RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 020361
(327 letters)
>gnl|CDD|212518 cd09992, HDAC_classII, Histone deacetylases and histone-like
deacetylases, classII. Class II histone deacetylases
are Zn-dependent enzymes that catalyze hydrolysis of
N(6)-acetyl-lysine residues of histones (EC 3.5.1.98)
and possibly other proteins to yield deacetylated
histones/other proteins. This group includes animal
HDAC4,5,6,7,8,9,10, fungal HOS3 and HDA1, plant HDA5 and
HDA15 as well as other eukaryotes, archaeal and
bacterial histone-like deacetylases. Eukaryotic
deacetylases mostly use histones (H2, H3, H4) as
substrates for deacetylation; however, non-histone
substrates are known (for example, tubulin). Substrates
for prokaryotic histone-like deacetylases are not known.
Histone acetylation/deacetylation process is important
for mediation of transcriptional regulation of many
genes. Histone deacetylases usually act via association
with DNA binding proteins to target specific chromatin
regions. Interaction partners of class II deacetylases
include 14-3-3 proteins, MEF2 family of transcriptional
factors, CtBP, calmodulin (CaM), SMRT, N-CoR, BCL6,
HP1alpha and SUMO. Histone deacetylases play a role in
the regulation of cell cycle, cell differentiation and
survival. Class II mammalian HDACs are differentially
inhibited by structurally diverse compounds with known
antitumor activities, thus presenting them as potential
drug targets for human diseases resulting from aberrant
acetylation.
Length = 291
Score = 379 bits (975), Expect = e-133
Identities = 131/281 (46%), Positives = 174/281 (61%), Gaps = 11/281 (3%)
Query: 11 EIIELKNFSPASVDDIASVHARAYVSGLEKAMDRASQQGIILIEGSGPTYATATTFQESL 70
+ + PA+ +++ VH Y+ +E + G ++ TY + +++ +L
Sbjct: 22 DRLVFVEPRPATEEELLRVHTPEYIERVE----ETCEAGGGYLDPD--TYVSPGSYEAAL 75
Query: 71 AAAGAGIALVDSVVAASKNRPDPPLGFALIRPPGHHAIPKGPMGFCVFGNVAIAARYAQR 130
AAGA +A VD+V++ FAL+RPPGHHA P MGFC+F NVAIAARYAQ+
Sbjct: 76 LAAGAALAAVDAVLSGEAEN-----AFALVRPPGHHAEPDRAMGFCLFNNVAIAARYAQK 130
Query: 131 AHGLKRVFIIDFDVHHGNGTNDAFYDDPDIFFLSTHQDGSYPGTGKIDEVGRGDGEGSTL 190
+GLKRV I+D+DVHHGNGT D FYDDP + + S HQ YPGTG +E G G GEG T+
Sbjct: 131 RYGLKRVLIVDWDVHHGNGTQDIFYDDPSVLYFSIHQYPFYPGTGAAEETGGGAGEGFTI 190
Query: 191 NLPLPGGSGDTAMRTVFHEVIVPCAQRFKPDLILVSAGYDAHVLDPLASLQFTTGTYYML 250
N+PLP GSGD F EV++P A+ F+PDL+LVSAG+DAH DPL + T Y L
Sbjct: 191 NVPLPPGSGDAEYLAAFEEVLLPIAREFQPDLVLVSAGFDAHRGDPLGGMNLTPEGYARL 250
Query: 251 AANIKQLAKDLCGSRCVFFLEGGYNLNSLSYSVADSFRAFL 291
+K+LA + CG R VF LEGGYNL +L+ SV A L
Sbjct: 251 TRLLKELADEHCGGRLVFVLEGGYNLEALAESVLAVLEALL 291
>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 = 325 bits (835), Expect = e-111
Identities = 123/273 (45%), Positives = 161/273 (58%), Gaps = 10/273 (3%)
Query: 19 SPASVDDIASVHARAYVSGLEKAMDRASQQGIILIEGSGPTYATATTFQESLAAAGAGIA 78
PA+ +++ VH+ YV LE+A + G I ++G T + +++ +L AAG +
Sbjct: 38 RPATEEELLLVHSPEYVEFLEEASLEEEELGRIGLDGD--TPVSPGSYEAALLAAGGTLE 95
Query: 79 LVDSVVAASKNRPDPPLGFALIRPPGHHAIPKGPMGFCVFGNVAIAARYAQRAHGLKRVF 138
D V++ FA +RPPGHHA GFC+F NVAIAARY + +GLKRV
Sbjct: 96 AADLVLSGEN-------AFAAVRPPGHHAERDRASGFCLFNNVAIAARYLLKRYGLKRVL 148
Query: 139 IIDFDVHHGNGTNDAFYDDPDIFFLSTHQDGSYPGTGKIDEVGRGDGEGSTLNLPLPGGS 198
I+D DVHHGNGT + FYDDP + +S HQD YPGTG DE G G GEG TLN+PLP G+
Sbjct: 149 IVDLDVHHGNGTQEIFYDDPRVLTISIHQDPFYPGTGFADETGEGAGEGYTLNIPLPPGT 208
Query: 199 GDTAMRTVFHEVIVPCAQRFKPDLILVSAGYDAHVLDPLASLQFTTGTYYMLAANIKQLA 258
GD F E+++P + F+PDLILVSAG+DAH DPL L TT Y + +LA
Sbjct: 209 GDEEYLAAFEEILLPALREFQPDLILVSAGFDAHAGDPLGGLNLTTEGYAERTRLLLELA 268
Query: 259 KDLCGSRCVFFLEGGYNLNSLSYSVADSFRAFL 291
G V LEGGYNL++L+ S A L
Sbjct: 269 DAYGG-PVVSVLEGGYNLDALARSAAAVLAGLL 300
>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 = 298 bits (766), Expect = e-101
Identities = 119/272 (43%), Positives = 158/272 (58%), Gaps = 14/272 (5%)
Query: 13 IELKNFSPASVDDIASVHARAYVSGLEKAMDRASQQGIILIEGSGPTYATATTFQESLAA 72
+ PA+ + + VH AYV LE A A ++G++ ++ T + + + +L A
Sbjct: 24 LRQLEAPPATREQLLRVHDAAYVDRLEAA---APEEGLVQLDPD--TAMSPGSLEAALRA 78
Query: 73 AGAGIALVDSVVAASKNRPDPPLGFALIRPPGHHAIPKGPMGFCVFGNVAIAARYAQRAH 132
AGA +A VD+V+A F +RPPGHHA MGFC+F NVAIAA +A H
Sbjct: 79 AGAVVAAVDAVMAGEARN-----AFCAVRPPGHHAERDKAMGFCLFNNVAIAAAHALAHH 133
Query: 133 GLKRVFIIDFDVHHGNGTNDAFYDDPDIFFLSTHQDGSYPGTGKIDEVGRGDGEGSTLNL 192
GL+RV I+DFDVHHGNGT D F DDP + F S+HQ YPGTG DE G G+ +N+
Sbjct: 134 GLERVAIVDFDVHHGNGTEDIFRDDPRVLFCSSHQHPLYPGTGAPDETGH----GNIVNV 189
Query: 193 PLPGGSGDTAMRTVFHEVIVPCAQRFKPDLILVSAGYDAHVLDPLASLQFTTGTYYMLAA 252
PLP G+G R + +P FKPDLIL+SAG+DAH DPLA L T Y +
Sbjct: 190 PLPAGTGGAEFREAVEDRWLPALDAFKPDLILISAGFDAHRDDPLAQLNLTEEDYAWITE 249
Query: 253 NIKQLAKDLCGSRCVFFLEGGYNLNSLSYSVA 284
+ +A C R V LEGGY+L++L+ SVA
Sbjct: 250 QLMDVADRYCDGRIVSVLEGGYDLSALARSVA 281
>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 = 295 bits (758), Expect = 7e-99
Identities = 111/306 (36%), Positives = 165/306 (53%), Gaps = 15/306 (4%)
Query: 20 PASVDDIASVHARAYVSGLEKAMDRASQQGIILIEGSGPTYATATTFQESLAAAGAGIAL 79
PA+ +++ VH Y+ ++ A E G T +++ +L AAG IA
Sbjct: 63 PATDEELLRVHTPEYIDRVKAASAAGGG------EAGGGTPFGPGSYEIALLAAGGAIAA 116
Query: 80 VDSVVAASKNRPDPPLGFALIRPPGHHAIPKGPMGFCVFGNVAIAARYAQRAHGLKRVFI 139
VD+V+ + +AL+RPPGHHA P MGFC+F NVAIAAR+A G+KRV +
Sbjct: 117 VDAVLDGEVDN-----AYALVRPPGHHAEPDQGMGFCLFNNVAIAARHALAVGGVKRVAV 171
Query: 140 IDFDVHHGNGTNDAFYDDPDIFFLSTHQDGSYP-GTGKIDEVGRGDGEGSTLNLPLPGGS 198
+D+DVHHGNGT FYDDPD+ +S HQD +P +G ++E G G GEG LN+PLP GS
Sbjct: 172 VDWDVHHGNGTQAIFYDDPDVLTISLHQDRCFPPDSGAVEERGEGAGEGYNLNIPLPPGS 231
Query: 199 GDTAMRTVFHEVIVPCAQRFKPDLILVSAGYDAHVLDPLASLQFTTGTYYMLAANIKQLA 258
GD A F +++P + F+P+LI+V++G+DA DPL + T+ + L ++ LA
Sbjct: 232 GDGAYLHAFERIVLPALRAFRPELIIVASGFDASAFDPLGRMMLTSDGFRALTRKLRDLA 291
Query: 259 KDLCGSRCVFFLEGGYNLNSLSYSVADSFRAFLGEPSKASEFDNPAILYEEPSAKV---K 315
+LCG R V EGGY+ + + G + ++ + +
Sbjct: 292 DELCGGRLVMVHEGGYSEAYVPFCGLAVLEELSGVRTGIADPLLYYPEAQGGQELQPHQR 351
Query: 316 QAIERV 321
AI+
Sbjct: 352 AAIDAA 357
>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 = 263 bits (673), Expect = 2e-86
Identities = 122/296 (41%), Positives = 173/296 (58%), Gaps = 16/296 (5%)
Query: 1 MELTSEFRGSEIIELKNFSPASVDDIASVHARAYVSGLEKAMDRASQQGIILIEGSGPTY 60
+EL + +EL PA+++++ VH+ YV LE + ++G ++G T
Sbjct: 32 LELLESSGLPDSLELVEPRPATLEELLLVHSPDYVEFLESL---SEEEGYGNLDGD--TP 86
Query: 61 ATATTFQESLAAAGAGIALVDSVVAASKNRPDPPLGFALIRPPGHHAIPKGPMGFCVFGN 120
+ T++ + AAG + VD+V+ N FAL+RPPGHHA GFC+F N
Sbjct: 87 VSPGTYEAARLAAGGALTAVDAVLEGEDNA------FALVRPPGHHAGRDRASGFCLFNN 140
Query: 121 VAIAARYAQRAHGLKRVFIIDFDVHHGNGTNDAFYDDPDIFFLSTHQDGS--YPGTGKID 178
VAIAA+Y + G+KRV IIDFDVHHGNGT + FYDD D+ +S HQDG YPGTG D
Sbjct: 141 VAIAAKYLLKK-GVKRVAIIDFDVHHGNGTQEIFYDDDDVLTVSLHQDGRPFYPGTGGAD 199
Query: 179 EVGRGDGEGSTLNLPLPGGSGDTAMRTVFHEVIVPCAQRFKPDLILVSAGYDAHVLDPLA 238
E+G G EG+ +N+PLP G+GD + E+++P + FKPDL++VSAG+DAH DPL
Sbjct: 200 EIGEG-KEGNNVNIPLPPGTGDDSYLEALEEIVLPLLEEFKPDLVIVSAGFDAHRGDPLG 258
Query: 239 SLQFTTGTYYMLAANIKQLAKDLCGSRCVFFLEGGYNLNSLSYSVADSFRAFLGEP 294
L T Y + +++LA+ G V LEGGYNL++L+ S+ G
Sbjct: 259 RLNLTEEGYAKIGRAVRKLAE-GYGGPVVAVLEGGYNLDALARSLVAFLAGLAGLV 313
>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 = 237 bits (606), Expect = 7e-77
Identities = 100/287 (34%), Positives = 132/287 (45%), Gaps = 33/287 (11%)
Query: 8 RGSEIIELKNFSPASVDDIASVHARAYVSGLEKAMDRASQQGIILIEGSGPTYATATTFQ 67
G + ++ I +VH YV LE A T + T++
Sbjct: 42 AGLGEVLPPR--DFGLEPILAVHDPDYVDFLETA--------------DTDTPISEGTWE 85
Query: 68 ESLAAAGAGIALVDSVVAASKNRPDPPLGFALIRPPGHHAIPKGPMGFCVFGNVAIAARY 127
+LAAA + D V+ +AL RPPGHHA GFC F N AIAA+Y
Sbjct: 86 AALAAADTALTAADLVLE------GERAAYALCRPPGHHAGRDRAGGFCYFNNAAIAAQY 139
Query: 128 AQRAHGLKRVFIIDFDVHHGNGTNDAFYDDPDIFFLSTHQDGS--YPGT-GKIDEVGRGD 184
+ RV I+D DVHHGNGT + FY+ PD+ ++S H D YP G DE G G+
Sbjct: 140 LRDRA--GRVAILDVDVHHGNGTQEIFYERPDVLYVSIHGDPRTFYPFFLGFADETGEGE 197
Query: 185 GEGSTLNLPLPGGSGDTAMRTVFHEVIVPCAQRFKPDLILVSAGYDAHVLDPLASLQFTT 244
GEG LNLPLP G+GD E + F PD ++VS G+D H DPL+ + TT
Sbjct: 198 GEGYNLNLPLPPGTGDDDYLAALDE-ALAAIAAFGPDALVVSLGFDTHEGDPLSDFKLTT 256
Query: 245 GTYYMLAANIKQLAKDLCGSRCVFFLEGGYNLNSLSYSVADSFRAFL 291
Y + I L VF EGGYN+++L + F
Sbjct: 257 EDYARIGRRIAALGL-----PTVFVQEGGYNVDALGRNAVAFLAGFE 298
>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 = 235 bits (602), Expect = 1e-75
Identities = 114/314 (36%), Positives = 170/314 (54%), Gaps = 23/314 (7%)
Query: 20 PASVDDIASVHARAYVSGLEKAMDRASQQGIILIEGSGPTYATATTFQESLAAAGAGIAL 79
A+ D++ H+ ++ ++ ++ L + Y ++Q +L AAG + +
Sbjct: 46 LATEDELLLCHSEEHLDEMKSLEKMKPRELNRLGKEYDSIYIHPDSYQCALLAAGCVLQV 105
Query: 80 VDSVVA-ASKNRPDPPLGFALIRPPGHHAIPKGPMGFCVFGNVAIAARYAQRAHGLKRVF 138
V++V+ S+N G A++RPPGHHA GFC F NVAIAARYAQ+ +GLKR+
Sbjct: 106 VEAVLTGESRN------GVAIVRPPGHHAEQDTACGFCFFNNVAIAARYAQKKYGLKRIL 159
Query: 139 IIDFDVHHGNGTNDAFYDDPDIFFLSTH--QDGS-YPGT--GKIDEVGRGDGEGSTLNLP 193
I+D+DVHHGNGT F DP + ++S H +GS +P + G D VG+G GEG +N+P
Sbjct: 160 IVDWDVHHGNGTQHMFESDPSVLYISLHRYDNGSFFPNSPEGNYDVVGKGKGEGFNVNIP 219
Query: 194 L-PGGSGDTAMRTVFHEVIVPCAQRFKPDLILVSAGYDAHVLDPLASLQFTTGTYYMLAA 252
GG GD F +V++P A F P+L+LVSAG+DA DPL + T Y +
Sbjct: 220 WNKGGMGDAEYIAAFQQVVLPIAYEFNPELVLVSAGFDAARGDPLGGCKVTPEGYAHMTH 279
Query: 253 NIKQLAKDLCGSRCVFFLEGGYNLNSLSYSVADSFRAFLGEPSKASEFDNPAILYEEPSA 312
+ LA G R + LEGGYNL S+S S++ + LG+P + P P +
Sbjct: 280 MLMSLA----GGRVIVILEGGYNLTSISESMSMCTKTLLGDPPPVLDLPRP------PCS 329
Query: 313 KVKQAIERVKHIHS 326
++I V +H
Sbjct: 330 SALKSINNVLQVHQ 343
>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 = 228 bits (584), Expect = 4e-73
Identities = 115/315 (36%), Positives = 165/315 (52%), Gaps = 26/315 (8%)
Query: 20 PASVDDIASVHARAYVSGLEK--AMDRASQQGIILIEGSGPTYATATTFQESLAAAGAGI 77
A D+I VH++ Y+ ++ M++ + L G Y +T++ + AAG+ I
Sbjct: 37 EAEEDEILLVHSQEYIDLVKSTETMEKEELES--LCSGYDSVYLCPSTYEAARLAAGSTI 94
Query: 78 ALVDSVVAASKNRPDPPLGFALIRPPGHHAIPKGPMGFCVFGNVAIAARYAQRAHGLKRV 137
LV +V+A GFALIRPPGHHA+ G+C+F NVAIAA+YA GLKR+
Sbjct: 95 ELVKAVMAGKI-----QNGFALIRPPGHHAMRNEANGYCIFNNVAIAAKYAIEKLGLKRI 149
Query: 138 FIIDFDVHHGNGTNDAFYDDPDIFFLSTH--QDGSY-PG--TGKIDEVGRGDGEGSTLNL 192
I+D+DVHHG GT FY+DP + + S H + G + P D +G G G G +N+
Sbjct: 150 LIVDWDVHHGQGTQQGFYEDPRVLYFSIHRYEHGRFWPHLFESDYDYIGVGHGYGFNVNV 209
Query: 193 PLPG-GSGDTAMRTVFHEVIVPCAQRFKPDLILVSAGYDAHVLDPLASLQFTTGTYYMLA 251
PL G GD +FH +++P A F+P+L+LVSAG+DA + DP + T Y L
Sbjct: 210 PLNQTGLGDADYLAIFHHILLPLALEFQPELVLVSAGFDASIGDPEGEMAVTPAGYAHLT 269
Query: 252 ANIKQLAKDLCGSRCVFFLEGGYNLNSLSYSVADSFRAFLGEPSKASEFDNPAILYEEPS 311
+L L G + + LEGGY L SL+ SV+ + R LG+P P + P
Sbjct: 270 ----RLLMGLAGGKLLLVLEGGYLLESLAESVSMTLRGLLGDPL-------PPLAPPIPI 318
Query: 312 AKVKQAIERVKHIHS 326
V + I S
Sbjct: 319 RSVLETILNAIAHLS 333
>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 = 214 bits (547), Expect = 5e-67
Identities = 107/268 (39%), Positives = 146/268 (54%), Gaps = 29/268 (10%)
Query: 72 AAGAGIALVDSVVAAS-KNRPDPPLGFALIRPPGHHAIPKGPMGFCVFGNVAIAARYAQR 130
A G I L V KN GFA++RPPGHHA P MGFC F +VAIAA+ Q+
Sbjct: 123 AVGCVIDLAFKVATGELKN------GFAVVRPPGHHAEPSQAMGFCFFNSVAIAAKQLQQ 176
Query: 131 AHGLKRVFIIDFDVHHGNGTNDAFYDDPDIFFLSTHQ--DGS-YPGTGKIDEVGRGDGEG 187
L+++ I+D+DVHHGNGT FY+DP++ ++S H+ DG+ +PGTG EVG G GEG
Sbjct: 177 KLKLRKILIVDWDVHHGNGTQQIFYEDPNVLYISLHRYDDGNFFPGTGAPTEVGSGAGEG 236
Query: 188 STLNLPLPGGS----GDTAMRTVFHEVIVPCAQRFKPDLILVSAGYDA---HVLDPLASL 240
+N+ GG GD F V++P A+ F PD++LVSAG+DA H PL
Sbjct: 237 FNVNIAWSGGLDPPMGDAEYLAAFRTVVMPIAREFSPDIVLVSAGFDAAEGHP-PPLGGY 295
Query: 241 QFTTGTY-YMLAANIKQLAKDLCGSRCVFFLEGGYNLNSLSYSVADSFRAFLG-EPSKAS 298
+ + + YM +QL L G + V LEGGY+L ++ + RA LG E S
Sbjct: 296 KVSPACFGYM----TRQLMN-LAGGKVVLALEGGYDLTAICDASEACVRALLGDELDPLS 350
Query: 299 EFDNPAILYEEPSAKVKQAIERVKHIHS 326
E L P+ ++E+V I S
Sbjct: 351 E----EELERRPNPNAVTSLEKVIAIQS 374
>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 = 207 bits (528), Expect = 5e-65
Identities = 103/289 (35%), Positives = 146/289 (50%), Gaps = 21/289 (7%)
Query: 17 NFSPASVDDIASVHARAYVSGLEKA--MDRASQQGIILIEGSGPTYATATTFQESLAAAG 74
A+ ++I VH+ + +E M + I Y T + + G
Sbjct: 30 PIREATKEEILLVHSEEHWDRVEATEKMSDEQLKDRTEIFERDSLYVNNDTAFCARLSCG 89
Query: 75 AGIALVDSVVAAS-KNRPDPPLGFALIRPPGHHAIPKGPMGFCVFGNVAIAARYAQ--RA 131
I +V KN FA++RPPGHHA P MGFC F NVA+AA++ Q
Sbjct: 90 GAIEACRAVAEGRVKN------AFAVVRPPGHHAEPDESMGFCFFNNVAVAAKWLQTEYP 143
Query: 132 HGLKRVFIIDFDVHHGNGTNDAFYDDPDIFFLSTH---QDGSYPGT--GKIDEVGRGDGE 186
+K++ I+D+D+HHGNGT AFYDDP++ ++S H G YPGT G + VG G G
Sbjct: 144 DKIKKILILDWDIHHGNGTQRAFYDDPNVLYISLHRFENGGFYPGTPYGDYESVGEGAGL 203
Query: 187 GSTLNLPLP-GGSGDTAMRTVFHEVIVPCAQRFKPDLILVSAGYDAHVLDPLASLQFTTG 245
G +N+P P GG GD F +++P A F PDL+++SAG+DA D L T
Sbjct: 204 GFNVNIPWPQGGMGDADYIYAFQRIVMPIAYEFDPDLVIISAGFDAADGDELGQCHVTPA 263
Query: 246 TYYMLAANIKQLAKDLCGSRCVFFLEGGYNLNSLSYSVADSFRAFLGEP 294
Y A++ + L G + V LEGGYNL+++S S + LGE
Sbjct: 264 GY----AHMTHMLMSLAGGKLVVALEGGYNLDAISDSALAVAKVLLGEA 308
>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 = 195 bits (498), Expect = 2e-60
Identities = 84/269 (31%), Positives = 124/269 (46%), Gaps = 22/269 (8%)
Query: 20 PASVDDIASVHARAYVSGLEKAMDRASQQGIILIE-----GSGPTYATATTFQESLAAAG 74
PA+ +++ H Y+ A+ AS+ G+ + + G
Sbjct: 47 PATEEELLLFHTPDYIE----AVKEASRGQEPEGRGRLGLGTEDNPVFPGMHEAAALVVG 102
Query: 75 AGIALVDSVVAASKNRPDPPLGFALIRPPG--HHAIPKGPMGFCVFGNVAIAARYAQRAH 132
+ V+ R F G HHA+ GFCV+ + A+A +
Sbjct: 103 GTLLAARLVLEGEARR-----AFNPA---GGLHHAMRGRASGFCVYNDAAVAIERLRD-K 153
Query: 133 GLKRVFIIDFDVHHGNGTNDAFYDDPDIFFLSTHQDGSY--PGTGKIDEVGRGDGEGSTL 190
G RV +D D HHG+G AFYDDP + +S H+ G Y PGTG +DE+G G+G G +
Sbjct: 154 GGLRVAYVDIDAHHGDGVQAAFYDDPRVLTISLHESGRYLFPGTGFVDEIGEGEGYGYAV 213
Query: 191 NLPLPGGSGDTAMRTVFHEVIVPCAQRFKPDLILVSAGYDAHVLDPLASLQFTTGTYYML 250
N+PLP G+GD F V+ P + F+PD+I+ G DAH DPL L + Y
Sbjct: 214 NIPLPPGTGDDEFLRAFEAVVPPLLRAFRPDVIVSQHGADAHAGDPLTHLNLSNRAYRAA 273
Query: 251 AANIKQLAKDLCGSRCVFFLEGGYNLNSL 279
I++LA + CG R + GGYN + +
Sbjct: 274 VRRIRELADEYCGGRWLALGGGGYNPDVV 302
>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 = 188 bits (478), Expect = 2e-57
Identities = 103/281 (36%), Positives = 150/281 (53%), Gaps = 17/281 (6%)
Query: 21 ASVDDIASVHARAYVSGLEKAMDRASQQGIILIEGSGPTYATATTFQESLAAAGAGIALV 80
AS +++ VH+ YV+ ++ ++ L + Y ++ + A G+ + LV
Sbjct: 38 ASEEELLLVHSPEYVALMKSTQYMTEEELRTLADTYDSVYLHPNSYSCACLAVGSVLQLV 97
Query: 81 DSVVAAS-KNRPDPPLGFALIRPPGHHAIPKGPMGFCVFGNVAIAARYAQRAHGLKRVFI 139
D V+ +N G A++RPPGHHA G+C+F NVAIAARYAQ+ HG++RV I
Sbjct: 98 DKVLGGEIRN------GLAIVRPPGHHAQHDKMDGYCMFNNVAIAARYAQQKHGVQRVLI 151
Query: 140 IDFDVHHGNGTNDAFYDDPDIFFLSTH--QDGSY-PGTGKIDE--VGRGDGEGSTLNLPL 194
+D+DVHHG GT F DP + + S H + G + P + D VG G GEG +N+P
Sbjct: 152 VDWDVHHGQGTQFIFEQDPSVLYFSIHRYEQGRFWPHLKESDSSAVGFGRGEGYNINVPW 211
Query: 195 PG-GSGDTAMRTVFHEVIVPCAQRFKPDLILVSAGYDAHVLDPLASLQFTTGTYYMLAAN 253
G D F V++P A F+P L+LV+AG+DA + DP + T + L
Sbjct: 212 NQVGMRDADYIAAFLHVLLPVALEFQPQLVLVAAGFDAVIGDPKGEMAATPACFAHLT-- 269
Query: 254 IKQLAKDLCGSRCVFFLEGGYNLNSLSYSVADSFRAFLGEP 294
L L G + + LEGGYNL SL+ V S +A LG+P
Sbjct: 270 --HLLMGLAGGKLILSLEGGYNLRSLAEGVCASLKALLGDP 308
>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 = 181 bits (462), Expect = 6e-55
Identities = 102/281 (36%), Positives = 149/281 (53%), Gaps = 17/281 (6%)
Query: 21 ASVDDIASVHARAYVSGLEKAMDRASQQGIILIEGSGPTYATATTFQESLAAAGAGIALV 80
AS ++I VH+ Y+S + + ++ + + Y TF + AAGA + LV
Sbjct: 38 ASEEEILLVHSPEYLSLVRETQVMNKEELMAISGKYDAVYFHPNTFHCARLAAGATLQLV 97
Query: 81 DSVVA-ASKNRPDPPLGFALIRPPGHHAIPKGPMGFCVFGNVAIAARYAQRAHGLKRVFI 139
D+V+ +N G AL+RPPGHH+ GFCVF NVAIAA YA++ +GL R+ I
Sbjct: 98 DAVLTGEVQN------GMALVRPPGHHSQRNAANGFCVFNNVAIAAEYAKKKYGLHRILI 151
Query: 140 IDFDVHHGNGTNDAFYDDPDIFFLSTH--QDGS---YPGTGKIDEVGRGDGEGSTLNLPL 194
+D+DVHHG G F +DP + + S H + + D VGRG G G +NLP
Sbjct: 152 VDWDVHHGQGIQYIFEEDPSVLYFSWHRYEHQRFWPFLRESDYDAVGRGKGLGFNINLPW 211
Query: 195 PG-GSGDTAMRTVFHEVIVPCAQRFKPDLILVSAGYDAHVLDPLASLQFTTGTYYMLAAN 253
G G+ F V++P A F P+L+LVSAG+D+ + DP + T + A+
Sbjct: 212 NKVGMGNADYLAAFFHVLLPLAFEFDPELVLVSAGFDSAIGDPEGQMCATPECF----AH 267
Query: 254 IKQLAKDLCGSRCVFFLEGGYNLNSLSYSVADSFRAFLGEP 294
+ L L G + LEGGY+L SL+ SV + + LG+P
Sbjct: 268 LTHLLMVLAGGKLCAVLEGGYHLESLAESVCMTVQTLLGDP 308
>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 = 182 bits (463), Expect = 3e-54
Identities = 107/266 (40%), Positives = 146/266 (54%), Gaps = 25/266 (9%)
Query: 72 AAGAGIALVDSVVAAS-KNRPDPPLGFALIRPPGHHAIPKGPMGFCVFGNVAIAARYAQR 130
A G I L V A KN GFA+IRPPGHHA MGFC F +VAIAA+ Q+
Sbjct: 126 AVGCLIELAFKVAAGELKN------GFAVIRPPGHHAEESTAMGFCFFNSVAIAAKLLQQ 179
Query: 131 AHGLKRVFIIDFDVHHGNGTNDAFYDDPDIFFLSTHQ--DGS-YPGTGKIDEVGRGDGEG 187
+ ++ I+D+D+HHGNGT AFY+DP++ ++S H+ DG+ +PG+G DEVG G G G
Sbjct: 180 KLNVGKILIVDWDIHHGNGTQQAFYNDPNVLYISLHRYDDGNFFPGSGAPDEVGAGPGVG 239
Query: 188 STLNLPLPGGS----GDTAMRTVFHEVIVPCAQRFKPDLILVSAGYDA---HVLDPLASL 240
+N+ GG GD T F V++P A F PD++LVSAG+DA H PL
Sbjct: 240 FNVNIAWTGGVDPPIGDVEYLTAFRTVVMPIANEFSPDVVLVSAGFDAVEGH-QSPLGGY 298
Query: 241 QFTTGTYYMLAANIKQLAKDLCGSRCVFFLEGGYNLNSLSYSVADSFRAFLGEPSKASEF 300
T + L KQL L G R V LEGG++L ++ + A LG + +
Sbjct: 299 SVTAKCFGHLT---KQLMT-LAGGRVVLALEGGHDLTAICDASEACVSALLGM--ELTPL 352
Query: 301 DNPAILYEEPSAKVKQAIERVKHIHS 326
DN +L ++P+ +ERV I S
Sbjct: 353 DN-TVLQQKPNDNAVATLERVIEIQS 377
>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 = 175 bits (445), Expect = 1e-51
Identities = 103/268 (38%), Positives = 146/268 (54%), Gaps = 29/268 (10%)
Query: 72 AAGAGIALVDSVVAAS-KNRPDPPLGFALIRPPGHHAIPKGPMGFCVFGNVAIAARYAQR 130
A G + LV V KN GFA++RPPGHHA PMGFC F +VAIAA+ Q+
Sbjct: 126 AVGCVVELVFKVATGELKN------GFAVVRPPGHHAEESTPMGFCYFNSVAIAAKLLQQ 179
Query: 131 AHGLKRVFIIDFDVHHGNGTNDAFYDDPDIFFLSTHQ--DGS-YPGTGKIDEVGRGDGEG 187
+ ++ I+D+DVHHGNGT AFY DP++ ++S H+ DG+ +PG+G DEVG G G G
Sbjct: 180 RLNVSKILIVDWDVHHGNGTQQAFYSDPNVLYMSLHRYDDGNFFPGSGAPDEVGTGPGVG 239
Query: 188 STLNLPLPGG----SGDTAMRTVFHEVIVPCAQRFKPDLILVSAGYDA---HVLDPLASL 240
+N+ GG GD F V++P A F PD++LVS+G+DA H PL
Sbjct: 240 FNVNMAFTGGLDPPMGDAEYLAAFRTVVMPIASEFAPDVVLVSSGFDAVEGHP-TPLGGY 298
Query: 241 QFTTGTYYMLAANIKQLAKDLCGSRCVFFLEGGYNLNSLSYSVADSFRAFLGEPSKASEF 300
+ + L + LA G R V LEGG++L ++ + A LG +E
Sbjct: 299 NLSAKCFGYLTKQLMGLA----GGRIVLALEGGHDLTAICDASEACVSALLG-----NEL 349
Query: 301 D--NPAILYEEPSAKVKQAIERVKHIHS 326
D +L + P+A +++E+V IHS
Sbjct: 350 DPLPEKVLQQRPNANAVRSMEKVMEIHS 377
>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 = 173 bits (439), Expect = 4e-51
Identities = 92/243 (37%), Positives = 133/243 (54%), Gaps = 22/243 (9%)
Query: 96 GFALIRPPGHHAIPKGPMGFCVFGNVAIAARYAQRAHGLKRVFIIDFDVHHGNGTNDAFY 155
GFA++RPPGHHA MGFC F +VAIA R Q+ ++ I+D+DVHHGNGT FY
Sbjct: 143 GFAVVRPPGHHADHSTAMGFCFFNSVAIACRQLQQQGKASKILIVDWDVHHGNGTQQTFY 202
Query: 156 DDPDIFFLSTHQ--DGS-YPGTGKIDEVGRGDGEGSTLNLPLPGG----SGDTAMRTVFH 208
DP + ++S H+ DG+ +PG+G +DEVG G GEG +N+ GG GD F
Sbjct: 203 QDPSVLYISLHRHDDGNFFPGSGAVDEVGAGSGEGFNVNVAWAGGLDPPMGDPEYLAAFR 262
Query: 209 EVIVPCAQRFKPDLILVSAGYDA---HVLDPLASLQFTTGTYYMLAANIKQLAKDLCGSR 265
V++P A+ F PDL+LVSAG+DA H PL + + + + LA G
Sbjct: 263 IVVMPIAREFSPDLVLVSAGFDAAEGHP-APLGGYHVSAKCFGYMTQQLMNLA----GGA 317
Query: 266 CVFFLEGGYNLNSLSYSVADSFRAFLGEPSKASEFD--NPAILYEEPSAKVKQAIERVKH 323
V LEGG++L ++ + A LG +E D + ++P+ +++E V
Sbjct: 318 VVLALEGGHDLTAICDASEACVAALLG-----NEVDPLSEESWKQKPNLNAIRSLEAVIR 372
Query: 324 IHS 326
+HS
Sbjct: 373 VHS 375
>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 = 159 bits (405), Expect = 5e-47
Identities = 75/278 (26%), Positives = 120/278 (43%), Gaps = 16/278 (5%)
Query: 13 IELKNFSPASVDDIASVHARAYVSGLEKAMDRASQQGIILIEGSGPTYATATTFQESLAA 72
IEL A+ + + VH Y++ L+ A+ + F+ + +
Sbjct: 18 IELIECREATEELLLKVHTEEYLNELKANFAVATITESKPVIFGPNFPVQRHYFRGARLS 77
Query: 73 AGAGIALVDSVVAASKNRPDPPLGFALIRPPGHHAIPKGPMGFCVFGNVAIAARYAQRAH 132
G + + V R FA++ GHHA GFC F +V +A ++ R
Sbjct: 78 TGGVVEAAELVAKGELER-----AFAVVGAGGHHAGKSRAWGFCYFNDVVLAIKFL-RER 131
Query: 133 GLKRVFIIDFDVHHGNGTNDAFYDDPDIFFLSTHQDGSYPGTGKIDEVGRGDGEGSTLNL 192
G+ R+ IID D HHG+GT +AFYDD + +S H YP GRG G+G +N+
Sbjct: 132 GISRILIIDTDAHHGDGTREAFYDDDRVLHMSFHNYDIYPF-------GRGKGKGYKINV 184
Query: 193 PLPGGSGDTAMRTVFHEVIVPCAQRFKPDLILVSAGYDAHVLDPLASLQFTTGTYYMLAA 252
PL G GD VI + F+P+++++ G+D H D L + + LA
Sbjct: 185 PLEDGLGDEEYLDAVERVISKVLEEFEPEVVVLQFGHDTHEGDRLGGFNLSEKGFVKLAE 244
Query: 253 NIKQLAKDLCGSRCVFFLEGGYNLNSLSYSVADSFRAF 290
+K+ A+ + L GGYN + + +
Sbjct: 245 IVKEFARGG---PILMVLGGGYNPEAAARIWTAIIKEL 279
>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 = 160 bits (406), Expect = 3e-46
Identities = 99/275 (36%), Positives = 144/275 (52%), Gaps = 20/275 (7%)
Query: 65 TFQESLAAAGAGIALVDSVVAASKNRPDPPL--GFALIRPPGHHAIPKGPMGFCVFGNVA 122
T L ++GA V V+ + L GFA++RPPGHHA MGFC F +VA
Sbjct: 110 TIWNELHSSGAARMAVGCVIELASKVASGELKNGFAVVRPPGHHAEESTAMGFCFFNSVA 169
Query: 123 IAARYAQRAHGLKRVFIIDFDVHHGNGTNDAFYDDPDIFFLSTHQ--DGS-YPGTGKIDE 179
I A+Y + + ++ I+D DVHHGNGT AFY DP I ++S H+ +G+ +PG+G +E
Sbjct: 170 ITAKYLRDQLNISKILIVDLDVHHGNGTQQAFYADPSILYISLHRYDEGNFFPGSGAPNE 229
Query: 180 VGRGDGEGSTLNLPLPGG----SGDTAMRTVFHEVIVPCAQRFKPDLILVSAGYDA---H 232
VG G GEG +N+ GG GD F ++ P A+ F PD++LVSAG+DA H
Sbjct: 230 VGTGLGEGYNINIAWTGGLDPPMGDVEYLEAFRTIVKPVAKEFDPDMVLVSAGFDALEGH 289
Query: 233 VLDPLASLQFTTGTYYMLAANIKQLAKDLCGSRCVFFLEGGYNLNSLSYSVADSFRAFLG 292
PL + T + L KQL L R V LEGG++L ++ + A LG
Sbjct: 290 T-PPLGGYKVTAKCFGHLT---KQLMT-LADGRVVLALEGGHDLTAICDASEACVNALLG 344
Query: 293 EPSKASEFDNPAILYEEPSAKVKQAIERVKHIHSL 327
+ D IL++ P+ +++++ I S
Sbjct: 345 NELEPLAED---ILHQSPNMNAVISLQKIIEIQSK 376
>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 = 112 bits (284), Expect = 3e-29
Identities = 54/136 (39%), Positives = 69/136 (50%), Gaps = 10/136 (7%)
Query: 105 HHAIPKGPMGFCVFGNVAIAARYAQRAHGLKRVFIIDFDVHHGNGTNDAFYDDPDIFFLS 164
HHA P GFCVF ++AIAAR ++RV I+D DVH GNGT F DDP +F S
Sbjct: 102 HHAFPDRGEGFCVFNDIAIAARVLLAEGLVRRVLIVDLDVHQGNGTAAIFADDPSVFTFS 161
Query: 165 THQDGSYPGTGKIDEVGRGDGEGSTLNLPLPGGSGDTAMRTVFHEVIVPCAQRFKPDLIL 224
H + +YP E S L++PLP G+GD E + F+PDL+
Sbjct: 162 MHGEKNYP----------FRKEPSDLDVPLPDGTGDDEYLAALEEALPRLLAEFRPDLVF 211
Query: 225 VSAGYDAHVLDPLASL 240
+AG D D L L
Sbjct: 212 YNAGVDVLAGDRLGRL 227
>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 = 105 bits (263), Expect = 7e-26
Identities = 77/271 (28%), Positives = 98/271 (36%), Gaps = 59/271 (21%)
Query: 56 SGPTYATATTFQESLAAAGAGIALVDSVVAASKNRPDPPLGFALIRPPGHHAIPKGPMGF 115
G Y + A GA VDSV P F IRPPGHH P GF
Sbjct: 73 QGDLYLCPESLDAIQGALGAVCEAVDSVFKP--ESPGTKRAFVAIRPPGHHCSESTPSGF 130
Query: 116 CVFGNVAIAARYAQRAHGLKRVFIIDFDVHHGNGTND----------------------- 152
C NV + A +A HG+ RV I+D D+HHGNGT D
Sbjct: 131 CWVNNVHVGAAHAYLTHGITRVVILDIDLHHGNGTQDIAWRINAEANKQALESSSYDDFK 190
Query: 153 -AFYDDPDIFFLSTHQDGSYP-GTGKIDEVG------RGDGEGSTLNLPLPGGSGDTAMR 204
A IF+ S H S+P G +V G N+ L + +
Sbjct: 191 PAGAPGLRIFYSSLHDINSFPCEDGDPAKVKDASVSIDGAHGQWIWNVHLQPWTTEED-- 248
Query: 205 TVFHEVIVPC-------AQRF-------KPD--LILVSAGYDAHVLDPLASLQ-----FT 243
F E+ P A F P L+ +SAG+DA + S+Q
Sbjct: 249 --FWELYYPKYRILFEKAAEFLRLTTAATPFKTLVFISAGFDASEHE-YESMQRHGVNVP 305
Query: 244 TGTYYMLAANIKQLAKDLCGSRCVFFLEGGY 274
T YY A + + A R + LEGGY
Sbjct: 306 TSFYYRFARDAVRFADAHAHGRLISVLEGGY 336
>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 = 101 bits (254), Expect = 8e-25
Identities = 40/134 (29%), Positives = 66/134 (49%), Gaps = 3/134 (2%)
Query: 105 HHAIPKGPMGFCVFGNVAIAARYAQRAHGLKRVFIIDFDVHHGNGTNDAFYDDPDIFFLS 164
HHA GFC ++ +A + H +RV ID D+HHG+G +AFY + +S
Sbjct: 127 HHAKKSEASGFCYVNDIVLAILELLKYH--QRVLYIDIDIHHGDGVEEAFYTTDRVMTVS 184
Query: 165 THQDGSY-PGTGKIDEVGRGDGEGSTLNLPLPGGSGDTAMRTVFHEVIVPCAQRFKPDLI 223
H+ G Y + ++G G G+ +N+PL G D + +F V+ + F+P +
Sbjct: 185 FHKFGEYFFPGTGLRDIGAGKGKYYAVNVPLKDGIDDESYLQIFEPVLSKVMEVFQPSAV 244
Query: 224 LVSAGYDAHVLDPL 237
++ G D+ D L
Sbjct: 245 VLQCGADSLAGDRL 258
>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 = 99.3 bits (248), Expect = 1e-23
Identities = 48/178 (26%), Positives = 77/178 (43%), Gaps = 9/178 (5%)
Query: 105 HHAIPKGPMGFCVFGNVAIAARYAQRAHGLKRVFIIDFDVHHGNGTNDAFYDDPDIFFLS 164
HHA GFC ++ + + RV +D D+HHG+G DAF + +S
Sbjct: 129 HHAQRDEASGFCYVNDIVLGILKLREK--FDRVLYVDLDLHHGDGVEDAFSFTSKVMTVS 186
Query: 165 THQ--DGSYPGTGKIDEVGRGDGEGSTLNLPLPGGSGDTAMRTVFHEVIVPCAQRFKPDL 222
H+ G +PGTG + +VG G G+ T+N+PL G D +F V+ F+P+
Sbjct: 187 LHKYSPGFFPGTGDVSDVGLGKGKYYTVNVPLRDGIQDEQYLQIFTAVVPEIVAAFRPEA 246
Query: 223 ILVSAGYDAHVLDPLASLQFTTGTYYMLAANIKQLAKDLCGSRCVFFLEGGYNLNSLS 280
+++ G D DP+ + T + + GGYNL + +
Sbjct: 247 VVLQCGADTLAGDPMGAFNLTPVGIGKCLKYVLG-----WKLPTLILGGGGYNLANTA 299
>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 = 98.1 bits (245), Expect = 1e-23
Identities = 50/173 (28%), Positives = 81/173 (46%), Gaps = 10/173 (5%)
Query: 105 HHAIPKGPMGFCVFGNVAIAARYAQRAHGLKRVFIIDFDVHHGNGTNDAFYDDPDIFFLS 164
HHA GFC ++ +A +RA +RVF +D D+HHG+G AF+ ++ S
Sbjct: 115 HHAQKSRASGFCYVNDIVLAILRLRRA-RFRRVFYLDLDLHHGDGVESAFFFSKNVLTCS 173
Query: 165 THQ--DGSYPGTGKIDEVGRGDGEGSTLNLPLPGGSGDTAMRTVFHEVIVPCAQRFKPDL 222
H+ G +PGTG + + LN+PL G D + + ++ P ++F+P++
Sbjct: 174 IHRYDPGFFPGTGSLKN----SSDKGMLNIPLKRGLSDKTLLRIIDSIVRPLIEKFEPEV 229
Query: 223 ILVSAGYDAHVLDPLASLQFTTGTYYMLAANIKQLAKDLCGSRCVFFLEGGYN 275
I++ G D DP T Y + I+ L K+ + GGYN
Sbjct: 230 IVIQCGCDGLSGDPHKEWNLTIRGY---GSVIELLLKEFKDKPTLLLGGGGYN 279
>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 = 92.5 bits (230), Expect = 1e-21
Identities = 45/129 (34%), Positives = 65/129 (50%), Gaps = 4/129 (3%)
Query: 105 HHAIPKGPMGFCVFGNVAIAARYAQRAHGLKRVFIIDFDVHHGNGTNDAFYDDPDIFFLS 164
HHA GFC ++ +A R RV ID DVHHG+G +AFY + LS
Sbjct: 131 HHAKKSEASGFCYVNDIVLAILNLLRYF--PRVLYIDIDVHHGDGVEEAFYRTDRVMTLS 188
Query: 165 THQDGS--YPGTGKIDEVGRGDGEGSTLNLPLPGGSGDTAMRTVFHEVIVPCAQRFKPDL 222
H+ +PGTG +D+ G G+ LN+PL G D +F +I P ++F+P
Sbjct: 189 FHKYNGEFFPGTGDLDDNGGTPGKHFALNVPLEDGIDDEQYNLLFKSIIGPTIEKFQPSA 248
Query: 223 ILVSAGYDA 231
I++ G D+
Sbjct: 249 IVLQCGADS 257
>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 = 91.0 bits (226), Expect = 1e-20
Identities = 46/152 (30%), Positives = 76/152 (50%), Gaps = 3/152 (1%)
Query: 105 HHAIPKGPMGFCVFGNVAIAARYAQRAHGLKRVFIIDFDVHHGNGTNDAFYDDPDIFFLS 164
HHA GFC ++ + R H +RV ID DVHHG+G +AFY + S
Sbjct: 133 HHAKKSEASGFCYVNDIVLGILELLRYH--QRVLYIDIDVHHGDGVEEAFYTTDRVMTCS 190
Query: 165 THQDGSY-PGTGKIDEVGRGDGEGSTLNLPLPGGSGDTAMRTVFHEVIVPCAQRFKPDLI 223
H+ G Y PGTG++ ++G G G+ +N+PL G D + +++F VI + ++P+ +
Sbjct: 191 FHKYGEYFPGTGELRDIGIGTGKNYAVNVPLRDGIDDESYKSIFEPVIKHVMEWYQPEAV 250
Query: 224 LVSAGYDAHVLDPLASLQFTTGTYYMLAANIK 255
++ G D+ D L + + +K
Sbjct: 251 VLQCGGDSLSGDRLGCFNLSMKGHANCVNFVK 282
>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 = 85.9 bits (212), Expect = 6e-19
Identities = 45/140 (32%), Positives = 70/140 (50%), Gaps = 3/140 (2%)
Query: 105 HHAIPKGPMGFCVFGNVAIAARYAQRAHGLKRVFIIDFDVHHGNGTNDAFYDDPDIFFLS 164
HHA GFC ++ +A + H +RV ID D+HHG+G +AFY + +S
Sbjct: 137 HHAKKSEASGFCYVNDIVLAILELLKYH--QRVLYIDIDIHHGDGVEEAFYTTDRVMTVS 194
Query: 165 THQDGSY-PGTGKIDEVGRGDGEGSTLNLPLPGGSGDTAMRTVFHEVIVPCAQRFKPDLI 223
H+ G Y PGTG + ++G G G+ +N PL G D + +F V+ + F+P +
Sbjct: 195 FHKYGEYFPGTGDLRDIGAGKGKYYAVNYPLRDGIDDESYEAIFKPVMSKVMEMFQPSAV 254
Query: 224 LVSAGYDAHVLDPLASLQFT 243
++ G D+ D L T
Sbjct: 255 VLQCGADSLSGDRLGCFNLT 274
>gnl|CDD|240251 PTZ00063, PTZ00063, histone deacetylase; Provisional.
Length = 436
Score = 82.2 bits (203), Expect = 2e-17
Identities = 45/140 (32%), Positives = 70/140 (50%), Gaps = 3/140 (2%)
Query: 105 HHAIPKGPMGFCVFGNVAIAARYAQRAHGLKRVFIIDFDVHHGNGTNDAFYDDPDIFFLS 164
HHA GFC ++ + + H RV ID DVHHG+G +AFY + +S
Sbjct: 137 HHAKRSEASGFCYINDIVLGILELLKYHA--RVMYIDIDVHHGDGVEEAFYVTHRVMTVS 194
Query: 165 THQDGSY-PGTGKIDEVGRGDGEGSTLNLPLPGGSGDTAMRTVFHEVIVPCAQRFKPDLI 223
H+ G + PGTG + ++G G+ ++N+PL G D + +F VI C + ++P I
Sbjct: 195 FHKFGDFFPGTGDVTDIGVAQGKYYSVNVPLNDGIDDDSFVDLFKPVISKCVEVYRPGAI 254
Query: 224 LVSAGYDAHVLDPLASLQFT 243
++ G D+ D L T
Sbjct: 255 VLQCGADSLTGDRLGRFNLT 274
>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 = 81.7 bits (202), Expect = 2e-17
Identities = 47/142 (33%), Positives = 69/142 (48%), Gaps = 4/142 (2%)
Query: 105 HHAIPKGPMGFCVFGNVAIAARYAQRAHGLKRVFIIDFDVHHGNGTNDAFYDDPDIFFLS 164
HHA GFC ++ IA + H RV ID D+HHG+G +AFY + +S
Sbjct: 132 HHAKKFEASGFCYVNDIVIAILELLKYH--PRVLYIDIDIHHGDGVQEAFYLTDRVMTVS 189
Query: 165 THQDGSY--PGTGKIDEVGRGDGEGSTLNLPLPGGSGDTAMRTVFHEVIVPCAQRFKPDL 222
H+ G+Y PGTG + EVG G ++N+PL G D + +F VI ++P
Sbjct: 190 FHKYGNYFFPGTGDMYEVGAESGRYYSVNVPLKDGIDDQSYLQLFKPVIQQVIDFYQPTC 249
Query: 223 ILVSAGYDAHVLDPLASLQFTT 244
I++ G D+ D L +
Sbjct: 250 IVLQCGADSLGCDRLGCFNLSI 271
>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 = 77.4 bits (190), Expect = 5e-16
Identities = 40/140 (28%), Positives = 67/140 (47%), Gaps = 3/140 (2%)
Query: 105 HHAIPKGPMGFCVFGNVAIAARYAQRAHGLKRVFIIDFDVHHGNGTNDAFYDDPDIFFLS 164
HHA GFC ++ +A + H +RV ID D+HHG+G +AFY + +S
Sbjct: 133 HHAKKSEASGFCYVNDIVLAILELLKYH--QRVLYIDIDIHHGDGVEEAFYTTDRVMTVS 190
Query: 165 -THQDGSYPGTGKIDEVGRGDGEGSTLNLPLPGGSGDTAMRTVFHEVIVPCAQRFKPDLI 223
+PGTG + ++G G G+ +N P+ G D + +F +I + ++P +
Sbjct: 191 FHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIISKVMEMYQPSAV 250
Query: 224 LVSAGYDAHVLDPLASLQFT 243
++ G D+ D L T
Sbjct: 251 VLQCGADSLSGDRLGCFNLT 270
>gnl|CDD|240374 PTZ00346, PTZ00346, histone deacetylase; Provisional.
Length = 429
Score = 73.5 bits (180), Expect = 1e-14
Identities = 43/142 (30%), Positives = 69/142 (48%), Gaps = 4/142 (2%)
Query: 105 HHAIPKGPMGFCVFGNVAIAARYAQRAHGLKRVFIIDFDVHHGNGTNDAFYDDPDIFFLS 164
HH+ GFC ++ + + H RV +D D+HHG+G ++AF +F LS
Sbjct: 154 HHSKCGECSGFCYVNDIVLGILELLKCH--DRVLYVDIDMHHGDGVDEAFCTSDRVFTLS 211
Query: 165 THQDGS--YPGTGKIDEVGRGDGEGSTLNLPLPGGSGDTAMRTVFHEVIVPCAQRFKPDL 222
H+ G +PGTG +VG G G ++NL + G D +F + +R+ PD
Sbjct: 212 LHKFGESFFPGTGHPRDVGYGRGRYYSMNLAVWDGITDFYYLGLFEHALHSIVRRYSPDA 271
Query: 223 ILVSAGYDAHVLDPLASLQFTT 244
I++ G D+ D L L ++
Sbjct: 272 IVLQCGADSLAGDRLGLLNLSS 293
>gnl|CDD|176107 cd08415, PBP2_LysR_opines_like, The C-terminal substrate-domain of
LysR-type transcriptional regulators involved in the
catabolism of opines and that of related regulators,
contains the type 2 periplasmic binding fold. This CD
includes the C-terminal substrate-domain of LysR-type
transcriptional regulators, OccR and NocR, involved in
the catabolism of opines and that of LysR for lysine
biosynthesis which clustered together in phylogenetic
trees. Opines, such as octopine and nopaline, are low
molecular weight compounds found in plant crown gall
tumors that are produced by the parasitic bacterium
Agrobacterium. There are at least 30 different opines
identified so far. Opines are utilized by
tumor-colonizing bacteria as a source of carbon,
nitrogen, and energy. NocR and OccR belong to the family
of LysR-type transcriptional regulators that positively
regulates the catabolism of nopaline and octopine,
respectively. Both nopaline and octopalin are arginine
derivatives. In Agrobacterium tumefaciens, NocR
regulates expression of the divergently transcribed nocB
and nocR genes of the nopaline catabolism (noc) region.
OccR protein activates the occQ operon of the Ti plasmid
in response to octopine. This operon encodes proteins
required for the uptake and catabolism of octopine. The
occ operon also encodes the TraR protein, which is a
quorum-sensing transcriptional regulator of the Ti
plasmid tra regulon. LysR is the transcriptional
activator of lysA gene encoding diaminopimelate
decarboxylase, an enzyme that catalyses the
decarboxylation of diaminopimelate to produce lysine.
This substrate-binding domain shows significant homology
to the type 2 periplasmic binding proteins (PBP2), which
are responsible for the uptake of a variety of
substrates such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis.
Length = 196
Score = 39.1 bits (92), Expect = 0.001
Identities = 19/45 (42%), Positives = 24/45 (53%), Gaps = 9/45 (20%)
Query: 69 SLAAAGAGIALVDSVVAASKN---------RPDPPLGFALIRPPG 104
+L AAG G+A+VD + AA RP P FAL+RP G
Sbjct: 138 ALVAAGLGVAIVDPLTAAGYAGAGLVVRPFRPAIPFEFALVRPAG 182
>gnl|CDD|219014 pfam06414, Zeta_toxin, Zeta toxin. This family consists of several
bacterial zeta toxin proteins. Zeta toxin is thought to
be part of a postregulational killing system in
bacteria. It relies on antitoxin/toxin systems that
secure stable inheritance of low and medium copy number
plasmids during cell division and kill cells that have
lost the plasmid.
Length = 191
Score = 32.6 bits (75), Expect = 0.15
Identities = 29/133 (21%), Positives = 44/133 (33%), Gaps = 30/133 (22%)
Query: 24 DDIASVHARAYVSGL-EKAMDRASQQGI-ILIEGSGPTYATATTFQESLAAAGAGIALVD 81
AS + S EK +D A ++G I++EG+ + A L AAG + +
Sbjct: 64 PKDASELTQPDASRWVEKLIDYAIERGYNIILEGTLRSPDVARKLARKLKAAGYEVEVY- 122
Query: 82 SVVAASKNRPDPPLG--FALIR-----------PPGHHAIPKGPMGFCVFGNVAIAARYA 128
VVA P L L R P H + + +
Sbjct: 123 -VVAV-----PPELSWLGVLDRYEEELAAGRRVPKEVHDA--------AYNGLPESVEAL 168
Query: 129 QRAHGLKRVFIID 141
+R R+ I D
Sbjct: 169 EREKLFDRILIKD 181
>gnl|CDD|212513 cd09987, Arginase_HDAC, Arginase-like and histone-like hydrolases.
Arginase-like/histone-like hydrolase superfamily
includes metal-dependent enzymes that belong to
Arginase-like amidino hydrolase family and
histone/histone-like deacetylase class I, II, IV family,
respectively. These enzymes catalyze hydrolysis of amide
bond. Arginases are known to be involved in control of
cellular levels of arginine and ornithine, in histidine
and arginine degradation and in clavulanic acid
biosynthesis. Deacetylases play a role in signal
transduction through histone and/or other protein
modification and can repress/activate transcription of a
number of different genes. They participate in different
cellular processes including cell cycle regulation, DNA
damage response, embryonic development, cytokine
signaling important for immune response and
post-translational control of the acetyl coenzyme A
synthetase. Mammalian histone deacetyases are known to
be involved in progression of different tumors. Specific
inhibitors of mammalian histone deacetylases are an
emerging class of promising novel anticancer drugs.
Length = 217
Score = 31.6 bits (72), Expect = 0.44
Identities = 29/149 (19%), Positives = 48/149 (32%), Gaps = 28/149 (18%)
Query: 105 HHAIPKGPMGFCVFGNVAIA---ARYAQRAHGLKRVFIIDFDVHHGNGTNDAFYD----- 156
+ G + + G+ +IA R H + +ID D HH T +AF
Sbjct: 19 VAVLKDGKVPVVLGGDHSIANGAIRAVAELHP--DLGVIDVDAHHDVRTPEAFGKGNHHT 76
Query: 157 ---------DPDIFFLSTHQDGSYPGTGKIDEVGRGDGEGSTLNLPLPGGSGDTAMRTVF 207
D+ +S G G + G + + + + VF
Sbjct: 77 PRHLLCEPLISDVHIVSIGIRGVSNG----EAGGAYARKLGVVYFSMTEVD-KLGLGDVF 131
Query: 208 HEVIVPCAQRFKPDLILVSAGYDAHVLDP 236
E++ K D + +S D LDP
Sbjct: 132 EEIVSYL--GDKGDNVYLSVDVD--GLDP 156
>gnl|CDD|225649 COG3107, LppC, Putative lipoprotein [General function prediction
only].
Length = 604
Score = 29.8 bits (67), Expect = 2.4
Identities = 30/154 (19%), Positives = 44/154 (28%), Gaps = 29/154 (18%)
Query: 9 GSEIIELKNFSPASVDDIA---------SVHARAYVSGLEKAMDRASQQ----GIILIEG 55
+ + LKNFS AS IA +V AR G A + + Q + I
Sbjct: 243 PTALTNLKNFSQASPSKIALLLPLTGQAAVFARTIQDGFLAAKNAPATQTAQVAELKIYD 302
Query: 56 SGPTYATATTFQESLAAAGAGIA---LVDSVVAASKNRPDPPLG-FALIRPPGHHAIPKG 111
+ GA L+ V A P+ AL +P
Sbjct: 303 TSA--QPLDAILAQAQQDGADFVVGPLLKPNVEALLASNQQPIPVLALNQPENSRNPA-- 358
Query: 112 PMGFCVFG-----NVAIAARYAQRAHGLKRVFII 140
C F AA + G + ++
Sbjct: 359 --QLCYFALSPEDEARDAANHL-WDQGKRNPLVL 389
>gnl|CDD|200502 cd11241, Sema_5, The Sema domain, a protein interacting module, of
semaphorin 5 (Sema5). Class 5 semaphorins are
transmembrane glycoproteins characterized by unique
thrombospondin specific repeats in the extracellular
region of the protein. There are three subfamilies in
class 5 semaphorins, namely 5A, 5B and 5C. Sema5A and
Sema5B function as guidance cues for optic and
corticofugal nerve development, respectively.
Sema5A-induced cell migration requires Met signaling.
Sema5C is an early development gene and may play a role
in odor-guided behavior. Sema5A is also implicated in
cancer. In a screening model for metastasis, the
Drosophila Sema5A ortholog, Dsema-5C, has been found to
be required in tumorigenicity and metastasis. Sema5A is
highly expressed in human pancreatic cancer cells and is
associated with tumor growth, invasion and metastasis.
Semaphorins are regulatory molecules involved in the
development of the nervous system and in axonal
guidance. They also play important roles in other
biological processes, such as angiogenesis, immune
regulation, respiration systems and cancer. The Sema
domain is located at the N-terminus and contains four
disulfide bonds formed by eight conserved cysteine
residues. It serves as a receptor-recognition and
-binding module.
Length = 438
Score = 29.4 bits (66), Expect = 2.9
Identities = 15/63 (23%), Positives = 22/63 (34%), Gaps = 5/63 (7%)
Query: 48 QGIILIEGSGPTYATATTFQESLAAAGAGIALVDSVVAASKNRP----DPPLGFALIRPP 103
QG + + YA TT +A + A A S + + N P + L P
Sbjct: 244 QGTFYLPETDLIYAVFTTNVNGIAGS-AICAFNLSAINQAFNGPFKYQENNGSAWLPTPN 302
Query: 104 GHH 106
H
Sbjct: 303 PHP 305
>gnl|CDD|222296 pfam13660, DUF4147, Domain of unknown function (DUF4147). This
domain is frequently found at the N-terminus of proteins
carrying the glycerate kinase-like domain MOFRL,
pfam05161.
Length = 227
Score = 28.6 bits (65), Expect = 3.4
Identities = 14/33 (42%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 55 GSGPTYATATTFQESLA-AAGAGIALVDSVVAA 86
SGPT TTF ++LA G+ L +SV A
Sbjct: 194 ASGPTVPDPTTFADALAILERYGLELPESVRAH 226
>gnl|CDD|223755 COG0683, LivK, ABC-type branched-chain amino acid transport
systems, periplasmic component [Amino acid transport and
metabolism].
Length = 366
Score = 28.9 bits (65), Expect = 3.7
Identities = 28/120 (23%), Positives = 37/120 (30%), Gaps = 19/120 (15%)
Query: 37 GLEKAMDRASQQGIILIEGSGPTYATATTFQESLAAAGAGIALV--DSVVAASKNRPDPP 94
A +Q G+ + G + S A AG+ L+ + R P
Sbjct: 66 AAAVARKLITQDGVDAVVG---PTTSGVALAASPVAEEAGVPLISPSATAPQLTGRGLKP 122
Query: 95 LGFALIRPPGHHAIPKGPMGFCVFGNVAIAARYAQRAHGLKRVFIIDFDVHHGNGTNDAF 154
F A AA Y + G KRV II D +G G DAF
Sbjct: 123 NVFRTGPTDNQQAAA--------------AADYLVKKGGKKRVAIIGDDYAYGEGLADAF 168
>gnl|CDD|217576 pfam03466, LysR_substrate, LysR substrate binding domain. The
structure of this domain is known and is similar to the
periplasmic binding proteins.
Length = 207
Score = 28.0 bits (63), Expect = 4.7
Identities = 15/53 (28%), Positives = 18/53 (33%), Gaps = 11/53 (20%)
Query: 69 SLAAAGAGIALV-DSVVAASKNR----------PDPPLGFALIRPPGHHAIPK 110
+ AAG GIAL+ S VA P P L+ G P
Sbjct: 142 AAVAAGLGIALLPRSAVARELADGRLVVLPLPDPPLPRPIYLVYRKGRRLSPA 194
>gnl|CDD|131814 TIGR02767, TraG-Ti, Ti-type conjugative transfer system protein
TraG. This protein is found in the Agrobacterium
tumefaciens Ti plasmid tra region responsible for
conjugative transfer of the entire plasmid among
Agrobacterium strains. The protein is distantly related
to the F-type conjugation system TraG protein. Both of
these systems are examples of type IV secretion systems.
Length = 623
Score = 28.7 bits (64), Expect = 5.8
Identities = 10/43 (23%), Positives = 18/43 (41%)
Query: 52 LIEGSGPTYATATTFQESLAAAGAGIALVDSVVAASKNRPDPP 94
+ S PT+ +A F + + GA I + + A + P
Sbjct: 95 YVASSVPTWQSALAFADPVTVIGASIGFISGMFALRISSTTAP 137
>gnl|CDD|176146 cd08457, PBP2_OccR, The C-terminal substrate-domain of LysR-type
transcriptional regulator, OccR, involved in the
catabolism of octopine, contains the type 2 periplasmic
binding fold. This CD includes the C-terminal
substrate-domain of LysR-type transcriptional regulator
OccR, which is involved in the catabolism of octopine.
Opines are low molecular weight compounds found in plant
crown gall tumors produced by the parasitic bacterium
Agrobacterium. There are at least 30 different opines
identified so far. Opines are utilized by
tumor-colonizing bacteria as a source of carbon,
nitrogen, and energy. In Agrobacterium tumefaciens,
OccR protein activates the occQ operon of the Ti plasmid
in response to octopine. This operon encodes proteins
required for the uptake and catabolism of octopine, an
arginine derivative. The occ operon also encodes the
TraR protein, which is a quorum-sensing transcriptional
regulator of the Ti plasmid tra regulon. This
substrate-binding domain shows significant homology to
the type 2 periplasmic binding proteins (PBP2), which
are responsible for the uptake of a variety of
substrates such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis.
Length = 196
Score = 27.8 bits (62), Expect = 6.2
Identities = 18/75 (24%), Positives = 27/75 (36%), Gaps = 15/75 (20%)
Query: 39 EKAMDRASQQGIILIEGSGPTYATATTFQESLAAAGAGIALVDSVVAASKN------RP- 91
E A+ + + +IE + T SL G GIA++D A RP
Sbjct: 114 EVALGKIGVKRRPIIE----VNLSHTAL--SLVREGLGIAIIDPATAIGLPLDGIVIRPF 167
Query: 92 --DPPLGFALIRPPG 104
GF ++R
Sbjct: 168 DTFIDAGFLVVRAAN 182
>gnl|CDD|218394 pfam05035, DGOK, 2-keto-3-deoxy-galactonokinase.
2-keto-3-deoxy-galactonokinase EC:2.7.1.58 catalyzes the
second step in D-galactonate degradation.
Length = 287
Score = 27.9 bits (63), Expect = 6.9
Identities = 24/66 (36%), Positives = 32/66 (48%), Gaps = 11/66 (16%)
Query: 24 DDIASVHARAYVSGL----EKA---MDRASQQGIILIEGSGPTYATATTFQESLAAAGAG 76
+A+ ARAY+SGL E A Q + LI GSG A A + +L AAG
Sbjct: 213 GGLAAAAARAYLSGLLIGAEVAAARPYFWLGQPVTLI-GSG---ALAALYATALEAAGVT 268
Query: 77 IALVDS 82
+ VD+
Sbjct: 269 VRAVDA 274
>gnl|CDD|238577 cd01172, RfaE_like, RfaE encodes a bifunctional ADP-heptose
synthase involved in the biosynthesis of the
lipopolysaccharide (LPS) core precursor
ADP-L-glycero-D-manno-heptose. LPS plays an important
role in maintaining the structural integrity of the
bacterial outer membrane of gram-negative bacteria. RfaE
consists of two domains, a sugar kinase domain,
represented here, and a domain belonging to the
cytidylyltransferase superfamily.
Length = 304
Score = 27.9 bits (63), Expect = 7.2
Identities = 11/41 (26%), Positives = 17/41 (41%), Gaps = 4/41 (9%)
Query: 46 SQQGIILIEGSGPTYATATTFQESLAAAGAGIALVDSVVAA 86
++G+ L E G +E GAG D+V+A
Sbjct: 227 GEEGMTLFERDGEVQHIPALAKEVYDVTGAG----DTVIAT 263
>gnl|CDD|238563 cd01143, YvrC, Periplasmic binding protein YvrC. These proteins
are predicted to function as initial receptors in ABC
transport of metal ions in eubacteria and archaea. They
belong to the TroA superfamily of periplasmic metal
binding proteins that share a distinct fold and ligand
binding mechanism. A typical TroA protein is comprised
of two globular subdomains connected by a single helix
and can bind the metal ion in the cleft between these
domains.
Length = 195
Score = 27.6 bits (62), Expect = 7.8
Identities = 9/19 (47%), Positives = 14/19 (73%)
Query: 219 KPDLILVSAGYDAHVLDPL 237
KPDL++VS+ A +L+ L
Sbjct: 60 KPDLVIVSSSSLAELLEKL 78
>gnl|CDD|213980 TIGR04367, HpnR_B12_rSAM, hopanoid C-3 methylase HpnR. Members of
this are family are a B12-binding domain/radical SAM
domain protein required for 3-methylhopanoid production.
Activity was confirmed by mutant phenotype by disrupting
this gene in Methylococcus capsulatus strain Bath. This
protein family should only occur in genomes that encode
a squalene-hopene cyclase (see TIGR01507) [Fatty acid
and phospholipid metabolism, Biosynthesis].
Length = 490
Score = 27.8 bits (62), Expect = 8.4
Identities = 31/85 (36%), Positives = 34/85 (40%), Gaps = 13/85 (15%)
Query: 173 GTGKIDEVGRGDGEGST---LNLPLPGGSGDTAMRTVFHEVIVPCAQRFKPDLILVSAGY 229
G ID V RG+GE S L GG T V E P RF P L
Sbjct: 111 AEGAIDCVLRGEGEASAPLLLEAVADGGDLLTVPGVVTLEGEGP-PPRFLPSLDEPRPAR 169
Query: 230 D--AH-------VLDPLASLQFTTG 245
D H VLDP AS++FT G
Sbjct: 170 DLLRHRRKYFIGVLDPCASIEFTRG 194
>gnl|CDD|216224 pfam00975, Thioesterase, Thioesterase domain. Peptide synthetases
are involved in the non-ribosomal synthesis of peptide
antibiotics. Next to the operons encoding these enzymes,
in almost all cases, are genes that encode proteins that
have similarity to the type II fatty acid thioesterases
of vertebrates. There are also modules within the
peptide synthetases that also share this similarity.
With respect to antibiotic production, thioesterases are
required for the addition of the last amino acid to the
peptide antibiotic, thereby forming a cyclic antibiotic.
Thioesterases (non-integrated) have molecular masses of
25-29 kDa.
Length = 224
Score = 27.3 bits (61), Expect = 9.8
Identities = 20/87 (22%), Positives = 33/87 (37%), Gaps = 18/87 (20%)
Query: 69 SLAAAGAGIALVDSVVAASKNRPDPPLG---------FALIRPPGHHAIPKGP---MGFC 116
+LA G A ++V + R +PPL +R P+GP G
Sbjct: 18 NLARRLPGTAEFNAVQLPGRERGEPPLTSIEELAEEYAEALRR----IQPEGPYALFGHS 73
Query: 117 VFGNVA--IAARYAQRAHGLKRVFIID 141
+ G +A +A R +R + + D
Sbjct: 74 MGGLLAFEVARRLERRGEEPAGLILSD 100
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 0.137 0.404
Gapped
Lambda K H
0.267 0.0867 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,268,413
Number of extensions: 1725299
Number of successful extensions: 1887
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1798
Number of HSP's successfully gapped: 64
Length of query: 327
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 230
Effective length of database: 6,635,264
Effective search space: 1526110720
Effective search space used: 1526110720
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 59 (26.3 bits)