RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 025519
(251 letters)
>gnl|CDD|212519 cd09993, HDAC_classIV, Histone deacetylase class IV also known as
histone deacetylase 11. Class IV histone deacetylases
(HDAC11; EC 3.5.1.98) are predicted Zn-dependent
enzymes. This class includes animal HDAC11, plant HDA2
and related bacterial deacetylases. Enzymes in this
subfamily participate in regulation of a number of
different processes through protein modification
(deacetylation). They catalyze hydrolysis of
N(6)-acetyl-lysine of histones (or other proteins) to
yield a deacetylated proteins. Histone deacetylases
often act as members of large multi-protein complexes
such as mSin3A or SMRT/N-CoR. Human HDAC11 does not
associate with them but can interact with HDAC6 in vivo.
It has been suggested that HDAC11 and HDAC6 may use
non-histone proteins as their substrates and play a role
other than to directly modulate chromatin structure. In
normal tissues, expression of HDAC11 is limited to
kidney, heart, brain, skeletal muscle and testis,
suggesting that its function might be tissue-specific.
In mammals, HDAC11 proteins are known to be involved in
progression of various tumors. HDAC11 plays an essential
role in regulating OX40 ligand (OX40L) expression in
Hodgkin lymphoma (HL); selective inhibition of HDAC11
expression significantly up-regulates OX40L and induces
apoptosis in HL cell lines. Thus, inhibition of HDAC11
could be a therapeutic drug option for antitumor immune
response in HL patients.
Length = 275
Score = 245 bits (627), Expect = 2e-81
Identities = 72/190 (37%), Positives = 97/190 (51%), Gaps = 9/190 (4%)
Query: 54 HPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIE 113
H F K+G + + L EG + IVEP A++EDLL VH YL+SL+S + E
Sbjct: 1 HRFPMRKYGLLREALLEEGLVLPEDIVEPEPATREDLLRVHDPEYLESLKSG---ELSRE 57
Query: 114 VPPVALFPNCLVQRKVLYPFRKQVGGTILAAKLAKERGWAINVGGGFHHCSADEGGGFCA 173
FP +++ R VGGTILAA+LA E G AIN+ GG HH D G GFC
Sbjct: 58 EIRRIGFPWSP---ELVERTRLAVGGTILAARLALEHGLAINLAGGTHHAFPDRGEGFCV 114
Query: 174 YADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRVYILDMFNPGIYPRDYEA 233
+ DI++ + + RV+I+DLD HQGNG F+ D V+ M YP
Sbjct: 115 FNDIAIAARVLLAEGLVRRVLIVDLDVHQGNGTAAIFADDPSVFTFSMHGEKNYPFR--- 171
Query: 234 RRFIDQKVEV 243
+ D V +
Sbjct: 172 KEPSDLDVPL 181
>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 = 157 bits (399), Expect = 3e-47
Identities = 65/188 (34%), Positives = 92/188 (48%), Gaps = 6/188 (3%)
Query: 60 KWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVAL 119
+ + + L G K ++E EA++E LL VH+E YL L+++ V+ I E PV
Sbjct: 1 RIRDLIEALKELGLRPKIELIECREATEELLLKVHTEEYLNELKANFAVATITESKPVIF 60
Query: 120 FPNCLVQRKVLYPFRKQVGGTILAAKLA----KERGWAINVGGGFHHCSADEGGGFCAYA 175
PN VQR R GG + AA+L ER +A+ VG G HH GFC +
Sbjct: 61 GPNFPVQRHYFRGARLSTGGVVEAAELVAKGELERAFAV-VGAGGHHAGKSRAWGFCYFN 119
Query: 176 DISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRVYILDMFNPGIYPRDYEARR 235
D+ L I + + ISR++IID DAH G+G + F D RV + N IYP +
Sbjct: 120 DVVLAIKFLR-ERGISRILIIDTDAHHGDGTREAFYDDDRVLHMSFHNYDIYPFGRGKGK 178
Query: 236 FIDQKVEV 243
V +
Sbjct: 179 GYKINVPL 186
>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 = 155 bits (394), Expect = 4e-46
Identities = 51/179 (28%), Positives = 83/179 (46%), Gaps = 7/179 (3%)
Query: 53 LHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIII 112
HP + + I + L G LD+ + P A++E+LL+VHS Y++ L+ +
Sbjct: 8 GHPENPERLEAILELLKESGLLDRLEFIAPRPATEEELLLVHSPEYVEFLEEA--SLEEE 65
Query: 113 EVPPVALFPNCLVQRKVLYPFRKQVGGTILAAKLA---KERGWAINVGGGFHHCSADEGG 169
E+ + L + V GGT+ AA L + A+ G HH D
Sbjct: 66 ELGRIGLDGDTPVSPGSYEAALLAAGGTLEAADLVLSGENAFAAVRPPG--HHAERDRAS 123
Query: 170 GFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRVYILDMFNPGIYP 228
GFC + ++++ Y + + RV+I+DLD H GNG ++ F D RV + + YP
Sbjct: 124 GFCLFNNVAIAARYLLKRYGLKRVLIVDLDVHHGNGTQEIFYDDPRVLTISIHQDPFYP 182
>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 = 114 bits (286), Expect = 6e-30
Identities = 55/202 (27%), Positives = 82/202 (40%), Gaps = 14/202 (6%)
Query: 32 IFKLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLL 91
+ K LIY P++ HP + + I + L S G D +VEP A+ E+LL
Sbjct: 1 MMKTALIYHPEFLEHEPP--PGHPENPDRLRLILELLESSGLPDSLELVEPRPATLEELL 58
Query: 92 VVHSESYLKSLQS-SPNVSIIIEVPPVALFPNCLVQRKVLYPFRKQVGGTILAAKLAKE- 149
+VHS Y++ L+S S + P + L GG + A E
Sbjct: 59 LVHSPDYVEFLESLSEEEGYGNLDGDTPVSPG-TYEAARLA-----AGGALTAVDAVLEG 112
Query: 150 -RGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEK 208
V HH D GFC + ++++ Y + + RV IID D H GNG ++
Sbjct: 113 EDNAFALVRPPGHHAGRDRASGFCLFNNVAIAAKYLLKK-GVKRVAIIDFDVHHGNGTQE 171
Query: 209 DFSSDSRVYILDM--FNPGIYP 228
F D V + + YP
Sbjct: 172 IFYDDDDVLTVSLHQDGRPFYP 193
>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 = 99.6 bits (249), Expect = 1e-24
Identities = 57/199 (28%), Positives = 84/199 (42%), Gaps = 28/199 (14%)
Query: 37 LIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSE 96
IYS +Y G HPF+ + L + G L +V P A++E+LL+ H+
Sbjct: 2 FIYSEEYLRYSFG--PNHPFNPPRLSLTKDLLRALGLLPPVDLVPPRPATEEELLLFHTP 59
Query: 97 SYLKSLQSSPNVSIIIEVPPVAL-------FPNC-----LVQRKVLYPFRKQVGGTILAA 144
Y+++++ + + L FP LV VGGT+LAA
Sbjct: 60 DYIEAVKEASRGQEPEGRGRLGLGTEDNPVFPGMHEAAALV-----------VGGTLLAA 108
Query: 145 KL--AKERGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQ 202
+L E A N GG HH GFC Y D ++ I RV +D+DAH
Sbjct: 109 RLVLEGEARRAFNPAGGLHHAMRGRASGFCVYNDAAVAIERL-RDKGGLRVAYVDIDAHH 167
Query: 203 GNGHEKDFSSDSRVYILDM 221
G+G + F D RV + +
Sbjct: 168 GDGVQAAFYDDPRVLTISL 186
>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 = 95.9 bits (239), Expect = 5e-23
Identities = 54/176 (30%), Positives = 85/176 (48%), Gaps = 24/176 (13%)
Query: 68 LSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVA--------- 118
+ + G L + +V+P A++E+L HS+ Y++ L+ + N E P
Sbjct: 30 IEAYGLLKQLRVVKPRVATEEELASFHSDEYIQFLKKASNEGDNDEEPSEQQEFGLGYDC 89
Query: 119 -LFPNCLVQRKVLYPFRKQVGG-TILAAKL--AKERGWAINVGGGFHHCSADEGGGFCAY 174
+F +Y + V G T+ AA+L + AIN GG+HH DE GFC
Sbjct: 90 PIFEG-------IYDYAAAVAGATLTAAQLLIDGKCKVAINWFGGWHHAQRDEASGFCYV 142
Query: 175 ADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRVYILDM--FNPGIYP 228
DI L I ++ RV+ +DLD H G+G E FS S+V + + ++PG +P
Sbjct: 143 NDIVLGILK--LREKFDRVLYVDLDLHHGDGVEDAFSFTSKVMTVSLHKYSPGFFP 196
>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 = 83.8 bits (208), Expect = 5e-19
Identities = 70/228 (30%), Positives = 92/228 (40%), Gaps = 55/228 (24%)
Query: 38 IYSPDYDISFLGIEKLHPFDSSKWGRIC---QFLSSEGFLDKNCIVEPLEASKEDLLVVH 94
Y PD + G + HP K RI + S G K I P A+ E+L H
Sbjct: 1 FYDPDVGNYYYG--QGHP---MKPHRIRMTHSLILSYGLYKKMEIYRPRPATAEELTKFH 55
Query: 95 SESYLKSLQSSP--------------NVSIIIEVPPVALFPNCLVQRKVLYPF-RKQVGG 139
S+ Y+ L+S NV E PV F LY + + GG
Sbjct: 56 SDDYIDFLRSVSPDNMKEFKKQLERFNVG---EDCPV--FDG-------LYEYCQLYAGG 103
Query: 140 TILAA-KLAK-ERGWAINVGGGFHHCSADEGGGFCAYADISLCI-----HYAFVQLNISR 192
+I AA KL + + AIN GG HH E GFC DI L I ++ R
Sbjct: 104 SIAAAVKLNRGQADIAINWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQ-------R 156
Query: 193 VMIIDLDAHQGNGHEKDFSSDSRVYIL------DMFNPGIYPRDYEAR 234
V+ ID+D H G+G E+ F + RV + + F PG RD A
Sbjct: 157 VLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKFGEYFFPGTGLRDIGAG 204
>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 = 74.5 bits (184), Expect = 1e-15
Identities = 48/173 (27%), Positives = 71/173 (41%), Gaps = 17/173 (9%)
Query: 63 RICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVALFPN 122
I + L EG LD+ VEP A++E+LL VH+ Y++ ++ E L P+
Sbjct: 10 AILEALEEEGLLDRLVFVEPRPATEEELLRVHTPEYIERVEE------TCEAGGGYLDPD 63
Query: 123 CLVQRKVLYPFRKQVGGTILAAKLAKERGWAINVGGGF-------HHCSADEGGGFCAYA 175
V G + A G A N F HH D GFC +
Sbjct: 64 TYVSPGSYEAALLAAGAALAAVDAV-LSGEAEN---AFALVRPPGHHAEPDRAMGFCLFN 119
Query: 176 DISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRVYILDMFNPGIYP 228
++++ YA + + RV+I+D D H GNG + F D V + YP
Sbjct: 120 NVAIAARYAQKRYGLKRVLIVDWDVHHGNGTQDIFYDDPSVLYFSIHQYPFYP 172
>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 = 73.8 bits (182), Expect = 2e-15
Identities = 44/162 (27%), Positives = 64/162 (39%), Gaps = 19/162 (11%)
Query: 74 LDKNC--IVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVALFPNCLVQRKVLY 131
L ++ I+EP A+++DL H + Y+ L + + P +
Sbjct: 34 LLQHFDEIIEPERATRKDLTKYHDKDYVDFLLK--KYGLEDDCPVFPFLSMYV------- 84
Query: 132 PFRKQVGGTILAAKLAK---ERGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQL 188
+ G ++ AK ER AIN GG HH GFC DI L I +
Sbjct: 85 --QLVAGSSLALAKHLITQVERDIAINWYGGRHHAQKSRASGFCYVNDIVLAIL-RLRRA 141
Query: 189 NISRVMIIDLDAHQGNGHEKDFSSDSRVYILD--MFNPGIYP 228
RV +DLD H G+G E F V ++PG +P
Sbjct: 142 RFRRVFYLDLDLHHGDGVESAFFFSKNVLTCSIHRYDPGFFP 183
>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 = 73.4 bits (181), Expect = 3e-15
Identities = 44/182 (24%), Positives = 70/182 (38%), Gaps = 29/182 (15%)
Query: 63 RICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYL---KSLQSSPNVSIIIEVPPVAL 119
RI L G D ++ P A+ E+LL VH+ Y+ K+ ++ E
Sbjct: 42 RIKNLLEVSGLSDHLVLITPRPATDEELLRVHTPEYIDRVKAASAAGGG----EAGGGTP 97
Query: 120 FPN------CLVQRKVLYPFRKQVGGTILAAKLAKE----RGWAINVGGGFHHCSADEGG 169
F L GG I A + +A+ G HH D+G
Sbjct: 98 FGPGSYEIALL-----------AAGGAIAAVDAVLDGEVDNAYALVRPPG-HHAEPDQGM 145
Query: 170 GFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRVYILDMFNPGIYPR 229
GFC + ++++ +A + RV ++D D H GNG + F D V + + +P
Sbjct: 146 GFCLFNNVAIAARHALAVGGVKRVAVVDWDVHHGNGTQAIFYDDPDVLTISLHQDRCFPP 205
Query: 230 DY 231
D
Sbjct: 206 DS 207
>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 = 70.7 bits (173), Expect = 3e-14
Identities = 50/160 (31%), Positives = 76/160 (47%), Gaps = 19/160 (11%)
Query: 68 LSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVS------IIIEVPPVALFP 121
L EG L++ V+ EAS+E+LL+VHS Y+ ++S+ ++ + V L P
Sbjct: 21 LIQEGLLERCVSVQAREASEEELLLVHSPEYVALMKSTQYMTEEELRTLADTYDSVYLHP 80
Query: 122 N-----CLVQRKVLYPFRKQVGGTILAAKLAKERGWAINVGGGFHHCSADEGGGFCAYAD 176
N CL VL K +GG I G AI G HH D+ G+C + +
Sbjct: 81 NSYSCACLAVGSVLQLVDKVLGGEI-------RNGLAIVRPPG-HHAQHDKMDGYCMFNN 132
Query: 177 ISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRV 216
+++ YA + + RV+I+D D H G G + F D V
Sbjct: 133 VAIAARYAQQKHGVQRVLIVDWDVHHGQGTQFIFEQDPSV 172
>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 = 68.3 bits (168), Expect = 2e-13
Identities = 47/170 (27%), Positives = 71/170 (41%), Gaps = 20/170 (11%)
Query: 68 LSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVALFPNCLVQR 127
L + G +E A++E LL VH +Y+ L+++ E V L P+ +
Sbjct: 15 LIASGLDRLLRQLEAPPATREQLLRVHDAAYVDRLEAA-----APEEGLVQLDPDTAMSP 69
Query: 128 KVLYPFRKQVGGTILA--AKLAKERGWAINVGGGF-------HHCSADEGGGFCAYADIS 178
L + G + A A +A G A N F HH D+ GFC + +++
Sbjct: 70 GSLEAALRAAGAVVAAVDAVMA---GEARNA---FCAVRPPGHHAERDKAMGFCLFNNVA 123
Query: 179 LCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRVYILDMFNPGIYP 228
+ +A + RV I+D D H GNG E F D RV +YP
Sbjct: 124 IAAAHALAHHGLERVAIVDFDVHHGNGTEDIFRDDPRVLFCSSHQHPLYP 173
>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 = 63.5 bits (155), Expect = 1e-11
Identities = 38/161 (23%), Positives = 74/161 (45%), Gaps = 11/161 (6%)
Query: 63 RICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVALFPN 122
I + L+ +G L++ + EA ++++L+VHS+ Y+ ++S+ + + + +
Sbjct: 16 AILERLTQDGLLERCVKIPAREAEEDEILLVHSQEYIDLVKSTETMEKEELESLCSGYDS 75
Query: 123 CLVQRKVLYPFRKQVGGTILAAKLAKERGWAINVGGGF-------HHCSADEGGGFCAYA 175
+ R G TI K + GF HH +E G+C +
Sbjct: 76 VYLCPSTYEAARLAAGSTIELVKAVMAGK----IQNGFALIRPPGHHAMRNEANGYCIFN 131
Query: 176 DISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRV 216
++++ YA +L + R++I+D D H G G ++ F D RV
Sbjct: 132 NVAIAAKYAIEKLGLKRILIVDWDVHHGQGTQQGFYEDPRV 172
>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 = 63.1 bits (154), Expect = 1e-11
Identities = 45/179 (25%), Positives = 76/179 (42%), Gaps = 18/179 (10%)
Query: 51 EKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSI 110
+ HP + RI + + G L++ + A++++LL+ HSE +L ++S +
Sbjct: 13 DPGHPECPQRISRIYERHNDLGLLERCLRLPSRLATEDELLLCHSEEHLDEMKSLEKMK- 71
Query: 111 IIEVPPVALFP-----NCLVQRKVLYPFRKQVGGTILAAKLAKERGWAINVGGGF----- 160
P L + + Y G +L A G + N G
Sbjct: 72 -----PRELNRLGKEYDSIYIHPDSYQCALLAAGCVLQVVEAVLTGESRN-GVAIVRPPG 125
Query: 161 HHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRV-YI 218
HH D GFC + ++++ YA + + R++I+D D H GNG + F SD V YI
Sbjct: 126 HHAEQDTACGFCFFNNVAIAARYAQKKYGLKRILIVDWDVHHGNGTQHMFESDPSVLYI 184
>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 = 62.1 bits (151), Expect = 3e-11
Identities = 50/152 (32%), Positives = 67/152 (44%), Gaps = 18/152 (11%)
Query: 79 IVEPLEASKEDLLVVHSESYLKSL-QSSP---NVSIIIEVPPVALFPNCLVQRKVLYPFR 134
E A++E+L H YL L + SP N + P + +C V +Y +
Sbjct: 43 TYEARAATREELRQFHDADYLDFLSKVSPENANQLRFDKAEPFNIGDDCPVFDG-MYDYC 101
Query: 135 KQVGGTILAA--KL-AKERGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNI- 190
+ G L A KL + + AIN GG HH E GFC DI L I LN+
Sbjct: 102 QLYAGASLDAARKLCSGQSDIAINWSGGLHHAKKSEASGFCYVNDIVLAI------LNLL 155
Query: 191 ---SRVMIIDLDAHQGNGHEKDFSSDSRVYIL 219
RV+ ID+D H G+G E+ F RV L
Sbjct: 156 RYFPRVLYIDIDVHHGDGVEEAFYRTDRVMTL 187
>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 = 61.6 bits (149), Expect = 4e-11
Identities = 55/188 (29%), Positives = 87/188 (46%), Gaps = 7/188 (3%)
Query: 34 KLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVV 93
K + Y D DI + HP + L + G K I P +A+ E++
Sbjct: 1 KKKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTKY 60
Query: 94 HSESYLKSLQS--SPNVS-IIIEVPPVALFPNCLVQRKVLYPFRKQVGGTILAA-KLAKE 149
HS+ Y+K L+S N+S ++ + +C V + + GG++ A KL ++
Sbjct: 61 HSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAGAVKLNRQ 120
Query: 150 R-GWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEK 208
+ A+N GG HH E GFC DI L I ++ + RV+ ID+D H G+G E+
Sbjct: 121 QTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAI-LELLKYH-QRVLYIDIDIHHGDGVEE 178
Query: 209 DFSSDSRV 216
F + RV
Sbjct: 179 AFYTTDRV 186
>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 = 61.2 bits (148), Expect = 6e-11
Identities = 57/199 (28%), Positives = 91/199 (45%), Gaps = 7/199 (3%)
Query: 34 KLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVV 93
K + Y D D+ + HP + L + G K I P +A+ E++
Sbjct: 5 KKKVCYYYDGDVGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKANAEEMTKY 64
Query: 94 HSESYLKSLQS--SPNVS-IIIEVPPVALFPNCLVQRKVLYPFRKQVGGTILAA-KLAKE 149
HS+ Y+K L+S N+S ++ + +C V + + GG++ +A KL K+
Sbjct: 65 HSDDYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSAGGSVASAVKLNKQ 124
Query: 150 R-GWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEK 208
+ A+N GG HH E GFC DI L I ++ + RV+ ID+D H G+G E+
Sbjct: 125 QTDIAVNWAGGLHHAKKSEASGFCYVNDIVLAI-LELLKYH-QRVLYIDIDIHHGDGVEE 182
Query: 209 DFSSDSRVYILDMFNPGIY 227
F + RV + G Y
Sbjct: 183 AFYTTDRVMTVSFHKYGEY 201
>gnl|CDD|240374 PTZ00346, PTZ00346, histone deacetylase; Provisional.
Length = 429
Score = 60.4 bits (146), Expect = 1e-10
Identities = 58/206 (28%), Positives = 96/206 (46%), Gaps = 21/206 (10%)
Query: 39 YSPDYDIS-FLGIEKLHPFDSSKWGRICQFLSSEGFLDKNC--IVEPLEASKEDLLVVHS 95
Y+ D +IS F+ + P+ I + L +D +C +V PL E+L+ H+
Sbjct: 30 YASDMNISAFVPQHAMKPYRVLAAMEIVRSLK----IDAHCRTVVPPL-VKVEELMAYHT 84
Query: 96 ESYLKSLQSSPNVSII--IEVPPVALFPNCLVQRKVLYPFRKQVGGTILAAKL--AKERG 151
++YL +L S + E V +C ++ GT++ A L + +
Sbjct: 85 DTYLANLGLHSCRSWLWNAETSKVFFSGDCPPVEGLMEHSIATASGTLMGAVLLNSGQVD 144
Query: 152 WAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFS 211
A++ GGG HH E GFC DI L I ++ + RV+ +D+D H G+G ++ F
Sbjct: 145 VAVHWGGGMHHSKCGECSGFCYVNDIVLGI-LELLKCH-DRVLYVDIDMHHGDGVDEAFC 202
Query: 212 SDSRVYILDM------FNPGI-YPRD 230
+ RV+ L + F PG +PRD
Sbjct: 203 TSDRVFTLSLHKFGESFFPGTGHPRD 228
>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 = 58.5 bits (141), Expect = 5e-10
Identities = 55/190 (28%), Positives = 86/190 (45%), Gaps = 28/190 (14%)
Query: 54 HPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIE 113
HP + + I L G L+K ++ +AS E++ +VHSE + SL N +
Sbjct: 24 HPEHAGRIQSIWSRLQETGLLNKCERIQGRKASLEEIQLVHSEHH--SLLYGTNPLDGQK 81
Query: 114 VPPVALFPNCLVQRKVLYP--------------------FRKQVGGTI-LAAKLAK---E 149
+ P L + + P R VG I LA+K+A +
Sbjct: 82 LDPRILLGDDSQKFFSSLPCGGLGVDSDTIWNELHSSGAARMAVGCVIELASKVASGELK 141
Query: 150 RGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKD 209
G+A+ G HH GFC + +++ Y QLNIS+++I+DLD H GNG ++
Sbjct: 142 NGFAVVRPPG-HHAEESTAMGFCFFNSVAITAKYLRDQLNISKILIVDLDVHHGNGTQQA 200
Query: 210 FSSD-SRVYI 218
F +D S +YI
Sbjct: 201 FYADPSILYI 210
>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 = 57.2 bits (138), Expect = 1e-09
Identities = 45/172 (26%), Positives = 76/172 (44%), Gaps = 13/172 (7%)
Query: 74 LDKNCIVEPL-EASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVALFPNCLVQRKVLYP 132
L + C+ P EAS+E++L+VHS YL ++ + ++ + + +
Sbjct: 26 LVQRCLRLPAREASEEEILLVHSPEYLSLVRETQVMNKEELMAISGKYDAVYFHPNTFHC 85
Query: 133 FRKQVGGT--ILAAKLAKE--RGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQL 188
R G T ++ A L E G A+ G HH + GFC + ++++ YA +
Sbjct: 86 ARLAAGATLQLVDAVLTGEVQNGMALVRPPG-HHSQRNAANGFCVFNNVAIAAEYAKKKY 144
Query: 189 NISRVMIIDLDAHQGNGHEKDFSSDSRV-------YILDMFNPGIYPRDYEA 233
+ R++I+D D H G G + F D V Y F P + DY+A
Sbjct: 145 GLHRILIVDWDVHHGQGIQYIFEEDPSVLYFSWHRYEHQRFWPFLRESDYDA 196
>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 = 56.6 bits (137), Expect = 2e-09
Identities = 55/191 (28%), Positives = 89/191 (46%), Gaps = 22/191 (11%)
Query: 54 HPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSI--I 111
HP D S+ RI + L G +++ + EA+KE++L+VHSE + ++++ +S +
Sbjct: 3 HPEDPSRISRIFEKLKEAGLINRMLRIPIREATKEEILLVHSEEHWDRVEATEKMSDEQL 62
Query: 112 IEVPPVALFPNCLVQRKVLYPFRKQVGGTILAAKLAKERGWAINVGGGF-------HHCS 164
+ + + V + R GG I A + A G V F HH
Sbjct: 63 KDRTEIFERDSLYVNNDTAFCARLSCGGAIEACR-AVAEG---RVKNAFAVVRPPGHHAE 118
Query: 165 ADEGGGFCAYADISLCIHYAFVQLN----ISRVMIIDLDAHQGNGHEKDFSSDSRV-YI- 218
DE GFC + ++ + ++Q I +++I+D D H GNG ++ F D V YI
Sbjct: 119 PDESMGFCFFNNV--AVAAKWLQTEYPDKIKKILILDWDIHHGNGTQRAFYDDPNVLYIS 176
Query: 219 LDMF-NPGIYP 228
L F N G YP
Sbjct: 177 LHRFENGGFYP 187
>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 = 53.2 bits (128), Expect = 3e-08
Identities = 51/162 (31%), Positives = 65/162 (40%), Gaps = 31/162 (19%)
Query: 72 GFLDKNCIVEPLEASKEDLLVVHSESYLKSLQS-SPNVSIIIEVPPVALFPNCLVQRKV- 129
G K + +P AS D+ HSE Y+ LQ +P + F L Q V
Sbjct: 38 GLYKKMQVYKPYRASAHDMCRFHSEDYIDFLQRVTPQ--------NIQGFTKSLNQFNVG 89
Query: 130 --------LYPFRKQVGGTIL--AAKL-AKERGWAINVGGGFHHCSADEGGGFCAYADIS 178
L+ F G L A KL K AIN GG HH E GFC DI
Sbjct: 90 DDCPVFPGLFDFCSMYTGASLEGATKLNHKICDIAINWSGGLHHAKKFEASGFCYVNDIV 149
Query: 179 LCIHYAFVQLNI----SRVMIIDLDAHQGNGHEKDFSSDSRV 216
+ I L + RV+ ID+D H G+G ++ F RV
Sbjct: 150 IAI------LELLKYHPRVLYIDIDIHHGDGVQEAFYLTDRV 185
>gnl|CDD|212522 cd09998, HDAC_Hos3, Class II histone deacetylases Hos3 and related
proteins. Fungal histone deacetylase Hos3 from
Saccharomyces cerevisiae is a Zn-dependent enzyme
belonging to HDAC class II. It catalyzes hydrolysis of
an N(6)-acetyl-lysine residue of a histone to yield a
deacetylated histone (EC 3.5.1.98). Histone
acetylation/deacetylation process is important for
mediation of transcriptional regulation of many genes.
Histone deacetylases usually act via association with
DNA binding proteins to target specific chromatin
regions. Hos3 deacetylase is homodimer, in vitro it
shows specificity to H4, H3 and H2A.
Length = 353
Score = 52.5 bits (126), Expect = 5e-08
Identities = 18/45 (40%), Positives = 28/45 (62%)
Query: 161 HHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNG 205
HHCS GFC ++ + +A++ I+RV+I+D+D H GNG
Sbjct: 120 HHCSESTPSGFCWVNNVHVGAAHAYLTHGITRVVILDIDLHHGNG 164
>gnl|CDD|240251 PTZ00063, PTZ00063, histone deacetylase; Provisional.
Length = 436
Score = 52.1 bits (125), Expect = 7e-08
Identities = 47/150 (31%), Positives = 70/150 (46%), Gaps = 19/150 (12%)
Query: 79 IVEPLEASKEDLLVVHSESYLKSLQS-SP----NVSIIIEVPPVALFPNCLVQRKVLYPF 133
I P ++ + +L++ H E Y+ L S SP + + ++ V +C V L+ F
Sbjct: 48 IYRPHKSVEPELVLFHDEEYVDFLSSISPENYRDFTYQLKRFNVGEATDCPVFDG-LFEF 106
Query: 134 RKQ-VGGTILAA-KLAKERG-WAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNI 190
++ G +I A KL + +N GG HH E GFC DI L I L +
Sbjct: 107 QQSCAGASIDGAYKLNNHQADICVNWSGGLHHAKRSEASGFCYINDIVLGI------LEL 160
Query: 191 ----SRVMIIDLDAHQGNGHEKDFSSDSRV 216
+RVM ID+D H G+G E+ F RV
Sbjct: 161 LKYHARVMYIDIDVHHGDGVEEAFYVTHRV 190
>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 = 51.2 bits (123), Expect = 1e-07
Identities = 45/186 (24%), Positives = 79/186 (42%), Gaps = 35/186 (18%)
Query: 59 SKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVA 118
S W R L G +++ + +A+ E+L +VHSE + ++P + ++ +A
Sbjct: 33 SIWSR----LQETGLVNRCERLRGRKATLEELQLVHSEVHTLLYGTNPLSRLKLDPTKLA 88
Query: 119 LFPNCLVQRKVLY---------------------PFRKQVGGTI-LAAKLAK---ERGWA 153
P Q+ + R VG I LA K+A + G+A
Sbjct: 89 GLP----QKSFVRLPCGGIGVDSDTVWNELHTSNAARMAVGCVIDLAFKVATGELKNGFA 144
Query: 154 INVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSD 213
+ G HH + GFC + +++ +L + +++I+D D H GNG ++ F D
Sbjct: 145 VVRPPG-HHAEPSQAMGFCFFNSVAIAAKQLQQKLKLRKILIVDWDVHHGNGTQQIFYED 203
Query: 214 SRV-YI 218
V YI
Sbjct: 204 PNVLYI 209
>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 = 50.6 bits (121), Expect = 2e-07
Identities = 32/83 (38%), Positives = 44/83 (53%), Gaps = 8/83 (9%)
Query: 138 GGTI-LAAKLAKER-GWAINVGGGFHHCSADEGGGFCAYADISLCI--HYAFVQLNISRV 193
GG++ AA+L + + A+N GG HH E GFC DI L I + Q RV
Sbjct: 108 GGSMEGAARLNRGKCDIAVNWAGGLHHAKKSEASGFCYVNDIVLGILELLRYHQ----RV 163
Query: 194 MIIDLDAHQGNGHEKDFSSDSRV 216
+ ID+D H G+G E+ F + RV
Sbjct: 164 LYIDIDVHHGDGVEEAFYTTDRV 186
>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 = 47.7 bits (113), Expect = 2e-06
Identities = 30/90 (33%), Positives = 47/90 (52%), Gaps = 6/90 (6%)
Query: 134 RKQVGGTI-LAAKLAK---ERGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLN 189
R VG I LA K+A + G+A+ G HH GFC + +++ +LN
Sbjct: 124 RMAVGCLIELAFKVAAGELKNGFAVIRPPG-HHAEESTAMGFCFFNSVAIAAKLLQQKLN 182
Query: 190 ISRVMIIDLDAHQGNGHEKDFSSDSRV-YI 218
+ +++I+D D H GNG ++ F +D V YI
Sbjct: 183 VGKILIVDWDIHHGNGTQQAFYNDPNVLYI 212
>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 = 47.0 bits (111), Expect = 4e-06
Identities = 19/61 (31%), Positives = 33/61 (54%)
Query: 161 HHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRVYILD 220
HH GFC + +++ +LN+S+++I+D D H GNG ++ F SD V +
Sbjct: 154 HHAEESTPMGFCYFNSVAIAAKLLQQRLNVSKILIVDWDVHHGNGTQQAFYSDPNVLYMS 213
Query: 221 M 221
+
Sbjct: 214 L 214
>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 = 44.1 bits (105), Expect = 3e-05
Identities = 38/184 (20%), Positives = 62/184 (33%), Gaps = 41/184 (22%)
Query: 37 LIYSPDYDI-----SFLGIEKLHPFDS-SKWGRICQFLSSEGFLDKNCIVEPLEASKEDL 90
++YS D+ + + + ++ + I L G + ++ P + E +
Sbjct: 2 IVYSEDHLLHHPKTELSRGKLVPHPENPERAEAILDALKRAGLGE---VLPPRDFGLEPI 58
Query: 91 LVVHSESYLKSLQSSPNVSIIIEVPPVALFPNCLVQRKVLYPFRKQVGGTILAAKLAKE- 149
L VH Y+ L++ + + + AA L E
Sbjct: 59 LAVHDPDYVDFLET--------------ADTDTPISEGTWEAALAAADTALTAADLVLEG 104
Query: 150 RGWAINVG---GGFHHCSADEGGGFC-----AYADISLCIHYAFVQLNISRVMIIDLDAH 201
A + G HH D GGFC A A Y + RV I+D+D H
Sbjct: 105 ERAAYALCRPPG--HHAGRDRAGGFCYFNNAAIA-----AQYL--RDRAGRVAILDVDVH 155
Query: 202 QGNG 205
GNG
Sbjct: 156 HGNG 159
>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 = 41.9 bits (98), Expect = 1e-04
Identities = 27/83 (32%), Positives = 41/83 (49%), Gaps = 5/83 (6%)
Query: 140 TILAAKLAK---ERGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMII 196
T LA K+A + G+A+ G HH GFC + +++ Q S+++I+
Sbjct: 129 TDLAFKVASRELKNGFAVVRPPG-HHADHSTAMGFCFFNSVAIACRQLQQQGKASKILIV 187
Query: 197 DLDAHQGNGHEKDFSSDSRV-YI 218
D D H GNG ++ F D V YI
Sbjct: 188 DWDVHHGNGTQQTFYQDPSVLYI 210
>gnl|CDD|161785 TIGR00239, 2oxo_dh_E1, 2-oxoglutarate dehydrogenase, E1 component.
The 2-oxoglutarate dehydrogenase complex consists of
this thiamine pyrophosphate-binding subunit (E1),
dihydrolipoamide succinyltransferase (E2), and lipoamide
dehydrogenase (E3). The E1 ortholog from Corynebacterium
glutamicum is unusual in having an N-terminal extension
that resembles the dihydrolipoamide succinyltransferase
(E2) component of 2-oxoglutarate dehydrogenase [Energy
metabolism, TCA cycle].
Length = 929
Score = 31.8 bits (72), Expect = 0.41
Identities = 14/45 (31%), Positives = 25/45 (55%), Gaps = 3/45 (6%)
Query: 12 DAETLKRNRILSSKLYFDIPIFKLPLIYSPDYDISFLGIEKLHPF 56
D E +KR + S K+Y+D+ + D++ + IE+L+PF
Sbjct: 809 DPEGVKRLVLCSGKVYYDLHEQRRKN---GQKDVAIVRIEQLYPF 850
>gnl|CDD|227889 COG5602, SIN3, Histone deacetylase complex, SIN3 component
[Chromatin structure and dynamics].
Length = 1163
Score = 31.4 bits (71), Expect = 0.54
Identities = 19/61 (31%), Positives = 28/61 (45%), Gaps = 5/61 (8%)
Query: 1 MSSSSSPSVTTDAETLKRNRILSSKLYFDIPIFKLPLI-YSPDYDISFLGIEKLHPFDSS 59
MSS D E LK N L+F + IF++ +I Y ++ L I+ L SS
Sbjct: 742 MSSYLES----DKERLKANLKTIVSLFFLLCIFRIIIIVYERLLNVKGLNIDGLKADRSS 797
Query: 60 K 60
+
Sbjct: 798 R 798
>gnl|CDD|220524 pfam10021, DUF2263, Uncharacterized protein conserved in bacteria
(DUF2263). This domain, found in various hypothetical
bacterial and eukaryotic proteins, has no known
function.
Length = 149
Score = 28.5 bits (64), Expect = 2.0
Identities = 13/41 (31%), Positives = 17/41 (41%), Gaps = 6/41 (14%)
Query: 2 SSSSSPSVTTDAETLKRNRILSSKLYFDIPIFKLPLIYSPD 42
SS + E + +R S LY D +IYSPD
Sbjct: 108 RSSLYFCLIKYPEFYEFHRAQKSPLYPD------YMIYSPD 142
>gnl|CDD|239110 cd02619, Peptidase_C1, C1 Peptidase family (MEROPS database
nomenclature), also referred to as the papain family;
composed of two subfamilies of cysteine peptidases
(CPs), C1A (papain) and C1B (bleomycin hydrolase).
Papain-like enzymes are mostly endopeptidases with some
exceptions like cathepsins B, C, H and X, which are
exopeptidases. Papain-like CPs have different functions
in various organisms. Plant CPs are used to mobilize
storage proteins in seeds while mammalian CPs are
primarily lysosomal enzymes responsible for protein
degradation in the lysosome. Papain-like CPs are
synthesized as inactive proenzymes with N-terminal
propeptide regions, which are removed upon activation.
Bleomycin hydrolase (BH) is a CP that detoxifies
bleomycin by hydrolysis of an amide group. It acts as a
carboxypeptidase on its C-terminus to convert itself
into an aminopeptidase and peptide ligase. BH is found
in all tissues in mammals as well as in many other
eukaryotes. It forms a hexameric ring barrel structure
with the active sites imbedded in the central channel.
Some members of the C1 family are proteins classified as
non-peptidase homologs which lack peptidase activity or
have missing active site residues.
Length = 223
Score = 29.0 bits (65), Expect = 2.2
Identities = 13/85 (15%), Positives = 23/85 (27%), Gaps = 6/85 (7%)
Query: 172 CAYADISLCIH---YAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRVYILDMFNPGIYP 228
+ + I +V L+ + I D G D + + GI P
Sbjct: 27 AYALESAYRIKGGEDEYVDLSPQYLYICANDECLGINGSCDGGGPLSALLKLVALKGIPP 86
Query: 229 RD---YEARRFIDQKVEVVVNNQYT 250
+ Y A ++ N
Sbjct: 87 EEDYPYGAESDGEEPKSEAALNAAK 111
>gnl|CDD|218127 pfam04522, DUF585, Protein of unknown function (DUF585). This
region represents the N terminus of bromovirus 2a
protein, and is always found N terminal to a predicted
RNA-dependent RNA polymerase region (pfam00978).
Length = 248
Score = 28.7 bits (64), Expect = 2.4
Identities = 10/30 (33%), Positives = 16/30 (53%), Gaps = 2/30 (6%)
Query: 55 PFDSSKWGRICQFLSS--EGFLDKNCIVEP 82
PFD ++WG C +++ EGF + I
Sbjct: 73 PFDQARWGSCCLNVTNLAEGFTGRRLIPLA 102
>gnl|CDD|170182 PRK09965, PRK09965, 3-phenylpropionate dioxygenase ferredoxin
subunit; Provisional.
Length = 106
Score = 27.4 bits (61), Expect = 3.5
Identities = 10/22 (45%), Positives = 14/22 (63%), Gaps = 1/22 (4%)
Query: 70 SEGFLDKNCIVE-PLEASKEDL 90
SEG+L+ + VE PL A+ L
Sbjct: 50 SEGYLEDDATVECPLHAASFCL 71
>gnl|CDD|182938 PRK11062, nhaR, transcriptional activator NhaR; Provisional.
Length = 296
Score = 27.3 bits (61), Expect = 7.0
Identities = 16/51 (31%), Positives = 25/51 (49%), Gaps = 8/51 (15%)
Query: 113 EVPPVALFPNCLVQRKVLYPFRKQVGGTILAAKLAK---ERGWAINVGGGF 160
+P FP CL +R++L P R+ T+L KL +G + + G F
Sbjct: 177 PLPEKP-FPACLEERRLLIPGRR----TMLGRKLLNWFNSQGLNVEILGEF 222
>gnl|CDD|234515 TIGR04234, seadorna_RNAP, seadornavirus RNA-directed RNA
polymerase. Members of this protein family are the
seadornavirus VP1 protein, the RNA-directed RNA
polymerase.
Length = 1144
Score = 27.5 bits (61), Expect = 7.7
Identities = 22/73 (30%), Positives = 35/73 (47%), Gaps = 12/73 (16%)
Query: 56 FDSSKWGRICQF-------LSSEGFLDKNC----IVEPLEASKEDLLVVHSESYLKSLQS 104
FDSS+ GRI + +++E F N +++ LE S L + SESY + L+
Sbjct: 570 FDSSQGGRISKAHADGVRRVANEYFPGTNTDLSDVLDLLELSMSKFLYITSESYERPLKY 629
Query: 105 SPNVSIIIEVPPV 117
+ I+ E V
Sbjct: 630 KSD-GIVAEAAGV 641
>gnl|CDD|236291 PRK08565, PRK08565, DNA-directed RNA polymerase subunit B;
Provisional.
Length = 1103
Score = 27.2 bits (61), Expect = 9.2
Identities = 12/26 (46%), Positives = 15/26 (57%), Gaps = 6/26 (23%)
Query: 53 LHPFDSSKWGRICQFLSSEGFLDKNC 78
LH ++WGRIC F + EG NC
Sbjct: 437 LHG---TQWGRICPFETPEG---PNC 456
>gnl|CDD|221999 pfam13236, CLU, Clustered mitochondria. The CLU domain (CLUstered
mitochondria) is a eukaryotic domain found in proteins
from fungi, protozoa, plants to humans. It is required
for correct functioning of the mitochondria and
mitochondrial transport although the exact function of
the domain is unknown. In Dictyostelium the full-length
protein is required for a very late step in fission of
the outer mitochondrial membrane suggesting that
mitochondria are transported along microtubules, as in
mammalian cells, rather than along actin filaments, as
in budding yeast. Disruption of the protein-impaired
cytokinesis and caused mitochondria to cluster at the
cell centre. It is likely that CLU functions in a novel
pathway that positions mitochondria within the cell
based on their physiological state. Disruption of the
CLU pathway may enhance oxidative damage, alter gene
expression, cause mitochondria to cluster at microtubule
plus ends, and lead eventually to mitochondrial failure.
Length = 222
Score = 26.8 bits (60), Expect = 9.6
Identities = 7/23 (30%), Positives = 11/23 (47%), Gaps = 2/23 (8%)
Query: 210 FSSDSRVYILDMFNPGIYPRDYE 232
+D R Y+LD+ +P D
Sbjct: 200 LGTDGRKYVLDLAR--TFPPDIN 220
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.321 0.138 0.416
Gapped
Lambda K H
0.267 0.0776 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,865,262
Number of extensions: 1224311
Number of successful extensions: 1043
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1011
Number of HSP's successfully gapped: 54
Length of query: 251
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 156
Effective length of database: 6,723,972
Effective search space: 1048939632
Effective search space used: 1048939632
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 (21.9 bits)
S2: 58 (26.0 bits)