RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 010834
(499 letters)
>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 = 654 bits (1690), Expect = 0.0
Identities = 244/381 (64%), Positives = 310/381 (81%), Gaps = 2/381 (0%)
Query: 17 RKVCYFYDPEVGNYYYGQGHPMKPHRIRMTHALLAHYGLLQNMQVLKPFPARERDLCRFH 76
++V YFYDP+VGN++YG GHPMKPHR+ +TH+L+ HYGL + MQV KP+ A D+CRFH
Sbjct: 1 KRVAYFYDPDVGNFHYGPGHPMKPHRLALTHSLVLHYGLYKKMQVYKPYRASAHDMCRFH 60
Query: 77 ADDYVSFLRSITPETQQDQLRQLKRFNVGEDCPVFDGLFSFCQTYAGGSVGGAVKLNHGL 136
++DY+ FL+ +TP+ Q + L +FNVG+DCPVF GLF FC Y G S+ GA KLNH +
Sbjct: 61 SEDYIDFLQRVTPQNIQGFTKSLNQFNVGDDCPVFPGLFDFCSMYTGASLEGATKLNHKI 120
Query: 137 CDIAINWAGGLHHAKKCEASGFCYVNDIVLAILELLKQHERVLYVDIDIHHGDGVEEAFY 196
CDIAINW+GGLHHAKK EASGFCYVNDIV+AILELLK H RVLY+DIDIHHGDGV+EAFY
Sbjct: 121 CDIAINWSGGLHHAKKFEASGFCYVNDIVIAILELLKYHPRVLYIDIDIHHGDGVQEAFY 180
Query: 197 TTDRVMTVSFHKFGDY-FPGTGDIRDIGYSKGKFYSLNVPLDDGIDDESYHYLFKPIIGK 255
TDRVMTVSFHK+G+Y FPGTGD+ ++G G++YS+NVPL DGIDD+SY LFKP+I +
Sbjct: 181 LTDRVMTVSFHKYGNYFFPGTGDMYEVGAESGRYYSVNVPLKDGIDDQSYLQLFKPVIQQ 240
Query: 256 VMEVFRPGAVVLQCGADSLSGDRLGCFNLSIKGHAECVKFMRSFNVPLLLLGGGGYTIRN 315
V++ ++P +VLQCGADSL DRLGCFNLSIKGH ECV+F++SFN+PLL+LGGGGYT+RN
Sbjct: 241 VIDFYQPTCIVLQCGADSLGCDRLGCFNLSIKGHGECVEFVKSFNIPLLVLGGGGYTVRN 300
Query: 316 VARCWCYETGVALGVEVDDKMPQHEYYEYFGPDYTLH-VAPSNMENKNSRQLLEEIRNKL 374
VARCW YET + + E+ +++P +EY+EYF PD+TLH + +EN+NS+Q L++IR +
Sbjct: 301 VARCWTYETSLLVDEEISNELPYNEYFEYFAPDFTLHPDVSTRIENQNSKQYLDQIRQTV 360
Query: 375 LEYLSKLQHAPSVQFQERPPD 395
E L L HAPSVQ Q+ PPD
Sbjct: 361 FENLKMLNHAPSVQMQDVPPD 381
>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 = 633 bits (1635), Expect = 0.0
Identities = 227/306 (74%), Positives = 267/306 (87%)
Query: 22 FYDPEVGNYYYGQGHPMKPHRIRMTHALLAHYGLLQNMQVLKPFPARERDLCRFHADDYV 81
FYDP+VGNYYYGQGHPMKPHRIRMTH+L+ YGL + M++ +P PA +L +FH+DDY+
Sbjct: 1 FYDPDVGNYYYGQGHPMKPHRIRMTHSLILSYGLYKKMEIYRPRPATAEELTKFHSDDYI 60
Query: 82 SFLRSITPETQQDQLRQLKRFNVGEDCPVFDGLFSFCQTYAGGSVGGAVKLNHGLCDIAI 141
FLRS++P+ ++ +QL+RFNVGEDCPVFDGL+ +CQ YAGGS+ AVKLN G DIAI
Sbjct: 61 DFLRSVSPDNMKEFKKQLERFNVGEDCPVFDGLYEYCQLYAGGSIAAAVKLNRGQADIAI 120
Query: 142 NWAGGLHHAKKCEASGFCYVNDIVLAILELLKQHERVLYVDIDIHHGDGVEEAFYTTDRV 201
NWAGGLHHAKK EASGFCYVNDIVLAILELLK H+RVLY+DIDIHHGDGVEEAFYTTDRV
Sbjct: 121 NWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRV 180
Query: 202 MTVSFHKFGDYFPGTGDIRDIGYSKGKFYSLNVPLDDGIDDESYHYLFKPIIGKVMEVFR 261
MTVSFHKFG+YF +RDIG KGK+Y++NVPL DGIDDESY +F+P++ KVMEVF+
Sbjct: 181 MTVSFHKFGEYFFPGTGLRDIGAGKGKYYAVNVPLKDGIDDESYLQIFEPVLSKVMEVFQ 240
Query: 262 PGAVVLQCGADSLSGDRLGCFNLSIKGHAECVKFMRSFNVPLLLLGGGGYTIRNVARCWC 321
P AVVLQCGADSL+GDRLGCFNLSIKGHA+CVKF++SFN+PLL+LGGGGYT+RNVARCW
Sbjct: 241 PSAVVLQCGADSLAGDRLGCFNLSIKGHAKCVKFVKSFNIPLLVLGGGGYTLRNVARCWT 300
Query: 322 YETGVA 327
YET V
Sbjct: 301 YETAVL 306
>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 = 607 bits (1567), Expect = 0.0
Identities = 240/375 (64%), Positives = 301/375 (80%)
Query: 16 KRKVCYFYDPEVGNYYYGQGHPMKPHRIRMTHALLAHYGLLQNMQVLKPFPARERDLCRF 75
K+KV YFYD +VGNY YG GHPMKPHRIRM H+L+ +YGL + M++ + PA + ++ +F
Sbjct: 1 KKKVAYFYDSDVGNYAYGPGHPMKPHRIRMAHSLVMNYGLYKKMEIYRAKPATKNEMTQF 60
Query: 76 HADDYVSFLRSITPETQQDQLRQLKRFNVGEDCPVFDGLFSFCQTYAGGSVGGAVKLNHG 135
H D+Y+ FL +TP+ + ++ ++NVG+DCPVFDGLF FC AGGS+ GA +LN G
Sbjct: 61 HTDEYIDFLSRVTPDNMEKFQKEQVKYNVGDDCPVFDGLFEFCSISAGGSMEGAARLNRG 120
Query: 136 LCDIAINWAGGLHHAKKCEASGFCYVNDIVLAILELLKQHERVLYVDIDIHHGDGVEEAF 195
CDIA+NWAGGLHHAKK EASGFCYVNDIVL ILELL+ H+RVLY+DID+HHGDGVEEAF
Sbjct: 121 KCDIAVNWAGGLHHAKKSEASGFCYVNDIVLGILELLRYHQRVLYIDIDVHHGDGVEEAF 180
Query: 196 YTTDRVMTVSFHKFGDYFPGTGDIRDIGYSKGKFYSLNVPLDDGIDDESYHYLFKPIIGK 255
YTTDRVMT SFHK+G+YFPGTG++RDIG GK Y++NVPL DGIDDESY +F+P+I
Sbjct: 181 YTTDRVMTCSFHKYGEYFPGTGELRDIGIGTGKNYAVNVPLRDGIDDESYKSIFEPVIKH 240
Query: 256 VMEVFRPGAVVLQCGADSLSGDRLGCFNLSIKGHAECVKFMRSFNVPLLLLGGGGYTIRN 315
VME ++P AVVLQCG DSLSGDRLGCFNLS+KGHA CV F++SFN+P+L+LGGGGYT+RN
Sbjct: 241 VMEWYQPEAVVLQCGGDSLSGDRLGCFNLSMKGHANCVNFVKSFNLPMLVLGGGGYTMRN 300
Query: 316 VARCWCYETGVALGVEVDDKMPQHEYYEYFGPDYTLHVAPSNMENKNSRQLLEEIRNKLL 375
VAR W +ETG+ G E+D +P +EYYEY+GPDY L+V PSNMEN N+ + L++I ++
Sbjct: 301 VARTWAFETGLLAGEELDKDLPYNEYYEYYGPDYELNVRPSNMENHNTPEYLDKITTAVI 360
Query: 376 EYLSKLQHAPSVQFQ 390
E L APSVQ Q
Sbjct: 361 ENLRNTSFAPSVQMQ 375
>gnl|CDD|240251 PTZ00063, PTZ00063, histone deacetylase; Provisional.
Length = 436
Score = 599 bits (1547), Expect = 0.0
Identities = 254/406 (62%), Positives = 319/406 (78%), Gaps = 7/406 (1%)
Query: 16 KRKVCYFYDPEVGNYYYGQGHPMKPHRIRMTHALLAHYGLLQNMQVLKPFPARERDLCRF 75
+++V YFYDP++G+YYYG GHPMKP RIRM HAL+ Y L ++M++ +P + E +L F
Sbjct: 3 RKRVSYFYDPDIGSYYYGPGHPMKPQRIRMAHALILSYDLYKHMEIYRPHKSVEPELVLF 62
Query: 76 HADDYVSFLRSITPETQQDQLRQLKRFNVGE--DCPVFDGLFSFCQTYAGGSVGGAVKLN 133
H ++YV FL SI+PE +D QLKRFNVGE DCPVFDGLF F Q+ AG S+ GA KLN
Sbjct: 63 HDEEYVDFLSSISPENYRDFTYQLKRFNVGEATDCPVFDGLFEFQQSCAGASIDGAYKLN 122
Query: 134 HGLCDIAINWAGGLHHAKKCEASGFCYVNDIVLAILELLKQHERVLYVDIDIHHGDGVEE 193
+ DI +NW+GGLHHAK+ EASGFCY+NDIVL ILELLK H RV+Y+DID+HHGDGVEE
Sbjct: 123 NHQADICVNWSGGLHHAKRSEASGFCYINDIVLGILELLKYHARVMYIDIDVHHGDGVEE 182
Query: 194 AFYTTDRVMTVSFHKFGDYFPGTGDIRDIGYSKGKFYSLNVPLDDGIDDESYHYLFKPII 253
AFY T RVMTVSFHKFGD+FPGTGD+ DIG ++GK+YS+NVPL+DGIDD+S+ LFKP+I
Sbjct: 183 AFYVTHRVMTVSFHKFGDFFPGTGDVTDIGVAQGKYYSVNVPLNDGIDDDSFVDLFKPVI 242
Query: 254 GKVMEVFRPGAVVLQCGADSLSGDRLGCFNLSIKGHAECVKFMRSFNVPLLLLGGGGYTI 313
K +EV+RPGA+VLQCGADSL+GDRLG FNL+IKGHA CV+F+RS N+PLL+LGGGGYTI
Sbjct: 243 SKCVEVYRPGAIVLQCGADSLTGDRLGRFNLTIKGHAACVEFVRSLNIPLLVLGGGGYTI 302
Query: 314 RNVARCWCYETGVALG--VEVDDKMPQHEYYEYFGPDYTLHVAPSNMENKNSRQLLEEIR 371
RNVARCW YETGV L E+ D++ ++YY+Y+ PD+ LH+ PSN+ N NS + LE+I+
Sbjct: 303 RNVARCWAYETGVILNKHDEMSDQISLNDYYDYYAPDFQLHLQPSNIPNYNSPEHLEKIK 362
Query: 372 NKLLEYLSKLQHAPSVQFQERPPDSELPEADEDQEDGDERWDPDSD 417
K+LE L L+HAP VQF PPD + D D ED ++ SD
Sbjct: 363 VKILENLRYLEHAPGVQFAYVPPD--FFDRDIDDED-EKNQYELSD 405
>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 = 572 bits (1474), Expect = 0.0
Identities = 257/370 (69%), Positives = 315/370 (85%)
Query: 12 TDGVKRKVCYFYDPEVGNYYYGQGHPMKPHRIRMTHALLAHYGLLQNMQVLKPFPARERD 71
+ G K+KVCY+YD +VGNYYYGQGHPMKPHRIRMTH LL +YGL + M++ +P A +
Sbjct: 1 SQGTKKKVCYYYDGDVGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKANAEE 60
Query: 72 LCRFHADDYVSFLRSITPETQQDQLRQLKRFNVGEDCPVFDGLFSFCQTYAGGSVGGAVK 131
+ ++H+DDY+ FLRSI P+ + +Q++RFNVGEDCPVFDGLF FCQ AGGSV AVK
Sbjct: 61 MTKYHSDDYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSAGGSVASAVK 120
Query: 132 LNHGLCDIAINWAGGLHHAKKCEASGFCYVNDIVLAILELLKQHERVLYVDIDIHHGDGV 191
LN DIA+NWAGGLHHAKK EASGFCYVNDIVLAILELLK H+RVLY+DIDIHHGDGV
Sbjct: 121 LNKQQTDIAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGV 180
Query: 192 EEAFYTTDRVMTVSFHKFGDYFPGTGDIRDIGYSKGKFYSLNVPLDDGIDDESYHYLFKP 251
EEAFYTTDRVMTVSFHK+G+YFPGTGD+RDIG KGK+Y++N PL DGIDDESY +FKP
Sbjct: 181 EEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNYPLRDGIDDESYEAIFKP 240
Query: 252 IIGKVMEVFRPGAVVLQCGADSLSGDRLGCFNLSIKGHAECVKFMRSFNVPLLLLGGGGY 311
++ KVME+F+P AVVLQCGADSLSGDRLGCFNL+IKGHA+CV+F++SFN+P+L+LGGGGY
Sbjct: 241 VMSKVMEMFQPSAVVLQCGADSLSGDRLGCFNLTIKGHAKCVEFVKSFNLPMLMLGGGGY 300
Query: 312 TIRNVARCWCYETGVALGVEVDDKMPQHEYYEYFGPDYTLHVAPSNMENKNSRQLLEEIR 371
TIRNVARCW YET VAL E+ +++P ++Y+EYFGPD+ LH++PSNM N+N+ + LE+I+
Sbjct: 301 TIRNVARCWTYETAVALDSEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTNEYLEKIK 360
Query: 372 NKLLEYLSKL 381
+L E L L
Sbjct: 361 QRLFENLRML 370
>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 = 553 bits (1426), Expect = 0.0
Identities = 250/366 (68%), Positives = 312/366 (85%)
Query: 16 KRKVCYFYDPEVGNYYYGQGHPMKPHRIRMTHALLAHYGLLQNMQVLKPFPARERDLCRF 75
K+KVCY+YD ++GNYYYGQGHPMKPHRIRMTH LL +YGL + M++ +P A ++ ++
Sbjct: 1 KKKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTKY 60
Query: 76 HADDYVSFLRSITPETQQDQLRQLKRFNVGEDCPVFDGLFSFCQTYAGGSVGGAVKLNHG 135
H+D+Y+ FLRSI P+ + +Q++RFNVGEDCPVFDGLF FCQ GGSV GAVKLN
Sbjct: 61 HSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAGAVKLNRQ 120
Query: 136 LCDIAINWAGGLHHAKKCEASGFCYVNDIVLAILELLKQHERVLYVDIDIHHGDGVEEAF 195
D+A+NWAGGLHHAKK EASGFCYVNDIVLAILELLK H+RVLY+DIDIHHGDGVEEAF
Sbjct: 121 QTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAF 180
Query: 196 YTTDRVMTVSFHKFGDYFPGTGDIRDIGYSKGKFYSLNVPLDDGIDDESYHYLFKPIIGK 255
YTTDRVMTVSFHK+G+YFPGTGD+RDIG KGK+Y++N P+ DGIDDESY +FKPII K
Sbjct: 181 YTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIISK 240
Query: 256 VMEVFRPGAVVLQCGADSLSGDRLGCFNLSIKGHAECVKFMRSFNVPLLLLGGGGYTIRN 315
VME+++P AVVLQCGADSLSGDRLGCFNL++KGHA+CV+ +++FN+PLL+LGGGGYTIRN
Sbjct: 241 VMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTIRN 300
Query: 316 VARCWCYETGVALGVEVDDKMPQHEYYEYFGPDYTLHVAPSNMENKNSRQLLEEIRNKLL 375
VARCW YET VAL E+ +++P ++Y+EYFGPD+ LH++PSNM N+N+ + +E+I+ +L
Sbjct: 301 VARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEYMEKIKQRLF 360
Query: 376 EYLSKL 381
E L L
Sbjct: 361 ENLRML 366
>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 = 468 bits (1207), Expect = e-165
Identities = 187/311 (60%), Positives = 236/311 (75%), Gaps = 2/311 (0%)
Query: 19 VCYFYDPEVGNYYYGQGHPMKPHRIRMTHALLAHYGLLQNMQVLKPFPARERDLCRFHAD 78
V Y ++ V +Y++G+ HPMKP R+ +T L+ YGL + M + A +L +FH
Sbjct: 1 VSYHFNSRVEDYHFGRTHPMKPFRLTLTKHLVMGYGLHKAMDTYEARAATREELRQFHDA 60
Query: 79 DYVSFLRSITPETQ-QDQLRQLKRFNVGEDCPVFDGLFSFCQTYAGGSVGGAVKLNHGLC 137
DY+ FL ++PE Q + + + FN+G+DCPVFDG++ +CQ YAG S+ A KL G
Sbjct: 61 DYLDFLSKVSPENANQLRFDKAEPFNIGDDCPVFDGMYDYCQLYAGASLDAARKLCSGQS 120
Query: 138 DIAINWAGGLHHAKKCEASGFCYVNDIVLAILELLKQHERVLYVDIDIHHGDGVEEAFYT 197
DIAINW+GGLHHAKK EASGFCYVNDIVLAIL LL+ RVLY+DID+HHGDGVEEAFY
Sbjct: 121 DIAINWSGGLHHAKKSEASGFCYVNDIVLAILNLLRYFPRVLYIDIDVHHGDGVEEAFYR 180
Query: 198 TDRVMTVSFHKF-GDYFPGTGDIRDIGYSKGKFYSLNVPLDDGIDDESYHYLFKPIIGKV 256
TDRVMT+SFHK+ G++FPGTGD+ D G + GK ++LNVPL+DGIDDE Y+ LFK IIG
Sbjct: 181 TDRVMTLSFHKYNGEFFPGTGDLDDNGGTPGKHFALNVPLEDGIDDEQYNLLFKSIIGPT 240
Query: 257 MEVFRPGAVVLQCGADSLSGDRLGCFNLSIKGHAECVKFMRSFNVPLLLLGGGGYTIRNV 316
+E F+P A+VLQCGADSL GDRLG FNL+IK H CVKF++SF +P+L++GGGGYT RNV
Sbjct: 241 IEKFQPSAIVLQCGADSLGGDRLGQFNLNIKAHGACVKFVKSFGIPMLVVGGGGYTPRNV 300
Query: 317 ARCWCYETGVA 327
AR WCYET VA
Sbjct: 301 ARAWCYETAVA 311
>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 = 416 bits (1071), Expect = e-143
Identities = 169/366 (46%), Positives = 242/366 (66%), Gaps = 4/366 (1%)
Query: 19 VCYFYDPEVGNYYYGQGHPMKPHRIRMTHALLAHYGLLQNMQVLKPFPARERDLCRFHAD 78
V Y + PE N P P+R M H+L+ YGLL+ ++V+KP A E +L FH+D
Sbjct: 1 VVYIHSPEYVNLC--DRLPKVPNRASMVHSLIEAYGLLKQLRVVKPRVATEEELASFHSD 58
Query: 79 DYVSFLRSITPETQQDQLRQ-LKRFNVGEDCPVFDGLFSFCQTYAGGSVGGAVKLNHGLC 137
+Y+ FL+ + E D+ + F +G DCP+F+G++ + AG ++ A L G C
Sbjct: 59 EYIQFLKKASNEGDNDEEPSEQQEFGLGYDCPIFEGIYDYAAAVAGATLTAAQLLIDGKC 118
Query: 138 DIAINWAGGLHHAKKCEASGFCYVNDIVLAILELLKQHERVLYVDIDIHHGDGVEEAFYT 197
+AINW GG HHA++ EASGFCYVNDIVL IL+L ++ +RVLYVD+D+HHGDGVE+AF
Sbjct: 119 KVAINWFGGWHHAQRDEASGFCYVNDIVLGILKLREKFDRVLYVDLDLHHGDGVEDAFSF 178
Query: 198 TDRVMTVSFHKFGD-YFPGTGDIRDIGYSKGKFYSLNVPLDDGIDDESYHYLFKPIIGKV 256
T +VMTVS HK+ +FPGTGD+ D+G KGK+Y++NVPL DGI DE Y +F ++ ++
Sbjct: 179 TSKVMTVSLHKYSPGFFPGTGDVSDVGLGKGKYYTVNVPLRDGIQDEQYLQIFTAVVPEI 238
Query: 257 MEVFRPGAVVLQCGADSLSGDRLGCFNLSIKGHAECVKFMRSFNVPLLLLGGGGYTIRNV 316
+ FRP AVVLQCGAD+L+GD +G FNL+ G +C+K++ + +P L+LGGGGY + N
Sbjct: 239 VAAFRPEAVVLQCGADTLAGDPMGAFNLTPVGIGKCLKYVLGWKLPTLILGGGGYNLANT 298
Query: 317 ARCWCYETGVALGVEVDDKMPQHEYYEYFGPDYTLHVAPSNMENKNSRQLLEEIRNKLLE 376
ARCW Y TG+ LG + +P HE++ +GPDY L ++PS + N Q +E+I +
Sbjct: 299 ARCWTYLTGLILGEPLSSDIPDHEFFTSYGPDYELEISPSLRPDLNEDQYIEKILETIKG 358
Query: 377 YLSKLQ 382
L +
Sbjct: 359 NLKNVV 364
>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 = 341 bits (877), Expect = e-114
Identities = 105/339 (30%), Positives = 166/339 (48%), Gaps = 19/339 (5%)
Query: 21 YFYDPEVGNYYYGQGHPMKPHRIRMTHALLAHYGLLQNMQVLKPFPARERDLCRFHADDY 80
Y PE + GHP P R+R+ LL GL ++++++P PA +L H+ DY
Sbjct: 6 LIYHPEFLEHEPPPGHPENPDRLRLILELLESSGLPDSLELVEPRPATLEELLLVHSPDY 65
Query: 81 VSFLRSITPETQQDQLRQLKRFNVGEDCPVFDGLFSFCQTYAGGSVGGAVKLNHGLCDIA 140
V FL S++ E N+ D PV G + + AGG++ + G +
Sbjct: 66 VEFLESLSEEEGY--------GNLDGDTPVSPGTYEAARLAAGGALTAVDAVLEGEDNAF 117
Query: 141 INWAGGLHHAKKCEASGFCYVNDIVLAILELLKQ-HERVLYVDIDIHHGDGVEEAFYTTD 199
HHA + ASGFC N++ +A LLK+ +RV +D D+HHG+G +E FY D
Sbjct: 118 ALVRPPGHHAGRDRASGFCLFNNVAIAAKYLLKKGVKRVAIIDFDVHHGNGTQEIFYDDD 177
Query: 200 RVMTVSFHKFG-DYFPGTGDIRDIGYSKGKFYSLNVPLDDGIDDESYHYLFKPIIGKVME 258
V+TVS H+ G ++PGTG +IG + ++N+PL G D+SY + I+ ++E
Sbjct: 178 DVLTVSLHQDGRPFYPGTGGADEIG-EGKEGNNVNIPLPPGTGDDSYLEALEEIVLPLLE 236
Query: 259 VFRPGAVVLQCGADSLSGDRLGCFNLSIKGHAECVKFMRSF----NVPLLLLGGGGYTIR 314
F+P V++ G D+ GD LG NL+ +G+A+ + +R P++ + GGY +
Sbjct: 237 EFKPDLVIVSAGFDAHRGDPLGRLNLTEEGYAKIGRAVRKLAEGYGGPVVAVLEGGYNLD 296
Query: 315 NVARCWCYETGVALGVEV----DDKMPQHEYYEYFGPDY 349
+AR G+ + E F DY
Sbjct: 297 ALARSLVAFLAGLAGLVEEELEEPLPEDLELRRAFRADY 335
>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 = 326 bits (837), Expect = e-109
Identities = 121/312 (38%), Positives = 165/312 (52%), Gaps = 15/312 (4%)
Query: 20 CYFYDPEVGNYYYGQGHPMKPHRIRMTHALLAHYGLLQNMQVLKPFPARERDLCRFHADD 79
+ Y E Y +G HP P R+ +T LL GLL + ++ P PA E +L FH D
Sbjct: 1 AFIYSEEYLRYSFGPNHPFNPPRLSLTKDLLRALGLLPPVDLVPPRPATEEELLLFHTPD 60
Query: 80 YVSFLR--SITPETQQDQLRQLKRFNVG-EDCPVFDGLFSFCQTYAGGSVGGAVKLNHGL 136
Y+ ++ S E + R +G ED PVF G+ GG++ A + G
Sbjct: 61 YIEAVKEASRGQEPEGRG-----RLGLGTEDNPVFPGMHEAAALVVGGTLLAARLVLEGE 115
Query: 137 CDIAINWAGGLHHAKKCEASGFCYVNDIVLAILELLKQH-ERVLYVDIDIHHGDGVEEAF 195
A N AGGLHHA + ASGFC ND +AI L + RV YVDID HHGDGV+ AF
Sbjct: 116 ARRAFNPAGGLHHAMRGRASGFCVYNDAAVAIERLRDKGGLRVAYVDIDAHHGDGVQAAF 175
Query: 196 YTTDRVMTVSFHKFGDY-FPGTGDIRDIGYSKGKFYSLNVPLDDGIDDESYHYLFKPIIG 254
Y RV+T+S H+ G Y FPGTG + +IG +G Y++N+PL G D+ + F+ ++
Sbjct: 176 YDDPRVLTISLHESGRYLFPGTGFVDEIGEGEGYGYAVNIPLPPGTGDDEFLRAFEAVVP 235
Query: 255 KVMEVFRPGAVVLQCGADSLSGDRLGCFNLSIKGHAECVKFMR-----SFNVPLLLLGGG 309
++ FRP +V Q GAD+ +GD L NLS + + V+ +R L LGGG
Sbjct: 236 PLLRAFRPDVIVSQHGADAHAGDPLTHLNLSNRAYRAAVRRIRELADEYCGGRWLALGGG 295
Query: 310 GYTIRNVARCWC 321
GY VAR W
Sbjct: 296 GYNPDVVARAWA 307
>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 = 318 bits (818), Expect = e-106
Identities = 103/305 (33%), Positives = 159/305 (52%), Gaps = 15/305 (4%)
Query: 31 YYGQGHPMKPHRIRMTHALLAHYGLLQNMQVLKPFPARERDLCRFHADDYVSFLRSITPE 90
G GHP P R+ LL GLL ++ + P PA E +L H+ +YV FL + E
Sbjct: 4 GSGLGHPENPERLEAILELLKESGLLDRLEFIAPRPATEEELLLVHSPEYVEFLEEASLE 63
Query: 91 TQQDQLRQLKRFNVGEDCPVFDGLFSFCQTYAGGSVGGAVKLNHGL-CDIAINWAGGLHH 149
++ L R + D PV G + AGG++ A + G A+ G HH
Sbjct: 64 EEE-----LGRIGLDGDTPVSPGSYEAALLAAGGTLEAADLVLSGENAFAAVRPPG--HH 116
Query: 150 AKKCEASGFCYVNDIVLAILELLKQH--ERVLYVDIDIHHGDGVEEAFYTTDRVMTVSFH 207
A++ ASGFC N++ +A LLK++ +RVL VD+D+HHG+G +E FY RV+T+S H
Sbjct: 117 AERDRASGFCLFNNVAIAARYLLKRYGLKRVLIVDLDVHHGNGTQEIFYDDPRVLTISIH 176
Query: 208 KFGDYFPGTGDIRDIGYSKGKFYSLNVPLDDGIDDESYHYLFKPIIGKVMEVFRPGAVVL 267
+ ++PGTG + G G+ Y+LN+PL G DE Y F+ I+ + F+P +++
Sbjct: 177 QDP-FYPGTGFADETGEGAGEGYTLNIPLPPGTGDEEYLAAFEEILLPALREFQPDLILV 235
Query: 268 QCGADSLSGDRLGCFNLSIKGHAECVKFMRSF----NVPLLLLGGGGYTIRNVARCWCYE 323
G D+ +GD LG NL+ +G+AE + + P++ + GGY + +AR
Sbjct: 236 SAGFDAHAGDPLGGLNLTTEGYAERTRLLLELADAYGGPVVSVLEGGYNLDALARSAAAV 295
Query: 324 TGVAL 328
L
Sbjct: 296 LAGLL 300
>gnl|CDD|240374 PTZ00346, PTZ00346, histone deacetylase; Provisional.
Length = 429
Score = 292 bits (749), Expect = 2e-94
Identities = 144/295 (48%), Positives = 195/295 (66%), Gaps = 2/295 (0%)
Query: 36 HPMKPHRIRMTHALLAHYGLLQNMQVLKPFPARERDLCRFHADDYVSFLRSITPETQQDQ 95
H MKP+R+ ++ + + + + P + +L +H D Y++ L + +
Sbjct: 43 HAMKPYRVLAAMEIVRSLKIDAHCRTVVPPLVKVEELMAYHTDTYLANLGLHSCRSWLWN 102
Query: 96 LRQLKRFNVGEDCPVFDGLFSFCQTYAGGSVGGAVKLNHGLCDIAINWAGGLHHAKKCEA 155
K F G DCP +GL A G++ GAV LN G D+A++W GG+HH+K E
Sbjct: 103 AETSKVFFSG-DCPPVEGLMEHSIATASGTLMGAVLLNSGQVDVAVHWGGGMHHSKCGEC 161
Query: 156 SGFCYVNDIVLAILELLKQHERVLYVDIDIHHGDGVEEAFYTTDRVMTVSFHKFGD-YFP 214
SGFCYVNDIVL ILELLK H+RVLYVDID+HHGDGV+EAF T+DRV T+S HKFG+ +FP
Sbjct: 162 SGFCYVNDIVLGILELLKCHDRVLYVDIDMHHGDGVDEAFCTSDRVFTLSLHKFGESFFP 221
Query: 215 GTGDIRDIGYSKGKFYSLNVPLDDGIDDESYHYLFKPIIGKVMEVFRPGAVVLQCGADSL 274
GTG RD+GY +G++YS+N+ + DGI D Y LF+ + ++ + P A+VLQCGADSL
Sbjct: 222 GTGHPRDVGYGRGRYYSMNLAVWDGITDFYYLGLFEHALHSIVRRYSPDAIVLQCGADSL 281
Query: 275 SGDRLGCFNLSIKGHAECVKFMRSFNVPLLLLGGGGYTIRNVARCWCYETGVALG 329
+GDRLG NLS GH +CV+ +R +P+L LGGGGYTIRNVA+ W YET + G
Sbjct: 282 AGDRLGLLNLSSFGHGQCVQAVRDLGIPMLALGGGGYTIRNVAKLWAYETSILTG 336
>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 = 284 bits (730), Expect = 3e-93
Identities = 121/292 (41%), Positives = 173/292 (59%), Gaps = 24/292 (8%)
Query: 42 RIRMTHALLAHYGLLQNM-QVLKPFPARERDLCRFHADDYVSFLRSITPETQQDQLRQLK 100
R + H+L+ YGLLQ+ ++++P A +DL ++H DYV FL LK
Sbjct: 21 RSSLVHSLIRAYGLLQHFDEIIEPERATRKDLTKYHDKDYVDFL--------------LK 66
Query: 101 RFNVGEDCPVFDGLFSFCQTYAGGSVGGAVKLNHGL-CDIAINWAGGLHHAKKCEASGFC 159
++ + +DCPVF L + Q AG S+ A L + DIAINW GG HHA+K ASGFC
Sbjct: 67 KYGLEDDCPVFPFLSMYVQLVAGSSLALAKHLITQVERDIAINWYGGRHHAQKSRASGFC 126
Query: 160 YVNDIVLAILELLKQH-ERVLYVDIDIHHGDGVEEAFYTTDRVMTVSFHKFGD-YFPGTG 217
YVNDIVLAIL L + RV Y+D+D+HHGDGVE AF+ + V+T S H++ +FPGTG
Sbjct: 127 YVNDIVLAILRLRRARFRRVFYLDLDLHHGDGVESAFFFSKNVLTCSIHRYDPGFFPGTG 186
Query: 218 DIRDIGYSKGKFYSLNVPLDDGIDDESYHYLFKPIIGKVMEVFRPGAVVLQCGADSLSGD 277
+++ LN+PL G+ D++ + I+ ++E F P +V+QCG D LSGD
Sbjct: 187 SLKN----SSDKGMLNIPLKRGLSDKTLLRIIDSIVRPLIEKFEPEVIVIQCGCDGLSGD 242
Query: 278 RLGCFNLSIKGHAECVKF-MRSF-NVPLLLLGGGGYTIRNVARCWCYETGVA 327
+NL+I+G+ ++ ++ F + P LLLGGGGY AR W Y T +
Sbjct: 243 PHKEWNLTIRGYGSVIELLLKEFKDKPTLLLGGGGYNHTEAARAWTYLTSMV 294
>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 = 283 bits (725), Expect = 1e-92
Identities = 108/287 (37%), Positives = 147/287 (51%), Gaps = 15/287 (5%)
Query: 42 RIRMTHALLAHYGLLQNMQVLKPFPARERDLCRFHADDYVSFLRSITPETQQDQLRQLKR 101
RIR L GL +++++ A E L + H ++Y++ L++ + K
Sbjct: 1 RIRDLIEALKELGLRPKIELIECREATEELLLKVHTEEYLNELKANFAVATITES---KP 57
Query: 102 FNVGEDCPVFDGLFSFCQTYAGGSVGGAVKLNHGLCDIAINWA-GGLHHAKKCEASGFCY 160
G + PV F + GG V A + G + A G HHA K A GFCY
Sbjct: 58 VIFGPNFPVQRHYFRGARLSTGGVVEAAELVAKGELERAFAVVGAGGHHAGKSRAWGFCY 117
Query: 161 VNDIVLAILELLKQ-HERVLYVDIDIHHGDGVEEAFYTTDRVMTVSFHKFGDYFPGTGDI 219
ND+VLAI L ++ R+L +D D HHGDG EAFY DRV+ +SFH + Y G G
Sbjct: 118 FNDVVLAIKFLRERGISRILIIDTDAHHGDGTREAFYDDDRVLHMSFHNYDIYPFGRG-- 175
Query: 220 RDIGYSKGKFYSLNVPLDDGIDDESYHYLFKPIIGKVMEVFRPGAVVLQCGADSLSGDRL 279
KGK Y +NVPL+DG+ DE Y + +I KV+E F P VVLQ G D+ GDRL
Sbjct: 176 ------KGKGYKINVPLEDGLGDEEYLDAVERVISKVLEEFEPEVVVLQFGHDTHEGDRL 229
Query: 280 GCFNLSIKGHAECVKFMRSFN--VPLLLLGGGGYTIRNVARCWCYET 324
G FNLS KG + + ++ F P+L++ GGGY AR W
Sbjct: 230 GGFNLSEKGFVKLAEIVKEFARGGPILMVLGGGYNPEAAARIWTAII 276
>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 = 160 bits (407), Expect = 2e-45
Identities = 80/299 (26%), Positives = 132/299 (44%), Gaps = 32/299 (10%)
Query: 36 HPMKPHRIRMTHALLAHYGLLQNMQVLKPFPARERDLCRFHADDYVSFLRSITPETQQDQ 95
HP +P R+ L GLL + ++P PA E +L R H +Y+ +
Sbjct: 1 HPERPERLLAILEALEEEGLLDRLVFVEPRPATEEELLRVHTPEYIERVEET-------- 52
Query: 96 LRQLKRFNVGEDCPVFDGLFSFC-QTY--AGGSVGGAVKLNHGLCDIAINWAGGL----- 147
D +Y A + G A+ + A L
Sbjct: 53 --------CEAGGGYLDPDTYVSPGSYEAALLAAGAALAAVDAVLSGEAENAFALVRPPG 104
Query: 148 HHAKKCEASGFCYVNDIVLAILELLKQH--ERVLYVDIDIHHGDGVEEAFYTTDRVMTVS 205
HHA+ A GFC N++ +A K++ +RVL VD D+HHG+G ++ FY V+ S
Sbjct: 105 HHAEPDRAMGFCLFNNVAIAARYAQKRYGLKRVLIVDWDVHHGNGTQDIFYDDPSVLYFS 164
Query: 206 FHKFGDYFPGTGDIRDIGYSKGKFYSLNVPLDDGIDDESYHYLFKPIIGKVMEVFRPGAV 265
H++ ++PGTG + G G+ +++NVPL G D Y F+ ++ + F+P V
Sbjct: 165 IHQY-PFYPGTGAAEETGGGAGEGFTINVPLPPGSGDAEYLAAFEEVLLPIAREFQPDLV 223
Query: 266 VLQCGADSLSGDRLGCFNLSIKGHAECVKFMRSF-----NVPLLLLGGGGYTIRNVARC 319
++ G D+ GD LG NL+ +G+A + ++ L+ + GGY + +A
Sbjct: 224 LVSAGFDAHRGDPLGGMNLTPEGYARLTRLLKELADEHCGGRLVFVLEGGYNLEALAES 282
>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 = 153 bits (390), Expect = 4e-43
Identities = 90/291 (30%), Positives = 132/291 (45%), Gaps = 33/291 (11%)
Query: 36 HPMKPHRIRMTHALLAHYGLLQNMQVLKPFPARERDLCRFHADDYV-SFLRSITPETQQD 94
H + + L GL+ +++P PA DL R H +Y+ S
Sbjct: 1 HRFPMRKYGLLREALLEEGLVLPEDIVEPEPATREDLLRVHDPEYLESLKSGELSR---- 56
Query: 95 QLRQLKRFNVGEDCPVFDGLFSFCQTYAGGSVGGA-VKLNHGLCDIAINWAGGLHHAKKC 153
+ + F P L + GG++ A + L HG +AIN AGG HHA
Sbjct: 57 EEIRRIGF------PWSPELVERTRLAVGGTILAARLALEHG---LAINLAGGTHHAFPD 107
Query: 154 EASGFCYVNDIVLAILELLKQH--ERVLYVDIDIHHGDGVEEAFYTTDRVMTVSFHKFGD 211
GFC NDI +A LL + RVL VD+D+H G+G F V T S H
Sbjct: 108 RGEGFCVFNDIAIAARVLLAEGLVRRVLIVDLDVHQGNGTAAIFADDPSVFTFSMHG-EK 166
Query: 212 YFPGTGDIRDIGYSKGKFYSLNVPLDDGIDDESYHYLFKPIIGKVMEVFRPGAVVLQCGA 271
+P S L+VPL DG D+ Y + + +++ FRP V G
Sbjct: 167 NYP-----FRKEPS-----DLDVPLPDGTGDDEYLAALEEALPRLLAEFRPDLVFYNAGV 216
Query: 272 DSLSGDRLGCFNLSIKGHAE----CVKFMRSFNVPLLLLGGGGYTIRNVAR 318
D L+GDRLG +LS++G E ++F R+ +P+ ++ GGGY+ R++AR
Sbjct: 217 DVLAGDRLGRLSLSLEGLRERDRLVLRFARARGIPVAMVLGGGYS-RDIAR 266
>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 = 147 bits (374), Expect = 5e-40
Identities = 75/271 (27%), Positives = 120/271 (44%), Gaps = 30/271 (11%)
Query: 22 FYDPEVGNYYYGQGHPMKPHRIRMTHALLAHYGLLQNMQVLKPFPARERDLCRFHADDYV 81
+ P G HP P R LL GL ++ ++ P PA + +L R H +Y+
Sbjct: 19 LFLPVGGLLVQPGRHPENPETKRRIKNLLEVSGLSDHLVLITPRPATDEELLRVHTPEYI 78
Query: 82 SFLRSITPETQQDQLRQLKRFNVGEDC---PVFDGLFSFCQTYAGGS-------VGGAVK 131
D+++ GE P G + AGG+ + G V
Sbjct: 79 ------------DRVKAASAAGGGEAGGGTPFGPGSYEIALLAAGGAIAAVDAVLDGEVD 126
Query: 132 LNHGLCDIAINWAGGLHHAKKCEASGFCYVNDIVLAILELLKQH--ERVLYVDIDIHHGD 189
+ L G HHA+ + GFC N++ +A L +RV VD D+HHG+
Sbjct: 127 NAYALV----RPPG--HHAEPDQGMGFCLFNNVAIAARHALAVGGVKRVAVVDWDVHHGN 180
Query: 190 GVEEAFYTTDRVMTVSFHKFGDYFPGTGDIRDIGYSKGKFYSLNVPLDDGIDDESYHYLF 249
G + FY V+T+S H+ + P +G + + G G+ Y+LN+PL G D +Y + F
Sbjct: 181 GTQAIFYDDPDVLTISLHQDRCFPPDSGAVEERGEGAGEGYNLNIPLPPGSGDGAYLHAF 240
Query: 250 KPIIGKVMEVFRPGAVVLQCGADSLSGDRLG 280
+ I+ + FRP +++ G D+ + D LG
Sbjct: 241 ERIVLPALRAFRPELIIVASGFDASAFDPLG 271
>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 = 138 bits (350), Expect = 3e-37
Identities = 82/294 (27%), Positives = 125/294 (42%), Gaps = 37/294 (12%)
Query: 35 GHPMKPHRIRMTHALLAHYGLLQNMQVLKPFPARERDLCRFHADDYVSFLRSITPETQQD 94
HP P R L GL +VL P + H DYV FL + D
Sbjct: 24 PHPENPERAEAILDALKRAGL---GEVLPPRDFGLEPILAVHDPDYVDFLETA------D 74
Query: 95 QLRQLKRFNVGEDCPVFDGLFSFCQTYAGGSVGGAVKLNHGLCDIAINWAGGL-----HH 149
D P+ +G + A ++ A + G A L HH
Sbjct: 75 T-----------DTPISEGTWEAALAAADTALTAADLVLEGE-----RAAYALCRPPGHH 118
Query: 150 AKKCEASGFCYVNDIVLAILELLKQHERVLYVDIDIHHGDGVEEAFYTTDRVMTVSFHKF 209
A + A GFCY N+ +A L + RV +D+D+HHG+G +E FY V+ VS H
Sbjct: 119 AGRDRAGGFCYFNNAAIAAQYLRDRAGRVAILDVDVHHGNGTQEIFYERPDVLYVSIH-- 176
Query: 210 GD---YFPGT-GDIRDIGYSKGKFYSLNVPLDDGIDDESYHYLFKPIIGKVMEVFRPGAV 265
GD ++P G + G +G+ Y+LN+PL G D+ Y + + F P A+
Sbjct: 177 GDPRTFYPFFLGFADETGEGEGEGYNLNLPLPPGTGDDDYLAALDEALAAIAA-FGPDAL 235
Query: 266 VLQCGADSLSGDRLGCFNLSIKGHAECVKFMRSFNVPLLLLGGGGYTIRNVARC 319
V+ G D+ GD L F L+ + +A + + + +P + + GGY + + R
Sbjct: 236 VVSLGFDTHEGDPLSDFKLTTEDYARIGRRIAALGLPTVFVQEGGYNVDALGRN 289
>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 = 137 bits (347), Expect = 2e-36
Identities = 82/306 (26%), Positives = 141/306 (46%), Gaps = 26/306 (8%)
Query: 32 YGQGHPMKPHRIRMTHALLAHYGLLQNMQVLKPFPARERDLCRFHADDYVSFLRSITPET 91
+ H P R+ L GLL+ + A E ++ H+ +Y+ ++S T
Sbjct: 3 WDSNHIECPERLEAILERLTQDGLLERCVKIPAREAEEDEILLVHSQEYIDLVKS----T 58
Query: 92 QQDQLRQLKRFNVGEDCPVFDGLFSFCQTY-----AGGSVGGAVKLN-HGLC--DIAINW 143
+ + +L+ C +D ++ TY A GS VK G A+
Sbjct: 59 ETMEKEELESL-----CSGYDSVYLCPSTYEAARLAAGSTIELVKAVMAGKIQNGFALIR 113
Query: 144 AGGLHHAKKCEASGFCYVNDIVLAILELLKQH--ERVLYVDIDIHHGDGVEEAFYTTDRV 201
G HHA + EA+G+C N++ +A +++ +R+L VD D+HHG G ++ FY RV
Sbjct: 114 PPG-HHAMRNEANGYCIFNNVAIAAKYAIEKLGLKRILIVDWDVHHGQGTQQGFYEDPRV 172
Query: 202 MTVSFHKF--GDYFPG--TGDIRDIGYSKGKFYSLNVPLDD-GIDDESYHYLFKPIIGKV 256
+ S H++ G ++P D IG G +++NVPL+ G+ D Y +F I+ +
Sbjct: 173 LYFSIHRYEHGRFWPHLFESDYDYIGVGHGYGFNVNVPLNQTGLGDADYLAIFHHILLPL 232
Query: 257 MEVFRPGAVVLQCGADSLSGDRLGCFNLSIKGHAECVKFMRSFNVP-LLLLGGGGYTIRN 315
F+P V++ G D+ GD G ++ G+A + + LLL+ GGY + +
Sbjct: 233 ALEFQPELVLVSAGFDASIGDPEGEMAVTPAGYAHLTRLLMGLAGGKLLLVLEGGYLLES 292
Query: 316 VARCWC 321
+A
Sbjct: 293 LAESVS 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 = 127 bits (322), Expect = 6e-33
Identities = 86/327 (26%), Positives = 153/327 (46%), Gaps = 32/327 (9%)
Query: 23 YDPEVGNYY--YGQGHPMKPHRIRMTHALLAHYGLLQNMQVLKPFPARERDLCRFHADDY 80
YD + N++ + GHP P RI + GLL+ L A E +L H++++
Sbjct: 1 YDQRMMNHHNLWDPGHPECPQRISRIYERHNDLGLLERCLRLPSRLATEDELLLCHSEEH 60
Query: 81 VSFLRSITPETQQDQLRQLKRFNVGEDCP-VFDGLFSFCQTYAGGSVGGAVKL---NHGL 136
+ ++S+ ++ R K ++ P + C A G V V+
Sbjct: 61 LDEMKSLEKMKPRELNRLGKEYDSIYIHPDSYQ-----CALLAAGCVLQVVEAVLTGESR 115
Query: 137 CDIAINWAGGLHHAKKCEASGFCYVNDIVLAILELLKQH--ERVLYVDIDIHHGDGVEEA 194
+AI G HHA++ A GFC+ N++ +A K++ +R+L VD D+HHG+G +
Sbjct: 116 NGVAIVRPPG-HHAEQDTACGFCFFNNVAIAARYAQKKYGLKRILIVDWDVHHGNGTQHM 174
Query: 195 FYTTDRVMTVSFHKF--GDYFPGT--GDIRDIGYSKGKFYSLNVPLD-DGIDDESYHYLF 249
F + V+ +S H++ G +FP + G+ +G KG+ +++N+P + G+ D Y F
Sbjct: 175 FESDPSVLYISLHRYDNGSFFPNSPEGNYDVVGKGKGEGFNVNIPWNKGGMGDAEYIAAF 234
Query: 250 KPIIGKVMEVFRPGAVVLQCGADSLSGDRLGCFNLSIKGHAECVKFMRSFNVPLLLLGG- 308
+ ++ + F P V++ G D+ GD LG ++ +G+A + S L GG
Sbjct: 235 QQVVLPIAYEFNPELVLVSAGFDAARGDPLGGCKVTPEGYAHMTHMLMS------LAGGR 288
Query: 309 ------GGYTIRNVARCWCYETGVALG 329
GGY + +++ T LG
Sbjct: 289 VIVILEGGYNLTSISESMSMCTKTLLG 315
>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 = 123 bits (312), Expect = 8e-32
Identities = 81/306 (26%), Positives = 141/306 (46%), Gaps = 34/306 (11%)
Query: 35 GHPMKPHRIRMTHALLAHYGLLQNMQVLKPFPARERDLCRFHADDYVSFLRSITPETQQD 94
HP P RI L GL+ M + A + ++ H++++ + + + +
Sbjct: 2 PHPEDPSRISRIFEKLKEAGLINRMLRIPIREATKEEILLVHSEEHWDRVEATEKMSDEQ 61
Query: 95 QLRQLKRFNVGEDCPVFDGLFSFCQTYAGGSVGGAVKLNHGLCD------IAINWAGGLH 148
+ + F D + +FC A S GGA++ + + A+ G H
Sbjct: 62 LKDRTEIF--ERDSLYVNNDTAFC---ARLSCGGAIEACRAVAEGRVKNAFAVVRPPG-H 115
Query: 149 HAKKCEASGFCYVNDIVLAILELLKQHE----RVLYVDIDIHHGDGVEEAFYTTDRVMTV 204
HA+ E+ GFC+ N++ +A L ++ ++L +D DIHHG+G + AFY V+ +
Sbjct: 116 HAEPDESMGFCFFNNVAVAAKWLQTEYPDKIKKILILDWDIHHGNGTQRAFYDDPNVLYI 175
Query: 205 SFHKF--GDYFPGT--GDIRDIGYSKGKFYSLNVPLDD-GIDDESYHYLFKPIIGKVMEV 259
S H+F G ++PGT GD +G G +++N+P G+ D Y Y F+ I+ +
Sbjct: 176 SLHRFENGGFYPGTPYGDYESVGEGAGLGFNVNIPWPQGGMGDADYIYAFQRIVMPIAYE 235
Query: 260 FRPGAVVLQCGADSLSGDRLGCFNLSIKGHAECVKFMRSFNVPLLLLGG-------GGYT 312
F P V++ G D+ GD LG +++ G+A + S L GG GGY
Sbjct: 236 FDPDLVIISAGFDAADGDELGQCHVTPAGYAHMTHMLMS------LAGGKLVVALEGGYN 289
Query: 313 IRNVAR 318
+ ++
Sbjct: 290 LDAISD 295
>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 = 115 bits (291), Expect = 8e-30
Identities = 39/235 (16%), Positives = 62/235 (26%), Gaps = 51/235 (21%)
Query: 117 FCQTYAGGSVGGAVKLNHGLCDIAINWAGGLHHAKKCEASGFCYVNDIVLAILELLKQHE 176
+ AG V + + G H+ N + A+ EL H
Sbjct: 10 AHELLAGVVVAVLKD-----GKVPVVLGG--DHSI---------ANGAIRAVAEL---HP 50
Query: 177 RVLYVDIDIHHGDGVEEAFY--------------TTDRVMTVSFHKFGDYFPGTGDIRDI 222
+ +D+D HH EAF V VS G G
Sbjct: 51 DLGVIDVDAHHDVRTPEAFGKGNHHTPRHLLCEPLISDVHIVSIGIRGVSNGEAG----- 105
Query: 223 GYSKGKFYSLNVPLDDGIDDESYHYLFKPIIGKVMEVFRPGAVVLQCGADSLSGD----- 277
G K + + + D +F+ I+ + + V L D L
Sbjct: 106 GAYARKLGVVYFSMTEV-DKLGLGDVFEEIVSYLG--DKGDNVYLSVDVDGLDPSFAPGT 162
Query: 278 -RLGCFNLSIKGHAECVKFMRSFNVPLLLLGGGGYTI----RNVARCWCYETGVA 327
G LS + + + N+ + L + AR T
Sbjct: 163 GTPGPGGLSYREGLYITERIAKTNLVVGLDIVEVNPLLDETGRTARLAAALTLEL 217
>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 = 108 bits (272), Expect = 2e-26
Identities = 75/258 (29%), Positives = 111/258 (43%), Gaps = 26/258 (10%)
Query: 36 HPMKPHRIRMTHALLAHYGLLQNMQVLKPFPARERDLCRFHADDYVSFLRSITPETQQDQ 95
HP P R+ L GL + ++ L+ PA L R H YV L + PE Q
Sbjct: 1 HPESPERLEAILDALIASGLDRLLRQLEAPPATREQLLRVHDAAYVDRLEAAAPEEGLVQ 60
Query: 96 LRQLKRFNVGEDCPVFDGLFSFCQTYAGGSVGGAV------KLNHGLCDIAINWAGGLHH 149
L D + G A G+V AV + + C A+ G HH
Sbjct: 61 L--------DPDTAMSPGSLE-AALRAAGAVVAAVDAVMAGEARNAFC--AVRPPG--HH 107
Query: 150 AKKCEASGFCYVNDIVLAILELLKQH--ERVLYVDIDIHHGDGVEEAFYTTDRVMTVSFH 207
A++ +A GFC N++ +A L H ERV VD D+HHG+G E+ F RV+ S H
Sbjct: 108 AERDKAMGFCLFNNVAIAAAHALAHHGLERVAIVDFDVHHGNGTEDIFRDDPRVLFCSSH 167
Query: 208 KFGDYFPGTGDIRDIGYSKGKFYSLNVPLDDGIDDESYHYLFKPIIGKVMEVFRPGAVVL 267
+ +PGTG + G+ +NVPL G + + ++ F+P +++
Sbjct: 168 QHP-LYPGTGAPDETGHG----NIVNVPLPAGTGGAEFREAVEDRWLPALDAFKPDLILI 222
Query: 268 QCGADSLSGDRLGCFNLS 285
G D+ D L NL+
Sbjct: 223 SAGFDAHRDDPLAQLNLT 240
>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 = 102 bits (256), Expect = 9e-24
Identities = 48/159 (30%), Positives = 85/159 (53%), Gaps = 14/159 (8%)
Query: 148 HHAKKCEASGFCYVNDIVLA--ILELLKQHERVLYVDIDIHHGDGVEEAFYTTDRVMTVS 205
HHA+ +A GFC+ N + +A L+ + ++L VD D+HHG+G ++ FY V+ +S
Sbjct: 151 HHAEPSQAMGFCFFNSVAIAAKQLQQKLKLRKILIVDWDVHHGNGTQQIFYEDPNVLYIS 210
Query: 206 FHKF--GDYFPGTGDIRDIGYSKGKFYSLNVPLDDGID----DESYHYLFKPIIGKVMEV 259
H++ G++FPGTG ++G G+ +++N+ G+D D Y F+ ++ +
Sbjct: 211 LHRYDDGNFFPGTGAPTEVGSGAGEGFNVNIAWSGGLDPPMGDAEYLAAFRTVVMPIARE 270
Query: 260 FRPGAVVLQCGADSLSG--DRLGCFNLSIKGHAECVKFM 296
F P V++ G D+ G LG + +S C +M
Sbjct: 271 FSPDIVLVSAGFDAAEGHPPPLGGYKVS----PACFGYM 305
>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 = 97.2 bits (242), Expect = 3e-22
Identities = 87/313 (27%), Positives = 143/313 (45%), Gaps = 32/313 (10%)
Query: 36 HPMKPHRIRMTHALLAHYGLLQNMQVLKPFPAR---ERDLCRFHADDYVSFLRSITPETQ 92
P P R+ L GLL+ AR E +L H+ +YV+ ++S T
Sbjct: 7 FPECPERLHAIREKLIQEGLLER---CVSVQAREASEEELLLVHSPEYVALMKS-TQYMT 62
Query: 93 QDQLRQLKRFNVGEDCPVFDGLF----SF-CQTYAGGSVGGAV-KLNHG-LCD-IAINWA 144
+++LR L +D ++ S+ C A GSV V K+ G + + +AI
Sbjct: 63 EEELRTLAD--------TYDSVYLHPNSYSCACLAVGSVLQLVDKVLGGEIRNGLAIVRP 114
Query: 145 GGLHHAKKCEASGFCYVNDIVLAILELLKQH--ERVLYVDIDIHHGDGVEEAFYTTDRVM 202
G HHA+ + G+C N++ +A ++H +RVL VD D+HHG G + F V+
Sbjct: 115 PG-HHAQHDKMDGYCMFNNVAIAARYAQQKHGVQRVLIVDWDVHHGQGTQFIFEQDPSVL 173
Query: 203 TVSFHKF--GDYFP--GTGDIRDIGYSKGKFYSLNVPLDD-GIDDESYHYLFKPIIGKVM 257
S H++ G ++P D +G+ +G+ Y++NVP + G+ D Y F ++ V
Sbjct: 174 YFSIHRYEQGRFWPHLKESDSSAVGFGRGEGYNINVPWNQVGMRDADYIAAFLHVLLPVA 233
Query: 258 EVFRPGAVVLQCGADSLSGDRLGCFNLSIKGHAECVKFMRSFNVPLLLLG-GGGYTIRNV 316
F+P V++ G D++ GD G + A + L+L GGY +R++
Sbjct: 234 LEFQPQLVLVAAGFDAVIGDPKGEMAATPACFAHLTHLLMGLAGGKLILSLEGGYNLRSL 293
Query: 317 ARCWCYETGVALG 329
A C LG
Sbjct: 294 AEGVCASLKALLG 306
>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 = 97.8 bits (243), Expect = 6e-22
Identities = 51/155 (32%), Positives = 90/155 (58%), Gaps = 14/155 (9%)
Query: 148 HHAKKCEASGFCYVNDIVLAILELLKQH---ERVLYVDIDIHHGDGVEEAFYTTDRVMTV 204
HHA++ A GFC+ N + +A +LL+Q ++L VD DIHHG+G ++AFY V+ +
Sbjct: 154 HHAEESTAMGFCFFNSVAIAA-KLLQQKLNVGKILIVDWDIHHGNGTQQAFYNDPNVLYI 212
Query: 205 SFHKF--GDYFPGTGDIRDIGYSKGKFYSLNVPLDDGID----DESYHYLFKPIIGKVME 258
S H++ G++FPG+G ++G G +++N+ G+D D Y F+ ++ +
Sbjct: 213 SLHRYDDGNFFPGSGAPDEVGAGPGVGFNVNIAWTGGVDPPIGDVEYLTAFRTVVMPIAN 272
Query: 259 VFRPGAVVLQCGADSLSGDR--LGCFNLSIK--GH 289
F P V++ G D++ G + LG ++++ K GH
Sbjct: 273 EFSPDVVLVSAGFDAVEGHQSPLGGYSVTAKCFGH 307
>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 = 96.3 bits (239), Expect = 2e-21
Identities = 56/173 (32%), Positives = 96/173 (55%), Gaps = 19/173 (10%)
Query: 148 HHAKKCEASGFCYVNDIVLAILELLKQH---ERVLYVDIDIHHGDGVEEAFYTTDRVMTV 204
HHA++ GFCY N + +A +LL+Q ++L VD D+HHG+G ++AFY+ V+ +
Sbjct: 154 HHAEESTPMGFCYFNSVAIAA-KLLQQRLNVSKILIVDWDVHHGNGTQQAFYSDPNVLYM 212
Query: 205 SFHKF--GDYFPGTGDIRDIGYSKGKFYSLNVPLDDGID----DESYHYLFKPIIGKVME 258
S H++ G++FPG+G ++G G +++N+ G+D D Y F+ ++ +
Sbjct: 213 SLHRYDDGNFFPGSGAPDEVGTGPGVGFNVNMAFTGGLDPPMGDAEYLAAFRTVVMPIAS 272
Query: 259 VFRPGAVVLQCGADSLSGD--RLGCFNLSIKGHAECVKFMRSFNVPLLLLGGG 309
F P V++ G D++ G LG +NLS A+C ++ L+ L GG
Sbjct: 273 EFAPDVVLVSSGFDAVEGHPTPLGGYNLS----AKCFGYLTK---QLMGLAGG 318
>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 = 93.9 bits (233), Expect = 8e-21
Identities = 51/154 (33%), Positives = 87/154 (56%), Gaps = 12/154 (7%)
Query: 148 HHAKKCEASGFCYVNDIVLAILELLKQHE--RVLYVDIDIHHGDGVEEAFYTTDRVMTVS 205
HHA++ A GFC+ N + + L Q ++L VD+D+HHG+G ++AFY ++ +S
Sbjct: 152 HHAEESTAMGFCFFNSVAITAKYLRDQLNISKILIVDLDVHHGNGTQQAFYADPSILYIS 211
Query: 206 FHKF--GDYFPGTGDIRDIGYSKGKFYSLNVPLDDGID----DESYHYLFKPIIGKVMEV 259
H++ G++FPG+G ++G G+ Y++N+ G+D D Y F+ I+ V +
Sbjct: 212 LHRYDEGNFFPGSGAPNEVGTGLGEGYNINIAWTGGLDPPMGDVEYLEAFRTIVKPVAKE 271
Query: 260 FRPGAVVLQCGADSLSGDR--LGCFNLSIK--GH 289
F P V++ G D+L G LG + ++ K GH
Sbjct: 272 FDPDMVLVSAGFDALEGHTPPLGGYKVTAKCFGH 305
>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 = 92.8 bits (230), Expect = 2e-20
Identities = 54/172 (31%), Positives = 93/172 (54%), Gaps = 17/172 (9%)
Query: 148 HHAKKCEASGFCYVNDIVLAILELLKQHE--RVLYVDIDIHHGDGVEEAFYTTDRVMTVS 205
HHA A GFC+ N + +A +L +Q + ++L VD D+HHG+G ++ FY V+ +S
Sbjct: 152 HHADHSTAMGFCFFNSVAIACRQLQQQGKASKILIVDWDVHHGNGTQQTFYQDPSVLYIS 211
Query: 206 FHKF--GDYFPGTGDIRDIGYSKGKFYSLNVPLDDGID----DESYHYLFKPIIGKVMEV 259
H+ G++FPG+G + ++G G+ +++NV G+D D Y F+ ++ +
Sbjct: 212 LHRHDDGNFFPGSGAVDEVGAGSGEGFNVNVAWAGGLDPPMGDPEYLAAFRIVVMPIARE 271
Query: 260 FRPGAVVLQCGADSLSGD--RLGCFNLSIKGHAECVKFMRSFNVPLLLLGGG 309
F P V++ G D+ G LG +++S A+C +M L+ L GG
Sbjct: 272 FSPDLVLVSAGFDAAEGHPAPLGGYHVS----AKCFGYMTQ---QLMNLAGG 316
>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 = 87.6 bits (217), Expect = 6e-19
Identities = 80/323 (24%), Positives = 141/323 (43%), Gaps = 46/323 (14%)
Query: 40 PHRIRMTHALLAHYGLLQNMQVLKPFPARE---RDLCRFHADDYVSFLRSITPETQQDQL 96
P R+ ++ L YGL+Q PARE ++ H+ +Y+S +R ETQ
Sbjct: 11 PERLTASYERLRQYGLVQR---CLRLPAREASEEEILLVHSPEYLSLVR----ETQVMNK 63
Query: 97 RQLKRFNVGEDCPVFDGLFSFCQTY--AGGSVGGAVKLNHGLCDIAINWAGGL-----HH 149
+L + +D ++ T+ A + G ++L + + L HH
Sbjct: 64 EELMAISGK-----YDAVYFHPNTFHCARLAAGATLQLVDAVLTGEVQNGMALVRPPGHH 118
Query: 150 AKKCEASGFCYVNDIVLAILELLKQH--ERVLYVDIDIHHGDGVEEAFYTTDRVMTVSFH 207
+++ A+GFC N++ +A K++ R+L VD D+HHG G++ F V+ S+H
Sbjct: 119 SQRNAANGFCVFNNVAIAAEYAKKKYGLHRILIVDWDVHHGQGIQYIFEEDPSVLYFSWH 178
Query: 208 KF--GDYFPG--TGDIRDIGYSKGKFYSLNVPLDD-GIDDESYHYLFKPIIGKVMEVFRP 262
++ ++P D +G KG +++N+P + G+ + Y F ++ + F P
Sbjct: 179 RYEHQRFWPFLRESDYDAVGRGKGLGFNINLPWNKVGMGNADYLAAFFHVLLPLAFEFDP 238
Query: 263 GAVVLQCGADSLSGDRLGCFNLSIKGHAECVKFMRSFNVPLLLLGG-------GGYTIRN 315
V++ G DS GD G + EC + + L GG GGY + +
Sbjct: 239 ELVLVSAGFDSAIGDPEGQMCAT----PECFAHLTHLLMV--LAGGKLCAVLEGGYHLES 292
Query: 316 VARCWCYETGVALGVEVDDKMPQ 338
+A C LG D +P+
Sbjct: 293 LAESVCMTVQTLLG----DPLPR 311
>gnl|CDD|212522 cd09998, HDAC_Hos3, Class II histone deacetylases Hos3 and related
proteins. Fungal histone deacetylase Hos3 from
Saccharomyces cerevisiae is a Zn-dependent enzyme
belonging to HDAC class II. It catalyzes hydrolysis of
an N(6)-acetyl-lysine residue of a histone to yield a
deacetylated histone (EC 3.5.1.98). Histone
acetylation/deacetylation process is important for
mediation of transcriptional regulation of many genes.
Histone deacetylases usually act via association with
DNA binding proteins to target specific chromatin
regions. Hos3 deacetylase is homodimer, in vitro it
shows specificity to H4, H3 and H2A.
Length = 353
Score = 52.1 bits (125), Expect = 3e-07
Identities = 39/171 (22%), Positives = 63/171 (36%), Gaps = 46/171 (26%)
Query: 148 HHAKKCEASGFCYVNDIVLAILELLKQH--ERVLYVDIDIHHGDGVEE------------ 193
HH + SGFC+VN++ + H RV+ +DID+HHG+G ++
Sbjct: 120 HHCSESTPSGFCWVNNVHVGAAHAYLTHGITRVVILDIDLHHGNGTQDIAWRINAEANKQ 179
Query: 194 ------------AFYTTDRVMTVSFHKFGDYFPGTGD---IRD----IGYSKGKFYSLNV 234
A R+ S H + GD ++D I + G++ NV
Sbjct: 180 ALESSSYDDFKPAGAPGLRIFYSSLHDINSFPCEDGDPAKVKDASVSIDGAHGQWIW-NV 238
Query: 235 PLDDGIDDESYHYLFKP----IIGKVMEVFRP--------GAVVLQCGADS 273
L +E + L+ P + K E R V + G D+
Sbjct: 239 HLQPWTTEEDFWELYYPKYRILFEKAAEFLRLTTAATPFKTLVFISAGFDA 289
>gnl|CDD|205674 pfam13496, DUF4120, Domain of unknown function (DUF4120). Based on
Bacteroides thetaiotaomicron gene BT_2585, a putative
uncharacterized protein. As seen in gene expression
experiments
(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22
31), it appears to be upregulated in the presence of
host or vs when in culture.
Length = 95
Score = 34.8 bits (80), Expect = 0.015
Identities = 25/78 (32%), Positives = 34/78 (43%), Gaps = 13/78 (16%)
Query: 72 LCRFHADDYVSFLRSITPETQQDQLRQLKRFNVGEDCPVFDGL--------FSFCQTYAG 123
LC+ H + V + +SI T Q + +LK++ +CP L F F Q Y
Sbjct: 3 LCQEHYEKVVQYAKSIGDTTLQKCIERLKQWEKNPNCPCEIELYYDFAPYSFGFTQRYPD 62
Query: 124 GS---VGGAVKLNHGLCD 138
G VGG L HG D
Sbjct: 63 GRTGIVGGL--LYHGQPD 78
>gnl|CDD|217861 pfam04050, Upf2, Up-frameshift suppressor 2. Transcripts
harbouring premature signals for translation termination
are recognised and rapidly degraded by eukaryotic cells
through a pathway known as nonsense-mediated mRNA decay.
In Saccharomyces cerevisiae, three trans-acting factors
(Upf1 to Upf3) are required for nonsense-mediated mRNA
decay.
Length = 171
Score = 35.0 bits (81), Expect = 0.038
Identities = 29/72 (40%), Positives = 39/72 (54%), Gaps = 9/72 (12%)
Query: 395 DSELPEADEDQE--DGDERWDPDSDMDVDDERKSLPNRVKR--EAVEPEQK---DREGLK 447
D ELPE DED E D +E PD + D + + + V R E V+PE + DRE K
Sbjct: 13 DEELPEEDEDDESSDEEEVDLPDDEQDEESDSEEEQIFVTRQEEEVDPEAEAEFDREFEK 72
Query: 448 GMAE--QARGFD 457
MAE ++R F+
Sbjct: 73 MMAESLESRKFE 84
>gnl|CDD|226894 COG4499, COG4499, Predicted membrane protein [Function unknown].
Length = 434
Score = 35.5 bits (82), Expect = 0.060
Identities = 18/74 (24%), Positives = 37/74 (50%), Gaps = 6/74 (8%)
Query: 357 NMENKNSRQLLEEIRNKLLEYLSKL-----QHAPSVQFQERPPDSELPEADEDQEDGDER 411
++ ++LL+E KL +Y KL + S + + + + +L + +E+++ E+
Sbjct: 361 DLSGDKRQELLKEYNKKLQDYTKKLGEVKDETDASEEAEAKAKEEKL-KQEENEKKQKEQ 419
Query: 412 WDPDSDMDVDDERK 425
D D + DERK
Sbjct: 420 ADEDKEKRQKDERK 433
>gnl|CDD|177433 PHA02608, 67, prohead core protein; Provisional.
Length = 80
Score = 31.3 bits (71), Expect = 0.17
Identities = 15/33 (45%), Positives = 20/33 (60%)
Query: 391 ERPPDSELPEADEDQEDGDERWDPDSDMDVDDE 423
E P D + E D+D +D D++ D D D D DDE
Sbjct: 48 EEPEDDDDDEDDDDDDDKDDKDDDDDDDDEDDE 80
>gnl|CDD|99747 cd06454, KBL_like, KBL_like; this family belongs to the pyridoxal
phosphate (PLP)-dependent aspartate aminotransferase
superfamily (fold I). The major groups in this CD
corresponds to serine palmitoyltransferase (SPT),
5-aminolevulinate synthase (ALAS),
8-amino-7-oxononanoate synthase (AONS), and
2-amino-3-ketobutyrate CoA ligase (KBL). SPT is
responsible for the condensation of L-serine with
palmitoyl-CoA to produce 3-ketodihydrospingosine, the
reaction of the first step in sphingolipid biosynthesis.
ALAS is involved in heme biosynthesis; it catalyzes the
synthesis of 5-aminolevulinic acid from glycine and
succinyl-coenzyme A. AONS catalyses the decarboxylative
condensation of l-alanine and pimeloyl-CoA in the first
committed step of biotin biosynthesis. KBL catalyzes the
second reaction step of the metabolic degradation
pathway for threonine converting 2-amino-3-ketobutyrate,
to glycine and acetyl-CoA. The members of this CD are
widely found in all three forms of life.
Length = 349
Score = 33.7 bits (78), Expect = 0.19
Identities = 24/84 (28%), Positives = 42/84 (50%), Gaps = 16/84 (19%)
Query: 167 AILELLKQHERVLYVDIDIH-------HGDGVEEAFYTTDRV--MTVSFHK----FGDYF 213
+++L K++ +L+VD + H HG GVEE TD V + + K G Y
Sbjct: 153 ELVDLAKKYGAILFVD-EAHSVGVYGPHGRGVEEFGGLTDDVDIIMGTLGKAFGAVGGYI 211
Query: 214 PGTGDIRD--IGYSKGKFYSLNVP 235
G+ ++ D Y++G +S ++P
Sbjct: 212 AGSKELIDYLRSYARGFIFSTSLP 235
>gnl|CDD|227880 COG5593, COG5593, Nucleic-acid-binding protein possibly involved in
ribosomal biogenesis [Translation, ribosomal structure
and biogenesis].
Length = 821
Score = 33.9 bits (77), Expect = 0.20
Identities = 25/97 (25%), Positives = 33/97 (34%), Gaps = 7/97 (7%)
Query: 400 EADEDQEDGDERWDPDSDMDVDDERKSLPNRVKREAVE--PEQKDREGLKGMAEQARGFD 457
E D D + D D SD DDE K + E E EGL + G
Sbjct: 702 EDDSDDSELDFAEDDFSDSTSDDEPKLDAIDDEDAKSEGSQESDQEEGLDEIFYSFDGEQ 761
Query: 458 MIADDSISTKVLDMSSMPIDEPSIKVEQENMSKASDH 494
+D + D SS E E+EN ++
Sbjct: 762 DNSDSFAESSEEDESSEEEKE-----EEENKEVSAKR 793
>gnl|CDD|200381 TIGR04130, FnlA, UDP-N-acetylglucosamine
4,6-dehydratase/5-epimerase. The FnlA enzyme is the
first step in the biosynthesis of UDP-FucNAc from
UDP-GlcNAc in E. coli (along with FnlB and FnlC). The
proteins identified by this model include FnlA homologs
in the O-antigen clusters of O4, O25, O26, O29 (Shigella
D11), O118, O145 and O172 serotype strains, all of which
produce O-antigens containing FucNAc (or the further
modified FucNAm). A homolog from Pseudomonas aerugiosa
serotype O11, WbjB, also involved in the biosynthesis of
UDP-FucNAc has been characterized and is now believed to
carry out both the initial 4,6-dehydratase reaction and
the subsequent epimerization of the resulting methyl
group at C-5. A phylogenetic tree of related sequences
shows a distinct clade of enzymes involved in the
biosynthesis of UDP-QuiNAc (Qui=qinovosamine). This
clade appears to be descendant from the common ancestor
of the Pseudomonas and E. coli fucose-biosynthesis
enzymes. It has been hypothesized that the first step in
the biosynthesis of these two compounds may be the same,
and thus that these enzymes all have the same function.
At present, lacking sufficient confirmation of this, the
current model trusted cutoff only covers the tree
segment surrounding the E. coli genes. The clades
containing the Pseudomonas and QuiNAc biosynthesis
enzymes score above the noise cutoff. Immediately below
the noise cutoff are enzymes involved in the
biosynthesis of UDP-RhaNAc (Rha=rhamnose), which again
may or may not produce the same product.
Length = 337
Score = 31.9 bits (72), Expect = 0.68
Identities = 19/66 (28%), Positives = 35/66 (53%), Gaps = 3/66 (4%)
Query: 161 VNDIVLAILELLKQHERVLYVDIDIHHGDGVEEAFYTTDRVMTVSFHKFGDYFPGTGDIR 220
+ + +A+ ELL HE + + I HG+ + EA + + + ++ GDY+ D+R
Sbjct: 231 IETLAIALKELLNAHEHPVNI-IGTRHGEKLYEALLSREEM--IAAIDMGDYYRVPPDLR 287
Query: 221 DIGYSK 226
D+ Y K
Sbjct: 288 DLNYGK 293
>gnl|CDD|133451 cd05212, NAD_bind_m-THF_DH_Cyclohyd_like, NAD(P) binding domain of
methylene-tetrahydrofolate dehydrogenase and
methylene-tetrahydrofolate dehydrogenase/cyclohydrolase.
NAD(P) binding domains of methylene-tetrahydrofolate
dehydrogenase (m-THF DH) and m-THF DH/cyclohydrolase
bifunctional enzymes (m-THF DH/cyclohydrolase). M-THF is
a versatile carrier of activated one-carbon units. The
major one-carbon folate donors are N-5
methyltetrahydrofolate, N5,N10-m-THF, and
N10-formayltetrahydrofolate. The oxidation of metabolic
intermediate m-THF to m-THF requires the enzyme m-THF
DH. In addition, most DHs also have an associated
cyclohydrolase activity which catalyzes its hydrolysis
to N10-formyltetrahydrofolate. m-THF DH is typically
found as part of a multifunctional protein in
eukaryotes. NADP-dependent m-THF DH in mammals, birds
and yeast are components of a trifunctional enzyme with
DH, cyclohydrolase, and synthetase activities. Certain
eukaryotic cells also contain homodimeric bifunctional
DH/cyclodrolase form. In bacteria, mono-functional DH,
as well as bifunctional DH/cyclodrolase are found. In
addition, yeast (S. cerevisiae) also express a
monofunctional DH. M-THF DH, like other amino acid
DH-like NAD(P)-binding domains, is a member of the
Rossmann fold superfamily which includes glutamate,
leucine, and phenylalanine DHs, m-THF DH,
methylene-tetrahydromethanopterin DH, m-THF
DH/cyclohydrolase, Shikimate DH-like proteins, malate
oxidoreductases, and glutamyl tRNA reductase. Amino acid
DHs catalyze the deamination of amino acids to keto
acids with NAD(P)+ as a cofactor. The NAD(P)-binding
Rossmann fold superfamily includes a wide variety of
protein families including NAD(P)- binding domains of
alcohol DHs, tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate DH, lactate/malate DHs,
formate/glycerate DHs, siroheme synthases,
6-phosphogluconate DH, amino acid DHs, repressor rex,
NAD-binding potassium channel domain, CoA-binding, and
ornithine cyclodeaminase-like domains. These domains
have an alpha-beta-alpha configuration. NAD binding
involves numerous hydrogen and van der Waals contacts.
Length = 140
Score = 30.6 bits (69), Expect = 0.81
Identities = 18/64 (28%), Positives = 25/64 (39%), Gaps = 17/64 (26%)
Query: 258 EVFRPGAVVLQCGADSLSGDRLGCFNLSIKGHAECVKFMRSFNVPLLLLGG---GGYTIR 314
E +PGA V+ C LSGD +K A S VP+ G ++
Sbjct: 88 EWIKPGATVINCSPTKLSGD-------DVKESA-------SLYVPMTGGVGKLTVAMRMQ 133
Query: 315 NVAR 318
N+ R
Sbjct: 134 NMVR 137
>gnl|CDD|233222 TIGR00986, 3a0801s05tom22, mitochondrial import receptor subunit
Tom22. The mitochondrial protein translocase (MPT)
family, which brings nuclearly encoded preproteins into
mitochondria, is very complex with 19 currently
identified protein constituents.These proteins include
several chaperone proteins, four proteins of the outer
membrane translocase (Tom) import receptor, five
proteins of the Tom channel complex, five proteins of
the inner membrane translocase (Tim) and three "motor"
proteins. This family is specific for the Tom22 proteins
[Transport and binding proteins, Amino acids, peptides
and amines].
Length = 145
Score = 30.3 bits (68), Expect = 1.2
Identities = 16/54 (29%), Positives = 24/54 (44%), Gaps = 3/54 (5%)
Query: 387 VQFQERPPDSELPEADEDQEDGDERWDPDSDMDVDDERKSLPNRVK--REAVEP 438
Q E+ E E DED D D DSD + E ++ +R+ ++ V P
Sbjct: 12 FQQPEQQTVVEPEEDDEDFTDVDSEDSVDSDFE-SLEEETFTDRIYALKDIVPP 64
>gnl|CDD|187819 cd09688, Cas5_I-C, CRISPR/Cas system-associated RAMP superfamily
protein Cas5. CRISPR (Clustered Regularly Interspaced
Short Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Cas5 is a RAMP superfamily protein; Subunit of the
Cascade complex; in subtype I-C this protein might be
the endoribonuclease that generates crRNAs; also known
as DevS family.
Length = 174
Score = 30.5 bits (69), Expect = 1.4
Identities = 14/57 (24%), Positives = 20/57 (35%), Gaps = 2/57 (3%)
Query: 389 FQERPPDSELPEADEDQEDGDERWDPDSDMDVDDERKSLPNRVKREAVEPEQKDREG 445
P +E PE E + D S + + +L R+ PE DR G
Sbjct: 76 KNIDDPKNENPEYQEVLSNIDFIVWVISG--NEGAQPTLAERIVEALTNPESVDRFG 130
>gnl|CDD|217595 pfam03514, GRAS, GRAS family transcription factor. Sequence
analysis of the products of the GRAS (GAI, RGA, SCR)
gene family indicates that they share a variable
amino-terminus and a highly conserved carboxyl-terminus
that contains five recognisable motifs. Proteins in the
GRAS family are transcription factors that seem to be
involved in development and other processes. Mutation of
the SCARECROW (SCR) gene results in a radial pattern
defect, loss of a ground tissue layer, in the root. The
PAT1 protein is involved in phytochrome A signal
transduction.
Length = 372
Score = 31.1 bits (71), Expect = 1.5
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 167 AILELLKQHERVLYVDIDIHHG 188
AILE + ERV +D DI G
Sbjct: 101 AILEAFEGEERVHIIDFDIGQG 122
>gnl|CDD|217450 pfam03247, Prothymosin, Prothymosin/parathymosin family.
Prothymosin alpha and parathymosin are two ubiquitous
small acidic nuclear proteins that are thought to be
involved in cell cycle progression, proliferation, and
cell differentiation.
Length = 106
Score = 29.2 bits (65), Expect = 1.7
Identities = 12/51 (23%), Positives = 23/51 (45%)
Query: 391 ERPPDSELPEADEDQEDGDERWDPDSDMDVDDERKSLPNRVKREAVEPEQK 441
+ D E+ E +E ED +E + + ++E ++ KR A + E
Sbjct: 44 AQEGDDEMEEEEEVDEDDEEEEGEGEEEEGEEEEETEGATGKRAAEDEEDD 94
>gnl|CDD|232962 TIGR00409, proS_fam_II, prolyl-tRNA synthetase, family II.
Prolyl-tRNA synthetase is a class II tRNA synthetase and
is recognized by pfam model tRNA-synt_2b, which
recognizes tRNA synthetases for Gly, His, Ser, and Pro.
The prolyl-tRNA synthetases are divided into two widely
divergent groups. This group includes enzymes from
Escherichia coli, Bacillus subtilis, Aquifex aeolicus,
the spirochete Treponema pallidum, Synechocystis
PCC6803, and one of the two prolyL-tRNA synthetases of
Saccharomyces cerevisiae. The other group includes the
Pro-specific domain of a human multifunctional tRNA
ligase and the prolyl-tRNA synthetases from the Archaea,
the Mycoplasmas, and the spirochete Borrelia burgdorferi
[Protein synthesis, tRNA aminoacylation].
Length = 568
Score = 30.9 bits (70), Expect = 1.8
Identities = 15/54 (27%), Positives = 26/54 (48%), Gaps = 7/54 (12%)
Query: 349 YTLHVAPSNMENKNSRQLLEEIRNKLLEYLSKLQHAPSVQFQERP----PDSEL 398
Y + + NM+++ +QL EE+ ++L L++ ER DSEL
Sbjct: 474 YDVVIVVMNMKDEEQQQLAEELYSEL---LAQGVDVLLDDRNERAGVKFADSEL 524
>gnl|CDD|218704 pfam05701, DUF827, Plant protein of unknown function (DUF827).
This family consists of several plant proteins of
unknown function. Several sequences in this family are
described as being "myosin heavy chain-like".
Length = 484
Score = 30.3 bits (68), Expect = 2.3
Identities = 20/100 (20%), Positives = 41/100 (41%), Gaps = 11/100 (11%)
Query: 397 ELPEADEDQEDGDERWDPDSDMDVDDERKSLPNRVKREAVEPEQKDREGLKGMAEQARG- 455
EL EA+++ E + DP+ D++ E + +++E + E+A+
Sbjct: 210 ELKEAEKELERLKQDLDPEKDLEKLAEASAELESLQKE--ISIMASVASVLKELEEAKAN 267
Query: 456 FDMIADDSISTKVLDMSSMPIDEPSIKVEQENMSKASDHM 495
+ A++ S + L S+K E E K + +
Sbjct: 268 LEKAAEEEKSLRNLVE--------SLKQELEEEKKELEEL 299
>gnl|CDD|215340 PLN02634, PLN02634, probable pectinesterase.
Length = 359
Score = 30.3 bits (68), Expect = 2.3
Identities = 19/83 (22%), Positives = 40/83 (48%), Gaps = 10/83 (12%)
Query: 153 CEASGFCYVNDIV-----LAILELLKQHERVLYV----DIDIHHGDGVEEAFYTTDRVMT 203
E +GF +V V L + + Q+ R++Y D + HG G ++ +T+++ T
Sbjct: 251 EEKTGFAFVGCRVTGTGPLYVGRAMGQYSRIVYAYTYFDAVVAHG-GWDDWDHTSNKSKT 309
Query: 204 VSFHKFGDYFPGTGDIRDIGYSK 226
F + + PG +R + +++
Sbjct: 310 AFFGVYNCWGPGAAAVRGVSWAR 332
>gnl|CDD|218312 pfam04889, Cwf_Cwc_15, Cwf15/Cwc15 cell cycle control protein.
This family represents Cwf15/Cwc15 (from
Schizosaccharomyces pombe and Saccharomyces cerevisiae
respectively) and their homologues. The function of
these proteins is unknown, but they form part of the
spliceosome and are thus thought to be involved in mRNA
splicing.
Length = 241
Score = 30.1 bits (68), Expect = 2.6
Identities = 16/82 (19%), Positives = 35/82 (42%), Gaps = 6/82 (7%)
Query: 376 EYLSKLQHAPSVQFQERPPDSELPEADEDQEDGDERWDPDSDMDVDDERKSLP---NRVK 432
+ ++ R D++ ++ D + D+ D D +DE +L ++K
Sbjct: 99 DDEEDEIKRKRIEEDARNSDADDSDSSSDSDSSDDDSDDDDS---EDETAALLRELEKIK 155
Query: 433 REAVEPEQKDREGLKGMAEQAR 454
+E E ++++ E E+AR
Sbjct: 156 KERAEEKEREEEEKAAEEEKAR 177
>gnl|CDD|185749 cd09236, V_AnPalA_UmRIM20_like, Protein-interacting V-domains of
Aspergillus nidulans PalA/RIM20, Ustilago maydis RIM20,
and related proteins. This family belongs to the
V_Alix_like superfamily which includes the V-shaped (V)
domains of Bro1 and Rim20 from Saccharomyces cerevisiae,
mammalian Alix (apoptosis-linked gene-2 interacting
protein X), His-Domain type N23 protein tyrosine
phosphatase (HD-PTP, also known as PTPN23), and related
domains. Aspergillus nidulas PalA/RIM20 and Ustilago
maydis RIM20, like Saccharomyces cerevisiae Rim20,
participate in the response to the external pH via the
Pal/Rim101 pathway; however, Saccharomyces cerevisiae
Rim20 does not belong to this family. This pathway is a
signaling cascade resulting in the activation of the
transcription factor PacC/Rim101. The mammalian Alix
V-domain (belonging to a different family) contains a
binding site, partially conserved in the superfamily,
for the retroviral late assembly (L) domain YPXnL motif.
Aspergillus nidulas PalA binds a nonviral YPXnL motif
(tandem YPXL/I motifs within PacC). The Alix V-domain is
also a dimerization domain. In addition to this
V-domain, members of the V_Alix_like superfamily also
have an N-terminal Bro1-like domain, which has been
shown to bind CHMP4/Snf7, a component of the ESCRT-III
complex.
Length = 353
Score = 30.0 bits (68), Expect = 2.6
Identities = 25/74 (33%), Positives = 36/74 (48%), Gaps = 11/74 (14%)
Query: 349 YTLHVAPS-------NMENKNSRQLLEEIRNKLLEYLSKLQHAPSVQFQERP---PDSEL 398
+ +H+A S + N++ LEE+ N+ L L S+Q E+P P S L
Sbjct: 2 FGVHLAISIYDDRKDRLVNESIIDELEELTNRAHSTLRSLNLPGSLQALEKPLGLPPSLL 61
Query: 399 PEADE-DQEDGDER 411
A+E QEDG ER
Sbjct: 62 RHAEEIRQEDGLER 75
>gnl|CDD|222926 PHA02745, PHA02745, hypothetical protein; Provisional.
Length = 265
Score = 29.9 bits (67), Expect = 2.7
Identities = 19/105 (18%), Positives = 37/105 (35%), Gaps = 15/105 (14%)
Query: 362 NSRQLLEEIRNKLLEYLSKLQHAPSVQFQERPPDSELPEADEDQEDGDERWDPDSDMDVD 421
+ E R L S+++ F++ D ++ + D +E VD
Sbjct: 27 RPSVIKEPTRRNYLSNCSQVKKLLEDLFEDISGDLDIRTSTGDYVSEEE-----HFGRVD 81
Query: 422 ----DERKSLPNRVKREAVEPEQKD------REGLKGMAEQARGF 456
DE + L +++ + + E R L + +Q R F
Sbjct: 82 TQEVDEFRGLNAKIRDKVLPIEDNKHDNSETRNPLNKIRQQIRKF 126
>gnl|CDD|217503 pfam03344, Daxx, Daxx Family. The Daxx protein (also known as the
Fas-binding protein) is thought to play a role in
apoptosis, but precise role played by Daxx remains to be
determined. Daxx forms a complex with Axin.
Length = 715
Score = 30.3 bits (68), Expect = 3.3
Identities = 16/68 (23%), Positives = 32/68 (47%), Gaps = 7/68 (10%)
Query: 385 PSVQFQERPPDSELPEADEDQEDGDERWDPDSDMDVDDERKSLPNRVKREAVEPEQKDRE 444
PS+ QE + + E +E++E+ +E + + +DE + E VE + E
Sbjct: 432 PSMASQESEEEESVEEEEEEEEEEEEEEQESEEEEGEDEEEE-------EEVEADNGSEE 484
Query: 445 GLKGMAEQ 452
++G +E
Sbjct: 485 EMEGSSEG 492
>gnl|CDD|226920 COG4547, CobT, Cobalamin biosynthesis protein CobT
(nicotinate-mononucleotide:5, 6-dimethylbenzimidazole
phosphoribosyltransferase) [Coenzyme metabolism].
Length = 620
Score = 29.8 bits (67), Expect = 3.6
Identities = 23/77 (29%), Positives = 35/77 (45%), Gaps = 5/77 (6%)
Query: 386 SVQFQERPPDSELPEADEDQEDGDERWDPDSDMDVDDERKSLPNRVKREAVEPEQKDREG 445
S+ E D + E D D+EDGD+ PD++ D + R+ + E E E D EG
Sbjct: 215 SMDMAEETGD-DGIEEDADEEDGDDD-QPDNNEDSEAGREESEGSDESEEDEAEATDGEG 272
Query: 446 LKGMAEQARGFDMIADD 462
+G + A + D
Sbjct: 273 EEGEMDAA---EASEDS 286
>gnl|CDD|221323 pfam11931, DUF3449, Domain of unknown function (DUF3449). This
presumed domain is functionally uncharacterized. This
domain is found in eukaryotes. This domain is typically
between 181 to 207 amino acids in length. This domain
has two conserved sequence motifs: PIP and CEICG. The
domain carries a zinc-finger domain of the C2H2-type.
Length = 187
Score = 28.8 bits (65), Expect = 4.4
Identities = 13/68 (19%), Positives = 31/68 (45%), Gaps = 4/68 (5%)
Query: 361 KNSRQLLEEIRNKLLEYLSKLQHAPSVQFQERPPDSELPEADEDQEDGDERWDPDSDMDV 420
+ +LL++ R +E + + Q ++ +ER ++ D ++ D+ D D + +
Sbjct: 8 EKLAELLKKEREDTIENVERKQ---ALTEEERQASADESSEDASEDGSDDDSDDDEEEPI 64
Query: 421 DDERKSLP 428
+ LP
Sbjct: 65 YNPLN-LP 71
>gnl|CDD|227496 COG5167, VID27, Protein involved in vacuole import and degradation
[Intracellular trafficking and secretion].
Length = 776
Score = 29.6 bits (66), Expect = 4.5
Identities = 14/70 (20%), Positives = 31/70 (44%), Gaps = 2/70 (2%)
Query: 357 NMENKNSRQLLEEIRNKLLEYLSKLQHAPSVQFQERPPDSELPEADEDQEDGDERWDPDS 416
N E + +L+ L + + + ++ + R P+ E +E+ ED ++ D
Sbjct: 343 NEEAERKDYILDSSSVPLEKQFDDILYFEKMEIENRNPEES--EHEEEVEDYEDENDHSK 400
Query: 417 DMDVDDERKS 426
+ DDE ++
Sbjct: 401 RICDDDELEN 410
>gnl|CDD|218538 pfam05285, SDA1, SDA1. This family consists of several SDA1
protein homologues. SDA1 is a Saccharomyces cerevisiae
protein which is involved in the control of the actin
cytoskeleton. The protein is essential for cell
viability and is localised in the nucleus.
Length = 317
Score = 29.2 bits (66), Expect = 5.0
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 400 EADEDQEDGDERWDPDSDMDVDDE 423
+D +D +E W+ + D D DDE
Sbjct: 92 LESDDDDDEEEEWEVEEDEDSDDE 115
>gnl|CDD|227466 COG5137, COG5137, Histone chaperone involved in gene silencing
[Transcription / Chromatin structure and dynamics].
Length = 279
Score = 29.2 bits (65), Expect = 5.2
Identities = 14/58 (24%), Positives = 25/58 (43%), Gaps = 2/58 (3%)
Query: 388 QFQERPPDSELPEADEDQEDGDERWDPDSDMDVDDERKSLPNRVKREAVEPEQKDREG 445
E PP P+ D ++E+ E D + + ++ RE E E+++ EG
Sbjct: 163 DNDEAPP--AQPDVDNEEEERLEESDGREEEEDEEVGSDSYGEGNRELNEEEEEEAEG 218
>gnl|CDD|219293 pfam07093, SGT1, SGT1 protein. This family consists of several
eukaryotic SGT1 proteins. Human SGT1 or hSGT1 is known
to suppress GCR2 and is highly expressed in the muscle
and heart. The function of this family is unknown
although it has been speculated that SGT1 may be
functionally analogous to the Gcr2p protein of
Saccharomyces cerevisiae which is known to be a
regulatory factor of glycolytic gene expression.
Length = 557
Score = 29.3 bits (66), Expect = 5.3
Identities = 27/141 (19%), Positives = 51/141 (36%), Gaps = 24/141 (17%)
Query: 355 PSNMENKNSRQLLEEIRNKLLEYLSKLQHAPSVQFQERPPDSELPEADEDQEDGDERWDP 414
SN E+ N LEE+ + + E+L+K+ +F + + DED ++ D+ D
Sbjct: 402 KSNKEDANEVDDLEEVVSSMEEFLNKVSSFEGAEFAD--------DEDEDDDEPDDSEDK 453
Query: 415 DSDMDVDDERKSLPNRVKREAVEPEQKDREGLKGMAEQARGFDMIADDSISTKVLDMSSM 474
D D D+ + L + + + + + D DD
Sbjct: 454 DVSFDEDEFFEFL-----KNMLGLKDDEIDNDLPDDSDDADEDDDEDDD----------- 497
Query: 475 PIDEPSIKVEQENMSKASDHM 495
++ S E + + D M
Sbjct: 498 EDEDSSSDSTLEELEEYMDQM 518
>gnl|CDD|222808 PHA00666, PHA00666, putative protease.
Length = 233
Score = 28.9 bits (64), Expect = 5.3
Identities = 21/90 (23%), Positives = 37/90 (41%), Gaps = 4/90 (4%)
Query: 384 APSVQFQERPPDSELPEADEDQEDGDERWDPDSDMDVDDERK--SLPNRVKREAVEPEQK 441
AP + D P A D+ +GD++ D D + K P + + +A E +
Sbjct: 38 APQGDPTQEEGDKPQPAAGADKPEGDKKADGDKPEEKKPGEKPEGAPEKYEFQAAEGVEL 97
Query: 442 DREGLKGMAEQARGFDMIADDSISTKVLDM 471
D L AR ++ + + KV+D+
Sbjct: 98 DTGALGAFEPVARELNLTNEQ--AQKVVDL 125
>gnl|CDD|218133 pfam04533, Herpes_U44, Herpes virus U44 protein. This is a family
of proteins from dsDNA beta-herpesvirinae and
gamma-herpesvirinae viruses. The function is not known,
and the proteins are named variously as U44, BSRF1,
UL71, and M71. The family BSRF1 has been merged into
this.
Length = 211
Score = 28.5 bits (64), Expect = 5.9
Identities = 13/56 (23%), Positives = 20/56 (35%), Gaps = 3/56 (5%)
Query: 362 NSRQLLEEIRNKLLEYLSKLQHAPSVQFQERPPDSELPEADEDQEDGDERWDPDSD 417
NS+ EI L Q P + + P+ ELP+A +G +
Sbjct: 158 NSKAWATEIDPILHSETGLYQALPPIVTE---PEPELPKAILKPPEGKGTTKAQAS 210
>gnl|CDD|117592 pfam09026, Cenp-B_dimeris, Centromere protein B dimerisation
domain. The centromere protein B (CENP-B) dimerisation
domain is composed of two alpha-helices, which are
folded into an antiparallel configuration. Dimerisation
of CENP-B is mediated by this domain, in which monomers
dimerise to form a symmetrical, antiparallel, four-helix
bundle structure with a large hydrophobic patch in which
23 residues of one monomer form van der Waals contacts
with the other monomer. This CENP-B dimer configuration
may be suitable for capturing two distant CENP-B boxes
during centromeric heterochromatin formation.
Length = 101
Score = 27.4 bits (60), Expect = 6.1
Identities = 14/45 (31%), Positives = 25/45 (55%)
Query: 385 PSVQFQERPPDSELPEADEDQEDGDERWDPDSDMDVDDERKSLPN 429
P++ F E DS+ +E+ +D ++ D D D D DD+ +P+
Sbjct: 1 PTLHFLEGEEDSDSDSDEEEDDDDEDEEDDDEDDDEDDDEVPVPS 45
>gnl|CDD|218003 pfam04281, Tom22, Mitochondrial import receptor subunit Tom22. The
mitochondrial protein translocase family, which is
responsible for movement of nuclear encoded pre-proteins
into mitochondria, is very complex with at least 19
components. These proteins include several chaperone
proteins, four proteins of the outer membrane
translocase (Tom) import receptor, five proteins of the
Tom channel complex, five proteins of the inner membrane
translocase (Tim) and three "motor" proteins. This
family represents the Tom22 proteins. The N terminal
region of Tom22 has been shown to have chaperone-like
activity, and the C terminal region faces the
intermembrane face.
Length = 136
Score = 28.0 bits (63), Expect = 6.2
Identities = 14/60 (23%), Positives = 28/60 (46%), Gaps = 2/60 (3%)
Query: 386 SVQFQERPPDSELPEADEDQEDGDERWDPDSDMDVDDERKSLPNRVK--REAVEPEQKDR 443
+ Q + P + E +D ++ D D D D D E ++L +R+ ++ V P + +
Sbjct: 11 TFQEKPAAPKNLAQEESDDDDEDDTDTDSDISDDSDFENETLYDRIVALKDIVPPTTRRK 70
>gnl|CDD|115203 pfam06531, DUF1108, Protein of unknown function (DUF1108). This
family consists of several bacterial proteins from
Staphylococcus aureus as well as a number of phage
proteins. The function of this family is unknown.
Length = 86
Score = 27.1 bits (60), Expect = 6.6
Identities = 16/47 (34%), Positives = 22/47 (46%), Gaps = 8/47 (17%)
Query: 455 GFD-----MIADDSISTKVLDMSSMPIDEPSIKVEQEN-MSKASDHM 495
GFD IS +V DM+++PI I V EN + A D +
Sbjct: 17 GFDFKLSVKKRHYGISIQVKDMNNVPIK--GIHVIDENDLYTALDIL 61
>gnl|CDD|164995 PHA02600, FII, major tail tube protein; Provisional.
Length = 169
Score = 28.1 bits (63), Expect = 6.8
Identities = 20/61 (32%), Positives = 29/61 (47%), Gaps = 10/61 (16%)
Query: 97 RQLKRFNVGEDCPVFDGLFSFC---------QTYAGGSVGGAVKLNHGLCDIAINWA-GG 146
R+LK FNV D + G+ + Y GG + G VK++ GL D+ + W GG
Sbjct: 5 RKLKNFNVFNDGASYQGVVEEVTLPKLTRKLEAYRGGGMNGPVKVDMGLEDLELEWTVGG 64
Query: 147 L 147
Sbjct: 65 F 65
>gnl|CDD|220284 pfam09538, FYDLN_acid, Protein of unknown function (FYDLN_acid).
Members of this family are bacterial proteins with a
conserved motif [KR]FYDLN, sometimes flanked by a pair
of CXXC motifs, followed by a long region of low
complexity sequence in which roughly half the residues
are Asp and Glu, including multiple runs of five or more
acidic residues. The function of members of this family
is unknown.
Length = 104
Score = 27.3 bits (61), Expect = 7.0
Identities = 11/29 (37%), Positives = 17/29 (58%)
Query: 395 DSELPEADEDQEDGDERWDPDSDMDVDDE 423
D L + D+D +D D D D+D+DD+
Sbjct: 65 DVVLDDDDDDDDDDDLPDLDDDDVDLDDD 93
>gnl|CDD|237047 PRK12298, obgE, GTPase CgtA; Reviewed.
Length = 390
Score = 28.7 bits (65), Expect = 7.3
Identities = 15/72 (20%), Positives = 28/72 (38%), Gaps = 12/72 (16%)
Query: 363 SRQLLEEIRNKLLEYLSKLQ--------HAPSVQF---QERPPDSELPEADEDQEDGDER 411
S ++E+ L+ ++ + V+F E E ++D +D D+
Sbjct: 317 SGLGVKELCWDLMTFIEENPREEAEEAEAPEKVEFMWDDYHREQLEEVEEEDD-DDWDDD 375
Query: 412 WDPDSDMDVDDE 423
WD D D V+
Sbjct: 376 WDEDDDEGVEVI 387
>gnl|CDD|222264 pfam13614, AAA_31, AAA domain. This family includes a wide variety
of AAA domains including some that have lost essential
nucleotide binding residues in the P-loop.
Length = 145
Score = 27.6 bits (62), Expect = 8.1
Identities = 15/71 (21%), Positives = 29/71 (40%), Gaps = 15/71 (21%)
Query: 170 ELLKQHERVLYVDIDIHHGD----------GVEEAFYTTDRVM-TVSFHKFG-DYFPG-- 215
L ++ +VLY+D++ + GD G+ + Y R+ + G DY
Sbjct: 24 SLAEEGPKVLYLDLEEYSGDLALFLGLEPKGLSDLLYYLKRLDSMLIQAMGGLDYLAPPR 83
Query: 216 -TGDIRDIGYS 225
D+R++
Sbjct: 84 NPEDLREVSPE 94
>gnl|CDD|233816 TIGR02302, aProt_lowcomp, TIGR02302 family protein. Members of
this family are long (~850 residue) bacterial proteins
from the alpha Proteobacteria. Each has 2-3 predicted
transmembrane helices near the N-terminus and a long
C-terminal region that includes stretches of
Gln/Gly-rich low complexity sequence, predicted by TMHMM
to be outside the membrane. In Bradyrhizobium japonicum,
two tandem reading frames are together homologous the
single members found in other species; the cutoffs
scores are set low enough that the longer scores above
the trusted cutoff and the shorter above the noise
cutoff for this model.
Length = 851
Score = 28.8 bits (64), Expect = 8.2
Identities = 16/46 (34%), Positives = 25/46 (54%), Gaps = 10/46 (21%)
Query: 346 GPDYTLHVA-PSNMENKNSRQLLEEIRNKL---------LEYLSKL 381
G + L V P ++ + +R++LEEIR KL L+YL +L
Sbjct: 802 GLGFGLTVKIPGEIDVQRARRILEEIRRKLGDSLRPQIELDYLERL 847
>gnl|CDD|223049 PHA03334, PHA03334, putative DNA polymerase catalytic subunit;
Provisional.
Length = 1545
Score = 29.1 bits (65), Expect = 8.3
Identities = 25/130 (19%), Positives = 40/130 (30%), Gaps = 20/130 (15%)
Query: 386 SVQFQERPPDSELPEADEDQEDGDERWD-PDSDMDVDDER----KSLPNRVKREAVEP-- 438
SV FQ P D+E D + +ER + + E + + E V+
Sbjct: 814 SVMFQLPPDDAETYLEDTVTLEDEERAPLEYTLEEWSAEAVNHVTKAKTKREGETVQSIL 873
Query: 439 EQKDREGLKGMAEQARGFD------MIADDSISTKVLDMSSM------PIDEPSI-KVEQ 485
+ M E+ R D D V + + P I K+
Sbjct: 874 SDLNTVLYDDMIERLRYVDEGGSVEPFKDGEDWWVVDPLDGIWTYVRDPFSSELITKLCY 933
Query: 486 ENMSKASDHM 495
EN S + +
Sbjct: 934 ENTSTVTCRL 943
>gnl|CDD|239449 cd03333, chaperonin_like, chaperonin_like superfamily. Chaperonins
are involved in productive folding of proteins. They
share a common general morphology, a double toroid of 2
stacked rings, each composed of 7-9 subunits. There are
2 main chaperonin groups. The symmetry of type I is
seven-fold and they are found in eubacteria (GroEL) and
in organelles of eubacterial descent (hsp60 and RBP).
The symmetry of type II is eight- or nine-fold and they
are found in archea (thermosome), thermophilic bacteria
(TF55) and in the eukaryotic cytosol (CTT). Their
common function is to sequester nonnative proteins
inside their central cavity and promote folding by using
energy derived from ATP hydrolysis. This superfamily
also contains related domains from Fab1-like
phosphatidylinositol 3-phosphate (PtdIns3P) 5-kinases
that only contain the intermediate and apical domains.
Length = 209
Score = 28.2 bits (64), Expect = 8.7
Identities = 19/66 (28%), Positives = 27/66 (40%), Gaps = 20/66 (30%)
Query: 232 LNVPLD------DGIDDESYHYLFKPIIGKVMEVFRPGAVVLQ-----CGA------DSL 274
L+ PL+ GIDD + HYL +M V R L+ GA + L
Sbjct: 88 LDCPLEYVVIAEKGIDDLALHYL---AKAGIMAVRRVKKEDLERIARATGATIVSSLEDL 144
Query: 275 SGDRLG 280
+ + LG
Sbjct: 145 TPEDLG 150
>gnl|CDD|219939 pfam08619, Nha1_C, Alkali metal cation/H+ antiporter Nha1 C
terminus. The C terminus of the plasma membrane Nha1
antiporter plays an important role in the immediate cell
response to hypo-osmotic shock which prevents an
execessive loss of ions and water. This domain is found
with pfam00999.
Length = 430
Score = 28.6 bits (64), Expect = 9.0
Identities = 16/61 (26%), Positives = 27/61 (44%), Gaps = 3/61 (4%)
Query: 358 MENKNSRQLLEEIRNKLLEYLSKLQHAPSVQFQERPPDSELPEADEDQEDGD-ERWDPDS 416
++K+ +L +++ + LL S+ + P + D ED D ER D DS
Sbjct: 343 TDSKSEEKLEDDLAHSLL--GSEASERRKNREPSSSSPPSRPRSRRDSEDEDTERDDSDS 400
Query: 417 D 417
D
Sbjct: 401 D 401
>gnl|CDD|227559 COG5234, CIN1, Beta-tubulin folding cofactor D [Posttranslational
modification, protein turnover, chaperones /
Cytoskeleton].
Length = 993
Score = 28.8 bits (64), Expect = 9.4
Identities = 13/84 (15%), Positives = 24/84 (28%), Gaps = 4/84 (4%)
Query: 18 KVCYFYDPEVGNYYYGQGHPMKPHRIRMTHA-LLAHYGL-LQNMQVLKPFPARE--RDLC 73
+ C + G + + + LL LQ L F A DL
Sbjct: 763 RRCEALTNIGNRISFRNGPNVDGGVLNELNISLLEIPNSFLQAFYGLTVFTADGLGSDLA 822
Query: 74 RFHADDYVSFLRSITPETQQDQLR 97
Y+++ + ++ R
Sbjct: 823 VKCFSFYIAYSYQLEDSFKKSNSR 846
>gnl|CDD|222912 PHA02624, PHA02624, large T antigen; Provisional.
Length = 647
Score = 28.4 bits (64), Expect = 9.5
Identities = 17/84 (20%), Positives = 32/84 (38%), Gaps = 4/84 (4%)
Query: 365 QLLEEIRNKLLEYLSKLQHAPSVQFQERPPDSELPEADEDQEDGDERWDPD----SDMDV 420
+ L + KL E + + + Q P PE ++ E+ +E+WD D ++
Sbjct: 53 KRLNSLYKKLQEGVKSARQSFGTQDSSEIPTYGTPEWEQWWEEFNEKWDEDLFCDEELSS 112
Query: 421 DDERKSLPNRVKREAVEPEQKDRE 444
D+ P + E E +
Sbjct: 113 SDDEDEPPPPSPPPSQEEESQSSS 136
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 0.139 0.427
Gapped
Lambda K H
0.267 0.0776 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 26,399,431
Number of extensions: 2660171
Number of successful extensions: 3120
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2983
Number of HSP's successfully gapped: 92
Length of query: 499
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 398
Effective length of database: 6,457,848
Effective search space: 2570223504
Effective search space used: 2570223504
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: 61 (27.2 bits)