Citrus Sinensis ID: 027427

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220---
Protein Sequence
MSSSSSPSVTTDAETLKRNRILSSKLYFDIPIFKLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVALFPNCLVQRKVLYPFRKQVGGTILAAKLAKERGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRSCLYSGYV
Secondary Structure (PSIPRED)
ccccccccccccHHHHHHHHHcccccccccccccccEEEcccccccccccccccccccHHHHHHHHHHHHccccccccEEccccccHHHHHccccHHHHHHHHcccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHccEEEEccccccccccccccccHHHHHHHHHHHHHHHHccccEEEEEEccccccHHHHHHHcccccEEEEEEcc
Secondary Structure Prediction (SSPRO)
ccccccccccccHHHHHHcccccccccccccccccEEEEEEcccccccccccccccccHHHHHHHHHHHHccHHccEEEEccccccHHHHHHHccHHHHHHHHHccHHHHHHHHHHHHHccccccccccHHHHHEccccHHHHHHHHccccEEEEcccccHHccccccccHHHHHHHHHHHHHHHHHccccEEEEEEEEcccccccEEEEEccccEEEEEEEc
Coil and Loop (DISEMBL)
mssssspsvttdaetlkrnrilssklyfdipifklpliyspdydisflgieklhpfdsskwgricqflssegfldkncivepleaskeDLLVVHSESYLKslqsspnvsiiievppvalfpnclvqrkvLYPFRKQVGGTILAAKLAKERGwainvgggfhhcsadegggfcayADISLCIHYAFVQLNISRVMIIdldahqgnghekdfssdsrsclysgyv
Flexible Loop (DISEMBL)
mssssspsvttdaetlkrnrilssklyFDIPIFKLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVALFPNCLVQRKVLYPFRKQVGGTILAAKLAKERGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQgnghekdfssdsrsclysgyv
Low Complexity Region (SEG)
MssssspsVTTDAETLKRNRILSSKLYFDIPIFKLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVALFPNCLVQRKVLYPFRKQVGGTILAAKLAKERGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRSCLYSGYV
Disordered region (IsUnstruct)
******************NRILSSKLYFDIPIFKLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVALFPNCLVQRKVLYPFRKQVGGTILAAKLAKERGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDA***********************
Disordered Region (DISOPRED)
*****************************IPIFKLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPN*****EVPPVALFPNCLVQRKVLYPFRKQVGGTILAAKLAKERGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRSCLYSGYV
Disordered Region (DISEMBL)
**************TLKRNRILSSKLYFDIPIFKLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVALFPNCLVQRKVLYPFRKQVGGTILAAKLAKERGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQG********************
Disordered Region (DISPRO)
***************LKRNRILSSKLYFDIPIFKLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVALFPNCLVQRKVLYPFRKQVGGTILAAKLAKERGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRSCLYSGYV
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSSSSSPSVTTDAETLKRNRILSSKLYFDIPIFKLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVALFPNCLVQRKVLYPFRKQVGGTILAAKLAKERGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRSCLYSGYV
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	223	2.2.26 [Sep-21-2011]
Q944K3	387	Histone deacetylase 2 OS=	yes	no	0.991	0.571	0.719	8e-93
Q9GKU5	347	Histone deacetylase 11 OS	N/A	no	0.896	0.576	0.587	2e-68
Q96DB2	347	Histone deacetylase 11 OS	yes	no	0.896	0.576	0.587	2e-68
Q91WA3	347	Histone deacetylase 11 OS	yes	no	0.896	0.576	0.587	9e-68
P28606	300	Uncharacterized protein S	yes	no	0.780	0.58	0.296	1e-14
Q6GFX3	389	Acetoin utilization prote	yes	no	0.735	0.421	0.300	4e-14
Q8NW34	389	Acetoin utilization prote	yes	no	0.735	0.421	0.294	2e-13
Q6G8J2	389	Acetoin utilization prote	yes	no	0.735	0.421	0.294	2e-13
Q5HF39	389	Acetoin utilization prote	yes	no	0.735	0.421	0.294	3e-13
P64376	389	Acetoin utilization prote	yes	no	0.735	0.421	0.294	4e-13

>sp|Q944K3|HDA2_ARATH Histone deacetylase 2 OS=Arabidopsis thaliana GN=HDA2 PE=1 SV=2

 Score =  339 bits (870), Expect = 8e-93,   Method: Compositional matrix adjust.
 Identities = 159/221 (71%), Positives = 185/221 (83%)

Query: 2   SSSSSPSVTTDAETLKRNRILSSKLYFDIPIFKLPLIYSPDYDISFLGIEKLHPFDSSKW 61
           S  SS S+ T  E L+R RIL+SKLYFD+P+ K+ +IYS  YDISF+GIEKLHPFDSSKW
Sbjct: 41  SEISSFSMATHPEALRRERILNSKLYFDVPLSKVSIIYSSSYDISFMGIEKLHPFDSSKW 100

Query: 62  GRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVALFP 121
           GR+C+FL S+GFL++  IVEPLEASK DLLVVHSE+YL SL+SS  V+ I EV PVA FP
Sbjct: 101 GRVCKFLVSDGFLEEKAIVEPLEASKIDLLVVHSENYLNSLKSSATVARITEVAPVAFFP 160

Query: 122 NCLVQRKVLYPFRKQVGGTILAAKLAKERGWAINVGGGFHHCSADEGGGFCAYADISLCI 181
           N LVQ+KVLYPFRKQVGGTILAAKLA ERGWAIN+GGGFHHC+A+ GGGFCA+ADISLCI
Sbjct: 161 NFLVQQKVLYPFRKQVGGTILAAKLATERGWAINIGGGFHHCTAERGGGFCAFADISLCI 220

Query: 182 HYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRSCLYSGY 222
           H+AF++L ISRVMIIDLDAHQGNGHE D   D+R  +   Y
Sbjct: 221 HFAFLRLRISRVMIIDLDAHQGNGHETDLGDDNRVYILDMY 261

Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Histone deacetylases act via the formation of large multiprotein complexes.
Arabidopsis thaliana (taxid: 3702)
EC: 3EC: .EC: 5EC: .EC: 1EC: .EC: 9EC: 8

>sp|Q9GKU5|HDA11_MACFA Histone deacetylase 11 OS=Macaca fascicularis GN=HDAC11 PE=2 SV=2

 Score =  258 bits (660), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 118/201 (58%), Positives = 147/201 (73%), Gaps = 1/201 (0%)

Query: 23  SSKLYFDIPIFKLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEP 82
           +++LY  +P  + P++YSP Y+I+F+G+EKLHPFD+ KWG++  FL  E  L  + +VE 
Sbjct: 4   TTQLYQHVPETRWPIVYSPRYNITFMGLEKLHPFDAGKWGKVINFLKEEKLLSDSMLVEA 63

Query: 83  LEASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVALFPNCLVQRKVLYPFRKQVGGTIL 142
            EAS+EDLLVVH+  YL  L+ S  V+ I E+PPV   PN LVQRKVL P R Q GGTI+
Sbjct: 64  REASEEDLLVVHTRRYLNELKWSFAVATITEIPPVIFLPNFLVQRKVLRPLRTQTGGTIM 123

Query: 143 AAKLAKERGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLN-ISRVMIIDLDAH 201
           A KLA ERGWAINVGGGFHHCS+D GGGFCAYADI+L I + F ++  ISR  IIDLDAH
Sbjct: 124 AGKLAVERGWAINVGGGFHHCSSDRGGGFCAYADITLAIKFLFERVEGISRATIIDLDAH 183

Query: 202 QGNGHEKDFSSDSRSCLYSGY 222
           QGNGHE+DF  D R  +   Y
Sbjct: 184 QGNGHERDFMDDKRVYIMDVY 204

Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Histone deacetylases act via the formation of large multiprotein complexes.

Macaca fascicularis (taxid: 9541)

EC: 3

EC: .

EC: 5

EC: .

EC: 1

EC: .

EC: 9

EC: 8

>sp|Q96DB2|HDA11_HUMAN Histone deacetylase 11 OS=Homo sapiens GN=HDAC11 PE=1 SV=1

 Score =  258 bits (660), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 118/201 (58%), Positives = 147/201 (73%), Gaps = 1/201 (0%)

Query: 23  SSKLYFDIPIFKLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEP 82
           +++LY  +P  + P++YSP Y+I+F+G+EKLHPFD+ KWG++  FL  E  L  + +VE 
Sbjct: 4   TTQLYQHVPETRWPIVYSPRYNITFMGLEKLHPFDAGKWGKVINFLKEEKLLSDSMLVEA 63

Query: 83  LEASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVALFPNCLVQRKVLYPFRKQVGGTIL 142
            EAS+EDLLVVH+  YL  L+ S  V+ I E+PPV   PN LVQRKVL P R Q GGTI+
Sbjct: 64  REASEEDLLVVHTRRYLNELKWSFAVATITEIPPVIFLPNFLVQRKVLRPLRTQTGGTIM 123

Query: 143 AAKLAKERGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLN-ISRVMIIDLDAH 201
           A KLA ERGWAINVGGGFHHCS+D GGGFCAYADI+L I + F ++  ISR  IIDLDAH
Sbjct: 124 AGKLAVERGWAINVGGGFHHCSSDRGGGFCAYADITLAIKFLFERVEGISRATIIDLDAH 183

Query: 202 QGNGHEKDFSSDSRSCLYSGY 222
           QGNGHE+DF  D R  +   Y
Sbjct: 184 QGNGHERDFMDDKRVYIMDVY 204

Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Histone deacetylases act via the formation of large multiprotein complexes.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 5

EC: .

EC: 1

EC: .

EC: 9

EC: 8

>sp|Q91WA3|HDA11_MOUSE Histone deacetylase 11 OS=Mus musculus GN=Hdac11 PE=2 SV=1

 Score =  256 bits (654), Expect = 9e-68,   Method: Compositional matrix adjust.
 Identities = 118/201 (58%), Positives = 146/201 (72%), Gaps = 1/201 (0%)

Query: 23  SSKLYFDIPIFKLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEP 82
           +++LY  +P  + P++YSP Y+I+F+G+EKLHPFD+ KWG++  FL  E  L    +VE 
Sbjct: 4   ATQLYQHVPEKRWPIVYSPRYNITFMGLEKLHPFDAGKWGKVINFLKEEKLLSDGMLVEA 63

Query: 83  LEASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVALFPNCLVQRKVLYPFRKQVGGTIL 142
            EAS+EDLLVVH+  YL  L+ S  V+ I E+PPV   PN LVQRKVL P R Q GGTI+
Sbjct: 64  REASEEDLLVVHTRRYLNELKWSFVVATITEIPPVIFLPNFLVQRKVLRPLRTQTGGTIM 123

Query: 143 AAKLAKERGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLN-ISRVMIIDLDAH 201
           A KLA ERGWAINVGGGFHHCS+D GGGFCAYADI+L I + F ++  ISR  IIDLDAH
Sbjct: 124 AGKLAVERGWAINVGGGFHHCSSDRGGGFCAYADITLAIKFLFERVEGISRATIIDLDAH 183

Query: 202 QGNGHEKDFSSDSRSCLYSGY 222
           QGNGHE+DF  D R  +   Y
Sbjct: 184 QGNGHERDFMGDKRVYIMDVY 204

Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Histone deacetylases act via the formation of large multiprotein complexes.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 5

EC: .

EC: 1

EC: .

EC: 9

EC: 8

>sp|P28606|Y1628_SYNP2 Uncharacterized protein SYNPCC7002_A1628 OS=Synechococcus sp. (strain ATCC 27264 / PCC 7002 / PR-6) GN=SYNPCC7002_A1628 PE=3 SV=2

 Score = 79.7 bits (195), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 56/189 (29%), Positives = 84/189 (44%), Gaps = 15/189 (7%)

Query: 35  LPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVH 94
            P++Y PDY      I + H F   K+  +   L  +G +    + +P    +  L +VH
Sbjct: 3   FPVVYHPDY---VTPIPEEHRFPMPKFRLLHGLLLEDGVIQPEQVYQPQLPDRAWLELVH 59

Query: 95  SESYLKSL---QSSPNVSIIIEVPPVALFPNCLVQRKVLYPFRKQVGGTILAAKLAKERG 151
              Y+ +      +P     I +P    +   +VQR +       VGGTIL A+LA E G
Sbjct: 60  EPDYVTAYCQGTLTPKAQRRIGLP----WSAGVVQRTL-----TAVGGTILTAQLALEHG 110

Query: 152 WAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFS 211
            A N  GG HH     G GFC   D+++       +    R++I+DLD HQG+G    F 
Sbjct: 111 LACNTAGGTHHAFPGYGSGFCILNDLAIATRTIQQRGLAQRILIVDLDVHQGDGTAFIFQ 170

Query: 212 SDSRSCLYS 220
            D     +S
Sbjct: 171 DDPTVFTFS 179

Putative deacetylase.

Synechococcus sp. (strain ATCC 27264 / PCC 7002 / PR-6) (taxid: 32049)

>sp|Q6GFX3|ACUC_STAAR Acetoin utilization protein AcuC OS=Staphylococcus aureus (strain MRSA252) GN=acuC PE=3 SV=1

 Score = 78.2 bits (191), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 52/173 (30%), Positives = 84/173 (48%), Gaps = 9/173 (5%)

Query: 54  HPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIE 113
           HPF+  +     + L +   L    IV+P  A+ ++L+++H   Y+++++ + +  II E
Sbjct: 25  HPFNQMRLKLTTELLLNANLLSPEQIVQPRIATDDELMLIHKYDYVEAIKHASH-GIISE 83

Query: 114 VPPVALFPNCLVQRKVLYPFRKQ---VGGTILAAKLAKERGWAIN---VGGGFHHCSADE 167
              +    N     +  +  R     VGG +  A L    G A+N   +GGG HH     
Sbjct: 84  DEAMKYGLNDEENGQFKHMHRHSATIVGGALTLADLIMS-GKALNGCHLGGGLHHAQPGR 142

Query: 168 GGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRSCLYS 220
             GFC Y DI++   Y   + N  RV+IID DAH G+G +  F +D+    YS
Sbjct: 143 ASGFCIYNDIAITAQYLAKEYN-QRVLIIDTDAHHGDGTQWSFYADNHVTTYS 194

Role in growth on acetoin or butanediol. Involved in the breakdown of these compounds used as a carbon source.

Staphylococcus aureus (strain MRSA252) (taxid: 282458)

>sp|Q8NW34|ACUC_STAAW Acetoin utilization protein AcuC OS=Staphylococcus aureus (strain MW2) GN=acuC PE=3 SV=1

 Score = 75.9 bits (185), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 51/173 (29%), Positives = 82/173 (47%), Gaps = 9/173 (5%)

Query: 54  HPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIE 113
           HPF+  +     + L +   L    IV+P  A+ ++L+++H   Y+++++ + +  II E
Sbjct: 25  HPFNQMRLKLTTELLLNANLLSPEQIVQPRIATDDELMLIHKYDYVEAIKHASH-GIISE 83

Query: 114 VPPVALFPNCLVQRKVLYPFRKQ---VGGTILAAKLAKERGWAIN---VGGGFHHCSADE 167
                   N     +  +  R     VGG +  A L    G  +N   +GGG HH     
Sbjct: 84  DEAKKYGLNDEENSQFKHMHRHSATIVGGALTLADLIMS-GKVLNGCHLGGGLHHAQPGR 142

Query: 168 GGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRSCLYS 220
             GFC Y DI++   Y   + N  RV+IID DAH G+G +  F +D+    YS
Sbjct: 143 ASGFCIYNDIAITAQYLAKEYN-QRVLIIDTDAHHGDGTQWSFYADNHVTTYS 194

Role in growth on acetoin or butanediol. Involved in the breakdown of these compounds used as a carbon source.

Staphylococcus aureus (strain MW2) (taxid: 196620)

>sp|Q6G8J2|ACUC_STAAS Acetoin utilization protein AcuC OS=Staphylococcus aureus (strain MSSA476) GN=acuC PE=3 SV=1

 Score = 75.9 bits (185), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 51/173 (29%), Positives = 82/173 (47%), Gaps = 9/173 (5%)

Query: 54  HPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIE 113
           HPF+  +     + L +   L    IV+P  A+ ++L+++H   Y+++++ + +  II E
Sbjct: 25  HPFNQMRLKLTTELLLNANLLSPEQIVQPRIATDDELMLIHKYDYVEAIKHASH-GIISE 83

Query: 114 VPPVALFPNCLVQRKVLYPFRKQ---VGGTILAAKLAKERGWAIN---VGGGFHHCSADE 167
                   N     +  +  R     VGG +  A L    G  +N   +GGG HH     
Sbjct: 84  DEAKKYGLNDEENSQFKHMHRHSATIVGGALTLADLIMS-GKVLNGCHLGGGLHHAQPGR 142

Query: 168 GGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRSCLYS 220
             GFC Y DI++   Y   + N  RV+IID DAH G+G +  F +D+    YS
Sbjct: 143 ASGFCIYNDIAITAQYLAKEYN-QRVLIIDTDAHHGDGTQWSFYADNHVTTYS 194

Role in growth on acetoin or butanediol. Involved in the breakdown of these compounds used as a carbon source.

Staphylococcus aureus (strain MSSA476) (taxid: 282459)

>sp|Q5HF39|ACUC_STAAC Acetoin utilization protein AcuC OS=Staphylococcus aureus (strain COL) GN=acuC PE=3 SV=1

 Score = 75.5 bits (184), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 51/173 (29%), Positives = 82/173 (47%), Gaps = 9/173 (5%)

Query: 54  HPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIE 113
           HPF+  +     + L +   L    IV+P  A+ ++L+++H   Y+++++ + +  II E
Sbjct: 25  HPFNQMRLKLTTELLLNANLLSPEQIVQPRIATDDELMLIHKYDYVEAIKHASH-GIISE 83

Query: 114 VPPVALFPNCLVQRKVLYPFRKQ---VGGTILAAKLAKERGWAIN---VGGGFHHCSADE 167
                   N     +  +  R     VGG +  A L    G  +N   +GGG HH     
Sbjct: 84  DEAKKYGLNDEENGQFKHMHRHSATIVGGALTLADLIMS-GKVLNGCHLGGGLHHAQPGR 142

Query: 168 GGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRSCLYS 220
             GFC Y DI++   Y   + N  RV+IID DAH G+G +  F +D+    YS
Sbjct: 143 ASGFCIYNDIAITAQYLAKEYN-QRVLIIDTDAHHGDGTQWSFYADNHVTTYS 194

Role in growth on acetoin or butanediol. Involved in the breakdown of these compounds used as a carbon source.

Staphylococcus aureus (strain COL) (taxid: 93062)

>sp|P64376|ACUC_STAAN Acetoin utilization protein AcuC OS=Staphylococcus aureus (strain N315) GN=acuC PE=1 SV=1

 Score = 75.1 bits (183), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 51/173 (29%), Positives = 82/173 (47%), Gaps = 9/173 (5%)

Query: 54  HPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIE 113
           HPF+  +     + L +   L    IV+P  A+ ++L+++H   Y+++++ + +  II E
Sbjct: 25  HPFNQMRLKLTTELLLNANLLSPEQIVQPRIATGDELMLIHKYDYVEAIKHASH-GIISE 83

Query: 114 VPPVALFPNCLVQRKVLYPFRKQ---VGGTILAAKLAKERGWAIN---VGGGFHHCSADE 167
                   N     +  +  R     VGG +  A L    G  +N   +GGG HH     
Sbjct: 84  DEAKKYGLNDEENGQFKHMHRHSATIVGGALTLADLIMS-GKVLNGCHLGGGLHHAQPGR 142

Query: 168 GGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRSCLYS 220
             GFC Y DI++   Y   + N  RV+IID DAH G+G +  F +D+    YS
Sbjct: 143 ASGFCIYNDIAITAQYIAKEYN-QRVLIIDTDAHHGDGTQWSFYADNHVTTYS 194

Role in growth on acetoin or butanediol. Involved in the breakdown of these compounds used as a carbon source.

Staphylococcus aureus (strain N315) (taxid: 158879)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	223
255550810	342	histone deacetylase, putative [Ricinus c	0.991	0.646	0.787	3e-99
357437493	350	Histone deacetylase [Medicago truncatula	0.982	0.625	0.808	4e-99
388493714	348	unknown [Lotus japonicus]	0.982	0.629	0.810	9e-99
225429480	359	PREDICTED: histone deacetylase 2 [Vitis	0.937	0.582	0.808	2e-97
356564065	348	PREDICTED: histone deacetylase 2-like [G	0.977	0.626	0.779	3e-97
326522206	352	predicted protein [Hordeum vulgare subsp	0.995	0.630	0.723	3e-92
242096222	350	hypothetical protein SORBIDRAFT_10g02255	0.995	0.634	0.711	9e-92
297812823	387	hypothetical protein ARALYDRAFT_489451 [	0.991	0.571	0.723	1e-91
30690103	387	histone deacetylase 2 [Arabidopsis thali	0.991	0.571	0.719	4e-91
115468630	352	Os06g0571100 [Oryza sativa Japonica Grou	0.905	0.573	0.772	5e-91

>gi|255550810|ref|XP_002516453.1| histone deacetylase, putative [Ricinus communis] gi|223544273|gb|EEF45794.1| histone deacetylase, putative [Ricinus communis]

 Score =  367 bits (941), Expect = 3e-99,   Method: Compositional matrix adjust.
 Identities = 174/221 (78%), Positives = 195/221 (88%)

Query: 2   SSSSSPSVTTDAETLKRNRILSSKLYFDIPIFKLPLIYSPDYDISFLGIEKLHPFDSSKW 61
           S   S S T D+ TL+RNRI+SSKLYFDIP+ K+P+IYSP YDISFLGIEKLHPFDSSKW
Sbjct: 16  SRQMSSSTTADSLTLRRNRIISSKLYFDIPLSKVPIIYSPAYDISFLGIEKLHPFDSSKW 75

Query: 62  GRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVALFP 121
           GR+C+FL +EG LDKN IVEPLEASK+DLLVVH ESYL SL+SS NV+ IIEVPPV+LFP
Sbjct: 76  GRVCRFLVTEGVLDKNSIVEPLEASKDDLLVVHLESYLSSLRSSANVATIIEVPPVSLFP 135

Query: 122 NCLVQRKVLYPFRKQVGGTILAAKLAKERGWAINVGGGFHHCSADEGGGFCAYADISLCI 181
           NCLVQ+KVL+PFRKQVGGTILAAKLAKERGWAINVGGGFHHCS+ +GGGFCAYADISLCI
Sbjct: 136 NCLVQQKVLFPFRKQVGGTILAAKLAKERGWAINVGGGFHHCSSGKGGGFCAYADISLCI 195

Query: 182 HYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRSCLYSGY 222
           H+AFV+L ISRVMIIDLDAHQGNGHE DF  D+R  +   Y
Sbjct: 196 HFAFVRLRISRVMIIDLDAHQGNGHEMDFYDDNRIYILDMY 236

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357437493|ref|XP_003589022.1| Histone deacetylase [Medicago truncatula] gi|355478070|gb|AES59273.1| Histone deacetylase [Medicago truncatula]

 Score =  366 bits (939), Expect = 4e-99,   Method: Compositional matrix adjust.
 Identities = 177/219 (80%), Positives = 193/219 (88%)

Query: 4   SSSPSVTTDAETLKRNRILSSKLYFDIPIFKLPLIYSPDYDISFLGIEKLHPFDSSKWGR 63
           SS PS +   +TL RNRILS+KLYFD+P  K+PLIYS  YDISFLGIEKLHPFDSSKWGR
Sbjct: 2   SSPPSCSAADDTLMRNRILSTKLYFDVPPSKVPLIYSDSYDISFLGIEKLHPFDSSKWGR 61

Query: 64  ICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVALFPNC 123
           IC+FL S G LDKN IVEPLEASK+DLLVVHSESYL SL+ S NV+ IIEVPPVALFPNC
Sbjct: 62  ICKFLISFGVLDKNRIVEPLEASKDDLLVVHSESYLNSLKESSNVAKIIEVPPVALFPNC 121

Query: 124 LVQRKVLYPFRKQVGGTILAAKLAKERGWAINVGGGFHHCSADEGGGFCAYADISLCIHY 183
           LVQRKVL+PFRKQVGGTILAAKLAKERGWAINVGGGFHHCSA+ GGGFCAYADISLCIH+
Sbjct: 122 LVQRKVLFPFRKQVGGTILAAKLAKERGWAINVGGGFHHCSAENGGGFCAYADISLCIHF 181

Query: 184 AFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRSCLYSGY 222
           AFVQLNISRV+IIDLDAHQGNGHE DF+ D+R  +   Y
Sbjct: 182 AFVQLNISRVIIIDLDAHQGNGHEMDFADDNRVYILDMY 220

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388493714|gb|AFK34923.1| unknown [Lotus japonicus]

 Score =  365 bits (936), Expect = 9e-99,   Method: Compositional matrix adjust.
 Identities = 180/222 (81%), Positives = 192/222 (86%), Gaps = 3/222 (1%)

Query: 1   MSSSSSPSVTTDAETLKRNRILSSKLYFDIPIFKLPLIYSPDYDISFLGIEKLHPFDSSK 60
           MSSSSS    TDA  L RNRILSSKLYFD+P  K+PLIYS  YDISFLGIEKLHPFDSSK
Sbjct: 1   MSSSSS---GTDALALARNRILSSKLYFDVPPSKVPLIYSESYDISFLGIEKLHPFDSSK 57

Query: 61  WGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVALF 120
           WGRIC FL S   LDK CIVEPLEASK+DLLVVHSESYL SL+ S NV+ IIEVPPVALF
Sbjct: 58  WGRICGFLVSFDVLDKKCIVEPLEASKDDLLVVHSESYLNSLKESSNVATIIEVPPVALF 117

Query: 121 PNCLVQRKVLYPFRKQVGGTILAAKLAKERGWAINVGGGFHHCSADEGGGFCAYADISLC 180
           PNCLVQ KVL+PFRKQVGGTILA KLAKERGWAINVGGGFHHCSA++GGGFCAYADISLC
Sbjct: 118 PNCLVQNKVLFPFRKQVGGTILAVKLAKERGWAINVGGGFHHCSAEKGGGFCAYADISLC 177

Query: 181 IHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRSCLYSGY 222
           IH+AFV+LNISRVMIIDLDAHQGNGHE DF+ DSR  +   Y
Sbjct: 178 IHFAFVRLNISRVMIIDLDAHQGNGHETDFADDSRVYILDMY 219

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225429480|ref|XP_002277742.1| PREDICTED: histone deacetylase 2 [Vitis vinifera] gi|296081627|emb|CBI20632.3| unnamed protein product [Vitis vinifera]

 Score =  360 bits (925), Expect = 2e-97,   Method: Compositional matrix adjust.
 Identities = 169/209 (80%), Positives = 190/209 (90%)

Query: 14  ETLKRNRILSSKLYFDIPIFKLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGF 73
           ETL+R RILSSKLYFD+P+ K+P+IYS  YDI+FLG+EKLHPFDSSKWGRIC+FL  +G 
Sbjct: 21  ETLRRGRILSSKLYFDVPLTKVPIIYSSSYDIAFLGMEKLHPFDSSKWGRICRFLILDGA 80

Query: 74  LDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVALFPNCLVQRKVLYPF 133
           L+KN IVEPLEASK+DLLVVHSESYL SL++S NV++IIEVPPVAL PNCLVQ+KVLYPF
Sbjct: 81  LEKNHIVEPLEASKDDLLVVHSESYLNSLKTSLNVAVIIEVPPVALLPNCLVQQKVLYPF 140

Query: 134 RKQVGGTILAAKLAKERGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRV 193
           RKQVGGTILAAKLAKERGWAINVGGGFHHCSA +GGGFCAYADISLCIHYAF++LNISRV
Sbjct: 141 RKQVGGTILAAKLAKERGWAINVGGGFHHCSAGKGGGFCAYADISLCIHYAFIRLNISRV 200

Query: 194 MIIDLDAHQGNGHEKDFSSDSRSCLYSGY 222
           MIIDLDAHQGNGHE DFS+D R  +   Y
Sbjct: 201 MIIDLDAHQGNGHELDFSNDRRVYILDMY 229

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356564065|ref|XP_003550277.1| PREDICTED: histone deacetylase 2-like [Glycine max]

 Score =  360 bits (924), Expect = 3e-97,   Method: Compositional matrix adjust.
 Identities = 173/222 (77%), Positives = 192/222 (86%), Gaps = 4/222 (1%)

Query: 1   MSSSSSPSVTTDAETLKRNRILSSKLYFDIPIFKLPLIYSPDYDISFLGIEKLHPFDSSK 60
           MSSSS+     DAE L+RNRILSSKLYFD+   K+PLIYS  YDI FLGIEKLHPFDSSK
Sbjct: 1   MSSSSA----NDAEALRRNRILSSKLYFDVSPSKVPLIYSASYDIEFLGIEKLHPFDSSK 56

Query: 61  WGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVALF 120
           WGRIC FL S G LDK C+VEPLEASK+DLLVVHSESYL +L+ S  V++I+EVPPVAL 
Sbjct: 57  WGRICGFLVSFGILDKKCVVEPLEASKDDLLVVHSESYLNTLKQSSKVAMIVEVPPVALI 116

Query: 121 PNCLVQRKVLYPFRKQVGGTILAAKLAKERGWAINVGGGFHHCSADEGGGFCAYADISLC 180
           PNCLVQ+KVL+PFRKQVGGTILAAKLAKERGWAIN+GGGFHHCSA +GGGFCAYADISLC
Sbjct: 117 PNCLVQQKVLFPFRKQVGGTILAAKLAKERGWAINMGGGFHHCSAQKGGGFCAYADISLC 176

Query: 181 IHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRSCLYSGY 222
           IH+AFV+LNISRVMIIDLDAHQGNGHE DF+ DSR  +   Y
Sbjct: 177 IHFAFVRLNISRVMIIDLDAHQGNGHEMDFAYDSRVYILDMY 218

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|326522206|dbj|BAK04231.1| predicted protein [Hordeum vulgare subsp. vulgare]

 Score =  343 bits (880), Expect = 3e-92,   Method: Compositional matrix adjust.
 Identities = 162/224 (72%), Positives = 194/224 (86%), Gaps = 2/224 (0%)

Query: 1   MSSSSSPSVT--TDAETLKRNRILSSKLYFDIPIFKLPLIYSPDYDISFLGIEKLHPFDS 58
           MSSSS+ +V   T A+ L+RNRILSSKLYFD+P  K P++YS  YDI+FLGIEK+HPFDS
Sbjct: 1   MSSSSAAAVPGGTPADALRRNRILSSKLYFDVPGSKAPVVYSTAYDIAFLGIEKMHPFDS 60

Query: 59  SKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVA 118
           SKWGRIC+FL+ EG L+KN +VEPLEAS+EDLLVVH+E+YL SL+SS  V+ I+EVPP+ 
Sbjct: 61  SKWGRICRFLTKEGHLEKNRVVEPLEASQEDLLVVHTEAYLNSLRSSFRVAAIVEVPPLT 120

Query: 119 LFPNCLVQRKVLYPFRKQVGGTILAAKLAKERGWAINVGGGFHHCSADEGGGFCAYADIS 178
           L PN LVQ+++LYPFRKQVGG+IL+AKLA ERGWAINVGGGFHHCSA+EGGGFCAYADIS
Sbjct: 121 LIPNWLVQQRLLYPFRKQVGGSILSAKLALERGWAINVGGGFHHCSAEEGGGFCAYADIS 180

Query: 179 LCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRSCLYSGY 222
           LCI +AFV+LNISRVMIIDL AHQGNG+EKDF++D R  +   Y
Sbjct: 181 LCIQFAFVRLNISRVMIIDLGAHQGNGYEKDFANDGRVYILDMY 224

Source: Hordeum vulgare subsp. vulgare

Species: Hordeum vulgare

Genus: Hordeum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242096222|ref|XP_002438601.1| hypothetical protein SORBIDRAFT_10g022550 [Sorghum bicolor] gi|241916824|gb|EER89968.1| hypothetical protein SORBIDRAFT_10g022550 [Sorghum bicolor]

 Score =  342 bits (876), Expect = 9e-92,   Method: Compositional matrix adjust.
 Identities = 158/222 (71%), Positives = 191/222 (86%)

Query: 1   MSSSSSPSVTTDAETLKRNRILSSKLYFDIPIFKLPLIYSPDYDISFLGIEKLHPFDSSK 60
           M+SSSSP+ T   E L++ RILSSKLY ++P  K P++YSP YDISFLG+EKLHPFDS+K
Sbjct: 1   MASSSSPAPTLAGEALRQKRILSSKLYLEVPSSKAPVVYSPAYDISFLGLEKLHPFDSAK 60

Query: 61  WGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVALF 120
           WGRIC++L+ EG+LDK  +V+PLEA KEDLLVVH+E+YL SL+SS  VS I+EVPPV+L 
Sbjct: 61  WGRICRYLTREGYLDKKRMVDPLEACKEDLLVVHTEAYLNSLKSSFRVSNIVEVPPVSLV 120

Query: 121 PNCLVQRKVLYPFRKQVGGTILAAKLAKERGWAINVGGGFHHCSADEGGGFCAYADISLC 180
           PN +V +K+LYPFRKQVGG+IL+AKLA ERGWAINVGGGFHHCSADEGGGFCAYADISLC
Sbjct: 121 PNWIVHKKLLYPFRKQVGGSILSAKLALERGWAINVGGGFHHCSADEGGGFCAYADISLC 180

Query: 181 IHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRSCLYSGY 222
           I +AF +LNIS V+IIDLDAHQGNGHEKDF++D R  ++  Y
Sbjct: 181 IQFAFARLNISSVLIIDLDAHQGNGHEKDFANDGRVYIFDMY 222

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297812823|ref|XP_002874295.1| hypothetical protein ARALYDRAFT_489451 [Arabidopsis lyrata subsp. lyrata] gi|297320132|gb|EFH50554.1| hypothetical protein ARALYDRAFT_489451 [Arabidopsis lyrata subsp. lyrata]

 Score =  341 bits (875), Expect = 1e-91,   Method: Compositional matrix adjust.
 Identities = 160/221 (72%), Positives = 186/221 (84%)

Query: 2   SSSSSPSVTTDAETLKRNRILSSKLYFDIPIFKLPLIYSPDYDISFLGIEKLHPFDSSKW 61
           S  SS S+ T  E L+R RIL+SKLYFD+P+ K+ +IYS  YDISF+GIEKLHPFDSSKW
Sbjct: 41  SEMSSFSMATHPEALRRERILNSKLYFDVPLSKVSIIYSSAYDISFMGIEKLHPFDSSKW 100

Query: 62  GRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVALFP 121
           GR+C+FL S+GFL++  IVEPLEASK DLLVVHSE+YL SL+SS  V+ I EVPPVA FP
Sbjct: 101 GRVCKFLVSDGFLEEKAIVEPLEASKIDLLVVHSENYLNSLKSSATVARITEVPPVAFFP 160

Query: 122 NCLVQRKVLYPFRKQVGGTILAAKLAKERGWAINVGGGFHHCSADEGGGFCAYADISLCI 181
           N LVQ+KVLYPFRKQVGGTILAAKLA ERGWAIN+GGGFHHC+A+ GGGFCA+ADISLCI
Sbjct: 161 NFLVQQKVLYPFRKQVGGTILAAKLATERGWAINIGGGFHHCTAERGGGFCAFADISLCI 220

Query: 182 HYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRSCLYSGY 222
           H+AF++L ISRVMIIDLDAHQGNGHE D   D+R  +   Y
Sbjct: 221 HFAFLRLRISRVMIIDLDAHQGNGHETDLGDDNRVYILDMY 261

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|30690103|ref|NP_568480.2| histone deacetylase 2 [Arabidopsis thaliana] gi|145558941|sp|Q944K3.2|HDA2_ARATH RecName: Full=Histone deacetylase 2 gi|332006134|gb|AED93517.1| histone deacetylase 2 [Arabidopsis thaliana]

 Score =  339 bits (870), Expect = 4e-91,   Method: Compositional matrix adjust.
 Identities = 159/221 (71%), Positives = 185/221 (83%)

Query: 2   SSSSSPSVTTDAETLKRNRILSSKLYFDIPIFKLPLIYSPDYDISFLGIEKLHPFDSSKW 61
           S  SS S+ T  E L+R RIL+SKLYFD+P+ K+ +IYS  YDISF+GIEKLHPFDSSKW
Sbjct: 41  SEISSFSMATHPEALRRERILNSKLYFDVPLSKVSIIYSSSYDISFMGIEKLHPFDSSKW 100

Query: 62  GRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVALFP 121
           GR+C+FL S+GFL++  IVEPLEASK DLLVVHSE+YL SL+SS  V+ I EV PVA FP
Sbjct: 101 GRVCKFLVSDGFLEEKAIVEPLEASKIDLLVVHSENYLNSLKSSATVARITEVAPVAFFP 160

Query: 122 NCLVQRKVLYPFRKQVGGTILAAKLAKERGWAINVGGGFHHCSADEGGGFCAYADISLCI 181
           N LVQ+KVLYPFRKQVGGTILAAKLA ERGWAIN+GGGFHHC+A+ GGGFCA+ADISLCI
Sbjct: 161 NFLVQQKVLYPFRKQVGGTILAAKLATERGWAINIGGGFHHCTAERGGGFCAFADISLCI 220

Query: 182 HYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRSCLYSGY 222
           H+AF++L ISRVMIIDLDAHQGNGHE D   D+R  +   Y
Sbjct: 221 HFAFLRLRISRVMIIDLDAHQGNGHETDLGDDNRVYILDMY 261

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|115468630|ref|NP_001057914.1| Os06g0571100 [Oryza sativa Japonica Group] gi|54291235|dbj|BAD61930.1| putative HDA2 [Oryza sativa Japonica Group] gi|113595954|dbj|BAF19828.1| Os06g0571100 [Oryza sativa Japonica Group] gi|125555796|gb|EAZ01402.1| hypothetical protein OsI_23434 [Oryza sativa Indica Group] gi|215704748|dbj|BAG94776.1| unnamed protein product [Oryza sativa Japonica Group]

 Score =  339 bits (870), Expect = 5e-91,   Method: Compositional matrix adjust.
 Identities = 156/202 (77%), Positives = 183/202 (90%)

Query: 14  ETLKRNRILSSKLYFDIPIFKLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGF 73
           + L+R+RILSSKLY D+P  K P++YSP YDI+FLGIEKLHPFDSSKWGRIC+FL+ EG 
Sbjct: 16  DPLRRDRILSSKLYLDVPGSKAPVVYSPAYDIAFLGIEKLHPFDSSKWGRICKFLTKEGH 75

Query: 74  LDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVALFPNCLVQRKVLYPF 133
           L+KN +VEPLEA+K+DLLVVHSESYL SL+SS  V+ I+E+PPVA  PN LVQ+K+LYPF
Sbjct: 76  LEKNRVVEPLEATKDDLLVVHSESYLNSLKSSLKVASIVELPPVAFIPNWLVQQKLLYPF 135

Query: 134 RKQVGGTILAAKLAKERGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRV 193
           RKQVGG+IL+AKLA ERGWAINVGGGFHHCSA++GGGFCAYADISLCI +AFV+LNISRV
Sbjct: 136 RKQVGGSILSAKLALERGWAINVGGGFHHCSAEQGGGFCAYADISLCIQFAFVRLNISRV 195

Query: 194 MIIDLDAHQGNGHEKDFSSDSR 215
           MIIDLDAHQGNGHEKDF++D R
Sbjct: 196 MIIDLDAHQGNGHEKDFANDGR 217

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	223
TAIR|locus:2180657	387	HDA2 "AT5G26040" [Arabidopsis	0.959	0.552	0.724	3.1e-83
UNIPROTKB|Q96DB2	347	HDAC11 "Histone deacetylase 11	0.896	0.576	0.587	1.6e-61
UNIPROTKB|Q9GKU5	347	HDAC11 "Histone deacetylase 11	0.896	0.576	0.587	1.6e-61
UNIPROTKB|I3LTU6	275	LOC100738481 "Uncharacterized	0.896	0.727	0.587	3.4e-61
MGI|MGI:2385252	347	Hdac11 "histone deacetylase 11	0.896	0.576	0.587	3.4e-61
RGD|1311706	347	Hdac11 "histone deacetylase 11	0.896	0.576	0.587	3.4e-61
UNIPROTKB|F1NYW6	357	HDAC11 "Uncharacterized protei	0.892	0.557	0.57	2.4e-60
UNIPROTKB|F1MWX4	386	HDAC11 "Uncharacterized protei	0.892	0.515	0.575	6.4e-60
ZFIN|ZDB-GENE-040704-7	366	hdac11 "histone deacetylase 11	0.892	0.543	0.565	1.7e-59
UNIPROTKB|B5MCV5	204	HDAC11 "Histone deacetylase 11	0.784	0.857	0.613	6.1e-55

TAIR|locus:2180657 HDA2 "AT5G26040" [Arabidopsis thaliana (taxid:3702)]

 Score = 834 (298.6 bits), Expect = 3.1e-83, P = 3.1e-83
 Identities = 155/214 (72%), Positives = 181/214 (84%)

Query:     9 VTTDAETLKRNRILSSKLYFDIPIFKLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFL 68
             + T  E L+R RIL+SKLYFD+P+ K+ +IYS  YDISF+GIEKLHPFDSSKWGR+C+FL
Sbjct:    48 MATHPEALRRERILNSKLYFDVPLSKVSIIYSSSYDISFMGIEKLHPFDSSKWGRVCKFL 107

Query:    69 SSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVALFPNCLVQRK 128
              S+GFL++  IVEPLEASK DLLVVHSE+YL SL+SS  V+ I EV PVA FPN LVQ+K
Sbjct:   108 VSDGFLEEKAIVEPLEASKIDLLVVHSENYLNSLKSSATVARITEVAPVAFFPNFLVQQK 167

Query:   129 VLYPFRKQVGGTILAAKLAKERGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQL 188
             VLYPFRKQVGGTILAAKLA ERGWAIN+GGGFHHC+A+ GGGFCA+ADISLCIH+AF++L
Sbjct:   168 VLYPFRKQVGGTILAAKLATERGWAINIGGGFHHCTAERGGGFCAFADISLCIHFAFLRL 227

Query:   189 NISRVMIIDLDAHQGNGHEKDFSSDSRSCLYSGY 222
              ISRVMIIDLDAHQGNGHE D   D+R  +   Y
Sbjct:   228 RISRVMIIDLDAHQGNGHETDLGDDNRVYILDMY 261

GO:0004407 "histone deacetylase activity" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|Q96DB2 HDAC11 "Histone deacetylase 11" [Homo sapiens (taxid:9606)]

 Score = 629 (226.5 bits), Expect = 1.6e-61, P = 1.6e-61
 Identities = 118/201 (58%), Positives = 147/201 (73%)

Query:    23 SSKLYFDIPIFKLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEP 82
             +++LY  +P  + P++YSP Y+I+F+G+EKLHPFD+ KWG++  FL  E  L  + +VE 
Sbjct:     4 TTQLYQHVPETRWPIVYSPRYNITFMGLEKLHPFDAGKWGKVINFLKEEKLLSDSMLVEA 63

Query:    83 LEASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVALFPNCLVQRKVLYPFRKQVGGTIL 142
              EAS+EDLLVVH+  YL  L+ S  V+ I E+PPV   PN LVQRKVL P R Q GGTI+
Sbjct:    64 REASEEDLLVVHTRRYLNELKWSFAVATITEIPPVIFLPNFLVQRKVLRPLRTQTGGTIM 123

Query:   143 AAKLAKERGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLN-ISRVMIIDLDAH 201
             A KLA ERGWAINVGGGFHHCS+D GGGFCAYADI+L I + F ++  ISR  IIDLDAH
Sbjct:   124 AGKLAVERGWAINVGGGFHHCSSDRGGGFCAYADITLAIKFLFERVEGISRATIIDLDAH 183

Query:   202 QGNGHEKDFSSDSRSCLYSGY 222
             QGNGHE+DF  D R  +   Y
Sbjct:   184 QGNGHERDFMDDKRVYIMDVY 204

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0032041 "NAD-dependent histone deacetylase activity (H3-K14 specific)" evidence=IEA

GO:0046969 "NAD-dependent histone deacetylase activity (H3-K9 specific)" evidence=IEA

GO:0046970 "NAD-dependent histone deacetylase activity (H4-K16 specific)" evidence=IEA

GO:0097372 "NAD-dependent histone deacetylase activity (H3-K18 specific)" evidence=IEA

GO:0014003 "oligodendrocyte development" evidence=IEA

GO:0000118 "histone deacetylase complex" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0016568 "chromatin modification" evidence=TAS

GO:0004407 "histone deacetylase activity" evidence=IDA

GO:0016575 "histone deacetylation" evidence=IDA

GO:0008134 "transcription factor binding" evidence=TAS

GO:0005886 "plasma membrane" evidence=IDA

UNIPROTKB|Q9GKU5 HDAC11 "Histone deacetylase 11" [Macaca fascicularis (taxid:9541)]

 Score = 629 (226.5 bits), Expect = 1.6e-61, P = 1.6e-61
 Identities = 118/201 (58%), Positives = 147/201 (73%)

Query:    23 SSKLYFDIPIFKLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEP 82
             +++LY  +P  + P++YSP Y+I+F+G+EKLHPFD+ KWG++  FL  E  L  + +VE 
Sbjct:     4 TTQLYQHVPETRWPIVYSPRYNITFMGLEKLHPFDAGKWGKVINFLKEEKLLSDSMLVEA 63

Query:    83 LEASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVALFPNCLVQRKVLYPFRKQVGGTIL 142
              EAS+EDLLVVH+  YL  L+ S  V+ I E+PPV   PN LVQRKVL P R Q GGTI+
Sbjct:    64 REASEEDLLVVHTRRYLNELKWSFAVATITEIPPVIFLPNFLVQRKVLRPLRTQTGGTIM 123

Query:   143 AAKLAKERGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLN-ISRVMIIDLDAH 201
             A KLA ERGWAINVGGGFHHCS+D GGGFCAYADI+L I + F ++  ISR  IIDLDAH
Sbjct:   124 AGKLAVERGWAINVGGGFHHCSSDRGGGFCAYADITLAIKFLFERVEGISRATIIDLDAH 183

Query:   202 QGNGHEKDFSSDSRSCLYSGY 222
             QGNGHE+DF  D R  +   Y
Sbjct:   184 QGNGHERDFMDDKRVYIMDVY 204

GO:0000118 "histone deacetylase complex" evidence=TAS

GO:0004407 "histone deacetylase activity" evidence=TAS

GO:0005634 "nucleus" evidence=TAS

GO:0005737 "cytoplasm" evidence=TAS

GO:0008134 "transcription factor binding" evidence=TAS

GO:0016568 "chromatin modification" evidence=TAS

GO:0016575 "histone deacetylation" evidence=TAS

UNIPROTKB|I3LTU6 LOC100738481 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 626 (225.4 bits), Expect = 3.4e-61, P = 3.4e-61
 Identities = 118/201 (58%), Positives = 146/201 (72%)

Query:    23 SSKLYFDIPIFKLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEP 82
             +++LY  +P  + P++YSP Y+I+F+G+EKLHPFD+ KWG++  FL  E  L  + +VE 
Sbjct:     3 TTQLYQHVPETRWPIVYSPRYNITFMGLEKLHPFDAGKWGKVISFLKEEKLLTDSMLVEA 62

Query:    83 LEASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVALFPNCLVQRKVLYPFRKQVGGTIL 142
              EAS EDLLVVH+  YL  L+ S  V+ I E+PPV   PN LVQRKVL P R Q GGTI+
Sbjct:    63 REASDEDLLVVHTRRYLNELKWSFAVATITEIPPVIFLPNFLVQRKVLKPLRTQTGGTIM 122

Query:   143 AAKLAKERGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLN-ISRVMIIDLDAH 201
             A KLA ERGWAINVGGGFHHCS+D GGGFCAYADI+L I + F ++  ISR  IIDLDAH
Sbjct:   123 AGKLAVERGWAINVGGGFHHCSSDRGGGFCAYADITLAIKFLFERVEGISRATIIDLDAH 182

Query:   202 QGNGHEKDFSSDSRSCLYSGY 222
             QGNGHE+DF  D R  +   Y
Sbjct:   183 QGNGHERDFMGDKRVYIMDVY 203

GO:0016787 "hydrolase activity" evidence=IEA

MGI|MGI:2385252 Hdac11 "histone deacetylase 11" [Mus musculus (taxid:10090)]

 Score = 626 (225.4 bits), Expect = 3.4e-61, P = 3.4e-61
 Identities = 118/201 (58%), Positives = 146/201 (72%)

Query:    23 SSKLYFDIPIFKLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEP 82
             +++LY  +P  + P++YSP Y+I+F+G+EKLHPFD+ KWG++  FL  E  L    +VE 
Sbjct:     4 ATQLYQHVPEKRWPIVYSPRYNITFMGLEKLHPFDAGKWGKVINFLKEEKLLSDGMLVEA 63

Query:    83 LEASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVALFPNCLVQRKVLYPFRKQVGGTIL 142
              EAS+EDLLVVH+  YL  L+ S  V+ I E+PPV   PN LVQRKVL P R Q GGTI+
Sbjct:    64 REASEEDLLVVHTRRYLNELKWSFVVATITEIPPVIFLPNFLVQRKVLRPLRTQTGGTIM 123

Query:   143 AAKLAKERGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLN-ISRVMIIDLDAH 201
             A KLA ERGWAINVGGGFHHCS+D GGGFCAYADI+L I + F ++  ISR  IIDLDAH
Sbjct:   124 AGKLAVERGWAINVGGGFHHCSSDRGGGFCAYADITLAIKFLFERVEGISRATIIDLDAH 183

Query:   202 QGNGHEKDFSSDSRSCLYSGY 222
             QGNGHE+DF  D R  +   Y
Sbjct:   184 QGNGHERDFMGDKRVYIMDVY 204

GO:0000118 "histone deacetylase complex" evidence=ISO;TAS

GO:0004407 "histone deacetylase activity" evidence=ISO;TAS

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=ISO;TAS

GO:0005737 "cytoplasm" evidence=TAS

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0008134 "transcription factor binding" evidence=TAS

GO:0014003 "oligodendrocyte development" evidence=ISO

GO:0016568 "chromatin modification" evidence=TAS

GO:0016575 "histone deacetylation" evidence=ISO

GO:0016787 "hydrolase activity" evidence=IEA

GO:0031078 "histone deacetylase activity (H3-K14 specific)" evidence=IEA

GO:0032041 "NAD-dependent histone deacetylase activity (H3-K14 specific)" evidence=IEA

GO:0032129 "histone deacetylase activity (H3-K9 specific)" evidence=IEA

GO:0034739 "histone deacetylase activity (H4-K16 specific)" evidence=IEA

GO:0046969 "NAD-dependent histone deacetylase activity (H3-K9 specific)" evidence=IEA

GO:0046970 "NAD-dependent histone deacetylase activity (H4-K16 specific)" evidence=IEA

GO:0070932 "histone H3 deacetylation" evidence=IEA

GO:0070933 "histone H4 deacetylation" evidence=IEA

RGD|1311706 Hdac11 "histone deacetylase 11" [Rattus norvegicus (taxid:10116)]

 Score = 626 (225.4 bits), Expect = 3.4e-61, P = 3.4e-61
 Identities = 118/201 (58%), Positives = 146/201 (72%)

Query:    23 SSKLYFDIPIFKLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEP 82
             +++LY  +P  + P++YSP Y+I+F+G+EKLHPFD+ KWG++  FL  E  L    +VE 
Sbjct:     4 ATQLYQHVPEKRWPIVYSPRYNITFMGLEKLHPFDAGKWGKVINFLKEEKLLSDGMLVEA 63

Query:    83 LEASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVALFPNCLVQRKVLYPFRKQVGGTIL 142
              EAS+EDLLVVH+  YL  L+ S  V+ I E+PPV   PN LVQRKVL P R Q GGTI+
Sbjct:    64 REASEEDLLVVHTRRYLNELKWSFVVATITEIPPVIFLPNFLVQRKVLRPLRTQTGGTIM 123

Query:   143 AAKLAKERGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLN-ISRVMIIDLDAH 201
             A KLA ERGWAINVGGGFHHCS+D GGGFCAYADI+L I + F ++  ISR  IIDLDAH
Sbjct:   124 AGKLAVERGWAINVGGGFHHCSSDRGGGFCAYADITLAIKFLFERVEGISRATIIDLDAH 183

Query:   202 QGNGHEKDFSSDSRSCLYSGY 222
             QGNGHE+DF  D R  +   Y
Sbjct:   184 QGNGHERDFMGDKRVYIMDVY 204

GO:0000118 "histone deacetylase complex" evidence=IEA;ISO

GO:0003674 "molecular_function" evidence=ND

GO:0004407 "histone deacetylase activity" evidence=IEA;ISO

GO:0005634 "nucleus" evidence=ISO;IDA

GO:0005886 "plasma membrane" evidence=IEA;ISO

GO:0014003 "oligodendrocyte development" evidence=IMP

GO:0016575 "histone deacetylation" evidence=ISO

UNIPROTKB|F1NYW6 HDAC11 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 618 (222.6 bits), Expect = 2.4e-60, P = 2.4e-60
 Identities = 114/200 (57%), Positives = 147/200 (73%)

Query:    24 SKLYFDIPIFKLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPL 83
             ++LY  +P    P++YSPDY+I+F+G+EKLHPFD+ KWG++  FL  E  +  + IV+  
Sbjct:     4 TELYEGVPPTCWPIVYSPDYNITFMGLEKLHPFDAGKWGKVINFLKEEKLIGDDLIVQAR 63

Query:    84 EASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVALFPNCLVQRKVLYPFRKQVGGTILA 143
             EA+ EDLLVVH+  YL  L+ S  V+ I E+PPV   PN LVQRKVL P R Q GGTI+A
Sbjct:    64 EATDEDLLVVHTRRYLNKLKWSFVVATITEIPPVLFLPNFLVQRKVLKPLRTQTGGTIMA 123

Query:   144 AKLAKERGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQL-NISRVMIIDLDAHQ 202
              KLA +RGWAINVGGGFHHCS+D+GGGFCAYADI+L I + F ++  +S+  IIDLDAHQ
Sbjct:   124 GKLAVDRGWAINVGGGFHHCSSDKGGGFCAYADITLAIKFLFERVPGVSKATIIDLDAHQ 183

Query:   203 GNGHEKDFSSDSRSCLYSGY 222
             GNGHE+DF +D R  +   Y
Sbjct:   184 GNGHERDFMNDHRVYIMDAY 203

GO:0000118 "histone deacetylase complex" evidence=IEA

GO:0004407 "histone deacetylase activity" evidence=IEA

GO:0005886 "plasma membrane" evidence=IEA

UNIPROTKB|F1MWX4 HDAC11 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 614 (221.2 bits), Expect = 6.4e-60, P = 6.4e-60
 Identities = 115/200 (57%), Positives = 144/200 (72%)

Query:    24 SKLYFDIPIFKLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPL 83
             ++LY  +P  + P++YSP Y+I+FLG+EKLHPFD+ KWG++   L  E  L  + +VE  
Sbjct:     4 TQLYQHVPDSRWPIVYSPRYNITFLGLEKLHPFDAGKWGKVISLLKEEKLLSDSMLVEAR 63

Query:    84 EASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVALFPNCLVQRKVLYPFRKQVGGTILA 143
             EAS EDLLVVH+  YL  L+ S  V+ I E+PPV   PN LVQRKVL P R Q GGTI+A
Sbjct:    64 EASDEDLLVVHTRRYLNELKWSFAVATITEIPPVIFLPNFLVQRKVLRPLRTQTGGTIMA 123

Query:   144 AKLAKERGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLN-ISRVMIIDLDAHQ 202
              KLA +RGWAINVGGGFHHCS+D GGGFCAYADI+L I + F ++  IS+  I+DLDAHQ
Sbjct:   124 GKLAVDRGWAINVGGGFHHCSSDRGGGFCAYADITLAIKFLFDRVEGISKATIVDLDAHQ 183

Query:   203 GNGHEKDFSSDSRSCLYSGY 222
             GNGHE+DF  D R  +   Y
Sbjct:   184 GNGHERDFMGDKRVYIMDVY 203

GO:0005886 "plasma membrane" evidence=IEA

GO:0004407 "histone deacetylase activity" evidence=IEA

GO:0000118 "histone deacetylase complex" evidence=IEA

ZFIN|ZDB-GENE-040704-7 hdac11 "histone deacetylase 11" [Danio rerio (taxid:7955)]

 Score = 610 (219.8 bits), Expect = 1.7e-59, P = 1.7e-59
 Identities = 113/200 (56%), Positives = 147/200 (73%)

Query:    24 SKLYFDIPIFKLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPL 83
             ++LY ++P   LP++YSP+Y+I+F+G+EKLHPFD+ KWG++ +FL  E F+    IV   
Sbjct:    16 TELYAEVPASCLPIVYSPEYNITFMGLEKLHPFDAGKWGKVIRFLKEEQFITDEIIVLAR 75

Query:    84 EASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVALFPNCLVQRKVLYPFRKQVGGTILA 143
             EAS+ DLLVVH+  YL  L+ S  V+ I E+PP+   PN LVQRKVL P R Q GGTI+A
Sbjct:    76 EASEADLLVVHTARYLNRLKWSLVVATITEIPPLLFLPNFLVQRKVLRPLRTQTGGTIMA 135

Query:   144 AKLAKERGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLN-ISRVMIIDLDAHQ 202
              KLA +RGWAINVGGGFHHCS+D+GGGFCAYADI+L I + F ++  ++   IIDLDAHQ
Sbjct:   136 GKLAIDRGWAINVGGGFHHCSSDKGGGFCAYADITLAIKFLFERVEGVASATIIDLDAHQ 195

Query:   203 GNGHEKDFSSDSRSCLYSGY 222
             GNGHE+DF  D R  +   Y
Sbjct:   196 GNGHERDFLEDRRVYIMDVY 215

GO:0016787 "hydrolase activity" evidence=IEA

UNIPROTKB|B5MCV5 HDAC11 "Histone deacetylase 11" [Homo sapiens (taxid:9606)]

 Score = 567 (204.7 bits), Expect = 6.1e-55, P = 6.1e-55
 Identities = 108/176 (61%), Positives = 128/176 (72%)

Query:    48 LGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPN 107
             +G+EKLHPFD+ KWG++  FL  E  L  + +VE  EAS+EDLLVVH+  YL  L+ S  
Sbjct:     1 MGLEKLHPFDAGKWGKVINFLKEEKLLSDSMLVEAREASEEDLLVVHTRRYLNELKWSFA 60

Query:   108 VSIIIEVPPVALFPNCLVQRKVLYPFRKQVGGTILAAKLAKERGWAINVGGGFHHCSADE 167
             V+ I E+PPV   PN LVQRKVL P R Q GGTI+A KLA ERGWAINVGGGFHHCS+D 
Sbjct:    61 VATITEIPPVIFLPNFLVQRKVLRPLRTQTGGTIMAGKLAVERGWAINVGGGFHHCSSDR 120

Query:   168 GGGFCAYADISLCIHYAFVQLN-ISRVMIIDLDAHQGNGHEKDFSSDSRSCLYSGY 222
             GGGFCAYADI+L I + F ++  ISR  IIDLDAHQGNGHE+DF  D R  +   Y
Sbjct:   121 GGGFCAYADITLAIKFLFERVEGISRATIIDLDAHQGNGHERDFMDDKRVYIMDVY 176

GO:0016787 "hydrolase activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0014003 "oligodendrocyte development" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q944K3	HDA2_ARATH	3, ., 5, ., 1, ., 9, 8	0.7194	0.9910	0.5710	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.5.1.98	0.914
3rd Layer	3.5.1	0.921

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00032175001 SubName- Full=Chromosome chr4 scaffold_6, whole genome shotgun sequence; (351 aa) (Vitis vinifera)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	223
cd09993	275	cd09993, HDAC_classIV, Histone deacetylase class I	6e-72
cd09301	279	cd09301, HDAC, Histone deacetylase (HDAC) classes	1e-42
pfam00850	300	pfam00850, Hist_deacetyl, Histone deacetylase doma	2e-41
COG0123	340	COG0123, AcuC, Deacetylases, including yeast histo	1e-27
cd09994	313	cd09994, HDAC_AcuC_like, Class I histone deacetyla	2e-24
cd10000	364	cd10000, HDAC8, Histone deacetylase 8 (HDAC8)	2e-19
cd09991	306	cd09991, HDAC_classI, Class I histone deacetylases	3e-17
cd09992	291	cd09992, HDAC_classII, Histone deacetylases and hi	8e-15
cd11682	337	cd11682, HDAC6-dom1, Histone deacetylase 6, domain	9e-15
cd09996	359	cd09996, HDAC_classII_1, Histone deacetylases and	7e-14
cd11680	294	cd11680, HDAC_Hos1, Class I histone deacetylases H	1e-12
cd11599	288	cd11599, HDAC_classII_2, Histone deacetylases and	3e-11
cd10002	336	cd10002, HDAC10_HDAC6-dom1, Histone deacetylase 6,	3e-11
cd10011	366	cd10011, HDAC2, Histone deacetylase 2 (HDAC2)	7e-11
cd10003	350	cd10003, HDAC6-dom2, Histone deacetylase 6, domain	1e-10
cd10010	371	cd10010, HDAC1, Histone deacetylase 1 (HDAC1)	2e-10
cd11598	311	cd11598, HDAC_Hos2, Class I histone deacetylases i	2e-10
cd10009	379	cd10009, HDAC9, Histone deacetylase 9	5e-10
cd11683	337	cd11683, HDAC10, Histone deacetylase 10	2e-09
cd11600	313	cd11600, HDAC_Clr3, Class II Histone deacetylase C	5e-09
cd09998	353	cd09998, HDAC_Hos3, Class II histone deacetylases	4e-08
cd10005	381	cd10005, HDAC3, Histone deacetylase 3 (HDAC3)	7e-08
PTZ00346	429	PTZ00346, PTZ00346, histone deacetylase; Provision	1e-07
PTZ00063	436	PTZ00063, PTZ00063, histone deacetylase; Provision	1e-07
cd11681	377	cd11681, HDAC_classIIa, Histone deacetylases, clas	4e-07
cd10004	375	cd10004, RPD3-like, reduced potassium dependency-3	5e-07
cd10007	420	cd10007, HDAC5, Histone deacetylase 5	7e-06
cd10006	409	cd10006, HDAC4, Histone deacetylase 4	1e-05
cd10001	298	cd10001, HDAC_classII_APAH, Histone deacetylase cl	2e-05
cd10008	378	cd10008, HDAC7, Histone deacetylase 7	3e-04

>gnl|CDD|212519 cd09993, HDAC_classIV, Histone deacetylase class IV also known as histone deacetylase 11

 Score =  219 bits (561), Expect = 6e-72
 Identities = 66/162 (40%), Positives = 88/162 (54%), Gaps = 6/162 (3%)

Query: 54  HPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIE 113
           H F   K+G + + L  EG +    IVEP  A++EDLL VH   YL+SL+S     +  E
Sbjct: 1   HRFPMRKYGLLREALLEEGLVLPEDIVEPEPATREDLLRVHDPEYLESLKSG---ELSRE 57

Query: 114 VPPVALFPNCLVQRKVLYPFRKQVGGTILAAKLAKERGWAINVGGGFHHCSADEGGGFCA 173
                 FP      +++   R  VGGTILAA+LA E G AIN+ GG HH   D G GFC 
Sbjct: 58  EIRRIGFPWSP---ELVERTRLAVGGTILAARLALEHGLAINLAGGTHHAFPDRGEGFCV 114

Query: 174 YADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSR 215
           + DI++       +  + RV+I+DLD HQGNG    F+ D  
Sbjct: 115 FNDIAIAARVLLAEGLVRRVLIVDLDVHQGNGTAAIFADDPS 156

Class IV histone deacetylases (HDAC11; EC 3.5.1.98) are predicted Zn-dependent enzymes. This class includes animal HDAC11, plant HDA2 and related bacterial deacetylases. Enzymes in this subfamily participate in regulation of a number of different processes through protein modification (deacetylation). They catalyze hydrolysis of N(6)-acetyl-lysine of histones (or other proteins) to yield a deacetylated proteins. Histone deacetylases often act as members of large multi-protein complexes such as mSin3A or SMRT/N-CoR. Human HDAC11 does not associate with them but can interact with HDAC6 in vivo. It has been suggested that HDAC11 and HDAC6 may use non-histone proteins as their substrates and play a role other than to directly modulate chromatin structure. In normal tissues, expression of HDAC11 is limited to kidney, heart, brain, skeletal muscle and testis, suggesting that its function might be tissue-specific. In mammals, HDAC11 proteins are known to be involved in progression of various tumors. HDAC11 plays an essential role in regulating OX40 ligand (OX40L) expression in Hodgkin lymphoma (HL); selective inhibition of HDAC11 expression significantly up-regulates OX40L and induces apoptosis in HL cell lines. Thus, inhibition of HDAC11 could be a therapeutic drug option for antitumor immune response in HL patients. Length = 275

>gnl|CDD|212512 cd09301, HDAC, Histone deacetylase (HDAC) classes I, II, IV and related proteins

 Score =  144 bits (366), Expect = 1e-42
 Identities = 59/160 (36%), Positives = 83/160 (51%), Gaps = 6/160 (3%)

Query: 60  KWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVAL 119
           +   + + L   G   K  ++E  EA++E LL VH+E YL  L+++  V+ I E  PV  
Sbjct: 1   RIRDLIEALKELGLRPKIELIECREATEELLLKVHTEEYLNELKANFAVATITESKPVIF 60

Query: 120 FPNCLVQRKVLYPFRKQVGGTILAAKLA----KERGWAINVGGGFHHCSADEGGGFCAYA 175
            PN  VQR      R   GG + AA+L      ER +A+ VG G HH       GFC + 
Sbjct: 61  GPNFPVQRHYFRGARLSTGGVVEAAELVAKGELERAFAV-VGAGGHHAGKSRAWGFCYFN 119

Query: 176 DISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSR 215
           D+ L I +   +  ISR++IID DAH G+G  + F  D R
Sbjct: 120 DVVLAIKFLR-ERGISRILIIDTDAHHGDGTREAFYDDDR 158

The HDAC/HDAC-like family includes Zn-dependent histone deacetylase classes I, II and IV (class III HDACs, also called sirtuins, are NAD-dependent and structurally unrelated, and therefore not part of this family). Histone deacetylases catalyze hydrolysis of N(6)-acetyl-lysine residues in histone amino termini to yield a deacetylated histone (EC 3.5.1.98), as opposed to the acetylation reaction by some histone acetyltransferases (EC 2.3.1.48). Deacetylases of this family are involved in signal transduction through histone and other protein modification, and can repress/activate transcription of a number of different genes. They usually act via the formation of large multiprotein complexes. They are involved in various cellular processes, including cell cycle regulation, DNA damage response, embryonic development, cytokine signaling important for immune response and post-translational control of the acetyl coenzyme A synthetase. In mammals, they are known to be involved in progression of different tumors. Specific inhibitors of mammalian histone deacetylases are an emerging class of promising novel anticancer drugs. Length = 279

>gnl|CDD|216151 pfam00850, Hist_deacetyl, Histone deacetylase domain

 Score =  142 bits (360), Expect = 2e-41
 Identities = 48/166 (28%), Positives = 78/166 (46%), Gaps = 7/166 (4%)

Query: 53  LHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIII 112
            HP +  +   I + L   G LD+   + P  A++E+LL+VHS  Y++ L+ +       
Sbjct: 8   GHPENPERLEAILELLKESGLLDRLEFIAPRPATEEELLLVHSPEYVEFLEEA--SLEEE 65

Query: 113 EVPPVALFPNCLVQRKVLYPFRKQVGGTILAAKLA---KERGWAINVGGGFHHCSADEGG 169
           E+  + L  +  V            GGT+ AA L    +    A+   G  HH   D   
Sbjct: 66  ELGRIGLDGDTPVSPGSYEAALLAAGGTLEAADLVLSGENAFAAVRPPG--HHAERDRAS 123

Query: 170 GFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSR 215
           GFC + ++++   Y   +  + RV+I+DLD H GNG ++ F  D R
Sbjct: 124 GFCLFNNVAIAARYLLKRYGLKRVLIVDLDVHHGNGTQEIFYDDPR 169

Histones can be reversibly acetylated on several lysine residues. Regulation of transcription is caused in part by this mechanism. Histone deacetylases catalyze the removal of the acetyl group. Histone deacetylases are related to other proteins. Length = 300

>gnl|CDD|223201 COG0123, AcuC, Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]

 Score =  107 bits (268), Expect = 1e-27
 Identities = 53/192 (27%), Positives = 78/192 (40%), Gaps = 12/192 (6%)

Query: 32  IFKLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLL 91
           + K  LIY P++          HP +  +   I + L S G  D   +VEP  A+ E+LL
Sbjct: 1   MMKTALIYHPEFLEHEPP--PGHPENPDRLRLILELLESSGLPDSLELVEPRPATLEELL 58

Query: 92  VVHSESYLKSLQS-SPNVSIIIEVPPVALFPNCLVQRKVLYPFRKQVGGTILAAKLAKE- 149
           +VHS  Y++ L+S S             + P    +   L       GG + A     E 
Sbjct: 59  LVHSPDYVEFLESLSEEEGYGNLDGDTPVSPG-TYEAARLA-----AGGALTAVDAVLEG 112

Query: 150 -RGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEK 208
                  V    HH   D   GFC + ++++   Y   +  + RV IID D H GNG ++
Sbjct: 113 EDNAFALVRPPGHHAGRDRASGFCLFNNVAIAAKYLLKK-GVKRVAIIDFDVHHGNGTQE 171

Query: 209 DFSSDSRSCLYS 220
            F  D      S
Sbjct: 172 IFYDDDDVLTVS 183

Length = 340

>gnl|CDD|212520 cd09994, HDAC_AcuC_like, Class I histone deacetylase AcuC (Acetoin utilization protein)-like enzymes

 Score = 98.0 bits (245), Expect = 2e-24
 Identities = 57/198 (28%), Positives = 82/198 (41%), Gaps = 28/198 (14%)

Query: 37  LIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSE 96
            IYS +Y     G    HPF+  +       L + G L    +V P  A++E+LL+ H+ 
Sbjct: 2   FIYSEEYLRYSFG--PNHPFNPPRLSLTKDLLRALGLLPPVDLVPPRPATEEELLLFHTP 59

Query: 97  SYLKSLQSSPNVSIIIEVPPVAL-------FPNC-----LVQRKVLYPFRKQVGGTILAA 144
            Y+++++ +           + L       FP       LV           VGGT+LAA
Sbjct: 60  DYIEAVKEASRGQEPEGRGRLGLGTEDNPVFPGMHEAAALV-----------VGGTLLAA 108

Query: 145 KL--AKERGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQ 202
           +L    E   A N  GG HH       GFC Y D ++ I          RV  +D+DAH 
Sbjct: 109 RLVLEGEARRAFNPAGGLHHAMRGRASGFCVYNDAAVAIERL-RDKGGLRVAYVDIDAHH 167

Query: 203 GNGHEKDFSSDSRSCLYS 220
           G+G +  F  D R    S
Sbjct: 168 GDGVQAAFYDDPRVLTIS 185

AcuC (Acetoin utilization protein) is a class I deacetylase found only in bacteria and is involved in post-translational control of the acetyl-coenzyme A synthetase (AcsA). Deacetylase AcuC works in coordination with deacetylase SrtN (class III), possibly to maintain AcsA in active (deacetylated) form and let the cell grow under low concentration of acetate. B. subtilis AcuC is a member of operon acuABC; this operon is repressed by the presence of glucose and does not show induction by acetoin; acetoin is a bacterial fermentation product that can be converted to acetate via the butanediol cycle in absence of other carbon sources. Inactivation of AcuC leads to slower growth and lower cell yield under low-acetate conditions in Bacillus subtilis. In general, Class I histone deacetylases (HDACs) are Zn-dependent enzymes that catalyze hydrolysis of N(6)-acetyl-lysine residues in histone amino termini to yield a deacetylated histone (EC 3.5.1.98). Enzymes belonging to this group participate in regulation of a number of processes through protein (mostly different histones) modification (deacetylation). Class I histone deacetylases in general act via the formation of large multiprotein complexes. Members of this class are involved in cell cycle regulation, DNA damage response, embryonic development, cytokine signaling important for immune response and in posttranslational control of the acetyl coenzyme A synthetase. Length = 313

>gnl|CDD|212524 cd10000, HDAC8, Histone deacetylase 8 (HDAC8)

 Score = 84.7 bits (210), Expect = 2e-19
 Identities = 50/161 (31%), Positives = 76/161 (47%), Gaps = 22/161 (13%)

Query: 68  LSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVA--------- 118
           + + G L +  +V+P  A++E+L   HS+ Y++ L+ + N     E P            
Sbjct: 30  IEAYGLLKQLRVVKPRVATEEELASFHSDEYIQFLKKASNEGDNDEEPSEQQEFGLGYDC 89

Query: 119 -LFPNCLVQRKVLYPFRKQVGG-TILAAKL--AKERGWAINVGGGFHHCSADEGGGFCAY 174
            +F         +Y +   V G T+ AA+L    +   AIN  GG+HH   DE  GFC  
Sbjct: 90  PIFEG-------IYDYAAAVAGATLTAAQLLIDGKCKVAINWFGGWHHAQRDEASGFCYV 142

Query: 175 ADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSR 215
            DI L I    ++    RV+ +DLD H G+G E  FS  S+
Sbjct: 143 NDIVLGILK--LREKFDRVLYVDLDLHHGDGVEDAFSFTSK 181

HDAC8 is a Zn-dependent class I histone deacetylase that catalyzes hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone (EC 3.5.1.98). Histone acetylation/deacetylation process is important for mediation of transcriptional regulation of many genes. Histone deacetylases usually act via association with DNA binding proteins to target specific chromatin regions. HDAC8 is found in human cytoskeleton-bound protein fraction and insoluble cell pellets. It plays a crucial role in intramembraneous bone formation; germline deletion of HDAC8 is detrimental to skull bone formation. HDAC8 is possibly associated with the smooth muscle actin cytockeleton and may regulate the contractive capacity of smooth muscle cells. HDAC8 is also involved in the metabolic control of the estrogen receptor related receptor (ERR)-alpha/peroxisome proliferator activated receptor (PPAR) gamma coactivator 1 alpha (PGC1-alpha) transcriptional complex as well as in the development of neuroblastoma and T-cell lymphoma. HDAC8-selective small-molecule inhibitors could be a therapeutic drug option for these diseases. Length = 364

>gnl|CDD|212517 cd09991, HDAC_classI, Class I histone deacetylases

 Score = 78.4 bits (194), Expect = 3e-17
 Identities = 63/203 (31%), Positives = 83/203 (40%), Gaps = 49/203 (24%)

Query: 38  IYSPDYDISFLGIEKLHPFDSSKWGRIC---QFLSSEGFLDKNCIVEPLEASKEDLLVVH 94
            Y PD    + G  + HP    K  RI      + S G   K  I  P  A+ E+L   H
Sbjct: 1   FYDPDVGNYYYG--QGHP---MKPHRIRMTHSLILSYGLYKKMEIYRPRPATAEELTKFH 55

Query: 95  SESYLKSLQSSP--------------NVSIIIEVPPVALFPNCLVQRKVLYPF-RKQVGG 139
           S+ Y+  L+S                NV    E  PV  F         LY + +   GG
Sbjct: 56  SDDYIDFLRSVSPDNMKEFKKQLERFNVG---EDCPV--FDG-------LYEYCQLYAGG 103

Query: 140 TILAA-KLAK-ERGWAINVGGGFHHCSADEGGGFCAYADISLCI-----HYAFVQLNISR 192
           +I AA KL + +   AIN  GG HH    E  GFC   DI L I     ++        R
Sbjct: 104 SIAAAVKLNRGQADIAINWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQ-------R 156

Query: 193 VMIIDLDAHQGNGHEKDFSSDSR 215
           V+ ID+D H G+G E+ F +  R
Sbjct: 157 VLYIDIDIHHGDGVEEAFYTTDR 179

Class I histone deacetylases (HDACs) are Zn-dependent enzymes that catalyze hydrolysis of N(6)-acetyl-lysine residues in histone amino termini to yield a deacetylated histone (EC 3.5.1.98). Enzymes belonging to this group participate in regulation of a number of processes through protein (mostly different histones) modification (deacetylation). Class I histone deacetylases in general act via the formation of large multiprotein complexes. This group includes animal HDAC1, HDAC2, HDAC3, HDAC8, fungal RPD3, HOS1 and HOS2, plant HDA9, protist, archaeal and bacterial (AcuC) deacetylases. Members of this class are involved in cell cycle regulation, DNA damage response, embryonic development, cytokine signaling important for immune response and in posttranslational control of the acetyl coenzyme A synthetase. In mammals, they are known to be involved in progression of various tumors. Specific inhibitors of mammalian histone deacetylases are an emerging class of promising novel anticancer drugs. Length = 306

>gnl|CDD|212518 cd09992, HDAC_classII, Histone deacetylases and histone-like deacetylases, classII

 Score = 71.4 bits (176), Expect = 8e-15
 Identities = 43/150 (28%), Positives = 64/150 (42%), Gaps = 17/150 (11%)

Query: 63  RICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVALFPN 122
            I + L  EG LD+   VEP  A++E+LL VH+  Y++ ++         E     L P+
Sbjct: 10  AILEALEEEGLLDRLVFVEPRPATEEELLRVHTPEYIERVEE------TCEAGGGYLDPD 63

Query: 123 CLVQRKVLYPFRKQVGGTILAAKLAKERGWAINVGGGF-------HHCSADEGGGFCAYA 175
             V            G  + A       G A N    F       HH   D   GFC + 
Sbjct: 64  TYVSPGSYEAALLAAGAALAAVDAV-LSGEAEN---AFALVRPPGHHAEPDRAMGFCLFN 119

Query: 176 DISLCIHYAFVQLNISRVMIIDLDAHQGNG 205
           ++++   YA  +  + RV+I+D D H GNG
Sbjct: 120 NVAIAARYAQKRYGLKRVLIVDWDVHHGNG 149

Class II histone deacetylases are Zn-dependent enzymes that catalyze hydrolysis of N(6)-acetyl-lysine residues of histones (EC 3.5.1.98) and possibly other proteins to yield deacetylated histones/other proteins. This group includes animal HDAC4,5,6,7,8,9,10, fungal HOS3 and HDA1, plant HDA5 and HDA15 as well as other eukaryotes, archaeal and bacterial histone-like deacetylases. Eukaryotic deacetylases mostly use histones (H2, H3, H4) as substrates for deacetylation; however, non-histone substrates are known (for example, tubulin). Substrates for prokaryotic histone-like deacetylases are not known. Histone acetylation/deacetylation process is important for mediation of transcriptional regulation of many genes. Histone deacetylases usually act via association with DNA binding proteins to target specific chromatin regions. Interaction partners of class II deacetylases include 14-3-3 proteins, MEF2 family of transcriptional factors, CtBP, calmodulin (CaM), SMRT, N-CoR, BCL6, HP1alpha and SUMO. Histone deacetylases play a role in the regulation of cell cycle, cell differentiation and survival. Class II mammalian HDACs are differentially inhibited by structurally diverse compounds with known antitumor activities, thus presenting them as potential drug targets for human diseases resulting from aberrant acetylation. Length = 291

>gnl|CDD|212545 cd11682, HDAC6-dom1, Histone deacetylase 6, domain 1

 Score = 71.4 bits (175), Expect = 9e-15
 Identities = 50/164 (30%), Positives = 77/164 (46%), Gaps = 19/164 (11%)

Query: 68  LSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVS------IIIEVPPVALFP 121
           L  EG L++   V+  EAS+E+LL+VHS  Y+  ++S+  ++      +      V L P
Sbjct: 21  LIQEGLLERCVSVQAREASEEELLLVHSPEYVALMKSTQYMTEEELRTLADTYDSVYLHP 80

Query: 122 N-----CLVQRKVLYPFRKQVGGTILAAKLAKERGWAINVGGGFHHCSADEGGGFCAYAD 176
           N     CL    VL    K +GG I         G AI    G HH   D+  G+C + +
Sbjct: 81  NSYSCACLAVGSVLQLVDKVLGGEI-------RNGLAIVRPPG-HHAQHDKMDGYCMFNN 132

Query: 177 ISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRSCLYS 220
           +++   YA  +  + RV+I+D D H G G +  F  D     +S
Sbjct: 133 VAIAARYAQQKHGVQRVLIVDWDVHHGQGTQFIFEQDPSVLYFS 176

Histone deacetylases 6 are class IIb Zn-dependent enzymes that catalyze hydrolysis of N(6)-acetyl-lysine of a histone to yield a deacetylated histone (EC 3.5.1.98). Histone acetylation/deacetylation process is important for mediation of transcriptional regulation of many genes. HDACs usually act via association with DNA binding proteins to target specific chromatin regions. HDAC6 is the only histone deacetylase with internal duplication of two catalytic domains which appear to function independently of each other, and also has a C-terminal ubiquitin-binding domain. It is located in the cytoplasm and associates with microtubule motor complex, functioning as the tubulin deacetylase and regulating microtubule-dependent cell motility. Known interaction partners of HDAC6 are alpha tubulin (substrate) and ubiquitin-like modifier FAT10 (also known as Ubiquitin D or UBD). Length = 337

>gnl|CDD|212521 cd09996, HDAC_classII_1, Histone deacetylases and histone-like deacetylases, classII

 Score = 69.1 bits (170), Expect = 7e-14
 Identities = 41/166 (24%), Positives = 64/166 (38%), Gaps = 29/166 (17%)

Query: 63  RICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYL---KSLQSSPNVSIIIEVPPVAL 119
           RI   L   G  D   ++ P  A+ E+LL VH+  Y+   K+  ++       E      
Sbjct: 42  RIKNLLEVSGLSDHLVLITPRPATDEELLRVHTPEYIDRVKAASAAGGG----EAGGGTP 97

Query: 120 FPN------CLVQRKVLYPFRKQVGGTILAAKLAKE----RGWAINVGGGFHHCSADEGG 169
           F         L             GG I A     +      +A+    G HH   D+G 
Sbjct: 98  FGPGSYEIALL-----------AAGGAIAAVDAVLDGEVDNAYALVRPPG-HHAEPDQGM 145

Query: 170 GFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSR 215
           GFC + ++++   +A     + RV ++D D H GNG +  F  D  
Sbjct: 146 GFCLFNNVAIAARHALAVGGVKRVAVVDWDVHHGNGTQAIFYDDPD 191

This subfamily includes bacterial as well as eukaryotic Class II histone deacetylase (HDAC) and related proteins. Deacetylases of class II are Zn-dependent enzymes that catalyze hydrolysis of N(6)-acetyl-lysine residues of histones (EC 3.5.1.98) and possibly other proteins to yield deacetylated histones/other proteins. Included in this family is a bacterial HDAC-like amidohydrolase (Bordetella/Alcaligenes species FB18817, denoted as FB188 HDAH) shown to be most similar in sequence and function to class II HDAC6 domain 3 or b (HDAC6b). FB188 HDAH is able to remove the acetyl moiety from acetylated histones, and can be inhibited by common HDAC inhibitors such as SAHA (suberoylanilide hydroxamic acid) as well as class II-specific but not class I specific inhibitors. Length = 359

>gnl|CDD|212543 cd11680, HDAC_Hos1, Class I histone deacetylases Hos1 and related proteins

 Score = 65.0 bits (159), Expect = 1e-12
 Identities = 40/147 (27%), Positives = 57/147 (38%), Gaps = 17/147 (11%)

Query: 74  LDKNC--IVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVALFPNCLVQRKVLY 131
           L ++   I+EP  A+++DL   H + Y+  L       +  + P        +       
Sbjct: 34  LLQHFDEIIEPERATRKDLTKYHDKDYVDFLLK--KYGLEDDCPVFPFLSMYV------- 84

Query: 132 PFRKQVGGTILAAKLAK---ERGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQL 188
             +   G ++  AK      ER  AIN  GG HH       GFC   DI L I     + 
Sbjct: 85  --QLVAGSSLALAKHLITQVERDIAINWYGGRHHAQKSRASGFCYVNDIVLAIL-RLRRA 141

Query: 189 NISRVMIIDLDAHQGNGHEKDFSSDSR 215
              RV  +DLD H G+G E  F     
Sbjct: 142 RFRRVFYLDLDLHHGDGVESAFFFSKN 168

Saccharomyces cerevisiae Hos1 is responsible for Smc3 deacetylation. Smc3 is an important player during the establishment of sister chromatid cohesion. Hos1 belongs to the class I histone deacetylases (HDACs). HDACs are Zn-dependent enzymes that catalyze hydrolysis of N(6)-acetyl-lysine residues in histone amino termini to yield a deacetylated histone (EC 3.5.1.98). Enzymes belonging to this group participate in regulation of a number of processes through protein (mostly different histones) modification (deacetylation). Class I histone deacetylases in general act via the formation of large multiprotein complexes. Other class I HDACs are animal HDAC1, HDAC2, HDAC3, HDAC8, fungal RPD3 and HOS2, plant HDA9, protist, archaeal and bacterial (AcuC) deacetylases. Members of this class are involved in cell cycle regulation, DNA damage response, embryonic development, cytokine signaling important for immune response and in posttranslational control of the acetyl coenzyme A synthetase. Length = 294

>gnl|CDD|212541 cd11599, HDAC_classII_2, Histone deacetylases and histone-like deacetylases, classII

 Score = 61.0 bits (149), Expect = 3e-11
 Identities = 44/157 (28%), Positives = 67/157 (42%), Gaps = 20/157 (12%)

Query: 68  LSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVALFPNCLVQR 127
           L + G       +E   A++E LL VH  +Y+  L+++       E   V L P+  +  
Sbjct: 15  LIASGLDRLLRQLEAPPATREQLLRVHDAAYVDRLEAA-----APEEGLVQLDPDTAMSP 69

Query: 128 KVLYPFRKQVGGTILA--AKLAKERGWAINVGGGF-------HHCSADEGGGFCAYADIS 178
             L    +  G  + A  A +A   G A N    F       HH   D+  GFC + +++
Sbjct: 70  GSLEAALRAAGAVVAAVDAVMA---GEARNA---FCAVRPPGHHAERDKAMGFCLFNNVA 123

Query: 179 LCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSR 215
           +   +A     + RV I+D D H GNG E  F  D R
Sbjct: 124 IAAAHALAHHGLERVAIVDFDVHHGNGTEDIFRDDPR 160

This subfamily includes eukaryotic as well as bacterial Class II histone deacetylase (HDAC) and related proteins. Deacetylases of class II are Zn-dependent enzymes that catalyze hydrolysis of N(6)-acetyl-lysine residues of histones (EC 3.5.1.98) and possibly other proteins to yield deacetylated histones/other proteins. In D. discoideum, where four homologs (HdaA, HdaB, HdaC, HdaD) have been identified, HDAC activity is important for regulating the timing of gene expression during development. Also, inhibition of HDAC activity by trichostatin A is shown to cause hyperacetylation of the histone and a delay in cell aggregation and differentiation. Length = 288

>gnl|CDD|212526 cd10002, HDAC10_HDAC6-dom1, Histone deacetylase 6, domain 1 and histone deacetylase 10

 Score = 61.6 bits (150), Expect = 3e-11
 Identities = 38/165 (23%), Positives = 75/165 (45%), Gaps = 11/165 (6%)

Query: 63  RICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVALFPN 122
            I + L+ +G L++   +   EA ++++L+VHS+ Y+  ++S+  +         + + +
Sbjct: 16  AILERLTQDGLLERCVKIPAREAEEDEILLVHSQEYIDLVKSTETMEKEELESLCSGYDS 75

Query: 123 CLVQRKVLYPFRKQVGGTILAAKLAKERGWAINVGGGF-------HHCSADEGGGFCAYA 175
             +        R   G TI   K          +  GF       HH   +E  G+C + 
Sbjct: 76  VYLCPSTYEAARLAAGSTIELVKAVMAGK----IQNGFALIRPPGHHAMRNEANGYCIFN 131

Query: 176 DISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRSCLYS 220
           ++++   YA  +L + R++I+D D H G G ++ F  D R   +S
Sbjct: 132 NVAIAAKYAIEKLGLKRILIVDWDVHHGQGTQQGFYEDPRVLYFS 176

Histone deacetylases 6 and 10 are class IIb Zn-dependent enzymes that catalyze hydrolysis of N(6)-acetyl-lysine of a histone to yield a deacetylated histone (EC 3.5.1.98). Histone acetylation/deacetylation process is important for mediation of transcriptional regulation of many genes. HDACs usually act via association with DNA binding proteins to target specific chromatin regions. HDAC6 is the only histone deacetylase with internal duplication of two catalytic domains which appear to function independently of each other, and also has a C-terminal ubiquitin-binding domain. It is located in the cytoplasm and associates with microtubule motor complex, functioning as the tubulin deacetylase and regulating microtubule-dependent cell motility. HDAC10 has an N-terminal deacetylase domain and a C-terminal pseudo-repeat that shares significant similarity with its catalytic domain. It is located in the nucleus and cytoplasm, and is involved in regulation of melanogenesis. It transcriptionally down-regulates thioredoxin-interacting protein (TXNIP), leading to altered reactive oxygen species (ROS) signaling in human gastric cancer cells. Known interaction partners of HDAC6 are alpha tubulin (substrate) and ubiquitin-like modifier FAT10 (also known as Ubiquitin D or UBD) while interaction partners of HDAC10 are Pax3, KAP1, hsc70 and HDAC3 proteins. Length = 336

>gnl|CDD|212535 cd10011, HDAC2, Histone deacetylase 2 (HDAC2)

 Score = 60.5 bits (146), Expect = 7e-11
 Identities = 54/187 (28%), Positives = 86/187 (45%), Gaps = 7/187 (3%)

Query: 34  KLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVV 93
           K  + Y  D DI      + HP    +       L + G   K  I  P +A+ E++   
Sbjct: 1   KKKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTKY 60

Query: 94  HSESYLKSLQS--SPNVS-IIIEVPPVALFPNCLVQRKVLYPFRKQVGGTILAA-KLAKE 149
           HS+ Y+K L+S    N+S    ++    +  +C V   +    +   GG++  A KL ++
Sbjct: 61  HSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAGAVKLNRQ 120

Query: 150 R-GWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEK 208
           +   A+N  GG HH    E  GFC   DI L I    ++ +  RV+ ID+D H G+G E+
Sbjct: 121 QTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAI-LELLKYH-QRVLYIDIDIHHGDGVEE 178

Query: 209 DFSSDSR 215
            F +  R
Sbjct: 179 AFYTTDR 185

Histone deacetylase 2 (HDAC2) is a Zn-dependent class I enzyme that catalyzes hydrolysis of N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone (EC 3.5.1.98). Histone acetylation/deacetylation process is important for mediation of transcriptional regulation of many genes. HDAC2 is involved in regulation through association with DNA binding proteins to target specific chromatin regions. It forms transcriptional repressor complexes by associating with several proteins, including the mammalian zinc-finger transcription factor YY1, thus playing an important role in transcriptional regulation, cell cycle progression and developmental events. Additionally, a few non-histone HDAC2 substrates have been found. HDAC2 plays a role in embryonic development and cytokine signaling important for immune response, and is over-expressed in several solid tumors including oral, prostate, ovarian, endometrial and gastric cancer. It participates in DNA-damage response, along with HDAC1; together, they can promote DNA non-homologous end-joining. HDAC2 is considered an important cancer prognostic marker. Inhibitors specifically targeting HDAC2 could be a therapeutic drug option. Length = 366

>gnl|CDD|212527 cd10003, HDAC6-dom2, Histone deacetylase 6, domain 2

 Score = 60.0 bits (146), Expect = 1e-10
 Identities = 45/179 (25%), Positives = 76/179 (42%), Gaps = 18/179 (10%)

Query: 51  EKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSI 110
           +  HP    +  RI +  +  G L++   +    A++++LL+ HSE +L  ++S   +  
Sbjct: 13  DPGHPECPQRISRIYERHNDLGLLERCLRLPSRLATEDELLLCHSEEHLDEMKSLEKMK- 71

Query: 111 IIEVPPVALFP-----NCLVQRKVLYPFRKQVGGTILAAKLAKERGWAINVGGGF----- 160
                P  L       + +      Y       G +L    A   G + N G        
Sbjct: 72  -----PRELNRLGKEYDSIYIHPDSYQCALLAAGCVLQVVEAVLTGESRN-GVAIVRPPG 125

Query: 161 HHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRSCLY 219
           HH   D   GFC + ++++   YA  +  + R++I+D D H GNG +  F SD  S LY
Sbjct: 126 HHAEQDTACGFCFFNNVAIAARYAQKKYGLKRILIVDWDVHHGNGTQHMFESDP-SVLY 183

Histone deacetylase 6 is a class IIb Zn-dependent enzyme that catalyzes hydrolysis of N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone (EC 3.5.1.98). Histone acetylation/deacetylation process is important for mediation of transcriptional regulation of many genes. HDACs usually act via association with DNA binding proteins to target specific chromatin regions. HDAC6 is the only histone deacetylase with internal duplication of two catalytic domains which appear to function independently of each other, and also has a C-terminal ubiquitin-binding domain. It is located in the cytoplasm and associates with microtubule motor complex, functioning as the tubulin deacetylase and regulating microtubule-dependent cell motility. Known interaction partners of HDAC6 are alpha tubulin and ubiquitin-like modifier FAT10 (also known as Ubiquitin D or UBD). Length = 350

>gnl|CDD|212534 cd10010, HDAC1, Histone deacetylase 1 (HDAC1)

 Score = 59.3 bits (143), Expect = 2e-10
 Identities = 54/187 (28%), Positives = 87/187 (46%), Gaps = 7/187 (3%)

Query: 34  KLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVV 93
           K  + Y  D D+      + HP    +       L + G   K  I  P +A+ E++   
Sbjct: 5   KKKVCYYYDGDVGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKANAEEMTKY 64

Query: 94  HSESYLKSLQS--SPNVS-IIIEVPPVALFPNCLVQRKVLYPFRKQVGGTILAA-KLAKE 149
           HS+ Y+K L+S    N+S    ++    +  +C V   +    +   GG++ +A KL K+
Sbjct: 65  HSDDYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSAGGSVASAVKLNKQ 124

Query: 150 R-GWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEK 208
           +   A+N  GG HH    E  GFC   DI L I    ++ +  RV+ ID+D H G+G E+
Sbjct: 125 QTDIAVNWAGGLHHAKKSEASGFCYVNDIVLAI-LELLKYH-QRVLYIDIDIHHGDGVEE 182

Query: 209 DFSSDSR 215
            F +  R
Sbjct: 183 AFYTTDR 189

Histone deacetylase 1 (HDAC1) is a Zn-dependent class I enzyme that catalyzes hydrolysis of N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone (EC 3.5.1.98). Histone acetylation/deacetylation process is important for mediation of transcriptional regulation of many genes. HDAC1 is involved in regulation through association with DNA binding proteins to target specific chromatin regions. In particular, HDAC1 appears to play a major role in pre-implantation embryogenesis in establishing a repressive chromatin state. Its interaction with retinoblastoma tumor-suppressor protein is essential in the control of cell proliferation and differentiation. Together with metastasis-associated protein-2 (MTA2), it deacetylates p53, thereby modulating its effect on cell growth and apoptosis. It participates in DNA-damage response, along with HDAC2; together, they promote DNA non-homologous end-joining. HDAC1 is also involved in tumorogenesis; its overexpression modulates cancer progression. Specific inhibitors of HDAC1 are currently used in cancer therapy. Length = 371

>gnl|CDD|212540 cd11598, HDAC_Hos2, Class I histone deacetylases including ScHos2 and SpPhd1

 Score = 59.0 bits (143), Expect = 2e-10
 Identities = 48/148 (32%), Positives = 65/148 (43%), Gaps = 18/148 (12%)

Query: 79  IVEPLEASKEDLLVVHSESYLKSL-QSSP---NVSIIIEVPPVALFPNCLVQRKVLYPFR 134
             E   A++E+L   H   YL  L + SP   N     +  P  +  +C V    +Y + 
Sbjct: 43  TYEARAATREELRQFHDADYLDFLSKVSPENANQLRFDKAEPFNIGDDCPVFDG-MYDYC 101

Query: 135 KQVGGTILAA--KL-AKERGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNI- 190
           +   G  L A  KL + +   AIN  GG HH    E  GFC   DI L I      LN+ 
Sbjct: 102 QLYAGASLDAARKLCSGQSDIAINWSGGLHHAKKSEASGFCYVNDIVLAI------LNLL 155

Query: 191 ---SRVMIIDLDAHQGNGHEKDFSSDSR 215
               RV+ ID+D H G+G E+ F    R
Sbjct: 156 RYFPRVLYIDIDVHHGDGVEEAFYRTDR 183

This subfamily includes Class I histone deacetylase (HDAC) Hos2 from Saccharomyces cerevisiae as well as a histone deacetylase Phd1 from Schizosaccharomyces pombe. Hos2 binds to the coding regions of genes during gene activation, specifically it deacetylates the lysines in H3 and H4 histone tails. It is preferentially associated with genes of high activity genome-wide and is shown to be necessary for efficient transcription. Thus, Hos2 is directly required for gene activation in contrast to other class I histone deacetylases. Protein encoded by phd1 is inhibited by trichostatin A (TSA), a specific inhibitor of histone deacetylase, and is involved in the meiotic cell cycle in S. pombe. Class 1 HDACs are Zn-dependent enzymes that catalyze hydrolysis of N(6)-acetyl-lysine residues in histone amino termini to yield a deacetylated histone (EC 3.5.1.98). Length = 311

>gnl|CDD|212533 cd10009, HDAC9, Histone deacetylase 9

 Score = 58.1 bits (140), Expect = 5e-10
 Identities = 55/190 (28%), Positives = 85/190 (44%), Gaps = 28/190 (14%)

Query: 54  HPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIE 113
           HP  + +   I   L   G L+K   ++  +AS E++ +VHSE +  SL    N     +
Sbjct: 24  HPEHAGRIQSIWSRLQETGLLNKCERIQGRKASLEEIQLVHSEHH--SLLYGTNPLDGQK 81

Query: 114 VPPVALFPNCLVQRKVLYP--------------------FRKQVGGTI-LAAKLAK---E 149
           + P  L  +   +     P                     R  VG  I LA+K+A    +
Sbjct: 82  LDPRILLGDDSQKFFSSLPCGGLGVDSDTIWNELHSSGAARMAVGCVIELASKVASGELK 141

Query: 150 RGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKD 209
            G+A+    G HH       GFC +  +++   Y   QLNIS+++I+DLD H GNG ++ 
Sbjct: 142 NGFAVVRPPG-HHAEESTAMGFCFFNSVAITAKYLRDQLNISKILIVDLDVHHGNGTQQA 200

Query: 210 FSSDSRSCLY 219
           F +D  S LY
Sbjct: 201 FYADP-SILY 209

Histone deacetylase 9 is a class IIa Zn-dependent enzyme that catalyzes hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone (EC 3.5.1.98). Histone acetylation/deacetylation process is important for mediation of transcriptional regulation of many genes. Histone deacetylases usually act via association with DNA binding proteins to target specific chromatin regions. Class IIa histone deacetylases are signal-dependent co-repressors, they have N-terminal regulatory domain with two or three conserved serine residues, phosphorylation of these residues is important for ability to shuttle between the nucleus and cytoplasm and act as transcriptional co-repressors. HDAC9 is involved in regulation of gene expression and dendritic growth in developing cortical neurons. It also plays a role in hematopoiesis. Its deregulated expression may be associated with some human cancers. HDAC5 and HDAC9 have been found to be significantly up-regulated in high-risk medulloblastoma compared with low-risk and may potentially be novel drug targets. Length = 379

>gnl|CDD|212546 cd11683, HDAC10, Histone deacetylase 10

 Score = 56.4 bits (136), Expect = 2e-09
 Identities = 41/151 (27%), Positives = 70/151 (46%), Gaps = 7/151 (4%)

Query: 74  LDKNCIVEPL-EASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVALFPNCLVQRKVLYP 132
           L + C+  P  EAS+E++L+VHS  YL  ++ +  ++    +     +          + 
Sbjct: 26  LVQRCLRLPAREASEEEILLVHSPEYLSLVRETQVMNKEELMAISGKYDAVYFHPNTFHC 85

Query: 133 FRKQVGGT--ILAAKLAKE--RGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQL 188
            R   G T  ++ A L  E   G A+    G HH   +   GFC + ++++   YA  + 
Sbjct: 86  ARLAAGATLQLVDAVLTGEVQNGMALVRPPG-HHSQRNAANGFCVFNNVAIAAEYAKKKY 144

Query: 189 NISRVMIIDLDAHQGNGHEKDFSSDSRSCLY 219
            + R++I+D D H G G +  F  D  S LY
Sbjct: 145 GLHRILIVDWDVHHGQGIQYIFEEDP-SVLY 174

Histone deacetylases 10 are class IIb Zn-dependent enzymes that catalyze hydrolysis of N(6)-acetyl-lysine of a histone to yield a deacetylated histone (EC 3.5.1.98). Histone acetylation/deacetylation process is important for mediation of transcriptional regulation of many genes. HDACs usually act via association with DNA binding proteins to target specific chromatin regions. HDAC10 has an N-terminal deacetylase domain and a C-terminal pseudo-repeat that shares significant similarity with its catalytic domain. It is located in the nucleus and cytoplasm, and is involved in regulation of melanogenesis. It transcriptionally down-regulates thioredoxin-interacting protein (TXNIP), leading to altered reactive oxygen species (ROS) signaling in human gastric cancer cells. Known interaction partners of HDAC10 are Pax3, KAP1, hsc70 and HDAC3 proteins. Length = 337

>gnl|CDD|212542 cd11600, HDAC_Clr3, Class II Histone deacetylase Clr3 and similar proteins

 Score = 55.0 bits (133), Expect = 5e-09
 Identities = 48/179 (26%), Positives = 83/179 (46%), Gaps = 20/179 (11%)

Query: 54  HPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSI--I 111
           HP D S+  RI + L   G +++   +   EA+KE++L+VHSE +   ++++  +S   +
Sbjct: 3   HPEDPSRISRIFEKLKEAGLINRMLRIPIREATKEEILLVHSEEHWDRVEATEKMSDEQL 62

Query: 112 IEVPPVALFPNCLVQRKVLYPFRKQVGGTILAAKLAKERGWAINVGGGF-------HHCS 164
            +   +    +  V     +  R   GG I A + A   G    V   F       HH  
Sbjct: 63  KDRTEIFERDSLYVNNDTAFCARLSCGGAIEACR-AVAEG---RVKNAFAVVRPPGHHAE 118

Query: 165 ADEGGGFCAYADISLCIHYAFVQLN----ISRVMIIDLDAHQGNGHEKDFSSDSRSCLY 219
            DE  GFC + ++   +   ++Q      I +++I+D D H GNG ++ F  D  + LY
Sbjct: 119 PDESMGFCFFNNV--AVAAKWLQTEYPDKIKKILILDWDIHHGNGTQRAFYDDP-NVLY 174

Clr3 is a class II Histone deacetylase Zn-dependent enzyme that catalyzes hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone (EC 3.5.1.98). Clr3 is the homolog of the class-II HDAC HdaI in S. cerevisiae, and is essential for silencing in heterochromatin regions, such as centromeric regions, ribosomal DNA, the mating-type region and telomeric loci. Clr3 has also been implicated in the regulation of stress-related genes; the histone acetyltransferase, Gcn5, in S. cerevisiae, preferentially acetylates global histone H3K14 while Clr3 preferentially deacetylates H3K14ac, and therefore, interplay between Gcn5 and Clr3 is crucial for the regulation of many stress-response genes. Length = 313

>gnl|CDD|212522 cd09998, HDAC_Hos3, Class II histone deacetylases Hos3 and related proteins

 Score = 52.1 bits (125), Expect = 4e-08
 Identities = 18/45 (40%), Positives = 28/45 (62%)

Query: 161 HHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNG 205
           HHCS     GFC   ++ +   +A++   I+RV+I+D+D H GNG
Sbjct: 120 HHCSESTPSGFCWVNNVHVGAAHAYLTHGITRVVILDIDLHHGNG 164

Fungal histone deacetylase Hos3 from Saccharomyces cerevisiae is a Zn-dependent enzyme belonging to HDAC class II. It catalyzes hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone (EC 3.5.1.98). Histone acetylation/deacetylation process is important for mediation of transcriptional regulation of many genes. Histone deacetylases usually act via association with DNA binding proteins to target specific chromatin regions. Hos3 deacetylase is homodimer, in vitro it shows specificity to H4, H3 and H2A. Length = 353

>gnl|CDD|212529 cd10005, HDAC3, Histone deacetylase 3 (HDAC3)

 Score = 51.6 bits (124), Expect = 7e-08
 Identities = 49/156 (31%), Positives = 63/156 (40%), Gaps = 31/156 (19%)

Query: 72  GFLDKNCIVEPLEASKEDLLVVHSESYLKSLQS-SPNVSIIIEVPPVALFPNCLVQRKV- 129
           G   K  + +P  AS  D+   HSE Y+  LQ  +P          +  F   L Q  V 
Sbjct: 38  GLYKKMQVYKPYRASAHDMCRFHSEDYIDFLQRVTPQ--------NIQGFTKSLNQFNVG 89

Query: 130 --------LYPFRKQVGGTIL--AAKL-AKERGWAINVGGGFHHCSADEGGGFCAYADIS 178
                   L+ F     G  L  A KL  K    AIN  GG HH    E  GFC   DI 
Sbjct: 90  DDCPVFPGLFDFCSMYTGASLEGATKLNHKICDIAINWSGGLHHAKKFEASGFCYVNDIV 149

Query: 179 LCIHYAFVQLNI----SRVMIIDLDAHQGNGHEKDF 210
           + I      L +     RV+ ID+D H G+G ++ F
Sbjct: 150 IAI------LELLKYHPRVLYIDIDIHHGDGVQEAF 179

HDAC3 is a Zn-dependent class I histone deacetylase that catalyzes hydrolysis of N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone (EC 3.5.1.98). Histone acetylation/deacetylation process is important for mediation of transcriptional regulation of many genes. In order to target specific chromatin regions, HDAC3 can interact with DNA-binding proteins (transcriptional factors) either directly or after forming complexes with a number of other proteins, as observed for the SMPT/N-CoR complex which recruits human HDAC3 to specific chromatin loci and activates deacetylation. Human HDAC3 is also involved in deacetylation of non-histone substrates such as RelA, SPY and p53 factors. This protein can also down-regulate p53 function and subsequently modulate cell growth and apoptosis. This gene is therefore regarded as a potential tumor suppressor gene. HDAC3 plays a role in various physiological processes, including subcellular protein localization, cell cycle progression, cell differentiation, apoptosis and survival. HDAC3 has been found to be overexpressed in some tumors including leukemia, lung carcinoma, colon cancer and maxillary carcinoma. Thus, inhibitors precisely targeting HDAC3 (in some cases together with retinoic acid or hyperthermia) could be a therapeutic drug option. Length = 381

>gnl|CDD|240374 PTZ00346, PTZ00346, histone deacetylase; Provisional

 Score = 51.2 bits (122), Expect = 1e-07
 Identities = 50/184 (27%), Positives = 85/184 (46%), Gaps = 14/184 (7%)

Query: 39  YSPDYDIS-FLGIEKLHPFDSSKWGRICQFLSSEGFLDKNC--IVEPLEASKEDLLVVHS 95
           Y+ D +IS F+    + P+       I + L     +D +C  +V PL    E+L+  H+
Sbjct: 30  YASDMNISAFVPQHAMKPYRVLAAMEIVRSLK----IDAHCRTVVPPL-VKVEELMAYHT 84

Query: 96  ESYLKSLQSSPNVSII--IEVPPVALFPNCLVQRKVLYPFRKQVGGTILAAKL--AKERG 151
           ++YL +L      S +   E   V    +C     ++        GT++ A L  + +  
Sbjct: 85  DTYLANLGLHSCRSWLWNAETSKVFFSGDCPPVEGLMEHSIATASGTLMGAVLLNSGQVD 144

Query: 152 WAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFS 211
            A++ GGG HH    E  GFC   DI L I    ++ +  RV+ +D+D H G+G ++ F 
Sbjct: 145 VAVHWGGGMHHSKCGECSGFCYVNDIVLGI-LELLKCH-DRVLYVDIDMHHGDGVDEAFC 202

Query: 212 SDSR 215
           +  R
Sbjct: 203 TSDR 206

Length = 429

>gnl|CDD|240251 PTZ00063, PTZ00063, histone deacetylase; Provisional

 Score = 51.0 bits (122), Expect = 1e-07
 Identities = 45/144 (31%), Positives = 68/144 (47%), Gaps = 19/144 (13%)

Query: 79  IVEPLEASKEDLLVVHSESYLKSLQS-SP----NVSIIIEVPPVALFPNCLVQRKVLYPF 133
           I  P ++ + +L++ H E Y+  L S SP    + +  ++   V    +C V    L+ F
Sbjct: 48  IYRPHKSVEPELVLFHDEEYVDFLSSISPENYRDFTYQLKRFNVGEATDCPVFDG-LFEF 106

Query: 134 RKQ-VGGTILAA-KLAKERG-WAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNI 190
           ++   G +I  A KL   +    +N  GG HH    E  GFC   DI L I      L +
Sbjct: 107 QQSCAGASIDGAYKLNNHQADICVNWSGGLHHAKRSEASGFCYINDIVLGI------LEL 160

Query: 191 ----SRVMIIDLDAHQGNGHEKDF 210
               +RVM ID+D H G+G E+ F
Sbjct: 161 LKYHARVMYIDIDVHHGDGVEEAF 184

Length = 436

>gnl|CDD|212544 cd11681, HDAC_classIIa, Histone deacetylases, class IIa

 Score = 49.3 bits (118), Expect = 4e-07
 Identities = 44/186 (23%), Positives = 79/186 (42%), Gaps = 35/186 (18%)

Query: 59  SKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVA 118
           S W R    L   G +++   +   +A+ E+L +VHSE +     ++P   + ++   +A
Sbjct: 33  SIWSR----LQETGLVNRCERLRGRKATLEELQLVHSEVHTLLYGTNPLSRLKLDPTKLA 88

Query: 119 LFPNCLVQRKVLY---------------------PFRKQVGGTI-LAAKLAK---ERGWA 153
             P    Q+  +                        R  VG  I LA K+A    + G+A
Sbjct: 89  GLP----QKSFVRLPCGGIGVDSDTVWNELHTSNAARMAVGCVIDLAFKVATGELKNGFA 144

Query: 154 INVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSD 213
           +    G HH    +  GFC +  +++       +L + +++I+D D H GNG ++ F  D
Sbjct: 145 VVRPPG-HHAEPSQAMGFCFFNSVAIAAKQLQQKLKLRKILIVDWDVHHGNGTQQIFYED 203

Query: 214 SRSCLY 219
             + LY
Sbjct: 204 P-NVLY 208

Class IIa histone deacetylases are Zn-dependent enzymes that catalyze hydrolysis of N(6)-acetyl-lysine residues of histones (EC 3.5.1.98) to yield deacetylated histones. This subclass includes animal HDAC4, HDAC5, HDAC7, and HDCA9. Histone acetylation/deacetylation process is important for mediation of transcriptional regulation of many genes. Histone deacetylases usually act via association with DNA binding proteins to target specific chromatin regions. Class IIa histone deacetylases are signal-dependent co-repressors, they have N-terminal regulatory domain with two or three conserved serine residues, phosphorylation of these residues is important for ability to shuttle between the nucleus and cytoplasm and act as transcriptional co-repressors. HDAC9 is involved in regulation of gene expression and dendritic growth in developing cortical neurons. It also plays a role in hematopoiesis. HDAC7 is involved in regulation of myocyte migration and differentiation. HDAC5 is involved in integration of chronic drug (cocaine) addiction and depression with changes in chromatin structure and gene expression. HDAC4 participates in regulation of chondrocyte hypertrophy and skeletogenesis. Length = 377

>gnl|CDD|212528 cd10004, RPD3-like, reduced potassium dependency-3 (RPD3)-like

 Score = 49.0 bits (117), Expect = 5e-07
 Identities = 31/82 (37%), Positives = 43/82 (52%), Gaps = 8/82 (9%)

Query: 138 GGTI-LAAKLAKER-GWAINVGGGFHHCSADEGGGFCAYADISLCI--HYAFVQLNISRV 193
           GG++  AA+L + +   A+N  GG HH    E  GFC   DI L I     + Q    RV
Sbjct: 108 GGSMEGAARLNRGKCDIAVNWAGGLHHAKKSEASGFCYVNDIVLGILELLRYHQ----RV 163

Query: 194 MIIDLDAHQGNGHEKDFSSDSR 215
           + ID+D H G+G E+ F +  R
Sbjct: 164 LYIDIDVHHGDGVEEAFYTTDR 185

Proteins of the Rpd3-like family are class I Zn-dependent Histone deacetylases that catalyze hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone (EC 3.5.1.98). RPD3 is the yeast homolog of class I HDACs. The main function of RPD3-like group members is regulation of a number of different processes through protein (mostly different histones) modification (deacetylation). This group includes fungal RPD3 and acts via the formation of large multiprotein complexes. Members of this group are involved in cell cycle regulation, DNA damage response, embryonic development and cytokine signaling important for immune response. Histone deacetylation by yeast RPD3 represses genes regulated by the Ash1 and Ume6 DNA-binding proteins. In mammals, they are known to be involved in progression of various tumors. Specific inhibitors of mammalian histone deacetylases could be a therapeutic drug option. Length = 375

>gnl|CDD|212531 cd10007, HDAC5, Histone deacetylase 5

 Score = 45.7 bits (108), Expect = 7e-06
 Identities = 29/90 (32%), Positives = 47/90 (52%), Gaps = 6/90 (6%)

Query: 134 RKQVGGTI-LAAKLAK---ERGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLN 189
           R  VG  I LA K+A    + G+A+    G HH       GFC +  +++       +LN
Sbjct: 124 RMAVGCLIELAFKVAAGELKNGFAVIRPPG-HHAEESTAMGFCFFNSVAIAAKLLQQKLN 182

Query: 190 ISRVMIIDLDAHQGNGHEKDFSSDSRSCLY 219
           + +++I+D D H GNG ++ F +D  + LY
Sbjct: 183 VGKILIVDWDIHHGNGTQQAFYNDP-NVLY 211

Histone deacetylase 5 is a class IIa Zn-dependent enzyme that catalyzes hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone (EC 3.5.1.98). Histone acetylation/deacetylation process is important for mediation of transcriptional regulation of many genes. Histone deacetylases usually act via association with DNA binding proteins to target specific chromatin regions. Class IIa histone deacetylases are signal-dependent co-repressors, having N-terminal regulatory domain with two or three conserved serine residues; phosphorylation of these residues is important for ability to shuttle between the nucleus and cytoplasm and act as transcriptional co-repressors. HDAC5 is involved in integration of chronic drug (cocaine) addiction and depression with changes in chromatin structure and gene expression; cocaine regulates HDAC5 function to antagonize the rewarding impact of cocaine, possibly by blocking drug-stimulated gene expression that supports drug-induced behavioral change. It is also involved in regulation of angiogenesis and cell cycle as well as immune system development. HDAC5 and HDAC9 have been found to be significantly up-regulated in high-risk medulloblastoma compared with low-risk and may potentially be novel drug targets. Length = 420

>gnl|CDD|212530 cd10006, HDAC4, Histone deacetylase 4

 Score = 45.0 bits (106), Expect = 1e-05
 Identities = 18/53 (33%), Positives = 30/53 (56%)

Query: 161 HHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSD 213
           HH       GFC +  +++       +LN+S+++I+D D H GNG ++ F SD
Sbjct: 154 HHAEESTPMGFCYFNSVAIAAKLLQQRLNVSKILIVDWDVHHGNGTQQAFYSD 206

Histone deacetylase 4 is a class IIa Zn-dependent enzyme that catalyzes hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone (EC 3.5.1.98). Histone acetylation/deacetylation process is important for mediation of transcriptional regulation of many genes. Histone deacetylases usually act via association with DNA binding proteins to target specific chromatin regions. Class IIa histone deacetylases are signal-dependent co-repressors, having N-terminal regulatory domain with two or three conserved serine residues; phosphorylation of these residues is important for ability to shuttle between the nucleus and cytoplasm and act as transcriptional co-repressors. HDAC4 participates in regulation of chondrocyte hypertrophy and skeletogenesis. However, biological substrates for HDAC4 have not been identified; only low lysine deacetylation activity has been demonstrated and active site mutant has enhanced activity toward acetylated lysines. HDAC4 does not bind DNA directly, but through transcription factors MEF2C (myocyte enhancer factor-2C) and MEF2D. Other known interaction partners of the protein are 14-3-3 proteins, SMRT and N-CoR co-repressors, BCL6, HP1, SUMO-1 ubiquitin-like protein, and ANKRA2. It appears to interact in a multiprotein complex with RbAp48 and HDAC3. Furthermore, HDAC4 is required for TGFbeta1-induced myofibroblastic differentiation. Length = 409

>gnl|CDD|212525 cd10001, HDAC_classII_APAH, Histone deacetylase class IIa

 Score = 44.5 bits (106), Expect = 2e-05
 Identities = 38/184 (20%), Positives = 62/184 (33%), Gaps = 41/184 (22%)

Query: 37  LIYSPDYDI-----SFLGIEKLHPFDS-SKWGRICQFLSSEGFLDKNCIVEPLEASKEDL 90
           ++YS D+ +          + +   ++  +   I   L   G  +   ++ P +   E +
Sbjct: 2   IVYSEDHLLHHPKTELSRGKLVPHPENPERAEAILDALKRAGLGE---VLPPRDFGLEPI 58

Query: 91  LVVHSESYLKSLQSSPNVSIIIEVPPVALFPNCLVQRKVLYPFRKQVGGTILAAKLAKE- 149
           L VH   Y+  L++                 +  +               + AA L  E 
Sbjct: 59  LAVHDPDYVDFLET--------------ADTDTPISEGTWEAALAAADTALTAADLVLEG 104

Query: 150 RGWAINVG---GGFHHCSADEGGGFC-----AYADISLCIHYAFVQLNISRVMIIDLDAH 201
              A  +    G  HH   D  GGFC     A A       Y   +    RV I+D+D H
Sbjct: 105 ERAAYALCRPPG--HHAGRDRAGGFCYFNNAAIA-----AQYL--RDRAGRVAILDVDVH 155

Query: 202 QGNG 205
            GNG
Sbjct: 156 HGNG 159

This subfamily includes bacterial acetylpolyamine amidohydrolase (APAH) as well as other Class II histone deacetylase (HDAC) and related proteins. Deacetylases of class II are Zn-dependent enzymes that catalyze hydrolysis of N(6)-acetyl-lysine residues of histones (EC 3.5.1.98) and possibly other proteins to yield deacetylated histones/other proteins. Mycoplana ramosa APAH exhibits broad substrate specificity and catalyzes the deacetylation of polyamines such as putrescine, spermidine, and spermine by cleavage of a non-peptide amide bond. Length = 298

>gnl|CDD|212532 cd10008, HDAC7, Histone deacetylase 7

 Score = 40.8 bits (95), Expect = 3e-04
 Identities = 27/83 (32%), Positives = 41/83 (49%), Gaps = 5/83 (6%)

Query: 140 TILAAKLAK---ERGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMII 196
           T LA K+A    + G+A+    G HH       GFC +  +++       Q   S+++I+
Sbjct: 129 TDLAFKVASRELKNGFAVVRPPG-HHADHSTAMGFCFFNSVAIACRQLQQQGKASKILIV 187

Query: 197 DLDAHQGNGHEKDFSSDSRSCLY 219
           D D H GNG ++ F  D  S LY
Sbjct: 188 DWDVHHGNGTQQTFYQDP-SVLY 209

Histone deacetylase 7 is a class IIa Zn-dependent enzyme that catalyzes hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone (EC 3.5.1.98). Histone acetylation/deacetylation process is important for mediation of transcriptional regulation of many genes. Histone deacetylases usually act via association with DNA binding proteins to target specific chromatin regions. Class IIa histone deacetylases are signal-dependent co-repressors, having N-terminal regulatory domain with two or three conserved serine residues; phosphorylation of these residues is important for ability to shuttle between the nucleus and cytoplasm and act as transcriptional co-repressors. HDAC7 is involved in regulation of myocyte migration and differentiation. Known interaction partners of class IIa HDAC7 are myocyte enhancer factors - MEF2A, -2C, and -2D, 14-3-3 proteins, SMRT and N-CoR co-repressors, HDAC3, ETA (endothelin receptor). This enzyme is also involved in the development of the immune system as well as brain and heart development. Multiple alternatively spliced transcript variants encoding several isoforms have been found for this gene. Length = 378

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	223
COG0123	340	AcuC Deacetylases, including yeast histone deacety	100.0
PTZ00063	436	histone deacetylase; Provisional	100.0
PTZ00346	429	histone deacetylase; Provisional	100.0
PF00850	311	Hist_deacetyl: Histone deacetylase domain; InterPr	100.0
KOG1342	425	consensus Histone deacetylase complex, catalytic c	100.0
KOG1344	324	consensus Predicted histone deacetylase [Chromatin	100.0
KOG1343	797	consensus Histone deacetylase complex, catalytic c	99.96
KOG1343	797	consensus Histone deacetylase complex, catalytic c	99.91

>COG0123 AcuC Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]

Probab=100.00  E-value=5.5e-55  Score=392.49  Aligned_cols=182  Identities=30%  Similarity=0.426  Sum_probs=165.6

Q ss_pred             CceeEEeCcccccccCCCCCCCCCCchHHHHHHHHHHHCCCCCCceEecCCCCCHHHHhccCCHHHHHHHhcCCCccccc
Q 027427           33 FKLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIII  112 (223)
Q Consensus        33 ~~~~ivy~~~~~~h~~~~~~~Hpe~p~R~~~i~~~L~~~gl~~~~~~~~p~~a~~e~l~~vHs~~Yv~~l~~~~~~~~~~  112 (223)
                      +++.++|++.+..|.++  .+|||+|.|++.+.++|++.|+...+++++|+++++++|++||+++||++|++.+...+  
T Consensus         2 ~~~~~~~~~~~~~~~~~--~~Hpe~p~R~~~~~~~l~~~~~~~~~~~~~p~~~~~~~l~~vH~~~yv~~l~~~~~~~~--   77 (340)
T COG0123           2 MKTALIYHPEFLEHEPP--PGHPENPDRLRLILELLESSGLPDSLELVEPRPATLEELLLVHSPDYVEFLESLSEEEG--   77 (340)
T ss_pred             CcceEeeCHHHhcCCCC--CCCCCChHHHHHHHHHHHhcCccccccccCCCcCCHHHHHhhCCHHHHHHHHHhccccc--
Confidence            57889999999888654  78999999999999999999988888999999999999999999999999999886521  


Q ss_pred             cCCCcccCCCcccccccHHHHHHHhhHHHHHHHHHhhc---CcEeecCCCCCCCCCCCCCcccccchHHHHHHHHHHhcC
Q 027427          113 EVPPVALFPNCLVQRKVLYPFRKQVGGTILAAKLAKER---GWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLN  189 (223)
Q Consensus       113 e~~~~~~~~d~~~~~~~~~~a~~a~Gg~l~aa~~~~~~---~~a~~~~~G~HHA~~~~~~GFC~fNnvAIAa~~l~~~~~  189 (223)
                         ...++.||++++++++++++++|+++.|++.++++   .++..+||| |||++++++|||+|||+||||++|+++ +
T Consensus        78 ---~~~~d~d~~~s~~~~~~a~~a~G~al~A~~~v~~g~~~~~~~~rppg-HHA~~~~a~GFC~fNn~Aiaa~~l~~~-~  152 (340)
T COG0123          78 ---YGNLDGDTPVSPGTYEAARLAAGGALTAVDAVLEGEDNAFALVRPPG-HHAGRDRASGFCLFNNVAIAAKYLLKK-G  152 (340)
T ss_pred             ---cccccCCCccChHHHHHHHHHhhHHHHHHHHHHcCccceEEECCCCc-ccccCCCCceeeeecHHHHHHHHHHHc-C
Confidence               23567899999999999999999999999999974   345555555 999999999999999999999999988 8


Q ss_pred             CCeEEEEecCCcCCchhhHhhhcCCCEEEEeccC
Q 027427          190 ISRVMIIDLDAHQGNGHEKDFSSDSRSCLYSGYV  223 (223)
Q Consensus       190 ~~RV~IiD~DvHHGnGTq~if~~d~~Vl~iSlH~  223 (223)
                      .+||+|||||||||||||+|||+|++|+|+|+||
T Consensus       153 ~~RVaIiD~DvHHGnGTqeify~~~~V~~~S~H~  186 (340)
T COG0123         153 VKRVAIIDFDVHHGNGTQEIFYDDDDVLTVSLHQ  186 (340)
T ss_pred             CCcEEEEEecCCCChhhHHHHccCCCeEEEeccC
Confidence            9999999999999999999999999999999997

>PTZ00063 histone deacetylase; Provisional

Probab=100.00  E-value=1.6e-54  Score=398.29  Aligned_cols=188  Identities=24%  Similarity=0.355  Sum_probs=167.9

Q ss_pred             CCceeEEeCcccccccCCCCCCCCCCchHHHHHHHHHHHCCCCCCceEecCCCCCHHHHhccCCHHHHHHHhcCCCcccc
Q 027427           32 IFKLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSII  111 (223)
Q Consensus        32 ~~~~~ivy~~~~~~h~~~~~~~Hpe~p~R~~~i~~~L~~~gl~~~~~~~~p~~a~~e~l~~vHs~~Yv~~l~~~~~~~~~  111 (223)
                      +.++.++|+|+|..|.++  .+|||+|.|++.+.++|+++|+...+++++|++|+.++|.+||+++||++|++.++....
T Consensus         3 ~~~v~~~yd~~~~~h~~g--~~HP~~P~Rl~~~~~ll~~~gl~~~~~~~~p~~At~eeL~~vHs~~YI~~L~~~~~~~~~   80 (436)
T PTZ00063          3 RKRVSYFYDPDIGSYYYG--PGHPMKPQRIRMAHALILSYDLYKHMEIYRPHKSVEPELVLFHDEEYVDFLSSISPENYR   80 (436)
T ss_pred             CceEEEEECccccCcCCc--CcCCcChHHHHHHHHHHHhCCCcccCeEecCCCCCHHHHHHhCCHHHHHHHHHhChhhcc
Confidence            567999999999999765  689999999999999999999999999999999999999999999999999987653211


Q ss_pred             ---ccCCCcccC--CCcccccccHHHHHHHhhHHHHHHHHHhhc--CcEeecCCCCCCCCCCCCCcccccchHHHHHHHH
Q 027427          112 ---IEVPPVALF--PNCLVQRKVLYPFRKQVGGTILAAKLAKER--GWAINVGGGFHHCSADEGGGFCAYADISLCIHYA  184 (223)
Q Consensus       112 ---~e~~~~~~~--~d~~~~~~~~~~a~~a~Gg~l~aa~~~~~~--~~a~~~~~G~HHA~~~~~~GFC~fNnvAIAa~~l  184 (223)
                         .......++  +||++++++++++++++||+|.|++.++++  ++|+||+||+|||++++++|||+|||+||||++|
T Consensus        81 ~~~~~~~~f~lg~~~D~pv~~gl~~~a~~aaGgsl~Aa~~l~~g~~~iAin~~GG~HHA~~~~A~GFC~~NdiaiAi~~L  160 (436)
T PTZ00063         81 DFTYQLKRFNVGEATDCPVFDGLFEFQQSCAGASIDGAYKLNNHQADICVNWSGGLHHAKRSEASGFCYINDIVLGILEL  160 (436)
T ss_pred             cchhhhhhcccCCCCCCCcccHHHHHHHHHHhHHHHHHHHHHcCCCCEEeeCCCCCCCCccCCCCceeeecHHHHHHHHH
Confidence               011112233  599999999999999999999999998853  5899999999999999999999999999999999


Q ss_pred             HHhcCCCeEEEEecCCcCCchhhHhhhcCCCEEEEeccC
Q 027427          185 FVQLNISRVMIIDLDAHQGNGHEKDFSSDSRSCLYSGYV  223 (223)
Q Consensus       185 ~~~~~~~RV~IiD~DvHHGnGTq~if~~d~~Vl~iSlH~  223 (223)
                      ++.+  +||+|||||||||||||++||+||+|+|||+|+
T Consensus       161 ~~~~--~RVliID~DvHHGdGtqe~F~~~~~VltvS~H~  197 (436)
T PTZ00063        161 LKYH--ARVMYIDIDVHHGDGVEEAFYVTHRVMTVSFHK  197 (436)
T ss_pred             HHhC--CeEEEEeCCCCCCcchHHHhccCCCeEEEEecc
Confidence            9864  799999999999999999999999999999996

>PTZ00346 histone deacetylase; Provisional

Probab=100.00  E-value=5.8e-54  Score=392.70  Aligned_cols=187  Identities=26%  Similarity=0.349  Sum_probs=162.0

Q ss_pred             CceeEE----eCcccccccCCCCCCCCCCchHHHHHHHHHHHCCCCCCceEecCCCCCHHHHhccCCHHHHHHHhcCCCc
Q 027427           33 FKLPLI----YSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNV  108 (223)
Q Consensus        33 ~~~~iv----y~~~~~~h~~~~~~~Hpe~p~R~~~i~~~L~~~gl~~~~~~~~p~~a~~e~l~~vHs~~Yv~~l~~~~~~  108 (223)
                      .++.+|    |.+++..+.+  +++|||+|+|++.++++|++.|+...+++++|++|+.++|++||+++||++|++....
T Consensus        20 ~~~~~~~~~~y~~~~~~~~~--~~~HPe~P~Rl~~~~~ll~~~gl~~~~~~~~p~~At~eeL~~vHs~~YI~~l~~~~~~   97 (429)
T PTZ00346         20 GRVALIDTSGYASDMNISAF--VPQHAMKPYRVLAAMEIVRSLKIDAHCRTVVPPLVKVEELMAYHTDTYLANLGLHSCR   97 (429)
T ss_pred             ceeEEEecCccccccccccC--CCcCCCCHHHHHHHHHHHHhcCCcccCeeecCCCCCHHHHHHhCCHHHHHHHHHhccc
Confidence            446788    5556665544  4789999999999999999999998899999999999999999999999999874321


Q ss_pred             cc--cccCCCcccCCCcccccccHHHHHHHhhHHHHHHHHHhhc--CcEeecCCCCCCCCCCCCCcccccchHHHHHHHH
Q 027427          109 SI--IIEVPPVALFPNCLVQRKVLYPFRKQVGGTILAAKLAKER--GWAINVGGGFHHCSADEGGGFCAYADISLCIHYA  184 (223)
Q Consensus       109 ~~--~~e~~~~~~~~d~~~~~~~~~~a~~a~Gg~l~aa~~~~~~--~~a~~~~~G~HHA~~~~~~GFC~fNnvAIAa~~l  184 (223)
                      ..  ..+.....+++||++++++++++++++||++.|++.++++  ++|++++||+|||++++++|||+|||+||||++|
T Consensus        98 ~~~~~~~~~~~~~d~Dtpv~~~~~~~a~laaGgsl~Aa~~v~~g~~~~Ai~~pGG~HHA~~~~a~GFC~fNdvAIAa~~l  177 (429)
T PTZ00346         98 SWLWNAETSKVFFSGDCPPVEGLMEHSIATASGTLMGAVLLNSGQVDVAVHWGGGMHHSKCGECSGFCYVNDIVLGILEL  177 (429)
T ss_pred             ccccccccccccccCCCCCChHHHHHHHHHHHHHHHHHHHHHcCCCCEEEeCCCCcCcCCCCCCCcchHHhHHHHHHHHH
Confidence            10  0011223456899999999999999999999999999854  5799999999999999999999999999999999


Q ss_pred             HHhcCCCeEEEEecCCcCCchhhHhhhcCCCEEEEeccC
Q 027427          185 FVQLNISRVMIIDLDAHQGNGHEKDFSSDSRSCLYSGYV  223 (223)
Q Consensus       185 ~~~~~~~RV~IiD~DvHHGnGTq~if~~d~~Vl~iSlH~  223 (223)
                      +++  .+||+|||||||||||||+|||+||+|||||+||
T Consensus       178 l~~--~~RVliID~DVHHGnGTqeiF~~dp~Vl~vSiHq  214 (429)
T PTZ00346        178 LKC--HDRVLYVDIDMHHGDGVDEAFCTSDRVFTLSLHK  214 (429)
T ss_pred             HHc--CCeEEEEeCCCCCCchHHHHHcCCCCeEEEEecC
Confidence            986  4799999999999999999999999999999996

>PF00850 Hist_deacetyl: Histone deacetylase domain; InterPro: IPR023801 Regulation of transcription is, in part, modulated by reversible histone acetylation on several lysine

Probab=100.00  E-value=2.8e-53  Score=378.44  Aligned_cols=174  Identities=28%  Similarity=0.414  Sum_probs=135.0

Q ss_pred             CcccccccCCCCCCCCCCchHHHHHHHHHHHC-CCCCCceEecCCCCCHHHHhccCCHHHHHHHhcCCCcccccc-CCCc
Q 027427           40 SPDYDISFLGIEKLHPFDSSKWGRICQFLSSE-GFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIE-VPPV  117 (223)
Q Consensus        40 ~~~~~~h~~~~~~~Hpe~p~R~~~i~~~L~~~-gl~~~~~~~~p~~a~~e~l~~vHs~~Yv~~l~~~~~~~~~~e-~~~~  117 (223)
                      ||.|. +.  ++++|||+|+|++.+.+.|++. ++++.      ++++.++|++|||++||++|++.+......+ ....
T Consensus         1 ~~~~~-~~--~~~~Hpe~p~R~~~i~~~L~~~~~l~~~------~~a~~~~L~~vH~~~Yv~~l~~~~~~~~~~~~~~~~   71 (311)
T PF00850_consen    1 HPQYQ-HQ--LGDGHPESPERLESIVEALKESYGLLPR------RPATDEELLRVHDPEYVDFLESASKEAKEEEEAGSP   71 (311)
T ss_dssp             ----T-T---CCTTSSSCTHHHHHHHHHHHHTTTGGGG----------HHHHTTTS-HHHHHHHHHHHHHTSGCTHHHHH
T ss_pred             CCccc-CC--CCCCcCCCHHHHHHHHHHHHHhcCCCCC------CCCCHHHHHHcCCHHHHHHHHHhccccccccccccc
Confidence            56776 32  4578999999999999999986 77644      9999999999999999999998764332111 0000


Q ss_pred             ---c-c-CCCcccccccHHHHHHHhhHHHHHHHHHhh----cCcEeecCCCCCCCCCCCCCcccccchHHHHHHHHHHhc
Q 027427          118 ---A-L-FPNCLVQRKVLYPFRKQVGGTILAAKLAKE----RGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQL  188 (223)
Q Consensus       118 ---~-~-~~d~~~~~~~~~~a~~a~Gg~l~aa~~~~~----~~~a~~~~~G~HHA~~~~~~GFC~fNnvAIAa~~l~~~~  188 (223)
                         . . +.||++++++++++++++|+++.|++.+++    ++||+++||| |||.+++++|||+|||+||||+||++++
T Consensus        72 ~~~~~~~~~dt~~~~~~~~~a~~a~g~~l~a~~~v~~g~~~~~~a~~rppg-HHA~~~~a~GFC~~Nnvaiaa~~l~~~~  150 (311)
T PF00850_consen   72 EFPNILDDGDTPISPGSWEAARLAAGGTLEAADAVLSGEIKNAFALVRPPG-HHAERDRAMGFCYFNNVAIAAKYLRKKY  150 (311)
T ss_dssp             HHCCBTSSSSSEBCTTHHHHHHHHHHHHHHHHHHHHTTSSSEEEEEESS---TT-BTTBBBTTBSS-HHHHHHHHHHHTT
T ss_pred             ccccccCCCCcceehHHHHHHHHHHHHHHHHHHhhhcccccceeeecCccc-cccCcCcCcceeeeccHHHHHHHHhhcc
Confidence               0 1 579999999999999999999999999994    4799997777 9999999999999999999999999988


Q ss_pred             CCCeEEEEecCCcCCchhhHhhhcCCCEEEEeccC
Q 027427          189 NISRVMIIDLDAHQGNGHEKDFSSDSRSCLYSGYV  223 (223)
Q Consensus       189 ~~~RV~IiD~DvHHGnGTq~if~~d~~Vl~iSlH~  223 (223)
                      +++||+|||||||||||||+|||+||+|+|+|||+
T Consensus       151 ~~~rV~iiD~DvHhGnGtq~if~~d~~V~~~SiH~  185 (311)
T PF00850_consen  151 GLKRVAIIDFDVHHGNGTQEIFYDDPRVLYISIHQ  185 (311)
T ss_dssp             TTSSEEEEE-SSS--HHHHHHTTT-SSEEEEEEEE
T ss_pred             ccceEEEEEeCCCCcccchhheeCCCCEEecCccc
Confidence            99999999999999999999999999999999996

Histone deacetylases (HDA) catalyse the removal of the acetyl group. Histone deacetylases, acetoin utilization proteins and acetylpolyamine amidohydrolases are all members of this ancient protein superfamily []. HDAs function in multi-subunit complexes, reversing the acetylation of histones by histone acetyltransferases [, ], and are also believed to deacetylate general transcription factors such as TFIIF and sequence-specific transcription factors such as p53 []. Thus, HDAs contribute to the regulation of transcription, in particular transcriptional repression []. At N-terminal tails of histones, removal of the acetyl group from the epsilon-amino group of a lysine side chain will restore its positivecharge, which may stabilise the histone-DNA interaction and prevent activating transcription factors binding to promoter elements []. HDAs play important roles in the cell cycle and differentiation, and their deregulation can contribute to the development of cancer [, ]. This entry represents the structural domain found in histone deacetylases. It consists of a 3-layer(alpha-beta-alpha) sandwich.; PDB: 4A69_A 2VQV_A 2VQO_A 2VQJ_A 2VQQ_B 2VQM_A 2VQW_G 3MAX_C 3MEN_D 1T64_B ....

>KOG1342 consensus Histone deacetylase complex, catalytic component RPD3 [Chromatin structure and dynamics]

Probab=100.00  E-value=2.5e-44  Score=319.74  Aligned_cols=189  Identities=27%  Similarity=0.370  Sum_probs=168.7

Q ss_pred             CCCCceeEEeCcccccccCCCCCCCCCCchHHHHHHHHHHHCCCCCCceEecCCCCCHHHHhccCCHHHHHHHhcCCCcc
Q 027427           30 IPIFKLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVS  109 (223)
Q Consensus        30 ~~~~~~~ivy~~~~~~h~~~~~~~Hpe~p~R~~~i~~~L~~~gl~~~~~~~~p~~a~~e~l~~vHs~~Yv~~l~~~~~~~  109 (223)
                      ..+.++.+.|+++-...  .++.+||++|.|++.+.+++..+||...+++.+|..|+.+|+.++||+|||++|++..+..
T Consensus         4 ~~k~~V~y~yd~~vg~~--~Yg~~hpmkP~R~~mth~Lv~~YgL~k~M~i~~p~~a~~~dm~~FHt~eYi~fL~~V~p~n   81 (425)
T KOG1342|consen    4 LIKRRVSYFYDPDVGNF--HYGQGHPMKPHRIRMTHSLVLNYGLYKKMEIYRPDKASAQDMTRFHTDEYINFLQSVTPEN   81 (425)
T ss_pred             cCCceEEEEecCccccc--cccCCCCCCcceehhhhHHHHhcchhhceeeccCCCCCHHHHHhhchHHHHHHHhhCCccc
Confidence            45667888888887554  3568999999999999999999999999999999999999999999999999999988754


Q ss_pred             cc---ccCCCcccCCCcccccccHHHHHHHhhHHHHHHHHHhh--cCcEeecCCCCCCCCCCCCCcccccchHHHHHHHH
Q 027427          110 II---IEVPPVALFPNCLVQRKVLYPFRKQVGGTILAAKLAKE--RGWAINVGGGFHHCSADEGGGFCAYADISLCIHYA  184 (223)
Q Consensus       110 ~~---~e~~~~~~~~d~~~~~~~~~~a~~a~Gg~l~aa~~~~~--~~~a~~~~~G~HHA~~~~~~GFC~fNnvAIAa~~l  184 (223)
                      ..   .+...+.+..||+++.++++.+++.+||+|.||+.+-.  ..+|+||.||.|||+++.|+|||++||++++|..|
T Consensus        82 ~~~~~~~~~~fNvg~DCPvF~gL~~fC~~~~GgSl~aa~kLn~~~~dIaINW~GGlHHAKK~eASGFCYvNDIVL~ILeL  161 (425)
T KOG1342|consen   82 METFNKELKQFNVGEDCPVFDGLYDYCQLYTGGSLNAAQKLNRGECDIAINWAGGLHHAKKSEASGFCYVNDIVLGILEL  161 (425)
T ss_pred             ccccchHHHhcCCCCCCccccCHHHHHHHhcccchHHHHHhCCCCceEEEecCcccccccccccCcceeehHHHHHHHHH
Confidence            31   12223456789999999999999999999999987653  35899999999999999999999999999999999


Q ss_pred             HHhcCCCeEEEEecCCcCCchhhHhhhcCCCEEEEecc
Q 027427          185 FVQLNISRVMIIDLDAHQGNGHEKDFSSDSRSCLYSGY  222 (223)
Q Consensus       185 ~~~~~~~RV~IiD~DvHHGnGTq~if~~d~~Vl~iSlH  222 (223)
                      ++.+  +||++||+|+|||||+|++||..+||||+|+|
T Consensus       162 lK~h--~RVLYIDIDvHHGDGVEeAFy~TDRVmTvSfH  197 (425)
T KOG1342|consen  162 LKYH--KRVLYIDIDVHHGDGVEEAFYTTDRVMTVSFH  197 (425)
T ss_pred             HHhC--CceEEEEecccCCccHHHHHhccceeEEEEEE
Confidence            9874  69999999999999999999999999999999

>KOG1344 consensus Predicted histone deacetylase [Chromatin structure and dynamics]

Probab=100.00  E-value=9.4e-39  Score=269.27  Aligned_cols=200  Identities=59%  Similarity=1.043  Sum_probs=187.7

Q ss_pred             hcccccccCCCCceeEEeCcccccccCCCCCCCCCCchHHHHHHHHHHHCCCCCCceEecCCCCCHHHHhccCCHHHHHH
Q 027427           22 LSSKLYFDIPIFKLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKS  101 (223)
Q Consensus        22 ~~~~~~~~~~~~~~~ivy~~~~~~h~~~~~~~Hpe~p~R~~~i~~~L~~~gl~~~~~~~~p~~a~~e~l~~vHs~~Yv~~  101 (223)
                      +-++.|+..|..+++|||++.|...+.++.+.|||+..++..|.+.|.+.++++.-.+++|.++++++|++|||.+|++.
T Consensus         3 ~~~kly~~vp~~k~pIvyS~~Y~i~FmGlEkLHPFDa~Kwg~v~kfL~~~~~l~d~~lvEp~e~t~e~L~rvHtr~YLks   82 (324)
T KOG1344|consen    3 VWVKLYDAVPAGKLPIVYSRNYAIRFMGLEKLHPFDAAKWGHVHKFLCAMNLLTDETLVEPNEATKEDLLRVHTRKYLKS   82 (324)
T ss_pred             eeeeecccCccccccEEecCccceeecchhhcCcCcccchhHHHHHHHHhccccccccccCcccCHHHHHhHhhHHHHHH
Confidence            45678899999999999999999999899899999999999999999999999888899999999999999999999999


Q ss_pred             HhcCCCccccccCCCcccCCCcccccccHHHHHHHhhHHHHHHHHHhhcCcEeecCCCCCCCCCCCCCcccccchHHHHH
Q 027427          102 LQSSPNVSIIIEVPPVALFPNCLVQRKVLYPFRKQVGGTILAAKLAKERGWAINVGGGFHHCSADEGGGFCAYADISLCI  181 (223)
Q Consensus       102 l~~~~~~~~~~e~~~~~~~~d~~~~~~~~~~a~~a~Gg~l~aa~~~~~~~~a~~~~~G~HHA~~~~~~GFC~fNnvAIAa  181 (223)
                      ++.....+.+.|.+...+.|++++.+..+...++.+||++.|++++++.|+|+|.+|||||+..++++|||.|-|+.+|+
T Consensus        83 lr~s~~vA~I~EiP~v~flPn~~iqrk~LrPlR~QagGtilA~kLAle~GWAINvGGGFHHcss~rGGGFC~yADItl~I  162 (324)
T KOG1344|consen   83 LRWSIKVAQITEIPFVGFLPNCIIQRKLLRPLRLQAGGTILAAKLALERGWAINVGGGFHHCSSSRGGGFCAYADITLAI  162 (324)
T ss_pred             hhccceeeEEEeccccccCchhhhhhhhccceeeccCceeehhhhhhhcCeEEeecCccceeccCCCCceeehhhHHHHH
Confidence            99877777788999889999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhcCCCeEEEEecCCcCCchhhHhhhcCCCEEEEecc
Q 027427          182 HYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRSCLYSGY  222 (223)
Q Consensus       182 ~~l~~~~~~~RV~IiD~DvHHGnGTq~if~~d~~Vl~iSlH  222 (223)
                      ..+.++..+.|++|||+|+|+|||.+.-|.+| .|..+.++
T Consensus       163 ~~lFer~~isr~mivDLDAHQGNghErdf~~~-~vyi~d~y  202 (324)
T KOG1344|consen  163 FFLFERKAISRAMIVDLDAHQGNGHERDFEDD-AVYIFDMY  202 (324)
T ss_pred             HHHHhhhhhhheEEEecccccCCccccccccc-eeehhhhh
Confidence            99999888999999999999999999999988 77665543

>KOG1343 consensus Histone deacetylase complex, catalytic component HDA1 [Chromatin structure and dynamics]

Probab=99.96  E-value=9.2e-31  Score=254.59  Aligned_cols=162  Identities=25%  Similarity=0.298  Sum_probs=124.3

Q ss_pred             CCCCCCchHHHHHHHHHHHCCCCCCceEecCCCCCHHHHhccCCHHHHHHHhcCCCccc-------cccCCCcccCCCcc
Q 027427           52 KLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSI-------IIEVPPVALFPNCL  124 (223)
Q Consensus        52 ~~Hpe~p~R~~~i~~~L~~~gl~~~~~~~~p~~a~~e~l~~vHs~~Yv~~l~~~~~~~~-------~~e~~~~~~~~d~~  124 (223)
                      ..||+.|.|   ....+. .|++.+|+.+    |+.++|+.||+.+|+..+........       ..++..++.++|+.
T Consensus       463 ~~~~~~p~r---~~t~~~-~gl~~~c~r~----at~~el~~vHs~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~dt~  534 (797)
T KOG1343|consen  463 SRSPESPAR---FTTGLH-TGLLGKCERI----ATLEELQLVHSEAHVLLYGSRKLLGDLSLKFESRLPCGGIGVDSDTW  534 (797)
T ss_pred             cCCcccchh---hhcccc-cccccccccc----cchhhhhhcccchhhcccchhhhcccccchhhhhccccceeecccHH
Confidence            368999999   222232 7888889877    99999999999999999652211110       01223344455655


Q ss_pred             ccccc-HHHHHHHhhHHHHHHHHHhhcCcEeecCCCCCCCCCCCCCcccccchHHHHHHHHHHhcCCCeEEEEecCCcCC
Q 027427          125 VQRKV-LYPFRKQVGGTILAAKLAKERGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQG  203 (223)
Q Consensus       125 ~~~~~-~~~a~~a~Gg~l~aa~~~~~~~~a~~~~~G~HHA~~~~~~GFC~fNnvAIAa~~l~~~~~~~RV~IiD~DvHHG  203 (223)
                      ++... ..++++++++.+..+..+. .|||++|||| |||....++|||+|||+|||+++++..+.++||+|+|||||||
T Consensus       535 ~~~~~ssga~~~av~~v~~~~~~~~-~g~avvRppG-Hha~~~~a~gfc~fn~vaiaak~l~~~~~~~rilivdwDvhhg  612 (797)
T KOG1343|consen  535 WNELHSSGAARLAVGCVIELAFKVA-SGFAVVRPPG-HHAEASTAMGFCFFNSVAIAAKLLQQRSKASRILIVDWDVHHG  612 (797)
T ss_pred             HHHHHHHHHHHHhcchhhhhhhhhh-cceeEecCCc-cccccCCcceeeeecchhhhhHHhhhhhhhcceEEEeecccCC
Confidence            54432 2244555555555554443 3899999999 9999999999999999999999999988889999999999999


Q ss_pred             chhhHhhhcCCCEEEEeccC
Q 027427          204 NGHEKDFSSDSRSCLYSGYV  223 (223)
Q Consensus       204 nGTq~if~~d~~Vl~iSlH~  223 (223)
                      ||||.+||.|++|+|+|+|.
T Consensus       613 ngtq~~f~~~~~vlyislhr  632 (797)
T KOG1343|consen  613 NGTQQAFYSDPSVLYISLHR  632 (797)
T ss_pred             cceeeeeccCccccccccch
Confidence            99999999999999999984

>KOG1343 consensus Histone deacetylase complex, catalytic component HDA1 [Chromatin structure and dynamics]

Probab=99.91  E-value=2.9e-25  Score=216.34  Aligned_cols=190  Identities=17%  Similarity=0.183  Sum_probs=156.9

Q ss_pred             CceeEEeCcccccccCCCCCCCC-CCchHHHHHHHHHHHCCCCCCceEecC-CCCCHHHHhccCCHHHHHHHhcCCCccc
Q 027427           33 FKLPLIYSPDYDISFLGIEKLHP-FDSSKWGRICQFLSSEGFLDKNCIVEP-LEASKEDLLVVHSESYLKSLQSSPNVSI  110 (223)
Q Consensus        33 ~~~~ivy~~~~~~h~~~~~~~Hp-e~p~R~~~i~~~L~~~gl~~~~~~~~p-~~a~~e~l~~vHs~~Yv~~l~~~~~~~~  110 (223)
                      .++.++|++.+..|....+..|+ +.++|++.+.+.+.+.++.+++.+..+ +.+++++++.+|+++|++.+........
T Consensus        29 ~~~~l~~~~~~~~h~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~v~~ke~~~~~~~t~~~~~  108 (797)
T KOG1343|consen   29 IQKQLLFAEFQKQHENQQELLEKEEKLERLRQIEEELERHRLEQPLLILRNKREAKESAVASVHVKEKLQEFLLSKKMTA  108 (797)
T ss_pred             hhhhhhhhhhhhhhhcccccccchhhhhHHHHHHHHhhccCCccccccccchhhcccchhcccccHHHHHHHHhhhhhcc
Confidence            56889999999999633334455 999999999999999999888876666 9999999999999999999987652211


Q ss_pred             cccC-CCcccCCCcccccccHHHHHHHhhHHHHHHHHHh----hcCcEeecCCCCCCCCCCCCCcccccchHHHHHHHHH
Q 027427          111 IIEV-PPVALFPNCLVQRKVLYPFRKQVGGTILAAKLAK----ERGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAF  185 (223)
Q Consensus       111 ~~e~-~~~~~~~d~~~~~~~~~~a~~a~Gg~l~aa~~~~----~~~~a~~~~~G~HHA~~~~~~GFC~fNnvAIAa~~l~  185 (223)
                      .... ....-.+..++++.++..+..+.|+.+...+.++    .++++.++++| |||.++...|||+|||||++++...
T Consensus       109 e~~l~~~~~~~~~~~~~~~s~~~a~~a~~~~~~~~~~~~~~~~~n~~a~v~p~~-hhsep~~~~~~cl~n~Va~~~~~~~  187 (797)
T KOG1343|consen  109 EEGLNHSSSRYPSLYYTSASHSSADQASGSLSGSYKAVLAGKASNGKADFRPPG-HHSEPNLKVGFCLFNNVAERRSSPL  187 (797)
T ss_pred             hhhhhcccCCCCcceecCCchhhhcccCcccccccccccCCcccCccCcCCCCC-CccccchhcchhHHHHHHHHhhccc
Confidence            0000 0011245777888889999999999998666654    46789999988 9999999999999999999999988


Q ss_pred             HhcCCCeEEEEecCCcCCchhhHhhhc--CCCEEEEeccC
Q 027427          186 VQLNISRVMIIDLDAHQGNGHEKDFSS--DSRSCLYSGYV  223 (223)
Q Consensus       186 ~~~~~~RV~IiD~DvHHGnGTq~if~~--d~~Vl~iSlH~  223 (223)
                      .++..+||+|+|||+|||+|||..|++  |++|+++|+|+
T Consensus       188 ~~~~~rri~i~d~dvh~g~Gtq~~~~~~~d~~vl~~s~~r  227 (797)
T KOG1343|consen  188 LRRKKRRILIVDWDVHHGPGTQPSSPNNGDQRVLYFSLHR  227 (797)
T ss_pred             cccccceeEeecccccCCCCCCCccCCCcccccccccchh
Confidence            887789999999999999999999999  99999999985

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	223
3max_A	367	Crystal Structure Of Human Hdac2 Complexed With An		8e-11
3ezp_A	388	Crystal Structure Analysis Of Human Hdac8 D101n Var		2e-10
3f07_A	388	Crystal Structure Analysis Of Human Hdac8 Complexed		6e-10
3sff_A	378	Crystal Structure Of Human Hdac8 Inhibitor Complex,		6e-10
1t64_A	377	Crystal Structure Of Human Hdac8 Complexed With Tri		6e-10
3mz3_A	389	Crystal Structure Of Co2+ Hdac8 Complexed With M344		6e-10
2v5w_A	388	Crystal Structure Of Hdac8-Substrate Complex Length		6e-10
2v5x_A	388	Crystal Structure Of Hdac8-Inhibitor Complex Length		7e-10
3ezt_A	388	Crystal Structure Analysis Of Human Hdac8 D101e Var		9e-10
3ew8_A	388	Crystal Structure Analysis Of Human Hdac8 D101l Var		1e-09
3mz4_A	389	Crystal Structure Of D101l Mn2+ Hdac8 Complexed Wit		1e-09
3f06_A	388	Crystal Structure Analysis Of Human Hdac8 D101a Var		1e-09
3ewf_A	388	Crystal Structure Analysis Of Human Hdac8 H143a Var		8e-09
1c3p_A	375	Crystal Structure Of An Hdac Homolog From Aquifex A		8e-09
1c3r_A	375	Crystal Structure Of An Hdac Homolog Complexed With		9e-09
4a69_A	376	Structure Of Hdac3 Bound To Corepressor And Inosito		4e-08
3c0y_A	423	Crystal Structure Of Catalytic Domain Of Human Hist		4e-06
1zz0_A	369	Crystal Structure Of A Hdac-Like Protein With Aceta		6e-06
2vcg_A	375	Crystal Structure Of A Hdac-like Protein Hdah From		6e-06
2vqo_A	413	Structure Of Hdac4 Catalytic Domain With A Gain-Of-		2e-05
2vqq_A	413	Structure Of Hdac4 Catalytic Domain (A Double Cyste		2e-05
2vqw_G	413	Structure Of Inhibitor-Free Hdac4 Catalytic Domain		2e-05
2vqj_A	413	Structure Of Hdac4 Catalytic Domain Bound To A Trif		2e-05

>pdb|3MAX|A Chain A, Crystal Structure Of Human Hdac2 Complexed With An N-(2-Amin Benzamide Length = 367

Iteration: 1
 Score = 63.5 bits (153), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 54/187 (28%), Positives = 86/187 (45%), Gaps = 7/187 (3%)
Query: 34  KLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVV 93
           K  + Y  D DI      + HP    +       L + G   K  I  P +A+ E++   
Sbjct: 2   KKKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTKY 61
Query: 94  HSESYLKSLQS--SPNVS-IIIEVPPVALFPNCLVQRKVLYPFRKQVGGTILAA-KLAKE 149
           HS+ Y+K L+S    N+S    ++    +  +C V   +    +   GG++  A KL ++
Sbjct: 62  HSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAGAVKLNRQ 121
Query: 150 R-GWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEK 208
           +   A+N  GG HH    E  GFC   DI L I    ++ +  RV+ ID+D H G+G E+
Sbjct: 122 QTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAI-LELLKYH-QRVLYIDIDIHHGDGVEE 179
Query: 209 DFSSDSR 215
            F +  R
Sbjct: 180 AFYTTDR 186

>pdb|3EZP|A Chain A, Crystal Structure Analysis Of Human Hdac8 D101n Variant Length = 388

Iteration: 1
 Score = 62.8 bits (151), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 52/191 (27%), Positives = 84/191 (43%), Gaps = 16/191 (8%)
Query: 30  IPIFKLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKED 89
           +P++    IYSP+Y      + K+      +   +   + +     +  IV+P  AS E+
Sbjct: 15  VPVY----IYSPEYVSMCDSLAKI----PKRASMVHSLIEAYALHKQMRIVKPKVASMEE 66
Query: 90  LLVVHSESYLKSLQ--SSPNVSIIIEVPPVALFPNCLVQRKVLYPFRKQVGGTILAAKLA 147
           +   H+++YL+ LQ  S        +     L  NC     + + +   +GG  + A   
Sbjct: 67  MATFHTDAYLQHLQKVSQEGDDDHPDSIEYGLGYNCPATEGI-FDYAAAIGGATITAAQC 125
Query: 148 KERGW---AINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGN 204
              G    AIN  GG+HH   DE  GFC   D  L I    ++    R++ +DLD H G+
Sbjct: 126 LIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGI--LRLRRKFERILYVDLDLHHGD 183
Query: 205 GHEKDFSSDSR 215
           G E  FS  S+
Sbjct: 184 GVEDAFSFTSK 194

>pdb|3F07|A Chain A, Crystal Structure Analysis Of Human Hdac8 Complexed With Apha In A New Monoclinic Crystal Form Length = 388

Iteration: 1
 Score = 60.8 bits (146), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 51/191 (26%), Positives = 84/191 (43%), Gaps = 16/191 (8%)
Query: 30  IPIFKLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKED 89
           +P++    IYSP+Y      + K+      +   +   + +     +  IV+P  AS E+
Sbjct: 15  VPVY----IYSPEYVSMCDSLAKI----PKRASMVHSLIEAYALHKQMRIVKPKVASMEE 66
Query: 90  LLVVHSESYLKSLQ--SSPNVSIIIEVPPVALFPNCLVQRKVLYPFRKQVGGTILAAKLA 147
           +   H+++YL+ LQ  S        +     L  +C     + + +   +GG  + A   
Sbjct: 67  MATFHTDAYLQHLQKVSQEGDDDHPDSIEYGLGYDCPATEGI-FDYAAAIGGATITAAQC 125
Query: 148 KERGW---AINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGN 204
              G    AIN  GG+HH   DE  GFC   D  L I    ++    R++ +DLD H G+
Sbjct: 126 LIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGI--LRLRRKFERILYVDLDLHHGD 183
Query: 205 GHEKDFSSDSR 215
           G E  FS  S+
Sbjct: 184 GVEDAFSFTSK 194

>pdb|3SFF|A Chain A, Crystal Structure Of Human Hdac8 Inhibitor Complex, An Amino Acid Derived Inhibitor Length = 378

Iteration: 1
 Score = 60.8 bits (146), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 51/191 (26%), Positives = 84/191 (43%), Gaps = 16/191 (8%)
Query: 30  IPIFKLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKED 89
           +P++    IYSP+Y      + K+      +   +   + +     +  IV+P  AS E+
Sbjct: 16  VPVY----IYSPEYVSMCDSLAKI----PKRASMVHSLIEAYALHKQMRIVKPKVASMEE 67
Query: 90  LLVVHSESYLKSLQ--SSPNVSIIIEVPPVALFPNCLVQRKVLYPFRKQVGGTILAAKLA 147
           +   H+++YL+ LQ  S        +     L  +C     + + +   +GG  + A   
Sbjct: 68  MATFHTDAYLQHLQKVSQEGDDDHPDSIEYGLGYDCPATEGI-FDYAAAIGGATITAAQC 126
Query: 148 KERGW---AINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGN 204
              G    AIN  GG+HH   DE  GFC   D  L I    ++    R++ +DLD H G+
Sbjct: 127 LIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGI--LRLRRKFERILYVDLDLHHGD 184
Query: 205 GHEKDFSSDSR 215
           G E  FS  S+
Sbjct: 185 GVEDAFSFTSK 195

>pdb|1T64|A Chain A, Crystal Structure Of Human Hdac8 Complexed With Trichostatin A Length = 377

Iteration: 1
 Score = 60.8 bits (146), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 51/191 (26%), Positives = 84/191 (43%), Gaps = 16/191 (8%)
Query: 30  IPIFKLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKED 89
           +P++    IYSP+Y      + K+      +   +   + +     +  IV+P  AS E+
Sbjct: 15  VPVY----IYSPEYVSMCDSLAKI----PKRASMVHSLIEAYALHKQMRIVKPKVASMEE 66
Query: 90  LLVVHSESYLKSLQ--SSPNVSIIIEVPPVALFPNCLVQRKVLYPFRKQVGGTILAAKLA 147
           +   H+++YL+ LQ  S        +     L  +C     + + +   +GG  + A   
Sbjct: 67  MATFHTDAYLQHLQKVSQEGDDDHPDSIEYGLGYDCPATEGI-FDYAAAIGGATITAAQC 125
Query: 148 KERGW---AINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGN 204
              G    AIN  GG+HH   DE  GFC   D  L I    ++    R++ +DLD H G+
Sbjct: 126 LIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGI--LRLRRKFERILYVDLDLHHGD 183
Query: 205 GHEKDFSSDSR 215
           G E  FS  S+
Sbjct: 184 GVEDAFSFTSK 194

>pdb|3MZ3|A Chain A, Crystal Structure Of Co2+ Hdac8 Complexed With M344 Length = 389

Iteration: 1
 Score = 60.8 bits (146), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 51/191 (26%), Positives = 84/191 (43%), Gaps = 16/191 (8%)
Query: 30  IPIFKLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKED 89
           +P++    IYSP+Y      + K+      +   +   + +     +  IV+P  AS E+
Sbjct: 15  VPVY----IYSPEYVSMCDSLAKI----PKRASMVHSLIEAYALHKQMRIVKPKVASMEE 66
Query: 90  LLVVHSESYLKSLQ--SSPNVSIIIEVPPVALFPNCLVQRKVLYPFRKQVGGTILAAKLA 147
           +   H+++YL+ LQ  S        +     L  +C     + + +   +GG  + A   
Sbjct: 67  MATFHTDAYLQHLQKVSQEGDDDHPDSIEYGLGYDCPATEGI-FDYAAAIGGATITAAQC 125
Query: 148 KERGW---AINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGN 204
              G    AIN  GG+HH   DE  GFC   D  L I    ++    R++ +DLD H G+
Sbjct: 126 LIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGI--LRLRRKFERILYVDLDLHHGD 183
Query: 205 GHEKDFSSDSR 215
           G E  FS  S+
Sbjct: 184 GVEDAFSFTSK 194

>pdb|2V5W|A Chain A, Crystal Structure Of Hdac8-Substrate Complex Length = 388

Iteration: 1
 Score = 60.8 bits (146), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 51/191 (26%), Positives = 84/191 (43%), Gaps = 16/191 (8%)
Query: 30  IPIFKLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKED 89
           +P++    IYSP+Y      + K+      +   +   + +     +  IV+P  AS E+
Sbjct: 15  VPVY----IYSPEYVSMCDSLAKI----PKRASMVHSLIEAYALHKQMRIVKPKVASMEE 66
Query: 90  LLVVHSESYLKSLQ--SSPNVSIIIEVPPVALFPNCLVQRKVLYPFRKQVGGTILAAKLA 147
           +   H+++YL+ LQ  S        +     L  +C     + + +   +GG  + A   
Sbjct: 67  MATFHTDAYLQHLQKVSQEGDDDHPDSIEYGLGYDCPATEGI-FDYAAAIGGATITAAQC 125
Query: 148 KERGW---AINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGN 204
              G    AIN  GG+HH   DE  GFC   D  L I    ++    R++ +DLD H G+
Sbjct: 126 LIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGI--LRLRRKFERILYVDLDLHHGD 183
Query: 205 GHEKDFSSDSR 215
           G E  FS  S+
Sbjct: 184 GVEDAFSFTSK 194

>pdb|2V5X|A Chain A, Crystal Structure Of Hdac8-Inhibitor Complex Length = 388

Iteration: 1
 Score = 60.5 bits (145), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 51/191 (26%), Positives = 84/191 (43%), Gaps = 16/191 (8%)
Query: 30  IPIFKLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKED 89
           +P++    IYSP+Y      + K+      +   +   + +     +  IV+P  AS E+
Sbjct: 15  VPVY----IYSPEYVSMCDSLAKI----PKRADMVHSLIEAYALHKQMRIVKPKVASMEE 66
Query: 90  LLVVHSESYLKSLQ--SSPNVSIIIEVPPVALFPNCLVQRKVLYPFRKQVGGTILAAKLA 147
           +   H+++YL+ LQ  S        +     L  +C     + + +   +GG  + A   
Sbjct: 67  MATFHTDAYLQHLQKVSQEGDDDHPDSIEYGLGYDCPATEGI-FDYAAAIGGATITAAQC 125
Query: 148 KERGW---AINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGN 204
              G    AIN  GG+HH   DE  GFC   D  L I    ++    R++ +DLD H G+
Sbjct: 126 LIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGI--LRLRRKFERILYVDLDLHHGD 183
Query: 205 GHEKDFSSDSR 215
           G E  FS  S+
Sbjct: 184 GVEDAFSFTSK 194

>pdb|3EZT|A Chain A, Crystal Structure Analysis Of Human Hdac8 D101e Variant Length = 388

Iteration: 1
 Score = 60.1 bits (144), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 51/191 (26%), Positives = 83/191 (43%), Gaps = 16/191 (8%)
Query: 30  IPIFKLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKED 89
           +P++    IYSP+Y      + K+      +   +   + +     +  IV+P  AS E+
Sbjct: 15  VPVY----IYSPEYVSMCDSLAKI----PKRASMVHSLIEAYALHKQMRIVKPKVASMEE 66
Query: 90  LLVVHSESYLKSLQ--SSPNVSIIIEVPPVALFPNCLVQRKVLYPFRKQVGGTILAAKLA 147
           +   H+++YL+ LQ  S        +     L   C     + + +   +GG  + A   
Sbjct: 67  MATFHTDAYLQHLQKVSQEGDDDHPDSIEYGLGYECPATEGI-FDYAAAIGGATITAAQC 125
Query: 148 KERGW---AINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGN 204
              G    AIN  GG+HH   DE  GFC   D  L I    ++    R++ +DLD H G+
Sbjct: 126 LIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGI--LRLRRKFERILYVDLDLHHGD 183
Query: 205 GHEKDFSSDSR 215
           G E  FS  S+
Sbjct: 184 GVEDAFSFTSK 194

>pdb|3EW8|A Chain A, Crystal Structure Analysis Of Human Hdac8 D101l Variant Length = 388

Iteration: 1
 Score = 59.7 bits (143), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 52/194 (26%), Positives = 85/194 (43%), Gaps = 22/194 (11%)
Query: 30  IPIFKLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKED 89
           +P++    IYSP+Y      + K+      +   +   + +     +  IV+P  AS E+
Sbjct: 15  VPVY----IYSPEYVSMCDSLAKI----PKRASMVHSLIEAYALHKQMRIVKPKVASMEE 66
Query: 90  LLVVHSESYLKSLQ-----SSPNVSIIIEVPPVALFPNCLVQRKVLYPFRKQVGGTILAA 144
           +   H+++YL+ LQ        +    IE     L P      + ++ +   +GG  + A
Sbjct: 67  MATFHTDAYLQHLQKVSQEGDDDHPDSIEYGLGYLCP----ATEGIFDYAAAIGGATITA 122
Query: 145 KLAKERGW---AINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAH 201
                 G    AIN  GG+HH   DE  GFC   D  L I    ++    R++ +DLD H
Sbjct: 123 AQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGI--LRLRRKFERILYVDLDLH 180
Query: 202 QGNGHEKDFSSDSR 215
            G+G E  FS  S+
Sbjct: 181 HGDGVEDAFSFTSK 194

>pdb|3MZ4|A Chain A, Crystal Structure Of D101l Mn2+ Hdac8 Complexed With M344 Length = 389

Iteration: 1
 Score = 59.7 bits (143), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 52/194 (26%), Positives = 85/194 (43%), Gaps = 22/194 (11%)
Query: 30  IPIFKLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKED 89
           +P++    IYSP+Y      + K+      +   +   + +     +  IV+P  AS E+
Sbjct: 15  VPVY----IYSPEYVSMCDSLAKI----PKRASMVHSLIEAYALHKQMRIVKPKVASMEE 66
Query: 90  LLVVHSESYLKSLQ-----SSPNVSIIIEVPPVALFPNCLVQRKVLYPFRKQVGGTILAA 144
           +   H+++YL+ LQ        +    IE     L P      + ++ +   +GG  + A
Sbjct: 67  MATFHTDAYLQHLQKVSQEGDDDHPDSIEYGLGYLCP----ATEGIFDYAAAIGGATITA 122
Query: 145 KLAKERGW---AINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAH 201
                 G    AIN  GG+HH   DE  GFC   D  L I    ++    R++ +DLD H
Sbjct: 123 AQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGI--LRLRRKFERILYVDLDLH 180
Query: 202 QGNGHEKDFSSDSR 215
            G+G E  FS  S+
Sbjct: 181 HGDGVEDAFSFTSK 194

>pdb|3F06|A Chain A, Crystal Structure Analysis Of Human Hdac8 D101a Variant. Length = 388

Iteration: 1
 Score = 59.7 bits (143), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 51/191 (26%), Positives = 83/191 (43%), Gaps = 16/191 (8%)
Query: 30  IPIFKLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKED 89
           +P++    IYSP+Y      + K+      +   +   + +     +  IV+P  AS E+
Sbjct: 15  VPVY----IYSPEYVSMCDSLAKI----PKRASMVHSLIEAYALHKQMRIVKPKVASMEE 66
Query: 90  LLVVHSESYLKSLQ--SSPNVSIIIEVPPVALFPNCLVQRKVLYPFRKQVGGTILAAKLA 147
           +   H+++YL+ LQ  S        +     L   C     + + +   +GG  + A   
Sbjct: 67  MATFHTDAYLQHLQKVSQEGDDDHPDSIEYGLGYACPATEGI-FDYAAAIGGATITAAQC 125
Query: 148 KERGW---AINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGN 204
              G    AIN  GG+HH   DE  GFC   D  L I    ++    R++ +DLD H G+
Sbjct: 126 LIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGI--LRLRRKFERILYVDLDLHHGD 183
Query: 205 GHEKDFSSDSR 215
           G E  FS  S+
Sbjct: 184 GVEDAFSFTSK 194

>pdb|3EWF|A Chain A, Crystal Structure Analysis Of Human Hdac8 H143a Variant Complexed With Substrate. Length = 388

Iteration: 1
 Score = 57.0 bits (136), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 50/191 (26%), Positives = 83/191 (43%), Gaps = 16/191 (8%)
Query: 30  IPIFKLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKED 89
           +P++    IYSP+Y      + K+      +   +   + +     +  IV+P  AS E+
Sbjct: 15  VPVY----IYSPEYVSMCDSLAKI----PKRASMVHSLIEAYALHKQMRIVKPKVASMEE 66
Query: 90  LLVVHSESYLKSLQ--SSPNVSIIIEVPPVALFPNCLVQRKVLYPFRKQVGGTILAAKLA 147
           +   H+++YL+ LQ  S        +     L  +C     + + +   +GG  + A   
Sbjct: 67  MATFHTDAYLQHLQKVSQEGDDDHPDSIEYGLGYDCPATEGI-FDYAAAIGGATITAAQC 125
Query: 148 KERGW---AINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGN 204
              G    AIN  GG+H    DE  GFC   D  L I    ++    R++ +DLD H G+
Sbjct: 126 LIDGMCKVAINWSGGWHAAKKDEASGFCYLNDAVLGI--LRLRRKFERILYVDLDLHHGD 183
Query: 205 GHEKDFSSDSR 215
           G E  FS  S+
Sbjct: 184 GVEDAFSFTSK 194

>pdb|1C3P|A Chain A, Crystal Structure Of An Hdac Homolog From Aquifex Aeolicus Length = 375

Iteration: 1
 Score = 57.0 bits (136), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 40/163 (24%), Positives = 72/163 (44%), Gaps = 6/163 (3%)
Query: 52  KLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSII 111
           K HP    +   + +F  +   +D+  +++   A+KE+LL+ H+E Y+ +L  +     +
Sbjct: 19  KNHPLKIPRVSLLLRFKDAMNLIDEKELIKSRPATKEELLLFHTEDYINTLMEAERCQCV 78
Query: 112 ----IEVPPVALFPNCLVQRKVLYPFRKQVGGTILAAKLAKERGWAINVGGGFHHCSADE 167
                E   +  + N  V   +        G T+ A +   +   A N  GG HH     
Sbjct: 79  PKGAREKYNIGGYENP-VSYAMFTGSSLATGSTVQAIEEFLKGNVAFNPAGGMHHAFKSR 137
Query: 168 GGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDF 210
             GFC   + ++ I Y   +    R++ IDLDAH  +G ++ F
Sbjct: 138 ANGFCYINNPAVGIEY-LRKKGFKRILYIDLDAHHCDGVQEAF 179

>pdb|1C3R|A Chain A, Crystal Structure Of An Hdac Homolog Complexed With Trichostatin A Length = 375

Iteration: 1
 Score = 56.6 bits (135), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 40/163 (24%), Positives = 72/163 (44%), Gaps = 6/163 (3%)
Query: 52  KLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSII 111
           K HP    +   + +F  +   +D+  +++   A+KE+LL+ H+E Y+ +L  +     +
Sbjct: 19  KNHPLKIPRVSLLLRFKDAMNLIDEKELIKSRPATKEELLLFHTEDYINTLMEAERSQSV 78
Query: 112 ----IEVPPVALFPNCLVQRKVLYPFRKQVGGTILAAKLAKERGWAINVGGGFHHCSADE 167
                E   +  + N  V   +        G T+ A +   +   A N  GG HH     
Sbjct: 79  PKGAREKYNIGGYENP-VSYAMFTGSSLATGSTVQAIEEFLKGNVAFNPAGGMHHAFKSR 137
Query: 168 GGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDF 210
             GFC   + ++ I Y   +    R++ IDLDAH  +G ++ F
Sbjct: 138 ANGFCYINNPAVGIEY-LRKKGFKRILYIDLDAHHCDGVQEAF 179

>pdb|4A69|A Chain A, Structure Of Hdac3 Bound To Corepressor And Inositol Tetraphosphate Length = 376

Iteration: 1
 Score = 54.7 bits (130), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 46/182 (25%), Positives = 73/182 (40%), Gaps = 7/182 (3%)
Query: 39  YSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESY 98
           Y  D D+        HP    +       +   G   K  + +P +AS+ D+   HSE Y
Sbjct: 7   YFYDPDVGNFHYGAGHPMKPHRLALTHSLVLHYGLYKKMIVFKPYQASQHDMCRFHSEDY 66
Query: 99  LKSLQSSPNVSIIIEVPPVALF---PNCLVQRKVLYPFRKQVGGTILAAKLAKER--GWA 153
           +  LQ     ++      +  F    +C V   +     +  G ++  A     +    A
Sbjct: 67  IDFLQRVSPTNMQGFTKSLNAFNVGDDCPVFPGLFEFCSRYTGASLQGATQLNNKICDIA 126
Query: 154 INVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSD 213
           IN  GG HH    E  GFC   DI + I    ++ +  RV+ ID+D H G+G ++ F   
Sbjct: 127 INWAGGLHHAKKFEASGFCYVNDIVIGI-LELLKYH-PRVLYIDIDIHHGDGVQEAFYLT 184
Query: 214 SR 215
            R
Sbjct: 185 DR 186

>pdb|3C0Y|A Chain A, Crystal Structure Of Catalytic Domain Of Human Histone Deacetylase Hdac7 Length = 423

Iteration: 1
 Score = 48.1 bits (113), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 61/237 (25%), Positives = 93/237 (39%), Gaps = 39/237 (16%)
Query: 14  ETLKRNRILSSKLYFDIPIFKLPLIYSPDYDISFL------GIEKLHPFDSSKWGRICQF 67
           E   + R+LSS    + P   LP      YD   L      G    HP  + +   I   
Sbjct: 18  EPASQARVLSSS---ETPARTLPFTTGLIYDSVMLKHQCSCGDNSRHPEHAGRIQSIWSR 74
Query: 68  LSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVALFPNCLVQR 127
           L   G   +   +   +AS E+L  VHSE ++    ++P   + ++   +A     L QR
Sbjct: 75  LQERGLRSQCECLRGRKASLEELQSVHSERHVLLYGTNPLSRLKLDNGKLA---GLLAQR 131
Query: 128 K-VLYP--------------------FRKQVGG-TILAAKLAK---ERGWAINVGGGFHH 162
             V+ P                     R   G  T LA K+A    + G+A+    G HH
Sbjct: 132 MFVMLPCGGVGVDTDTIWNELHSSNAARWAAGSVTDLAFKVASRELKNGFAVVRPPG-HH 190
Query: 163 CSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRSCLY 219
                  GFC +  +++       Q   S+++I+D D H GNG ++ F  D  S LY
Sbjct: 191 ADHSTAMGFCFFNSVAIACRQLQQQSKASKILIVDWDVHHGNGTQQTFYQDP-SVLY 246

>pdb|1ZZ0|A Chain A, Crystal Structure Of A Hdac-Like Protein With Acetate Bound Length = 369

Iteration: 1
 Score = 47.4 bits (111), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 40/165 (24%), Positives = 77/165 (46%), Gaps = 14/165 (8%)
Query: 54  HPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIE 113
           HP D+ +  R  + + + G ++    +  + A+  D+L  HS ++L++++   N+    +
Sbjct: 39  HP-DTKR--RFHELVCASGQIEHLTPIAAVAATDADILRAHSAAHLENMKRVSNLPTGGD 95
Query: 114 VPP-VALFPNCLVQRKVLYPFRKQVGGTI-LAAKLAK---ERGWAINVGGGFHHCSADEG 168
               + +  N  ++       R   GG + L  ++A      G+A+ V    HH   +  
Sbjct: 96  TGDGITMMGNGGLEIA-----RLSAGGAVELTRRVATGELSAGYAL-VNPPGHHAPHNAA 149
Query: 169 GGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSD 213
            GFC + + S+   YA   L + RV I+D D H GNG +  + +D
Sbjct: 150 MGFCIFNNTSVAAGYARAVLGMERVAILDWDVHHGNGTQDIWWND 194

>pdb|2VCG|A Chain A, Crystal Structure Of A Hdac-like Protein Hdah From Bordetella Sp. With The Bound Inhibitor St-17 Length = 375

Iteration: 1
 Score = 47.4 bits (111), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 40/165 (24%), Positives = 77/165 (46%), Gaps = 14/165 (8%)
Query: 54  HPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIE 113
           HP D+ +  R  + + + G ++    +  + A+  D+L  HS ++L++++   N+    +
Sbjct: 45  HP-DTKR--RFHELVCASGQIEHLTPIAAVAATDADILRAHSAAHLENMKRVSNLPTGGD 101
Query: 114 VPP-VALFPNCLVQRKVLYPFRKQVGGTI-LAAKLAK---ERGWAINVGGGFHHCSADEG 168
               + +  N  ++       R   GG + L  ++A      G+A+ V    HH   +  
Sbjct: 102 TGDGITMMGNGGLEIA-----RLSAGGAVELTRRVATGELSAGYAL-VNPPGHHAPHNAA 155
Query: 169 GGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSD 213
            GFC + + S+   YA   L + RV I+D D H GNG +  + +D
Sbjct: 156 MGFCIFNNTSVAAGYARAVLGMERVAILDWDVHHGNGTQDIWWND 200

>pdb|2VQO|A Chain A, Structure Of Hdac4 Catalytic Domain With A Gain-Of-Function Muation Bound To A Trifluoromethylketone Inhbitor Length = 413

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 45/195 (23%), Positives = 76/195 (38%), Gaps = 29/195 (14%)
Query: 49  GIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPN- 107
           G    HP  + +   I   L   G   K   +   +A+ E+L  VHSE++     ++P  
Sbjct: 26  GSSSSHPEHAGRIQSIWSRLQETGLRGKCEAIRGRKATLEELQTVHSEAHTLLYGTNPLN 85
Query: 108 -------------VSIIIEVPPVALFPNCLVQRKVLYPFRKQVGGTILAAKLAKERGWAI 154
                         S+ + +P   +     V    ++      G   LA     E  + +
Sbjct: 86  RQKLDSKKLLGSLASVFVRLPCGGVG----VDSDTIWNEVHSAGAARLAVGCVVELVFKV 141
Query: 155 NVG---GGF-------HHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGN 204
             G    GF       HH       GFC +  +++       +L++S+++I+D D H GN
Sbjct: 142 ATGELKNGFAVVRPPGHHAEESTPMGFCYFNSVAVAAKLLQQRLSVSKILIVDWDVHHGN 201
Query: 205 GHEKDFSSDSRSCLY 219
           G ++ F SD  S LY
Sbjct: 202 GTQQAFYSDP-SVLY 215

>pdb|2VQQ|A Chain A, Structure Of Hdac4 Catalytic Domain (A Double Cysteine-To- Alanine Mutant) Bound To A Trifluoromethylketone Inhbitor Length = 413

Iteration: 1
 Score = 45.8 bits (107), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 45/195 (23%), Positives = 76/195 (38%), Gaps = 29/195 (14%)
Query: 49  GIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPN- 107
           G    HP  + +   I   L   G   K   +   +A+ E+L  VHSE++     ++P  
Sbjct: 26  GSSSSHPEHAGRIQSIWSRLQETGLRGKCEAIRGRKATLEELQTVHSEAHTLLYGTNPLN 85
Query: 108 -------------VSIIIEVPPVALFPNCLVQRKVLYPFRKQVGGTILAAKLAKERGWAI 154
                         S+ + +P   +     V    ++      G   LA     E  + +
Sbjct: 86  RQKLDSKKLLGSLASVFVRLPCGGVG----VDSDTIWNEVHSAGAARLAVGCVVELVFKV 141
Query: 155 NVG---GGF-------HHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGN 204
             G    GF       HH       GFC +  +++       +L++S+++I+D D H GN
Sbjct: 142 ATGELKNGFAVVRPPGHHAEESTPMGFCYFNSVAVAAKLLQQRLSVSKILIVDWDVHHGN 201
Query: 205 GHEKDFSSDSRSCLY 219
           G ++ F SD  S LY
Sbjct: 202 GTQQAFYSDP-SVLY 215

>pdb|2VQW|G Chain G, Structure Of Inhibitor-Free Hdac4 Catalytic Domain (With Gain-Of-Function Mutation His332tyr) Length = 413

Iteration: 1
 Score = 45.8 bits (107), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 45/195 (23%), Positives = 76/195 (38%), Gaps = 29/195 (14%)
Query: 49  GIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPN- 107
           G    HP  + +   I   L   G   K   +   +A+ E+L  VHSE++     ++P  
Sbjct: 26  GSSSSHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHTLLYGTNPLN 85
Query: 108 -------------VSIIIEVPPVALFPNCLVQRKVLYPFRKQVGGTILAAKLAKERGWAI 154
                         S+ + +P   +     V    ++      G   LA     E  + +
Sbjct: 86  RQKLDSKKLLGSLASVFVRLPCGGVG----VDSDTIWNEVHSAGAARLAVGCVVELVFKV 141
Query: 155 NVG---GGF-------HHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGN 204
             G    GF       HH       GFC +  +++       +L++S+++I+D D H GN
Sbjct: 142 ATGELKNGFAVVRPPGHHAEESTPMGFCYFNSVAVAAKLLQQRLSVSKILIVDWDVHHGN 201
Query: 205 GHEKDFSSDSRSCLY 219
           G ++ F SD  S LY
Sbjct: 202 GTQQAFYSDP-SVLY 215

>pdb|2VQJ|A Chain A, Structure Of Hdac4 Catalytic Domain Bound To A Trifluoromethylketone Inhbitor Length = 413

Iteration: 1
 Score = 45.4 bits (106), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 45/195 (23%), Positives = 76/195 (38%), Gaps = 29/195 (14%)
Query: 49  GIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPN- 107
           G    HP  + +   I   L   G   K   +   +A+ E+L  VHSE++     ++P  
Sbjct: 26  GSSSSHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHTLLYGTNPLN 85
Query: 108 -------------VSIIIEVPPVALFPNCLVQRKVLYPFRKQVGGTILAAKLAKERGWAI 154
                         S+ + +P   +     V    ++      G   LA     E  + +
Sbjct: 86  RQKLDSKKLLGSLASVFVRLPCGGVG----VDSDTIWNEVHSAGAARLAVGCVVELVFKV 141
Query: 155 NVG---GGF-------HHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGN 204
             G    GF       HH       GFC +  +++       +L++S+++I+D D H GN
Sbjct: 142 ATGELKNGFAVVRPPGHHAEESTPMGFCYFNSVAVAAKLLQQRLSVSKILIVDWDVHHGN 201
Query: 205 GHEKDFSSDSRSCLY 219
           G ++ F SD  S LY
Sbjct: 202 GTQQAFYSDP-SVLY 215

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	223
3ew8_A	388	HD8, histone deacetylase 8; hydrolase, HDAC, metal	2e-32
1c3p_A	375	Protein (HDLP (histone deacetylase-like protein) )	2e-30
3max_A	367	HD2, histone deacetylase 2; class 2, HDAC, foot po	1e-29
4a69_A	376	Histone deacetylase 3,; transcription, hydrolase;	1e-27
2pqp_A	421	HD7A, histone deacetylase 7A; HDAC, structural gen	9e-19
3q9b_A	341	Acetylpolyamine amidohydrolase; HDAC, polyamines,	9e-17
1zz1_A	369	Histone deacetylase-like amidohydrolase; HET: SHH;	9e-16
3men_A	362	Acetylpolyamine aminohydrolase; histone deacetylas	5e-15

>3ew8_A HD8, histone deacetylase 8; hydrolase, HDAC, metalloenzyme, arginase fold, HDAC8, histon deacetylase, hydroxamate inhibitor, unliganded; HET: B3N; 1.80A {Homo sapiens} PDB: 3f06_A* 3ezp_A* 3ezt_A* 3f0r_A* 3f07_A* 2v5w_A* 2v5x_A* 3ewf_A* 3mz4_A* 3mz6_A* 3mz7_A* 3rqd_A* 3mz3_A* 1t64_A* 1t67_A* 1t69_A* 1vkg_A* 1w22_A* 3sff_A* 3sfh_A* Length = 388

 Score =  119 bits (301), Expect = 2e-32
 Identities = 51/188 (27%), Positives = 77/188 (40%), Gaps = 10/188 (5%)

Query: 37  LIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSE 96
            IYSP+Y    + +         +   +   + +     +  IV+P  AS E++   H++
Sbjct: 18  YIYSPEY----VSMCDSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVASMEEMATFHTD 73

Query: 97  SYLKSLQ--SSPNVSIIIEVPPVALFPNCLVQRKVLYPFRKQVGGTILAAK--LAKERGW 152
           +YL+ LQ  S        +     L   C     +        G TI AA+  +      
Sbjct: 74  AYLQHLQKVSQEGDDDHPDSIEYGLGYLCPATEGIFDYAAAIGGATITAAQCLIDGMCKV 133

Query: 153 AINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSS 212
           AIN  GG+HH   DE  GFC   D  L I     +    R++ +DLD H G+G E  FS 
Sbjct: 134 AINWSGGWHHAKKDEASGFCYLNDAVLGILRL--RRKFERILYVDLDLHHGDGVEDAFSF 191

Query: 213 DSRSCLYS 220
            S+    S
Sbjct: 192 TSKVMTVS 199

>1c3p_A Protein (HDLP (histone deacetylase-like protein) ); alpha/beta fold, lyase; 1.80A {Aquifex aeolicus} SCOP: c.42.1.2 PDB: 1c3r_A* 1c3s_A* Length = 375

 Score =  114 bits (288), Expect = 2e-30
 Identities = 43/196 (21%), Positives = 78/196 (39%), Gaps = 24/196 (12%)

Query: 37  LIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSE 96
           LI + DY          HP    +   + +F  +   +D+  +++   A+KE+LL+ H+E
Sbjct: 6   LIGTLDYGKYRYPKN--HPLKIPRVSLLLRFKDAMNLIDEKELIKSRPATKEELLLFHTE 63

Query: 97  SYLKSLQSSPNVSIIIEVP-----------PVALFPNCLVQRKVLYPF-RKQVGGTILAA 144
            Y+ +L  +     + +             PV            ++       G T+ A 
Sbjct: 64  DYINTLMEAERCQCVPKGAREKYNIGGYENPV--SYA-------MFTGSSLATGSTVQAI 114

Query: 145 KLAKERGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGN 204
           +   +   A N  GG HH       GFC   + ++ I Y   +    R++ IDLDAH  +
Sbjct: 115 EEFLKGNVAFNPAGGMHHAFKSRANGFCYINNPAVGIEYL-RKKGFKRILYIDLDAHHCD 173

Query: 205 GHEKDFSSDSRSCLYS 220
           G ++ F    +  + S
Sbjct: 174 GVQEAFYDTDQVFVLS 189

>3max_A HD2, histone deacetylase 2; class 2, HDAC, foot pocket, hydrolase; HET: LLX NHE; 2.05A {Homo sapiens} Length = 367

 Score =  112 bits (281), Expect = 1e-29
 Identities = 50/189 (26%), Positives = 78/189 (41%), Gaps = 9/189 (4%)

Query: 37  LIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSE 96
             Y  D    + G  + HP    +       L + G   K  I  P +A+ E++   HS+
Sbjct: 7   YYYDGDIGNYYYG--QGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTKYHSD 64

Query: 97  SYLKSLQS-SPN--VSIIIEVPPVALFPNCLVQRKVLYPFRKQVGGTILAAK--LAKERG 151
            Y+K L+S  P+       ++    +  +C V   +    +   GG++  A     ++  
Sbjct: 65  EYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAGAVKLNRQQTD 124

Query: 152 WAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFS 211
            A+N  GG HH    E  GFC   DI L I          RV+ ID+D H G+G E+ F 
Sbjct: 125 MAVNWAGGLHHAKKSEASGFCYVNDIVLAILEL--LKYHQRVLYIDIDIHHGDGVEEAFY 182

Query: 212 SDSRSCLYS 220
           +  R    S
Sbjct: 183 TTDRVMTVS 191

>4a69_A Histone deacetylase 3,; transcription, hydrolase; HET: I0P; 2.06A {Homo sapiens} Length = 376

 Score =  107 bits (268), Expect = 1e-27
 Identities = 49/189 (25%), Positives = 71/189 (37%), Gaps = 9/189 (4%)

Query: 37  LIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSE 96
             Y PD      G    HP    +       +   G   K  + +P +AS+ D+   HSE
Sbjct: 7   YFYDPDVGNFHYG--AGHPMKPHRLALTHSLVLHYGLYKKMIVFKPYQASQHDMCRFHSE 64

Query: 97  SYLKSLQSSPNVSIIIEVPPVALF---PNCLVQRKVLYPFRKQVGGTILAAK--LAKERG 151
            Y+  LQ     ++      +  F    +C V   +     +  G ++  A     K   
Sbjct: 65  DYIDFLQRVSPTNMQGFTKSLNAFNVGDDCPVFPGLFEFCSRYTGASLQGATQLNNKICD 124

Query: 152 WAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFS 211
            AIN  GG HH    E  GFC   DI + I          RV+ ID+D H G+G ++ F 
Sbjct: 125 IAINWAGGLHHAKKFEASGFCYVNDIVIGILEL--LKYHPRVLYIDIDIHHGDGVQEAFY 182

Query: 212 SDSRSCLYS 220
              R    S
Sbjct: 183 LTDRVMTVS 191

>3q9b_A Acetylpolyamine amidohydrolase; HDAC, polyamines, arginase fold, deacetylase, hydrolase-HYDR inhibitor complex; HET: B3N; 2.25A {Mycoplana ramosa} PDB: 3q9f_A* 3q9c_A* 3q9e_A* Length = 341

 Score = 76.7 bits (189), Expect = 9e-17
 Identities = 38/183 (20%), Positives = 61/183 (33%), Gaps = 36/183 (19%)

Query: 63  RICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVALFPN 122
            I   +   GF D   +V P     E +L VH   YL  L+++ +          A+  +
Sbjct: 35  WILAAVKEAGFDD---VVAPARHGLETVLKVHDAGYLNFLETAWDRWKAAGYKGEAIATS 91

Query: 123 CLVQRKVLYPFRKQVG---------------GTILAAKLAKERGWAIN----VGGGF--- 160
             V+R          G               GT  AA  +     AI+    +  G    
Sbjct: 92  FPVRRTSPRIPTDIEGQIGYYCNAAETAISPGTWEAALSSM--ASAIDGADLIAAGHKAA 149

Query: 161 --------HHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSS 212
                   HH   D  GG+C   + ++      +     ++ I+D+D H GNG +  F  
Sbjct: 150 FSLCRPPGHHAGIDMFGGYCFINNAAVAAQRL-LDKGAKKIAILDVDFHHGNGTQDIFYE 208

Query: 213 DSR 215
              
Sbjct: 209 RGD 211

>1zz1_A Histone deacetylase-like amidohydrolase; HET: SHH; 1.57A {Alcaligenaceae bacterium} PDB: 1zz0_A* 1zz3_A* 2gh6_A* 2vcg_A* Length = 369

 Score = 73.9 bits (182), Expect = 9e-16
 Identities = 33/160 (20%), Positives = 64/160 (40%), Gaps = 15/160 (9%)

Query: 63  RICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIEVPPVALFPN 122
           R  + + + G ++    +  + A+  D+L  HS ++L++++   N    +          
Sbjct: 45  RFHELVCASGQIEHLTPIAAVAATDADILRAHSAAHLENMKRVSN----LPTGGDTGDGI 100

Query: 123 CLVQRKVLYPFRKQVGGTILAAKLAKERGWAINVGGGF-------HHCSADEGGGFCAYA 175
            ++    L   R   GG +   +          +  G+       HH   +   GFC + 
Sbjct: 101 TMMGNGGLEIARLSAGGAVELTRRVATG----ELSAGYALVNPPGHHAPHNAAMGFCIFN 156

Query: 176 DISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSR 215
           + S+   YA   L + RV I+D D H GNG +  + +D  
Sbjct: 157 NTSVAAGYARAVLGMERVAILDWDVHHGNGTQDIWWNDPS 196

>3men_A Acetylpolyamine aminohydrolase; histone deacetylase; 2.20A {Burkholderia pseudomallei 1710B} Length = 362

 Score = 71.7 bits (176), Expect = 5e-15
 Identities = 37/213 (17%), Positives = 64/213 (30%), Gaps = 43/213 (20%)

Query: 38  IYSPDY------DISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLL 91
            + PD            G  ++      +  R+     + GF     + EP +     + 
Sbjct: 25  YFHPDQSLHHPRTYFSRGRMRMPQEVPERAARLVAAAFAMGFP----VREPDDFGIAPIA 80

Query: 92  VVHSESYLKSLQS-SPNVSIIIEVPPVALFPNCLVQR-KVLYPFRKQVG----------- 138
            VH   YL+ L++       + E        N  V+    L     Q             
Sbjct: 81  AVHDTHYLRFLETVHREWKAMPEDWGDEAMSNIFVREPNALRGVLAQAARHLADGSCPVG 140

Query: 139 -GTILAAKLAKERGWAI--------NVGGGF-------HHCSADEGGGFCAYADISLCIH 182
             T  AA  +     A+             +       HH   D  GGFC   + ++   
Sbjct: 141 EHTWRAAYWSA--QSALAAAAAVRDGAPAAYALCRPPGHHARVDAAGGFCYLNNAAIAAQ 198

Query: 183 YAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSR 215
               +   +RV ++D D H G G ++ F +   
Sbjct: 199 AL--RARHARVAVLDTDMHHGQGIQEIFYARRD 229

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	223
2pqp_A	421	HD7A, histone deacetylase 7A; HDAC, structural gen	100.0
1zz1_A	369	Histone deacetylase-like amidohydrolase; HET: SHH;	100.0
4a69_A	376	Histone deacetylase 3,; transcription, hydrolase;	100.0
3max_A	367	HD2, histone deacetylase 2; class 2, HDAC, foot po	100.0
1c3p_A	375	Protein (HDLP (histone deacetylase-like protein) )	100.0
2vqm_A	413	HD4, histone deacetylase 4; inhibitor, repressor,	100.0
3q9b_A	341	Acetylpolyamine amidohydrolase; HDAC, polyamines,	100.0
3ew8_A	388	HD8, histone deacetylase 8; hydrolase, HDAC, metal	100.0
3men_A	362	Acetylpolyamine aminohydrolase; histone deacetylas	100.0

>1zz1_A Histone deacetylase-like amidohydrolase; HET: SHH; 1.57A {Alcaligenaceae bacterium} PDB: 1zz0_A* 1zz3_A* 2gh6_A* 2vcg_A*

Probab=100.00  E-value=2.9e-59  Score=423.66  Aligned_cols=182  Identities=21%  Similarity=0.313  Sum_probs=168.1

Q ss_pred             CceeEEeCcccccccCCCCCC----------------CCCCchHHHHHHHHHHHCCCCCCceEecCCCCCHHHHhccCCH
Q 027427           33 FKLPLIYSPDYDISFLGIEKL----------------HPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSE   96 (223)
Q Consensus        33 ~~~~ivy~~~~~~h~~~~~~~----------------Hpe~p~R~~~i~~~L~~~gl~~~~~~~~p~~a~~e~l~~vHs~   96 (223)
                      |+++++|||+|..|.++  .+                |||+|+|++.|.+.|++.|+++.+++++|++|++++|++||++
T Consensus         1 m~t~~~y~~~~~~h~~~--~~~~~~~~~g~~~~~~~~Hpe~p~R~~~i~~~l~~~gl~~~~~~~~p~~a~~~~l~~vH~~   78 (369)
T 1zz1_A            1 MAIGYVWNTLYGWVDTG--TGSLAAANLTARMQPISHHLAHPDTKRRFHELVCASGQIEHLTPIAAVAATDADILRAHSA   78 (369)
T ss_dssp             -CEEEECCGGGGGCCCC--SSSSSCCBTTTTBCCCSSCTTCTHHHHHHHHHHHHTTGGGGSEECCCCCCCHHHHHTTSCH
T ss_pred             CeEEEEEchHHcccCCC--CcccccccccccccccCCCCCCHHHHHHHHHHHHhcCCCccceEeCCCcCCHHHHHHhccH
Confidence            57899999999999765  44                9999999999999999999999899999999999999999999


Q ss_pred             HHHHHHhcCCC-ccccccCCCcccCC-CcccccccHHHHHHHhhHHHHHHHHHhh----cCcEeecCCCCCCCCCCCCCc
Q 027427           97 SYLKSLQSSPN-VSIIIEVPPVALFP-NCLVQRKVLYPFRKQVGGTILAAKLAKE----RGWAINVGGGFHHCSADEGGG  170 (223)
Q Consensus        97 ~Yv~~l~~~~~-~~~~~e~~~~~~~~-d~~~~~~~~~~a~~a~Gg~l~aa~~~~~----~~~a~~~~~G~HHA~~~~~~G  170 (223)
                      +||++|++.+. ..      ...+++ ||++++++++++++++||++.|++.+++    ++||++|||| |||++++++|
T Consensus        79 ~Yv~~l~~~~~~~~------~~~l~~~dtp~~~~~~~~a~~aaG~~l~aa~~v~~g~~~~afa~~rppG-HHA~~~~a~G  151 (369)
T 1zz1_A           79 AHLENMKRVSNLPT------GGDTGDGITMMGNGGLEIARLSAGGAVELTRRVATGELSAGYALVNPPG-HHAPHNAAMG  151 (369)
T ss_dssp             HHHHHHHHHHHSTT------CEECSSSSCEECTTTHHHHHHHHHHHHHHHHHHHTTSCSEEEECCSSCC-TTCCTTCCBT
T ss_pred             HHHHHHHHhCcccc------ceecCCCCCCCChHHHHHHHHHHHHHHHHHHHHHhCCCcceEEEecCCc-cCcCCCCCCC
Confidence            99999998654 21      123566 9999999999999999999999999986    4689999999 9999999999


Q ss_pred             ccccchHHHHHHHHHHhcCCCeEEEEecCCcCCchhhHhhhcCCCEEEEeccC
Q 027427          171 FCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRSCLYSGYV  223 (223)
Q Consensus       171 FC~fNnvAIAa~~l~~~~~~~RV~IiD~DvHHGnGTq~if~~d~~Vl~iSlH~  223 (223)
                      ||+|||+||||++|++++|++||+|||||||||||||+|||+||+|+|||+|+
T Consensus       152 FC~fNnvAiAa~~l~~~~g~~RV~IvD~DvHHGnGTq~iF~~d~~Vl~~SiH~  204 (369)
T 1zz1_A          152 FCIFNNTSVAAGYARAVLGMERVAILDWDVHHGNGTQDIWWNDPSVLTISLHQ  204 (369)
T ss_dssp             TBSSCHHHHHHHHHHHTSCCSCEEEEECSSSCCHHHHHHTTTCTTEEEEEEEE
T ss_pred             chHhhHHHHHHHHHHHhcCCCeEEEEecCCCCchhhhHHhcCCCCEEEEeccC
Confidence            99999999999999999999999999999999999999999999999999996

>4a69_A Histone deacetylase 3,; transcription, hydrolase; HET: I0P; 2.06A {Homo sapiens}

Probab=100.00  E-value=2.6e-58  Score=417.57  Aligned_cols=188  Identities=25%  Similarity=0.374  Sum_probs=168.6

Q ss_pred             CCceeEEeCcccccccCCCCCCCCCCchHHHHHHHHHHHCCCCCCceEecCCCCCHHHHhccCCHHHHHHHhcCCCcccc
Q 027427           32 IFKLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSII  111 (223)
Q Consensus        32 ~~~~~ivy~~~~~~h~~~~~~~Hpe~p~R~~~i~~~L~~~gl~~~~~~~~p~~a~~e~l~~vHs~~Yv~~l~~~~~~~~~  111 (223)
                      +.++.++|||+|..|.++  ++|||+|+|++.|.++|++.|+++.+++++|++|++++|++||+++||++|++.+.....
T Consensus         2 ~~~~~~~y~~~~~~~~~g--~~HPe~p~Rl~~i~~~l~~~gl~~~~~~~~p~~At~e~L~~vHs~~Yi~~l~~~~~~~~~   79 (376)
T 4a69_A            2 AKTVAYFYDPDVGNFHYG--AGHPMKPHRLALTHSLVLHYGLYKKMIVFKPYQASQHDMCRFHSEDYIDFLQRVSPTNMQ   79 (376)
T ss_dssp             CCCEEEECCTTTTCCCCC--TTCSCCTHHHHHHHHHHHHTTGGGGSEEECCCCCCHHHHTTTSCHHHHHHHHHCCTTTGG
T ss_pred             CCeEEEEEChHHhCcCCC--CCCCcCHHHHHHHHHHHHhcCCCCCceEeCCCCCCHHHHHHhCCHHHHHHHHHhCcccch
Confidence            457999999999998754  789999999999999999999999999999999999999999999999999988754210


Q ss_pred             ---ccCCCcccCCCcccccccHHHHHHHhhHHHHHHHHHhhc--CcEeecCCCCCCCCCCCCCcccccchHHHHHHHHHH
Q 027427          112 ---IEVPPVALFPNCLVQRKVLYPFRKQVGGTILAAKLAKER--GWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFV  186 (223)
Q Consensus       112 ---~e~~~~~~~~d~~~~~~~~~~a~~a~Gg~l~aa~~~~~~--~~a~~~~~G~HHA~~~~~~GFC~fNnvAIAa~~l~~  186 (223)
                         .+.....+++||++++++++++++++||++.|++.++++  ++|++++||+|||++++++|||+|||+||||++|++
T Consensus        80 ~~~~~~~~~~l~~Dtpv~~~~~e~a~~aaGgtl~Aa~~v~~g~~~~A~~~~gG~HHA~~~~a~GFC~~NdvAiAa~~l~~  159 (376)
T 4a69_A           80 GFTKSLNAFNVGDDCPVFPGLFEFCSRYTGASLQGATQLNNKICDIAINWAGGLHHAKKFEASGFCYVNDIVIGILELLK  159 (376)
T ss_dssp             GGHHHHHHHTCSSSSCCCTTHHHHHHHHHHHHHHHHHHHHTTSCSEEEETTCCCTTCBTTBCBTTBSSCHHHHHHHHHTT
T ss_pred             hhhhhhceeccCCCCCcchHHHHHHHHHHHHHHHHHHHHHcCCcceeeeCCCCCCcCCcCCCCcchhhhHHHHHHHHHHH
Confidence               011123467899999999999999999999999988754  589999999999999999999999999999999997


Q ss_pred             hcCCCeEEEEecCCcCCchhhHhhhcCCCEEEEeccC
Q 027427          187 QLNISRVMIIDLDAHQGNGHEKDFSSDSRSCLYSGYV  223 (223)
Q Consensus       187 ~~~~~RV~IiD~DvHHGnGTq~if~~d~~Vl~iSlH~  223 (223)
                      +  .+||+|||||||||||||+|||+||+|||||+|+
T Consensus       160 ~--~~RV~ivD~DvHHGnGtq~iF~~d~~Vl~~S~H~  194 (376)
T 4a69_A          160 Y--HPRVLYIDIDIHHGDGVQEAFYLTDRVMTVSFHK  194 (376)
T ss_dssp             T--CSCEEEEECSSSCCHHHHHHTTTCSSEEEEEEEE
T ss_pred             h--CCcEEEEeccCCCCcchhhHhcCCCCEEEEeccc
Confidence            6  4999999999999999999999999999999995

>3max_A HD2, histone deacetylase 2; class 2, HDAC, foot pocket, hydrolase; HET: LLX NHE; 2.05A {Homo sapiens}

Probab=100.00  E-value=6.6e-58  Score=413.29  Aligned_cols=188  Identities=27%  Similarity=0.378  Sum_probs=169.2

Q ss_pred             CCceeEEeCcccccccCCCCCCCCCCchHHHHHHHHHHHCCCCCCceEecCCCCCHHHHhccCCHHHHHHHhcCCCcccc
Q 027427           32 IFKLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSII  111 (223)
Q Consensus        32 ~~~~~ivy~~~~~~h~~~~~~~Hpe~p~R~~~i~~~L~~~gl~~~~~~~~p~~a~~e~l~~vHs~~Yv~~l~~~~~~~~~  111 (223)
                      +.++.++|||+|..|.++  ++|||+|+|+++|.++|++.|+++.+++++|++|++++|++||+++||++|++.+.....
T Consensus         2 ~~~v~~~y~~~~~~~~~g--~~HPe~P~Rl~~i~~~L~~~gl~~~~~~~~p~~At~e~L~~vHs~~Yi~~l~~~~~~~~~   79 (367)
T 3max_A            2 KKKVCYYYDGDIGNYYYG--QGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTKYHSDEYIKFLRSIRPDNMS   79 (367)
T ss_dssp             CCCEEEECCGGGGGCCCC--TTCSCCTHHHHHHHHHHHHTTGGGGSEEECCCCCCHHHHTTTSCHHHHHHHHHCCGGGGG
T ss_pred             CCeEEEEECccccCcCCC--CCCCCCHHHHHHHHHHHHhcCCcccCeeeCCCCCCHHHHHhhCCHHHHHHHHHhCccccc
Confidence            468999999999999765  789999999999999999999999999999999999999999999999999987754211


Q ss_pred             ---ccCCCcccCCCcccccccHHHHHHHhhHHHHHHHHHhh--cCcEeecCCCCCCCCCCCCCcccccchHHHHHHHHHH
Q 027427          112 ---IEVPPVALFPNCLVQRKVLYPFRKQVGGTILAAKLAKE--RGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFV  186 (223)
Q Consensus       112 ---~e~~~~~~~~d~~~~~~~~~~a~~a~Gg~l~aa~~~~~--~~~a~~~~~G~HHA~~~~~~GFC~fNnvAIAa~~l~~  186 (223)
                         .+.....+++||++++++++++++++||++.|++.+++  .++|+++|||+|||++++++|||+|||+||||++|++
T Consensus        80 ~~~~~~~~~~l~~Dtp~~~~~~e~a~~aaGgsl~aa~~v~~~~~~~Ai~~pgG~HHA~~~~a~GFC~~NdvaiAa~~l~~  159 (367)
T 3max_A           80 EYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAGAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLK  159 (367)
T ss_dssp             GCHHHHHHTTCSSSSCCCTTHHHHHHHHHHHHHHHHHHHHTTSCSEEEETTCCCTTCBTTBCBTTBCSCHHHHHHHHHTT
T ss_pred             hhhhHhhhcCCCCCCCCchHHHHHHHHHHHHHHHHHHHhcccCcceEecCCCCCCcCCcCCCCCchhhhHHHHHHHHHHH
Confidence               00111345789999999999999999999999998874  4689999999999999999999999999999999987


Q ss_pred             hcCCCeEEEEecCCcCCchhhHhhhcCCCEEEEeccC
Q 027427          187 QLNISRVMIIDLDAHQGNGHEKDFSSDSRSCLYSGYV  223 (223)
Q Consensus       187 ~~~~~RV~IiD~DvHHGnGTq~if~~d~~Vl~iSlH~  223 (223)
                      .  .+||+|||||||||||||+|||+||+|+|+|+|+
T Consensus       160 ~--~~RV~ivD~DvHHGnGtq~iF~~d~~Vl~~S~H~  194 (367)
T 3max_A          160 Y--HQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHK  194 (367)
T ss_dssp             T--CSCEEEEECSSSCCHHHHHHTTTCSSEEEEEEEE
T ss_pred             c--CCcEEEEecCCCCCchhhHHhcCCCCEEEEeccc
Confidence            5  4999999999999999999999999999999995

>1c3p_A Protein (HDLP (histone deacetylase-like protein) ); alpha/beta fold, lyase; 1.80A {Aquifex aeolicus} SCOP: c.42.1.2 PDB: 1c3r_A* 1c3s_A*

Probab=100.00  E-value=2.6e-58  Score=418.19  Aligned_cols=188  Identities=23%  Similarity=0.329  Sum_probs=167.0

Q ss_pred             CceeEEeCcccccccCCCCCCCCCCchHHHHHHHHHHHCCCCCCceEecCCCCCHHHHhccCCHHHHHHHhcCCCccc--
Q 027427           33 FKLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSI--  110 (223)
Q Consensus        33 ~~~~ivy~~~~~~h~~~~~~~Hpe~p~R~~~i~~~L~~~gl~~~~~~~~p~~a~~e~l~~vHs~~Yv~~l~~~~~~~~--  110 (223)
                      ++++++|||+|..|.+  +++|||+|+|++.|+++|++.|+++.+++++|++|++++|++||+++||++|++.+....  
T Consensus         2 ~~t~~vy~~~~~~h~~--g~~Hpe~p~R~~~i~~~l~~~gl~~~~~~~~p~~at~~~l~~vH~~~Yv~~l~~~~~~~~~~   79 (375)
T 1c3p_A            2 KKVKLIGTLDYGKYRY--PKNHPLKIPRVSLLLRFKDAMNLIDEKELIKSRPATKEELLLFHTEDYINTLMEAERCQCVP   79 (375)
T ss_dssp             CCEEEEECGGGGGSCC--CTTCGGGSCCHHHHHHHHHHTTCCCGGGEEECCCCCHHHHTTTSCHHHHHHHHHHHHHTSCC
T ss_pred             ceEEEEECHHHcCCCC--CCCCCCCHHHHHHHHHHHHhcCCCCCCeEeCCCCCCHHHHHHhCCHHHHHHHHHhccccCCC
Confidence            4689999999999865  478999999999999999999999999999999999999999999999999987653210  


Q ss_pred             cccCCCccc-CCCcccccccHHHHHHHhhHHHHHHHHHhhcCcEeecCCCCCCCCCCCCCcccccchHHHHHHHHHHhcC
Q 027427          111 IIEVPPVAL-FPNCLVQRKVLYPFRKQVGGTILAAKLAKERGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLN  189 (223)
Q Consensus       111 ~~e~~~~~~-~~d~~~~~~~~~~a~~a~Gg~l~aa~~~~~~~~a~~~~~G~HHA~~~~~~GFC~fNnvAIAa~~l~~~~~  189 (223)
                      ..+.....+ ++||++++++++++++++||++.|++.+++++.|+++|||+|||++++++|||+|||+||||++|+++ |
T Consensus        80 ~~~~~~~~l~~~dtp~~~~~~~~a~~aaGg~l~aa~~v~~g~~a~~ppGG~HHA~~~~a~GFC~fNnvAiAa~~l~~~-g  158 (375)
T 1c3p_A           80 KGAREKYNIGGYENPVSYAMFTGSSLATGSTVQAIEEFLKGNVAFNPAGGMHHAFKSRANGFCYINNPAVGIEYLRKK-G  158 (375)
T ss_dssp             TTHHHHHCCSSSSSCSSTTTTHHHHHHHHHHHHHHHHHHTTCEEEETTCCCTTCBTTBCBTTBSSCHHHHHHHHHHHT-T
T ss_pred             hHHhhccccCCCCcccChhHHHHHHHHhhHHHHHHHHHHcCCceeecCcccceeeeccCCCceeecHHHHHHHHHHHh-C
Confidence            000011224 67999999999999999999999999999888788888888999999999999999999999999876 6


Q ss_pred             CCeEEEEecCCcCCchhhHhhhcCCCEEEEeccC
Q 027427          190 ISRVMIIDLDAHQGNGHEKDFSSDSRSCLYSGYV  223 (223)
Q Consensus       190 ~~RV~IiD~DvHHGnGTq~if~~d~~Vl~iSlH~  223 (223)
                      .+||+|||||||||||||+|||+||+|+|||+|+
T Consensus       159 ~~RV~IvD~DvHHGnGtq~iF~~dp~Vl~~SiH~  192 (375)
T 1c3p_A          159 FKRILYIDLDAHHCDGVQEAFYDTDQVFVLSLHQ  192 (375)
T ss_dssp             CCCEEEEECSSSCCHHHHHHHTTCSSEEEEEEEE
T ss_pred             CCeEEEEecCCCCCHHHHHHhccCCCEEEEeccc
Confidence            7999999999999999999999999999999995

>2vqm_A HD4, histone deacetylase 4; inhibitor, repressor, chromatin, coiled coil, transcription regulation, UBL conjugation, chromatin regulator; HET: HA3; 1.8A {Homo sapiens} PDB: 2vqj_A* 2vqw_G 2vqq_A* 2vqo_A* 2vqv_A* 3c10_A* 3c0z_A 3c0y_A*

Probab=100.00  E-value=1.3e-57  Score=418.19  Aligned_cols=193  Identities=22%  Similarity=0.279  Sum_probs=165.3

Q ss_pred             CCCCceeEEeCcccccccCCCC--CCCCCCchHHHHHHHHHHHCCCCCCceEecCCCCCHHHHhccCCHHHHHHHhcCCC
Q 027427           30 IPIFKLPLIYSPDYDISFLGIE--KLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPN  107 (223)
Q Consensus        30 ~~~~~~~ivy~~~~~~h~~~~~--~~Hpe~p~R~~~i~~~L~~~gl~~~~~~~~p~~a~~e~l~~vHs~~Yv~~l~~~~~  107 (223)
                      .|.++|++|||++|+.|.++++  ..|||+|+|++.|+++|++.|+.+.+++++|++|++++|++||+++||++++....
T Consensus         5 ~p~~~Tg~vyd~~~l~H~~~~g~~~~HPE~P~Rl~~i~~~L~~~gl~~~~~~~~p~~At~eeL~~vHs~~Yv~~~~~~~~   84 (413)
T 2vqm_A            5 KPRFTTGLVYDTLMLKHQCTCGSSSSHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHTLLYGTNPL   84 (413)
T ss_dssp             -CCSSEEEECCGGGCSCCCTTC-------CCCHHHHHHHHHHHHTHHHHSEEECCCCCCHHHHTTTSCHHHHHHHHSCGG
T ss_pred             CCCCeEEEEEcHHHhccCCCCCCCCCCCCCHHHHHHHHHHHHhCCCCcCCeEeCCCCCCHHHHHHhCCHHHHHHHhcCch
Confidence            4689999999999999987654  56999999999999999999999999999999999999999999999998876432


Q ss_pred             cccc----------------ccCCCcccCCCccccc-ccHHHHHHHhhHHHHHHHHHhh----cCcEeecCCCCCCCCCC
Q 027427          108 VSII----------------IEVPPVALFPNCLVQR-KVLYPFRKQVGGTILAAKLAKE----RGWAINVGGGFHHCSAD  166 (223)
Q Consensus       108 ~~~~----------------~e~~~~~~~~d~~~~~-~~~~~a~~a~Gg~l~aa~~~~~----~~~a~~~~~G~HHA~~~  166 (223)
                      ....                .......++.|+.++. .++.++++++|+++.|++.++.    ++||++|||| |||+++
T Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~dt~~~~~~s~~aA~laaG~~l~a~~~v~~g~~~~afa~vrppG-HHA~~~  163 (413)
T 2vqm_A           85 NRQKLDSKKLLGSLASVFVRLPCGGVGVDSDTIWNEVHSAGAARLAVGCVVELVFKVATGELKNGFAVVRPPG-HHAEES  163 (413)
T ss_dssp             GGCC----HHHHHHHHHEEECTTSCEEECTTSTHHHHHHHHHHHHHHHHHHHHHHHHHTTSSSEEEECCCSCC-TTCBTT
T ss_pred             hhhHhhhhhhccchhhhhhccccCCcCccCCccccchhHHHHHHHHHHHHHHHHHHHhcCCccceeeeccccc-ccCcCC
Confidence            2100                0112234566777665 6889999999999999999975    4689999998 999999


Q ss_pred             CCCcccccchHHHHHHHHHHhcCCCeEEEEecCCcCCchhhHhhhcCCCEEEEeccC
Q 027427          167 EGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRSCLYSGYV  223 (223)
Q Consensus       167 ~~~GFC~fNnvAIAa~~l~~~~~~~RV~IiD~DvHHGnGTq~if~~d~~Vl~iSlH~  223 (223)
                      +++|||+|||+||||+||+++++++||+|||||||||||||+|||+||+|+|+|+|+
T Consensus       164 ~a~GFC~~Nnvaiaa~~~~~~~~~~RV~ivD~DvHHGnGtq~iF~~d~~Vl~~S~H~  220 (413)
T 2vqm_A          164 TPMGFCYFNSVAVAAKLLQQRLSVSKILIVDWDVHHGNGTQQAFYSDPSVLYMSLHR  220 (413)
T ss_dssp             BCBTTBSSCHHHHHHHHHHHHSCCSCEEEEECSSSCCHHHHHHHTTCTTEEEEEEEE
T ss_pred             CCCCccccchHHHHHHHHHHhcCCCeEEEEecccCCCccHHHHHhcCcccccccchh
Confidence            999999999999999999999999999999999999999999999999999999995

>3q9b_A Acetylpolyamine amidohydrolase; HDAC, polyamines, arginase fold, deacetylase, hydrolase-HYDR inhibitor complex; HET: B3N; 2.25A {Mycoplana ramosa} PDB: 3q9f_A* 3q9c_A* 3q9e_A*

Probab=100.00  E-value=1.1e-56  Score=401.99  Aligned_cols=184  Identities=20%  Similarity=0.224  Sum_probs=161.3

Q ss_pred             eeEEeCcccccccCCCC------CCCCCCchHHHHHHHHHHHCCCCCCceEecCCCCCHHHHhccCCHHHHHHHhcCCCc
Q 027427           35 LPLIYSPDYDISFLGIE------KLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNV  108 (223)
Q Consensus        35 ~~ivy~~~~~~h~~~~~------~~Hpe~p~R~~~i~~~L~~~gl~~~~~~~~p~~a~~e~l~~vHs~~Yv~~l~~~~~~  108 (223)
                      +.++|+|+|+.|..+..      ..|||+|+|++.|+++|++.|+.   ++++|++|++++|++||+++||++|++.+..
T Consensus         1 m~~v~~~~~~~H~~~~~~~~G~~~~HPE~P~Rl~~i~~~L~~~gl~---~~~~p~~at~e~L~~vHs~~Yi~~l~~~~~~   77 (341)
T 3q9b_A            1 MRVIFSEDHKLRNAKTELYGGELVPPFEAPFRAEWILAAVKEAGFD---DVVAPARHGLETVLKVHDAGYLNFLETAWDR   77 (341)
T ss_dssp             CEEECCGGGGGCCCSCEEETTEEECCSSCTHHHHHHHHHHHHTTCC---CEECCCCCCSTTGGGTSCHHHHHHHHHHHHH
T ss_pred             CEEEECcHHhccCCcccccCCCcCCCCCChHHHHHHHHHHHhCCCC---ceeCCCCCCHHHHHHhCCHHHHHHHHHhhhh
Confidence            46899999999976521      25999999999999999999985   5789999999999999999999999876421


Q ss_pred             c-----c---cccC------------------CCcccCCCcccccccHHHHHHHhhHHHHHHHHHhh---cCcEeecCCC
Q 027427          109 S-----I---IIEV------------------PPVALFPNCLVQRKVLYPFRKQVGGTILAAKLAKE---RGWAINVGGG  159 (223)
Q Consensus       109 ~-----~---~~e~------------------~~~~~~~d~~~~~~~~~~a~~a~Gg~l~aa~~~~~---~~~a~~~~~G  159 (223)
                      +     +   ..+.                  ....+++||++++++|+++++++|+++.|++.+++   ++||++||||
T Consensus        78 ~~~~~~~~~~~~~~~p~~~~~~~~p~~~~~~~g~~~~d~dt~~~~~~~~aa~~aaG~~l~a~~~v~~g~~~afal~rppG  157 (341)
T 3q9b_A           78 WKAAGYKGEAIATSFPVRRTSPRIPTDIEGQIGYYCNAAETAISPGTWEAALSSMASAIDGADLIAAGHKAAFSLCRPPG  157 (341)
T ss_dssp             HHHTTCSSCBCCCBCCCTTCCCCCCSSHHHHHHHTBSBTTCCBCTTHHHHHHHHHHHHHHHHHHHHHTCSEEEECCSSCC
T ss_pred             hhhcccccccccccccccccccccccchhcccceeccCCCCCcChhHHHHHHHHHHHHHHHHHHHHhCCCceEecCCCCC
Confidence            1     0   0000                  01246789999999999999999999999999986   3699999999


Q ss_pred             CCCCCCCCCCcccccchHHHHHHHHHHhcCCCeEEEEecCCcCCchhhHhhhcCCCEEEEeccC
Q 027427          160 FHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRSCLYSGYV  223 (223)
Q Consensus       160 ~HHA~~~~~~GFC~fNnvAIAa~~l~~~~~~~RV~IiD~DvHHGnGTq~if~~d~~Vl~iSlH~  223 (223)
                       |||++++++|||+|||+||||++|+++ |++||+|||||||||||||+|||+||+|||+|+|+
T Consensus       158 -HHA~~~~a~GFC~~NnvaiAa~~l~~~-g~~RV~ivD~DvHHGnGtq~iF~~d~~Vl~~S~H~  219 (341)
T 3q9b_A          158 -HHAGIDMFGGYCFINNAAVAAQRLLDK-GAKKIAILDVDFHHGNGTQDIFYERGDVFFASLHG  219 (341)
T ss_dssp             -TTCBTTBBBTTBSSCHHHHHHHHHHHT-TCSCEEEEECSSSCCHHHHHHHTTCTTEEEEEEEE
T ss_pred             -CCCCCCCCCCccccCHHHHHHHHHHHc-CCCeEEEEecCCCCCcchhHHhcCCCCEEEEeccC
Confidence             999999999999999999999999985 69999999999999999999999999999999995

>3ew8_A HD8, histone deacetylase 8; hydrolase, HDAC, metalloenzyme, arginase fold, HDAC8, histon deacetylase, hydroxamate inhibitor, unliganded; HET: B3N; 1.80A {Homo sapiens} SCOP: c.42.1.2 PDB: 3f06_A* 3ezp_A* 3ezt_A* 3f0r_A* 3f07_A* 2v5w_A* 2v5x_A* 3ewf_A* 3mz4_A* 3mz6_A* 3mz7_A* 3rqd_A* 3mz3_A* 1t64_A* 1t67_A* 1t69_A* 1vkg_A* 1w22_A* 3sff_A* 3sfh_A*

Probab=100.00  E-value=1.1e-56  Score=407.26  Aligned_cols=190  Identities=26%  Similarity=0.296  Sum_probs=165.3

Q ss_pred             ccCCCCceeEEeCcccccccCCCCCCCCCCchHHHHHHHHHHHCCCCCCceEecCCCCCHHHHhccCCHHHHHHHhcCCC
Q 027427           28 FDIPIFKLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPN  107 (223)
Q Consensus        28 ~~~~~~~~~ivy~~~~~~h~~~~~~~Hpe~p~R~~~i~~~L~~~gl~~~~~~~~p~~a~~e~l~~vHs~~Yv~~l~~~~~  107 (223)
                      ...++.++.++|+|+|..|.    .+|||+|+|+++|.++|++.|+++.+++++|++|++++|++||+++||++|++.+.
T Consensus         9 ~~~~~~~~~~~y~~~~~~~~----~~HPe~P~Rl~~i~~ll~~~gl~~~~~~~~p~~At~e~L~~vHs~~Yi~~l~~~~~   84 (388)
T 3ew8_A            9 DSGQSLVPVYIYSPEYVSMC----DSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVASMEEMATFHTDAYLQHLQKVSQ   84 (388)
T ss_dssp             -----CCCEEECCHHHHHHH----TTCTTSTTHHHHHHHHHHHTTGGGGSEEECCCCCCHHHHTTTSCHHHHHHHHHHHH
T ss_pred             ccCCCCcEEEEEChHHhccC----CCCCCCcHHHHHHHHHHHHcCCcccCeEeCCCCCCHHHHHhhCCHHHHHHHHHhcc
Confidence            35667889999999999873    46999999999999999999999999999999999999999999999999998654


Q ss_pred             cccc--ccCCCcccCCCcccccccHHHHHHHhhHHHHHHHHHhhc--CcEeecCCCCCCCCCCCCCcccccchHHHHHHH
Q 027427          108 VSII--IEVPPVALFPNCLVQRKVLYPFRKQVGGTILAAKLAKER--GWAINVGGGFHHCSADEGGGFCAYADISLCIHY  183 (223)
Q Consensus       108 ~~~~--~e~~~~~~~~d~~~~~~~~~~a~~a~Gg~l~aa~~~~~~--~~a~~~~~G~HHA~~~~~~GFC~fNnvAIAa~~  183 (223)
                      ....  .+.....++.||++++++++++++++||++.|++.++++  ++|+++|||+|||++++++|||+|||+||||++
T Consensus        85 ~~~~~~~~~~~~~lg~Dtp~~~~~~e~a~~aaGgsl~Aa~~v~~g~~~~Ai~~pGG~HHA~~~~a~GFC~~NdiaiAa~~  164 (388)
T 3ew8_A           85 EGDDDHPDSIEYGLGYLCPATEGIFDYAAAIGGATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILR  164 (388)
T ss_dssp             HC--------CCSCSSSSCCCTTHHHHHHHHHHHHHHHHHHHHTTSCSEEEETTCCCTTCBTTBCBTTBSSCHHHHHHHH
T ss_pred             cccccchhhhhccCCCCCCCChhHHHHHHHHHHHHHHHHHHHHcCCCceeeecCCcccceeecCCCCchhhhHHHHHHHH
Confidence            2211  011223456799999999999999999999999999865  589999999999999999999999999999999


Q ss_pred             HHHhcCCCeEEEEecCCcCCchhhHhhhcCCCEEEEeccC
Q 027427          184 AFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRSCLYSGYV  223 (223)
Q Consensus       184 l~~~~~~~RV~IiD~DvHHGnGTq~if~~d~~Vl~iSlH~  223 (223)
                      |++.  .+||+|||||||||||||+|||+||+|||||+|+
T Consensus       165 l~~~--~~RV~ivD~DvHHGnGtq~iF~~d~~Vl~~S~H~  202 (388)
T 3ew8_A          165 LRRK--FERILYVDLDLHHGDGVEDAFSFTSKVMTVSLHK  202 (388)
T ss_dssp             HTTT--CSCEEEEECSSSCCHHHHHHTTTCSSEEEEEEEE
T ss_pred             HHhc--CCeEEEEecCCCCChhHHHHhccCCCEEEEecCC
Confidence            9864  7999999999999999999999999999999995

>3men_A Acetylpolyamine aminohydrolase; histone deacetylase; 2.20A {Burkholderia pseudomallei 1710B}

Probab=100.00  E-value=1.5e-56  Score=403.34  Aligned_cols=182  Identities=19%  Similarity=0.248  Sum_probs=159.9

Q ss_pred             eeEEeCcccccccCCCC------CCCCCCchHHHHHHHHHHHCCCCCCceEecCCCCCHHHHhccCCHHHHHHHhcCCCc
Q 027427           35 LPLIYSPDYDISFLGIE------KLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNV  108 (223)
Q Consensus        35 ~~ivy~~~~~~h~~~~~------~~Hpe~p~R~~~i~~~L~~~gl~~~~~~~~p~~a~~e~l~~vHs~~Yv~~l~~~~~~  108 (223)
                      +.++|||+|+.|..+..      ..|||+|+|++.|+++|++.|+    ++++|++|++++|++||+++||++|++.+..
T Consensus        22 M~~~~~~~~~~H~~~~~~~~G~~~~HPE~P~Rl~~i~~~L~~~gl----~~~~p~~At~e~L~~vHs~~YI~~l~~~~~~   97 (362)
T 3men_A           22 MLTYFHPDQSLHHPRTYFSRGRMRMPQEVPERAARLVAAAFAMGF----PVREPDDFGIAPIAAVHDTHYLRFLETVHRE   97 (362)
T ss_dssp             CEEECCGGGGGCCCCCEEETTEEECCCSCTHHHHHHHHHHHHTTC----CEECCCCCCSHHHHTTSCHHHHHHHHHHHHH
T ss_pred             eEEEEChHHHhhCCccccccCCcCCCCCChHHHHHHHHHHHhCCC----eEeCCCCCCHHHHHHhCCHHHHHHHHHhhhh
Confidence            56999999999986521      3699999999999999999997    6899999999999999999999999876421


Q ss_pred             cc------ccc-CC------------------CcccCCCcccccccHHHHHHHhhHHHHHHHHHhh---cCcEeecCCCC
Q 027427          109 SI------IIE-VP------------------PVALFPNCLVQRKVLYPFRKQVGGTILAAKLAKE---RGWAINVGGGF  160 (223)
Q Consensus       109 ~~------~~e-~~------------------~~~~~~d~~~~~~~~~~a~~a~Gg~l~aa~~~~~---~~~a~~~~~G~  160 (223)
                      +.      ..| ++                  ...+++||++++++|++|++++|+++.|++.+++   ++||++|||| 
T Consensus        98 ~~~~~~~~~~e~~p~~~p~~~~~p~~~~~~~g~~~~d~Dtpv~~~~~~aa~~aaG~~l~aa~~v~~g~~~afal~rPpG-  176 (362)
T 3men_A           98 WKAMPEDWGDEAMSNIFVREPNALRGVLAQAARHLADGSCPVGEHTWRAAYWSAQSALAAAAAVRDGAPAAYALCRPPG-  176 (362)
T ss_dssp             HHTSCGGGCSSBCCCBCCCSSCCCCSHHHHHHHHBCBTTCCBCTTHHHHHHHHHHHHHHHHHHHHTTCSEEEECCSSCC-
T ss_pred             hhhcccccccccccccccccccccccccccccccccCCCCccchhHHHHHHHHHHHHHHHHHHHHcCCCceEEeCCCCC-
Confidence            10      000 00                  0235789999999999999999999999999985   3699999999 


Q ss_pred             CCCCCCCCCcccccchHHHHHHHHHHhcCCCeEEEEecCCcCCchhhHhhhcCCCEEEEeccC
Q 027427          161 HHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRSCLYSGYV  223 (223)
Q Consensus       161 HHA~~~~~~GFC~fNnvAIAa~~l~~~~~~~RV~IiD~DvHHGnGTq~if~~d~~Vl~iSlH~  223 (223)
                      |||++++++|||+|||+||||++|+++  .+||+|||||||||||||+|||+||+|+|+|+|+
T Consensus       177 HHA~~~~a~GFC~fNnvAiAa~~l~~~--~~RV~ivD~DvHHGnGtq~iF~~d~~Vl~~S~H~  237 (362)
T 3men_A          177 HHARVDAAGGFCYLNNAAIAAQALRAR--HARVAVLDTDMHHGQGIQEIFYARRDVLYVSIHG  237 (362)
T ss_dssp             TTCBTTBBBTTBSSCHHHHHHHHHTTT--CSCEEEEECSSSCCHHHHHHTTTCSSEEEEEEEE
T ss_pred             CCCCCCCCCCccccCHHHHHHHHHHHc--CCeEEEEeCcCCCchhHhHHhcCCCCEEEEEecC
Confidence            999999999999999999999999987  6999999999999999999999999999999995

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	223
d1c3pa_	372	c.42.1.2 (A:) HDAC homologue {Aquifex aeolicus [Ta	9e-21
d1t64a_	364	c.42.1.2 (A:) Histone deacetylase 8, HDAC8 {Human	7e-18
d3c10a1	386	c.42.1.2 (A:515-900) Histone deacetylase 7, HDAC7	5e-16

>d1c3pa_ c.42.1.2 (A:) HDAC homologue {Aquifex aeolicus [TaxId: 63363]} Length = 372

class: Alpha and beta proteins (a/b)
fold: Arginase/deacetylase
superfamily: Arginase/deacetylase
family: Histone deacetylase, HDAC
domain: HDAC homologue
species: Aquifex aeolicus [TaxId: 63363]

 Score = 86.9 bits (214), Expect = 9e-21
 Identities = 42/187 (22%), Positives = 76/187 (40%), Gaps = 6/187 (3%)

Query: 34  KLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVV 93
           K+ LI + DY          HP    +   + +F  +   +D+  +++   A+KE+LL+ 
Sbjct: 2   KVKLIGTLDYGKYRYPKN--HPLKIPRVSLLLRFKDAMNLIDEKELIKSRPATKEELLLF 59

Query: 94  HSESYLKSLQSSPNVSIIIEVPPVALFP---NCLVQRKVLYPFRKQVGGTILAAKLAKER 150
           H+E Y+ +L  +     + +              V   +        G T+ A +   + 
Sbjct: 60  HTEDYINTLMEAERCQCVPKGAREKYNIGGYENPVSYAMFTGSSLATGSTVQAIEEFLKG 119

Query: 151 GWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDF 210
             A N  GG HH       GFC   + ++ I Y   +    R++ IDLDAH  +G ++ F
Sbjct: 120 NVAFNPAGGMHHAFKSRANGFCYINNPAVGIEYLR-KKGFKRILYIDLDAHHCDGVQEAF 178

Query: 211 SSDSRSC 217
               +  
Sbjct: 179 YDTDQVF 185

>d1t64a_ c.42.1.2 (A:) Histone deacetylase 8, HDAC8 {Human (Homo sapiens) [TaxId: 9606]} Length = 364

class: Alpha and beta proteins (a/b)
fold: Arginase/deacetylase
superfamily: Arginase/deacetylase
family: Histone deacetylase, HDAC
domain: Histone deacetylase 8, HDAC8
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 78.7 bits (193), Expect = 7e-18
 Identities = 51/194 (26%), Positives = 81/194 (41%), Gaps = 14/194 (7%)

Query: 30  IPIFKLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKED 89
           +P++    IYSP+Y    + +         +   +   + +     +  IV+P  AS E+
Sbjct: 2   VPVY----IYSPEY----VSMCDSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVASMEE 53

Query: 90  LLVVHSESYLKSLQ--SSPNVSIIIEVPPVALFPNCLVQRKVLYPFRKQVGGTILAAK-- 145
           +   H+++YL+ LQ  S        +     L  +C     +        G TI AA+  
Sbjct: 54  MATFHTDAYLQHLQKVSQEGDDDHPDSIEYGLGYDCPATEGIFDYAAAIGGATITAAQCL 113

Query: 146 LAKERGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNG 205
           +      AIN  GG+HH   DE  GFC   D  L I     +    R++ +DLD H G+G
Sbjct: 114 IDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRL--RRKFERILYVDLDLHHGDG 171

Query: 206 HEKDFSSDSRSCLY 219
            E  FS  S+    
Sbjct: 172 VEDAFSFTSKVMTV 185

>d3c10a1 c.42.1.2 (A:515-900) Histone deacetylase 7, HDAC7 {Human (Homo sapiens) [TaxId: 9606]} Length = 386

class: Alpha and beta proteins (a/b)
fold: Arginase/deacetylase
superfamily: Arginase/deacetylase
family: Histone deacetylase, HDAC
domain: Histone deacetylase 7, HDAC7
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 73.8 bits (180), Expect = 5e-16
 Identities = 37/206 (17%), Positives = 67/206 (32%), Gaps = 23/206 (11%)

Query: 37  LIYSPDYD--ISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVH 94
           LIY           G    HP  + +   I   L   G   +   +   +AS E+L  VH
Sbjct: 8   LIYDSVMLKHQCSCGDNSRHPEHAGRIQSIWSRLQERGLRSQCECLRGRKASLEELQSVH 67

Query: 95  SESYLKSLQSSP-----------------NVSIIIEVPPVALFPNCLVQRKVLYPFRKQV 137
           SE ++    ++P                  + +++    V +  + +          +  
Sbjct: 68  SERHVLLYGTNPLSRLKLDNGKLAGLLAQRMFVMLPCGGVGVDTDTIWNELHSSNAARWA 127

Query: 138 GGTILAAKLAKERG----WAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRV 193
            G++                  V    HH       GFC +  +++       Q   S++
Sbjct: 128 AGSVTDLAFKVASRELKNGFAVVRPPGHHADHSTAMGFCFFNSVAIACRQLQQQSKASKI 187

Query: 194 MIIDLDAHQGNGHEKDFSSDSRSCLY 219
           +I+D D H GNG ++ F  D      
Sbjct: 188 LIVDWDVHHGNGTQQTFYQDPSVLYI 213

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	223
d3c10a1	386	Histone deacetylase 7, HDAC7 {Human (Homo sapiens)	100.0
d1c3pa_	372	HDAC homologue {Aquifex aeolicus [TaxId: 63363]}	100.0
d1t64a_	364	Histone deacetylase 8, HDAC8 {Human (Homo sapiens)	100.0

>d3c10a1 c.42.1.2 (A:515-900) Histone deacetylase 7, HDAC7 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Arginase/deacetylase
superfamily: Arginase/deacetylase
family: Histone deacetylase, HDAC
domain: Histone deacetylase 7, HDAC7
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=3.8e-56  Score=403.78  Aligned_cols=190  Identities=22%  Similarity=0.269  Sum_probs=168.0

Q ss_pred             CceeEEeCcccccccCCCC--CCCCCCchHHHHHHHHHHHCCCCCCceEecCCCCCHHHHhccCCHHHHHHHhcCCCccc
Q 027427           33 FKLPLIYSPDYDISFLGIE--KLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSI  110 (223)
Q Consensus        33 ~~~~ivy~~~~~~h~~~~~--~~Hpe~p~R~~~i~~~L~~~gl~~~~~~~~p~~a~~e~l~~vHs~~Yv~~l~~~~~~~~  110 (223)
                      ..|++||||+|+.|.++++  ..|||+|+|++.|++.|++.|+.+.+++++|++|+.++|.+||+++||+++........
T Consensus         4 ~~Tg~vyd~~~l~H~~~~g~~~~HPE~p~Rl~~i~~~L~~~gl~~~~~~~~p~~a~~~~L~~vH~~~YI~~l~~~~~~~~   83 (386)
T d3c10a1           4 FTTGLIYDSVMLKHQCSCGDNSRHPEHAGRIQSIWSRLQERGLRSQCECLRGRKASLEELQSVHSERHVLLYGTNPLSRL   83 (386)
T ss_dssp             TCEEEECCGGGGGCCCTTCCGGGCSSCTHHHHHHHHHHHHTTCGGGSEEECCCCCCHHHHTTTSCHHHHHHHHCCTTCSC
T ss_pred             CCEEEEECHHHhcCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCccCCeEeCCCCCCHHHHHHhCCHHHHHHHhhchhhhh
Confidence            5689999999999987654  45999999999999999999999999999999999999999999999999976543210


Q ss_pred             c-----------------ccCCCcccCCCccccc-ccHHHHHHHhhHHHHHHHHHhh----cCcEeecCCCCCCCCCCCC
Q 027427          111 I-----------------IEVPPVALFPNCLVQR-KVLYPFRKQVGGTILAAKLAKE----RGWAINVGGGFHHCSADEG  168 (223)
Q Consensus       111 ~-----------------~e~~~~~~~~d~~~~~-~~~~~a~~a~Gg~l~aa~~~~~----~~~a~~~~~G~HHA~~~~~  168 (223)
                      .                 .......+++|+++++ .+++++++++|+++.|++.++.    ++||+++||| |||.++++
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~~d~dt~~~~~~s~~Aa~~aaG~~~~a~~~v~~~~~~~afa~~rppG-HHA~~~~~  162 (386)
T d3c10a1          84 KLDNGKLAGLLAQRMFVMLPCGGVGVDTDTIWNELHSSNAARWAAGSVTDLAFKVASRELKNGFAVVRPPG-HHADHSTA  162 (386)
T ss_dssp             CCCHHHHHHHHHC---CBCTTSCEESSSSCEECTTTHHHHHHHHHHHHHHHHHHHHTTSSSEEEECCSSCC-TTCBTTBC
T ss_pred             cccccccchhhhhhhhcccCCCCcccCCCcccCcchHHHHHHHHhhHHHHHHhhhhcCccccccccccccc-cccccccc
Confidence            0                 0012234567888877 7899999999999999999874    4689999998 99999999


Q ss_pred             CcccccchHHHHHHHHHHhcCCCeEEEEecCCcCCchhhHhhhcCCCEEEEeccC
Q 027427          169 GGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRSCLYSGYV  223 (223)
Q Consensus       169 ~GFC~fNnvAIAa~~l~~~~~~~RV~IiD~DvHHGnGTq~if~~d~~Vl~iSlH~  223 (223)
                      +|||+|||+||||+||+++++++||+|||||||||||||+|||+||+|+|+|+|+
T Consensus       163 ~GFC~fNdvAiaa~~l~~~~~~~rV~iiD~DvHhGnGTq~if~~~~~V~~~SiH~  217 (386)
T d3c10a1         163 MGFCFFNSVAIACRQLQQQSKASKILIVDWDVHHGNGTQQTFYQDPSVLYISLHR  217 (386)
T ss_dssp             BTTBSSCHHHHHHHHHHHHSTTCCEEEEECSSSCCHHHHHHHTTCTTEEEEEEEE
T ss_pred             CCcccccHHHHHHHHHHhhcccCCceEEecccCCCCceeeEeecccccccccccc
Confidence            9999999999999999999999999999999999999999999999999999995

>d1c3pa_ c.42.1.2 (A:) HDAC homologue {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: Arginase/deacetylase
superfamily: Arginase/deacetylase
family: Histone deacetylase, HDAC
domain: HDAC homologue
species: Aquifex aeolicus [TaxId: 63363]

Probab=100.00  E-value=3.9e-55  Score=395.28  Aligned_cols=188  Identities=23%  Similarity=0.341  Sum_probs=163.0

Q ss_pred             CceeEEeCcccccccCCCCCCCCCCchHHHHHHHHHHHCCCCCCceEecCCCCCHHHHhccCCHHHHHHHhcCCCccccc
Q 027427           33 FKLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIII  112 (223)
Q Consensus        33 ~~~~ivy~~~~~~h~~~~~~~Hpe~p~R~~~i~~~L~~~gl~~~~~~~~p~~a~~e~l~~vHs~~Yv~~l~~~~~~~~~~  112 (223)
                      .|+.+||+++|..|.++  ++|||+|+|+..++++|++.|+++.+++++|++|+.++|++|||++||++|++.+......
T Consensus         1 ~k~~li~~~d~~~~~~g--~~HPe~p~Rl~~i~~~L~~~gl~~~~~~~~p~~At~e~L~~vHs~~Yi~~l~~~~~~~~~~   78 (372)
T d1c3pa_           1 KKVKLIGTLDYGKYRYP--KNHPLKIPRVSLLLRFKDAMNLIDEKELIKSRPATKEELLLFHTEDYINTLMEAERCQCVP   78 (372)
T ss_dssp             CCEEEEECGGGGGSCCC--TTCGGGSCCHHHHHHHHHHTTCCCGGGEEECCCCCHHHHTTTSCHHHHHHHHHHHHHTSCC
T ss_pred             CeEEEEeChhhcCCCCC--CccCcCHHHHHHHHHHHHHcCCCCCCcEEcCCCCCHHHHHHhCCHHHHHHHHHhcccccCc
Confidence            47899999999988754  7899999999999999999999999999999999999999999999999998754322110


Q ss_pred             cCC--Cccc-CCCcccccccHHHHHHHhhHHHHHHHHHhhcCcEeecCCCCCCCCCCCCCcccccchHHHHHHHHHHhcC
Q 027427          113 EVP--PVAL-FPNCLVQRKVLYPFRKQVGGTILAAKLAKERGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLN  189 (223)
Q Consensus       113 e~~--~~~~-~~d~~~~~~~~~~a~~a~Gg~l~aa~~~~~~~~a~~~~~G~HHA~~~~~~GFC~fNnvAIAa~~l~~~~~  189 (223)
                      +..  .... ..++++++++++++++++|+++.|++.++++..++++|||+|||.+++++|||+|||+||||+|+++. +
T Consensus        79 ~~~~~~~~~~~~~~p~~~~~~~~a~~~~g~~~~a~~~~~~g~~a~~ppGG~HHA~~~~a~GFC~fNnvAiaa~~l~~~-~  157 (372)
T d1c3pa_          79 KGAREKYNIGGYENPVSYAMFTGSSLATGSTVQAIEEFLKGNVAFNPAGGMHHAFKSRANGFCYINNPAVGIEYLRKK-G  157 (372)
T ss_dssp             TTHHHHHCCSSSSSCSSTTTTHHHHHHHHHHHHHHHHHHTTCEEEETTCCCTTCBTTBCBTTBSSCHHHHHHHHHHHT-T
T ss_pred             ccccccccCCCcCCCCCHHHHHHHHHhhhhHHHHhhhhccccceeeccccccccccccceeeeecchHHHHHHHHHHh-c
Confidence            000  0011 24778889999999999999999999988766667777778999999999999999999999998765 6


Q ss_pred             CCeEEEEecCCcCCchhhHhhhcCCCEEEEeccC
Q 027427          190 ISRVMIIDLDAHQGNGHEKDFSSDSRSCLYSGYV  223 (223)
Q Consensus       190 ~~RV~IiD~DvHHGnGTq~if~~d~~Vl~iSlH~  223 (223)
                      ++||+|||||||||||||+|||+||+|+|+|+|+
T Consensus       158 ~~RV~ivD~DvHhGnGtq~if~~d~~V~~~SiH~  191 (372)
T d1c3pa_         158 FKRILYIDLDAHHCDGVQEAFYDTDQVFVLSLHQ  191 (372)
T ss_dssp             CCCEEEEECSSSCCHHHHHHHTTCSSEEEEEEEE
T ss_pred             cCceEEEeccccCCCceeEEEeecCCcccccccc
Confidence            8999999999999999999999999999999995

>d1t64a_ c.42.1.2 (A:) Histone deacetylase 8, HDAC8 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Arginase/deacetylase
superfamily: Arginase/deacetylase
family: Histone deacetylase, HDAC
domain: Histone deacetylase 8, HDAC8
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=1.1e-54  Score=390.94  Aligned_cols=182  Identities=28%  Similarity=0.361  Sum_probs=161.7

Q ss_pred             eE-EeCcccccccCCCCCCCCCCchHHHHHHHHHHHCCCCCCceEecCCCCCHHHHhccCCHHHHHHHhcCCCcccc--c
Q 027427           36 PL-IYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSII--I  112 (223)
Q Consensus        36 ~i-vy~~~~~~h~~~~~~~Hpe~p~R~~~i~~~L~~~gl~~~~~~~~p~~a~~e~l~~vHs~~Yv~~l~~~~~~~~~--~  112 (223)
                      +| ||+|+|..+.    ..|||+|.|++.+.++|+++||++.+++++|++|+.++|++||+++||++|++.+..+..  .
T Consensus         3 pvyiy~~~~~~~~----~~hP~~P~R~~~~~~ll~~~gl~~~~~~v~p~~At~~el~~vHs~~Yi~~l~~~~~~~~~~~~   78 (364)
T d1t64a_           3 PVYIYSPEYVSMC----DSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVASMEEMATFHTDAYLQHLQKVSQEGDDDHP   78 (364)
T ss_dssp             CEEECCHHHHHHH----TCSSSSCCHHHHHHHHHHHTTGGGGSEEECCCCCCHHHHTTTSCHHHHHHHHHHHHHCSSCCT
T ss_pred             CeEEeCHHHhccC----CCCCCCcHHHHHHHHHHHHcCCccCCEEeCCCCCCHHHHHHhCCHHHHHHHHHhhhccccccc
Confidence            45 8999998762    579999999999999999999999999999999999999999999999999876543321  1


Q ss_pred             cCCCcccCCCcccccccHHHHHHHhhHHHHHHHHHhhc--CcEeecCCCCCCCCCCCCCcccccchHHHHHHHHHHhcCC
Q 027427          113 EVPPVALFPNCLVQRKVLYPFRKQVGGTILAAKLAKER--GWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNI  190 (223)
Q Consensus       113 e~~~~~~~~d~~~~~~~~~~a~~a~Gg~l~aa~~~~~~--~~a~~~~~G~HHA~~~~~~GFC~fNnvAIAa~~l~~~~~~  190 (223)
                      +.....++.||++++++++++++++|+++.|++.++++  ..|++++||+|||++++++|||+|||+||||+++++  +.
T Consensus        79 ~~~~~~l~~d~p~~~~~~~~~~~~aG~~l~A~~~~~~g~~~~a~~~~gg~HHA~~~~a~GFC~~NdvaiA~~~~~~--~~  156 (364)
T d1t64a_          79 DSIEYGLGYDCPATEGIFDYAAAIGGATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRLRR--KF  156 (364)
T ss_dssp             TTTTTTCBTTBCCCTTHHHHHHHHHHHHHHHHHHHHTTSCSEEEETTCCCTTCBTTBCBTTBSSCHHHHHHHHHTT--TC
T ss_pred             hheeecCCCCCCCCchHHHHHHHHhhhHHHHHHHHHcCCcccccccCccccccccccccccccccHHHHHHHHHHh--hh
Confidence            11223466799999999999999999999999999865  478999999999999999999999999999998764  47


Q ss_pred             CeEEEEecCCcCCchhhHhhhcCCCEEEEeccC
Q 027427          191 SRVMIIDLDAHQGNGHEKDFSSDSRSCLYSGYV  223 (223)
Q Consensus       191 ~RV~IiD~DvHHGnGTq~if~~d~~Vl~iSlH~  223 (223)
                      +||+|||||||||||||+||++||+|+|+|+|+
T Consensus       157 ~RV~iiD~DvHhGnGtq~iF~~d~~V~~~SiH~  189 (364)
T d1t64a_         157 ERILYVDLDLHHGDGVEDAFSFTSKVMTVSLHK  189 (364)
T ss_dssp             SCEEEEECSSSCCHHHHHHHTTCSSEEEEEEEE
T ss_pred             ceEEEEecccCCCCceeeeeecCCccccccccc
Confidence            999999999999999999999999999999995