RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 032833
(132 letters)
>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 = 83.9 bits (208), Expect = 3e-20
Identities = 34/74 (45%), Positives = 46/74 (62%)
Query: 1 MTHMLNALSGGKLLVILEGGYNLRSISSSATSVIKVLLGENPGCELGDSAPSKSGLVTVL 60
MTHML +L+GG+++VILEGGYNL SIS S + K LLG+ P P S L ++
Sbjct: 277 MTHMLMSLAGGRVIVILEGGYNLTSISESMSMCTKTLLGDPPPVLDLPRPPCSSALKSIN 336
Query: 61 EVLKIQMNFWPSLA 74
VL++ +W SL
Sbjct: 337 NVLQVHQKYWKSLR 350
>gnl|CDD|212542 cd11600, HDAC_Clr3, Class II Histone deacetylase Clr3 and similar
proteins. Clr3 is a class II Histone deacetylase
Zn-dependent enzyme that catalyzes hydrolysis of an
N(6)-acetyl-lysine residue of a histone to yield a
deacetylated histone (EC 3.5.1.98). Clr3 is the homolog
of the class-II HDAC HdaI in S. cerevisiae, and is
essential for silencing in heterochromatin regions, such
as centromeric regions, ribosomal DNA, the mating-type
region and telomeric loci. Clr3 has also been implicated
in the regulation of stress-related genes; the histone
acetyltransferase, Gcn5, in S. cerevisiae,
preferentially acetylates global histone H3K14 while
Clr3 preferentially deacetylates H3K14ac, and therefore,
interplay between Gcn5 and Clr3 is crucial for the
regulation of many stress-response genes.
Length = 313
Score = 81.2 bits (201), Expect = 2e-19
Identities = 30/43 (69%), Positives = 35/43 (81%)
Query: 1 MTHMLNALSGGKLLVILEGGYNLRSISSSATSVIKVLLGENPG 43
MTHML +L+GGKL+V LEGGYNL +IS SA +V KVLLGE P
Sbjct: 268 MTHMLMSLAGGKLVVALEGGYNLDAISDSALAVAKVLLGEAPP 310
>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 = 7e-13
Identities = 27/70 (38%), Positives = 41/70 (58%), Gaps = 1/70 (1%)
Query: 1 MTHMLNALSGGKLLVILEGGYNLRSISSSATSVIKVLLGENPGCELGDSAPSKSGLVTVL 60
+T +L L+GGKLL++LEGGY L S++ S + ++ LLG+ P L P +S L T+L
Sbjct: 268 LTRLLMGLAGGKLLLVLEGGYLLESLAESVSMTLRGLLGD-PLPPLAPPIPIRSVLETIL 326
Query: 61 EVLKIQMNFW 70
+ W
Sbjct: 327 NAIAHLSPRW 336
>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 = 61.0 bits (148), Expect = 5e-12
Identities = 30/72 (41%), Positives = 45/72 (62%), Gaps = 4/72 (5%)
Query: 1 MTHMLNALSGGKLLVILEGGYNLRSISSSATSVIKVLLGENPGCELGDS--APSKSGLVT 58
+TH+L L+GGKL++ LEGGYNLRS++ + +K LLG+ C + +S AP +S L +
Sbjct: 268 LTHLLMGLAGGKLILSLEGGYNLRSLAEGVCASLKALLGDP--CPMLESPGAPCRSALAS 325
Query: 59 VLEVLKIQMNFW 70
V + FW
Sbjct: 326 VSCTISALEPFW 337
>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 = 59.9 bits (145), Expect = 1e-11
Identities = 26/70 (37%), Positives = 41/70 (58%)
Query: 1 MTHMLNALSGGKLLVILEGGYNLRSISSSATSVIKVLLGENPGCELGDSAPSKSGLVTVL 60
+TH+L L+GGKL +LEGGY+L S++ S ++ LLG+ G+ P +S L ++
Sbjct: 268 LTHLLMVLAGGKLCAVLEGGYHLESLAESVCMTVQTLLGDPLPRLSGEMTPCQSALESIQ 327
Query: 61 EVLKIQMNFW 70
V Q +W
Sbjct: 328 NVRAAQAPYW 337
>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 = 54.4 bits (132), Expect = 8e-10
Identities = 17/42 (40%), Positives = 28/42 (66%), Gaps = 4/42 (9%)
Query: 1 MTHMLNAL----SGGKLLVILEGGYNLRSISSSATSVIKVLL 38
+T +L L GG+L+ +LEGGYNL +++ S +V++ LL
Sbjct: 250 LTRLLKELADEHCGGRLVFVLEGGYNLEALAESVLAVLEALL 291
>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 = 53.1 bits (128), Expect = 3e-09
Identities = 23/73 (31%), Positives = 44/73 (60%), Gaps = 3/73 (4%)
Query: 1 MTHMLNALSGGKLLVILEGGYNLRSISSSATSVIKVLLGENP---GCELGDSAPSKSGLV 57
MT L L+GGK+++ LEGGY+L +I ++ + ++ LLG+ E + P+ + +
Sbjct: 305 MTRQLMNLAGGKVVLALEGGYDLTAICDASEACVRALLGDELDPLSEEELERRPNPNAVT 364
Query: 58 TVLEVLKIQMNFW 70
++ +V+ IQ +W
Sbjct: 365 SLEKVIAIQSPYW 377
>gnl|CDD|216151 pfam00850, Hist_deacetyl, Histone deacetylase domain. Histones can
be reversibly acetylated on several lysine residues.
Regulation of transcription is caused in part by this
mechanism. Histone deacetylases catalyze the removal of
the acetyl group. Histone deacetylases are related to
other proteins.
Length = 300
Score = 48.4 bits (116), Expect = 1e-07
Identities = 16/41 (39%), Positives = 25/41 (60%), Gaps = 3/41 (7%)
Query: 1 MTHML---NALSGGKLLVILEGGYNLRSISSSATSVIKVLL 38
T +L GG ++ +LEGGYNL +++ SA +V+ LL
Sbjct: 260 RTRLLLELADAYGGPVVSVLEGGYNLDALARSAAAVLAGLL 300
>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 = 45.8 bits (108), Expect = 1e-06
Identities = 27/99 (27%), Positives = 55/99 (55%), Gaps = 4/99 (4%)
Query: 1 MTHMLNALSGGKLLVILEGGYNLRSISSSATSVIKVLLGE--NPGCE-LGDSAPSKSGLV 57
+T L L+GG++++ LEGG++L +I ++ + + LLG +P E + P+ + +
Sbjct: 308 LTKQLMGLAGGRIVLALEGGHDLTAICDASEACVSALLGNELDPLPEKVLQQRPNANAVR 367
Query: 58 TVLEVLKIQMNFWPSLA-SRFTELQSLWEIYAAENKKKQ 95
++ +V++I +W L + T SL E EN++ +
Sbjct: 368 SMEKVMEIHSKYWRCLQRTTSTAGYSLIEAQTCENEEAE 406
>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 = 43.8 bits (103), Expect = 6e-06
Identities = 26/94 (27%), Positives = 46/94 (48%), Gaps = 4/94 (4%)
Query: 1 MTHMLNALSGGKLLVILEGGYNLRSISSSATSVIKVLLGENPG---CELGDSAPSKSGLV 57
+T L L+GG++++ LEGG++L +I ++ + + LLG + P+ + +
Sbjct: 308 LTKQLMTLAGGRVVLALEGGHDLTAICDASEACVSALLGMELTPLDNTVLQQKPNDNAVA 367
Query: 58 TVLEVLKIQMNFWPSLASRFTEL-QSLWEIYAAE 90
T+ V++IQ W L L SL E E
Sbjct: 368 TLERVIEIQSKHWSCLKRFAATLGFSLLEAQRGE 401
>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 = 2e-05
Identities = 20/73 (27%), Positives = 41/73 (56%), Gaps = 3/73 (4%)
Query: 1 MTHMLNALSGGKLLVILEGGYNLRSISSSATSVIKVLLGE--NPGCELG-DSAPSKSGLV 57
MT L L+GG +++ LEGG++L +I ++ + + LLG +P E P+ + +
Sbjct: 306 MTQQLMNLAGGAVVLALEGGHDLTAICDASEACVAALLGNEVDPLSEESWKQKPNLNAIR 365
Query: 58 TVLEVLKIQMNFW 70
++ V+++ +W
Sbjct: 366 SLEAVIRVHSKYW 378
>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 = 41.2 bits (97), Expect = 4e-05
Identities = 13/43 (30%), Positives = 24/43 (55%), Gaps = 3/43 (6%)
Query: 1 MTHMLNALS---GGKLLVILEGGYNLRSISSSATSVIKVLLGE 40
+ + L+ GG ++ +LEGGYNL +++ S + + L G
Sbjct: 270 IGRAVRKLAEGYGGPVVAVLEGGYNLDALARSLVAFLAGLAGL 312
>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 = 37.9 bits (89), Expect = 5e-04
Identities = 11/42 (26%), Positives = 25/42 (59%), Gaps = 4/42 (9%)
Query: 1 MTHML----NALSGGKLLVILEGGYNLRSISSSATSVIKVLL 38
+T L + G+++ +LEGGY+L +++ S + ++ L+
Sbjct: 247 ITEQLMDVADRYCDGRIVSVLEGGYDLSALARSVAAHVRALM 288
>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 = 36.5 bits (84), Expect = 0.002
Identities = 18/73 (24%), Positives = 45/73 (61%), Gaps = 3/73 (4%)
Query: 1 MTHMLNALSGGKLLVILEGGYNLRSISSSATSVIKVLLG---ENPGCELGDSAPSKSGLV 57
+T L L+ G++++ LEGG++L +I ++ + + LLG E ++ +P+ + ++
Sbjct: 306 LTKQLMTLADGRVVLALEGGHDLTAICDASEACVNALLGNELEPLAEDILHQSPNMNAVI 365
Query: 58 TVLEVLKIQMNFW 70
++ ++++IQ +W
Sbjct: 366 SLQKIIEIQSKYW 378
>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 = 33.6 bits (77), Expect = 0.018
Identities = 12/34 (35%), Positives = 20/34 (58%)
Query: 4 MLNALSGGKLLVILEGGYNLRSISSSATSVIKVL 37
+ GG +L++L GGYN + + T++IK L
Sbjct: 246 VKEFARGGPILMVLGGGYNPEAAARIWTAIIKEL 279
>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 = 32.5 bits (75), Expect = 0.043
Identities = 9/36 (25%), Positives = 18/36 (50%), Gaps = 1/36 (2%)
Query: 3 HMLNALSGGKLLVILEGGYNLRSISSSATSVIKVLL 38
+ AL G + + EGGYN+ ++ +A + +
Sbjct: 264 RRIAAL-GLPTVFVQEGGYNVDALGRNAVAFLAGFE 298
>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 = 29.8 bits (68), Expect = 0.33
Identities = 10/26 (38%), Positives = 16/26 (61%), Gaps = 4/26 (15%)
Query: 1 MTHMLNAL----SGGKLLVILEGGYN 22
+T L L GG+L+++ EGGY+
Sbjct: 283 LTRKLRDLADELCGGRLVMVHEGGYS 308
>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 = 28.2 bits (63), Expect = 1.3
Identities = 9/22 (40%), Positives = 16/22 (72%)
Query: 11 GKLLVILEGGYNLRSISSSATS 32
G+L+ +LEGGY+ R++ S +
Sbjct: 326 GRLISVLEGGYSDRALCSGVLA 347
>gnl|CDD|212119 cd10808, YdjC, Escherichia coli YdjC-like family of proteins.
Uncharacterized subfamily of YdjC-like family of
proteins. Included in this subfamily is the
uncharacterized Escherichia coli protein YdjC (also
known as ChbG), encoded by the chb
(N,N'-diacetylchitobiose, also called [GlcNAc]2) or cel
operon, which encodes enzymes involved in growth on an
N,N'-diacetylchitobiose carbon source. The molecular
function of this subfamily is unclear.
Length = 259
Score = 27.6 bits (62), Expect = 1.9
Identities = 10/50 (20%), Positives = 18/50 (36%)
Query: 80 LQSLWEIYAAENKKKQIKKIRRADAPIWWKWGRKRLLYQIIKGHLRVRSR 129
L + +I + I +R D P ++ K L + L V +
Sbjct: 134 LPGVLDIVLDLAARYGIPAVRIPDEPPFFARLAKSGLRRRAGVGLSVLAA 183
>gnl|CDD|193500 cd03879, M28_AAP, M28 Zn-Peptidase Aeromonas (Vibrio) proteolytica
aminopeptidase. Peptidase family M28; Aeromonas
(Vibrio) proteolytica aminopeptidase (AAP; leucine
aminopeptidase from Vibrio proteolyticus; Bacterial
leucyl aminopeptidase; E.C. 3.4.11.10) subfamily. AAP is
a small (32kDa), heat stable leucine aminopeptidase and
is active as a monomer. Similar forms of the enzyme have
been isolated from Escherichia coli and Staphylococcus
thermophilus. Leucine aminopeptidases, in general, play
important roles in many biological processes such as
protein catabolism, hormone degradation, regulation of
migration and cell proliferation, as well as HIV
infection and proliferation. AAP is a broad-specificity
enzyme, utilizing two zinc(II) ions in its active site
to remove N-terminal amino acids, with preference for
large hydrophobic amino acids in the P1 position of the
substrate, Leu being the most efficiently cleaved. It
can accommodate all residues, except Pro, Asp and Glu in
the P1' position.
Length = 285
Score = 27.2 bits (61), Expect = 2.6
Identities = 24/78 (30%), Positives = 36/78 (46%), Gaps = 21/78 (26%)
Query: 15 VILEGGYNLRSISSSATSVIKVLLGENPGCELGDSAPSKSGLVTVLEVLK--IQMNFWPS 72
V++ G + L SI+ S S G PG + D SG+ T+LE L+ ++ F P
Sbjct: 91 VVV-GAH-LDSINGSNPS-----NGRAPGAD--DDG---SGIATILEALRVLLESGFQPK 138
Query: 73 LASRFTELQSLWEIYAAE 90
++ W YAAE
Sbjct: 139 -----RTIEFHW--YAAE 149
>gnl|CDD|224000 COG1074, RecB, ATP-dependent exoDNAse (exonuclease V) beta subunit
(contains helicase and exonuclease domains) [DNA
replication, recombination, and repair].
Length = 1139
Score = 27.0 bits (60), Expect = 3.9
Identities = 11/64 (17%), Positives = 17/64 (26%), Gaps = 5/64 (7%)
Query: 60 LEVLKIQMNFWPSLASRFTELQSLWEIYAAENKKKQIKKIRRADAPIWWKW-----GRKR 114
L L W L +L +W + + KI I + G +
Sbjct: 631 LAALAQDEAEWEFLWENLRQLADIWRFRGVLAMWRALAKITPLHDLIAERLLSTNLGERD 690
Query: 115 LLYQ 118
L
Sbjct: 691 LTNG 694
>gnl|CDD|223885 COG0815, Lnt, Apolipoprotein N-acyltransferase [Cell envelope
biogenesis, outer membrane].
Length = 518
Score = 26.6 bits (59), Expect = 4.4
Identities = 22/101 (21%), Positives = 34/101 (33%), Gaps = 5/101 (4%)
Query: 7 ALSGGKLLVILEGGYNLRSISSSATSVIKVLLGENPGCELGDSAPSKSGLVTVLEVLKIQ 66
A++ V+L+ R + V+ + G C L A S L V +Q
Sbjct: 179 AVNALLASVLLKRATGGRLLLLGLLLVVLLAYG----CALLGLAGSVPVGEPTLTVALVQ 234
Query: 67 MNFWPSLASRFTELQSLWEIYAAENKKKQIKKIRRADAPIW 107
N L L L Y E + K ++ D +W
Sbjct: 235 GNIPQDLKWDADALARLIAGYLEEEFLAAVDK-QKPDLVVW 274
>gnl|CDD|173679 cd05588, STKc_aPKC, Catalytic domain of the Protein
Serine/Threonine Kinase, Atypical Protein Kinase C.
Serine/Threonine Kinases (STKs), Atypical Protein Kinase
C (aPKC) subfamily, catalytic (c) domain. STKs catalyze
the transfer of the gamma-phosphoryl group from ATP to
serine/threonine residues on protein substrates. The
aPKC subfamily is part of a larger superfamily that
includes the catalytic domains of other protein STKs,
protein tyrosine kinases, RIO kinases, aminoglycoside
phosphotransferase, choline kinase, and phosphoinositide
3-kinase. PKCs are classified into three groups
(classical, atypical, and novel) depending on their mode
of activation and the structural characteristics of
their regulatory domain. aPKCs only require
phosphatidylserine (PS) for activation. They contain a
C2-like region, instead of a calcium-binding (C2) region
found in classical PKCs, in their regulatory domain.
There are two aPKC isoforms, zeta and iota. aPKCs are
involved in many cellular functions including
proliferation, migration, apoptosis, polarity
maintenance and cytoskeletal regulation. They also play
a critical role in the regulation of glucose metabolism
and in the pathogenesis of type 2 diabetes.
Length = 329
Score = 26.3 bits (58), Expect = 5.0
Identities = 15/34 (44%), Positives = 21/34 (61%), Gaps = 1/34 (2%)
Query: 15 VILEGGYNL-RSISSSATSVIKVLLGENPGCELG 47
VILE + RS+S A+SV+K L ++P LG
Sbjct: 216 VILEKQIRIPRSLSVKASSVLKGFLNKDPKERLG 249
>gnl|CDD|173663 cd05572, STKc_cGK_PKG, Catalytic domain of the Protein
Serine/Threonine Kinase, cGMP-dependent protein kinase.
Serine/Threonine Kinases (STKs), cGMP-dependent protein
kinase (cGK or PKG) subfamily, catalytic (c) domain.
STKs catalyze the transfer of the gamma-phosphoryl group
from ATP to serine/threonine residues on protein
substrates. The cGK subfamily is part of a larger
superfamily that includes the catalytic domains of other
protein STKs, protein tyrosine kinases, RIO kinases,
aminoglycoside phosphotransferase, choline kinase, and
phosphoinositide 3-kinase. Mammals have two cGK isoforms
from different genes, cGKI and cGKII. cGKI exists as two
splice variants, cGKI-alpha and cGKI-beta. cGK consists
of an N-terminal regulatory domain containing a
dimerization and an autoinhibitory pseudosubstrate
region, two cGMP-binding domains, and a C-terminal
catalytic domain. Binding of cGMP to both binding sites
releases the inhibition of the catalytic center by the
pseudosubstrate region, allowing autophosphorylation and
activation of the kinase. cGKI is a soluble protein
expressed in all smooth muscles, platelets, cerebellum,
and kidney. It is also expressed at lower concentrations
in other tissues. cGKII is a membrane-bound protein that
is most abundantly expressed in the intestine. It is
also present in the brain nuclei, adrenal cortex,
kidney, lung, and prostate. cGKI is involved in the
regulation of smooth muscle tone, smooth cell
proliferation, and platelet activation. cGKII plays a
role in the regulation of secretion, such as renin
secretion by the kidney and aldosterone secretion by the
adrenal. It also regulates bone growth and the circadian
rhythm.
Length = 262
Score = 26.4 bits (59), Expect = 5.0
Identities = 14/35 (40%), Positives = 17/35 (48%), Gaps = 3/35 (8%)
Query: 16 ILEGGYNL---RSISSSATSVIKVLLGENPGCELG 47
IL+G L I +A +IK LL NP LG
Sbjct: 206 ILKGNGKLEFPNYIDKAAKDLIKQLLRRNPEERLG 240
>gnl|CDD|189007 cd09600, M1_APN_1, Peptidase M1 family containing Aminopeptidase N.
This family contains aminopeptidase N (APN; CD13;
Alanyl aminopeptidase; EC 3.4.11.2), a Type II integral
membrane protease belonging to the M1 gluzincin family.
It includes bacterial-type alanyl aminopeptidases as
well as PfA-M1 aminopeptidase (Plasmodium
falciparum-type). APN consists of a small N-terminal
cytoplasmic domain, a single transmembrane domain and a
large extracellular ectodomain that contains the active
site. It preferentially cleaves neutral amino acids from
the N-terminus of oligopeptides and, in higher
eukaryotes, is present in a variety of human tissues and
cell types (leukocyte, fibroblast, endothelial and
epithelial cells). APN expression is dysregulated in
inflammatory diseases such as chronic pain, rheumatoid
arthritis, multiple sclerosis, systemic sclerosis,
systemic lupus erythematosus,
polymyositis/dermatomyosytis and pulmonary sarcoidosis,
and is enhanced in tumor cells such as melanoma, renal,
prostate, pancreas, colon, gastric and thyroid cancers.
It is predominantly expressed on stem cells and on cells
of the granulocytic and monocytic lineages at distinct
stages of differentiation, thus considered a marker of
differentiation. Thus, APN inhibition may lead to the
development of anti-cancer and anti-inflammatory drugs.
APNs are also present in many pathogenic bacteria and
represent potential drug targets, Some APNs have been
used commercially, such as one from Lactococcus lactis
used in the food industry. APN also serves as a receptor
for coronaviruses, although the virus receptor
interaction site seems to be distinct from the enzymatic
site and aminopeptidase activity is not necessary for
viral infection. APNs have also been extensively studied
as putative Cry toxin receptors. Cry1 proteins are
pore-forming toxins that bind to the midgut epithelial
cell membrane of susceptible insect larvae, causing
extensive damage. Several different toxins, including
Cry1Aa, Cry1Ab, Cry1Ac, Cry1Ba, Cry1Ca and Cry1Fa, have
been shown to bind to APNs; however, a direct role of
APN in cytotoxicity has been yet to be firmly
established.
Length = 861
Score = 26.5 bits (59), Expect = 5.1
Identities = 11/46 (23%), Positives = 22/46 (47%), Gaps = 6/46 (13%)
Query: 62 VLKI-QMNFWPSLASRFTELQSLWEIYAAENK---KKQIKKIRRAD 103
++K+ + N P +A+R E S W+ + K +++I A
Sbjct: 804 IIKLDKFN--PQVAARLVEAFSRWKKLDEPRQSLMKAALERILAAP 847
>gnl|CDD|206725 cd04160, Arfrp1, Arf-related protein 1 (Arfrp1). Arfrp1
(Arf-related protein 1), formerly known as ARP, is a
membrane-associated Arf family member that lacks the
N-terminal myristoylation motif. Arfrp1 is mainly
associated with the trans-Golgi compartment and the
trans-Golgi network, where it regulates the targeting
of Arl1 and the GRIP domain-containing proteins,
golgin-97 and golgin-245, onto Golgi membranes. It is
also involved in the anterograde transport of the
vesicular stomatitis virus G protein from the Golgi to
the plasma membrane, and in the retrograde transport of
TGN38 and Shiga toxin from endosomes to the trans-Golgi
network. Arfrp1 also inhibits Arf/Sec7-dependent
activation of phospholipase D. Deletion of Arfrp1 in
mice causes embryonic lethality at the gastrulation
stage and apoptosis of mesodermal cells, indicating its
importance in development.
Length = 168
Score = 25.8 bits (57), Expect = 6.0
Identities = 14/30 (46%), Positives = 19/30 (63%), Gaps = 2/30 (6%)
Query: 61 EVLKIQMNFWPSLASRFTELQSLWEIYAAE 90
EV K ++ FW L + EL+SLW+ Y AE
Sbjct: 47 EVGKARLMFW-DLGGQ-EELRSLWDKYYAE 74
>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 = 26.0 bits (58), Expect = 6.5
Identities = 9/30 (30%), Positives = 15/30 (50%)
Query: 8 LSGGKLLVILEGGYNLRSISSSATSVIKVL 37
GG+ L + GGYN ++ + + VL
Sbjct: 284 YCGGRWLALGGGGYNPDVVARAWALLWAVL 313
>gnl|CDD|223621 COG0547, TrpD, Anthranilate phosphoribosyltransferase [Amino acid
transport and metabolism].
Length = 338
Score = 26.0 bits (58), Expect = 7.3
Identities = 9/22 (40%), Positives = 11/22 (50%)
Query: 47 GDSAPSKSGLVTVLEVLKIQMN 68
S SKSG VLE L + +
Sbjct: 113 NRSVSSKSGSADVLEALGVNLE 134
>gnl|CDD|237709 PRK14419, PRK14419, membrane protein; Provisional.
Length = 199
Score = 25.7 bits (57), Expect = 8.4
Identities = 20/91 (21%), Positives = 34/91 (37%), Gaps = 16/91 (17%)
Query: 1 MTHMLNALSGGKLLVILEGGYNLRSISSSATSVIKVL--LGENPGCELGDSAPSKSGLVT 58
+ ++L + G L G +LR I S +T VL +G+ P V
Sbjct: 10 LAYLLGSFPSGYLAGRWLKGIDLREIGSGSTGATNVLRNVGKGPAL-----------FVF 58
Query: 59 VLEVLKIQMNFWPSLASRFTELQSLWEIYAA 89
+++V K L + LQ ++ A
Sbjct: 59 IIDVGK---GVLAVLLAYALGLQPWLQVLAG 86
>gnl|CDD|240777 cd12331, RRM_NRD1_SEB1_like, RNA recognition motif in Saccharomyces
cerevisiae protein Nrd1, Schizosaccharomyces pombe
Rpb7-binding protein seb1 and similar proteins. This
subfamily corresponds to the RRM of Nrd1 and Seb1. Nrd1
is a novel heterogeneous nuclear ribonucleoprotein
(hnRNP)-like RNA-binding protein encoded by gene NRD1
(for nuclear pre-mRNA down-regulation) from yeast S.
cerevisiae. It is implicated in 3' end formation of
small nucleolar and small nuclear RNAs transcribed by
polymerase II, and plays a critical role in pre-mRNA
metabolism. Nrd1 contains an RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a short arginine-, serine-,
and glutamate-rich segment similar to the regions rich
in RE and RS dipeptides (RE/RS domains) in many metazoan
splicing factors, and a proline- and glutamine-rich
C-terminal domain (P+Q domain) similar to domains found
in several yeast hnRNPs. Disruption of NRD1 gene is
lethal to yeast cells. Its N-terminal domain is
sufficient for viability, which may facilitate
interactions with RNA polymerase II where Nrd1 may
function as an auxiliary factor. By contrast, the RRM,
RE/RS domains, and P+Q domain are dispensable. Seb1 is
an RNA-binding protein encoded by gene seb1 (for seven
binding) from fission yeast S. pombe. It is essential
for cell viability and bound directly to Rpb7 subunit of
RNA polymerase II. Seb1 is involved in processing of
polymerase II transcripts. It also contains one RRM
motif and a region rich in arginine-serine dipeptides
(RS domain).
Length = 79
Score = 24.8 bits (54), Expect = 8.7
Identities = 6/24 (25%), Positives = 14/24 (58%)
Query: 88 AAENKKKQIKKIRRADAPIWWKWG 111
AEN ++ +++ + D + +WG
Sbjct: 51 DAENAREAMEQYKSGDMQLRTRWG 74
>gnl|CDD|236966 PRK11747, dinG, ATP-dependent DNA helicase DinG; Provisional.
Length = 697
Score = 25.6 bits (57), Expect = 9.3
Identities = 9/37 (24%), Positives = 16/37 (43%), Gaps = 3/37 (8%)
Query: 60 LEVLKIQMNFWPSLASRFTELQSLWEIYAAENKKKQI 96
LE L +++ R L LW + A E+++
Sbjct: 385 LERLLLELGRA---LGRLEALSKLWRLAAKEDQESGA 418
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
0.319 0.134 0.406
Gapped
Lambda K H
0.267 0.0732 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,450,072
Number of extensions: 543557
Number of successful extensions: 508
Number of sequences better than 10.0: 1
Number of HSP's gapped: 505
Number of HSP's successfully gapped: 38
Length of query: 132
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 46
Effective length of database: 7,123,158
Effective search space: 327665268
Effective search space used: 327665268
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (24.2 bits)