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Conserved domains on  [gi|1039728092|ref|XP_017174976|]
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histone deacetylase 4 isoform X3 [Mus musculus]

Protein Classification

histone deacetylase 4( domain architecture ID 10178366)

histone deacetylase 4 (HD4) is a class IIa histone deacetylase that is responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4)

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HDAC4 cd10006
Histone deacetylase 4; Histone deacetylase 4 is a class IIa Zn-dependent enzyme that catalyzes ...
 651-1054 0e+00

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.


:

Pssm-ID: 212530 [Multi-domain]  Cd Length: 409  Bit Score: 914.42  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  651 KPRFTTGLVYDTLMLKHQCTCGNTNSHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHTLLYGTNPL 730
Cdd:cd10006      1 KPRFTTGLVYDTLMLKHQCTCGNSNSHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHTLLYGTNPL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  731 NRQKLDS-----SLTSVFVRLPCGGVGVDSDTIWNEVHSSGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEEST 805
Cdd:cd10006     81 NRQKLDSkkllgSLASVFVRLPCGGVGVDSDTIWNEVHSSGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEEST 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  806 PMGFCYFNSVAVAAKLLQQRLNVSKILIVDWDVHHGNGTQQAFYNDPNVLYMSLHRYDDGNFFPGSGAPDEVGTGPGVGF 885
Cdd:cd10006    161 PMGFCYFNSVAIAAKLLQQRLNVSKILIVDWDVHHGNGTQQAFYSDPNVLYMSLHRYDDGNFFPGSGAPDEVGTGPGVGF 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  886 NVNMAFTGGLEPPMGDAEYLAAFRTVVMPIANEFAPDVVLVSSGFDAVEGHPTPLGGYNLSAKCFGYLTKQLMGLAGGRL 965
Cdd:cd10006    241 NVNMAFTGGLDPPMGDAEYLAAFRTVVMPIASEFAPDVVLVSSGFDAVEGHPTPLGGYNLSAKCFGYLTKQLMGLAGGRI 320

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  966 VLALEGGHDLTAICDASEACVSALLGNELEPLPEKVLHQRPNANAVHSMEKVMDIHSKYWRCLQRLSSTVGHSLIEAQKC 1045
Cdd:cd10006    321 VLALEGGHDLTAICDASEACVSALLGNELDPLPEKVLQQRPNANAVRSMEKVMEIHSKYWRCLQRTTSTAGYSLIEAQTC 400


                   ....*....
gi 1039728092 1046 EKEEAETVT 1054
Cdd:cd10006    401 ENEEAETVT 409
ClassIIa_HDAC4_Gln-rich-N cd10162
Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase; This ...
 90-151 7.03e-33

Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase; This family consists of the glutamine-rich domain of histone deacetylase 4 (HDAC4). It belongs to a superfamily that consists of the glutamine-rich N-terminal helical extension to certain Class IIa histone deacetylases (HDACs), including HDAC4, HDAC5 and HDCA9; it is missing from HDAC7. This domain confers responsiveness to calcium signals and mediates interactions with transcription factors and cofactors, and it is able to repress transcription independently of the HDAC C-terminal, zinc-dependent catalytic domain. It has many intra- and inter-helical interactions which are possibly involved in reversible assembly and disassembly of proteins. HDACs regulate diverse cellular processes through enzymatic deacetylation of histone as well as non-histone proteins, in particular deacetylating N(6)-acetyl-lysine residues.


:

Pssm-ID: 197398 [Multi-domain]  Cd Length: 90  Bit Score: 122.23  E-value: 7.03e-33
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1039728092   90 AEFQRQHEQLSRQHEAQLHEHIKQQQEMLAMKHQQELLEHQRKLERHRQEQELEKQHREQKL 151
Cdd:cd10162     29 AEFQRQHEQLSRQHEAQLHEHIKQQQELLAMKHQQELLEHQRKLERHRQEQEMEKQQREQKL 90
 
Name Accession Description Interval E-value
HDAC4 cd10006
Histone deacetylase 4; Histone deacetylase 4 is a class IIa Zn-dependent enzyme that catalyzes ...
 651-1054 0e+00

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.


Pssm-ID: 212530 [Multi-domain]  Cd Length: 409  Bit Score: 914.42  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  651 KPRFTTGLVYDTLMLKHQCTCGNTNSHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHTLLYGTNPL 730
Cdd:cd10006      1 KPRFTTGLVYDTLMLKHQCTCGNSNSHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHTLLYGTNPL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  731 NRQKLDS-----SLTSVFVRLPCGGVGVDSDTIWNEVHSSGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEEST 805
Cdd:cd10006     81 NRQKLDSkkllgSLASVFVRLPCGGVGVDSDTIWNEVHSSGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEEST 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  806 PMGFCYFNSVAVAAKLLQQRLNVSKILIVDWDVHHGNGTQQAFYNDPNVLYMSLHRYDDGNFFPGSGAPDEVGTGPGVGF 885
Cdd:cd10006    161 PMGFCYFNSVAIAAKLLQQRLNVSKILIVDWDVHHGNGTQQAFYSDPNVLYMSLHRYDDGNFFPGSGAPDEVGTGPGVGF 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  886 NVNMAFTGGLEPPMGDAEYLAAFRTVVMPIANEFAPDVVLVSSGFDAVEGHPTPLGGYNLSAKCFGYLTKQLMGLAGGRL 965
Cdd:cd10006    241 NVNMAFTGGLDPPMGDAEYLAAFRTVVMPIASEFAPDVVLVSSGFDAVEGHPTPLGGYNLSAKCFGYLTKQLMGLAGGRI 320

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  966 VLALEGGHDLTAICDASEACVSALLGNELEPLPEKVLHQRPNANAVHSMEKVMDIHSKYWRCLQRLSSTVGHSLIEAQKC 1045
Cdd:cd10006    321 VLALEGGHDLTAICDASEACVSALLGNELDPLPEKVLQQRPNANAVRSMEKVMEIHSKYWRCLQRTTSTAGYSLIEAQTC 400


                   ....*....
gi 1039728092 1046 EKEEAETVT 1054
Cdd:cd10006    401 ENEEAETVT 409
Hist_deacetyl pfam00850
Histone deacetylase domain; Histones can be reversibly acetylated on several lysine residues. ...
 677-989 8.50e-126

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.


Pssm-ID: 425906 [Multi-domain]  Cd Length: 298  Bit Score: 385.82  E-value: 8.50e-126
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  677 HPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHtllygtnpLNRQKldsSLTSVFVRLPCGGVGVDSD 756
Cdd:pfam00850    1 HPENPERLKAILEALREAGLLPDLEIIAPRPATEEELLLVHSPEY--------LEFLE---EAAPEGGALLLLSYLSGDD 69

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  757 TIWNEVHSSGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEESTPMGFCYFNSVAVAAKLLQQRLNVSKILIVDW 836
Cdd:pfam00850   70 DTPVSPGSYEAALLAAGGTLAAADAVLSGEARNAFALVRPPGHHAERDRASGFCIFNNVAIAAKYLREKYGLKRVAIVDF 149

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  837 DVHHGNGTQQAFYNDPNVLYMSLHRYdDGNFFPGSGAPDEVGTGPGVGFNVNMAftggLEPPMGDAEYLAAFRTVVMPIA 916
Cdd:pfam00850  150 DVHHGNGTQEIFYDDPSVLTLSIHQY-PGGFYPGTGFADETGEGKGKGYTLNVP----LPPGTGDAEYLAAFEEILLPAL 224

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1039728092  917 NEFAPDVVLVSSGFDAVEGHptPLGGYNLSAKCFGYLTKQLMGLA---GGRLVLALEGGHDLTAICDASEACVSAL 989
Cdd:pfam00850  225 EEFQPDLILVSAGFDAHAGD--PLGGLNLTTEGFAEITRILLELAdplCIRVVSVLEGGYNLDALARSATAVLAAL 298
AcuC COG0123
Acetoin utilization deacetylase AcuC or a related deacetylase [Secondary metabolites ...
 656-991 5.01e-102

Acetoin utilization deacetylase AcuC or a related deacetylase [Secondary metabolites biosynthesis, transport and catabolism];


Pssm-ID: 439893 [Multi-domain]  Cd Length: 308  Bit Score: 323.21  E-value: 5.01e-102
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  656 TGLVYDTLMLKHQCTCGntnsHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHtllygtnplnrqkl 735
Cdd:COG0123      1 TALIYHPDYLLHDLGPG----HPEPPERLRAILDALEASGLLDDLELVEPPPATEEDLLRVHTPDY-------------- 62

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  736 dssLTSVFVRLPCGGVG-VDSDTIWNEvHSSGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEESTPMGFCYFNS 814
Cdd:COG0123     63 ---VDALRAASLDGGYGqLDPDTPVSP-GTWEAALLAAGGALAAADAVLEGEARNAFALVRPPGHHAERDRAMGFCLFNN 138

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  815 VAVAAKLLQQRlNVSKILIVDWDVHHGNGTQQAFYNDPNVLYMSLHRYddgNFFPGSGAPDEVGTGPGVGFNVNMAftgg 894
Cdd:COG0123    139 AAIAARYLLAK-GLERVAIVDFDVHHGNGTQDIFYDDPDVLTISIHQD---PLYPGTGAADETGEGAGEGSNLNVP---- 210

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  895 LEPPMGDAEYLAAFRTVVMPIANEFAPDVVLVSSGFDAVEGhpTPLGGYNLSAKCFGYLTKQLMGLA---GGRLVLALEG 971
Cdd:COG0123    211 LPPGTGDAEYLAALEEALLPALEAFKPDLIVVSAGFDAHAD--DPLGRLNLTTEGYAWRTRRVLELAdhcGGPVVSVLEG 288

                          330       340
                   ....*....|....*....|
gi 1039728092  972 GHDLTAICDASEACVSALLG 991
Cdd:COG0123    289 GYNLDALARSVAAHLETLLG 308
ClassIIa_HDAC4_Gln-rich-N cd10162
Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase; This ...
 90-151 7.03e-33

Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase; This family consists of the glutamine-rich domain of histone deacetylase 4 (HDAC4). It belongs to a superfamily that consists of the glutamine-rich N-terminal helical extension to certain Class IIa histone deacetylases (HDACs), including HDAC4, HDAC5 and HDCA9; it is missing from HDAC7. This domain confers responsiveness to calcium signals and mediates interactions with transcription factors and cofactors, and it is able to repress transcription independently of the HDAC C-terminal, zinc-dependent catalytic domain. It has many intra- and inter-helical interactions which are possibly involved in reversible assembly and disassembly of proteins. HDACs regulate diverse cellular processes through enzymatic deacetylation of histone as well as non-histone proteins, in particular deacetylating N(6)-acetyl-lysine residues.


Pssm-ID: 197398 [Multi-domain]  Cd Length: 90  Bit Score: 122.23  E-value: 7.03e-33
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1039728092   90 AEFQRQHEQLSRQHEAQLHEHIKQQQEMLAMKHQQELLEHQRKLERHRQEQELEKQHREQKL 151
Cdd:cd10162     29 AEFQRQHEQLSRQHEAQLHEHIKQQQELLAMKHQQELLEHQRKLERHRQEQEMEKQQREQKL 90
HDAC4_Gln pfam12203
Glutamine rich N terminal domain of histone deacetylase 4; This domain is found in eukaryotes, ...
 90-151 3.92e-25

Glutamine rich N terminal domain of histone deacetylase 4; This domain is found in eukaryotes, and is approximately 90 amino acids in length. The family is found in association with pfam00850. The domain forms an alpha helix which complexes to form a tetramer. The glutamine rich domains have many intra- and inter-helical interactions which are thought to be involved in reversible assembly and disassembly of proteins. The domain is part of histone deacetylase 4 (HDAC4) which removes acetyl groups from histones. This restores their positive charge to allow stronger DNA binding thus restricting transcriptional activity.


Pssm-ID: 403429 [Multi-domain]  Cd Length: 91  Bit Score: 100.31  E-value: 3.92e-25
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1039728092   90 AEFQRQHEQLSRQHEAQLHEHIKQQQEMLAMKHQQELLEHQRKLERHRQEQELEKQHREQKL 151
Cdd:pfam12203   30 AEFQKQHELLTRQHEAQLQEHIKQQQELLAMKQQQELLEQQRKLEQQRQEEELEKHRREQQL 91
PTZ00063 PTZ00063
histone deacetylase; Provisional
 799-963 1.57e-21

histone deacetylase; Provisional


Pssm-ID: 240251  Cd Length: 436  Bit Score: 98.73  E-value: 1.57e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  799 HHAEESTPMGFCYFNSVAVAA-KLLQQRlnvSKILIVDWDVHHGNGTQQAFYNDPNVLYMSLHRYddGNFFPGSGAPDEV 877
Cdd:PTZ00063   137 HHAKRSEASGFCYINDIVLGIlELLKYH---ARVMYIDIDVHHGDGVEEAFYVTHRVMTVSFHKF--GDFFPGTGDVTDI 211

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  878 GTGPGVGFNVNMAFTGGleppMGDAEYLAAFRTVVMPIANEFAPDVVLVSSGFDAVEGhpTPLGGYNLS----AKCFGYL 953
Cdd:PTZ00063   212 GVAQGKYYSVNVPLNDG----IDDDSFVDLFKPVISKCVEVYRPGAIVLQCGADSLTG--DRLGRFNLTikghAACVEFV 285

                          170
                   ....*....|...
gi 1039728092  954 TK---QLMGLAGG 963
Cdd:PTZ00063   286 RSlniPLLVLGGG 298
fliH PRK06800
flagellar assembly protein H; Validated
 91-196 5.14e-05

flagellar assembly protein H; Validated


Pssm-ID: 180700  Cd Length: 228  Bit Score: 46.02  E-value: 5.14e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092   91 EFQRQHEQLsRQHEAQLHEH---IKQQQEMLAMKHQQeLLEHQRKLERHRQEQELEKQHREQKLQQLKnkekgkesavas 167
Cdd:PRK06800    35 EIQKDHEEL-LAQQKSLHKElnqLRQEQQKLERERQQ-LLADREQFQEHVQQQMKEIEAARQQFQKEQ------------ 100

                           90       100
                   ....*....|....*....|....*....
gi 1039728092  168 TEVKMKLQEFVLNKKKALAHRNLNHCISS 196
Cdd:PRK06800   101 QETAYEWTELLWDQSFQLAEKIVNQAVDT 129
FliJ COG2882
Flagellar biosynthesis chaperone FliJ [Cell motility];
105-152 3.82e-04

Flagellar biosynthesis chaperone FliJ [Cell motility];


Pssm-ID: 442129 [Multi-domain]  Cd Length: 142  Bit Score: 41.81  E-value: 3.82e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1039728092  105 AQLHEHIKQQQEMLAM------KHQQELLEHQRKL-------ERHRQEQELEKQHREQKLQ 152
Cdd:COG2882     74 ARLDEAIEQQQQQVAQaeqqveQARQAWLEARQERkaleklkERRREEERQEENRREQKEL 134
sbcc TIGR00618
exonuclease SbcC; All proteins in this family for which functions are known are part of an ...
 98-188 7.82e-03

exonuclease SbcC; All proteins in this family for which functions are known are part of an exonuclease complex with sbcD homologs. This complex is involved in the initiation of recombination to regulate the levels of palindromic sequences in DNA. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 129705 [Multi-domain]  Cd Length: 1042  Bit Score: 40.34  E-value: 7.82e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092   98 QLSRQHEAQLHEHIKQQQEMLamkHQQELLEHQRKLErhrQEQELEKQHREQKLQQLKnKEKGKESAVASTEVKMKLQEF 177
Cdd:TIGR00618  605 EAEDMLACEQHALLRKLQPEQ---DLQDVRLHLQQCS---QELALKLTALHALQLTLT-QERVREHALSIRVLPKELLAS 677

                           90
                   ....*....|.
gi 1039728092  178 VLNKKKALAHR 188
Cdd:TIGR00618  678 RQLALQKMQSE 688
 
Name Accession Description Interval E-value
HDAC4 cd10006
Histone deacetylase 4; Histone deacetylase 4 is a class IIa Zn-dependent enzyme that catalyzes ...
 651-1054 0e+00

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.


Pssm-ID: 212530 [Multi-domain]  Cd Length: 409  Bit Score: 914.42  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  651 KPRFTTGLVYDTLMLKHQCTCGNTNSHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHTLLYGTNPL 730
Cdd:cd10006      1 KPRFTTGLVYDTLMLKHQCTCGNSNSHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHTLLYGTNPL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  731 NRQKLDS-----SLTSVFVRLPCGGVGVDSDTIWNEVHSSGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEEST 805
Cdd:cd10006     81 NRQKLDSkkllgSLASVFVRLPCGGVGVDSDTIWNEVHSSGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEEST 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  806 PMGFCYFNSVAVAAKLLQQRLNVSKILIVDWDVHHGNGTQQAFYNDPNVLYMSLHRYDDGNFFPGSGAPDEVGTGPGVGF 885
Cdd:cd10006    161 PMGFCYFNSVAIAAKLLQQRLNVSKILIVDWDVHHGNGTQQAFYSDPNVLYMSLHRYDDGNFFPGSGAPDEVGTGPGVGF 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  886 NVNMAFTGGLEPPMGDAEYLAAFRTVVMPIANEFAPDVVLVSSGFDAVEGHPTPLGGYNLSAKCFGYLTKQLMGLAGGRL 965
Cdd:cd10006    241 NVNMAFTGGLDPPMGDAEYLAAFRTVVMPIASEFAPDVVLVSSGFDAVEGHPTPLGGYNLSAKCFGYLTKQLMGLAGGRI 320

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  966 VLALEGGHDLTAICDASEACVSALLGNELEPLPEKVLHQRPNANAVHSMEKVMDIHSKYWRCLQRLSSTVGHSLIEAQKC 1045
Cdd:cd10006    321 VLALEGGHDLTAICDASEACVSALLGNELDPLPEKVLQQRPNANAVRSMEKVMEIHSKYWRCLQRTTSTAGYSLIEAQTC 400


                   ....*....
gi 1039728092 1046 EKEEAETVT 1054
Cdd:cd10006    401 ENEEAETVT 409
HDAC5 cd10007
Histone deacetylase 5; Histone deacetylase 5 is a class IIa Zn-dependent enzyme that catalyzes ...
 654-1062 0e+00

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.


Pssm-ID: 212531 [Multi-domain]  Cd Length: 420  Bit Score: 793.42  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  654 FTTGLVYDTLMLKHQCTCGNTNSHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHTLLYGTNPLNRQ 733
Cdd:cd10007      3 FTTGLVYDTFMLKHQCTCGNTNVHPEHAGRIQSVWSRLQETGLLGKCERVRGRKATLDEIQTVHSEHHTLLYGTSPLNRQ 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  734 KLDSS------LTSVFVRLPCGGVGVDSDTIWNEVHSSGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEESTPM 807
Cdd:cd10007     83 KLDSKkllgplSQKMYAVLPCGGIGVDSDTVWNEMHSSSAVRMAVGCLIELAFKVAAGELKNGFAVIRPPGHHAEESTAM 162

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  808 GFCYFNSVAVAAKLLQQRLNVSKILIVDWDVHHGNGTQQAFYNDPNVLYMSLHRYDDGNFFPGSGAPDEVGTGPGVGFNV 887
Cdd:cd10007    163 GFCFFNSVAIAAKLLQQKLNVGKILIVDWDIHHGNGTQQAFYNDPNVLYISLHRYDDGNFFPGSGAPDEVGAGPGVGFNV 242

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  888 NMAFTGGLEPPMGDAEYLAAFRTVVMPIANEFAPDVVLVSSGFDAVEGHPTPLGGYNLSAKCFGYLTKQLMGLAGGRLVL 967
Cdd:cd10007    243 NIAWTGGVDPPIGDVEYLTAFRTVVMPIANEFSPDVVLVSAGFDAVEGHQSPLGGYSVTAKCFGHLTKQLMTLAGGRVVL 322

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  968 ALEGGHDLTAICDASEACVSALLGNELEPLPEKVLHQRPNANAVHSMEKVMDIHSKYWRCLQRLSSTVGHSLIEAQKCEK 1047
Cdd:cd10007    323 ALEGGHDLTAICDASEACVSALLGMELTPLDNTVLQQKPNDNAVATLERVIEIQSKHWSCLKRFAATLGFSLLEAQRGEL 402

                          410
                   ....*....|....*
gi 1039728092 1048 EEAETVTAMASLSVG 1062
Cdd:cd10007    403 EEAETVSAMASLSVD 417
HDAC_classIIa cd11681
Histone deacetylases, class IIa; Class IIa histone deacetylases are Zn-dependent enzymes that ...
 654-1025 0e+00

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.


Pssm-ID: 212544 [Multi-domain]  Cd Length: 377  Bit Score: 792.70  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  654 FTTGLVYDTLMLKHQCTCGNTNSHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHTLLYGTNPLNRQ 733
Cdd:cd11681      1 FTTGLAYDPLMLKHQCICGNNSSHPEHGGRLQSIWSRLQETGLVNRCERLRGRKATLEELQLVHSEVHTLLYGTNPLSRL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  734 KLDSSL-----TSVFVRLPCGGVGVDSDTIWNEVHSSGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEESTPMG 808
Cdd:cd11681     81 KLDPTKlaglpQKSFVRLPCGGIGVDSDTVWNELHTSNAARMAVGCVIDLAFKVATGELKNGFAVVRPPGHHAEPSQAMG 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  809 FCYFNSVAVAAKLLQQRLNVSKILIVDWDVHHGNGTQQAFYNDPNVLYMSLHRYDDGNFFPGSGAPDEVGTGPGVGFNVN 888
Cdd:cd11681    161 FCFFNSVAIAAKQLQQKLKLRKILIVDWDVHHGNGTQQIFYEDPNVLYISLHRYDDGNFFPGTGAPTEVGSGAGEGFNVN 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  889 MAFTGGLEPPMGDAEYLAAFRTVVMPIANEFAPDVVLVSSGFDAVEGHPTPLGGYNLSAKCFGYLTKQLMGLAGGRLVLA 968
Cdd:cd11681    241 IAWSGGLDPPMGDAEYLAAFRTVVMPIAREFSPDIVLVSAGFDAAEGHPPPLGGYKVSPACFGYMTRQLMNLAGGKVVLA 320

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1039728092  969 LEGGHDLTAICDASEACVSALLGNELEPLPEKVLHQRPNANAVHSMEKVMDIHSKYW 1025
Cdd:cd11681    321 LEGGYDLTAICDASEACVRALLGDELDPLSEEELERRPNPNAVTSLEKVIAIQSPYW 377
HDAC7 cd10008
Histone deacetylase 7; Histone deacetylase 7 is a class IIa Zn-dependent enzyme that catalyzes ...
 654-1025 0e+00

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.


Pssm-ID: 212532 [Multi-domain]  Cd Length: 378  Bit Score: 709.85  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  654 FTTGLVYDTLMLKHQCTCGNTNSHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHTLLYGTNPLNRQ 733
Cdd:cd10008      1 FTTGLVYDSVMLKHQCSCGDNSNHPEHAGRIQSIWSRLQERGLRSQCECLRGRKASLEELQSVHSERHVLLYGTNPLSRL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  734 KLDSSLTS------VFVRLPCGGVGVDSDTIWNEVHSSGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEESTPM 807
Cdd:cd10008     81 KLDNGKLAgllaqrMFVMLPCGGVGVDTDTIWNELHSSNAARWAAGSVTDLAFKVASRELKNGFAVVRPPGHHADHSTAM 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  808 GFCYFNSVAVAAKLLQQRLNVSKILIVDWDVHHGNGTQQAFYNDPNVLYMSLHRYDDGNFFPGSGAPDEVGTGPGVGFNV 887
Cdd:cd10008    161 GFCFFNSVAIACRQLQQQGKASKILIVDWDVHHGNGTQQTFYQDPSVLYISLHRHDDGNFFPGSGAVDEVGAGSGEGFNV 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  888 NMAFTGGLEPPMGDAEYLAAFRTVVMPIANEFAPDVVLVSSGFDAVEGHPTPLGGYNLSAKCFGYLTKQLMGLAGGRLVL 967
Cdd:cd10008    241 NVAWAGGLDPPMGDPEYLAAFRIVVMPIAREFSPDLVLVSAGFDAAEGHPAPLGGYHVSAKCFGYMTQQLMNLAGGAVVL 320

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1039728092  968 ALEGGHDLTAICDASEACVSALLGNELEPLPEKVLHQRPNANAVHSMEKVMDIHSKYW 1025
Cdd:cd10008    321 ALEGGHDLTAICDASEACVAALLGNEVDPLSEESWKQKPNLNAIRSLEAVIRVHSKYW 378
HDAC9 cd10009
Histone deacetylase 9; Histone deacetylase 9 is a class IIa Zn-dependent enzyme that catalyzes ...
 654-1026 0e+00

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.


Pssm-ID: 212533 [Multi-domain]  Cd Length: 379  Bit Score: 635.90  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  654 FTTGLVYDTLMLKHQCTCGNTNSHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHTLLYGTNPLNRQ 733
Cdd:cd10009      1 SATGIAYDPLMLKHQCVCGNSTTHPEHAGRIQSIWSRLQETGLLNKCERIQGRKASLEEIQLVHSEHHSLLYGTNPLDGQ 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  734 KLDSSL------TSVFVRLPCGGVGVDSDTIWNEVHSSGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEESTPM 807
Cdd:cd10009     81 KLDPRIllgddsQKFFSSLPCGGLGVDSDTIWNELHSSGAARMAVGCVIELASKVASGELKNGFAVVRPPGHHAEESTAM 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  808 GFCYFNSVAVAAKLLQQRLNVSKILIVDWDVHHGNGTQQAFYNDPNVLYMSLHRYDDGNFFPGSGAPDEVGTGPGVGFNV 887
Cdd:cd10009    161 GFCFFNSVAITAKYLRDQLNISKILIVDLDVHHGNGTQQAFYADPSILYISLHRYDEGNFFPGSGAPNEVGTGLGEGYNI 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  888 NMAFTGGLEPPMGDAEYLAAFRTVVMPIANEFAPDVVLVSSGFDAVEGHPTPLGGYNLSAKCFGYLTKQLMGLAGGRLVL 967
Cdd:cd10009    241 NIAWTGGLDPPMGDVEYLEAFRTIVKPVAKEFDPDMVLVSAGFDALEGHTPPLGGYKVTAKCFGHLTKQLMTLADGRVVL 320

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1039728092  968 ALEGGHDLTAICDASEACVSALLGNELEPLPEKVLHQRPNANAVHSMEKVMDIHSKYWR 1026
Cdd:cd10009    321 ALEGGHDLTAICDASEACVNALLGNELEPLAEDILHQSPNMNAVISLQKIIEIQSKYWK 379
HDAC_classII cd09992
Histone deacetylases and histone-like deacetylases, classII; Class II histone deacetylases are ...
 677-990 8.06e-138

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.


Pssm-ID: 212518 [Multi-domain]  Cd Length: 291  Bit Score: 416.90  E-value: 8.06e-138
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  677 HPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHtllygtnplnrqkLDSSLTSVfvrlPCGGVGVDSD 756
Cdd:cd09992      1 HPERPERLLAILEALEEEGLLDRLVFVEPRPATEEELLRVHTPEY-------------IERVEETC----EAGGGYLDPD 63

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  757 TIWNEvHSSGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEESTPMGFCYFNSVAVAAKLLQQRLNVSKILIVDW 836
Cdd:cd09992     64 TYVSP-GSYEAALLAAGAALAAVDAVLSGEAENAFALVRPPGHHAEPDRAMGFCLFNNVAIAARYAQKRYGLKRVLIVDW 142

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  837 DVHHGNGTQQAFYNDPNVLYMSLHRYDdgnFFPGSGAPDEVGTGPGVGFNVNMAftggLEPPMGDAEYLAAFRTVVMPIA 916
Cdd:cd09992    143 DVHHGNGTQDIFYDDPSVLYFSIHQYP---FYPGTGAAEETGGGAGEGFTINVP----LPPGSGDAEYLAAFEEVLLPIA 215

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1039728092  917 NEFAPDVVLVSSGFDAVEGHptPLGGYNLSAKCFGYLTKQLMGLA----GGRLVLALEGGHDLTAICDASEACVSALL 990
Cdd:cd09992    216 REFQPDLVLVSAGFDAHRGD--PLGGMNLTPEGYARLTRLLKELAdehcGGRLVFVLEGGYNLEALAESVLAVLEALL 291
HDAC6-dom2 cd10003
Histone deacetylase 6, domain 2; Histone deacetylase 6 is a class IIb Zn-dependent enzyme that ...
 660-1028 4.43e-134

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).


Pssm-ID: 212527 [Multi-domain]  Cd Length: 350  Bit Score: 409.42  E-value: 4.43e-134
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  660 YDTLMLKHqCTCGNTNsHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHTllygtnplnrQKLDSSL 739
Cdd:cd10003      1 YDQRMMNH-HNLWDPG-HPECPQRISRIYERHNDLGLLERCLRLPSRLATEDELLLCHSEEHL----------DEMKSLE 68

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  740 TSVFVRLpcGGVGVDSDTIWNEVHSSGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEESTPMGFCYFNSVAVAA 819
Cdd:cd10003     69 KMKPREL--NRLGKEYDSIYIHPDSYQCALLAAGCVLQVVEAVLTGESRNGVAIVRPPGHHAEQDTACGFCFFNNVAIAA 146

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  820 KLLQQRLNVSKILIVDWDVHHGNGTQQAFYNDPNVLYMSLHRYDDGNFFPGS--GAPDEVGTGPGVGFNVNMAFTGGlep 897
Cdd:cd10003    147 RYAQKKYGLKRILIVDWDVHHGNGTQHMFESDPSVLYISLHRYDNGSFFPNSpeGNYDVVGKGKGEGFNVNIPWNKG--- 223

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  898 PMGDAEYLAAFRTVVMPIANEFAPDVVLVSSGFDAVEGhpTPLGGYNLSAKCFGYLTKQLMGLAGGRLVLALEGGHDLTA 977
Cdd:cd10003    224 GMGDAEYIAAFQQVVLPIAYEFNPELVLVSAGFDAARG--DPLGGCKVTPEGYAHMTHMLMSLAGGRVIVILEGGYNLTS 301

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1039728092  978 ICDASEACVSALLGnelEPLPEKVLHQRPNANAVHSMEKVMDIHSKYWRCL 1028
Cdd:cd10003    302 ISESMSMCTKTLLG---DPPPVLDLPRPPCSSALKSINNVLQVHQKYWKSL 349
Hist_deacetyl pfam00850
Histone deacetylase domain; Histones can be reversibly acetylated on several lysine residues. ...
 677-989 8.50e-126

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.


Pssm-ID: 425906 [Multi-domain]  Cd Length: 298  Bit Score: 385.82  E-value: 8.50e-126
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  677 HPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHtllygtnpLNRQKldsSLTSVFVRLPCGGVGVDSD 756
Cdd:pfam00850    1 HPENPERLKAILEALREAGLLPDLEIIAPRPATEEELLLVHSPEY--------LEFLE---EAAPEGGALLLLSYLSGDD 69

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  757 TIWNEVHSSGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEESTPMGFCYFNSVAVAAKLLQQRLNVSKILIVDW 836
Cdd:pfam00850   70 DTPVSPGSYEAALLAAGGTLAAADAVLSGEARNAFALVRPPGHHAERDRASGFCIFNNVAIAAKYLREKYGLKRVAIVDF 149

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  837 DVHHGNGTQQAFYNDPNVLYMSLHRYdDGNFFPGSGAPDEVGTGPGVGFNVNMAftggLEPPMGDAEYLAAFRTVVMPIA 916
Cdd:pfam00850  150 DVHHGNGTQEIFYDDPSVLTLSIHQY-PGGFYPGTGFADETGEGKGKGYTLNVP----LPPGTGDAEYLAAFEEILLPAL 224

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1039728092  917 NEFAPDVVLVSSGFDAVEGHptPLGGYNLSAKCFGYLTKQLMGLA---GGRLVLALEGGHDLTAICDASEACVSAL 989
Cdd:pfam00850  225 EEFQPDLILVSAGFDAHAGD--PLGGLNLTTEGFAEITRILLELAdplCIRVVSVLEGGYNLDALARSATAVLAAL 298
HDAC_Clr3 cd11600
Class II Histone deacetylase Clr3 and similar proteins; Clr3 is a class II Histone ...
 675-998 6.83e-118

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.


Pssm-ID: 212542 [Multi-domain]  Cd Length: 313  Bit Score: 365.51  E-value: 6.83e-118
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  675 NSHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAH------TLLYGTNPLNRQKLDSSLTSVFVrlpc 748
Cdd:cd11600      1 DPHPEDPSRISRIFEKLKEAGLINRMLRIPIREATKEEILLVHSEEHwdrveaTEKMSDEQLKDRTEIFERDSLYV---- 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  749 ggvgvdsdtiwNEvHSSGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEESTPMGFCYFNSVAVAAKLLQQRL-- 826
Cdd:cd11600     77 -----------NN-DTAFCARLSCGGAIEACRAVAEGRVKNAFAVVRPPGHHAEPDESMGFCFFNNVAVAAKWLQTEYpd 144

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  827 NVSKILIVDWDVHHGNGTQQAFYNDPNVLYMSLHRYDDGNFFPGS--GAPDEVGTGPGVGFNVNMAFTgglEPPMGDAEY 904
Cdd:cd11600    145 KIKKILILDWDIHHGNGTQRAFYDDPNVLYISLHRFENGGFYPGTpyGDYESVGEGAGLGFNVNIPWP---QGGMGDADY 221

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  905 LAAFRTVVMPIANEFAPDVVLVSSGFDAVEGhpTPLGGYNLSAKCFGYLTKQLMGLAGGRLVLALEGGHDLTAICDASEA 984
Cdd:cd11600    222 IYAFQRIVMPIAYEFDPDLVIISAGFDAADG--DELGQCHVTPAGYAHMTHMLMSLAGGKLVVALEGGYNLDAISDSALA 299

                          330
                   ....*....|....
gi 1039728092  985 CVSALLGNELEPLP 998
Cdd:cd11600    300 VAKVLLGEAPPKLP 313
HDAC cd09301
Histone deacetylase (HDAC) classes I, II, IV and related proteins; The HDAC/HDAC-like family ...
 683-989 2.12e-116

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.


Pssm-ID: 212512 [Multi-domain]  Cd Length: 279  Bit Score: 360.21  E-value: 2.12e-116
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  683 RIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHTLLYGTNPLNRQKLDSSltsvfvrlpcggVGVDSDTIWNEV 762
Cdd:cd09301      1 RIRDLIEALKELGLRPKIELIECREATEELLLKVHTEEYLNELKANFAVATITESK------------PVIFGPNFPVQR 68

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  763 HSSGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEESTPMGFCYFNSVAVAAKLLQQRlNVSKILIVDWDVHHGN 842
Cdd:cd09301     69 HYFRGARLSTGGVVEAAELVAKGELERAFAVVGAGGHHAGKSRAWGFCYFNDVVLAIKFLRER-GISRILIIDTDAHHGD 147

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  843 GTQQAFYNDPNVLYMSLHRYDDGNFfpgsgapdevGTGPGVGFNVNMAFTGGleppMGDAEYLAAFRTVVMPIANEFAPD 922
Cdd:cd09301    148 GTREAFYDDDRVLHMSFHNYDIYPF----------GRGKGKGYKINVPLEDG----LGDEEYLDAVERVISKVLEEFEPE 213

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1039728092  923 VVLVSSGFDAVEGHptPLGGYNLSAKCFGYLTKQLMGLA-GGRLVLALEGGHDLTAICDASEACVSAL 989
Cdd:cd09301    214 VVVLQFGHDTHEGD--RLGGFNLSEKGFVKLAEIVKEFArGGPILMVLGGGYNPEAAARIWTAIIKEL 279
AcuC COG0123
Acetoin utilization deacetylase AcuC or a related deacetylase [Secondary metabolites ...
 656-991 5.01e-102

Acetoin utilization deacetylase AcuC or a related deacetylase [Secondary metabolites biosynthesis, transport and catabolism];


Pssm-ID: 439893 [Multi-domain]  Cd Length: 308  Bit Score: 323.21  E-value: 5.01e-102
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  656 TGLVYDTLMLKHQCTCGntnsHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHtllygtnplnrqkl 735
Cdd:COG0123      1 TALIYHPDYLLHDLGPG----HPEPPERLRAILDALEASGLLDDLELVEPPPATEEDLLRVHTPDY-------------- 62

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  736 dssLTSVFVRLPCGGVG-VDSDTIWNEvHSSGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEESTPMGFCYFNS 814
Cdd:COG0123     63 ---VDALRAASLDGGYGqLDPDTPVSP-GTWEAALLAAGGALAAADAVLEGEARNAFALVRPPGHHAERDRAMGFCLFNN 138

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  815 VAVAAKLLQQRlNVSKILIVDWDVHHGNGTQQAFYNDPNVLYMSLHRYddgNFFPGSGAPDEVGTGPGVGFNVNMAftgg 894
Cdd:COG0123    139 AAIAARYLLAK-GLERVAIVDFDVHHGNGTQDIFYDDPDVLTISIHQD---PLYPGTGAADETGEGAGEGSNLNVP---- 210

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  895 LEPPMGDAEYLAAFRTVVMPIANEFAPDVVLVSSGFDAVEGhpTPLGGYNLSAKCFGYLTKQLMGLA---GGRLVLALEG 971
Cdd:COG0123    211 LPPGTGDAEYLAALEEALLPALEAFKPDLIVVSAGFDAHAD--DPLGRLNLTTEGYAWRTRRVLELAdhcGGPVVSVLEG 288

                          330       340
                   ....*....|....*....|
gi 1039728092  972 GHDLTAICDASEACVSALLG 991
Cdd:COG0123    289 GYNLDALARSVAAHLETLLG 308
HDAC10_HDAC6-dom1 cd10002
Histone deacetylase 6, domain 1 and histone deacetylase 10; Histone deacetylases 6 and 10 are ...
 676-1025 2.69e-99

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.


Pssm-ID: 212526 [Multi-domain]  Cd Length: 336  Bit Score: 316.94  E-value: 2.69e-99
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  676 SHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAH-TLLYGTNPLNRQKLDSsLTSVFvrlpcggvgvd 754
Cdd:cd10002      6 NHIECPERLEAILERLTQDGLLERCVKIPAREAEEDEILLVHSQEYiDLVKSTETMEKEELES-LCSGY----------- 73

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  755 sDTIWNEVHSSGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEESTPMGFCYFNSVAVAAKLLQQRLNVSKILIV 834
Cdd:cd10002     74 -DSVYLCPSTYEAARLAAGSTIELVKAVMAGKIQNGFALIRPPGHHAMRNEANGYCIFNNVAIAAKYAIEKLGLKRILIV 152

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  835 DWDVHHGNGTQQAFYNDPNVLYMSLHRYDDGNFFPGSGAP--DEVGTGPGVGFNVNMAF--TGgleppMGDAEYLAAFRT 910
Cdd:cd10002    153 DWDVHHGQGTQQGFYEDPRVLYFSIHRYEHGRFWPHLFESdyDYIGVGHGYGFNVNVPLnqTG-----LGDADYLAIFHH 227

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  911 VVMPIANEFAPDVVLVSSGFDAVEGhpTPLGGYNLSAKCFGYLTKQLMGLAGGRLVLALEGGHDLTAICDASEACVSALL 990
Cdd:cd10002    228 ILLPLALEFQPELVLVSAGFDASIG--DPEGEMAVTPAGYAHLTRLLMGLAGGKLLLVLEGGYLLESLAESVSMTLRGLL 305

                          330       340       350
                   ....*....|....*....|....*....|....*
gi 1039728092  991 GNELEPLPekvlHQRPNANAVHSMEKVMDIHSKYW 1025
Cdd:cd10002    306 GDPLPPLA----PPIPIRSVLETILNAIAHLSPRW 336
HDAC_classII_1 cd09996
Histone deacetylases and histone-like deacetylases, classII; This subfamily includes bacterial ...
 656-976 1.37e-89

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.


Pssm-ID: 212521 [Multi-domain]  Cd Length: 359  Bit Score: 291.77  E-value: 1.37e-89
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  656 TGLVYDTLMLKHqctcgNTNS----------------HPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSE 719
Cdd:cd09996      1 TGFVWDERYLWH-----DTGTgalflpvggllvqpgrHPENPETKRRIKNLLEVSGLSDHLVLITPRPATDEELLRVHTP 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  720 AHtllygtnpLNR-QKLDSSltsvfvrlpcGGVGVDSDTIWNEvHSSGAARLAVGCVVELVFKVATGELKNGFAVVRPPG 798
Cdd:cd09996     76 EY--------IDRvKAASAA----------GGGEAGGGTPFGP-GSYEIALLAAGGAIAAVDAVLDGEVDNAYALVRPPG 136

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  799 HHAEESTPMGFCYFNSVAVAAKLLQQRLNVSKILIVDWDVHHGNGTQQAFYNDPNVLYMSLHRydDGNFFPGSGAPDEVG 878
Cdd:cd09996    137 HHAEPDQGMGFCLFNNVAIAARHALAVGGVKRVAVVDWDVHHGNGTQAIFYDDPDVLTISLHQ--DRCFPPDSGAVEERG 214

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  879 TGPGVGFNVNMAftggLEPPMGDAEYLAAFRTVVMPIANEFAPDVVLVSSGFDAveGHPTPLGGYNLSAKCFGYLTKQLM 958
Cdd:cd09996    215 EGAGEGYNLNIP----LPPGSGDGAYLHAFERIVLPALRAFRPELIIVASGFDA--SAFDPLGRMMLTSDGFRALTRKLR 288

                          330       340
                   ....*....|....*....|..
gi 1039728092  959 GLA----GGRLVLALEGGHDLT 976
Cdd:cd09996    289 DLAdelcGGRLVMVHEGGYSEA 310
HDAC6-dom1 cd11682
Histone deacetylase 6, domain 1; Histone deacetylases 6 are class IIb Zn-dependent enzymes ...
 676-1025 7.98e-87

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).


Pssm-ID: 212545 [Multi-domain]  Cd Length: 337  Bit Score: 283.67  E-value: 7.98e-87
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  676 SHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHS-EAHTLLYGTNPLNRQKLdSSLTSVFvrlpcggvgvd 754
Cdd:cd11682      6 SFPECPERLHAIREKLIQEGLLERCVSVQAREASEEELLLVHSpEYVALMKSTQYMTEEEL-RTLADTY----------- 73

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  755 sDTIWNEVHSSGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEESTPMGFCYFNSVAVAAKLLQQRLNVSKILIV 834
Cdd:cd11682     74 -DSVYLHPNSYSCACLAVGSVLQLVDKVLGGEIRNGLAIVRPPGHHAQHDKMDGYCMFNNVAIAARYAQQKHGVQRVLIV 152

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  835 DWDVHHGNGTQQAFYNDPNVLYMSLHRYDDGNFFPGSGAPDE--VGTGPGVGFNVNMAFTgglEPPMGDAEYLAAFRTVV 912
Cdd:cd11682    153 DWDVHHGQGTQFIFEQDPSVLYFSIHRYEQGRFWPHLKESDSsaVGFGRGEGYNINVPWN---QVGMRDADYIAAFLHVL 229

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  913 MPIANEFAPDVVLVSSGFDAVEGHPTplGGYNLSAKCFGYLTKQLMGLAGGRLVLALEGGHDLTAICDASEACVSALLGn 992
Cdd:cd11682    230 LPVALEFQPQLVLVAAGFDAVIGDPK--GEMAATPACFAHLTHLLMGLAGGKLILSLEGGYNLRSLAEGVCASLKALLG- 306

                          330       340       350
                   ....*....|....*....|....*....|...
gi 1039728092  993 elEPLPEKVLHQRPNANAVHSMEKVMDIHSKYW 1025
Cdd:cd11682    307 --DPCPMLESPGAPCRSALASVSCTISALEPFW 337
HDAC_classII_2 cd11599
Histone deacetylases and histone-like deacetylases, classII; This subfamily includes ...
 677-990 1.18e-82

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.


Pssm-ID: 212541 [Multi-domain]  Cd Length: 288  Bit Score: 270.15  E-value: 1.18e-82
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  677 HPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHtllygtnplnrqkldssLTSVFVRLPC-GGVGVDS 755
Cdd:cd11599      1 HPESPERLEAILDALIASGLDRLLRQLEAPPATREQLLRVHDAAY-----------------VDRLEAAAPEeGLVQLDP 63

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  756 DTIWNEvHSSGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEESTPMGFCYFNSVAVAAKLLQQRLNVSKILIVD 835
Cdd:cd11599     64 DTAMSP-GSLEAALRAAGAVVAAVDAVMAGEARNAFCAVRPPGHHAERDKAMGFCLFNNVAIAAAHALAHHGLERVAIVD 142

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  836 WDVHHGNGTQQAFYNDPNVLYMSLHRYddgNFFPGSGAPDEvgTGPGVGFNVNM-AFTGGleppmgdAEYLAAFRTVVMP 914
Cdd:cd11599    143 FDVHHGNGTEDIFRDDPRVLFCSSHQH---PLYPGTGAPDE--TGHGNIVNVPLpAGTGG-------AEFREAVEDRWLP 210

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  915 IANEFAPDVVLVSSGFDAvegHPT-PLGGYNLSAKCFGYLTKQLMGLA----GGRLVLALEGGHDLTAICDASEACVSAL 989
Cdd:cd11599    211 ALDAFKPDLILISAGFDA---HRDdPLAQLNLTEEDYAWITEQLMDVAdrycDGRIVSVLEGGYDLSALARSVAAHVRAL 287


                   .
gi 1039728092  990 L 990
Cdd:cd11599    288 M 288
HDAC10 cd11683
Histone deacetylase 10; Histone deacetylases 10 are class IIb Zn-dependent enzymes that ...
 683-1025 1.40e-73

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.


Pssm-ID: 212546 [Multi-domain]  Cd Length: 337  Bit Score: 247.08  E-value: 1.40e-73
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  683 RIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHTLLYGTNPLNRQKLDSSLTSVFvrlpcggvgvdsDTIWNEV 762
Cdd:cd11683     13 RLTASYERLRQYGLVQRCLRLPAREASEEEILLVHSPEYLSLVRETQVMNKEELMAISGKY------------DAVYFHP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  763 HSSGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEESTPMGFCYFNSVAVAAKLLQQRLNVSKILIVDWDVHHGN 842
Cdd:cd11683     81 NTFHCARLAAGATLQLVDAVLTGEVQNGMALVRPPGHHSQRNAANGFCVFNNVAIAAEYAKKKYGLHRILIVDWDVHHGQ 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  843 GTQQAFYNDPNVLYMSLHRYDDGNFFPG--SGAPDEVGTGPGVGFNVNMAFTgglEPPMGDAEYLAAFRTVVMPIANEFA 920
Cdd:cd11683    161 GIQYIFEEDPSVLYFSWHRYEHQRFWPFlrESDYDAVGRGKGLGFNINLPWN---KVGMGNADYLAAFFHVLLPLAFEFD 237

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  921 PDVVLVSSGFDAVEGHPTplGGYNLSAKCFGYLTKQLMGLAGGRLVLALEGGHDLTAICDASEACVSALLGnelEPLPEK 1000
Cdd:cd11683    238 PELVLVSAGFDSAIGDPE--GQMCATPECFAHLTHLLMVLAGGKLCAVLEGGYHLESLAESVCMTVQTLLG---DPLPRL 312

                          330       340
                   ....*....|....*....|....*
gi 1039728092 1001 VLHQRPNANAVHSMEKVMDIHSKYW 1025
Cdd:cd11683    313 SGEMTPCQSALESIQNVRAAQAPYW 337
HDAC_classII_APAH cd10001
Histone deacetylase class IIa; This subfamily includes bacterial acetylpolyamine ...
 658-991 3.29e-69

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.


Pssm-ID: 212525 [Multi-domain]  Cd Length: 298  Bit Score: 233.58  E-value: 3.29e-69
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  658 LVYDTLMLKHQ----CTCGNTNSHPEHAGRIQSIWSRLQETGLRGKcecIRGRKATLEELQTVHSEAHtllygtnplnrq 733
Cdd:cd10001      2 IVYSEDHLLHHpkteLSRGKLVPHPENPERAEAILDALKRAGLGEV---LPPRDFGLEPILAVHDPDY------------ 66

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  734 kLDssltsvFVRlpcggvGVDSDTIWNEvHSSGAARLAVGCVVELVFKVATGElKNGFAVVRPPGHHAEESTPMGFCYFN 813
Cdd:cd10001     67 -VD------FLE------TADTDTPISE-GTWEAALAAADTALTAADLVLEGE-RAAYALCRPPGHHAGRDRAGGFCYFN 131

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  814 SVAVAAKLLQQRlnVSKILIVDWDVHHGNGTQQAFYNDPNVLYMSLHRyDDGNFFPG-SGAPDEVGTGPGVGFNVNMAft 892
Cdd:cd10001    132 NAAIAAQYLRDR--AGRVAILDVDVHHGNGTQEIFYERPDVLYVSIHG-DPRTFYPFfLGFADETGEGEGEGYNLNLP-- 206

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  893 ggLEPPMGDAEYLAAFRTVVMPIAnEFAPDVVLVSSGFDAVEGhpTPLGGYNLSAKCFGYLTKQLMGLaGGRLVLALEGG 972
Cdd:cd10001    207 --LPPGTGDDDYLAALDEALAAIA-AFGPDALVVSLGFDTHEG--DPLSDFKLTTEDYARIGRRIAAL-GLPTVFVQEGG 280

                          330
                   ....*....|....*....
gi 1039728092  973 HDLTAIcdaSEACVSALLG 991
Cdd:cd10001    281 YNVDAL---GRNAVAFLAG 296
HDAC_AcuC_like cd09994
Class I histone deacetylase AcuC (Acetoin utilization protein)-like enzymes; AcuC (Acetoin ...
 677-975 2.55e-49

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.


Pssm-ID: 212520 [Multi-domain]  Cd Length: 313  Bit Score: 177.75  E-value: 2.55e-49
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  677 HPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHtllygtnpLNRQKLDSSLTSVFVRLPCGgVGVDSD 756
Cdd:cd09994     17 HPFNPPRLSLTKDLLRALGLLPPVDLVPPRPATEEELLLFHTPDY--------IEAVKEASRGQEPEGRGRLG-LGTEDN 87

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  757 TIWNEVHSsgAARLAVGCVVELVFKVATGElknGFAVVRPPG--HHAEESTPMGFCYFNSVAVAAKLLQqRLNVSKILIV 834
Cdd:cd09994     88 PVFPGMHE--AAALVVGGTLLAARLVLEGE---ARRAFNPAGglHHAMRGRASGFCVYNDAAVAIERLR-DKGGLRVAYV 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  835 DWDVHHGNGTQQAFYNDPNVLYMSLHRyDDGNFFPGSGAPDEVGTGPGVGFNVNMAftggLEPPMGDAEYLAAFRTVVMP 914
Cdd:cd09994    162 DIDAHHGDGVQAAFYDDPRVLTISLHE-SGRYLFPGTGFVDEIGEGEGYGYAVNIP----LPPGTGDDEFLRAFEAVVPP 236

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1039728092  915 IANEFAPDVVLVSSGFDAVEGhpTPLGGYNLSAKCFGYLTKQLMGLA----GGRLVLALEGGHDL 975
Cdd:cd09994    237 LLRAFRPDVIVSQHGADAHAG--DPLTHLNLSNRAYRAAVRRIRELAdeycGGRWLALGGGGYNP 299
Arginase_HDAC cd09987
Arginase-like and histone-like hydrolases; Arginase-like/histone-like hydrolase superfamily ...
 763-989 3.94e-37

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.


Pssm-ID: 212513  Cd Length: 217  Bit Score: 139.05  E-value: 3.94e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  763 HSSGAARLAVGCVVELVFKVatgelKNGFAVVrppGHHAEestpmgfcyFNSVAVAAKLLQQRlnvskILIVDWDVHHGN 842
Cdd:cd09987      6 RKAEAHELLAGVVVAVLKDG-----KVPVVLG---GDHSI---------ANGAIRAVAELHPD-----LGVIDVDAHHDV 63

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  843 GTQQAFYN--------------DPNVLYMSLHRYDDGNFFPGsgapdevGTGPGVGFNVNMAFTGGLeppmgDAEYLAAF 908
Cdd:cd09987     64 RTPEAFGKgnhhtprhllceplISDVHIVSIGIRGVSNGEAG-------GAYARKLGVVYFSMTEVD-----KLGLGDVF 131

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  909 RTVVMPIanEFAPDVVLVSSGFDAVEGHPTP----LGGYNLSAKCFGYLTKQLMGLaGGRLVLALEGGHDL----TAICD 980
Cdd:cd09987    132 EEIVSYL--GDKGDNVYLSVDVDGLDPSFAPgtgtPGPGGLSYREGLYITERIAKT-NLVVGLDIVEVNPLldetGRTAR 208


                   ....*....
gi 1039728092  981 ASEACVSAL 989
Cdd:cd09987    209 LAAALTLEL 217
HDAC_classI cd09991
Class I histone deacetylases; Class I histone deacetylases (HDACs) are Zn-dependent enzymes ...
 677-963 8.00e-35

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.


Pssm-ID: 212517 [Multi-domain]  Cd Length: 306  Bit Score: 135.40  E-value: 8.00e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  677 HPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAH-TLLYGTNPLNrqklDSSLTSVFVRLpcgGVGVD- 754
Cdd:cd09991     15 HPMKPHRIRMTHSLILSYGLYKKMEIYRPRPATAEELTKFHSDDYiDFLRSVSPDN----MKEFKKQLERF---NVGEDc 87

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  755 --SDTIWNEVHSSGAArlAVGCVVELVFKVATgelkngfAVVRPPG--HHAEESTPMGFCYFNSVAVAA-KLLQ--QRln 827
Cdd:cd09991     88 pvFDGLYEYCQLYAGG--SIAAAVKLNRGQAD-------IAINWAGglHHAKKSEASGFCYVNDIVLAIlELLKyhQR-- 156

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  828 vskILIVDWDVHHGNGTQQAFYNDPNVLYMSLHRYddGNFFPGSGAPDEVGTGPGVGFNVNMAftggLEPPMGDAEYLAA 907
Cdd:cd09991    157 ---VLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKF--GEYFFPGTGLRDIGAGKGKYYAVNVP----LKDGIDDESYLQI 227

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1039728092  908 FRTVVMPIANEFAPDVVLVSSGFDAVEGhpTPLGGYNLS----AKCFGYLTK---QLMGLAGG 963
Cdd:cd09991    228 FEPVLSKVMEVFQPSAVVLQCGADSLAG--DRLGCFNLSikghAKCVKFVKSfniPLLVLGGG 288
ClassIIa_HDAC4_Gln-rich-N cd10162
Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase; This ...
 90-151 7.03e-33

Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase; This family consists of the glutamine-rich domain of histone deacetylase 4 (HDAC4). It belongs to a superfamily that consists of the glutamine-rich N-terminal helical extension to certain Class IIa histone deacetylases (HDACs), including HDAC4, HDAC5 and HDCA9; it is missing from HDAC7. This domain confers responsiveness to calcium signals and mediates interactions with transcription factors and cofactors, and it is able to repress transcription independently of the HDAC C-terminal, zinc-dependent catalytic domain. It has many intra- and inter-helical interactions which are possibly involved in reversible assembly and disassembly of proteins. HDACs regulate diverse cellular processes through enzymatic deacetylation of histone as well as non-histone proteins, in particular deacetylating N(6)-acetyl-lysine residues.


Pssm-ID: 197398 [Multi-domain]  Cd Length: 90  Bit Score: 122.23  E-value: 7.03e-33
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1039728092   90 AEFQRQHEQLSRQHEAQLHEHIKQQQEMLAMKHQQELLEHQRKLERHRQEQELEKQHREQKL 151
Cdd:cd10162     29 AEFQRQHEQLSRQHEAQLHEHIKQQQELLAMKHQQELLEHQRKLERHRQEQEMEKQQREQKL 90
HDAC8 cd10000
Histone deacetylase 8 (HDAC8); HDAC8 is a Zn-dependent class I histone deacetylase that ...
 670-1018 1.01e-32

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.


Pssm-ID: 212524 [Multi-domain]  Cd Length: 364  Bit Score: 130.92  E-value: 1.01e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  670 TCGNTNSHPEHAGRIQSIwsrLQETGLRGKCECIRGRKATLEELQTVHSEA--HTLLYGTNPLNRQKLDSSLTSVfvrlp 747
Cdd:cd10000     12 LCDRLPKVPNRASMVHSL---IEAYGLLKQLRVVKPRVATEEELASFHSDEyiQFLKKASNEGDNDEEPSEQQEF----- 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  748 cgGVGVDS---DTIWNEVHS-SGAARLAVGCVVELVFKVAtgelkngfavVRPPG--HHAEESTPMGFCYFNSVAVAAKL 821
Cdd:cd10000     84 --GLGYDCpifEGIYDYAAAvAGATLTAAQLLIDGKCKVA----------INWFGgwHHAQRDEASGFCYVNDIVLGILK 151

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  822 LQQRLnvSKILIVDWDVHHGNGTQQAFYNDPNVLYMSLHRYDDGnFFPGSGAPDEVGTGPGVGFNVNMAFTGGLEppmgD 901
Cdd:cd10000    152 LREKF--DRVLYVDLDLHHGDGVEDAFSFTSKVMTVSLHKYSPG-FFPGTGDVSDVGLGKGKYYTVNVPLRDGIQ----D 224

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  902 AEYLAAFRTVVMPIANEFAPDVVLVSSGFDAVEGhpTPLGGYNLSAKCFGYLTKQLMGLAGGRLVLAlEGGHDL--TAIC 979
Cdd:cd10000    225 EQYLQIFTAVVPEIVAAFRPEAVVLQCGADTLAG--DPMGAFNLTPVGIGKCLKYVLGWKLPTLILG-GGGYNLanTARC 301

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1039728092  980 DASeaCVSALLGNELEPL-----------PEKVLH----QRPNANAVHSMEKVM 1018
Cdd:cd10000    302 WTY--LTGLILGEPLSSDipdhefftsygPDYELEispsLRPDLNEDQYIEKIL 353
HDAC_classIV cd09993
Histone deacetylase class IV also known as histone deacetylase 11; Class IV histone ...
 687-947 1.28e-31

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.


Pssm-ID: 212519 [Multi-domain]  Cd Length: 275  Bit Score: 125.30  E-value: 1.28e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  687 IWSRLQETGLRGKCECIRGRKATLEELQTVHSEA--HTLLYGTN----------PLNRQKLDSSLTSVfvrlpcGGvgvd 754
Cdd:cd09993     11 LREALLEEGLVLPEDIVEPEPATREDLLRVHDPEylESLKSGELsreeirrigfPWSPELVERTRLAV------GG---- 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  755 sdTIwnevhssGAARLAvgcvvelvfkvatgeLKNGFAVvRPPG--HHAEESTPMGFCYFNSVAVAAKLLQQRLNVSKIL 832
Cdd:cd09993     81 --TI-------LAARLA---------------LEHGLAI-NLAGgtHHAFPDRGEGFCVFNDIAIAARVLLAEGLVRRVL 135

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  833 IVDWDVHHGNGTQQAFYNDPNVLYMSLHrydDGNFFPGSGAPDevgtgpgvGFNVnmaftgGLEPPMGDAEYLAAFRTVV 912
Cdd:cd09993    136 IVDLDVHQGNGTAAIFADDPSVFTFSMH---GEKNYPFRKEPS--------DLDV------PLPDGTGDDEYLAALEEAL 198

                          250       260       270
                   ....*....|....*....|....*....|....*
gi 1039728092  913 MPIANEFAPDVVLVSSGFDAVEGhpTPLGGYNLSA 947
Cdd:cd09993    199 PRLLAEFRPDLVFYNAGVDVLAG--DRLGRLSLSL 231
ClassIIa_HDAC_Gln-rich-N cd10149
Glutamine-rich N-terminal helical domain of various Class IIa histone deacetylases (HDAC4, ...
 90-151 9.28e-30

Glutamine-rich N-terminal helical domain of various Class IIa histone deacetylases (HDAC4, HDAC5 and HDCA9); This superfamily consists of a glutamine-rich N-terminal helical extension to certain Class IIa histone deacetylases (HDACs), including HDAC4, HDAC5 and HDAC9; it is missing in HDAC7. It is referred to as the glutamine-rich domain, and confers responsiveness to calcium signals and mediates interactions with transcription factors and cofactors. This domain is able to repress transcription independently of the HDAC's C-terminal, zinc-dependent catalytic domain. It has many intra- and inter-helical interactions which are possibly involved in reversible assembly and disassembly of proteins. HDACs regulate diverse cellular processes through enzymatic deacetylation of histone as well as non-histone proteins, in particular deacetylating N(6)-acetyl-lysine residues.


Pssm-ID: 197397 [Multi-domain]  Cd Length: 90  Bit Score: 113.25  E-value: 9.28e-30
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1039728092   90 AEFQRQHEQLSRQHEAQLHEHIKQQQEMLAMKHQQELLEHQRKLERHRQEQELEKQHREQKL 151
Cdd:cd10149     29 AEFQKQHENLTRQHEAQLQEHIKQQQEMLAIKQQQELLEKQRKLEQQRQEQELEKQRREQQL 90
HDAC_Hos1 cd11680
Class I histone deacetylases Hos1 and related proteins; Saccharomyces cerevisiae Hos1 is ...
 799-979 1.33e-28

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.


Pssm-ID: 212543 [Multi-domain]  Cd Length: 294  Bit Score: 116.98  E-value: 1.33e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  799 HHAEESTPMGFCYFNSVAVAAKLLQqRLNVSKILIVDWDVHHGNGTQQAFYNDPNVLYMSLHRYDDGnFFPGSGAPDEvg 878
Cdd:cd11680    115 HHAQKSRASGFCYVNDIVLAILRLR-RARFRRVFYLDLDLHHGDGVESAFFFSKNVLTCSIHRYDPG-FFPGTGSLKN-- 190

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  879 tgPGVGFNVNMAftggLEPPMGDAEYLAAFRTVVMPIANEFAPDVVLVSSGFDAVEGhpTPLGGYNLSAKCFGYLTKQLM 958
Cdd:cd11680    191 --SSDKGMLNIP----LKRGLSDKTLLRIIDSIVRPLIEKFEPEVIVIQCGCDGLSG--DPHKEWNLTIRGYGSVIELLL 262

                          170       180
                   ....*....|....*....|....
gi 1039728092  959 GLAGGRLVLALEGG---HDLTAIC 979
Cdd:cd11680    263 KEFKDKPTLLLGGGgynHTEAARA 286
HDAC_Hos2 cd11598
Class I histone deacetylases including ScHos2 and SpPhd1; This subfamily includes Class I ...
 799-951 2.31e-28

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).


Pssm-ID: 212540 [Multi-domain]  Cd Length: 311  Bit Score: 116.79  E-value: 2.31e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  799 HHAEESTPMGFCYFNSVAVAakLLQQRLNVSKILIVDWDVHHGNGTQQAFYNDPNVLYMSLHRYdDGNFFPGSGAPDEVG 878
Cdd:cd11598    131 HHAKKSEASGFCYVNDIVLA--ILNLLRYFPRVLYIDIDVHHGDGVEEAFYRTDRVMTLSFHKY-NGEFFPGTGDLDDNG 207

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1039728092  879 TGPGVGFNVNMAftggLEPPMGDAEYLAAFRTVVMPIANEFAPDVVLVSSGFDAVEGhpTPLGGYNLSAKCFG 951
Cdd:cd11598    208 GTPGKHFALNVP----LEDGIDDEQYNLLFKSIIGPTIEKFQPSAIVLQCGADSLGG--DRLGQFNLNIKAHG 274
HDAC4_Gln pfam12203
Glutamine rich N terminal domain of histone deacetylase 4; This domain is found in eukaryotes, ...
 90-151 3.92e-25

Glutamine rich N terminal domain of histone deacetylase 4; This domain is found in eukaryotes, and is approximately 90 amino acids in length. The family is found in association with pfam00850. The domain forms an alpha helix which complexes to form a tetramer. The glutamine rich domains have many intra- and inter-helical interactions which are thought to be involved in reversible assembly and disassembly of proteins. The domain is part of histone deacetylase 4 (HDAC4) which removes acetyl groups from histones. This restores their positive charge to allow stronger DNA binding thus restricting transcriptional activity.


Pssm-ID: 403429 [Multi-domain]  Cd Length: 91  Bit Score: 100.31  E-value: 3.92e-25
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1039728092   90 AEFQRQHEQLSRQHEAQLHEHIKQQQEMLAMKHQQELLEHQRKLERHRQEQELEKQHREQKL 151
Cdd:pfam12203   30 AEFQKQHELLTRQHEAQLQEHIKQQQELLAMKQQQELLEQQRKLEQQRQEEELEKHRREQQL 91
HDAC1 cd10010
Histone deacetylase 1 (HDAC1); Histone deacetylase 1 (HDAC1) is a Zn-dependent class I enzyme ...
 677-963 1.11e-24

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.


Pssm-ID: 212534 [Multi-domain]  Cd Length: 371  Bit Score: 107.46  E-value: 1.11e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  677 HPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAH-TLLYGTNPLNRQKLDSSLTSVFVRLPCGGVgvds 755
Cdd:cd10010     25 HPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKANAEEMTKYHSDDYiKFLRSIRPDNMSEYSKQMQRFNVGEDCPVF---- 100

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  756 DTIWNEVHSSGAARLAVGcvvelvfkVATGELKNGFAVVRPPG-HHAEESTPMGFCYFNSVAVAakLLQQRLNVSKILIV 834
Cdd:cd10010    101 DGLFEFCQLSAGGSVASA--------VKLNKQQTDIAVNWAGGlHHAKKSEASGFCYVNDIVLA--ILELLKYHQRVLYI 170

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  835 DWDVHHGNGTQQAFYNDPNVLYMSLHRYddGNFFPGSGAPDEVGTGPGVGFNVNMAFTGGLEppmgDAEYLAAFRTVVMP 914
Cdd:cd10010    171 DIDIHHGDGVEEAFYTTDRVMTVSFHKY--GEYFPGTGDLRDIGAGKGKYYAVNYPLRDGID----DESYEAIFKPVMSK 244

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1039728092  915 IANEFAPDVVLVSSGFDAVEGhpTPLGGYNLS----AKCFGYLTK---QLMGLAGG 963
Cdd:cd10010    245 VMEMFQPSAVVLQCGADSLSG--DRLGCFNLTikghAKCVEFVKSfnlPMLMLGGG 298
RPD3-like cd10004
reduced potassium dependency-3 (RPD3)-like; Proteins of the Rpd3-like family are class I ...
 677-963 4.65e-24

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.


Pssm-ID: 212528 [Multi-domain]  Cd Length: 375  Bit Score: 105.66  E-value: 4.65e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  677 HPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHT-LLYGTNPLNRQKLDSSLTSVfvrlpcgGVGVDS 755
Cdd:cd10004     21 HPMKPHRIRMAHSLVMNYGLYKKMEIYRAKPATKNEMTQFHTDEYIdFLSRVTPDNMEKFQKEQVKY-------NVGDDC 93

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  756 ---DTIWNEVHSS------GAARLAVGcvvelvfkvatgelKNGFAVVRPPG-HHAEESTPMGFCYFNSVAVAA-KLLQQ 824
Cdd:cd10004     94 pvfDGLFEFCSISaggsmeGAARLNRG--------------KCDIAVNWAGGlHHAKKSEASGFCYVNDIVLGIlELLRY 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  825 RlnvSKILIVDWDVHHGNGTQQAFYNDPNVLYMSLHRYddGNFFPGSGAPDEVGTGPGVGFNVNMAFTGGLEppmgDAEY 904
Cdd:cd10004    160 H---QRVLYIDIDVHHGDGVEEAFYTTDRVMTCSFHKY--GEYFPGTGELRDIGIGTGKNYAVNVPLRDGID----DESY 230

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1039728092  905 LAAFRTVVMPIANEFAPDVVLVSSGFDAVEGhpTPLGGYNLS----AKCFGYLTK---QLMGLAGG 963
Cdd:cd10004    231 KSIFEPVIKHVMEWYQPEAVVLQCGGDSLSG--DRLGCFNLSmkghANCVNFVKSfnlPMLVLGGG 294
HDAC_Hos3 cd09998
Class II histone deacetylases Hos3 and related proteins; Fungal histone deacetylase Hos3 from ...
 767-989 7.93e-23

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.


Pssm-ID: 212522 [Multi-domain]  Cd Length: 353  Bit Score: 101.37  E-value: 7.93e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  767 AARLAVGCV---VELVFKVATGELKNGFAVVRPPGHHAEESTPMGFCYFNSVAVAAKLLQQRLNVSKILIVDWDVHHGNG 843
Cdd:cd09998     85 AIQGALGAVceaVDSVFKPESPGTKRAFVAIRPPGHHCSESTPSGFCWVNNVHVGAAHAYLTHGITRVVILDIDLHHGNG 164

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  844 TQ------------------------QAFYNDPNVLYMSLHrydDGNFFP-GSGAPDEVGTGpgvgfNVNMAFTGG---- 894
Cdd:cd09998    165 TQdiawrinaeankqalesssyddfkPAGAPGLRIFYSSLH---DINSFPcEDGDPAKVKDA-----SVSIDGAHGqwiw 236

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  895 ---LEPPMGDAEYLAAFR---TVVMPIANEF------APD---VVLVSSGFDAVEGHPTPLG--GYNLSAKCFGYLTKQL 957
Cdd:cd09998    237 nvhLQPWTTEEDFWELYYpkyRILFEKAAEFlrlttaATPfktLVFISAGFDASEHEYESMQrhGVNVPTSFYYRFARDA 316

                          250       260       270
                   ....*....|....*....|....*....|....*.
gi 1039728092  958 MGLA----GGRLVLALEGGHDLTAICDASEACVSAL 989
Cdd:cd09998    317 VRFAdahaHGRLISVLEGGYSDRALCSGVLAHLTGL 352
ClassIIa_HDAC9_Gln-rich-N cd10163
Glutamine-rich N-terminal helical domain of HDAC9, a Class IIa histone deacetylase; This ...
 90-151 2.56e-22

Glutamine-rich N-terminal helical domain of HDAC9, a Class IIa histone deacetylase; This family consists of the glutamine-rich domain of histone deacetylase 9 (HDAC9). It belongs to a superfamily that consists of the glutamine-rich N-terminal helical extension to certain Class IIa histone deacetylases (HDACs), including HDAC4, HDAC5 and HDCA9; it is missing from HDAC7. This domain confers responsiveness to calcium signals and mediates interactions with transcription factors and cofactors, and it is able to repress transcription independently of the HDAC C-terminal, zinc-dependent catalytic domain. It has many intra- and inter-helical interactions which are possibly involved in reversible assembly and disassembly of proteins. HDACs regulate diverse cellular processes through enzymatic deacetylation of histone as well as non-histone proteins, in particular deacetylating N(6)-acetyl-lysine residues.


Pssm-ID: 197399 [Multi-domain]  Cd Length: 90  Bit Score: 92.12  E-value: 2.56e-22
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1039728092   90 AEFQRQHEQLSRQHEAQLHEHIKQQQEMLAMKHQQELLEHQRKLERHRQEQELEKQHREQKL 151
Cdd:cd10163     29 AEFQKQHENLTRQHQAQLQEHLKLQQELLAMKQQQELLEKEQKLEQQRQEQELERHRREQQL 90
HDAC3 cd10005
Histone deacetylase 3 (HDAC3); HDAC3 is a Zn-dependent class I histone deacetylase that ...
 677-951 6.47e-22

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.


Pssm-ID: 212529  Cd Length: 381  Bit Score: 99.01  E-value: 6.47e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  677 HPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHT-LLYGTNPLNRQKLDSSLTSVFVRLPC---GGVg 752
Cdd:cd10005     20 HPMKPHRLALTHSLVLHYGLYKKMQVYKPYRASAHDMCRFHSEDYIdFLQRVTPQNIQGFTKSLNQFNVGDDCpvfPGL- 98

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  753 VDSDTIWNEVHSSGAARLAVGCVvelvfKVA---TGELkngfavvrppgHHAEESTPMGFCYFNSVAVAA-KLLQQRlnv 828
Cdd:cd10005     99 FDFCSMYTGASLEGATKLNHKIC-----DIAinwSGGL-----------HHAKKFEASGFCYVNDIVIAIlELLKYH--- 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  829 SKILIVDWDVHHGNGTQQAFYNDPNVLYMSLHRYddGN-FFPGSGAPDEVGTGPGVGFNVNMAFTGGLEppmgDAEYLAA 907
Cdd:cd10005    160 PRVLYIDIDIHHGDGVQEAFYLTDRVMTVSFHKY--GNyFFPGTGDMYEVGAESGRYYSVNVPLKDGID----DQSYLQL 233

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|....
gi 1039728092  908 FRTVVMPIANEFAPDVVLVSSGFDAVEGhpTPLGGYNLSAKCFG 951
Cdd:cd10005    234 FKPVIQQVIDFYQPTCIVLQCGADSLGC--DRLGCFNLSIKGHG 275
PTZ00063 PTZ00063
histone deacetylase; Provisional
 799-963 1.57e-21

histone deacetylase; Provisional


Pssm-ID: 240251  Cd Length: 436  Bit Score: 98.73  E-value: 1.57e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  799 HHAEESTPMGFCYFNSVAVAA-KLLQQRlnvSKILIVDWDVHHGNGTQQAFYNDPNVLYMSLHRYddGNFFPGSGAPDEV 877
Cdd:PTZ00063   137 HHAKRSEASGFCYINDIVLGIlELLKYH---ARVMYIDIDVHHGDGVEEAFYVTHRVMTVSFHKF--GDFFPGTGDVTDI 211

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  878 GTGPGVGFNVNMAFTGGleppMGDAEYLAAFRTVVMPIANEFAPDVVLVSSGFDAVEGhpTPLGGYNLS----AKCFGYL 953
Cdd:PTZ00063   212 GVAQGKYYSVNVPLNDG----IDDDSFVDLFKPVISKCVEVYRPGAIVLQCGADSLTG--DRLGRFNLTikghAACVEFV 285

                          170
                   ....*....|...
gi 1039728092  954 TK---QLMGLAGG 963
Cdd:PTZ00063   286 RSlniPLLVLGGG 298
HDAC2 cd10011
Histone deacetylase 2 (HDAC2); Histone deacetylase 2 (HDAC2) is a Zn-dependent class I enzyme ...
 677-948 2.97e-20

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.


Pssm-ID: 212535 [Multi-domain]  Cd Length: 366  Bit Score: 93.97  E-value: 2.97e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  677 HPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAH-TLLYGTNPLNRQKLDSSLTSVFVRLPCGGVgvds 755
Cdd:cd10011     21 HPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTKYHSDEYiKFLRSIRPDNMSEYSKQMQRFNVGEDCPVF---- 96

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  756 DTIWNEVHSSGAARLAVGcvvelvfkVATGELKNGFAVVRPPG-HHAEESTPMGFCYFNSVAVAakLLQQRLNVSKILIV 834
Cdd:cd10011     97 DGLFEFCQLSTGGSVAGA--------VKLNRQQTDMAVNWAGGlHHAKKSEASGFCYVNDIVLA--ILELLKYHQRVLYI 166

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  835 DWDVHHGNGTQQAFYNDPNVlyMSLHRYDDGNFFPGSGAPDEVGTGPGVGFNVNMAFTGGLEppmgDAEYLAAFRTVVMP 914
Cdd:cd10011    167 DIDIHHGDGVEEAFYTTDRV--MTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGID----DESYGQIFKPIISK 240

                          250       260       270
                   ....*....|....*....|....*....|....
gi 1039728092  915 IANEFAPDVVLVSSGFDAVEGhpTPLGGYNLSAK 948
Cdd:cd10011    241 VMEMYQPSAVVLQCGADSLSG--DRLGCFNLTVK 272
PTZ00346 PTZ00346
histone deacetylase; Provisional
 799-972 1.26e-17

histone deacetylase; Provisional


Pssm-ID: 240374 [Multi-domain]  Cd Length: 429  Bit Score: 86.62  E-value: 1.26e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  799 HHAEESTPMGFCYFNSVAVAakLLQQRLNVSKILIVDWDVHHGNGTQQAFYNDPNVLYMSLHRYDDgNFFPGSGAPDEVG 878
Cdd:PTZ00346   154 HHSKCGECSGFCYVNDIVLG--ILELLKCHDRVLYVDIDMHHGDGVDEAFCTSDRVFTLSLHKFGE-SFFPGTGHPRDVG 230

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092  879 TGPGVGFNVNMAFTGGLEppmgDAEYLAAFRTVVMPIANEFAPDVVLVSSGFDAVEGhpTPLGGYNLSAKCFGYLTKQLM 958
Cdd:PTZ00346   231 YGRGRYYSMNLAVWDGIT----DFYYLGLFEHALHSIVRRYSPDAIVLQCGADSLAG--DRLGLLNLSSFGHGQCVQAVR 304

                          170
                   ....*....|....
gi 1039728092  959 GLagGRLVLALEGG 972
Cdd:PTZ00346   305 DL--GIPMLALGGG 316
ClassIIa_HDAC5_Gln-rich-N cd10164
Glutamine-rich N-terminal helical domain of HDAC5, a Class IIa histone deacetylase; This ...
 62-151 4.21e-15

Glutamine-rich N-terminal helical domain of HDAC5, a Class IIa histone deacetylase; This family consists of the glutamine-rich domain of histone deacetylase 5 (HDAC5). It belongs to a superfamily that consists of the glutamine-rich N-terminal helical extension to certain Class IIa histone deacetylases (HDACs), including HDAC4, HDAC5 and HDCA9; it is missing from HDAC7. This domain confers responsiveness to calcium signals and mediates interactions with transcription factors and cofactors, and it is able to repress transcription independently of the HDAC C-terminal, zinc-dependent catalytic domain. It has many intra- and inter-helical interactions which are possibly involved in reversible assembly and disassembly of proteins. HDACs regulate diverse cellular processes through enzymatic deacetylation of histone as well as non-histone proteins, in particular deacetylating N(6)-acetyl-lysine residues.


Pssm-ID: 197400 [Multi-domain]  Cd Length: 97  Bit Score: 71.78  E-value: 4.21e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092   62 EPALREQQLQQELLALKQKQQIQRQILIAEFQRQHEQLSRQHEAQLHEHIK---------QQQEMLAMKHQQElLEHQRK 132
Cdd:cd10164      1 DPSLREQQLQQELLLLKQQQQLQKQLLFAEFQKQHEHLTRQHEVQLQKHLKvraelfseqQQQEILAAKRQQE-LEQQRK 79

                           90
                   ....*....|....*....
gi 1039728092  133 LERHRQEqELEKQHREQKL 151
Cdd:cd10164     80 REQQRQE-ELEKQRLEQQL 97
GBP_C pfam02841
Guanylate-binding protein, C-terminal domain; Transcription of the anti-viral ...
 90-155 1.27e-06

Guanylate-binding protein, C-terminal domain; Transcription of the anti-viral guanylate-binding protein (GBP) is induced by interferon-gamma during macrophage induction. This family contains GBP1 and GPB2, both GTPases capable of binding GTP, GDP and GMP.


Pssm-ID: 460721 [Multi-domain]  Cd Length: 297  Bit Score: 51.52  E-value: 1.27e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1039728092   90 AEFQRQHEQLSRQHEAQLHEHIKQQQEMLAMKHQQELLEHQRKLERHRQEQEL--------EKQHREQKLQQLK 155
Cdd:pfam02841  224 REKQKEEEQMMEAQERSYQEHVKQLIEKMEAEREQLLAEQERMLEHKLQEQEEllkegfktEAESLQKEIQDLK 297
GBP_C cd16269
Guanylate-binding protein, C-terminal domain; Guanylate-binding protein (GBP), C-terminal ...
 93-157 1.10e-05

Guanylate-binding protein, C-terminal domain; Guanylate-binding protein (GBP), C-terminal domain. Guanylate-binding proteins (GBPs) are synthesized after activation of the cell by interferons. The biochemical properties of GBPs are clearly different from those of Ras-like and heterotrimeric GTP-binding proteins. They bind guanine nucleotides with low affinity (micromolar range), are stable in their absence, and have a high turnover GTPase. In addition to binding GDP/GTP, they have the unique ability to bind GMP with equal affinity and hydrolyze GTP not only to GDP, but also to GMP. This C-terminal domain has been shown to mediate inhibition of endothelial cell proliferation by inflammatory cytokines.


Pssm-ID: 293879 [Multi-domain]  Cd Length: 291  Bit Score: 48.34  E-value: 1.10e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1039728092   93 QRQHEQLSRQHEAQLHEHIKQQQEMLAMKHQQELLEHQRKLERHRQEQE-LEKQHREQKLQQLKNK 157
Cdd:cd16269    221 QRELEQKLEDQERSYEEHLRQLKEKMEEERENLLKEQERALESKLKEQEaLLEEGFKEQAELLQEE 286
fliH PRK06800
flagellar assembly protein H; Validated
 91-196 5.14e-05

flagellar assembly protein H; Validated


Pssm-ID: 180700  Cd Length: 228  Bit Score: 46.02  E-value: 5.14e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092   91 EFQRQHEQLsRQHEAQLHEH---IKQQQEMLAMKHQQeLLEHQRKLERHRQEQELEKQHREQKLQQLKnkekgkesavas 167
Cdd:PRK06800    35 EIQKDHEEL-LAQQKSLHKElnqLRQEQQKLERERQQ-LLADREQFQEHVQQQMKEIEAARQQFQKEQ------------ 100

                           90       100
                   ....*....|....*....|....*....
gi 1039728092  168 TEVKMKLQEFVLNKKKALAHRNLNHCISS 196
Cdd:PRK06800   101 QETAYEWTELLWDQSFQLAEKIVNQAVDT 129
tolA PRK09510
cell envelope integrity inner membrane protein TolA; Provisional
 91-186 6.08e-05

cell envelope integrity inner membrane protein TolA; Provisional


Pssm-ID: 236545 [Multi-domain]  Cd Length: 387  Bit Score: 46.72  E-value: 6.08e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092   91 EFQRQHEQLSRQHEAQ-LHEHIKQQQEMLAMKHQQELLEHQRKLERHR-QEQELEKQHREQ-KLQQLKNKEKGKESAVAS 167
Cdd:PRK09510    63 QYNRQQQQQKSAKRAEeQRKKKEQQQAEELQQKQAAEQERLKQLEKERlAAQEQKKQAEEAaKQAALKQKQAEEAAAKAA 142

                           90
                   ....*....|....*....
gi 1039728092  168 TEVKMKLQEfvlnKKKALA 186
Cdd:PRK09510   143 AAAKAKAEA----EAKRAA 157
TPH pfam13868
Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of ...
 93-190 1.40e-04

Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of eukaryotic proteins. Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). The family is in the trichohyalin-plectin-homology domain.


Pssm-ID: 464007 [Multi-domain]  Cd Length: 341  Bit Score: 45.29  E-value: 1.40e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092   93 QRQHEQLSRQHEAQLhEHIKQQQEMLAMKHQQE---LLEHQRKLERHRQEQ-----ELEKQHREQKLQQLKNKEKGKEsa 164
Cdd:pfam13868  231 ARQRQELQQAREEQI-ELKERRLAEEAEREEEEferMLRKQAEDEEIEQEEaekrrMKRLEHRRELEKQIEEREEQRA-- 307

                           90       100
                   ....*....|....*....|....*.
gi 1039728092  165 vasTEVKMKLQEFVLNKKKALAHRNL 190
Cdd:pfam13868  308 ---AEREEELEEGERLREEEAERRER 330
tolA PRK09510
cell envelope integrity inner membrane protein TolA; Provisional
 93-186 3.54e-04

cell envelope integrity inner membrane protein TolA; Provisional


Pssm-ID: 236545 [Multi-domain]  Cd Length: 387  Bit Score: 44.41  E-value: 3.54e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092   93 QRQHEQLSRQHEAQLHEHIKQQQEMLAMKHQQELLEHQRKLERHRQEQELEKQHREQKLQQLKNKEKGK--ESAVASTEV 170
Cdd:PRK09510    86 QQQAEELQQKQAAEQERLKQLEKERLAAQEQKKQAEEAAKQAALKQKQAEEAAAKAAAAAKAKAEAEAKraAAAAKKAAA 165

                           90
                   ....*....|....*.
gi 1039728092  171 KMKLQEFVLNKKKALA 186
Cdd:PRK09510   166 EAKKKAEAEAAKKAAA 181
FliJ COG2882
Flagellar biosynthesis chaperone FliJ [Cell motility];
105-152 3.82e-04

Flagellar biosynthesis chaperone FliJ [Cell motility];


Pssm-ID: 442129 [Multi-domain]  Cd Length: 142  Bit Score: 41.81  E-value: 3.82e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1039728092  105 AQLHEHIKQQQEMLAM------KHQQELLEHQRKL-------ERHRQEQELEKQHREQKLQ 152
Cdd:COG2882     74 ARLDEAIEQQQQQVAQaeqqveQARQAWLEARQERkaleklkERRREEERQEENRREQKEL 134
COG1340 COG1340
Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown];
90-181 6.20e-04

Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown];


Pssm-ID: 440951 [Multi-domain]  Cd Length: 297  Bit Score: 42.98  E-value: 6.20e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092   90 AEFQRQHEQLSRQHEaqlhEHIKQQQEMLAMKHQ-QELLEHQRKLERHRQEQELEKQhREQKLQQLKNKEKgkesavAST 168
Cdd:COG1340    216 KEIVEAQEKADELHE----EIIELQKELRELRKElKKLRKKQRALKREKEKEELEEK-AEEIFEKLKKGEK------LTT 284

                           90
                   ....*....|...
gi 1039728092  169 EVKMKLQEFVLNK 181
Cdd:COG1340    285 EELKLLQKSGLLE 297
DUF4515 pfam14988
Domain of unknown function (DUF4515); This family of proteins is found in bacteria and ...
 91-187 1.98e-03

Domain of unknown function (DUF4515); This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 198 and 469 amino acids in length. There are two completely conserved L residues that may be functionally important.


Pssm-ID: 405647 [Multi-domain]  Cd Length: 206  Bit Score: 40.91  E-value: 1.98e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092   91 EFQRQHEQLSRQHEAQLHEHIKQQQEMLAMKHQQ-----ELLEHQRKLER--HRQEQELE-----KQHREQKLQQLKNKE 158
Cdd:pfam14988   15 EKQKKIEKLWNQYVQECEEIERRRQELASRYTQQtaelqTQLLQKEKEQAslKKELQALRpfaklKESQEREIQDLEEEK 94

                           90       100
                   ....*....|....*....|....*....
gi 1039728092  159 KGKESAVASTEVKMKLQefVLNKKKALAH 187
Cdd:pfam14988   95 EKVRAETAEKDREAHLQ--FLKEKALLEK 121
DUF5401 pfam17380
Family of unknown function (DUF5401); This is a family of unknown function found in ...
 91-176 2.44e-03

Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea.


Pssm-ID: 375164 [Multi-domain]  Cd Length: 722  Bit Score: 42.03  E-value: 2.44e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092   91 EFQRQHEQLSRQHEAQLHEHIKQQQEMLAMKHQQELLEHQ-RKLERHRQEqELEKQHREQKLQQLKNKEKGKESAVASTE 169
Cdd:pfam17380  405 KILEEERQRKIQQQKVEMEQIRAEQEEARQREVRRLEEERaREMERVRLE-EQERQQQVERLRQQEEERKRKKLELEKEK 483


                   ....*..
gi 1039728092  170 VKMKLQE 176
Cdd:pfam17380  484 RDRKRAE 490
GBP_C cd16269
Guanylate-binding protein, C-terminal domain; Guanylate-binding protein (GBP), C-terminal ...
 90-176 3.30e-03

Guanylate-binding protein, C-terminal domain; Guanylate-binding protein (GBP), C-terminal domain. Guanylate-binding proteins (GBPs) are synthesized after activation of the cell by interferons. The biochemical properties of GBPs are clearly different from those of Ras-like and heterotrimeric GTP-binding proteins. They bind guanine nucleotides with low affinity (micromolar range), are stable in their absence, and have a high turnover GTPase. In addition to binding GDP/GTP, they have the unique ability to bind GMP with equal affinity and hydrolyze GTP not only to GDP, but also to GMP. This C-terminal domain has been shown to mediate inhibition of endothelial cell proliferation by inflammatory cytokines.


Pssm-ID: 293879 [Multi-domain]  Cd Length: 291  Bit Score: 40.64  E-value: 3.30e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092   90 AEFQRQHEQLSRQHEAQLhehikqQQEMLAMKHQQEllEHQRKLERhRQEQELEKQHREQ-KLQQLKNKEKGKESAVAST 168
Cdd:cd16269    207 AEAAEQERKLLEEQQREL------EQKLEDQERSYE--EHLRQLKE-KMEEERENLLKEQeRALESKLKEQEALLEEGFK 277


                   ....*...
gi 1039728092  169 EVKMKLQE 176
Cdd:cd16269    278 EQAELLQE 285
DUF5401 pfam17380
Family of unknown function (DUF5401); This is a family of unknown function found in ...
 91-176 5.08e-03

Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea.


Pssm-ID: 375164 [Multi-domain]  Cd Length: 722  Bit Score: 40.88  E-value: 5.08e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092   91 EFQRQHEQL--SRQHEAQLHEHIKQQQEMLAMKHQQEL-----LEHQRKLERHRQEQ---ELEKQHREQKLQ---QLKNK 157
Cdd:pfam17380  313 ERRRKLEEAekARQAEMDRQAAIYAEQERMAMERERELerirqEERKRELERIRQEEiamEISRMRELERLQmerQQKNE 392

                           90
                   ....*....|....*....
gi 1039728092  158 EKGKESAVAStevKMKLQE 176
Cdd:pfam17380  393 RVRQELEAAR---KVKILE 408
YhaN COG4717
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];
90-176 5.35e-03

Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];


Pssm-ID: 443752 [Multi-domain]  Cd Length: 641  Bit Score: 40.91  E-value: 5.35e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092   90 AEFQRQHEQLSRQHEaQLHEHIKQQQEMLAMKHQQELLEHQRKLERHRQeqelEKQHREQKLQQLKNKEKGKESAVASTE 169
Cdd:COG4717    159 RELEEELEELEAELA-ELQEELEELLEQLSLATEEELQDLAEELEELQQ----RLAELEEELEEAQEELEELEEELEQLE 233


                   ....*..
gi 1039728092  170 VKMKLQE 176
Cdd:COG4717    234 NELEAAA 240
MAP7 pfam05672
MAP7 (E-MAP-115) family; The organization of microtubules varies with the cell type and is ...
 90-176 5.94e-03

MAP7 (E-MAP-115) family; The organization of microtubules varies with the cell type and is presumably controlled by tissue-specific microtubule-associated proteins (MAPs). The 115-kDa epithelial MAP (E-MAP-115/MAP7) has been identified as a microtubule-stabilising protein predominantly expressed in cell lines of epithelial origin. The binding of this microtubule associated protein is nucleotide independent.


Pssm-ID: 461709 [Multi-domain]  Cd Length: 153  Bit Score: 38.48  E-value: 5.94e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092   90 AEFQRQHEQLSRQHEAQLHEHIKQQQEMLAMKHQQELLEHQRKLERHRQEQE-----------LEKQHREQKLQQLKNKE 158
Cdd:pfam05672   23 AREQREREEQERLEKEEEERLRKEELRRRAEEERARREEEARRLEEERRREEeerqrkaeeeaEEREQREQEEQERLQKQ 102

                           90
                   ....*....|....*...
gi 1039728092  159 KGKESAVASTEVKMKLQE 176
Cdd:pfam05672  103 KEEAEAKAREEAERQRQE 120
TPH pfam13868
Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of ...
 93-177 7.78e-03

Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of eukaryotic proteins. Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). The family is in the trichohyalin-plectin-homology domain.


Pssm-ID: 464007 [Multi-domain]  Cd Length: 341  Bit Score: 39.90  E-value: 7.78e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092   93 QRQHEQLSRQHEAQLHEHIKQQQEMLAMKHQQELLEHQRKLERHRQEQELEKQHREQKLQQLKNKEKGKEsavasTEVKM 172
Cdd:pfam13868  212 QEEQERKERQKEREEAEKKARQRQELQQAREEQIELKERRLAEEAEREEEEFERMLRKQAEDEEIEQEEA-----EKRRM 286


                   ....*
gi 1039728092  173 KLQEF 177
Cdd:pfam13868  287 KRLEH 291
sbcc TIGR00618
exonuclease SbcC; All proteins in this family for which functions are known are part of an ...
 98-188 7.82e-03

exonuclease SbcC; All proteins in this family for which functions are known are part of an exonuclease complex with sbcD homologs. This complex is involved in the initiation of recombination to regulate the levels of palindromic sequences in DNA. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 129705 [Multi-domain]  Cd Length: 1042  Bit Score: 40.34  E-value: 7.82e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092   98 QLSRQHEAQLHEHIKQQQEMLamkHQQELLEHQRKLErhrQEQELEKQHREQKLQQLKnKEKGKESAVASTEVKMKLQEF 177
Cdd:TIGR00618  605 EAEDMLACEQHALLRKLQPEQ---DLQDVRLHLQQCS---QELALKLTALHALQLTLT-QERVREHALSIRVLPKELLAS 677

                           90
                   ....*....|.
gi 1039728092  178 VLNKKKALAHR 188
Cdd:TIGR00618  678 RQLALQKMQSE 688
DDRGK pfam09756
DDRGK domain; This is a family of proteins of approximately 300 residues, found in plants and ...
 93-176 9.01e-03

DDRGK domain; This is a family of proteins of approximately 300 residues, found in plants and vertebrates. They contain a highly conserved DDRGK motif.


Pssm-ID: 370664 [Multi-domain]  Cd Length: 188  Bit Score: 38.48  E-value: 9.01e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728092   93 QRQHeqlsRQHEAQLHEHIKQQQEMLAMKHQQEllEHQRKLERHRQEQELEKQHREQKLQQLKNKEKGKESAVASTEVKM 172
Cdd:pfam09756   17 KRQQ----REAEEEEREEREKLEEKREEEYKER--EEREEEAEKEKEEEERKQEEEQERKEQEEYEKLKSQFVVEEEGTD 90


                   ....
gi 1039728092  173 KLQE 176
Cdd:pfam09756   91 KLSA 94
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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