RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8529
(436 letters)
>gnl|CDD|212519 cd09993, HDAC_classIV, Histone deacetylase class IV also known as
histone deacetylase 11. Class IV histone deacetylases
(HDAC11; EC 3.5.1.98) are predicted Zn-dependent
enzymes. This class includes animal HDAC11, plant HDA2
and related bacterial deacetylases. Enzymes in this
subfamily participate in regulation of a number of
different processes through protein modification
(deacetylation). They catalyze hydrolysis of
N(6)-acetyl-lysine of histones (or other proteins) to
yield a deacetylated proteins. Histone deacetylases
often act as members of large multi-protein complexes
such as mSin3A or SMRT/N-CoR. Human HDAC11 does not
associate with them but can interact with HDAC6 in vivo.
It has been suggested that HDAC11 and HDAC6 may use
non-histone proteins as their substrates and play a role
other than to directly modulate chromatin structure. In
normal tissues, expression of HDAC11 is limited to
kidney, heart, brain, skeletal muscle and testis,
suggesting that its function might be tissue-specific.
In mammals, HDAC11 proteins are known to be involved in
progression of various tumors. HDAC11 plays an essential
role in regulating OX40 ligand (OX40L) expression in
Hodgkin lymphoma (HL); selective inhibition of HDAC11
expression significantly up-regulates OX40L and induces
apoptosis in HL cell lines. Thus, inhibition of HDAC11
could be a therapeutic drug option for antitumor immune
response in HL patients.
Length = 275
Score = 325 bits (836), Expect = e-110
Identities = 98/291 (33%), Positives = 142/291 (48%), Gaps = 21/291 (7%)
Query: 130 HPFDSKKWKHIFNYLWKHIFNYLVEAKFITQDNIIEPQEVSEEQLLIAHTEKYLKSLKWS 189
H F +K+ + L +E + ++I+EP+ + E LL H +YL+SLK
Sbjct: 1 HRFPMRKYGLLREAL--------LEEGLVLPEDIVEPEPATREDLLRVHDPEYLESLKSG 52
Query: 190 FNVAAISEVCPLVAVPNYFVQKCYLRPMRYHVGGTLEAGFLALRRGWSINIGGGFHHASE 249
E + P + R VGGT+ A LAL G +IN+ GG HHA
Sbjct: 53 ---ELSREEIRRIGFPWS---PELVERTRLAVGGTILAARLALEHGLAINLAGGTHHAFP 106
Query: 250 TKGGGFCAYADISLLVKLLFQSKSISTAMIVDLDAHQGNGYEKDFMNETRIFIMETCITS 309
+G GFC + DI++ ++L + +IVDLD HQGNG F ++ +F +
Sbjct: 107 DRGEGFCVFNDIAIAARVLLAEGLVRRVLIVDLDVHQGNGTAAIFADDPSVFTFS--MHG 164
Query: 310 KA-----KEAIRCRIELAPYTEDQHYLEKIEAGLERSLRSFCPDIIVYNAGTDVLLNDPL 364
+ KE + L T D YL +E L R L F PD++ YNAG DVL D L
Sbjct: 165 EKNYPFRKEPSDLDVPLPDGTGDDEYLAALEEALPRLLAEFRPDLVFYNAGVDVLAGDRL 224
Query: 365 GLLAISPQGIIRRDELVFMKARERRVPIVMLTSGGYLKQTARIIADSILNL 415
G L++S +G+ RD LV AR R +P+ M+ GGY + AR++A L
Sbjct: 225 GRLSLSLEGLRERDRLVLRFARARGIPVAMVLGGGYSRDIARLVARHAQTL 275
Score = 105 bits (265), Expect = 8e-26
Identities = 28/64 (43%), Positives = 39/64 (60%)
Query: 4 GTLEAGFLALRRGWSINIGGGFHHASETKGGGFCAYADISLLVKLLFQSKSISTAMIVDL 63
GT+ A LAL G +IN+ GG HHA +G GFC + DI++ ++L + +IVDL
Sbjct: 80 GTILAARLALEHGLAINLAGGTHHAFPDRGEGFCVFNDIAIAARVLLAEGLVRRVLIVDL 139
Query: 64 DAHQ 67
D HQ
Sbjct: 140 DVHQ 143
>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 = 208 bits (530), Expect = 2e-64
Identities = 91/282 (32%), Positives = 143/282 (50%), Gaps = 15/282 (5%)
Query: 145 WKHIFNYLVEAKFITQDNIIEPQEVSEEQLLIAHTEKYLKSLKWSFNVAAISEVCPLVAV 204
+ + L E + +IE +E +EE LL HTE+YL LK +F VA I+E P++
Sbjct: 2 IRDLIEALKELGLRPKIELIECREATEELLLKVHTEEYLNELKANFAVATITESKPVIFG 61
Query: 205 PNYFVQKCYLRPMRYHVGGTLEAGFLA----LRRGWSINIGGGFHHASETKGGGFCAYAD 260
PN+ VQ+ Y R R GG +EA L L R +++ +G G HHA +++ GFC + D
Sbjct: 62 PNFPVQRHYFRGARLSTGGVVEAAELVAKGELERAFAV-VGAGGHHAGKSRAWGFCYFND 120
Query: 261 ISLLVKLLFQSKSISTAMIVDLDAHQGNGYEKDFMNETRIFIMETC------ITSKAKEA 314
+ L +K L + + IS +I+D DAH G+G + F ++ R+ M +
Sbjct: 121 VVLAIKFLRE-RGISRILIIDTDAHHGDGTREAFYDDDRVLHMSFHNYDIYPFGRGKGKG 179
Query: 315 IRCRIELAPYTEDQHYLEKIEAGLERSLRSFCPDIIVYNAGTDVLLNDPLGLLAISPQGI 374
+ + L D+ YL+ +E + + L F P+++V G D D LG +S +G
Sbjct: 180 YKINVPLEDGLGDEEYLDAVERVISKVLEEFEPEVVVLQFGHDTHEGDRLGGFNLSEKGF 239
Query: 375 IRRDELVFMKARERRVPIVMLTSGGY-LKQTARIIADSILNL 415
++ E+V A R PI+M+ GGY + ARI I L
Sbjct: 240 VKLAEIVKEFA--RGGPILMVLGGGYNPEAAARIWTAIIKEL 279
Score = 69.4 bits (170), Expect = 3e-13
Identities = 25/68 (36%), Positives = 40/68 (58%), Gaps = 6/68 (8%)
Query: 4 GTLEAGFLA----LRRGWSINIGGGFHHASETKGGGFCAYADISLLVKLLFQSKSISTAM 59
G +EA L L R +++ +G G HHA +++ GFC + D+ L +K L + + IS +
Sbjct: 80 GVVEAAELVAKGELERAFAV-VGAGGHHAGKSRAWGFCYFNDVVLAIKFLRE-RGISRIL 137
Query: 60 IVDLDAHQ 67
I+D DAH
Sbjct: 138 IIDTDAHH 145
>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 = 184 bits (469), Expect = 5e-55
Identities = 80/309 (25%), Positives = 129/309 (41%), Gaps = 28/309 (9%)
Query: 122 HFFKLEKLHPFDSKKWKHIFNYLWKHIFNYLVEAKFITQDNIIEPQEVSEEQLLIAHTEK 181
H HP + ++ + I L E+ + + I P+ +EE+LL+ H+ +
Sbjct: 1 HDTGSGLGHPENPERLEAILELL--------KESGLLDRLEFIAPRPATEEELLLVHSPE 52
Query: 182 YLKSLKWSFNVAAISEVCPLVAVPNYFVQKCYLRPMRYHVGGTLEAGFLALRR---GWSI 238
Y++ L+ + L + V GGTLEA L L ++
Sbjct: 53 YVEFLEEASLEEEELGRIGLD--GDTPVSPGSYEAALLAAGGTLEAADLVLSGENAFAAV 110
Query: 239 NIGGGFHHASETKGGGFCAYADISLLVKLLFQSKSISTAMIVDLDAHQGNGYEKDFMNET 298
G HHA + GFC + ++++ + L + + +IVDLD H GNG ++ F ++
Sbjct: 111 RPPG--HHAERDRASGFCLFNNVAIAARYLLKRYGLKRVLIVDLDVHHGNGTQEIFYDDP 168
Query: 299 RIFIM-------------ETCITSKAKEAIRCRIELAPYTEDQHYLEKIEAGLERSLRSF 345
R+ + A E I L P T D+ YL E L +LR F
Sbjct: 169 RVLTISIHQDPFYPGTGFADETGEGAGEGYTLNIPLPPGTGDEEYLAAFEEILLPALREF 228
Query: 346 CPDIIVYNAGTDVLLNDPLGLLAISPQGIIRRDELVFMKARERRVPIVMLTSGGYLKQTA 405
PD+I+ +AG D DPLG L ++ +G R L+ A P+V + GGY
Sbjct: 229 QPDLILVSAGFDAHAGDPLGGLNLTTEGYAERTRLLLELADAYGGPVVSVLEGGYNLDAL 288
Query: 406 RIIADSILN 414
A ++L
Sbjct: 289 ARSAAAVLA 297
Score = 59.9 bits (146), Expect = 5e-10
Identities = 21/67 (31%), Positives = 33/67 (49%), Gaps = 5/67 (7%)
Query: 4 GTLEAGFLALRR---GWSINIGGGFHHASETKGGGFCAYADISLLVKLLFQSKSISTAMI 60
GTLEA L L ++ G HHA + GFC + ++++ + L + + +I
Sbjct: 92 GTLEAADLVLSGENAFAAVRPPG--HHAERDRASGFCLFNNVAIAARYLLKRYGLKRVLI 149
Query: 61 VDLDAHQ 67
VDLD H
Sbjct: 150 VDLDVHH 156
>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 = 121 bits (306), Expect = 4e-31
Identities = 63/254 (24%), Positives = 103/254 (40%), Gaps = 22/254 (8%)
Query: 163 IIEPQEVSEEQLLIAHTEKYLKSLKWSFNVAAISEVCPLVAVPNYFVQKCYLRPMRYHVG 222
++EP+ + E+LL+ H+ Y++ L+ + V + L G
Sbjct: 46 LVEPRPATLEELLLVHSPDYVEFLESLSEEEGYGNLDGDTPVSPGTYEAARLA-----AG 100
Query: 223 GTLEAGFLALR--RGWSINIGGGFHHASETKGGGFCAYADISLLVKLLFQSKSISTAMIV 280
G L A L + HHA + GFC + ++++ K L K + I+
Sbjct: 101 GALTAVDAVLEGEDNAFALVRPPGHHAGRDRASGFCLFNNVAIAAKYL-LKKGVKRVAII 159
Query: 281 DLDAHQGNGYEKDFMNETRIFIM--------------ETCITSKAKEAIRCRIELAPYTE 326
D D H GNG ++ F ++ + + + KE I L P T
Sbjct: 160 DFDVHHGNGTQEIFYDDDDVLTVSLHQDGRPFYPGTGGADEIGEGKEGNNVNIPLPPGTG 219
Query: 327 DQHYLEKIEAGLERSLRSFCPDIIVYNAGTDVLLNDPLGLLAISPQGIIRRDELVFMKAR 386
D YLE +E + L F PD+++ +AG D DPLG L ++ +G + V A
Sbjct: 220 DDSYLEALEEIVLPLLEEFKPDLVIVSAGFDAHRGDPLGRLNLTEEGYAKIGRAVRKLAE 279
Query: 387 ERRVPIVMLTSGGY 400
P+V + GGY
Sbjct: 280 GYGGPVVAVLEGGY 293
Score = 52.4 bits (126), Expect = 2e-07
Identities = 17/66 (25%), Positives = 26/66 (39%), Gaps = 3/66 (4%)
Query: 4 GTLEAGFLALR--RGWSINIGGGFHHASETKGGGFCAYADISLLVKLLFQSKSISTAMIV 61
G L A L + HHA + GFC + ++++ K L K + I+
Sbjct: 101 GALTAVDAVLEGEDNAFALVRPPGHHAGRDRASGFCLFNNVAIAAKYL-LKKGVKRVAII 159
Query: 62 DLDAHQ 67
D D H
Sbjct: 160 DFDVHH 165
>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 = 109 bits (274), Expect = 7e-27
Identities = 73/283 (25%), Positives = 109/283 (38%), Gaps = 45/283 (15%)
Query: 157 FITQDNIIEPQEVSEEQLLIAHTEKYLKSLKWSFNVAAISEVCPLVAVPNY--------- 207
+ +++ P+ +EE+LL+ HT Y++++K S
Sbjct: 36 LLPPVDLVPPRPATEEELLLFHTPDYIEAVK------EASRGQEPEGRGRLGLGTEDNPV 89
Query: 208 FVQKCYLRPMRYHVGGTLEA--GFLALRRGWSINIGGGFHHASETKGGGFCAYADISLLV 265
F + VGGTL A L + N GG HHA + GFC Y D ++ +
Sbjct: 90 FPG-MHEAA-ALVVGGTLLAARLVLEGEARRAFNPAGGLHHAMRGRASGFCVYNDAAVAI 147
Query: 266 KLLFQSKSISTAMIVDLDAHQGNGYEKDFMNETRIF---IMETCI-----TSKAKEAIRC 317
+ L + K VD+DAH G+G + F ++ R+ + E+ T E
Sbjct: 148 ERL-RDKGGLRVAYVDIDAHHGDGVQAAFYDDPRVLTISLHESGRYLFPGTGFVDEIGEG 206
Query: 318 R-------IELAPYTEDQHYLEKIEAGLERSLRSFCPDIIVYNAGTDVLLNDPLGLLAIS 370
I L P T D +L EA + LR+F PD+IV G D DPL L +S
Sbjct: 207 EGYGYAVNIPLPPGTGDDEFLRAFEAVVPPLLRAFRPDVIVSQHGADAHAGDPLTHLNLS 266
Query: 371 PQGIIRRDELVFMKARE--RRV---PIVMLTSGGY-LKQTARI 407
+ + RE + L GGY AR
Sbjct: 267 NRAYRA----AVRRIRELADEYCGGRWLALGGGGYNPDVVARA 305
Score = 51.8 bits (125), Expect = 3e-07
Identities = 18/47 (38%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 20 NIGGGFHHASETKGGGFCAYADISLLVKLLFQSKSISTAMIVDLDAH 66
N GG HHA + GFC Y D ++ ++ L + K VD+DAH
Sbjct: 121 NPAGGLHHAMRGRASGFCVYNDAAVAIERL-RDKGGLRVAYVDIDAH 166
>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 = 81.0 bits (201), Expect = 4e-17
Identities = 66/299 (22%), Positives = 110/299 (36%), Gaps = 44/299 (14%)
Query: 146 KHIFNYLVEAKFITQDNIIEPQEVSEEQLLIAHTEKYLKSLKWSFNVAAISEVCPLVAVP 205
I L E + + +EP+ +EE+LL HT +Y++ ++ +
Sbjct: 9 LAILEALEEEGLLDRLVFVEPRPATEEELLRVHTPEYIERVE-----ETCEAGGGYLDPD 63
Query: 206 NYFVQKCYLRPMRYHVGGTLEAGFLALRRGWSINIGGGF-------HHASETKGGGFCAY 258
Y Y G L A L F HHA + GFC +
Sbjct: 64 TYVSPGSY-EAALLAAGAALAAVDAVLSGEAE----NAFALVRPPGHHAEPDRAMGFCLF 118
Query: 259 ADISLLVKLLFQSKSISTAMIVDLDAHQGNGYEKDFMNETRIFIMETCI----------T 308
++++ + + + +IVD D H GNG + F ++ + T
Sbjct: 119 NNVAIAARYAQKRYGLKRVLIVDWDVHHGNGTQDIFYDDPSVL----YFSIHQYPFYPGT 174
Query: 309 SKAKEAIR-------CRIELAPYTEDQHYLEKIEAGLERSLRSFCPDIIVYNAGTDVLLN 361
A+E + L P + D YL E L R F PD+++ +AG D
Sbjct: 175 GAAEETGGGAGEGFTINVPLPPGSGDAEYLAAFEEVLLPIAREFQPDLVLVSAGFDAHRG 234
Query: 362 DPLGLLAISPQG---IIRRDELVFMKARERRVPIVMLTSGGY-LKQTARIIADSILNLA 416
DPLG + ++P+G + R L + +V + GGY L+ A + + L
Sbjct: 235 DPLGGMNLTPEGYARLTRL--LKELADEHCGGRLVFVLEGGYNLEALAESVLAVLEALL 291
Score = 30.2 bits (69), Expect = 2.0
Identities = 11/41 (26%), Positives = 21/41 (51%)
Query: 26 HHASETKGGGFCAYADISLLVKLLFQSKSISTAMIVDLDAH 66
HHA + GFC + ++++ + + + +IVD D H
Sbjct: 105 HHAEPDRAMGFCLFNNVAIAARYAQKRYGLKRVLIVDWDVH 145
>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 = 72.8 bits (178), Expect = 5e-14
Identities = 79/336 (23%), Positives = 136/336 (40%), Gaps = 59/336 (17%)
Query: 130 HPFDSKKWKHIFNYLWKHIFNYLVEAKFITQDNIIEPQEVSEEQLLIAHTEKYLKSLK-- 187
HP + + N L NY + K I P + + E++ H+++Y+K L+
Sbjct: 21 HPMKPHRIRMTHNLL----LNYGLYRKM----EIYRPHKATAEEMTKYHSDEYIKFLRSI 72
Query: 188 ------------WSFNVAAISEVCPLVAVPNYFVQKCYLRPMRYHVGGTLEAGFLALRR- 234
FNV E CP V + + C L GG++ AG + L R
Sbjct: 73 RPDNMSEYSKQMQRFNVG---EDCP---VFDGLFEFCQLS-----TGGSV-AGAVKLNRQ 120
Query: 235 --GWSINIGGGFHHASETKGGGFCAYADISLLVKLLFQSKSISTAMIVDLDAHQGNGYEK 292
++N GG HHA +++ GFC DI L + L K + +D+D H G+G E+
Sbjct: 121 QTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELL--KYHQRVLYIDIDIHHGDGVEE 178
Query: 293 DFMNETRIFIMETC--------------ITSKAKEAIRCRIELAPYTEDQHYLEKIEAGL 338
F R+ + I + + + +D+ Y + + +
Sbjct: 179 AFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPII 238
Query: 339 ERSLRSFCPDIIVYNAGTDVLLNDPLGLLAISPQGIIRRDELVFMKARERRVPIVMLTSG 398
+ + + P +V G D L D LG ++ +G + E+V + +P++ML G
Sbjct: 239 SKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVV----KTFNLPLLMLGGG 294
Query: 399 GY-LKQTARIIADSILNLADLGLISR-PYNIWFIYY 432
GY ++ AR D + + PYN +F Y+
Sbjct: 295 GYTIRNVARCWTYETAVALDCEIPNELPYNDYFEYF 330
Score = 36.6 bits (84), Expect = 0.024
Identities = 21/63 (33%), Positives = 31/63 (49%), Gaps = 5/63 (7%)
Query: 8 AGFLALRR---GWSINIGGGFHHASETKGGGFCAYADISLLVKLLFQSKSISTAMIVDLD 64
AG + L R ++N GG HHA +++ GFC DI L + L K + +D+D
Sbjct: 112 AGAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELL--KYHQRVLYIDID 169
Query: 65 AHQ 67
H
Sbjct: 170 IHH 172
>gnl|CDD|240374 PTZ00346, PTZ00346, histone deacetylase; Provisional.
Length = 429
Score = 70.4 bits (172), Expect = 3e-13
Identities = 81/280 (28%), Positives = 123/280 (43%), Gaps = 54/280 (19%)
Query: 164 IEPQEVSEEQLLIAHTEKYLKSL------KWSFNVAAISEV-----CPLVAVPNYFVQKC 212
+ P V E+L+ HT+ YL +L W +N A S+V CP V +
Sbjct: 69 VVPPLVKVEELMAYHTDTYLANLGLHSCRSWLWN-AETSKVFFSGDCPPV--------EG 119
Query: 213 YLRPMRYHVGGTLEAGFLALRRGW---SINIGGGFHHASETKGGGFCAYADISL-LVKLL 268
+ GTL G + L G +++ GGG HH+ + GFC DI L +++LL
Sbjct: 120 LMEHSIATASGTL-MGAVLLNSGQVDVAVHWGGGMHHSKCGECSGFCYVNDIVLGILELL 178
Query: 269 FQSKSISTAMIVDLDAHQGNGYEKDFMNETRIFIMETCITSKAKEAI------------- 315
K + VD+D H G+G ++ F R+F + K E+
Sbjct: 179 ---KCHDRVLYVDIDMHHGDGVDEAFCTSDRVFTLS---LHKFGESFFPGTGHPRDVGYG 232
Query: 316 RCR---IELAPY--TEDQHYLEKIEAGLERSLRSFCPDIIVYNAGTDVLLNDPLGLLAIS 370
R R + LA + D +YL E L +R + PD IV G D L D LGLL +S
Sbjct: 233 RGRYYSMNLAVWDGITDFYYLGLFEHALHSIVRRYSPDAIVLQCGADSLAGDRLGLLNLS 292
Query: 371 PQGIIRRDELVFMKARERRVPIVMLTSGGY-LKQTARIIA 409
G + + V R+ +P++ L GGY ++ A++ A
Sbjct: 293 SFGHGQCVQAV----RDLGIPMLALGGGGYTIRNVAKLWA 328
Score = 31.5 bits (71), Expect = 0.93
Identities = 18/51 (35%), Positives = 28/51 (54%), Gaps = 4/51 (7%)
Query: 18 SINIGGGFHHASETKGGGFCAYADISL-LVKLLFQSKSISTAMIVDLDAHQ 67
+++ GGG HH+ + GFC DI L +++LL K + VD+D H
Sbjct: 146 AVHWGGGMHHSKCGECSGFCYVNDIVLGILELL---KCHDRVLYVDIDMHH 193
>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 = 66.2 bits (161), Expect = 6e-12
Identities = 79/338 (23%), Positives = 131/338 (38%), Gaps = 63/338 (18%)
Query: 130 HPFDSKKWKHIFNYLWKHIFNYLVEAKFITQDNIIEPQEVSEEQLLIAHTEKYLKSLK-- 187
HP + + N L NY + K I P + + E++ H++ Y+K L+
Sbjct: 25 HPMKPHRIRMTHNLL----LNYGLYRKM----EIYRPHKANAEEMTKYHSDDYIKFLRSI 76
Query: 188 ------------WSFNVAAISEVCPLVAVPNYFVQKCYLRPMRYHVGGTLEAGFLALRR- 234
FNV E CP V + + C L GG++ + ++
Sbjct: 77 RPDNMSEYSKQMQRFNVG---EDCP---VFDGLFEFCQLS-----AGGSVASAVKLNKQQ 125
Query: 235 -GWSINIGGGFHHASETKGGGFCAYADISLLVKLLFQSKSISTAMIVDLDAHQGNGYEKD 293
++N GG HHA +++ GFC DI L + L K + +D+D H G+G E+
Sbjct: 126 TDIAVNWAGGLHHAKKSEASGFCYVNDIVLAILELL--KYHQRVLYIDIDIHHGDGVEEA 183
Query: 294 FMNETRIFIME--------------TCITSKAKEAIRCRIELAPYTEDQHYLEKIEAGLE 339
F R+ + I + + L +D+ Y + +
Sbjct: 184 FYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNYPLRDGIDDESYEAIFKPVMS 243
Query: 340 RSLRSFCPDIIVYNAGTDVLLNDPLGLLAISPQGIIRRDELVFMKARERRVPIVMLTSGG 399
+ + F P +V G D L D LG ++ +G + E V + +P++ML GG
Sbjct: 244 KVMEMFQPSAVVLQCGADSLSGDRLGCFNLTIKGHAKCVEFV----KSFNLPMLMLGGGG 299
Query: 400 YLKQTARIIADSILNLADLGLISR-----PYNIWFIYY 432
Y T R +A + L S PYN +F Y+
Sbjct: 300 Y---TIRNVARCWTYETAVALDSEIPNELPYNDYFEYF 334
Score = 36.6 bits (84), Expect = 0.024
Identities = 17/50 (34%), Positives = 26/50 (52%), Gaps = 2/50 (4%)
Query: 18 SINIGGGFHHASETKGGGFCAYADISLLVKLLFQSKSISTAMIVDLDAHQ 67
++N GG HHA +++ GFC DI L + L K + +D+D H
Sbjct: 129 AVNWAGGLHHAKKSEASGFCYVNDIVLAILELL--KYHQRVLYIDIDIHH 176
>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 = 66.2 bits (162), Expect = 7e-12
Identities = 71/281 (25%), Positives = 118/281 (41%), Gaps = 56/281 (19%)
Query: 162 NIIEPQEVSEEQLLIAHTEKYLKSLKWSFNVAAISEV---------------CPLVAVPN 206
+++P+ +EE+L H+++Y++ LK + + CP+
Sbjct: 40 RVVKPRVATEEELASFHSDEYIQFLK---KASNEGDNDEEPSEQQEFGLGYDCPIFEGIY 96
Query: 207 YFVQKCYLRPMRYHVGGTLEAGFLALRRGW---SINIGGGFHHASETKGGGFCAYADISL 263
+ G TL A L L G +IN GG+HHA + GFC DI L
Sbjct: 97 DYAAAV--------AGATLTAAQL-LIDGKCKVAINWFGGWHHAQRDEASGFCYVNDIVL 147
Query: 264 -LVKLLFQSKSISTAMIVDLDAHQGNGYEKDFMNETRI-----------FIMETCITSKA 311
++KL + + + VDLD H G+G E F +++ F T S
Sbjct: 148 GILKLREKFDRV---LYVDLDLHHGDGVEDAFSFTSKVMTVSLHKYSPGFFPGTGDVSDV 204
Query: 312 KEAIRCR-----IELAPYTEDQHYLEKIEAGLERSLRSFCPDIIVYNAGTDVLLNDPLGL 366
+ + + L +D+ YL+ A + + +F P+ +V G D L DP+G
Sbjct: 205 GLG-KGKYYTVNVPLRDGIQDEQYLQIFTAVVPEIVAAFRPEAVVLQCGADTLAGDPMGA 263
Query: 367 LAISPQGIIRRDELVFMKARERRVPIVMLTSGGY-LKQTAR 406
++P GI + + V ++P ++L GGY L TAR
Sbjct: 264 FNLTPVGIGKCLKYVL----GWKLPTLILGGGGYNLANTAR 300
Score = 39.2 bits (92), Expect = 0.003
Identities = 20/50 (40%), Positives = 28/50 (56%), Gaps = 4/50 (8%)
Query: 18 SINIGGGFHHASETKGGGFCAYADISL-LVKLLFQSKSISTAMIVDLDAH 66
+IN GG+HHA + GFC DI L ++KL + + + VDLD H
Sbjct: 121 AINWFGGWHHAQRDEASGFCYVNDIVLGILKLREKFDRV---LYVDLDLH 167
>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 = 65.4 bits (160), Expect = 7e-12
Identities = 64/258 (24%), Positives = 101/258 (39%), Gaps = 34/258 (13%)
Query: 160 QDNIIEPQEVSEEQLLIAHTEKYLKSLKWSFNVAAISEVCPLVAVPNYFVQKCYLRPMRY 219
D IIEP+ + + L H + Y+ L + + + CP+ + +VQ
Sbjct: 38 FDEIIEPERATRKDLTKYHDKDYVDFLLKKYG---LEDDCPVFPFLSMYVQ--------L 86
Query: 220 HVGGTLEAGFLALR---RGWSINIGGGFHHASETKGGGFCAYADISLLVKLLFQSKSIST 276
G +L + R +IN GG HHA +++ GFC DI L + L +
Sbjct: 87 VAGSSLALAKHLITQVERDIAINWYGGRHHAQKSRASGFCYVNDIVLAILRL-RRARFRR 145
Query: 277 AMIVDLDAHQGNGYEKDFMNETRIFIMETC-----------ITSKAKEAIR---CRIELA 322
+DLD H G+G E F + TC T K + I L
Sbjct: 146 VFYLDLDLHHGDGVESAFFFSKNVL---TCSIHRYDPGFFPGTGSLKNSSDKGMLNIPLK 202
Query: 323 PYTEDQHYLEKIEAGLERSLRSFCPDIIVYNAGTDVLLNDPLGLLAISPQGIIRRDELVF 382
D+ L I++ + + F P++IV G D L DP ++ +G EL+
Sbjct: 203 RGLSDKTLLRIIDSIVRPLIEKFEPEVIVIQCGCDGLSGDPHKEWNLTIRGYGSVIELL- 261
Query: 383 MKARERRVPIVMLTSGGY 400
+ P ++L GGY
Sbjct: 262 -LKEFKDKPTLLLGGGGY 278
Score = 41.5 bits (98), Expect = 4e-04
Identities = 18/49 (36%), Positives = 25/49 (51%), Gaps = 1/49 (2%)
Query: 18 SINIGGGFHHASETKGGGFCAYADISLLVKLLFQSKSISTAMIVDLDAH 66
+IN GG HHA +++ GFC DI L + L + +DLD H
Sbjct: 107 AINWYGGRHHAQKSRASGFCYVNDIVLAILRL-RRARFRRVFYLDLDLH 154
>gnl|CDD|240251 PTZ00063, PTZ00063, histone deacetylase; Provisional.
Length = 436
Score = 64.4 bits (157), Expect = 3e-11
Identities = 74/306 (24%), Positives = 123/306 (40%), Gaps = 53/306 (17%)
Query: 163 IIEPQEVSEEQLLIAHTEKYLKSLKW--------------SFNVAAISEVCPLVAVPNYF 208
I P + E +L++ H E+Y+ L FNV ++ CP+ F
Sbjct: 48 IYRPHKSVEPELVLFHDEEYVDFLSSISPENYRDFTYQLKRFNVGEATD-CPVFDGLFEF 106
Query: 209 VQKCYLRPMRYHVGGTLEAGFLALRRGWS---INIGGGFHHASETKGGGFCAYADISL-L 264
Q C G +++ + L + +N GG HHA ++ GFC DI L +
Sbjct: 107 QQSC--------AGASIDGAY-KLNNHQADICVNWSGGLHHAKRSEASGFCYINDIVLGI 157
Query: 265 VKLLFQSKSISTAMIVDLDAHQGNGYEKDFMNETRIFIME--------------TCITSK 310
++LL K + M +D+D H G+G E+ F R+ + T I
Sbjct: 158 LELL---KYHARVMYIDIDVHHGDGVEEAFYVTHRVMTVSFHKFGDFFPGTGDVTDIGVA 214
Query: 311 AKEAIRCRIELAPYTEDQHYLEKIEAGLERSLRSFCPDIIVYNAGTDVLLNDPLGLLAIS 370
+ + L +D +++ + + + + + P IV G D L D LG ++
Sbjct: 215 QGKYYSVNVPLNDGIDDDSFVDLFKPVISKCVEVYRPGAIVLQCGADSLTGDRLGRFNLT 274
Query: 371 PQGIIRRDELVFMKARERRVPIVMLTSGGY-LKQTARIIA---DSILNLADLGLISRPYN 426
+G E V R +P+++L GGY ++ AR A ILN D N
Sbjct: 275 IKGHAACVEFV----RSLNIPLLVLGGGGYTIRNVARCWAYETGVILNKHDEMSDQISLN 330
Query: 427 IWFIYY 432
++ YY
Sbjct: 331 DYYDYY 336
Score = 38.6 bits (90), Expect = 0.006
Identities = 19/50 (38%), Positives = 28/50 (56%), Gaps = 4/50 (8%)
Query: 18 SINIGGGFHHASETKGGGFCAYADISL-LVKLLFQSKSISTAMIVDLDAH 66
+N GG HHA ++ GFC DI L +++LL K + M +D+D H
Sbjct: 129 CVNWSGGLHHAKRSEASGFCYINDIVLGILELL---KYHARVMYIDIDVH 175
>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 = 63.3 bits (154), Expect = 6e-11
Identities = 65/235 (27%), Positives = 109/235 (46%), Gaps = 36/235 (15%)
Query: 222 GGTLEAGFLALRRG---WSINIGGGFHHASETKGGGFCAYADISL-LVKLLFQSKSISTA 277
GG++E G L RG ++N GG HHA +++ GFC DI L +++LL + +
Sbjct: 108 GGSME-GAARLNRGKCDIAVNWAGGLHHAKKSEASGFCYVNDIVLGILELLRYHQRV--- 163
Query: 278 MIVDLDAHQGNGYEKDFMNETRIFIMETCITSKAKE------AIR-----------CRIE 320
+ +D+D H G+G E+ F R+ TC K E +R +
Sbjct: 164 LYIDIDVHHGDGVEEAFYTTDRVM---TCSFHKYGEYFPGTGELRDIGIGTGKNYAVNVP 220
Query: 321 LAPYTEDQHYLEKIEAGLERSLRSFCPDIIVYNAGTDVLLNDPLGLLAISPQGIIRRDEL 380
L +D+ Y E ++ + + P+ +V G D L D LG +S +G + +
Sbjct: 221 LRDGIDDESYKSIFEPVIKHVMEWYQPEAVVLQCGGDSLSGDRLGCFNLSMKG--HANCV 278
Query: 381 VFMKARERRVPIVMLTSGGY-LKQTARIIA--DSILNLADLGLISRPYNIWFIYY 432
F+K+ +P+++L GGY ++ AR A +L +L PYN ++ YY
Sbjct: 279 NFVKSFN--LPMLVLGGGGYTMRNVARTWAFETGLLAGEELDK-DLPYNEYYEYY 330
Score = 36.7 bits (85), Expect = 0.022
Identities = 17/51 (33%), Positives = 30/51 (58%), Gaps = 4/51 (7%)
Query: 18 SINIGGGFHHASETKGGGFCAYADISL-LVKLLFQSKSISTAMIVDLDAHQ 67
++N GG HHA +++ GFC DI L +++LL + + + +D+D H
Sbjct: 125 AVNWAGGLHHAKKSEASGFCYVNDIVLGILELLRYHQRV---LYIDIDVHH 172
>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 = 62.2 bits (152), Expect = 9e-11
Identities = 69/274 (25%), Positives = 119/274 (43%), Gaps = 44/274 (16%)
Query: 162 NIIEPQEVSEEQLLIAHTEKYLKSLKWSFNVAAISEVCPLVAVPNYFVQK-CYLRPMRYH 220
I P+ + E+L H++ Y+ L+ +V+ + + + V + C + Y
Sbjct: 39 EIYRPRPATAEELTKFHSDDYIDFLR---SVSPDNMKEFKKQLERFNVGEDCPVFDGLYE 95
Query: 221 -----VGGTLEAGFLALRRGWS---INIGGGFHHASETKGGGFCAYADISL-LVKLLFQS 271
GG++ A + L RG + IN GG HHA +++ GFC DI L +++LL
Sbjct: 96 YCQLYAGGSIAAA-VKLNRGQADIAINWAGGLHHAKKSEASGFCYVNDIVLAILELL--- 151
Query: 272 KSISTAMIVDLDAHQGNGYEKDFMNETRIFIMETC----------ITSKAKEAIRCR--- 318
K + +D+D H G+G E+ F R+ T + ++ I
Sbjct: 152 KYHQRVLYIDIDIHHGDGVEEAFYTTDRVM---TVSFHKFGEYFFPGTGLRD-IGAGKGK 207
Query: 319 -----IELAPYTEDQHYLEKIEAGLERSLRSFCPDIIVYNAGTDVLLNDPLGLLAISPQG 373
+ L +D+ YL+ E L + + F P +V G D L D LG +S +G
Sbjct: 208 YYAVNVPLKDGIDDESYLQIFEPVLSKVMEVFQPSAVVLQCGADSLAGDRLGCFNLSIKG 267
Query: 374 IIRRDELVFMKARERRVPIVMLTSGGY-LKQTAR 406
+ + V + +P+++L GGY L+ AR
Sbjct: 268 HAKCVKFV----KSFNIPLLVLGGGGYTLRNVAR 297
Score = 40.3 bits (95), Expect = 0.001
Identities = 23/78 (29%), Positives = 35/78 (44%), Gaps = 25/78 (32%)
Query: 19 INIGGGFHHASETKGGGFCAYADISL-LVKLLFQSKSISTAMIVDLDA------------ 65
IN GG HHA +++ GFC DI L +++LL K + +D+D
Sbjct: 120 INWAGGLHHAKKSEASGFCYVNDIVLAILELL---KYHQRVLYIDIDIHHGDGVEEAFYT 176
Query: 66 ---------HQFSDYYFP 74
H+F +Y+FP
Sbjct: 177 TDRVMTVSFHKFGEYFFP 194
>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 = 59.8 bits (146), Expect = 6e-10
Identities = 58/246 (23%), Positives = 88/246 (35%), Gaps = 43/246 (17%)
Query: 147 HIFNYLVEAKFITQDNIIEPQEVSEEQLLIAHTEKYLKSLKWSFNVAAISEVCPLVAV-P 205
I + L+ + +E + EQLL H Y+ + A + LV + P
Sbjct: 10 AILDALIASGLDRLLRQLEAPPATREQLLRVHDAAYVDR------LEAAAPEEGLVQLDP 63
Query: 206 NYFVQKCYLRPMRYHVGGTLEA-----------GFLALRR-GWSINIGGGFHHASETKGG 253
+ + L G + A F A+R G HHA K
Sbjct: 64 DTAMSPGSLEAALRAAGAVVAAVDAVMAGEARNAFCAVRPPG---------HHAERDKAM 114
Query: 254 GFCAYADISLLVKLLFQSKSISTAMIVDLDAHQGNGYEKDFMNETRIFIMETCI------ 307
GFC + ++++ + IVD D H GNG E F ++ R+ C
Sbjct: 115 GFCLFNNVAIAAAHALAHHGLERVAIVDFDVHHGNGTEDIFRDDPRVLF---CSSHQHPL 171
Query: 308 ---TSKAKEAIRCRI---ELAPYTEDQHYLEKIEAGLERSLRSFCPDIIVYNAGTDVLLN 361
T E I L T + E +E +L +F PD+I+ +AG D +
Sbjct: 172 YPGTGAPDETGHGNIVNVPLPAGTGGAEFREAVEDRWLPALDAFKPDLILISAGFDAHRD 231
Query: 362 DPLGLL 367
DPL L
Sbjct: 232 DPLAQL 237
Score = 29.0 bits (66), Expect = 4.4
Identities = 12/42 (28%), Positives = 18/42 (42%)
Query: 26 HHASETKGGGFCAYADISLLVKLLFQSKSISTAMIVDLDAHQ 67
HHA K GFC + ++++ + IVD D H
Sbjct: 106 HHAERDKAMGFCLFNNVAIAAAHALAHHGLERVAIVDFDVHH 147
>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 = 59.4 bits (144), Expect = 7e-10
Identities = 67/285 (23%), Positives = 111/285 (38%), Gaps = 62/285 (21%)
Query: 162 NIIEPQEVSEEQLLIAHTEKYLKSLKW---------------SFNVAAISEVCPLVAVPN 206
+ E + + E+L H YL L FN I + CP+
Sbjct: 42 DTYEARAATREELRQFHDADYLDFLSKVSPENANQLRFDKAEPFN---IGDDCPVFDGMY 98
Query: 207 YFVQKCYLRPMRYHVGGTLEAGFLALRRGWS---INIGGGFHHASETKGGGFCAYADISL 263
+ Q + G +L+A L G S IN GG HHA +++ GFC DI L
Sbjct: 99 DYCQL--------YAGASLDAA-RKLCSGQSDIAINWSGGLHHAKKSEASGFCYVNDIVL 149
Query: 264 -LVKLLFQSKSISTAMIVDLDAHQGNGYEKDFMNETRIFIM-----------------ET 305
++ LL + + +D+D H G+G E+ F R+ + +
Sbjct: 150 AILNLL---RYFPRVLYIDIDVHHGDGVEEAFYRTDRVMTLSFHKYNGEFFPGTGDLDDN 206
Query: 306 CITSKAKEAIRCRIELAPYTEDQHYLEKIEAGLERSLRSFCPDIIVYNAGTDVLLNDPLG 365
T A+ +E +D+ Y ++ + ++ F P IV G D L D LG
Sbjct: 207 GGTPGKHFALNVPLEDG--IDDEQYNLLFKSIIGPTIEKFQPSAIVLQCGADSLGGDRLG 264
Query: 366 LLAISPQGIIRRDELV-FMKARERRVPIVMLTSGGYLKQTARIIA 409
++ + V F+K+ +P++++ GGY T R +A
Sbjct: 265 QFNLNIKA---HGACVKFVKS--FGIPMLVVGGGGY---TPRNVA 301
Score = 34.4 bits (79), Expect = 0.10
Identities = 18/50 (36%), Positives = 28/50 (56%), Gaps = 4/50 (8%)
Query: 18 SINIGGGFHHASETKGGGFCAYADISL-LVKLLFQSKSISTAMIVDLDAH 66
+IN GG HHA +++ GFC DI L ++ LL + + +D+D H
Sbjct: 123 AINWSGGLHHAKKSEASGFCYVNDIVLAILNLL---RYFPRVLYIDIDVH 169
>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 = 59.5 bits (145), Expect = 9e-10
Identities = 62/259 (23%), Positives = 101/259 (38%), Gaps = 32/259 (12%)
Query: 164 IEPQEVSEEQLLIAHTEKYLKSLKWSFNVAAISEVCPLVAVPNYFVQKCYLRPMRYHVGG 223
I P+ ++E+LL HT +Y+ +K A S A GG
Sbjct: 59 ITPRPATDEELLRVHTPEYIDRVK------AASAAGGGEAGGGTPFGPGSYEIALLAAGG 112
Query: 224 TLEAGFLAL----RRGWSINIGGGFHHASETKGGGFCAYADISLLVKLLFQSKSISTAMI 279
+ A L +++ G HHA +G GFC + ++++ + + +
Sbjct: 113 AIAAVDAVLDGEVDNAYALVRPPG-HHAEPDQGMGFCLFNNVAIAARHALAVGGVKRVAV 171
Query: 280 VDLDAHQGNGYEKDFMNETRI-FI---METC----------ITSKAKEAIRCRIELAPYT 325
VD D H GNG + F ++ + I + C A E I L P +
Sbjct: 172 VDWDVHHGNGTQAIFYDDPDVLTISLHQDRCFPPDSGAVEERGEGAGEGYNLNIPLPPGS 231
Query: 326 EDQHYLEKIEAGLERSLRSFCPDIIVYNAGTDVLLNDPLGLLAISPQGIIRRDELVFMKA 385
D YL E + +LR+F P++I+ +G D DPLG + ++ G R
Sbjct: 232 GDGAYLHAFERIVLPALRAFRPELIIVASGFDASAFDPLGRMMLTSDG-FRALTRKLRDL 290
Query: 386 RER----RVPIVMLTSGGY 400
+ R +VM+ GGY
Sbjct: 291 ADELCGGR--LVMVHEGGY 307
Score = 39.1 bits (92), Expect = 0.003
Identities = 11/41 (26%), Positives = 20/41 (48%)
Query: 26 HHASETKGGGFCAYADISLLVKLLFQSKSISTAMIVDLDAH 66
HHA +G GFC + ++++ + + +VD D H
Sbjct: 137 HHAEPDQGMGFCLFNNVAIAARHALAVGGVKRVAVVDWDVH 177
>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 = 59.2 bits (144), Expect = 1e-09
Identities = 37/165 (22%), Positives = 70/165 (42%), Gaps = 21/165 (12%)
Query: 148 IFNYLVEAKFITQDNIIEPQEVSEEQLLIAHTEKYLKSLKWSFNVAAISEVCPLVAVPNY 207
I L + + + I +E E+++L+ H+++Y+ +K S E L ++ +
Sbjct: 17 ILERLTQDGLLERCVKIPAREAEEDEILLVHSQEYIDLVK-STE---TMEKEELESLCSG 72
Query: 208 FVQKCYLRPMRYH-----VGGTLEAGFLALRRGWSINIGGGF-------HHASETKGGGF 255
+ YL P Y G T+E + I GF HHA + G+
Sbjct: 73 Y-DSVYLCPSTYEAARLAAGSTIELVKAVMAGK----IQNGFALIRPPGHHAMRNEANGY 127
Query: 256 CAYADISLLVKLLFQSKSISTAMIVDLDAHQGNGYEKDFMNETRI 300
C + ++++ K + + +IVD D H G G ++ F + R+
Sbjct: 128 CIFNNVAIAAKYAIEKLGLKRILIVDWDVHHGQGTQQGFYEDPRV 172
Score = 31.5 bits (72), Expect = 0.85
Identities = 14/53 (26%), Positives = 24/53 (45%), Gaps = 7/53 (13%)
Query: 21 IGGGF-------HHASETKGGGFCAYADISLLVKLLFQSKSISTAMIVDLDAH 66
I GF HHA + G+C + ++++ K + + +IVD D H
Sbjct: 105 IQNGFALIRPPGHHAMRNEANGYCIFNNVAIAAKYAIEKLGLKRILIVDWDVH 157
>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 = 56.6 bits (136), Expect = 1e-08
Identities = 40/143 (27%), Positives = 60/143 (41%), Gaps = 22/143 (15%)
Query: 245 HHASETKGGGFCAYADISLLVKLLFQSKSISTAMIVDLDAHQGNGYEKDFMNETRIFIME 304
HHA E+ GFC + +++ K L +IS +IVDLD H GNG ++ F + I +
Sbjct: 152 HHAEESTAMGFCFFNSVAITAKYLRDQLNISKILIVDLDVHHGNGTQQAFYADPSILYIS 211
Query: 305 ----------------TCITSKAKEAIRCRIE----LAPYTEDQHYLEKIEAGLERSLRS 344
+ + E I L P D YLE ++ +
Sbjct: 212 LHRYDEGNFFPGSGAPNEVGTGLGEGYNINIAWTGGLDPPMGDVEYLEAFRTIVKPVAKE 271
Query: 345 FCPDIIVYNAGTDVL--LNDPLG 365
F PD+++ +AG D L PLG
Sbjct: 272 FDPDMVLVSAGFDALEGHTPPLG 294
Score = 40.8 bits (95), Expect = 0.001
Identities = 17/42 (40%), Positives = 24/42 (57%)
Query: 26 HHASETKGGGFCAYADISLLVKLLFQSKSISTAMIVDLDAHQ 67
HHA E+ GFC + +++ K L +IS +IVDLD H
Sbjct: 152 HHAEESTAMGFCFFNSVAITAKYLRDQLNISKILIVDLDVHH 193
>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 = 55.4 bits (133), Expect = 3e-08
Identities = 29/89 (32%), Positives = 47/89 (52%), Gaps = 5/89 (5%)
Query: 217 MRYHVGGTLEAGFLA----LRRGWSINIGGGFHHASETKGGGFCAYADISLLVKLLFQSK 272
+R VG +E F L+ G+++ G HHA E+ GFC + +++ KLL Q
Sbjct: 123 VRMAVGCLIELAFKVAAGELKNGFAVIRPPG-HHAEESTAMGFCFFNSVAIAAKLLQQKL 181
Query: 273 SISTAMIVDLDAHQGNGYEKDFMNETRIF 301
++ +IVD D H GNG ++ F N+ +
Sbjct: 182 NVGKILIVDWDIHHGNGTQQAFYNDPNVL 210
Score = 41.1 bits (96), Expect = 0.001
Identities = 16/42 (38%), Positives = 24/42 (57%)
Query: 26 HHASETKGGGFCAYADISLLVKLLFQSKSISTAMIVDLDAHQ 67
HHA E+ GFC + +++ KLL Q ++ +IVD D H
Sbjct: 154 HHAEESTAMGFCFFNSVAIAAKLLQQKLNVGKILIVDWDIHH 195
>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 = 54.7 bits (131), Expect = 4e-08
Identities = 30/90 (33%), Positives = 48/90 (53%), Gaps = 5/90 (5%)
Query: 218 RYHVGGTLEAGFLA----LRRGWSINIGGGFHHASETKGGGFCAYADISLLVKLLFQSKS 273
R VG +E F L+ G+++ G HHA E+ GFC + +++ KLL Q +
Sbjct: 124 RLAVGCVVELVFKVATGELKNGFAVVRPPG-HHAEESTPMGFCYFNSVAIAAKLLQQRLN 182
Query: 274 ISTAMIVDLDAHQGNGYEKDFMNETRIFIM 303
+S +IVD D H GNG ++ F ++ + M
Sbjct: 183 VSKILIVDWDVHHGNGTQQAFYSDPNVLYM 212
Score = 41.9 bits (98), Expect = 4e-04
Identities = 20/55 (36%), Positives = 32/55 (58%), Gaps = 1/55 (1%)
Query: 13 LRRGWSINIGGGFHHASETKGGGFCAYADISLLVKLLFQSKSISTAMIVDLDAHQ 67
L+ G+++ G HHA E+ GFC + +++ KLL Q ++S +IVD D H
Sbjct: 142 LKNGFAVVRPPG-HHAEESTPMGFCYFNSVAIAAKLLQQRLNVSKILIVDWDVHH 195
>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 = 53.1 bits (128), Expect = 1e-07
Identities = 57/266 (21%), Positives = 103/266 (38%), Gaps = 50/266 (18%)
Query: 146 KHIFNYLVEAKFITQDNIIEPQEVSEEQLLIAHTEKYLKSLKWSFNVAAISEVCPLVAVP 205
IF L EA I + I +E ++E++L+ H+E++ ++ + + + L
Sbjct: 11 SRIFEKLKEAGLINRMLRIPIREATKEEILLVHSEEHWDRVE-ATEKMSDEQ---LKDRT 66
Query: 206 NYFVQ-KCYLRPMRYH-----VGGTLEAGFLALRRGWSINIGGGF-------HHASETKG 252
F + Y+ GG +EA A+ G + F HHA +
Sbjct: 67 EIFERDSLYVNNDTAFCARLSCGGAIEAC-RAVAEG---RVKNAFAVVRPPGHHAEPDES 122
Query: 253 GGFCAYADISLLVKLLFQSK--SISTAMIVDLDAHQGNGYEKDFMNETRI-FI------- 302
GFC + ++++ K L I +I+D D H GNG ++ F ++ + +I
Sbjct: 123 MGFCFFNNVAVAAKWLQTEYPDKIKKILILDWDIHHGNGTQRAFYDDPNVLYISLHRFEN 182
Query: 303 -----------METCITSKAKEAIRCRIELAPYTE----DQHYLEKIEAGLERSLRSFCP 347
E+ A I P+ + D Y+ + + F P
Sbjct: 183 GGFYPGTPYGDYESV-GEGAGLGFNVNI---PWPQGGMGDADYIYAFQRIVMPIAYEFDP 238
Query: 348 DIIVYNAGTDVLLNDPLGLLAISPQG 373
D+++ +AG D D LG ++P G
Sbjct: 239 DLVIISAGFDAADGDELGQCHVTPAG 264
Score = 30.8 bits (70), Expect = 1.5
Identities = 13/43 (30%), Positives = 21/43 (48%), Gaps = 2/43 (4%)
Query: 26 HHASETKGGGFCAYADISLLVKLLFQSK--SISTAMIVDLDAH 66
HHA + GFC + ++++ K L I +I+D D H
Sbjct: 115 HHAEPDESMGFCFFNNVAVAAKWLQTEYPDKIKKILILDWDIH 157
>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 = 53.3 bits (128), Expect = 1e-07
Identities = 58/273 (21%), Positives = 107/273 (39%), Gaps = 42/273 (15%)
Query: 164 IEPQEVSEEQLLIAHTEKYLKSLKWSFNVAAISEVCPLVAVPNYFVQKCYLRPMRYHVGG 223
++ +E SEE+LL+ H+ +Y+ +K + + L + + + YL P Y
Sbjct: 33 VQAREASEEELLLVHSPEYVALMKSTQYMTEEE----LRTLADTY-DSVYLHPNSYSCA- 86
Query: 224 TLEAGFL----------ALRRGWSINIGGGFHHASETKGGGFCAYADISLLVKLLFQSKS 273
L G + +R G +I G HHA K G+C + ++++ + Q
Sbjct: 87 CLAVGSVLQLVDKVLGGEIRNGLAIVRPPG-HHAQHDKMDGYCMFNNVAIAARYAQQKHG 145
Query: 274 ISTAMIVDLDAHQGNGYEKDFMNETRIF---------------IMETCITSKAKEA-IRC 317
+ +IVD D H G G + F + + + E+ ++
Sbjct: 146 VQRVLIVDWDVHHGQGTQFIFEQDPSVLYFSIHRYEQGRFWPHLKESDSSAVGFGRGEGY 205
Query: 318 RIELAPYT----EDQHYLEKIEAGLERSLRSFCPDIIVYNAGTDVLLNDPLGLLAISPQG 373
I + P+ D Y+ L F P +++ AG D ++ DP G +A +P
Sbjct: 206 NINV-PWNQVGMRDADYIAAFLHVLLPVALEFQPQLVLVAAGFDAVIGDPKGEMAATPAC 264
Query: 374 IIRRDELVFMKARERRVPIVMLTSGGY-LKQTA 405
L+ A + +++ GGY L+ A
Sbjct: 265 FAHLTHLLMGLAGGK---LILSLEGGYNLRSLA 294
Score = 35.6 bits (82), Expect = 0.040
Identities = 19/69 (27%), Positives = 33/69 (47%), Gaps = 3/69 (4%)
Query: 13 LRRGWSINIGGGFHHASETKGGGFCAYADISLLVKLLFQSKSISTAMIVDLDAH--QFSD 70
+R G +I G HHA K G+C + ++++ + Q + +IVD D H Q +
Sbjct: 105 IRNGLAIVRPPG-HHAQHDKMDGYCMFNNVAIAARYAQQKHGVQRVLIVDWDVHHGQGTQ 163
Query: 71 YYFPSAHSI 79
+ F S+
Sbjct: 164 FIFEQDPSV 172
>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 = 52.7 bits (127), Expect = 1e-07
Identities = 48/173 (27%), Positives = 69/173 (39%), Gaps = 34/173 (19%)
Query: 223 GTLEAGFLALRR--GWSINIGGGFHHASETKGGGFCAYADISLLVKLLFQSKSISTAMIV 280
G L+ GF A+ R G HHA ++ GFC + +++ K L Q + +IV
Sbjct: 137 GELKNGF-AVVRPPG---------HHAEPSQAMGFCFFNSVAIAAKQLQQKLKLRKILIV 186
Query: 281 DLDAHQGNGYEKDFMNETRIFIME----------------TCITSKAKEAIRCRIE---- 320
D D H GNG ++ F + + + T + S A E I
Sbjct: 187 DWDVHHGNGTQQIFYEDPNVLYISLHRYDDGNFFPGTGAPTEVGSGAGEGFNVNIAWSGG 246
Query: 321 LAPYTEDQHYLEKIEAGLERSLRSFCPDIIVYNAGTDVLLNDP--LGLLAISP 371
L P D YL + R F PDI++ +AG D P LG +SP
Sbjct: 247 LDPPMGDAEYLAAFRTVVMPIAREFSPDIVLVSAGFDAAEGHPPPLGGYKVSP 299
Score = 38.9 bits (91), Expect = 0.004
Identities = 21/65 (32%), Positives = 31/65 (47%), Gaps = 12/65 (18%)
Query: 4 GTLEAGFLALRR--GWSINIGGGFHHASETKGGGFCAYADISLLVKLLFQSKSISTAMIV 61
G L+ GF A+ R G HHA ++ GFC + +++ K L Q + +IV
Sbjct: 137 GELKNGF-AVVRPPG---------HHAEPSQAMGFCFFNSVAIAAKQLQQKLKLRKILIV 186
Query: 62 DLDAH 66
D D H
Sbjct: 187 DWDVH 191
>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 = 52.8 bits (127), Expect = 2e-07
Identities = 58/215 (26%), Positives = 98/215 (45%), Gaps = 27/215 (12%)
Query: 237 SINIGGGFHHASETKGGGFCAYADISL-LVKLLFQSKSISTAMIVDLDAHQGNGYEKDFM 295
+IN GG HHA + + GFC DI + +++LL K + +D+D H G+G ++ F
Sbjct: 124 AINWSGGLHHAKKFEASGFCYVNDIVIAILELL---KYHPRVLYIDIDIHHGDGVQEAFY 180
Query: 296 NETRI-----------FIMETC----ITSKAKEAIRCRIELAPYTEDQHYLEKIEAGLER 340
R+ F T + +++ + L +DQ YL+ + +++
Sbjct: 181 LTDRVMTVSFHKYGNYFFPGTGDMYEVGAESGRYYSVNVPLKDGIDDQSYLQLFKPVIQQ 240
Query: 341 SLRSFCPDIIVYNAGTDVLLNDPLGLLAISPQGIIRRDELV-FMKARERRVPIVMLTSGG 399
+ + P IV G D L D LG +S +G E V F+K +P+++L GG
Sbjct: 241 VIDFYQPTCIVLQCGADSLGCDRLGCFNLSIKG---HGECVEFVK--SFNIPLLVLGGGG 295
Query: 400 Y-LKQTARIIADSILNLADLGLISR-PYNIWFIYY 432
Y ++ AR L D + + PYN +F Y+
Sbjct: 296 YTVRNVARCWTYETSLLVDEEISNELPYNEYFEYF 330
Score = 33.5 bits (77), Expect = 0.19
Identities = 18/50 (36%), Positives = 28/50 (56%), Gaps = 4/50 (8%)
Query: 18 SINIGGGFHHASETKGGGFCAYADISL-LVKLLFQSKSISTAMIVDLDAH 66
+IN GG HHA + + GFC DI + +++LL K + +D+D H
Sbjct: 124 AINWSGGLHHAKKFEASGFCYVNDIVIAILELL---KYHPRVLYIDIDIH 170
>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 = 52.2 bits (126), Expect = 2e-07
Identities = 60/289 (20%), Positives = 88/289 (30%), Gaps = 99/289 (34%)
Query: 161 DNIIEPQEVSEEQLLIAHTEKYLKSLKWSFNVAAISEVCPLVAVPNYFVQKCYLRPMRYH 220
++ P++ E +L H Y+ L+ A P+
Sbjct: 45 GEVLPPRDFGLEPILAVHDPDYVDFLE----TADTD--TPISE----------------- 81
Query: 221 VGGTLEAGFLA----------LRRGWSINI------GGGFHHASETKGGGFC-----AYA 259
GT EA A + G G HHA + GGFC A A
Sbjct: 82 --GTWEAALAAADTALTAADLVLEGERAAYALCRPPG---HHAGRDRAGGFCYFNNAAIA 136
Query: 260 DISLLVKLLFQSKSISTAMIVDLDAHQGNG-----YEKD--------------------F 294
L I+D+D H GNG YE+ F
Sbjct: 137 AQYLR-------DRAGRVAILDVDVHHGNGTQEIFYERPDVLYVSIHGDPRTFYPFFLGF 189
Query: 295 MNETRIFIMETCITSKAKEAIRCRIE--LAPYTEDQHYLEKIEAGLERSLRSFCPDIIVY 352
+ET E + L P T D YL ++ L + +F PD +V
Sbjct: 190 ADET-----------GEGEGEGYNLNLPLPPGTGDDDYLAALDEALAA-IAAFGPDALVV 237
Query: 353 NAGTDVLLNDPLGLLAISPQGIIRRDELVFMKARERRVPIVMLTSGGYL 401
+ G D DPL ++ + R + + +P V + GGY
Sbjct: 238 SLGFDTHEGDPLSDFKLTTEDYAR----IGRRIAALGLPTVFVQEGGYN 282
>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 = 51.6 bits (124), Expect = 4e-07
Identities = 35/169 (20%), Positives = 70/169 (41%), Gaps = 27/169 (15%)
Query: 147 HIFNYLVEAKFITQDNIIEPQEVSEEQLLIAHTEKYLKSLKWSFNVAAISEVCPLVAVPN 206
I+ + + + + + +E++LL+ H+E++L +K ++ ++ P
Sbjct: 25 RIYERHNDLGLLERCLRLPSRLATEDELLLCHSEEHLDEMK------SLEKMKP----RE 74
Query: 207 YFVQKC-----YLRPMRYHVGGTLEAGFL-----ALRRGWSINIGGGF-----HHASETK 251
Y+ P Y L AG + A+ G S N G HHA +
Sbjct: 75 LNRLGKEYDSIYIHPDSYQCA-LLAAGCVLQVVEAVLTGESRN-GVAIVRPPGHHAEQDT 132
Query: 252 GGGFCAYADISLLVKLLFQSKSISTAMIVDLDAHQGNGYEKDFMNETRI 300
GFC + ++++ + + + +IVD D H GNG + F ++ +
Sbjct: 133 ACGFCFFNNVAIAARYAQKKYGLKRILIVDWDVHHGNGTQHMFESDPSV 181
Score = 30.4 bits (69), Expect = 2.0
Identities = 16/56 (28%), Positives = 30/56 (53%), Gaps = 3/56 (5%)
Query: 345 FCPDIIVYNAGTDVLLNDPLGLLAISPQGIIRRDELVFMKARERRVPIVMLTSGGY 400
F P++++ +AG D DPLG ++P+G ++ A R ++++ GGY
Sbjct: 245 FNPELVLVSAGFDAARGDPLGGCKVTPEGYAHMTHMLMSLAGGR---VIVILEGGY 297
Score = 28.1 bits (63), Expect = 8.9
Identities = 11/41 (26%), Positives = 21/41 (51%)
Query: 26 HHASETKGGGFCAYADISLLVKLLFQSKSISTAMIVDLDAH 66
HHA + GFC + ++++ + + + +IVD D H
Sbjct: 126 HHAEQDTACGFCFFNNVAIAARYAQKKYGLKRILIVDWDVH 166
>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 = 48.1 bits (114), Expect = 5e-06
Identities = 38/170 (22%), Positives = 65/170 (38%), Gaps = 25/170 (14%)
Query: 218 RYHVGGTLEAGFLA----LRRGWSINIGGGFHHASETKGGGFCAYADISLLVKLLFQSKS 273
R+ G + F L+ G+++ G HHA + GFC + +++ + L Q
Sbjct: 122 RWAAGSVTDLAFKVASRELKNGFAVVRPPG-HHADHSTAMGFCFFNSVAIACRQLQQQGK 180
Query: 274 ISTAMIVDLDAHQGNGYEKDFMNETRIFIMETC----------------ITSKAKEAIRC 317
S +IVD D H GNG ++ F + + + + + + E
Sbjct: 181 ASKILIVDWDVHHGNGTQQTFYQDPSVLYISLHRHDDGNFFPGSGAVDEVGAGSGEGFNV 240
Query: 318 RIE----LAPYTEDQHYLEKIEAGLERSLRSFCPDIIVYNAGTDVLLNDP 363
+ L P D YL + R F PD+++ +AG D P
Sbjct: 241 NVAWAGGLDPPMGDPEYLAAFRIVVMPIAREFSPDLVLVSAGFDAAEGHP 290
Score = 35.8 bits (82), Expect = 0.037
Identities = 14/42 (33%), Positives = 21/42 (50%)
Query: 26 HHASETKGGGFCAYADISLLVKLLFQSKSISTAMIVDLDAHQ 67
HHA + GFC + +++ + L Q S +IVD D H
Sbjct: 152 HHADHSTAMGFCFFNSVAIACRQLQQQGKASKILIVDWDVHH 193
>gnl|CDD|212546 cd11683, HDAC10, Histone deacetylase 10. Histone deacetylases 10
are class IIb Zn-dependent enzymes that catalyze
hydrolysis of N(6)-acetyl-lysine of a histone to yield a
deacetylated histone (EC 3.5.1.98). Histone
acetylation/deacetylation process is important for
mediation of transcriptional regulation of many genes.
HDACs usually act via association with DNA binding
proteins to target specific chromatin regions. HDAC10
has an N-terminal deacetylase domain and a C-terminal
pseudo-repeat that shares significant similarity with
its catalytic domain. It is located in the nucleus and
cytoplasm, and is involved in regulation of
melanogenesis. It transcriptionally down-regulates
thioredoxin-interacting protein (TXNIP), leading to
altered reactive oxygen species (ROS) signaling in human
gastric cancer cells. Known interaction partners of
HDAC10 are Pax3, KAP1, hsc70 and HDAC3 proteins.
Length = 337
Score = 42.9 bits (101), Expect = 2e-04
Identities = 33/137 (24%), Positives = 60/137 (43%), Gaps = 13/137 (9%)
Query: 167 QEVSEEQLLIAHTEKYLKSLKWSFNVAAISEVCPLVAVPN--YFVQKCYLRPMRYHVGGT 224
+E SEE++L+ H+ +YL ++ V E+ + + YF + R G T
Sbjct: 36 REASEEEILLVHSPEYLSLVR-ETQVMNKEELMAISGKYDAVYFHPNTF-HCARLAAGAT 93
Query: 225 LEAGFLALRR----GWSINIGGGFHHASETKGGGFCAYADISLLVKLLFQSKSISTAMIV 280
L+ L G ++ G HH+ GFC + ++++ + + + +IV
Sbjct: 94 LQLVDAVLTGEVQNGMALVRPPG-HHSQRNAANGFCVFNNVAIAAEYAKKKYGLHRILIV 152
Query: 281 DLDAHQGNG----YEKD 293
D D H G G +E+D
Sbjct: 153 DWDVHHGQGIQYIFEED 169
Score = 30.2 bits (68), Expect = 2.0
Identities = 20/75 (26%), Positives = 33/75 (44%), Gaps = 10/75 (13%)
Query: 26 HHASETKGGGFCAYADISLLVKLLFQSKSISTAMIVDLDAH--QFSDYYF---PSA---- 76
HH+ GFC + ++++ + + + +IVD D H Q Y F PS
Sbjct: 117 HHSQRNAANGFCVFNNVAIAAEYAKKKYGLHRILIVDWDVHHGQGIQYIFEEDPSVLYFS 176
Query: 77 -HSIKRKRKVEFLKE 90
H + +R FL+E
Sbjct: 177 WHRYEHQRFWPFLRE 191
>gnl|CDD|240148 cd05017, SIS_PGI_PMI_1, The members of this protein family contain
the SIS (Sugar ISomerase) domain and have both the
phosphoglucose isomerase (PGI) and the phosphomannose
isomerase (PMI) functions. These functions catalyze the
reversible reactions of glucose 6-phosphate to fructose
6-phosphate, and mannose 6-phosphate to fructose
6-phosphate, respectively at an equal rate. This protein
contains two SIS domains. This alignment is based on the
first SIS domain.
Length = 119
Score = 30.7 bits (70), Expect = 0.51
Identities = 12/26 (46%), Positives = 16/26 (61%)
Query: 381 VFMKARERRVPIVMLTSGGYLKQTAR 406
+A+ER IV +TSGG L + AR
Sbjct: 62 AVEQAKERGAKIVAITSGGKLLEMAR 87
>gnl|CDD|153393 cd07923, Gallate_dioxygenase_C, The C-terminal domain of Gallate
Dioxygenase, which catalyzes the oxidization and
subsequent ring-opening of gallate. Gallate Dioxygenase
catalyzes the oxidization and subsequent ring-opening of
gallate, an intermediate in the degradation of the
aromatic compound, syringate. The reaction product of
gallate dioxygenase is 4-oxalomesaconate. The amino acid
sequence of the N-terminal and C-terminal regions of
gallate dioxygenase exhibits homology with the sequence
of the PCA 4,5-dioxygenase B (catalytic) and A subunits,
respectively. This model represents the C-terminal
domain, which is similar to the A subunit of PCA
4,5-dioxygenase (or LigAB). The enzyme is estimated to
be a homodimer according to the Escherichia coli enzyme.
Since enzymes in this subfamily have fused A and B
subunits, the dimer interface may resemble the tetramer
interface of classical LigAB enzymes. This enzyme
belongs to the class III extradiol dioxygenase family,
composed of enzymes which use a non-heme Fe(II) to
cleave aromatic rings between a hydroxylated carbon and
an adjacent non-hydroxylated carbon.
Length = 94
Score = 30.1 bits (68), Expect = 0.53
Identities = 19/46 (41%), Positives = 26/46 (56%), Gaps = 4/46 (8%)
Query: 86 EFLKERKALEDE--ITSEPQESVVTRPWPIVYRPEYNVHFFKLEKL 129
FL++ +AL DE +T E + + R W + R Y V FF LEKL
Sbjct: 23 RFLEDPEALFDEAGLTEEERTLIRNRDWIGMIR--YGVIFFVLEKL 66
>gnl|CDD|149036 pfam07746, LigA, Aromatic-ring-opening dioxygenase LigAB, LigA
subunit. This is a family of aromatic ring opening
dioxygenases which catalyze the ring-opening reaction of
protocatechuate and related compounds.
Length = 88
Score = 28.7 bits (65), Expect = 1.5
Identities = 15/59 (25%), Positives = 25/59 (42%), Gaps = 4/59 (6%)
Query: 86 EFLKERKALEDE--ITSEPQESVVTRPWPIVYRPEYNVHFFKLEKLHPFDSKKWKHIFN 142
FL + +A DE +T E + +V R W + +F+ L KL + I+
Sbjct: 16 RFLADEEAYLDEYGLTEEQKAAVRARDWNGLIA--LGGNFYYLAKLAAVLGLSNQDIYA 72
>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 = 30.5 bits (69), Expect = 1.6
Identities = 15/45 (33%), Positives = 25/45 (55%)
Query: 245 HHASETKGGGFCAYADISLLVKLLFQSKSISTAMIVDLDAHQGNG 289
HH SE+ GFC ++ + + + I+ +I+D+D H GNG
Sbjct: 120 HHCSESTPSGFCWVNNVHVGAAHAYLTHGITRVVILDIDLHHGNG 164
>gnl|CDD|180984 PRK07454, PRK07454, short chain dehydrogenase; Provisional.
Length = 241
Score = 29.9 bits (68), Expect = 2.2
Identities = 21/59 (35%), Positives = 28/59 (47%), Gaps = 4/59 (6%)
Query: 311 AKEAIRCRIELAPYTEDQHYLEKIEAGLERSLRSF-CPDIIVYNAG---TDVLLNDPLG 365
A E ++ A Y+ D E I G+ L F CPD+++ NAG T LL PL
Sbjct: 47 AAELRSTGVKAAAYSIDLSNPEAIAPGIAELLEQFGCPDVLINNAGMAYTGPLLEMPLS 105
>gnl|CDD|234537 TIGR04313, aro_clust_Mycop, aromatic cluster surface protein.
Members of this family are absolutely restricted to the
Mollicutes (Mycoplasma and Ureaplasma). All have a
signal peptide, usually of the lipoprotein type,
suggesting surface expression. Most members have lengths
of about 280 residues but some members have a nearly
full-length duplication. The mostly nearly invariant
residue, a Trp,is part of a strongly conserved 9-residue
motif, [ND]-W-[LY]-[WF]-X-[LF]-X-N-[LI], where X usually
is hydrophobic. Because the hydrophobic six-residue core
of this motif almost always contains three to four
aromatic residues, we name this family aromatic cluster
surface protein. Multiple paralogs may occur in a given
Mycoplasma, usually clustered on the genome.
Length = 297
Score = 30.1 bits (68), Expect = 2.4
Identities = 17/112 (15%), Positives = 35/112 (31%), Gaps = 13/112 (11%)
Query: 82 KRKVEFLKERKALEDEITSEPQESVVTRPWPIVYRPEYNVHFFKL------EKLHPFDSK 135
K +++K +K + E+ + + + I + FF +KL+ SK
Sbjct: 73 DEKNKYIKSQKNINSELYLKLLKLSLEYLNNINNSSSNDSDFFSYLYEKSKKKLNELFSK 132
Query: 136 KWKHIFNYLWKHIFNYLVEAKFITQDNIIEPQEVSEEQLLIAHTEKYLKSLK 187
W + K F + + Q + + H +L
Sbjct: 133 NWLWTLYNIDKFEFVFY---DYWDLFKKQNEQFNIDAK----HNSLFLGKFL 177
>gnl|CDD|184006 PRK13367, PRK13367, protocatechuate 4,5-dioxygenase; Provisional.
Length = 420
Score = 29.7 bits (67), Expect = 3.1
Identities = 19/51 (37%), Positives = 28/51 (54%), Gaps = 7/51 (13%)
Query: 81 RKRKVEFLKERKALEDE--ITSEPQESVVTRPWPIVYRPEYNVHFFKLEKL 129
R+R FL + +AL DE ++ E ++ + R W + Y V FF LEKL
Sbjct: 334 RER---FLADPEALYDEAGLSEEERDLIRRRDWRGLIH--YGVSFFLLEKL 379
>gnl|CDD|226355 COG3835, CdaR, Sugar diacid utilization regulator [Transcription /
Signal transduction mechanisms].
Length = 376
Score = 29.6 bits (67), Expect = 3.7
Identities = 15/71 (21%), Positives = 26/71 (36%), Gaps = 1/71 (1%)
Query: 72 YFPSAHSIKRKRKVEFLKERKALEDEITSEPQESVVTRPWPIVYRPEYNVHFFKLEKLHP 131
Y H+++R ++ E + D E VV +P R + VH ++EKL
Sbjct: 169 YNEQLHNLQRMARLIQSSESRR-NDVAILSLNERVVLKPALSAERWDREVHSKRIEKLLA 227
Query: 132 FDSKKWKHIFN 142
+
Sbjct: 228 RAKAYGRLSLR 238
>gnl|CDD|181536 PRK08674, PRK08674, bifunctional phosphoglucose/phosphomannose
isomerase; Validated.
Length = 337
Score = 29.2 bits (66), Expect = 4.6
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 381 VFMKARERRVPIVMLTSGGYLKQTAR 406
+A +R I+ +TSGG LK+ A+
Sbjct: 97 AVEQALKRGAKIIAITSGGKLKEMAK 122
>gnl|CDD|240112 cd04795, SIS, SIS domain. SIS (Sugar ISomerase) domains are found
in many phosphosugar isomerases and phosphosugar binding
proteins. SIS domains are also found in proteins that
regulate the expression of genes involved in synthesis
of phosphosugars.
Length = 87
Score = 27.3 bits (61), Expect = 4.8
Identities = 11/64 (17%), Positives = 22/64 (34%), Gaps = 6/64 (9%)
Query: 339 ERSLRSFCPDIIVYN------AGTDVLLNDPLGLLAISPQGIIRRDELVFMKARERRVPI 392
L +++ A LL ++A+S G A+E +P+
Sbjct: 18 LELLELTGIEVVALIATELEHASLLSLLRKGDVVIALSYSGRTEELLAALEIAKELGIPV 77
Query: 393 VMLT 396
+ +T
Sbjct: 78 IAIT 81
>gnl|CDD|184014 PRK13379, PRK13379, protocatechuate 4,5-dioxygenase subunit alpha;
Provisional.
Length = 119
Score = 27.6 bits (61), Expect = 6.1
Identities = 16/54 (29%), Positives = 29/54 (53%), Gaps = 4/54 (7%)
Query: 77 HSIKRKRKVEFLKERKALEDE--ITSEPQESVVTRPWPIVYRPEYNVHFFKLEK 128
H I+ + FL++ +AL E +T + +E + R W + + Y +FF +EK
Sbjct: 34 HMIRAPWRDRFLQDAEALMQEAGLTEQEKELIRARDWLGLVQ--YGANFFVIEK 85
>gnl|CDD|177538 PHA03136, PHA03136, thymidine kinase; Provisional.
Length = 378
Score = 28.9 bits (64), Expect = 6.5
Identities = 10/56 (17%), Positives = 18/56 (32%), Gaps = 6/56 (10%)
Query: 87 FLKERKALEDEITSEPQESVVTRPWP------IVYRPEYNVHFFKLEKLHPFDSKK 136
F ++K + S P I E +L+K+H F+ +
Sbjct: 263 FDDDKKECLEAADSPEIVGGKKNPSIDQTLFAIFAFDELCDEGERLKKVHEFNLQC 318
>gnl|CDD|197336 cd10281, Nape_like_AP-endo, Neisseria meningitides Nape-like
subfamily of the ExoIII family purinic/apyrimidinic (AP)
endonucleases. This subfamily includes Neisseria
meningitides Nape and related proteins. These are
Escherichia coli exonuclease III (ExoIII)-like AP
endonucleases and belong to the large EEP
(exonuclease/endonuclease/phosphatase) superfamily that
contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds. AP endonucleases participate in the DNA base
excision repair (BER) pathway. AP sites are one of the
most common lesions in cellular DNA. During BER the
damaged DNA is first recognized by DNA glycosylase. AP
endonucleases then catalyze the hydrolytic cleavage of
the phosphodiester bond 5' to the AP site, and this is
followed by the coordinated actions of DNA polymerase,
deoxyribose phosphatase, and DNA ligase. If left
unrepaired, AP sites block DNA replication, and have
both mutagenic and cytotoxic effects. AP endonucleases
can carry out a variety of excision and incision
reactions on DNA, including 3'-5' exonuclease,
3'-deoxyribose phosphodiesterase, 3'-phosphatase, and
occasionally, nonspecific DNase activities. Different AP
endonuclease enzymes catalyze the different reactions
with different efficiences. Many organisms have two AP
endonucleases, usually one is the dominant AP
endonuclease, the other has weak AP endonuclease
activity; for example, Neisseria meningitides Nape and
NExo. Nape, found in this subfamily, is the dominant AP
endonuclease. It exhibits strong AP endonuclease
activity, and also exhibits 3'-5'exonuclease and
3'-deoxyribose phosphodiesterase activities.
Length = 253
Score = 28.3 bits (64), Expect = 7.9
Identities = 10/48 (20%), Positives = 20/48 (41%), Gaps = 2/48 (4%)
Query: 72 YFPSA--HSIKRKRKVEFLKERKALEDEITSEPQESVVTRPWPIVYRP 117
Y PS +++ K+ FL E+ + +E +V + I +
Sbjct: 108 YVPSGSSGDERQEAKMAFLDAFLEHLKELRRKRREFIVCGDFNIAHTE 155
>gnl|CDD|236122 PRK07877, PRK07877, hypothetical protein; Provisional.
Length = 722
Score = 28.4 bits (64), Expect = 8.1
Identities = 8/14 (57%), Positives = 11/14 (78%)
Query: 384 KARERRVPIVMLTS 397
AR RR+P++M TS
Sbjct: 216 AARARRIPVLMATS 229
>gnl|CDD|177784 PLN00190, PLN00190, 60S ribosomal protein L21; Provisional.
Length = 158
Score = 27.8 bits (62), Expect = 8.6
Identities = 15/56 (26%), Positives = 24/56 (42%), Gaps = 3/56 (5%)
Query: 79 IKRKRKVEFLKERKALEDEITSEPQ---ESVVTRPWPIVYRPEYNVHFFKLEKLHP 131
++ R E RK DE +E + E + T+ P +P + V LE + P
Sbjct: 96 VQPSRCREEFLLRKKSNDEAKAEAKAKGEKISTKRQPKGPKPGFMVEGATLETVTP 151
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
0.323 0.139 0.422
Gapped
Lambda K H
0.267 0.0737 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 22,802,561
Number of extensions: 2277040
Number of successful extensions: 1947
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1900
Number of HSP's successfully gapped: 100
Length of query: 436
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 336
Effective length of database: 6,502,202
Effective search space: 2184739872
Effective search space used: 2184739872
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 60 (26.9 bits)