RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16742
(620 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 = 113 bits (286), Expect = 4e-28
Identities = 57/175 (32%), Positives = 68/175 (38%), Gaps = 71/175 (40%)
Query: 505 THHAFPDHGAGFCLMNDMALAARYLIRHGIVRKVLIVDLDVHQ----------------- 547
THHAFPD G GFC+ ND+A+AAR L+ G+VR+VLIVDLDVHQ
Sbjct: 101 THHAFPDRGEGFCVFNDIAIAARVLLAEGLVRRVLIVDLDVHQGNGTAAIFADDPSVFTF 160
Query: 548 --H------------TRSIPVPS-------LTVLSSCVPGL------------------- 567
H +P+P L L +P L
Sbjct: 161 SMHGEKNYPFRKEPSDLDVPLPDGTGDDEYLAALEEALPRLLAEFRPDLVFYNAGVDVLA 220
Query: 568 --------------YMRDYYVLDTAISAGIPVATVTGGGYCADIDQLAQRQTIIH 608
RD VL A + GIPVA V GGGY DI +L R
Sbjct: 221 GDRLGRLSLSLEGLRERDRLVLRFARARGIPVAMVLGGGYSRDIARLVARHAQTL 275
Score = 84.5 bits (210), Expect = 4e-18
Identities = 22/77 (28%), Positives = 38/77 (49%), Gaps = 1/77 (1%)
Query: 47 HRFPMSKFSKTFNYLVRDKVIDKSKQLIEPQQISESIAELVHTKEYVHKFFNGKTTEKEQ 106
HRFPM K+ L+ + ++ + ++EP+ + VH EY+ +G+ + +E
Sbjct: 1 HRFPMRKYGLLREALLEEGLV-LPEDIVEPEPATREDLLRVHDPEYLESLKSGELSREEI 59
Query: 107 KVTGFEWSAGLASRVRT 123
+ GF WS L R R
Sbjct: 60 RRIGFPWSPELVERTRL 76
Score = 76.4 bits (189), Expect = 2e-15
Identities = 29/45 (64%), Positives = 34/45 (75%)
Query: 419 GDGTAFIFDKDPAVFTFSMHCGRNYPFRKQCSDLDVAIDVGTDDA 463
G+GTA IF DP+VFTFSMH +NYPFRK+ SDLDV + GT D
Sbjct: 144 GNGTAAIFADDPSVFTFSMHGEKNYPFRKEPSDLDVPLPDGTGDD 188
Score = 75.6 bits (187), Expect = 5e-15
Identities = 24/44 (54%), Positives = 32/44 (72%)
Query: 197 YQATLKEHLPGILAQFKPDLVIYDAGVDPHQHDELGKLNLTDHG 240
Y A L+E LP +LA+F+PDLV Y+AGVD D LG+L+L+ G
Sbjct: 190 YLAALEEALPRLLAEFRPDLVFYNAGVDVLAGDRLGRLSLSLEG 233
>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 = 80.0 bits (198), Expect = 2e-16
Identities = 24/42 (57%), Positives = 33/42 (78%)
Query: 506 HHAFPDHGAGFCLMNDMALAARYLIRHGIVRKVLIVDLDVHQ 547
HHA D +GFCL N++A+AARYL++ +++VLIVDLDVH
Sbjct: 115 HHAERDRASGFCLFNNVAIAARYLLKRYGLKRVLIVDLDVHH 156
Score = 62.2 bits (152), Expect = 2e-10
Identities = 21/46 (45%), Positives = 26/46 (56%)
Query: 195 SGYQATLKEHLPGILAQFKPDLVIYDAGVDPHQHDELGKLNLTDHG 240
Y A +E L L +F+PDL++ AG D H D LG LNLT G
Sbjct: 211 EEYLAAFEEILLPALREFQPDLILVSAGFDAHAGDPLGGLNLTTEG 256
Score = 53.8 bits (130), Expect = 9e-08
Identities = 17/56 (30%), Positives = 23/56 (41%), Gaps = 10/56 (17%)
Query: 419 GDGTAFIFDKDPAVFTFSMHCGRNYPF----------RKQCSDLDVAIDVGTDDAG 464
G+GT IF DP V T S+H YP + L++ + GT D
Sbjct: 157 GNGTQEIFYDDPRVLTISIHQDPFYPGTGFADETGEGAGEGYTLNIPLPPGTGDEE 212
Score = 46.4 bits (111), Expect = 2e-05
Identities = 17/82 (20%), Positives = 27/82 (32%), Gaps = 5/82 (6%)
Query: 45 PNHRFPMSKFSKTFNYLVRDKVIDKSKQLIEPQQISESIAELVHTKEYVHKFFNGKTTEK 104
H + L ++D+ + I P+ +E LVH+ EYV E+
Sbjct: 7 LGHPENPERLEAILELLKESGLLDR-LEFIAPRPATEEELLLVHSPEYVEFLEEASLEEE 65
Query: 105 EQKVTGFE----WSAGLASRVR 122
E G + S G
Sbjct: 66 ELGRIGLDGDTPVSPGSYEAAL 87
Score = 36.8 bits (86), Expect = 0.024
Identities = 12/45 (26%), Positives = 18/45 (40%)
Query: 566 GLYMRDYYVLDTAISAGIPVATVTGGGYCADIDQLAQRQTIIHRA 610
G R +L+ A + G PV +V GGY D + +
Sbjct: 256 GYAERTRLLLELADAYGGPVVSVLEGGYNLDALARSAAAVLAGLL 300
>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 = 70.1 bits (172), Expect = 5e-13
Identities = 22/43 (51%), Positives = 32/43 (74%), Gaps = 1/43 (2%)
Query: 505 THHAFPDHGAGFCLMNDMALAARYLIRHGIVRKVLIVDLDVHQ 547
HHA D +GFCL N++A+AA+YL++ G V++V I+D DVH
Sbjct: 124 GHHAGRDRASGFCLFNNVAIAAKYLLKKG-VKRVAIIDFDVHH 165
Score = 57.0 bits (138), Expect = 1e-08
Identities = 23/45 (51%), Positives = 30/45 (66%)
Query: 196 GYQATLKEHLPGILAQFKPDLVIYDAGVDPHQHDELGKLNLTDHG 240
Y L+E + +L +FKPDLVI AG D H+ D LG+LNLT+ G
Sbjct: 222 SYLEALEEIVLPLLEEFKPDLVIVSAGFDAHRGDPLGRLNLTEEG 266
Score = 47.4 bits (113), Expect = 1e-05
Identities = 37/189 (19%), Positives = 52/189 (27%), Gaps = 75/189 (39%)
Query: 419 GDGTAFIFDKDPAVFTFSMHC--GRNYPFRKQC---------SDLDVAIDVGTDDAGNRT 467
G+GT IF D V T S+H YP +++++ + GT D
Sbjct: 166 GNGTQEIFYDDDDVLTVSLHQDGRPFYPGTGGADEIGEGKEGNNVNIPLPPGTGDD---- 221
Query: 468 VALTWVTFLSQRSEKMRNNGIFLFLLR-LSDPEINRFSTHHAFPDHGAGFCLMNDMALAA 526
+L L + P + F PD
Sbjct: 222 --------------------SYLEALEEIVLPLLEEFK-----PD--------------- 241
Query: 527 RYLIRHGIVRKVLIVDL--DVHQHTRSIPVPSLTVLSSCVPGLYMRDYYVLDTAISAGIP 584
++IV D H+ L L+ G V A G P
Sbjct: 242 -----------LVIVSAGFDAHRGDP------LGRLNLTEEGYAKIGRAVRKLAEGYGGP 284
Query: 585 VATVTGGGY 593
V V GGY
Sbjct: 285 VVAVLEGGY 293
Score = 40.8 bits (96), Expect = 0.002
Identities = 13/51 (25%), Positives = 22/51 (43%), Gaps = 1/51 (1%)
Query: 43 LPPNHRFPMSKFSKTFNYLVRDKVIDKSKQLIEPQQISESIAELVHTKEYV 93
PP H + L+ + S +L+EP+ + LVH+ +YV
Sbjct: 17 PPPGHPENPDRLRLILE-LLESSGLPDSLELVEPRPATLEELLLVHSPDYV 66
>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 = 68.7 bits (169), Expect = 1e-12
Identities = 23/41 (56%), Positives = 30/41 (73%)
Query: 506 HHAFPDHGAGFCLMNDMALAARYLIRHGIVRKVLIVDLDVH 546
HHA PD GFCL N++A+AARY + +++VLIVD DVH
Sbjct: 105 HHAEPDRAMGFCLFNNVAIAARYAQKRYGLKRVLIVDWDVH 145
Score = 49.8 bits (120), Expect = 2e-06
Identities = 21/45 (46%), Positives = 27/45 (60%)
Query: 196 GYQATLKEHLPGILAQFKPDLVIYDAGVDPHQHDELGKLNLTDHG 240
Y A +E L I +F+PDLV+ AG D H+ D LG +NLT G
Sbjct: 202 EYLAAFEEVLLPIAREFQPDLVLVSAGFDAHRGDPLGGMNLTPEG 246
Score = 38.2 bits (90), Expect = 0.007
Identities = 13/27 (48%), Positives = 16/27 (59%)
Query: 419 GDGTAFIFDKDPAVFTFSMHCGRNYPF 445
G+GT IF DP+V FS+H YP
Sbjct: 147 GNGTQDIFYDDPSVLYFSIHQYPFYPG 173
>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 = 65.7 bits (161), Expect = 2e-11
Identities = 23/41 (56%), Positives = 31/41 (75%)
Query: 506 HHAFPDHGAGFCLMNDMALAARYLIRHGIVRKVLIVDLDVH 546
HHA PD G GFCL N++A+AAR+ + G V++V +VD DVH
Sbjct: 137 HHAEPDQGMGFCLFNNVAIAARHALAVGGVKRVAVVDWDVH 177
Score = 33.3 bits (77), Expect = 0.33
Identities = 13/42 (30%), Positives = 21/42 (50%)
Query: 196 GYQATLKEHLPGILAQFKPDLVIYDAGVDPHQHDELGKLNLT 237
Y + + L F+P+L+I +G D D LG++ LT
Sbjct: 235 AYLHAFERIVLPALRAFRPELIIVASGFDASAFDPLGRMMLT 276
Score = 32.9 bits (76), Expect = 0.49
Identities = 13/26 (50%), Positives = 16/26 (61%)
Query: 419 GDGTAFIFDKDPAVFTFSMHCGRNYP 444
G+GT IF DP V T S+H R +P
Sbjct: 179 GNGTQAIFYDDPDVLTISLHQDRCFP 204
>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 = 63.3 bits (155), Expect = 6e-11
Identities = 17/42 (40%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 505 THHAFPDHGAGFCLMNDMALAARYLIRHGIVRKVLIVDLDVH 546
HHA +GFC+ ND A+A L G +V VD+D H
Sbjct: 126 LHHAMRGRASGFCVYNDAAVAIERLRDKGG-LRVAYVDIDAH 166
Score = 40.2 bits (95), Expect = 0.002
Identities = 13/36 (36%), Positives = 21/36 (58%)
Query: 205 LPGILAQFKPDLVIYDAGVDPHQHDELGKLNLTDHG 240
+P +L F+PD+++ G D H D L LNL++
Sbjct: 234 VPPLLRAFRPDVIVSQHGADAHAGDPLTHLNLSNRA 269
Score = 32.5 bits (75), Expect = 0.54
Identities = 10/20 (50%), Positives = 11/20 (55%)
Query: 419 GDGTAFIFDKDPAVFTFSMH 438
GDG F DP V T S+H
Sbjct: 168 GDGVQAAFYDDPRVLTISLH 187
Score = 30.6 bits (70), Expect = 2.0
Identities = 15/52 (28%), Positives = 25/52 (48%), Gaps = 1/52 (1%)
Query: 42 TLPPNHRFPMSKFSKTFNYLVRDKVIDKSKQLIEPQQISESIAELVHTKEYV 93
+ PNH F + S T + L+R + L+ P+ +E L HT +Y+
Sbjct: 12 SFGPNHPFNPPRLSLTKD-LLRALGLLPPVDLVPPRPATEEELLLFHTPDYI 62
Score = 29.1 bits (66), Expect = 7.4
Identities = 10/29 (34%), Positives = 15/29 (51%)
Query: 249 ISSEAGVDPHQHDELGKLNLTDHGVKYIL 277
I S+ G D H D L LNL++ + +
Sbjct: 246 IVSQHGADAHAGDPLTHLNLSNRAYRAAV 274
>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 = 57.5 bits (140), Expect = 5e-09
Identities = 21/43 (48%), Positives = 28/43 (65%), Gaps = 2/43 (4%)
Query: 506 HHAFPDHGAGFCLMNDMALAARYLI-RHGIVRKVLIVDLDVHQ 547
HHA D GFCL N++A+AA + + HG+ +V IVD DVH
Sbjct: 106 HHAERDKAMGFCLFNNVAIAAAHALAHHGL-ERVAIVDFDVHH 147
Score = 40.2 bits (95), Expect = 0.002
Identities = 16/30 (53%), Positives = 21/30 (70%)
Query: 209 LAQFKPDLVIYDAGVDPHQHDELGKLNLTD 238
L FKPDL++ AG D H+ D L +LNLT+
Sbjct: 212 LDAFKPDLILISAGFDAHRDDPLAQLNLTE 241
>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 = 1e-08
Identities = 19/43 (44%), Positives = 29/43 (67%), Gaps = 2/43 (4%)
Query: 506 HHAFPDHGAGFCLMNDMALAARYLI--RHGIVRKVLIVDLDVH 546
HHA PD GFC N++A+AA++L ++K+LI+D D+H
Sbjct: 115 HHAEPDESMGFCFFNNVAVAAKWLQTEYPDKIKKILILDWDIH 157
Score = 33.9 bits (78), Expect = 0.20
Identities = 15/30 (50%), Positives = 19/30 (63%)
Query: 208 ILAQFKPDLVIYDAGVDPHQHDELGKLNLT 237
I +F PDLVI AG D DELG+ ++T
Sbjct: 232 IAYEFDPDLVIISAGFDAADGDELGQCHVT 261
>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 = 55.9 bits (135), Expect = 1e-08
Identities = 18/42 (42%), Positives = 24/42 (57%), Gaps = 1/42 (2%)
Query: 506 HHAFPDHGAGFCLMNDMALAARYLIRHGIVRKVLIVDLDVHQ 547
HHA GFC ND+ LA ++L GI ++LI+D D H
Sbjct: 105 HHAGKSRAWGFCYFNDVVLAIKFLRERGI-SRILIIDTDAHH 145
Score = 44.0 bits (104), Expect = 1e-04
Identities = 13/41 (31%), Positives = 24/41 (58%)
Query: 197 YQATLKEHLPGILAQFKPDLVIYDAGVDPHQHDELGKLNLT 237
Y ++ + +L +F+P++V+ G D H+ D LG NL+
Sbjct: 195 YLDAVERVISKVLEEFEPEVVVLQFGHDTHEGDRLGGFNLS 235
>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 = 56.2 bits (136), Expect = 2e-08
Identities = 21/41 (51%), Positives = 27/41 (65%)
Query: 506 HHAFPDHGAGFCLMNDMALAARYLIRHGIVRKVLIVDLDVH 546
HHA P GFC N +A+AA+ L + +RK+LIVD DVH
Sbjct: 151 HHAEPSQAMGFCFFNSVAIAAKQLQQKLKLRKILIVDWDVH 191
>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 = 55.8 bits (135), Expect = 3e-08
Identities = 20/46 (43%), Positives = 31/46 (67%), Gaps = 2/46 (4%)
Query: 506 HHAFPDHGAGFCLMNDMALAARYLIRHGIVRKVLIVDLDVH--QHT 549
HHA + G+C+ N++A+AA+Y I ++++LIVD DVH Q T
Sbjct: 117 HHAMRNEANGYCIFNNVAIAAKYAIEKLGLKRILIVDWDVHHGQGT 162
Score = 30.0 bits (68), Expect = 4.2
Identities = 13/36 (36%), Positives = 21/36 (58%), Gaps = 1/36 (2%)
Query: 205 LPGILAQFKPDLVIYDAGVDPHQHDELGKLNLTDHG 240
LP + +F+P+LV+ AG D D G++ +T G
Sbjct: 230 LP-LALEFQPELVLVSAGFDASIGDPEGEMAVTPAG 264
>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 = 55.8 bits (135), Expect = 3e-08
Identities = 20/41 (48%), Positives = 28/41 (68%)
Query: 506 HHAFPDHGAGFCLMNDMALAARYLIRHGIVRKVLIVDLDVH 546
HHA D GFC N++A+AARY + ++++LIVD DVH
Sbjct: 126 HHAEQDTACGFCFFNNVAIAARYAQKKYGLKRILIVDWDVH 166
>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 = 53.3 bits (129), Expect = 1e-07
Identities = 19/41 (46%), Positives = 25/41 (60%), Gaps = 2/41 (4%)
Query: 506 HHAFPDHGAGFCLMNDMALAARYLIRHGIVRKVLIVDLDVH 546
HHA D GFC N+ A+AA+YL +V I+D+DVH
Sbjct: 117 HHAGRDRAGGFCYFNNAAIAAQYLRDRA--GRVAILDVDVH 155
Score = 43.3 bits (103), Expect = 2e-04
Identities = 16/43 (37%), Positives = 20/43 (46%), Gaps = 1/43 (2%)
Query: 196 GYQATLKEHLPGILAQFKPDLVIYDAGVDPHQHDELGKLNLTD 238
Y A L E L +A F PD ++ G D H+ D L LT
Sbjct: 215 DYLAALDEALA-AIAAFGPDALVVSLGFDTHEGDPLSDFKLTT 256
>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 = 52.5 bits (126), Expect = 3e-07
Identities = 25/48 (52%), Positives = 33/48 (68%), Gaps = 2/48 (4%)
Query: 500 INRFSTHHAFPDHGAGFCLMNDMALAARYL-IRHGIVRKVLIVDLDVH 546
I R HHA D G+C+ N++A+AARY +HG V++VLIVD DVH
Sbjct: 111 IVRPPGHHAQHDKMDGYCMFNNVAIAARYAQQKHG-VQRVLIVDWDVH 157
Score = 33.3 bits (76), Expect = 0.34
Identities = 12/20 (60%), Positives = 16/20 (80%)
Query: 419 GDGTAFIFDKDPAVFTFSMH 438
G GT FIF++DP+V FS+H
Sbjct: 159 GQGTQFIFEQDPSVLYFSIH 178
>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 = 50.8 bits (121), Expect = 1e-06
Identities = 20/42 (47%), Positives = 24/42 (57%)
Query: 506 HHAFPDHGAGFCLMNDMALAARYLIRHGIVRKVLIVDLDVHQ 547
HHA GFC N +A+A R L + G K+LIVD DVH
Sbjct: 152 HHADHSTAMGFCFFNSVAIACRQLQQQGKASKILIVDWDVHH 193
>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 = 47.2 bits (113), Expect = 1e-05
Identities = 16/41 (39%), Positives = 27/41 (65%), Gaps = 2/41 (4%)
Query: 506 HHAFPDHGAGFCLMNDMALAARYLIRHGIVRKVLIVDLDVH 546
HHA +GFC +ND+ LA L+++ ++VL +D+D+H
Sbjct: 127 HHAKKSEASGFCYVNDIVLAILELLKY--HQRVLYIDIDIH 165
Score = 31.0 bits (71), Expect = 1.9
Identities = 12/34 (35%), Positives = 17/34 (50%), Gaps = 2/34 (5%)
Query: 212 FKPDLVIYDAGVDPHQHDELGKLNLT--DHGECI 243
F+P V+ G D D LG NL+ H +C+
Sbjct: 239 FQPSAVVLQCGADSLAGDRLGCFNLSIKGHAKCV 272
>gnl|CDD|212524 cd10000, HDAC8, Histone deacetylase 8 (HDAC8). HDAC8 is a
Zn-dependent class I histone deacetylase that catalyzes
hydrolysis of an N(6)-acetyl-lysine residue of a histone
to yield a deacetylated histone (EC 3.5.1.98). Histone
acetylation/deacetylation process is important for
mediation of transcriptional regulation of many genes.
Histone deacetylases usually act via association with
DNA binding proteins to target specific chromatin
regions. HDAC8 is found in human cytoskeleton-bound
protein fraction and insoluble cell pellets. It plays a
crucial role in intramembraneous bone formation;
germline deletion of HDAC8 is detrimental to skull bone
formation. HDAC8 is possibly associated with the smooth
muscle actin cytockeleton and may regulate the
contractive capacity of smooth muscle cells. HDAC8 is
also involved in the metabolic control of the estrogen
receptor related receptor (ERR)-alpha/peroxisome
proliferator activated receptor (PPAR) gamma coactivator
1 alpha (PGC1-alpha) transcriptional complex as well as
in the development of neuroblastoma and T-cell lymphoma.
HDAC8-selective small-molecule inhibitors could be a
therapeutic drug option for these diseases.
Length = 364
Score = 46.2 bits (110), Expect = 3e-05
Identities = 18/41 (43%), Positives = 23/41 (56%), Gaps = 2/41 (4%)
Query: 506 HHAFPDHGAGFCLMNDMALAARYLIRHGIVRKVLIVDLDVH 546
HHA D +GFC +ND+ L L +VL VDLD+H
Sbjct: 129 HHAQRDEASGFCYVNDIVLGILKLREK--FDRVLYVDLDLH 167
Score = 30.0 bits (68), Expect = 3.5
Identities = 15/43 (34%), Positives = 23/43 (53%), Gaps = 2/43 (4%)
Query: 205 LPGILAQFKPDLVIYDAGVDPHQHDELGKLNLTDH--GECISS 245
+P I+A F+P+ V+ G D D +G NLT G+C+
Sbjct: 235 VPEIVAAFRPEAVVLQCGADTLAGDPMGAFNLTPVGIGKCLKY 277
>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 = 45.0 bits (106), Expect = 7e-05
Identities = 20/42 (47%), Positives = 25/42 (59%)
Query: 506 HHAFPDHGAGFCLMNDMALAARYLIRHGIVRKVLIVDLDVHQ 547
HHA GFC N +A+ A+YL + K+LIVDLDVH
Sbjct: 152 HHAEESTAMGFCFFNSVAITAKYLRDQLNISKILIVDLDVHH 193
>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 = 42.2 bits (99), Expect = 6e-04
Identities = 17/42 (40%), Positives = 27/42 (64%)
Query: 506 HHAFPDHGAGFCLMNDMALAARYLIRHGIVRKVLIVDLDVHQ 547
HH+ + GFC+ N++A+AA Y + + ++LIVD DVH
Sbjct: 117 HHSQRNAANGFCVFNNVAIAAEYAKKKYGLHRILIVDWDVHH 158
Score = 34.8 bits (80), Expect = 0.13
Identities = 24/71 (33%), Positives = 36/71 (50%), Gaps = 9/71 (12%)
Query: 405 HRALIMEIGLPCYDGDGTAFIFDKDPAVFTFSMH---CGRNYPFRKQCSDLDVAIDVGTD 461
HR LI++ + + G G +IF++DP+V FS H R +PF ++ SD D VG
Sbjct: 147 HRILIVDWDV--HHGQGIQYIFEEDPSVLYFSWHRYEHQRFWPFLRE-SDYDA---VGRG 200
Query: 462 DAGNRTVALTW 472
+ L W
Sbjct: 201 KGLGFNINLPW 211
>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 = 41.9 bits (98), Expect = 7e-04
Identities = 20/42 (47%), Positives = 25/42 (59%)
Query: 506 HHAFPDHGAGFCLMNDMALAARYLIRHGIVRKVLIVDLDVHQ 547
HHA GFC N +A+AA+ L + V K+LIVD DVH
Sbjct: 154 HHAEESTPMGFCYFNSVAIAAKLLQQRLNVSKILIVDWDVHH 195
>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 = 41.7 bits (98), Expect = 8e-04
Identities = 17/42 (40%), Positives = 26/42 (61%), Gaps = 2/42 (4%)
Query: 506 HHAFPDHGAGFCLMNDMALAARYLIRHGIVRKVLIVDLDVHQ 547
HHA +GFC +ND+ L L+R+ ++VL +D+DVH
Sbjct: 133 HHAKKSEASGFCYVNDIVLGILELLRYH--QRVLYIDIDVHH 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 = 41.5 bits (98), Expect = 8e-04
Identities = 18/41 (43%), Positives = 24/41 (58%), Gaps = 1/41 (2%)
Query: 506 HHAFPDHGAGFCLMNDMALAARYLIRHGIVRKVLIVDLDVH 546
HHA +GFC +ND+ LA L R R+V +DLD+H
Sbjct: 115 HHAQKSRASGFCYVNDIVLAILRLRRARF-RRVFYLDLDLH 154
>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 = 41.5 bits (97), Expect = 0.001
Identities = 19/42 (45%), Positives = 25/42 (59%)
Query: 506 HHAFPDHGAGFCLMNDMALAARYLIRHGIVRKVLIVDLDVHQ 547
HHA GFC N +A+AA+ L + V K+LIVD D+H
Sbjct: 154 HHAEESTAMGFCFFNSVAIAAKLLQQKLNVGKILIVDWDIHH 195
>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 = 38.6 bits (90), Expect = 0.007
Identities = 16/42 (38%), Positives = 26/42 (61%), Gaps = 2/42 (4%)
Query: 506 HHAFPDHGAGFCLMNDMALAARYLI-RHGIVRKVLIVDLDVH 546
HH +GFC +N++ + A + HGI R V+I+D+D+H
Sbjct: 120 HHCSESTPSGFCWVNNVHVGAAHAYLTHGITR-VVILDIDLH 160
>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 = 38.1 bits (88), Expect = 0.012
Identities = 16/42 (38%), Positives = 27/42 (64%), Gaps = 2/42 (4%)
Query: 506 HHAFPDHGAGFCLMNDMALAARYLIRHGIVRKVLIVDLDVHQ 547
HHA +GFC +ND+ LA L+++ ++VL +D+D+H
Sbjct: 133 HHAKKSEASGFCYVNDIVLAILELLKYH--QRVLYIDIDIHH 172
Score = 28.9 bits (64), Expect = 8.9
Identities = 14/49 (28%), Positives = 22/49 (44%), Gaps = 2/49 (4%)
Query: 197 YQATLKEHLPGILAQFKPDLVIYDAGVDPHQHDELGKLNLT--DHGECI 243
Y K + ++ ++P V+ G D D LG NLT H +C+
Sbjct: 230 YGQIFKPIISKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCV 278
>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 = 37.4 bits (87), Expect = 0.017
Identities = 18/41 (43%), Positives = 25/41 (60%), Gaps = 2/41 (4%)
Query: 506 HHAFPDHGAGFCLMNDMALAARYLIRHGIVRKVLIVDLDVH 546
HHA +GFC +ND+ LA L+R +VL +D+DVH
Sbjct: 131 HHAKKSEASGFCYVNDIVLAILNLLR--YFPRVLYIDIDVH 169
Score = 32.0 bits (73), Expect = 0.83
Identities = 14/50 (28%), Positives = 22/50 (44%), Gaps = 2/50 (4%)
Query: 197 YQATLKEHLPGILAQFKPDLVIYDAGVDPHQHDELGKLNLT--DHGECIS 244
Y K + + +F+P ++ G D D LG+ NL HG C+
Sbjct: 229 YNLLFKSIIGPTIEKFQPSAIVLQCGADSLGGDRLGQFNLNIKAHGACVK 278
>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 = 36.6 bits (84), Expect = 0.032
Identities = 16/42 (38%), Positives = 27/42 (64%), Gaps = 2/42 (4%)
Query: 506 HHAFPDHGAGFCLMNDMALAARYLIRHGIVRKVLIVDLDVHQ 547
HHA +GFC +ND+ LA L+++ ++VL +D+D+H
Sbjct: 137 HHAKKSEASGFCYVNDIVLAILELLKYH--QRVLYIDIDIHH 176
Score = 33.5 bits (76), Expect = 0.27
Identities = 16/49 (32%), Positives = 24/49 (48%), Gaps = 2/49 (4%)
Query: 197 YQATLKEHLPGILAQFKPDLVIYDAGVDPHQHDELGKLNLT--DHGECI 243
Y+A K + ++ F+P V+ G D D LG NLT H +C+
Sbjct: 234 YEAIFKPVMSKVMEMFQPSAVVLQCGADSLSGDRLGCFNLTIKGHAKCV 282
>gnl|CDD|233183 TIGR00916, 2A0604s01, protein-export membrane protein, SecD/SecF
family. The SecA,SecB,SecD,SecE,SecF,SecG and SecY
proteins form the protein translocation appartus in
prokaryotes. This family is specific for the SecD and
SecF proteins [Protein fate, Protein and peptide
secretion and trafficking].
Length = 192
Score = 35.3 bits (82), Expect = 0.042
Identities = 20/63 (31%), Positives = 34/63 (53%), Gaps = 7/63 (11%)
Query: 148 IAAVLADLICIAVYLTFFLQRRPVFFDIAAVLADLIHFMVGINTQPVSGYQATLKEHLPG 207
I A+L L+ + +Y+ + R IAA++ D+I ++G+ +S + ATL LPG
Sbjct: 50 IIALLIGLVLVLLYMLLRYEWRGAIAAIAALVHDVI-LILGV----LSLFGATLT--LPG 102
Query: 208 ILA 210
I
Sbjct: 103 IAG 105
>gnl|CDD|240374 PTZ00346, PTZ00346, histone deacetylase; Provisional.
Length = 429
Score = 35.8 bits (82), Expect = 0.057
Identities = 16/51 (31%), Positives = 26/51 (50%), Gaps = 2/51 (3%)
Query: 197 YQATLKEHLPGILAQFKPDLVIYDAGVDPHQHDELGKLNLTD--HGECISS 245
Y + L I+ ++ PD ++ G D D LG LNL+ HG+C+ +
Sbjct: 252 YLGLFEHALHSIVRRYSPDAIVLQCGADSLAGDRLGLLNLSSFGHGQCVQA 302
Score = 29.6 bits (66), Expect = 6.1
Identities = 16/43 (37%), Positives = 25/43 (58%), Gaps = 4/43 (9%)
Query: 506 HHAFPDHGAGFCLMNDMALAARYLIR-HGIVRKVLIVDLDVHQ 547
HH+ +GFC +ND+ L L++ H +VL VD+D+H
Sbjct: 154 HHSKCGECSGFCYVNDIVLGILELLKCHD---RVLYVDIDMHH 193
>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 = 35.5 bits (82), Expect = 0.077
Identities = 15/41 (36%), Positives = 26/41 (63%), Gaps = 2/41 (4%)
Query: 506 HHAFPDHGAGFCLMNDMALAARYLIRHGIVRKVLIVDLDVH 546
HHA +GFC +ND+ +A L+++ +VL +D+D+H
Sbjct: 132 HHAKKFEASGFCYVNDIVIAILELLKYH--PRVLYIDIDIH 170
Score = 28.9 bits (65), Expect = 8.8
Identities = 17/59 (28%), Positives = 27/59 (45%), Gaps = 5/59 (8%)
Query: 188 GINTQPVSGYQATLKEHLPGILAQFKPDLVIYDAGVDPHQHDELGKLNLT--DHGECIS 244
GI+ Q Y K + ++ ++P ++ G D D LG NL+ HGEC+
Sbjct: 224 GIDDQ---SYLQLFKPVIQQVIDFYQPTCIVLQCGADSLGCDRLGCFNLSIKGHGECVE 279
>gnl|CDD|237275 PRK13022, secF, preprotein translocase subunit SecF; Reviewed.
Length = 289
Score = 34.7 bits (81), Expect = 0.10
Identities = 14/43 (32%), Positives = 24/43 (55%), Gaps = 7/43 (16%)
Query: 150 AVLADLICIAVYLTFFLQRRPVFFDIAAVLADLIH---FMVGI 189
A+L L+ I +Y+ F + R F + A++A L+H +GI
Sbjct: 132 ALLVALVGILIYIAFRFEWR---FALGAIIA-LLHDVIITLGI 170
>gnl|CDD|240251 PTZ00063, PTZ00063, histone deacetylase; Provisional.
Length = 436
Score = 34.8 bits (80), Expect = 0.12
Identities = 15/41 (36%), Positives = 25/41 (60%), Gaps = 2/41 (4%)
Query: 506 HHAFPDHGAGFCLMNDMALAARYLIRHGIVRKVLIVDLDVH 546
HHA +GFC +ND+ L L+++ +V+ +D+DVH
Sbjct: 137 HHAKRSEASGFCYINDIVLGILELLKYHA--RVMYIDIDVH 175
>gnl|CDD|233213 TIGR00966, 3a0501s07, protein-export membrane protein SecF. This
bacterial protein is always found with the homologous
protein-export membrane protein SecD. In numerous
lineages, this protein occurs as a SecDF fusion protein
[Protein fate, Protein and peptide secretion and
trafficking].
Length = 246
Score = 32.2 bits (74), Expect = 0.66
Identities = 17/51 (33%), Positives = 27/51 (52%), Gaps = 5/51 (9%)
Query: 139 LQRRPVFFDIAAVLADLICIAVYLTFFLQRRPVFFDIAAVLADLIHFMVGI 189
L R+ V A+LA L+ I +Y+T + R I A++ D+I VG+
Sbjct: 96 LARKAVL----ALLAALVLILIYITVRFEWRFALGAIVALVHDVI-ITVGV 141
>gnl|CDD|223418 COG0341, SecF, Preprotein translocase subunit SecF [Intracellular
trafficking and secretion].
Length = 305
Score = 32.2 bits (74), Expect = 0.69
Identities = 15/43 (34%), Positives = 24/43 (55%), Gaps = 7/43 (16%)
Query: 150 AVLADLICIAVYLTFFLQRRPVFFDIAAVLADLIH---FMVGI 189
A+L L+ I +Y+ F + R F +AA+LA L+H +G
Sbjct: 139 ALLLALVGILIYVFFRFEWR---FALAAILA-LLHDVIITLGF 177
>gnl|CDD|237276 PRK13024, PRK13024, bifunctional preprotein translocase subunit
SecD/SecF; Reviewed.
Length = 755
Score = 30.2 bits (69), Expect = 3.7
Identities = 16/45 (35%), Positives = 23/45 (51%), Gaps = 7/45 (15%)
Query: 148 IAAVLADLICIAVYLTFFLQRRPVFFDIAAVLADLIH---FMVGI 189
I AVL LI I +Y+ R F + A+LA L+H ++G
Sbjct: 580 IIAVLIALIGILLYILI---RFEWTFSLGAILA-LLHDVLIVIGF 620
>gnl|CDD|216990 pfam02355, SecD_SecF, Protein export membrane protein. This family
consists of various prokaryotic SecD and SecF protein
export membrane proteins. This SecD and SecF proteins
are part of the multimeric protein export complex
comprising SecA, D, E, F, G, Y, and YajC. SecD and SecF
are required to maintain a proton motive force.
Length = 189
Score = 29.5 bits (67), Expect = 3.9
Identities = 12/40 (30%), Positives = 21/40 (52%), Gaps = 1/40 (2%)
Query: 150 AVLADLICIAVYLTFFLQRRPVFFDIAAVLADLIHFMVGI 189
A+L L+ I VY++ + R + A+ D+I VG+
Sbjct: 36 ALLGALLGILVYVSLRFEWRFALGAVIALAHDVI-ITVGV 74
>gnl|CDD|183530 PRK12444, PRK12444, threonyl-tRNA synthetase; Reviewed.
Length = 639
Score = 30.1 bits (68), Expect = 4.6
Identities = 21/76 (27%), Positives = 34/76 (44%), Gaps = 17/76 (22%)
Query: 47 HRFPMSKFSKTFNYLVRDKVI--DKSKQLIEPQQISESIAELVHTKEYVHKFFNGKTTEK 104
HR +FS N L+R + D + + P QI + I ++ +YV+K F
Sbjct: 365 HR---HEFSGALNGLLRVRTFCQDDAHLFVTPDQIEDEIKSVMAQIDYVYKTF------- 414
Query: 105 EQKVTGFEWSAGLASR 120
GFE+ L++R
Sbjct: 415 -----GFEYEVELSTR 425
>gnl|CDD|233999 TIGR02757, TIGR02757, TIGR02757 family protein. Members of this
uncharacterized protein family are found sporadically,
so far only among spirochetes, epsilon and delta
proteobacteria, and Bacteroides. The function is unknown
and its gene neighborhoods show little conservation
[Hypothetical proteins, Conserved].
Length = 229
Score = 29.3 bits (66), Expect = 5.1
Identities = 15/62 (24%), Positives = 25/62 (40%), Gaps = 12/62 (19%)
Query: 499 EINRFSTHHAFPDHGAGFCLMNDMALAARYLIR---------HGIVRKVLIVDLDVHQHT 549
++N ++ A P G+ +N M L R++IR LI+ LD H
Sbjct: 126 KLNSYNNTIADPSGGSPLKRLN-MFL--RWMIRKDEVDLGIWESFKPSDLILPLDTHVFR 182
Query: 550 RS 551
+
Sbjct: 183 IA 184
>gnl|CDD|212571 cd11698, DHR2_DOCK9, Dock Homology Region 2, a GEF domain, of Class
D Dedicator of Cytokinesis 9. Dock9, also called
Zizimin1, is an atypical guanine nucleotide exchange
factor (GEF) that lacks the conventional Dbl homology
(DH) domain. As a GEF, it activates the small GTPase
Cdc42 by exchanging bound GDP for free GTP. It plays
important roles in spine formation and dendritic growth.
DOCK proteins are divided into four classes (A-D) based
on sequence similarity and domain architecture; class D
includes Dock9, 10 and 11. All DOCKs contain two
homology domains: the DHR-1 (Dock homology region-1),
also called CZH1 (CED-5, Dock180, and MBC-zizimin
homology 1), and DHR-2 (also called CZH2 or Docker). The
DHR-1 domain binds
phosphatidylinositol-3,4,5-triphosphate. This alignment
model represents the DHR-2 domain of Dock9, which
contains the catalytic GEF activity for Cdc42. Class D
DOCKs also contain a Pleckstrin homology (PH) domain at
the N-terminus.
Length = 415
Score = 29.6 bits (66), Expect = 5.5
Identities = 30/121 (24%), Positives = 48/121 (39%), Gaps = 29/121 (23%)
Query: 514 AGFCLMNDMALAARYLIRHGIVRK----------------VLIVDL---DVHQHTRSIPV 554
A C ++ AL A YL R G+ R+ ++ D+ DVH + +
Sbjct: 23 AAMCYVHVAALVAEYLTRKGMFRQGCTAFRVITPNIDEEASMMEDVGMQDVHFNEDVL-- 80
Query: 555 PSLTVLSSCVPGLYMRDYYVLDTAI-SAGIPVATVTGGGYCADIDQLAQRQTIIHRAATH 613
+ +L C GL+ + Y L I IP+ D ++LA +HRA +
Sbjct: 81 --MELLEQCADGLWKAERYELIADIYKLIIPIYE-----KRRDFERLAHLYDTLHRAYSK 133
Query: 614 V 614
V
Sbjct: 134 V 134
>gnl|CDD|223706 COG0633, Fdx, Ferredoxin [Energy production and conversion].
Length = 102
Score = 27.8 bits (62), Expect = 5.6
Identities = 8/23 (34%), Positives = 11/23 (47%)
Query: 573 YVLDTAISAGIPVATVTGGGYCA 595
+L+ A GIP+ GG C
Sbjct: 24 TLLEAAERNGIPIEYACRGGACG 46
>gnl|CDD|206172 pfam14002, YniB, YniB-like protein. The YniB-like protein family
includes the E. coli YniB protein, which is functionally
uncharacterized. This family of proteins is found in
bacteria. Proteins in this family are approximately 180
amino acids in length. This family of proteins are
integral membrane proteins.
Length = 166
Score = 28.8 bits (65), Expect = 6.0
Identities = 17/54 (31%), Positives = 27/54 (50%), Gaps = 8/54 (14%)
Query: 143 PVFFDIAAVLADLICIAVYLTFFLQRRPVFFDIAAVLADLIHFMVGI---NTQP 193
+F I A+++ LI + +L F L++ I AV+ D I MV + NT
Sbjct: 5 LIF--IPALISTLISLLKFLYFHLEKGTG---INAVMNDFIKVMVEMVRFNTPF 53
>gnl|CDD|235139 PRK03612, PRK03612, spermidine synthase; Provisional.
Length = 521
Score = 29.4 bits (67), Expect = 6.6
Identities = 9/21 (42%), Positives = 15/21 (71%)
Query: 524 LAARYLIRHGIVRKVLIVDLD 544
LA R ++++ V +V +VDLD
Sbjct: 310 LALREVLKYPDVEQVTLVDLD 330
>gnl|CDD|233544 TIGR01717, AMP-nucleosdse, AMP nucleosidase. This model represents
the AMP nucleosidase from proteobacteria but also
including a sequence from Corynebacterium, a
gram-positive organism. The species from E. coli has
been most well studied.
Length = 477
Score = 29.0 bits (65), Expect = 8.5
Identities = 13/52 (25%), Positives = 20/52 (38%), Gaps = 12/52 (23%)
Query: 568 YMRDYYVLDTAISAGIPVATVTGGGYCADIDQLAQRQTIIHRAATHVYKERG 619
Y+R+ +VLD + IP I +A+ Q + A V G
Sbjct: 317 YLREDHVLDAVLPPDIP------------IPAIAEVQRALEDAVAEVTGRPG 356
>gnl|CDD|204381 pfam10027, DUF2269, Predicted integral membrane protein (DUF2269).
Members of this family of bacterial hypothetical
integral membrane proteins have no known function.
Length = 150
Score = 28.0 bits (63), Expect = 9.2
Identities = 16/56 (28%), Positives = 23/56 (41%), Gaps = 6/56 (10%)
Query: 148 IAAVL--ADLICIAVYLTF-FLQRRPVFFDIAA---VLADLIHFMVGINTQPVSGY 197
++AVL I A Y+ P AA VLAD + + QP++G
Sbjct: 9 LSAVLLFGTGIGTAFYMLRARRTGDPAVIARAARRVVLADWLFTAPAVILQPITGL 64
>gnl|CDD|163625 cd07382, MPP_DR1281, Deinococcus radiodurans DR1281 and related
proteins, metallophosphatase domain. DR1281 is an
uncharacterized Deinococcus radiodurans protein with a
domain that belongs to the metallophosphatase (MPP)
superfamily. MPPs are functionally diverse, but all
share a conserved domain with an active site consisting
of two metal ions (usually manganese, iron, or zinc)
coordinated with octahedral geometry by a cage of
histidine, aspartate, and asparagine residues. The MPP
superfamily includes: Mre11/SbcD-like exonucleases,
Dbr1-like RNA lariat debranching enzymes, YfcE-like
phosphodiesterases, purple acid phosphatases (PAPs),
YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 255
Score = 28.6 bits (65), Expect = 9.4
Identities = 11/24 (45%), Positives = 16/24 (66%), Gaps = 1/24 (4%)
Query: 195 SGYQATLKEHLPGILAQFKPDLVI 218
G +A +KEHLP + ++K D VI
Sbjct: 12 PGRKA-VKEHLPKLKKEYKIDFVI 34
>gnl|CDD|224606 COG1692, COG1692, Calcineurin-like phosphoesterase [General
function prediction only].
Length = 266
Score = 28.4 bits (64), Expect = 9.5
Identities = 9/19 (47%), Positives = 14/19 (73%)
Query: 200 TLKEHLPGILAQFKPDLVI 218
+KEHLP + +++K D VI
Sbjct: 17 AVKEHLPQLKSKYKIDFVI 35
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
0.325 0.139 0.426
Gapped
Lambda K H
0.267 0.0772 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 32,383,778
Number of extensions: 3254712
Number of successful extensions: 3918
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3898
Number of HSP's successfully gapped: 104
Length of query: 620
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 517
Effective length of database: 6,369,140
Effective search space: 3292845380
Effective search space used: 3292845380
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 62 (27.6 bits)