromutase [Carbohydrate transport and
metabolism].
Length = 509
Score = 28.8 bits (65), Expect = 6.1
Identities = 22/75 (29%), Positives = 39/75 (52%), Gaps = 11/75 (14%)
Query: 258 HAMTELVVPAIQKFEPNMIVL------VVGQDSSAFDPNGRQCLTMDGYREMGRIVRSLA 311
+T+ +V AI+K + ++IVL +VG + F+ + +D +GRIV ++
Sbjct: 374 KEVTDALVEAIEKGKYDLIVLNYANPDMVGH-TGNFEATIKAVEAVD--ECLGRIVDAVK 430
Query: 312 DRYSGGRLLIVQEGG 326
+GG LLI + G
Sbjct: 431 K--NGGTLLITADHG 443
>gnl|CDD|215721 pfam00107, ADH_zinc_N, Zinc-binding dehydrogenase.
Length = 131
Score = 26.9 bits (60), Expect = 9.7
Identities = 8/20 (40%), Positives = 11/20 (55%)
Query: 172 LAVQLALNSGCGKVVVIDID 191
AVQLA G +V+ +D
Sbjct: 5 AAVQLAKALGAARVIAVDRS 24
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 0.139 0.428
Gapped
Lambda K H
0.267 0.0674 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 20,607,731
Number of extensions: 2052525
Number of successful extensions: 1976
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1869
Number of HSP's successfully gapped: 50
Length of query: 386
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 287
Effective length of database: 6,546,556
Effective search space: 1878861572
Effective search space used: 1878861572
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 60 (27.0 bits)