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Conserved domains on  [gi|2085259879|ref|XP_043089610|]
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histone deacetylase 5 isoform X6 [Puntigrus tetrazona]

Protein Classification

histone deacetylase 5( domain architecture ID 10178376)

histone deacetylase 5 (HD5) 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)

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HDAC5 cd10007
Histone deacetylase 5; Histone deacetylase 5 is a class IIa Zn-dependent enzyme that catalyzes ...
 647-1066 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: 924.00  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  647 HLFTTGLVYDTFMLKHQCICGNTNIHPEHAGRIQSVWSRLQETGLLGRCERIRGRKATLDEIQTVHSEYHTLLYGTSPLN 726
Cdd:cd10007      1 HLFTTGLVYDTFMLKHQCTCGNTNVHPEHAGRIQSVWSRLQETGLLGKCERVRGRKATLDEIQTVHSEHHTLLYGTSPLN 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  727 RQKLDSKKLLGPISQKMYAVLPCGGIGVDSDTVWNEMHSSGAVRMAVGCVIELAFKVAAGELKNGFAVVRPPGHHAEEST 806
Cdd:cd10007     81 RQKLDSKKLLGPLSQKMYAVLPCGGIGVDSDTVWNEMHSSSAVRMAVGCLIELAFKVAAGELKNGFAVIRPPGHHAEEST 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  807 AMGFCFFNSVAITAKLLQQKLGVGKILIIDWDIHHGNGTQQAFYNDPNVLYISLHRYDDGNFFPGSGAPEEVGVGPGEGF 886
Cdd:cd10007    161 AMGFCFFNSVAIAAKLLQQKLNVGKILIVDWDIHHGNGTQQAFYNDPNVLYISLHRYDDGNFFPGSGAPDEVGAGPGVGF 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  887 NVNIAWTGGVEPPMGDVEYLTAFRTVVMPIANEFSPDVVLVSAGFDAVEGHQSPLGGYNVTAKCFGHLTKQLMKLAGGRV 966
Cdd:cd10007    241 NVNIAWTGGVDPPIGDVEYLTAFRTVVMPIANEFSPDVVLVSAGFDAVEGHQSPLGGYSVTAKCFGHLTKQLMTLAGGRV 320

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  967 VLALEGGHDLTAICDASESCVAALLGDELDPLPLTVLQQKPCPKATASLERVIEIQSKHWTSLQRLAPTVGHSLLDAQRR 1046
Cdd:cd10007    321 VLALEGGHDLTAICDASEACVSALLGMELTPLDNTVLQQKPNDNAVATLERVIEIQSKHWSCLKRFAATLGFSLLEAQRG 400

                          410       420
                   ....*....|....*....|
gi 2085259879 1047 EKDEADTLTAMASLTVDNDQ 1066
Cdd:cd10007    401 ELEEAETVSAMASLSVDTEQ 420
ClassIIa_HDAC5_Gln-rich-N cd10164
Glutamine-rich N-terminal helical domain of HDAC5, a Class IIa histone deacetylase; This ...
 52-139 3.94e-30

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: 114.92  E-value: 3.94e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879   52 DPALREKQLQHELLLLKQQQELQKQLLFAEFQKQHEVLTRQHEVQLQEHLK---------QQQEILAAKRQQELEQKRKL 122
Cdd:cd10164      1 DPSLREQQLQQELLLLKQQQQLQKQLLFAEFQKQHEHLTRQHEVQLQKHLKvraelfseqQQQEILAAKRQQELEQQRKR 80

                           90
                   ....*....|....*..
gi 2085259879  123 EQQRHEEMEKQRLEQQL 139
Cdd:cd10164     81 EQQRQEELEKQRLEQQL 97
 
Name Accession Description Interval E-value
HDAC5 cd10007
Histone deacetylase 5; Histone deacetylase 5 is a class IIa Zn-dependent enzyme that catalyzes ...
 647-1066 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: 924.00  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  647 HLFTTGLVYDTFMLKHQCICGNTNIHPEHAGRIQSVWSRLQETGLLGRCERIRGRKATLDEIQTVHSEYHTLLYGTSPLN 726
Cdd:cd10007      1 HLFTTGLVYDTFMLKHQCTCGNTNVHPEHAGRIQSVWSRLQETGLLGKCERVRGRKATLDEIQTVHSEHHTLLYGTSPLN 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  727 RQKLDSKKLLGPISQKMYAVLPCGGIGVDSDTVWNEMHSSGAVRMAVGCVIELAFKVAAGELKNGFAVVRPPGHHAEEST 806
Cdd:cd10007     81 RQKLDSKKLLGPLSQKMYAVLPCGGIGVDSDTVWNEMHSSSAVRMAVGCLIELAFKVAAGELKNGFAVIRPPGHHAEEST 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  807 AMGFCFFNSVAITAKLLQQKLGVGKILIIDWDIHHGNGTQQAFYNDPNVLYISLHRYDDGNFFPGSGAPEEVGVGPGEGF 886
Cdd:cd10007    161 AMGFCFFNSVAIAAKLLQQKLNVGKILIVDWDIHHGNGTQQAFYNDPNVLYISLHRYDDGNFFPGSGAPDEVGAGPGVGF 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  887 NVNIAWTGGVEPPMGDVEYLTAFRTVVMPIANEFSPDVVLVSAGFDAVEGHQSPLGGYNVTAKCFGHLTKQLMKLAGGRV 966
Cdd:cd10007    241 NVNIAWTGGVDPPIGDVEYLTAFRTVVMPIANEFSPDVVLVSAGFDAVEGHQSPLGGYSVTAKCFGHLTKQLMTLAGGRV 320

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  967 VLALEGGHDLTAICDASESCVAALLGDELDPLPLTVLQQKPCPKATASLERVIEIQSKHWTSLQRLAPTVGHSLLDAQRR 1046
Cdd:cd10007    321 VLALEGGHDLTAICDASEACVSALLGMELTPLDNTVLQQKPNDNAVATLERVIEIQSKHWSCLKRFAATLGFSLLEAQRG 400

                          410       420
                   ....*....|....*....|
gi 2085259879 1047 EKDEADTLTAMASLTVDNDQ 1066
Cdd:cd10007    401 ELEEAETVSAMASLSVDTEQ 420
Hist_deacetyl pfam00850
Histone deacetylase domain; Histones can be reversibly acetylated on several lysine residues. ...
 672-990 1.22e-123

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: 380.43  E-value: 1.22e-123
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  672 HPEHAGRIQSVWSRLQETGLLGRCERIRGRKATLDEIQTVHSEYHTLLYGTSPLNRQKLDSKKLLGpisqkmyavlpcgg 751
Cdd:pfam00850    1 HPENPERLKAILEALREAGLLPDLEIIAPRPATEEELLLVHSPEYLEFLEEAAPEGGALLLLSYLS-------------- 66

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  752 igvDSDTVWNEMHSSGAVRMAVGCVIELAFKVAAGELKNGFAVVRPPGHHAEESTAMGFCFFNSVAITAKLLQQKLGVGK 831
Cdd:pfam00850   67 ---GDDDTPVSPGSYEAALLAAGGTLAAADAVLSGEARNAFALVRPPGHHAERDRASGFCIFNNVAIAAKYLREKYGLKR 143

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  832 ILIIDWDIHHGNGTQQAFYNDPNVLYISLHRYdDGNFFPGSGAPEEVGVGPGEGFNVNIAWTGGveppMGDVEYLTAFRT 911
Cdd:pfam00850  144 VAIVDFDVHHGNGTQEIFYDDPSVLTLSIHQY-PGGFYPGTGFADETGEGKGKGYTLNVPLPPG----TGDAEYLAAFEE 218

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  912 VVMPIANEFSPDVVLVSAGFDAVEGHqsPLGGYNVTAKCFGHLTKQLMKLA---GGRVVLALEGGHDLTAICDASESCVA 988
Cdd:pfam00850  219 ILLPALEEFQPDLILVSAGFDAHAGD--PLGGLNLTTEGFAEITRILLELAdplCIRVVSVLEGGYNLDALARSATAVLA 296


                   ..
gi 2085259879  989 AL 990
Cdd:pfam00850  297 AL 298
AcuC COG0123
Acetoin utilization deacetylase AcuC or a related deacetylase [Secondary metabolites ...
 651-992 4.96e-101

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


Pssm-ID: 439893 [Multi-domain]  Cd Length: 308  Bit Score: 320.90  E-value: 4.96e-101
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  651 TGLVYDTFMLKHQCicGNTniHPEHAGRIQSVWSRLQETGLLGRCERIRGRKATLDEIQTVHSEYHtllygtsplnrqkL 730
Cdd:COG0123      1 TALIYHPDYLLHDL--GPG--HPEPPERLRAILDALEASGLLDDLELVEPPPATEEDLLRVHTPDY-------------V 63

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  731 DskkllgpisqKMYAVLPCGGIG-VDSDTVWNEmHSSGAVRMAVGCVIELAFKVAAGELKNGFAVVRPPGHHAEESTAMG 809
Cdd:COG0123     64 D----------ALRAASLDGGYGqLDPDTPVSP-GTWEAALLAAGGALAAADAVLEGEARNAFALVRPPGHHAERDRAMG 132

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  810 FCFFNSVAITAKLLQQKlGVGKILIIDWDIHHGNGTQQAFYNDPNVLYISLHRYddgNFFPGSGAPEEVGVGPGEGFNVN 889
Cdd:COG0123    133 FCLFNNAAIAARYLLAK-GLERVAIVDFDVHHGNGTQDIFYDDPDVLTISIHQD---PLYPGTGAADETGEGAGEGSNLN 208

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  890 IAwtggVEPPMGDVEYLTAFRTVVMPIANEFSPDVVLVSAGFDAvegHQS-PLGGYNVTAKCFGHLTKQLMKLA---GGR 965
Cdd:COG0123    209 VP----LPPGTGDAEYLAALEEALLPALEAFKPDLIVVSAGFDA---HADdPLGRLNLTTEGYAWRTRRVLELAdhcGGP 281

                          330       340
                   ....*....|....*....|....*..
gi 2085259879  966 VVLALEGGHDLTAICDASESCVAALLG 992
Cdd:COG0123    282 VVSVLEGGYNLDALARSVAAHLETLLG 308
ClassIIa_HDAC5_Gln-rich-N cd10164
Glutamine-rich N-terminal helical domain of HDAC5, a Class IIa histone deacetylase; This ...
 52-139 3.94e-30

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: 114.92  E-value: 3.94e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879   52 DPALREKQLQHELLLLKQQQELQKQLLFAEFQKQHEVLTRQHEVQLQEHLK---------QQQEILAAKRQQELEQKRKL 122
Cdd:cd10164      1 DPSLREQQLQQELLLLKQQQQLQKQLLFAEFQKQHEHLTRQHEVQLQKHLKvraelfseqQQQEILAAKRQQELEQQRKR 80

                           90
                   ....*....|....*..
gi 2085259879  123 EQQRHEEMEKQRLEQQL 139
Cdd:cd10164     81 EQQRQEELEKQRLEQQL 97
PTZ00063 PTZ00063
histone deacetylase; Provisional
 800-964 1.17e-22

histone deacetylase; Provisional


Pssm-ID: 240251  Cd Length: 436  Bit Score: 102.20  E-value: 1.17e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  800 HHAEESTAMGFCFFNSVAI-TAKLLQQKlgvGKILIIDWDIHHGNGTQQAFYNDPNVLYISLHRYddGNFFPGSGAPEEV 878
Cdd:PTZ00063   137 HHAKRSEASGFCYINDIVLgILELLKYH---ARVMYIDIDVHHGDGVEEAFYVTHRVMTVSFHKF--GDFFPGTGDVTDI 211

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  879 GVGPGEGFNVNIAWTGGveppMGDVEYLTAFRTVVMPIANEFSPDVVLVSAGFDAVEGHQspLGGYNVT----AKCFGHL 954
Cdd:PTZ00063   212 GVAQGKYYSVNVPLNDG----IDDDSFVDLFKPVISKCVEVYRPGAIVLQCGADSLTGDR--LGRFNLTikghAACVEFV 285

                          170
                   ....*....|...
gi 2085259879  955 TK---QLMKLAGG 964
Cdd:PTZ00063   286 RSlniPLLVLGGG 298
HDAC4_Gln pfam12203
Glutamine rich N terminal domain of histone deacetylase 4; This domain is found in eukaryotes, ...
 51-139 1.48e-20

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: 87.22  E-value: 1.48e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879   51 VDPALREKQLQHELLLLKQQQELQKQLLFAEFQKQHEVLTRQHEVQLQEHLKQQQEILAAKRQQEL-EQKRKLEQQRHE- 128
Cdd:pfam12203    1 VDPLLREQQLQQELLLLKQQQQIQKQLLIAEFQKQHELLTRQHEAQLQEHIKQQQELLAMKQQQELlEQQRKLEQQRQEe 80

                           90
                   ....*....|.
gi 2085259879  129 EMEKQRLEQQL 139
Cdd:pfam12203   81 ELEKHRREQQL 91
tolA PRK09510
cell envelope integrity inner membrane protein TolA; Provisional
 83-161 1.33e-04

cell envelope integrity inner membrane protein TolA; Provisional


Pssm-ID: 236545 [Multi-domain]  Cd Length: 387  Bit Score: 45.57  E-value: 1.33e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2085259879   83 QKQHEVLTRQHEVQLQEHLKQQQEilaakRQQELEQKRKLEQQRHEEMEKQRleqQLIMLRNKEKGKESAIASTEVKLK 161
Cdd:PRK09510    78 EEQRKKKEQQQAEELQQKQAAEQE-----RLKQLEKERLAAQEQKKQAEEAA---KQAALKQKQAEEAAAKAAAAAKAK 148
tolA_full TIGR02794
TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the ...
 81-171 3.92e-03

TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB. [Transport and binding proteins, Other, Cellular processes, Pathogenesis]


Pssm-ID: 274303 [Multi-domain]  Cd Length: 346  Bit Score: 40.60  E-value: 3.92e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879   81 EFQKQHEVLTRQHEVQLQEHLKQQQEILAAKRQQELEQKRKLE----QQRHEEMEKQRLEQqlimlRNKEKGKESAIAST 156
Cdd:TIGR02794   95 EQRAAAEKAAKQAEQAAKQAEEKQKQAEEAKAKQAAEAKAKAEaeaeRKAKEEAAKQAEEE-----AKAKAAAEAKKKAE 169

                           90
                   ....*....|....*
gi 2085259879  157 EVKLKLQEFLLSKKE 171
Cdd:TIGR02794  170 EAKKKAEAEAKAKAE 184
 
Name Accession Description Interval E-value
HDAC5 cd10007
Histone deacetylase 5; Histone deacetylase 5 is a class IIa Zn-dependent enzyme that catalyzes ...
 647-1066 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: 924.00  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  647 HLFTTGLVYDTFMLKHQCICGNTNIHPEHAGRIQSVWSRLQETGLLGRCERIRGRKATLDEIQTVHSEYHTLLYGTSPLN 726
Cdd:cd10007      1 HLFTTGLVYDTFMLKHQCTCGNTNVHPEHAGRIQSVWSRLQETGLLGKCERVRGRKATLDEIQTVHSEHHTLLYGTSPLN 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  727 RQKLDSKKLLGPISQKMYAVLPCGGIGVDSDTVWNEMHSSGAVRMAVGCVIELAFKVAAGELKNGFAVVRPPGHHAEEST 806
Cdd:cd10007     81 RQKLDSKKLLGPLSQKMYAVLPCGGIGVDSDTVWNEMHSSSAVRMAVGCLIELAFKVAAGELKNGFAVIRPPGHHAEEST 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  807 AMGFCFFNSVAITAKLLQQKLGVGKILIIDWDIHHGNGTQQAFYNDPNVLYISLHRYDDGNFFPGSGAPEEVGVGPGEGF 886
Cdd:cd10007    161 AMGFCFFNSVAIAAKLLQQKLNVGKILIVDWDIHHGNGTQQAFYNDPNVLYISLHRYDDGNFFPGSGAPDEVGAGPGVGF 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  887 NVNIAWTGGVEPPMGDVEYLTAFRTVVMPIANEFSPDVVLVSAGFDAVEGHQSPLGGYNVTAKCFGHLTKQLMKLAGGRV 966
Cdd:cd10007    241 NVNIAWTGGVDPPIGDVEYLTAFRTVVMPIANEFSPDVVLVSAGFDAVEGHQSPLGGYSVTAKCFGHLTKQLMTLAGGRV 320

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  967 VLALEGGHDLTAICDASESCVAALLGDELDPLPLTVLQQKPCPKATASLERVIEIQSKHWTSLQRLAPTVGHSLLDAQRR 1046
Cdd:cd10007    321 VLALEGGHDLTAICDASEACVSALLGMELTPLDNTVLQQKPNDNAVATLERVIEIQSKHWSCLKRFAATLGFSLLEAQRG 400

                          410       420
                   ....*....|....*....|
gi 2085259879 1047 EKDEADTLTAMASLTVDNDQ 1066
Cdd:cd10007    401 ELEEAETVSAMASLSVDTEQ 420
HDAC_classIIa cd11681
Histone deacetylases, class IIa; Class IIa histone deacetylases are Zn-dependent enzymes that ...
 649-1026 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: 810.81  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  649 FTTGLVYDTFMLKHQCICGNTNIHPEHAGRIQSVWSRLQETGLLGRCERIRGRKATLDEIQTVHSEYHTLLYGTSPLNRQ 728
Cdd:cd11681      1 FTTGLAYDPLMLKHQCICGNNSSHPEHGGRLQSIWSRLQETGLVNRCERLRGRKATLEELQLVHSEVHTLLYGTNPLSRL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  729 KLDSKKLLGpISQKMYAVLPCGGIGVDSDTVWNEMHSSGAVRMAVGCVIELAFKVAAGELKNGFAVVRPPGHHAEESTAM 808
Cdd:cd11681     81 KLDPTKLAG-LPQKSFVRLPCGGIGVDSDTVWNELHTSNAARMAVGCVIDLAFKVATGELKNGFAVVRPPGHHAEPSQAM 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  809 GFCFFNSVAITAKLLQQKLGVGKILIIDWDIHHGNGTQQAFYNDPNVLYISLHRYDDGNFFPGSGAPEEVGVGPGEGFNV 888
Cdd:cd11681    160 GFCFFNSVAIAAKQLQQKLKLRKILIVDWDVHHGNGTQQIFYEDPNVLYISLHRYDDGNFFPGTGAPTEVGSGAGEGFNV 239

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  889 NIAWTGGVEPPMGDVEYLTAFRTVVMPIANEFSPDVVLVSAGFDAVEGHQSPLGGYNVTAKCFGHLTKQLMKLAGGRVVL 968
Cdd:cd11681    240 NIAWSGGLDPPMGDAEYLAAFRTVVMPIAREFSPDIVLVSAGFDAAEGHPPPLGGYKVSPACFGYMTRQLMNLAGGKVVL 319

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2085259879  969 ALEGGHDLTAICDASESCVAALLGDELDPLPLTVLQQKPCPKATASLERVIEIQSKHW 1026
Cdd:cd11681    320 ALEGGYDLTAICDASEACVRALLGDELDPLSEEELERRPNPNAVTSLEKVIAIQSPYW 377
HDAC4 cd10006
Histone deacetylase 4; Histone deacetylase 4 is a class IIa Zn-dependent enzyme that catalyzes ...
 646-1055 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: 786.92  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  646 KHLFTTGLVYDTFMLKHQCICGNTNIHPEHAGRIQSVWSRLQETGLLGRCERIRGRKATLDEIQTVHSEYHTLLYGTSPL 725
Cdd:cd10006      1 KPRFTTGLVYDTLMLKHQCTCGNSNSHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHTLLYGTNPL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  726 NRQKLDSKKLLGPISQkMYAVLPCGGIGVDSDTVWNEMHSSGAVRMAVGCVIELAFKVAAGELKNGFAVVRPPGHHAEES 805
Cdd:cd10006     81 NRQKLDSKKLLGSLAS-VFVRLPCGGVGVDSDTIWNEVHSSGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEES 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  806 TAMGFCFFNSVAITAKLLQQKLGVGKILIIDWDIHHGNGTQQAFYNDPNVLYISLHRYDDGNFFPGSGAPEEVGVGPGEG 885
Cdd:cd10006    160 TPMGFCYFNSVAIAAKLLQQRLNVSKILIVDWDVHHGNGTQQAFYSDPNVLYMSLHRYDDGNFFPGSGAPDEVGTGPGVG 239

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  886 FNVNIAWTGGVEPPMGDVEYLTAFRTVVMPIANEFSPDVVLVSAGFDAVEGHQSPLGGYNVTAKCFGHLTKQLMKLAGGR 965
Cdd:cd10006    240 FNVNMAFTGGLDPPMGDAEYLAAFRTVVMPIASEFAPDVVLVSSGFDAVEGHPTPLGGYNLSAKCFGYLTKQLMGLAGGR 319

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  966 VVLALEGGHDLTAICDASESCVAALLGDELDPLPLTVLQQKPCPKATASLERVIEIQSKHWTSLQRLAPTVGHSLLDAQR 1045
Cdd:cd10006    320 IVLALEGGHDLTAICDASEACVSALLGNELDPLPEKVLQQRPNANAVRSMEKVMEIHSKYWRCLQRTTSTAGYSLIEAQT 399

                          410
                   ....*....|
gi 2085259879 1046 REKDEADTLT 1055
Cdd:cd10006    400 CENEEAETVT 409
HDAC7 cd10008
Histone deacetylase 7; Histone deacetylase 7 is a class IIa Zn-dependent enzyme that catalyzes ...
 649-1026 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: 699.84  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  649 FTTGLVYDTFMLKHQCICGNTNIHPEHAGRIQSVWSRLQETGLLGRCERIRGRKATLDEIQTVHSEYHTLLYGTSPLNRQ 728
Cdd:cd10008      1 FTTGLVYDSVMLKHQCSCGDNSNHPEHAGRIQSIWSRLQERGLRSQCECLRGRKASLEELQSVHSERHVLLYGTNPLSRL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  729 KLDSKKLLGPISQKMYAVLPCGGIGVDSDTVWNEMHSSGAVRMAVGCVIELAFKVAAGELKNGFAVVRPPGHHAEESTAM 808
Cdd:cd10008     81 KLDNGKLAGLLAQRMFVMLPCGGVGVDTDTIWNELHSSNAARWAAGSVTDLAFKVASRELKNGFAVVRPPGHHADHSTAM 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  809 GFCFFNSVAITAKLLQQKLGVGKILIIDWDIHHGNGTQQAFYNDPNVLYISLHRYDDGNFFPGSGAPEEVGVGPGEGFNV 888
Cdd:cd10008    161 GFCFFNSVAIACRQLQQQGKASKILIVDWDVHHGNGTQQTFYQDPSVLYISLHRHDDGNFFPGSGAVDEVGAGSGEGFNV 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  889 NIAWTGGVEPPMGDVEYLTAFRTVVMPIANEFSPDVVLVSAGFDAVEGHQSPLGGYNVTAKCFGHLTKQLMKLAGGRVVL 968
Cdd:cd10008    241 NVAWAGGLDPPMGDPEYLAAFRIVVMPIAREFSPDLVLVSAGFDAAEGHPAPLGGYHVSAKCFGYMTQQLMNLAGGAVVL 320

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2085259879  969 ALEGGHDLTAICDASESCVAALLGDELDPLPLTVLQQKPCPKATASLERVIEIQSKHW 1026
Cdd:cd10008    321 ALEGGHDLTAICDASEACVAALLGNEVDPLSEESWKQKPNLNAIRSLEAVIRVHSKYW 378
HDAC9 cd10009
Histone deacetylase 9; Histone deacetylase 9 is a class IIa Zn-dependent enzyme that catalyzes ...
 649-1026 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: 672.11  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  649 FTTGLVYDTFMLKHQCICGNTNIHPEHAGRIQSVWSRLQETGLLGRCERIRGRKATLDEIQTVHSEYHTLLYGTSPLNRQ 728
Cdd:cd10009      1 SATGIAYDPLMLKHQCVCGNSTTHPEHAGRIQSIWSRLQETGLLNKCERIQGRKASLEEIQLVHSEHHSLLYGTNPLDGQ 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  729 KLDSKKLLGPISQKMYAVLPCGGIGVDSDTVWNEMHSSGAVRMAVGCVIELAFKVAAGELKNGFAVVRPPGHHAEESTAM 808
Cdd:cd10009     81 KLDPRILLGDDSQKFFSSLPCGGLGVDSDTIWNELHSSGAARMAVGCVIELASKVASGELKNGFAVVRPPGHHAEESTAM 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  809 GFCFFNSVAITAKLLQQKLGVGKILIIDWDIHHGNGTQQAFYNDPNVLYISLHRYDDGNFFPGSGAPEEVGVGPGEGFNV 888
Cdd:cd10009    161 GFCFFNSVAITAKYLRDQLNISKILIVDLDVHHGNGTQQAFYADPSILYISLHRYDEGNFFPGSGAPNEVGTGLGEGYNI 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  889 NIAWTGGVEPPMGDVEYLTAFRTVVMPIANEFSPDVVLVSAGFDAVEGHQSPLGGYNVTAKCFGHLTKQLMKLAGGRVVL 968
Cdd:cd10009    241 NIAWTGGLDPPMGDVEYLEAFRTIVKPVAKEFDPDMVLVSAGFDALEGHTPPLGGYKVTAKCFGHLTKQLMTLADGRVVL 320

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2085259879  969 ALEGGHDLTAICDASESCVAALLGDELDPLPLTVLQQKPCPKATASLERVIEIQSKHW 1026
Cdd:cd10009    321 ALEGGHDLTAICDASEACVNALLGNELEPLAEDILHQSPNMNAVISLQKIIEIQSKYW 378
HDAC6-dom2 cd10003
Histone deacetylase 6, domain 2; Histone deacetylase 6 is a class IIb Zn-dependent enzyme that ...
 655-1029 2.85e-142

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: 430.99  E-value: 2.85e-142
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  655 YDTFMLKHQCICgNTNiHPEHAGRIQSVWSRLQETGLLGRCERIRGRKATLDEIQTVHSEYHtllygtspLNRQKLDSKK 734
Cdd:cd10003      1 YDQRMMNHHNLW-DPG-HPECPQRISRIYERHNDLGLLERCLRLPSRLATEDELLLCHSEEH--------LDEMKSLEKM 70

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  735 LLGPISQKmyavlpcggiGVDSDTVWNEMHSSGAVRMAVGCVIELAFKVAAGELKNGFAVVRPPGHHAEESTAMGFCFFN 814
Cdd:cd10003     71 KPRELNRL----------GKEYDSIYIHPDSYQCALLAAGCVLQVVEAVLTGESRNGVAIVRPPGHHAEQDTACGFCFFN 140

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  815 SVAITAKLLQQKLGVGKILIIDWDIHHGNGTQQAFYNDPNVLYISLHRYDDGNFFPGS--GAPEEVGVGPGEGFNVNIAW 892
Cdd:cd10003    141 NVAIAARYAQKKYGLKRILIVDWDVHHGNGTQHMFESDPSVLYISLHRYDNGSFFPNSpeGNYDVVGKGKGEGFNVNIPW 220

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  893 TGGvepPMGDVEYLTAFRTVVMPIANEFSPDVVLVSAGFDAVEGhqSPLGGYNVTAKCFGHLTKQLMKLAGGRVVLALEG 972
Cdd:cd10003    221 NKG---GMGDAEYIAAFQQVVLPIAYEFNPELVLVSAGFDAARG--DPLGGCKVTPEGYAHMTHMLMSLAGGRVIVILEG 295

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 2085259879  973 GHDLTAICDASESCVAALLGdelDPLPLTVLQQKPCPKATASLERVIEIQSKHWTSL 1029
Cdd:cd10003    296 GYNLTSISESMSMCTKTLLG---DPPPVLDLPRPPCSSALKSINNVLQVHQKYWKSL 349
HDAC_classII cd09992
Histone deacetylases and histone-like deacetylases, classII; Class II histone deacetylases are ...
 672-991 8.16e-141

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: 424.99  E-value: 8.16e-141
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  672 HPEHAGRIQSVWSRLQETGLLGRCERIRGRKATLDEIQTVHSEYHTllygtsplnrqkldskkllgpisQKMYAVLPCGG 751
Cdd:cd09992      1 HPERPERLLAILEALEEEGLLDRLVFVEPRPATEEELLRVHTPEYI-----------------------ERVEETCEAGG 57

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  752 IGVDSDTVWNEmHSSGAVRMAVGCVIELAFKVAAGELKNGFAVVRPPGHHAEESTAMGFCFFNSVAITAKLLQQKLGVGK 831
Cdd:cd09992     58 GYLDPDTYVSP-GSYEAALLAAGAALAAVDAVLSGEAENAFALVRPPGHHAEPDRAMGFCLFNNVAIAARYAQKRYGLKR 136

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  832 ILIIDWDIHHGNGTQQAFYNDPNVLYISLHRYDdgnFFPGSGAPEEVGVGPGEGFNVNIAWTGGveppMGDVEYLTAFRT 911
Cdd:cd09992    137 VLIVDWDVHHGNGTQDIFYDDPSVLYFSIHQYP---FYPGTGAAEETGGGAGEGFTINVPLPPG----SGDAEYLAAFEE 209

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  912 VVMPIANEFSPDVVLVSAGFDAVEGHqsPLGGYNVTAKCFGHLTKQLMKLA----GGRVVLALEGGHDLTAICDASESCV 987
Cdd:cd09992    210 VLLPIAREFQPDLVLVSAGFDAHRGD--PLGGMNLTPEGYARLTRLLKELAdehcGGRLVFVLEGGYNLEALAESVLAVL 287


                   ....
gi 2085259879  988 AALL 991
Cdd:cd09992    288 EALL 291
Hist_deacetyl pfam00850
Histone deacetylase domain; Histones can be reversibly acetylated on several lysine residues. ...
 672-990 1.22e-123

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: 380.43  E-value: 1.22e-123
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  672 HPEHAGRIQSVWSRLQETGLLGRCERIRGRKATLDEIQTVHSEYHTLLYGTSPLNRQKLDSKKLLGpisqkmyavlpcgg 751
Cdd:pfam00850    1 HPENPERLKAILEALREAGLLPDLEIIAPRPATEEELLLVHSPEYLEFLEEAAPEGGALLLLSYLS-------------- 66

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  752 igvDSDTVWNEMHSSGAVRMAVGCVIELAFKVAAGELKNGFAVVRPPGHHAEESTAMGFCFFNSVAITAKLLQQKLGVGK 831
Cdd:pfam00850   67 ---GDDDTPVSPGSYEAALLAAGGTLAAADAVLSGEARNAFALVRPPGHHAERDRASGFCIFNNVAIAAKYLREKYGLKR 143

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  832 ILIIDWDIHHGNGTQQAFYNDPNVLYISLHRYdDGNFFPGSGAPEEVGVGPGEGFNVNIAWTGGveppMGDVEYLTAFRT 911
Cdd:pfam00850  144 VAIVDFDVHHGNGTQEIFYDDPSVLTLSIHQY-PGGFYPGTGFADETGEGKGKGYTLNVPLPPG----TGDAEYLAAFEE 218

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  912 VVMPIANEFSPDVVLVSAGFDAVEGHqsPLGGYNVTAKCFGHLTKQLMKLA---GGRVVLALEGGHDLTAICDASESCVA 988
Cdd:pfam00850  219 ILLPALEEFQPDLILVSAGFDAHAGD--PLGGLNLTTEGFAEITRILLELAdplCIRVVSVLEGGYNLDALARSATAVLA 296


                   ..
gi 2085259879  989 AL 990
Cdd:pfam00850  297 AL 298
HDAC_Clr3 cd11600
Class II Histone deacetylase Clr3 and similar proteins; Clr3 is a class II Histone ...
 672-999 6.46e-123

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: 379.00  E-value: 6.46e-123
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  672 HPEHAGRIQSVWSRLQETGLLGRCERIRGRKATLDEIQTVHSEYH-TLLYGTSPLNRQKLDSKKllgpisqKMYavlpcg 750
Cdd:cd11600      3 HPEDPSRISRIFEKLKEAGLINRMLRIPIREATKEEILLVHSEEHwDRVEATEKMSDEQLKDRT-------EIF------ 69

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  751 gigvDSDTVWNEMHSSGAVRMAVGCVIELAFKVAAGELKNGFAVVRPPGHHAEESTAMGFCFFNSVAITAKLLQQKL--G 828
Cdd:cd11600     70 ----ERDSLYVNNDTAFCARLSCGGAIEACRAVAEGRVKNAFAVVRPPGHHAEPDESMGFCFFNNVAVAAKWLQTEYpdK 145

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  829 VGKILIIDWDIHHGNGTQQAFYNDPNVLYISLHRYDDGNFFPGS--GAPEEVGVGPGEGFNVNIAWTggvEPPMGDVEYL 906
Cdd:cd11600    146 IKKILILDWDIHHGNGTQRAFYDDPNVLYISLHRFENGGFYPGTpyGDYESVGEGAGLGFNVNIPWP---QGGMGDADYI 222

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  907 TAFRTVVMPIANEFSPDVVLVSAGFDAVEGhqSPLGGYNVTAKCFGHLTKQLMKLAGGRVVLALEGGHDLTAICDASESC 986
Cdd:cd11600    223 YAFQRIVMPIAYEFDPDLVIISAGFDAADG--DELGQCHVTPAGYAHMTHMLMSLAGGKLVVALEGGYNLDAISDSALAV 300

                          330
                   ....*....|...
gi 2085259879  987 VAALLGDELDPLP 999
Cdd:cd11600    301 AKVLLGEAPPKLP 313
HDAC10_HDAC6-dom1 cd10002
Histone deacetylase 6, domain 1 and histone deacetylase 10; Histone deacetylases 6 and 10 are ...
 672-1026 3.11e-105

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: 333.12  E-value: 3.11e-105
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  672 HPEHAGRIQSVWSRLQETGLLGRCERIRGRKATLDEIQTVHS-EYHTLLYGTSPLNRQKLDSKkllgpisqkmyavlpCG 750
Cdd:cd10002      7 HIECPERLEAILERLTQDGLLERCVKIPAREAEEDEILLVHSqEYIDLVKSTETMEKEELESL---------------CS 71

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  751 GIgvdsDTVWNEMHSSGAVRMAVGCVIELAFKVAAGELKNGFAVVRPPGHHAEESTAMGFCFFNSVAITAKLLQQKLGVG 830
Cdd:cd10002     72 GY----DSVYLCPSTYEAARLAAGSTIELVKAVMAGKIQNGFALIRPPGHHAMRNEANGYCIFNNVAIAAKYAIEKLGLK 147

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  831 KILIIDWDIHHGNGTQQAFYNDPNVLYISLHRYDDGNFFPGSGAPE--EVGVGPGEGFNVNIAW--TGgveppMGDVEYL 906
Cdd:cd10002    148 RILIVDWDVHHGQGTQQGFYEDPRVLYFSIHRYEHGRFWPHLFESDydYIGVGHGYGFNVNVPLnqTG-----LGDADYL 222

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  907 TAFRTVVMPIANEFSPDVVLVSAGFDAVEGhqSPLGGYNVTAKCFGHLTKQLMKLAGGRVVLALEGGHDLTAICDASESC 986
Cdd:cd10002    223 AIFHHILLPLALEFQPELVLVSAGFDASIG--DPEGEMAVTPAGYAHLTRLLMGLAGGKLLLVLEGGYLLESLAESVSMT 300

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|
gi 2085259879  987 VAALLGDELDPLPLtvlqQKPCPKATASLERVIEIQSKHW 1026
Cdd:cd10002    301 LRGLLGDPLPPLAP----PIPIRSVLETILNAIAHLSPRW 336
HDAC cd09301
Histone deacetylase (HDAC) classes I, II, IV and related proteins; The HDAC/HDAC-like family ...
 678-990 3.92e-102

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: 322.46  E-value: 3.92e-102
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  678 RIQSVWSRLQETGLLGRCERIRGRKATLDEIQTVHSEYHTLLYGTSPLNRQKLDSKKllgpisqkmyavlpcggiGVDSD 757
Cdd:cd09301      1 RIRDLIEALKELGLRPKIELIECREATEELLLKVHTEEYLNELKANFAVATITESKP------------------VIFGP 62

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  758 TVWNEMHSSGAVRMAVGCVIELAFKVAAGELKNGFAVVRPPGHHAEESTAMGFCFFNSVAITAKLLQQKlGVGKILIIDW 837
Cdd:cd09301     63 NFPVQRHYFRGARLSTGGVVEAAELVAKGELERAFAVVGAGGHHAGKSRAWGFCYFNDVVLAIKFLRER-GISRILIIDT 141

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  838 DIHHGNGTQQAFYNDPNVLYISLHRYDDGNFfpgsgapeevGVGPGEGFNVNIAWTGGveppMGDVEYLTAFRTVVMPIA 917
Cdd:cd09301    142 DAHHGDGTREAFYDDDRVLHMSFHNYDIYPF----------GRGKGKGYKINVPLEDG----LGDEEYLDAVERVISKVL 207

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2085259879  918 NEFSPDVVLVSAGFDAVEGHqsPLGGYNVTAKCFGHLTKQLMKLA-GGRVVLALEGGHDLTAICDASESCVAAL 990
Cdd:cd09301    208 EEFEPEVVVLQFGHDTHEGD--RLGGFNLSEKGFVKLAEIVKEFArGGPILMVLGGGYNPEAAARIWTAIIKEL 279
AcuC COG0123
Acetoin utilization deacetylase AcuC or a related deacetylase [Secondary metabolites ...
 651-992 4.96e-101

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


Pssm-ID: 439893 [Multi-domain]  Cd Length: 308  Bit Score: 320.90  E-value: 4.96e-101
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  651 TGLVYDTFMLKHQCicGNTniHPEHAGRIQSVWSRLQETGLLGRCERIRGRKATLDEIQTVHSEYHtllygtsplnrqkL 730
Cdd:COG0123      1 TALIYHPDYLLHDL--GPG--HPEPPERLRAILDALEASGLLDDLELVEPPPATEEDLLRVHTPDY-------------V 63

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  731 DskkllgpisqKMYAVLPCGGIG-VDSDTVWNEmHSSGAVRMAVGCVIELAFKVAAGELKNGFAVVRPPGHHAEESTAMG 809
Cdd:COG0123     64 D----------ALRAASLDGGYGqLDPDTPVSP-GTWEAALLAAGGALAAADAVLEGEARNAFALVRPPGHHAERDRAMG 132

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  810 FCFFNSVAITAKLLQQKlGVGKILIIDWDIHHGNGTQQAFYNDPNVLYISLHRYddgNFFPGSGAPEEVGVGPGEGFNVN 889
Cdd:COG0123    133 FCLFNNAAIAARYLLAK-GLERVAIVDFDVHHGNGTQDIFYDDPDVLTISIHQD---PLYPGTGAADETGEGAGEGSNLN 208

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  890 IAwtggVEPPMGDVEYLTAFRTVVMPIANEFSPDVVLVSAGFDAvegHQS-PLGGYNVTAKCFGHLTKQLMKLA---GGR 965
Cdd:COG0123    209 VP----LPPGTGDAEYLAALEEALLPALEAFKPDLIVVSAGFDA---HADdPLGRLNLTTEGYAWRTRRVLELAdhcGGP 281

                          330       340
                   ....*....|....*....|....*..
gi 2085259879  966 VVLALEGGHDLTAICDASESCVAALLG 992
Cdd:COG0123    282 VVSVLEGGYNLDALARSVAAHLETLLG 308
HDAC6-dom1 cd11682
Histone deacetylase 6, domain 1; Histone deacetylases 6 are class IIb Zn-dependent enzymes ...
 672-1026 7.50e-90

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: 291.76  E-value: 7.50e-90
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  672 HPEHAGRIQSVWSRLQETGLLGRCERIRGRKATLDEIQTVHS-EYHTLLYGTSPLNRQKLDSkkllgpISQKMyavlpcg 750
Cdd:cd11682      7 FPECPERLHAIREKLIQEGLLERCVSVQAREASEEELLLVHSpEYVALMKSTQYMTEEELRT------LADTY------- 73

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  751 gigvdsDTVWNEMHSSGAVRMAVGCVIELAFKVAAGELKNGFAVVRPPGHHAEESTAMGFCFFNSVAITAKLLQQKLGVG 830
Cdd:cd11682     74 ------DSVYLHPNSYSCACLAVGSVLQLVDKVLGGEIRNGLAIVRPPGHHAQHDKMDGYCMFNNVAIAARYAQQKHGVQ 147

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  831 KILIIDWDIHHGNGTQQAFYNDPNVLYISLHRYDDGNFFP--GSGAPEEVGVGPGEGFNVNIAWTggvEPPMGDVEYLTA 908
Cdd:cd11682    148 RVLIVDWDVHHGQGTQFIFEQDPSVLYFSIHRYEQGRFWPhlKESDSSAVGFGRGEGYNINVPWN---QVGMRDADYIAA 224

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  909 FRTVVMPIANEFSPDVVLVSAGFDAVEGhqSPLGGYNVTAKCFGHLTKQLMKLAGGRVVLALEGGHDLTAICDASESCVA 988
Cdd:cd11682    225 FLHVLLPVALEFQPQLVLVAAGFDAVIG--DPKGEMAATPACFAHLTHLLMGLAGGKLILSLEGGYNLRSLAEGVCASLK 302

                          330       340       350
                   ....*....|....*....|....*....|....*...
gi 2085259879  989 ALLGdelDPLPLTVLQQKPCPKATASLERVIEIQSKHW 1026
Cdd:cd11682    303 ALLG---DPCPMLESPGAPCRSALASVSCTISALEPFW 337
HDAC_classII_1 cd09996
Histone deacetylases and histone-like deacetylases, classII; This subfamily includes bacterial ...
 651-977 2.81e-83

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: 274.82  E-value: 2.81e-83
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  651 TGLVYDTFMLKHqcicgNTN----------------IHPEHAGRIQSVWSRLQETGLLGRCERIRGRKATLDEIQTVHSE 714
Cdd:cd09996      1 TGFVWDERYLWH-----DTGtgalflpvggllvqpgRHPENPETKRRIKNLLEVSGLSDHLVLITPRPATDEELLRVHTP 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  715 YHtllygtspLNRQKLDSKKllgpisqkmyavlpcGGIGVDSDTVWNEmHSSGAVRMAVGCVIELAFKVAAGELKNGFAV 794
Cdd:cd09996     76 EY--------IDRVKAASAA---------------GGGEAGGGTPFGP-GSYEIALLAAGGAIAAVDAVLDGEVDNAYAL 131

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  795 VRPPGHHAEESTAMGFCFFNSVAITAKLLQQKLGVGKILIIDWDIHHGNGTQQAFYNDPNVLYISLHRydDGNFFPGSGA 874
Cdd:cd09996    132 VRPPGHHAEPDQGMGFCLFNNVAIAARHALAVGGVKRVAVVDWDVHHGNGTQAIFYDDPDVLTISLHQ--DRCFPPDSGA 209

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  875 PEEVGVGPGEGFNVNIawtggvepPM----GDVEYLTAFRTVVMPIANEFSPDVVLVSAGFDAveGHQSPLGGYNVTAKC 950
Cdd:cd09996    210 VEERGEGAGEGYNLNI--------PLppgsGDGAYLHAFERIVLPALRAFRPELIIVASGFDA--SAFDPLGRMMLTSDG 279

                          330       340       350
                   ....*....|....*....|....*....|.
gi 2085259879  951 FGHLTKQLMKLA----GGRVVLALEGGHDLT 977
Cdd:cd09996    280 FRALTRKLRDLAdelcGGRLVMVHEGGYSEA 310
HDAC_classII_2 cd11599
Histone deacetylases and histone-like deacetylases, classII; This subfamily includes ...
 672-991 2.11e-81

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: 267.07  E-value: 2.11e-81
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  672 HPEHAGRIQSVWSRLQETGLLGRCERIRGRKATLDEIQTVHSEYHtllygtsplnrqkldskkllgpISQKMYAVLPCGG 751
Cdd:cd11599      1 HPESPERLEAILDALIASGLDRLLRQLEAPPATREQLLRVHDAAY----------------------VDRLEAAAPEEGL 58

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  752 IGVDSDTVWNEmHSSGAVRMAVGCVIELAFKVAAGELKNGFAVVRPPGHHAEESTAMGFCFFNSVAITAKLLQQKLGVGK 831
Cdd:cd11599     59 VQLDPDTAMSP-GSLEAALRAAGAVVAAVDAVMAGEARNAFCAVRPPGHHAERDKAMGFCLFNNVAIAAAHALAHHGLER 137

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  832 ILIIDWDIHHGNGTQQAFYNDPNVLYISLHRYddgNFFPGSGAPEEVGVGpgegfN-VNIAWTGGVEPPmgdvEYLTAFR 910
Cdd:cd11599    138 VAIVDFDVHHGNGTEDIFRDDPRVLFCSSHQH---PLYPGTGAPDETGHG-----NiVNVPLPAGTGGA----EFREAVE 205

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  911 TVVMPIANEFSPDVVLVSAGFDAvegHQS-PLGGYNVTAKCFGHLTKQLMKLA----GGRVVLALEGGHDLTAICDASES 985
Cdd:cd11599    206 DRWLPALDAFKPDLILISAGFDA---HRDdPLAQLNLTEEDYAWITEQLMDVAdrycDGRIVSVLEGGYDLSALARSVAA 282


                   ....*.
gi 2085259879  986 CVAALL 991
Cdd:cd11599    283 HVRALM 288
HDAC10 cd11683
Histone deacetylase 10; Histone deacetylases 10 are class IIb Zn-dependent enzymes that ...
 678-1026 3.89e-78

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: 259.79  E-value: 3.89e-78
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  678 RIQSVWSRLQETGLLGRCERIRGRKATLDEIQTVHSEYHTLLYGTSplnrQKLDSKKLLGpISQKMyavlpcggigvdsD 757
Cdd:cd11683     13 RLTASYERLRQYGLVQRCLRLPAREASEEEILLVHSPEYLSLVRET----QVMNKEELMA-ISGKY-------------D 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  758 TVWNEMHSSGAVRMAVGCVIELAFKVAAGELKNGFAVVRPPGHHAEESTAMGFCFFNSVAITAKLLQQKLGVGKILIIDW 837
Cdd:cd11683     75 AVYFHPNTFHCARLAAGATLQLVDAVLTGEVQNGMALVRPPGHHSQRNAANGFCVFNNVAIAAEYAKKKYGLHRILIVDW 154

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  838 DIHHGNGTQQAFYNDPNVLYISLHRYDDGNFFPG--SGAPEEVGVGPGEGFNVNIAWTggvEPPMGDVEYLTAFRTVVMP 915
Cdd:cd11683    155 DVHHGQGIQYIFEEDPSVLYFSWHRYEHQRFWPFlrESDYDAVGRGKGLGFNINLPWN---KVGMGNADYLAAFFHVLLP 231

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  916 IANEFSPDVVLVSAGFDAVEGhqSPLGGYNVTAKCFGHLTKQLMKLAGGRVVLALEGGHDLTAICDASESCVAALLGdel 995
Cdd:cd11683    232 LAFEFDPELVLVSAGFDSAIG--DPEGQMCATPECFAHLTHLLMVLAGGKLCAVLEGGYHLESLAESVCMTVQTLLG--- 306

                          330       340       350
                   ....*....|....*....|....*....|.
gi 2085259879  996 DPLPLTVLQQKPCPKATASLERVIEIQSKHW 1026
Cdd:cd11683    307 DPLPRLSGEMTPCQSALESIQNVRAAQAPYW 337
HDAC_classII_APAH cd10001
Histone deacetylase class IIa; This subfamily includes bacterial acetylpolyamine ...
 672-992 2.71e-68

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: 230.89  E-value: 2.71e-68
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  672 HPEHAGRIQSVWSRLQETGLLgrcERIRGRKATLDEIQTVHS-EYHTLLYGtsplnrqkldskkllgpisqkmyavlpcg 750
Cdd:cd10001     25 HPENPERAEAILDALKRAGLG---EVLPPRDFGLEPILAVHDpDYVDFLET----------------------------- 72

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  751 gigVDSDTVWNEmHSSGAVRMAVGCVIELAFKVAAGElKNGFAVVRPPGHHAEESTAMGFCFFNSVAITAKLLQQKlgVG 830
Cdd:cd10001     73 ---ADTDTPISE-GTWEAALAAADTALTAADLVLEGE-RAAYALCRPPGHHAGRDRAGGFCYFNNAAIAAQYLRDR--AG 145

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  831 KILIIDWDIHHGNGTQQAFYNDPNVLYISLHRyDDGNFFPG-SGAPEEVGVGPGEGFNVNIAwtggVEPPMGDVEYLTAF 909
Cdd:cd10001    146 RVAILDVDVHHGNGTQEIFYERPDVLYVSIHG-DPRTFYPFfLGFADETGEGEGEGYNLNLP----LPPGTGDDDYLAAL 220

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  910 RTVVMPIAnEFSPDVVLVSAGFDAVEGhqSPLGGYNVTAKCFGHLTKQLMKLaGGRVVLALEGGHDLTAIcdaSESCVAA 989
Cdd:cd10001    221 DEALAAIA-AFGPDALVVSLGFDTHEG--DPLSDFKLTTEDYARIGRRIAAL-GLPTVFVQEGGYNVDAL---GRNAVAF 293


                   ...
gi 2085259879  990 LLG 992
Cdd:cd10001    294 LAG 296
HDAC_AcuC_like cd09994
Class I histone deacetylase AcuC (Acetoin utilization protein)-like enzymes; AcuC (Acetoin ...
 672-976 2.46e-50

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: 180.45  E-value: 2.46e-50
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  672 HPEHAGRIQSVWSRLQETGLLGRCERIRGRKATLDEIQTVHS-EYHTLLYGTSPlNRQKLDSKKLlgpisqkmyavlpcg 750
Cdd:cd09994     17 HPFNPPRLSLTKDLLRALGLLPPVDLVPPRPATEEELLLFHTpDYIEAVKEASR-GQEPEGRGRL--------------- 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  751 GIGVDSDTVWNEMHSsgAVRMAVGCVIELAFKVAAGElknGFAVVRPPG--HHAEESTAMGFCFFNSVAITAKLLQQKlG 828
Cdd:cd09994     81 GLGTEDNPVFPGMHE--AAALVVGGTLLAARLVLEGE---ARRAFNPAGglHHAMRGRASGFCVYNDAAVAIERLRDK-G 154

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  829 VGKILIIDWDIHHGNGTQQAFYNDPNVLYISLHRyDDGNFFPGSGAPEEVGVGPGEGFNVNIAwtggVEPPMGDVEYLTA 908
Cdd:cd09994    155 GLRVAYVDIDAHHGDGVQAAFYDDPRVLTISLHE-SGRYLFPGTGFVDEIGEGEGYGYAVNIP----LPPGTGDDEFLRA 229

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2085259879  909 FRTVVMPIANEFSPDVVLVSAGFDAVEGhqSPLGGYNVTAKCFGHLTKQLMKLA----GGRVVLALEGGHDL 976
Cdd:cd09994    230 FEAVVPPLLRAFRPDVIVSQHGADAHAG--DPLTHLNLSNRAYRAAVRRIRELAdeycGGRWLALGGGGYNP 299
HDAC8 cd10000
Histone deacetylase 8 (HDAC8); HDAC8 is a Zn-dependent class I histone deacetylase that ...
 677-997 1.72e-33

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: 133.23  E-value: 1.72e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  677 GRIQSVWSRLQETGLLGRCERIRGRKATLDEIQTVHS-EYHTLLYGTSplnrQKLDSkkllgpisQKMYAVLPCGGIGVD 755
Cdd:cd10000     21 NRASMVHSLIEAYGLLKQLRVVKPRVATEEELASFHSdEYIQFLKKAS----NEGDN--------DEEPSEQQEFGLGYD 88

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  756 SDTVWNEMHssgAVRMAVGCVIELAFKVAAGELKngFAVVRPPG-HHAEESTAMGFCFFNSVAITAKLLQQKLGvgKILI 834
Cdd:cd10000     89 CPIFEGIYD---YAAAVAGATLTAAQLLIDGKCK--VAINWFGGwHHAQRDEASGFCYVNDIVLGILKLREKFD--RVLY 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  835 IDWDIHHGNGTQQAFYNDPNVLYISLHRYDDGnFFPGSGAPEEVGVGPGEGFNVNIAWTGGVEppmgDVEYLTAFRTVVM 914
Cdd:cd10000    162 VDLDLHHGDGVEDAFSFTSKVMTVSLHKYSPG-FFPGTGDVSDVGLGKGKYYTVNVPLRDGIQ----DEQYLQIFTAVVP 236

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  915 PIANEFSPDVVLVSAGFDAVEGhqSPLGGYNVTAKCFGHLTKQLMK------LAGGrvvlaleGGHDL--TAICDAseSC 986
Cdd:cd10000    237 EIVAAFRPEAVVLQCGADTLAG--DPMGAFNLTPVGIGKCLKYVLGwklptlILGG-------GGYNLanTARCWT--YL 305

                          330
                   ....*....|.
gi 2085259879  987 VAALLGDELDP 997
Cdd:cd10000    306 TGLILGEPLSS 316
HDAC_Hos1 cd11680
Class I histone deacetylases Hos1 and related proteins; Saccharomyces cerevisiae Hos1 is ...
 800-980 3.57e-31

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: 124.30  E-value: 3.57e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  800 HHAEESTAMGFCFFNSVAITAKLLQQKlGVGKILIIDWDIHHGNGTQQAFYNDPNVLYISLHRYDDGnFFPGSGAPEEvg 879
Cdd:cd11680    115 HHAQKSRASGFCYVNDIVLAILRLRRA-RFRRVFYLDLDLHHGDGVESAFFFSKNVLTCSIHRYDPG-FFPGTGSLKN-- 190

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  880 vgPGEGFNVNIAwtggVEPPMGDVEYLTAFRTVVMPIANEFSPDVVLVSAGFDAVEGhqSPLGGYNVTAKCFGHLTKQLM 959
Cdd:cd11680    191 --SSDKGMLNIP----LKRGLSDKTLLRIIDSIVRPLIEKFEPEVIVIQCGCDGLSG--DPHKEWNLTIRGYGSVIELLL 262

                          170       180
                   ....*....|....*....|....
gi 2085259879  960 KLAGGRVVLALEGG---HDLTAIC 980
Cdd:cd11680    263 KEFKDKPTLLLGGGgynHTEAARA 286
HDAC_classI cd09991
Class I histone deacetylases; Class I histone deacetylases (HDACs) are Zn-dependent enzymes ...
 672-988 5.95e-31

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: 124.23  E-value: 5.95e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  672 HPEHAGRIQSVWSRLQETGLLGRCERIRGRKATLDEIQTVHS-EYHTLLYGTSPLNRQKLdsKKLLgpisqKMYavlpcg 750
Cdd:cd09991     15 HPMKPHRIRMTHSLILSYGLYKKMEIYRPRPATAEELTKFHSdDYIDFLRSVSPDNMKEF--KKQL-----ERF------ 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  751 GIGVDSdTVWNEMHSsgAVRMAVGCVIELAFKVAAGELKngfAVVRPPG--HHAEESTAMGFCFFNSV--AITaKLLQQK 826
Cdd:cd09991     82 NVGEDC-PVFDGLYE--YCQLYAGGSIAAAVKLNRGQAD---IAINWAGglHHAKKSEASGFCYVNDIvlAIL-ELLKYH 154

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  827 lgvGKILIIDWDIHHGNGTQQAFYNDPNVLYISLHRYddGNFFPGSGAPEEVGVGPGEGFNVNIA-WTGgveppMGDVEY 905
Cdd:cd09991    155 ---QRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKF--GEYFFPGTGLRDIGAGKGKYYAVNVPlKDG-----IDDESY 224

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  906 LTAFRTVVMPIANEFSPDVVLVSAGFDAVEGhqSPLGGYNVT----AKCFghltkQLMKLAGGRVVLALEGGHDL--TAI 979
Cdd:cd09991    225 LQIFEPVLSKVMEVFQPSAVVLQCGADSLAG--DRLGCFNLSikghAKCV-----KFVKSFNIPLLVLGGGGYTLrnVAR 297


                   ....*....
gi 2085259879  980 CDASESCVA 988
Cdd:cd09991    298 CWTYETAVL 306
ClassIIa_HDAC5_Gln-rich-N cd10164
Glutamine-rich N-terminal helical domain of HDAC5, a Class IIa histone deacetylase; This ...
 52-139 3.94e-30

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: 114.92  E-value: 3.94e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879   52 DPALREKQLQHELLLLKQQQELQKQLLFAEFQKQHEVLTRQHEVQLQEHLK---------QQQEILAAKRQQELEQKRKL 122
Cdd:cd10164      1 DPSLREQQLQQELLLLKQQQQLQKQLLFAEFQKQHEHLTRQHEVQLQKHLKvraelfseqQQQEILAAKRQQELEQQRKR 80

                           90
                   ....*....|....*..
gi 2085259879  123 EQQRHEEMEKQRLEQQL 139
Cdd:cd10164     81 EQQRQEELEKQRLEQQL 97
HDAC_classIV cd09993
Histone deacetylase class IV also known as histone deacetylase 11; Class IV histone ...
 682-948 1.32e-29

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: 119.14  E-value: 1.32e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  682 VWSRLQETGLLGRCERIRGRKATLDEIQTVHS-EY-HTLLYGTspLNRQKLDSKKLlgPISQKMyaVLPcggigvdsdtv 759
Cdd:cd09993     11 LREALLEEGLVLPEDIVEPEPATREDLLRVHDpEYlESLKSGE--LSREEIRRIGF--PWSPEL--VER----------- 73

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  760 wnemhssgaVRMAVGCVIeLAFKVAageLKNGFAVvRPPG--HHAEESTAMGFCFFNSVAITAKLLQQKLGVGKILIIDW 837
Cdd:cd09993     74 ---------TRLAVGGTI-LAARLA---LEHGLAI-NLAGgtHHAFPDRGEGFCVFNDIAIAARVLLAEGLVRRVLIVDL 139

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  838 DIHHGNGTQQAFYNDPNVLYISLHrydDGNFFPGSGAPEEVGVgpgegfnvniawtgGVEPPMGDVEYLTAFRTVVMPIA 917
Cdd:cd09993    140 DVHQGNGTAAIFADDPSVFTFSMH---GEKNYPFRKEPSDLDV--------------PLPDGTGDDEYLAALEEALPRLL 202

                          250       260       270
                   ....*....|....*....|....*....|.
gi 2085259879  918 NEFSPDVVLVSAGFDAVEGhqSPLGGYNVTA 948
Cdd:cd09993    203 AEFRPDLVFYNAGVDVLAG--DRLGRLSLSL 231
HDAC_Hos2 cd11598
Class I histone deacetylases including ScHos2 and SpPhd1; This subfamily includes Class I ...
 701-956 1.76e-29

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: 119.87  E-value: 1.76e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  701 RKATLDEIQTVHSE-YHTLLYGTSPLNRQKLDSKKL----LG---PISQKMYAVLpcggigvdsdtvwnemhssgavRMA 772
Cdd:cd11598     47 RAATREELRQFHDAdYLDFLSKVSPENANQLRFDKAepfnIGddcPVFDGMYDYC----------------------QLY 104

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  773 VGCVIELAFKVAAGelKNGFAVVRPPG-HHAEESTAMGFCFFNSVAITakLLQQKLGVGKILIIDWDIHHGNGTQQAFYN 851
Cdd:cd11598    105 AGASLDAARKLCSG--QSDIAINWSGGlHHAKKSEASGFCYVNDIVLA--ILNLLRYFPRVLYIDIDVHHGDGVEEAFYR 180

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  852 DPNVLYISLHRYdDGNFFPGSGAPEEVGVGPGEGFNVNIAWTGGVeppmGDVEYLTAFRTVVMPIANEFSPDVVLVSAGF 931
Cdd:cd11598    181 TDRVMTLSFHKY-NGEFFPGTGDLDDNGGTPGKHFALNVPLEDGI----DDEQYNLLFKSIIGPTIEKFQPSAIVLQCGA 255

                          250       260
                   ....*....|....*....|....*
gi 2085259879  932 DAVEGHQspLGGYNVTAKCFGHLTK 956
Cdd:cd11598    256 DSLGGDR--LGQFNLNIKAHGACVK 278
Arginase_HDAC cd09987
Arginase-like and histone-like hydrolases; Arginase-like/histone-like hydrolase superfamily ...
 763-993 2.53e-29

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: 116.71  E-value: 2.53e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  763 MHSSGAVRMAVGCVIELAFKVaagelKNGFAVVrppGHHAEestamgfcfFNSVAITAKLLQQKLGVgkiliIDWDIHHG 842
Cdd:cd09987      5 IRKAEAHELLAGVVVAVLKDG-----KVPVVLG---GDHSI---------ANGAIRAVAELHPDLGV-----IDVDAHHD 62

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  843 NGTQQAFYN--------------DPNVLYISLHRYDDGNFFPGsgapeevGVGPGEGFNVNIAWTGGveppmGDVEYLTA 908
Cdd:cd09987     63 VRTPEAFGKgnhhtprhllceplISDVHIVSIGIRGVSNGEAG-------GAYARKLGVVYFSMTEV-----DKLGLGDV 130

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  909 FRTVVMPIanEFSPDVVLVSAGFDAVEGHQSP----LGGYNVTAKCFGHLTKQLMKLaGGRVVLALEGGHDLTAICDASE 984
Cdd:cd09987    131 FEEIVSYL--GDKGDNVYLSVDVDGLDPSFAPgtgtPGPGGLSYREGLYITERIAKT-NLVVGLDIVEVNPLLDETGRTA 207


                   ....*....
gi 2085259879  985 SCVAALLGD 993
Cdd:cd09987    208 RLAAALTLE 216
RPD3-like cd10004
reduced potassium dependency-3 (RPD3)-like; Proteins of the Rpd3-like family are class I ...
 672-953 3.84e-26

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: 111.82  E-value: 3.84e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  672 HPEHAGRIQSVWSRLQETGLLGRCERIRGRKATLDEIQTVHS-EYHTLLYGTSPLNR---QKLDSKKLLG---PISQKMY 744
Cdd:cd10004     21 HPMKPHRIRMAHSLVMNYGLYKKMEIYRAKPATKNEMTQFHTdEYIDFLSRVTPDNMekfQKEQVKYNVGddcPVFDGLF 100

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  745 AVlpCGGIGVDSdtvwnemhSSGAVRMAVG-CVIELAFkvaAGELkngfavvrppgHHAEESTAMGFCFFNSVAITA-KL 822
Cdd:cd10004    101 EF--CSISAGGS--------MEGAARLNRGkCDIAVNW---AGGL-----------HHAKKSEASGFCYVNDIVLGIlEL 156

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  823 LQQKlgvGKILIIDWDIHHGNGTQQAFYNDPNVLYISLHRYddGNFFPGSGAPEEVGVGPGEGFNVNIAWTGGVEppmgD 902
Cdd:cd10004    157 LRYH---QRVLYIDIDVHHGDGVEEAFYTTDRVMTCSFHKY--GEYFPGTGELRDIGIGTGKNYAVNVPLRDGID----D 227

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|.
gi 2085259879  903 VEYLTAFRTVVMPIANEFSPDVVLVSAGFDAVEGHQspLGGYNVTAKcfGH 953
Cdd:cd10004    228 ESYKSIFEPVIKHVMEWYQPEAVVLQCGGDSLSGDR--LGCFNLSMK--GH 274
HDAC_Hos3 cd09998
Class II histone deacetylases Hos3 and related proteins; Fungal histone deacetylase Hos3 from ...
 768-990 3.20e-25

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: 108.69  E-value: 3.20e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  768 AVRMAVGCV---IELAFKVAAGELKNGFAVVRPPGHHAEESTAMGFCFFNSVAITAKLLQQKLGVGKILIIDWDIHHGNG 844
Cdd:cd09998     85 AIQGALGAVceaVDSVFKPESPGTKRAFVAIRPPGHHCSESTPSGFCWVNNVHVGAAHAYLTHGITRVVILDIDLHHGNG 164

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  845 TQ------------------------QAFYNDPNVLYISLHrydDGNFFP-GSGAPEEVGVGpgegfNVNIA-------W 892
Cdd:cd09998    165 TQdiawrinaeankqalesssyddfkPAGAPGLRIFYSSLH---DINSFPcEDGDPAKVKDA-----SVSIDgahgqwiW 236

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  893 TGGVEPPMGDVEYLTAFR---TVVMPIANEF-------SPD--VVLVSAGFDAVEGHQSPLG--GYNVTAKCFGHLTKQL 958
Cdd:cd09998    237 NVHLQPWTTEEDFWELYYpkyRILFEKAAEFlrlttaaTPFktLVFISAGFDASEHEYESMQrhGVNVPTSFYYRFARDA 316

                          250       260       270
                   ....*....|....*....|....*....|....*.
gi 2085259879  959 MKLA----GGRVVLALEGGHDLTAICDASESCVAAL 990
Cdd:cd09998    317 VRFAdahaHGRLISVLEGGYSDRALCSGVLAHLTGL 352
ClassIIa_HDAC_Gln-rich-N cd10149
Glutamine-rich N-terminal helical domain of various Class IIa histone deacetylases (HDAC4, ...
 52-139 9.76e-24

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: 96.30  E-value: 9.76e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879   52 DPALREKQLQHELLLLKQQQELQKQLLFAEFQKQHEVLTRQHEVQLQEHLKQQQEILAAKRQQEL-EQKRKLEQQRHE-E 129
Cdd:cd10149      1 DPVLREQQLQQELLALKQQQQIQKQLLIAEFQKQHENLTRQHEAQLQEHIKQQQEMLAIKQQQELlEKQRKLEQQRQEqE 80

                           90
                   ....*....|
gi 2085259879  130 MEKQRLEQQL 139
Cdd:cd10149     81 LEKQRREQQL 90
HDAC1 cd10010
Histone deacetylase 1 (HDAC1); Histone deacetylase 1 (HDAC1) is a Zn-dependent class I enzyme ...
 672-953 1.18e-23

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: 104.38  E-value: 1.18e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  672 HPEHAGRIQSVWSRLQETGLLGRCERIRGRKATLDEIQTVHSE-YHTLLYGTSPLNRQKLdSKKLlgpisQKMYAVLPCG 750
Cdd:cd10010     25 HPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKANAEEMTKYHSDdYIKFLRSIRPDNMSEY-SKQM-----QRFNVGEDCP 98

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  751 GIgvDSDTVWNEMHSSGAVRMAVgcvielafkvAAGELKNGFAVVRPPG-HHAEESTAMGFCFFNSVAITA-KLLQQKlg 828
Cdd:cd10010     99 VF--DGLFEFCQLSAGGSVASAV----------KLNKQQTDIAVNWAGGlHHAKKSEASGFCYVNDIVLAIlELLKYH-- 164

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  829 vGKILIIDWDIHHGNGTQQAFYNDPNVLYISLHRYddGNFFPGSGAPEEVGVGPGEGFNVNIAWTGGVEppmgDVEYLTA 908
Cdd:cd10010    165 -QRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKY--GEYFPGTGDLRDIGAGKGKYYAVNYPLRDGID----DESYEAI 237

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|....*
gi 2085259879  909 FRTVVMPIANEFSPDVVLVSAGFDAVEGHQspLGGYNVTAKcfGH 953
Cdd:cd10010    238 FKPVMSKVMEMFQPSAVVLQCGADSLSGDR--LGCFNLTIK--GH 278
PTZ00063 PTZ00063
histone deacetylase; Provisional
 800-964 1.17e-22

histone deacetylase; Provisional


Pssm-ID: 240251  Cd Length: 436  Bit Score: 102.20  E-value: 1.17e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  800 HHAEESTAMGFCFFNSVAI-TAKLLQQKlgvGKILIIDWDIHHGNGTQQAFYNDPNVLYISLHRYddGNFFPGSGAPEEV 878
Cdd:PTZ00063   137 HHAKRSEASGFCYINDIVLgILELLKYH---ARVMYIDIDVHHGDGVEEAFYVTHRVMTVSFHKF--GDFFPGTGDVTDI 211

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  879 GVGPGEGFNVNIAWTGGveppMGDVEYLTAFRTVVMPIANEFSPDVVLVSAGFDAVEGHQspLGGYNVT----AKCFGHL 954
Cdd:PTZ00063   212 GVAQGKYYSVNVPLNDG----IDDDSFVDLFKPVISKCVEVYRPGAIVLQCGADSLTGDR--LGRFNLTikghAACVEFV 285

                          170
                   ....*....|...
gi 2085259879  955 TK---QLMKLAGG 964
Cdd:PTZ00063   286 RSlniPLLVLGGG 298
HDAC3 cd10005
Histone deacetylase 3 (HDAC3); HDAC3 is a Zn-dependent class I histone deacetylase that ...
 800-953 5.51e-21

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: 96.31  E-value: 5.51e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  800 HHAEESTAMGFCFFNSVAITA-KLLQQKlgvGKILIIDWDIHHGNGTQQAFYNDPNVLYISLHRYddGN-FFPGSGAPEE 877
Cdd:cd10005    132 HHAKKFEASGFCYVNDIVIAIlELLKYH---PRVLYIDIDIHHGDGVQEAFYLTDRVMTVSFHKY--GNyFFPGTGDMYE 206

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2085259879  878 VGVGPGEGFNVNIAWTGGVEppmgDVEYLTAFRTVVMPIANEFSPDVVLVSAGFDAVEGHQspLGGYNVTAKcfGH 953
Cdd:cd10005    207 VGAESGRYYSVNVPLKDGID----DQSYLQLFKPVIQQVIDFYQPTCIVLQCGADSLGCDR--LGCFNLSIK--GH 274
HDAC2 cd10011
Histone deacetylase 2 (HDAC2); Histone deacetylase 2 (HDAC2) is a Zn-dependent class I enzyme ...
 672-953 1.32e-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: 95.13  E-value: 1.32e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  672 HPEHAGRIQSVWSRLQETGLLGRCERIRGRKATLDEIQTVHS-EYHTLLYGTSPLNRQKLdSKKLlgpisQKMYAVLPCG 750
Cdd:cd10011     21 HPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTKYHSdEYIKFLRSIRPDNMSEY-SKQM-----QRFNVGEDCP 94

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  751 GIgvDSDTVWNEMHSSGAVRMAVGC---VIELAFKVAAGElkngfavvrppgHHAEESTAMGFCFFNSVAITA-KLLQQK 826
Cdd:cd10011     95 VF--DGLFEFCQLSTGGSVAGAVKLnrqQTDMAVNWAGGL------------HHAKKSEASGFCYVNDIVLAIlELLKYH 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  827 lgvGKILIIDWDIHHGNGTQQAFYNDPNVLYISlhRYDDGNFFPGSGAPEEVGVGPGEGFNVNIAWTGGVEppmgDVEYL 906
Cdd:cd10011    161 ---QRVLYIDIDIHHGDGVEEAFYTTDRVMTVS--FHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGID----DESYG 231

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|....*..
gi 2085259879  907 TAFRTVVMPIANEFSPDVVLVSAGFDAVEGHQspLGGYNVTAKcfGH 953
Cdd:cd10011    232 QIFKPIISKVMEMYQPSAVVLQCGADSLSGDR--LGCFNLTVK--GH 274
HDAC4_Gln pfam12203
Glutamine rich N terminal domain of histone deacetylase 4; This domain is found in eukaryotes, ...
 51-139 1.48e-20

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: 87.22  E-value: 1.48e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879   51 VDPALREKQLQHELLLLKQQQELQKQLLFAEFQKQHEVLTRQHEVQLQEHLKQQQEILAAKRQQEL-EQKRKLEQQRHE- 128
Cdd:pfam12203    1 VDPLLREQQLQQELLLLKQQQQIQKQLLIAEFQKQHELLTRQHEAQLQEHIKQQQELLAMKQQQELlEQQRKLEQQRQEe 80

                           90
                   ....*....|.
gi 2085259879  129 EMEKQRLEQQL 139
Cdd:pfam12203   81 ELEKHRREQQL 91
ClassIIa_HDAC9_Gln-rich-N cd10163
Glutamine-rich N-terminal helical domain of HDAC9, a Class IIa histone deacetylase; This ...
 52-139 1.91e-19

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: 84.03  E-value: 1.91e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879   52 DPALREKQLQHELLLLKQQQELQKQLLFAEFQKQHEVLTRQHEVQLQEHLKQQQEILAAKRQQE-LEQKRKLEQQRHE-E 129
Cdd:cd10163      1 DPTVREKQLQQELLLIQQQQQIQKQLLIAEFQKQHENLTRQHQAQLQEHLKLQQELLAMKQQQElLEKEQKLEQQRQEqE 80

                           90
                   ....*....|
gi 2085259879  130 MEKQRLEQQL 139
Cdd:cd10163     81 LERHRREQQL 90
ClassIIa_HDAC4_Gln-rich-N cd10162
Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase; This ...
 52-139 2.02e-19

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: 84.09  E-value: 2.02e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879   52 DPALREKQLQHELLLLKQQQELQKQLLFAEFQKQHEVLTRQHEVQLQEHLKQQQEILAAKRQQE-LEQKRKLEQQRHE-E 129
Cdd:cd10162      1 EPALREQQLQQELLALKQKQQIQRQLLIAEFQRQHEQLSRQHEAQLHEHIKQQQELLAMKHQQElLEHQRKLERHRQEqE 80

                           90
                   ....*....|
gi 2085259879  130 MEKQRLEQQL 139
Cdd:cd10162     81 MEKQQREQKL 90
PTZ00346 PTZ00346
histone deacetylase; Provisional
 800-973 1.36e-18

histone deacetylase; Provisional


Pssm-ID: 240374 [Multi-domain]  Cd Length: 429  Bit Score: 89.70  E-value: 1.36e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  800 HHAEESTAMGFCFFNSVAItaKLLQQKLGVGKILIIDWDIHHGNGTQQAFYNDPNVLYISLHRYDDgNFFPGSGAPEEVG 879
Cdd:PTZ00346   154 HHSKCGECSGFCYVNDIVL--GILELLKCHDRVLYVDIDMHHGDGVDEAFCTSDRVFTLSLHKFGE-SFFPGTGHPRDVG 230

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879  880 VGPGEGFNVNIA-WTGgveppMGDVEYLTAFRTVVMPIANEFSPDVVLVSAGFDAVEGHQspLGGYNVTAKCFGHLTKQL 958
Cdd:PTZ00346   231 YGRGRYYSMNLAvWDG-----ITDFYYLGLFEHALHSIVRRYSPDAIVLQCGADSLAGDR--LGLLNLSSFGHGQCVQAV 303

                          170
                   ....*....|....*
gi 2085259879  959 MKLagGRVVLALEGG 973
Cdd:PTZ00346   304 RDL--GIPMLALGGG 316
TPH pfam13868
Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of ...
 94-146 6.54e-05

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: 46.45  E-value: 6.54e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2085259879   94 EVQLQEHLKQQQEILAAKRQQELEQKRKLEQQrHEEMEKQRLEQQLIMLRNKE 146
Cdd:pfam13868   50 EEERERALEEEEEKEEERKEERKRYRQELEEQ-IEEREQKRQEEYEEKLQERE 101
tolA PRK09510
cell envelope integrity inner membrane protein TolA; Provisional
 83-161 1.33e-04

cell envelope integrity inner membrane protein TolA; Provisional


Pssm-ID: 236545 [Multi-domain]  Cd Length: 387  Bit Score: 45.57  E-value: 1.33e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2085259879   83 QKQHEVLTRQHEVQLQEHLKQQQEilaakRQQELEQKRKLEQQRHEEMEKQRleqQLIMLRNKEKGKESAIASTEVKLK 161
Cdd:PRK09510    78 EEQRKKKEQQQAEELQQKQAAEQE-----RLKQLEKERLAAQEQKKQAEEAA---KQAALKQKQAEEAAAKAAAAAKAK 148
TPH pfam13868
Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of ...
 83-150 2.31e-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: 44.52  E-value: 2.31e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2085259879   83 QKQHEVLTRQHEVQLQEHLKQQQEILAAKRQQELEQKRKLEQQRHEEMEKQRLEQQLIMLRNKEKGKE 150
Cdd:pfam13868   60 EEEKEEERKEERKRYRQELEEQIEEREQKRQEEYEEKLQEREQMDEIVERIQEEDQAEAEEKLEKQRQ 127
DUF5401 pfam17380
Family of unknown function (DUF5401); This is a family of unknown function found in ...
 81-164 2.93e-04

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: 45.11  E-value: 2.93e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879   81 EFQKQHEVLTRQHE-VQLQEHLKQQQ-EILaakRQQELEQKRK-LEQQRhEEMEKQRLEQQLIMLRNKE-KGKESAIAST 156
Cdd:pfam17380  436 EVRRLEEERAREMErVRLEEQERQQQvERL---RQQEEERKRKkLELEK-EKRDRKRAEEQRRKILEKElEERKQAMIEE 511


                   ....*...
gi 2085259879  157 EVKLKLQE 164
Cdd:pfam17380  512 ERKRKLLE 519
MAP7 pfam05672
MAP7 (E-MAP-115) family; The organization of microtubules varies with the cell type and is ...
 83-146 3.02e-04

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: 42.34  E-value: 3.02e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879   83 QKQHEVLTRQHEV--QLQEHLKQQQEILAAKRQQELEQKRKLEQQRHEEM---------------EKQRLEQQLIMLRNK 145
Cdd:pfam05672   50 RRAEEERARREEEarRLEEERRREEEERQRKAEEEAEEREQREQEEQERLqkqkeeaeakareeaERQRQEREKIMQQEE 129


                   .
gi 2085259879  146 E 146
Cdd:pfam05672  130 Q 130
PTZ00121 PTZ00121
MAEBL; Provisional
 80-171 3.45e-04

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 45.13  E-value: 3.45e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879   80 AEFQKQHEVLTRQHEVQLQEHLKQQQEILAAKRQQELEQKRKLEQQRH---------EEMEKQRLEQQLIMLRNKEKGK- 149
Cdd:PTZ00121  1530 AEEAKKADEAKKAEEKKKADELKKAEELKKAEEKKKAEEAKKAEEDKNmalrkaeeaKKAEEARIEEVMKLYEEEKKMKa 1609

                           90       100
                   ....*....|....*....|..
gi 2085259879  150 ESAIASTEVKLKLQEflLSKKE 171
Cdd:PTZ00121  1610 EEAKKAEEAKIKAEE--LKKAE 1629
GBP_C pfam02841
Guanylate-binding protein, C-terminal domain; Transcription of the anti-viral ...
 79-144 3.50e-04

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: 43.82  E-value: 3.50e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2085259879   79 FAEFQKQHEVLTRQHEVQLQEHLKQQQEILAAKRQQEL-EQKRKLEQ--QRHEEMEKQRLEQQLIMLRN 144
Cdd:pfam02841  223 LREKQKEEEQMMEAQERSYQEHVKQLIEKMEAEREQLLaEQERMLEHklQEQEELLKEGFKTEAESLQK 291
ERM_helical pfam20492
Ezrin/radixin/moesin, alpha-helical domain; The ERM family consists of three closely-related ...
 80-139 5.47e-04

Ezrin/radixin/moesin, alpha-helical domain; The ERM family consists of three closely-related proteins, ezrin, radixin and moesin. Ezrin was first identified as a constituent of microvilli, radixin as a barbed, end-capping actin-modulating protein from isolated junctional fractions, and moesin as a heparin binding protein. A tumour suppressor molecule responsible for neurofibromatosis type 2 (NF2) is highly similar to ERM proteins and has been designated merlin (moesin-ezrin-radixin-like protein). ERM molecules contain 3 domains, an N-terminal globular domain, an extended alpha-helical domain and a charged C-terminal domain (pfam00769). Ezrin, radixin and merlin also contain a polyproline linker region between the helical and C-terminal domains. The N-terminal domain is highly conserved and is also found in merlin, band 4.1 proteins and members of the band 4.1 superfamily, designated the FERM domain. ERM proteins crosslink actin filaments with plasma membranes. They co-localize with CD44 at actin filament plasma membrane interaction sites, associating with CD44 via their N-terminal domains and with actin filaments via their C-terminal domains. This is the alpha-helical domain, which is involved in intramolecular masking of protein-protein interaction sites, regulating the activity of this proteins.


Pssm-ID: 466641 [Multi-domain]  Cd Length: 120  Bit Score: 40.67  E-value: 5.47e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2085259879   80 AEFQKQHEVLTRQHE--VQLQEHLKQQQE--ILAAKRQQELEQ-KRKLEQQRHEEM-EKQRLEQQL 139
Cdd:pfam20492   20 EETKKAQEELEESEEtaEELEEERRQAEEeaERLEQKRQEAEEeKERLEESAEMEAeEKEQLEAEL 85
GBP_C cd16269
Guanylate-binding protein, C-terminal domain; Guanylate-binding protein (GBP), C-terminal ...
 83-145 1.34e-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: 42.18  E-value: 1.34e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2085259879   83 QKQHEVLTRQHEVQLQEHLKQQQEILAAKRQQELEQKRKLEQQR---HEEMEKQRLEQQLIMLRNK 145
Cdd:cd16269    221 QRELEQKLEDQERSYEEHLRQLKEKMEEERENLLKEQERALESKlkeQEALLEEGFKEQAELLQEE 286
Pinin_SDK_memA pfam04696
pinin/SDK/memA/ protein conserved region; Members of this family have very varied ...
 84-172 2.84e-03

pinin/SDK/memA/ protein conserved region; Members of this family have very varied localizations within the eukaryotic cell. pinin is known to localize at the desmosomes and is implicated in anchoring intermediate filaments to the desmosomal plaque. SDK2/3 is a dynamically localized nuclear protein thought to be involved in modulation of alternative pre-mRNA splicing. memA is a tumour marker preferentially expressed in human melanoma cell lines. A common feature of the members of this family is that they may all participate in regulating protein-protein interactions.


Pssm-ID: 461396 [Multi-domain]  Cd Length: 130  Bit Score: 39.20  E-value: 2.84e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879   84 KQHEVLTRQHEV--QLQEHLKQQQE---ILAAKRQQELEQKRKLEQQRHEEMEKQRLEQQLIMLRNKEkgkesaiastev 158
Cdd:pfam04696   27 KQKEKEERRAEIekRLEEKAKQEKEeleERKREEREELFEERRAEQIELRALEEKLELKELMETWHEN------------ 94

                           90
                   ....*....|....
gi 2085259879  159 KLKLQEFLLSKKEP 172
Cdd:pfam04696   95 LKALANFLKTKTEP 108
RNase_Y_N pfam12072
RNase Y N-terminal region;
80-171 3.04e-03

RNase Y N-terminal region;


Pssm-ID: 463456 [Multi-domain]  Cd Length: 201  Bit Score: 40.25  E-value: 3.04e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879   80 AEFQKqhEVLTRQHEVQLQEH-LKQQQEILaAKRQQELEQK-RKLEQQRHE-EMEKQRLEQ------QLIMLRNKEKGKE 150
Cdd:pfam12072   67 AEAER--ELKERRNELQRQERrLLQKEETL-DRKDESLEKKeESLEKKEKElEAQQQQLEEkeeeleELIEEQRQELERI 143

                           90       100
                   ....*....|....*....|.
gi 2085259879  151 SAIASTEVKlklqEFLLSKKE 171
Cdd:pfam12072  144 SGLTSEEAK----EILLDEVE 160
tolA_full TIGR02794
TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the ...
 81-171 3.92e-03

TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB. [Transport and binding proteins, Other, Cellular processes, Pathogenesis]


Pssm-ID: 274303 [Multi-domain]  Cd Length: 346  Bit Score: 40.60  E-value: 3.92e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879   81 EFQKQHEVLTRQHEVQLQEHLKQQQEILAAKRQQELEQKRKLE----QQRHEEMEKQRLEQqlimlRNKEKGKESAIAST 156
Cdd:TIGR02794   95 EQRAAAEKAAKQAEQAAKQAEEKQKQAEEAKAKQAAEAKAKAEaeaeRKAKEEAAKQAEEE-----AKAKAAAEAKKKAE 169

                           90
                   ....*....|....*
gi 2085259879  157 EVKLKLQEFLLSKKE 171
Cdd:TIGR02794  170 EAKKKAEAEAKAKAE 184
GBP_C cd16269
Guanylate-binding protein, C-terminal domain; Guanylate-binding protein (GBP), C-terminal ...
 80-169 4.60e-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: 40.25  E-value: 4.60e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879   80 AEFQKQHEVLTRQHEVqLQEHLKQQQEILAAKRQQELEQKRKLEQQRHEEMEKQRLEQQLIMlrnkekgkesaiastEVK 159
Cdd:cd16269    201 EAERAKAEAAEQERKL-LEEQQRELEQKLEDQERSYEEHLRQLKEKMEEERENLLKEQERAL---------------ESK 264

                           90
                   ....*....|
gi 2085259879  160 LKLQEFLLSK 169
Cdd:cd16269    265 LKEQEALLEE 274
fliH PRK06800
flagellar assembly protein H; Validated
 81-142 6.56e-03

flagellar assembly protein H; Validated


Pssm-ID: 180700  Cd Length: 228  Bit Score: 39.47  E-value: 6.56e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2085259879   81 EFQKQHEVLtRQHEVQLQEH---LKQQQEILAAKRQQELEQKRKLEQQRHE---EMEKQRL----EQQLIML 142
Cdd:PRK06800    35 EIQKDHEEL-LAQQKSLHKElnqLRQEQQKLERERQQLLADREQFQEHVQQqmkEIEAARQqfqkEQQETAY 105
PRK12704 PRK12704
phosphodiesterase; Provisional
 80-163 6.59e-03

phosphodiesterase; Provisional


Pssm-ID: 237177 [Multi-domain]  Cd Length: 520  Bit Score: 40.53  E-value: 6.59e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879   80 AEFQKqhEVLTRQHEVQLQEH-LKQQQEILAaKRQQELEQK-RKLEQQ-------------RHEEMEKQRLEQQLIMLR- 143
Cdd:PRK12704    71 NEFEK--ELRERRNELQKLEKrLLQKEENLD-RKLELLEKReEELEKKekeleqkqqelekKEEELEELIEEQLQELERi 147

                           90       100
                   ....*....|....*....|...
gi 2085259879  144 ---NKEKGKESAIASTEVKLKLQ 163
Cdd:PRK12704   148 sglTAEEAKEILLEKVEEEARHE 170
TPH pfam13868
Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of ...
 83-146 6.70e-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: 6.70e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2085259879   83 QKQHEVLTRQHEVQLQEHLKQQQEILAAKRQQElEQKRKLEQQRHEEMEKQRLEQQLIMLRNKE 146
Cdd:pfam13868  181 EKEREIARLRAQQEKAQDEKAERDELRAKLYQE-EQERKERQKEREEAEKKARQRQELQQAREE 243
DUF5401 pfam17380
Family of unknown function (DUF5401); This is a family of unknown function found in ...
 91-164 6.83e-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: 40.49  E-value: 6.83e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879   91 RQHEVQLQEHLKQQQEILAAKRQQEL------EQKRKLEQQRHE----EMEKQRLEQQLIMLRNK--EKGKESAIASTEV 158
Cdd:pfam17380  325 RQAEMDRQAAIYAEQERMAMERERELerirqeERKRELERIRQEeiamEISRMRELERLQMERQQknERVRQELEAARKV 404


                   ....*.
gi 2085259879  159 KLKLQE 164
Cdd:pfam17380  405 KILEEE 410
DUF5401 pfam17380
Family of unknown function (DUF5401); This is a family of unknown function found in ...
 81-147 7.25e-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: 40.49  E-value: 7.25e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2085259879   81 EFQKQHEVLTRQHEVQLQEHLKQQQEILAAKRQQELEQKRKLEQQRHEEMEKQRLE-----QQLIMLRNKEK 147
Cdd:pfam17380  399 EAARKVKILEEERQRKIQQQKVEMEQIRAEQEEARQREVRRLEEERAREMERVRLEeqerqQQVERLRQQEE 470
CCDC34 pfam13904
Coiled-coil domain-containing protein 3; This family is found in eukaryotes; it has several ...
 89-171 8.66e-03

Coiled-coil domain-containing protein 3; This family is found in eukaryotes; it has several conserved tryptophan residues. The function is not known.


Pssm-ID: 464032 [Multi-domain]  Cd Length: 221  Bit Score: 38.92  E-value: 8.66e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085259879   89 LTRQHEVQLQEHLKQQQEilAAKRQQELEQKRKLEQQRHEEMEKQRLEQQLIMLRNKEKGKESAIAST------------ 156
Cdd:pfam13904   61 LAAKQRQRQKELQAQKEE--REKEEQEAELRKRLAKEKYQEWLQRKARQQTKKREESHKQKAAESASKslakperkvsqe 138

                           90
                   ....*....|....*
gi 2085259879  157 EVKLKLQEFLLSKKE 171
Cdd:pfam13904  139 EAKEVLQEWERKKLE 153
 
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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