Citrus Sinensis ID: 036514

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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-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------33
Protein Sequence
MPADRHFMRLDILEIKSHIERKLGAAKSDKYFSLLTRYLSLKISKSEFDRLCIGTIGRENVRLHNRLLRSIIQNACLSKTPPPKEPKVDGFERGKVPNGYQRSCLQSLCKDIPQSSRKGMTPALRDCKLKDFPSPLGPRGKSHSIACQDSVPKIQEQLSTNELFSLGSRPPGSVEDGEEVDQAAGSPSIYSRSPVKAPLGIPINGKGTPKLLHKSSTDAYYTGICQNHGELPDAYSLRKRLEKKLEMEGLKVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATELNPQILGNDWPSQLEIFSCMHQKIYD
Secondary Structure (PSIPRED)
cccccccccccHHHHHHHHHHHHccccHHHHHHHHHHHHHccccHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHcccccccccccccccccccccHHHHHHccccccccccccccccccccccccccccccccccccccccHHHcccccccHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHcccccccccHHHHHHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
cccccccccccHHHHHHHHHHHHcHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHcHHcHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHccHcccccccccccccccHHHHHHcccccccccccccEcccccEccccccccccccccccccccHHHHcccccccHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccEEEHHHHHHHHHHcHHHccccHHHHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
mpadrhfmRLDILEIKSHIERKLGAAKSDKYFSLLTRYLSLKISKSEFDRLCIGTIGRENVRLHNRLLRSIIQNaclsktpppkepkvdgfergkvpngyqrSCLQSLckdipqssrkgmtpalrdcklkdfpsplgprgkshsiacqdsvpkiqeqlstnelfslgsrppgsvedgeevdqaagspsiysrspvkaplgipingkgtpkllhksstdaYYTGIcqnhgelpdAYSLRKRLEKKLEMEGLKVSVDCANLLNNGLDVFMKRLIKPClelagsrsghkhssfsASILDFQVatelnpqilgndwpsqLEIFSCMHQKIYD
Flexible Loop (DISEMBL)
MPADRHFMRLDILEIKSHIERklgaaksdkyFSLLTRYLSlkisksefdrlCIGTIGRENVRLHNRLLRSIIqnaclsktpppkepkvdgfergkvpngyqrSCLQSLCKdipqssrkgmtpalrdcKLKDFPSPLGPRGKSHSIACQDSVPKIQEQLSTNELFSLGSRPPGSVEDGEEVDQAagspsiysrspvkapLGIPINGKGTPKLLHKSSTDAYYTGICQNHGELPDAYSLRKRLEKKLEMEGLKVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATELNPQILGNDWPSQLEIFSCMHQKIYD
Low Complexity Region (SEG)
MPADRHFMRLDILEIKSHIERKLGAAKSDKYFSLLTRYLSLKISKSEFDRLCIGTIGRENVRLHNRLLRSIIQNACLSKTPPPKEPKVDGFERGKVPNGYQRSCLQSLCKDIPQSSRKGMTPALRDCKLKDFPSPLGPRGKSHSIACQDSVPKIQEQLSTNELFSLGSRPPGSVEDGEEVDQAAGSPSIYSRSPVKAPLGIPINGKGTPKLLHKSSTDAYYTGICQNHGELPDAYSLRKRLEKKLEMEGLKVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATELNPQILGNDWPSQLEIFSCMHQKIYD
Disordered region (IsUnstruct)
******FMRLDILEIKSHIERKLGAAKSDKYFSLLTRYLSLKISKSEFDRLCIGTIGRENVRLHNRLLRSIIQNACL*************************************************************************************************************************************LLHKSSTDAYYTGICQNHGELPDAYSLRKRLEKKLEMEGLKVSVDCANLLNNGLDVFMKRLIKPCLELAGS*******SFSASILDFQVATELNPQILGNDWPSQLEIFSCMHQ****
Disordered Region (DISOPRED)
************LEIKSHIERKLGAAKSDKYFSLLTRYLSLKISKSEFDRLCIGTIGRENVRLHNRLLRSIIQNAC********************************************************************************************************************SPVKAPLGIPING******************ICQNHGELPDAYSLRKRLEKKLEMEGLKVSVDCANLLNNGLDVFMKRLIKPCL*******************DFQVATELNPQILGNDWPSQLEIFSCMHQKIY*
Disordered Region (DISEMBL)
MPADRHFMRLDILEIKSHIERKLGAAKSDKYFSLLTRYLSLKISKSEFDRLCIGTIGRENVRLHNRLLRSIIQNACLSKTPPPKEPKVDGFERGKVPNGYQRSCLQSLCKDIPQSSRKGMTPALRDCKLKDFPSP*********IACQDSVPKIQEQLSTNELFSLG********************SIYSRSPVKAPLGIPINGKGTPKLLHKSSTDAYYTGICQNHGELPDAYSLRKRLEKKLEMEGLKVSVDCANLLNNGLDVFMKRLIKPCLELA*********SFSASILDFQVATELNPQILGNDWPSQLEIFSCMHQKIYD
Disordered Region (DISPRO)
********RLDILEIKSHIERKLGAAKSDKYFSLLTRYLSLKISKSEFDRLCIGTIGRENVRLHNRLLRSIIQNACLSKTPPP**********************************************************************************************************YSRSPVKAPLGIPINGKG***********AYYTGICQNHGELPDAYSLRKRLEKKLEMEGLKVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATELNPQILGNDWPSQLEIFSCMHQKIYD
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MPADRHFMRLDILEIKSHIERKLGAAKSDKYFSLLTRYLSLKISKSEFDRLCIGTIGRENVRLHNRLLRSIIQNACLSKTPPPKEPKVDGFERGKVPNGYQRSCLQSLCKDIPQSSRKGMTPALRDCKLKDFPSPLGPRGKSHSIACQDSVPKIQEQLSTNELFSLGSRPPGSVEDGEEVDQAAGSPSIYSRSPVKAPLGIPINGKGTPKLLHKSSTDAYYTGICQNHGELPDAYSLRKRLEKKLEMEGLKVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATELNPQILGNDWPSQLEIFSCMHQKIYD
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

No hits with e-value below 0.001 by BLAST

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	328
255568559	354	conserved hypothetical protein [Ricinus	0.963	0.892	0.628	1e-112
225438964	331	PREDICTED: uncharacterized protein LOC10	0.966	0.957	0.652	1e-111
147772915	355	hypothetical protein VITISV_007567 [Viti	0.966	0.892	0.612	1e-110
147783361	354	hypothetical protein VITISV_008500 [Viti	0.978	0.906	0.536	3e-92
225428953	354	PREDICTED: uncharacterized protein LOC10	0.978	0.906	0.536	1e-91
224105687	338	predicted protein [Populus trichocarpa]	0.966	0.937	0.535	2e-88
224105691	355	predicted protein [Populus trichocarpa]	0.966	0.892	0.515	4e-88
356565509	363	PREDICTED: uncharacterized protein LOC10	0.972	0.878	0.568	8e-87
224060715	341	predicted protein [Populus trichocarpa]	0.960	0.923	0.523	2e-86
255573127	357	conserved hypothetical protein [Ricinus	0.975	0.896	0.495	1e-85

>gi|255568559|ref|XP_002525253.1| conserved hypothetical protein [Ricinus communis] gi|223535411|gb|EEF37081.1| conserved hypothetical protein [Ricinus communis]

 Score =  409 bits (1052), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 215/342 (62%), Positives = 246/342 (71%), Gaps = 26/342 (7%)

Query: 1   MPADRHFMRLDILEIKSHIERKLGAAKSDKYFSLLTRYLSLKISKSEFDRLCIGTIGREN 60
           MPA RH  R+D LEIK  IERKLG  K+ KYF LLT++LSLKISK +FDRLCIGTIG+EN
Sbjct: 1   MPAARHCSRIDTLEIKLQIERKLGHLKAQKYFDLLTKFLSLKISKCDFDRLCIGTIGKEN 60

Query: 61  VRLHNRLLRSIIQNACLSKTPPPKEPKVDGFERGKVPNGYQRSCLQSLCKDIPQSSRKGM 120
           VRLHN LLRSII+NA LSK PPPKE K +     K PNGYQ+ CLQSLCKD  QS RKG 
Sbjct: 61  VRLHNHLLRSIIKNAHLSKMPPPKEAKAEDALGVKTPNGYQKGCLQSLCKDFLQSPRKGR 120

Query: 121 TPALRDCKLKDFPSPLGPRGKSHSIACQDSVPKIQEQLSTNELFSLGSRPPGSVEDGEEV 180
           +  L + K +D PSPL P GKSH+    DS+PK QEQ S  EL SLGSRPPGSVEDGEEV
Sbjct: 121 S-ILSERKFRDRPSPLRPHGKSHNFGFDDSMPKNQEQQSATELLSLGSRPPGSVEDGEEV 179

Query: 181 DQAAGSPSIYSRSPVKAPLGIPINGKGTPKLLHKSSTDAYYTGICQNHGELPDAYSLRKR 240
           DQAAGSPSIYSRSPV+APLGIP N KG  K+L       Y+   C N GELPD   LRKR
Sbjct: 180 DQAAGSPSIYSRSPVRAPLGIPFNTKGARKVLCNPLASCYHMDTCHNSGELPDTKLLRKR 239

Query: 241 LEKKLEMEGLKVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSS----------- 289
           L++KLEMEG+KVSVDCANLLN+GLDVF+KRLIKPC++LAGS+ G K ++           
Sbjct: 240 LQQKLEMEGVKVSVDCANLLNSGLDVFLKRLIKPCMDLAGSKFGQKQTTQGHARAIPRLS 299

Query: 290 --------------FSASILDFQVATELNPQILGNDWPSQLE 317
                          SAS+LDF++A ELNPQILG +W  QLE
Sbjct: 300 GMQPVGYLQKPSGFISASMLDFRLAMELNPQILGENWSMQLE 341

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225438964|ref|XP_002279502.1| PREDICTED: uncharacterized protein LOC100257838 [Vitis vinifera]

 Score =  407 bits (1045), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 210/322 (65%), Positives = 249/322 (77%), Gaps = 5/322 (1%)

Query: 1   MPADRHFMRLDILEIKSHIERKLGAAKSDKYFSLLTRYLSLKISKSEFDRLCIGTIGREN 60
           M   R+F R+  LE+K  IE+KLG AK++KYF LLT+YLSLK+SK+EF++LCI TIGREN
Sbjct: 1   MLVGRNFSRIHTLELKIQIEKKLGRAKAEKYFDLLTKYLSLKLSKNEFNKLCIDTIGREN 60

Query: 61  VRLHNRLLRSIIQNACLSKTPPPKEPKVDGFERGKVPNGYQRSCLQSLCKDI-PQSSRKG 119
           V LHN+L+ SII+NACLSK+PPPK+ K +G    KV NGYQRS LQS+C+D+ PQS RKG
Sbjct: 61  VLLHNQLIGSIIKNACLSKSPPPKQSKTEGSLNVKVANGYQRSSLQSICRDVFPQSPRKG 120

Query: 120 MTPALRDCKLKDFPSPLGPRGKSHSIACQDSVPKIQEQLSTNELFSLGSRPPG---SVED 176
            TP+LRD K +D PSPLGP GK+HS+ C+D+VPKIQEQ S  EL SLGSRPPG   SVED
Sbjct: 121 RTPSLRDRKFRDRPSPLGPHGKNHSVVCEDTVPKIQEQQSATELLSLGSRPPGEVNSVED 180

Query: 177 GEEVDQAAGSPSIYSRSPVKAPLGIPINGKGTPKLLHKSSTDAYYTGICQNHGELPDAYS 236
           GEEV+QAA SP I+SRSPV APLGIP     T K+L   +  A+    CQ  GELPD +S
Sbjct: 181 GEEVEQAARSPGIHSRSPVTAPLGIPKTTIVTRKVLCNEAPSAFQIESCQIMGELPDTHS 240

Query: 237 LRKRLEKKLEMEGLKVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHS-SFSASIL 295
           LR RLE+KLEMEG K+S DC +LLNNGLDVF+KRLIKPCLELA SR   K + S  ASIL
Sbjct: 241 LRNRLEQKLEMEGFKISGDCISLLNNGLDVFLKRLIKPCLELASSRYVQKPAGSIPASIL 300

Query: 296 DFQVATELNPQILGNDWPSQLE 317
           DF+VA ELNP ILG DWP +LE
Sbjct: 301 DFRVAMELNPYILGEDWPVKLE 322

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147772915|emb|CAN71564.1| hypothetical protein VITISV_007567 [Vitis vinifera]

 Score =  404 bits (1039), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 212/346 (61%), Positives = 251/346 (72%), Gaps = 29/346 (8%)

Query: 1   MPADRHFMRLDILEIKSHIERKLGAAKSDKYFSLLTRYLSLKISKSEFDRLCIGTIGREN 60
           M   R+F R+  LE+K  IE+KLG AK++KYF LLT+YLSLK+SK+EF++LCI TIGREN
Sbjct: 1   MLVGRNFSRIHTLELKIQIEKKLGRAKAEKYFDLLTKYLSLKLSKNEFNKLCIDTIGREN 60

Query: 61  VRLHNRLLRSIIQNACLSKTPPPKEPKVDGFERGKVPNGYQRSCLQSLCKDI-PQSSRKG 119
           V LHN+L+ SII+NACLSK+PPPK+ K +G    KV NGYQRS LQS+C+D+ PQS RKG
Sbjct: 61  VLLHNQLIGSIIKNACLSKSPPPKQSKTEGSLNVKVANGYQRSSLQSICRDVFPQSPRKG 120

Query: 120 MTPALRDCKLKDFPSPLGPRGKSHSIACQDSVPKIQEQLSTNELFSLGSRPPG---SVED 176
            TP+LRD K +D PSPLGP GK+HS+ C+D+VPKIQEQ S  EL SLGSRPPG   SVED
Sbjct: 121 RTPSLRDRKFRDRPSPLGPHGKNHSVVCEDTVPKIQEQQSATELLSLGSRPPGEVNSVED 180

Query: 177 GEEVDQAAGSPSIYSRSPVKAPLGIPINGKGTPKLLHKSSTDAYYTGICQNHGELPDAYS 236
           GEEV+QAA SP I+SRSPV APLGIP     T K+L   +  A+    CQ  GELPD +S
Sbjct: 181 GEEVEQAARSPGIHSRSPVTAPLGIPKTTXVTRKVLCNEAPSAFQIESCQIMGELPDTHS 240

Query: 237 LRKRLEKKLEMEGLKVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKH--------- 287
           LR RLE+KLEMEG K+S DC +LLNNGLDVF+KRLIKPCLELA SRSG KH         
Sbjct: 241 LRNRLEQKLEMEGFKISGDCISLLNNGLDVFLKRLIKPCLELASSRSGQKHLSQKHGHVV 300

Query: 288 ----------------SSFSASILDFQVATELNPQILGNDWPSQLE 317
                            S  ASILDF+VA +LNP ILG DWP +LE
Sbjct: 301 SGPKGMWPVRYVQKPAGSIPASILDFRVAMDLNPYILGEDWPVKLE 346

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147783361|emb|CAN72960.1| hypothetical protein VITISV_008500 [Vitis vinifera]

 Score =  344 bits (882), Expect = 3e-92,   Method: Compositional matrix adjust.
 Identities = 189/352 (53%), Positives = 231/352 (65%), Gaps = 31/352 (8%)

Query: 1   MPADRHFMRLDILEIKSHIERKLGAAKSDKYFSLLTRYLSLKISKSEFDRLCIGTIGREN 60
           M  +++F R+D LE+K+ I R++G  K++KYF  L R  SLK+SK EFD+ C+ TIGREN
Sbjct: 1   MVPNQNFTRIDTLELKALIVRRIGRQKAEKYFDQLKRLFSLKLSKREFDKFCLWTIGREN 60

Query: 61  VRLHNRLLRSIIQNACLSKTPPPKEPKVDGFERGKVPNGYQRSCLQSLCKD-IPQSSRKG 119
           + LHNRL+ SI++NACLSK PP K   V   +  KV NGYQR+CLQSL  D  P S RKG
Sbjct: 61  IPLHNRLIGSILKNACLSKVPPLKGRNVGVPKDVKVANGYQRNCLQSLYGDAFPPSPRKG 120

Query: 120 MTPALRDCKLKDFPSPLGPRGKSHSIACQDSVPKIQEQLSTNELFSLGSRPPG---SVED 176
            +   RD + +D  SPLGP GK  S+AC++   K QEQ S  EL SLGSRPPG   SVED
Sbjct: 121 RSQVNRDRRFRDRLSPLGPLGKPQSVACEELASKAQEQQSATELLSLGSRPPGEVVSVED 180

Query: 177 GEEVDQAAGSPSIYSRSPVKAPLGIPINGKGTPKLLHKSSTDAYYTGICQNHGELPDAYS 236
           GEEV+Q AGSPS+ SRSPV+AP GI +N  G   L + S  + Y+   C N GELPD  S
Sbjct: 181 GEEVEQLAGSPSVQSRSPVRAPFGISMNMGGRKSLCNGSVCN-YHPETCHNSGELPDTGS 239

Query: 237 LRKRLEKKLEMEGLKVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKH--------- 287
           LR  LE+KLEMEG  VS+DC NLLNN LDVF+KRLI+PCL+L GSR G++H         
Sbjct: 240 LRSHLERKLEMEGFSVSMDCVNLLNNSLDVFLKRLIEPCLQLVGSRCGNEHLRQLNAQTL 299

Query: 288 ----------------SSFSASILDFQVATELNPQILGNDWPSQLEIFSCMH 323
                               AS+LDF+VA ELNPQILG DWP QLE   C+H
Sbjct: 300 PGMNRILPGRYIQKSRKPKYASVLDFRVAMELNPQILGEDWPVQLEKI-CLH 350

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225428953|ref|XP_002263494.1| PREDICTED: uncharacterized protein LOC100256708 [Vitis vinifera]

 Score =  342 bits (878), Expect = 1e-91,   Method: Compositional matrix adjust.
 Identities = 189/352 (53%), Positives = 231/352 (65%), Gaps = 31/352 (8%)

Query: 1   MPADRHFMRLDILEIKSHIERKLGAAKSDKYFSLLTRYLSLKISKSEFDRLCIGTIGREN 60
           M  +++F R+D LE+K+ I R++G  K++KYF  L R  SLK+SK EFD+ C+ TIGREN
Sbjct: 1   MVPNQNFTRIDTLELKALIVRRIGRQKAEKYFDQLKRLFSLKLSKREFDKFCLWTIGREN 60

Query: 61  VRLHNRLLRSIIQNACLSKTPPPKEPKVDGFERGKVPNGYQRSCLQSLCKD-IPQSSRKG 119
           + LHNRL+ SI++NACLSK PP K   V   +  KV NGYQR+CLQSL  D  P S RKG
Sbjct: 61  IPLHNRLIGSILKNACLSKVPPLKGRNVGVPKDVKVANGYQRNCLQSLYGDAFPPSPRKG 120

Query: 120 MTPALRDCKLKDFPSPLGPRGKSHSIACQDSVPKIQEQLSTNELFSLGSRPPG---SVED 176
            +   RD + +D  SPLGP GK  S+AC++   K QEQ S  EL SLGSRPPG   SVED
Sbjct: 121 RSQVNRDRRFRDRLSPLGPLGKPQSVACEELASKAQEQQSATELLSLGSRPPGEVVSVED 180

Query: 177 GEEVDQAAGSPSIYSRSPVKAPLGIPINGKGTPKLLHKSSTDAYYTGICQNHGELPDAYS 236
           GEEV+Q AGSPS+ SRSPV+AP GI +N  G   L + S  + Y+   C N GELPD  S
Sbjct: 181 GEEVEQLAGSPSVQSRSPVRAPFGISMNMGGRKSLCNGSICN-YHPETCHNSGELPDTGS 239

Query: 237 LRKRLEKKLEMEGLKVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKH--------- 287
           LR  LE+KLEMEG  VS+DC NLLNN LDVF+KRLI+PCL+L GSR G++H         
Sbjct: 240 LRSHLERKLEMEGFGVSMDCVNLLNNSLDVFLKRLIEPCLQLVGSRCGNEHLRQLNAQTL 299

Query: 288 ----------------SSFSASILDFQVATELNPQILGNDWPSQLEIFSCMH 323
                               AS+LDF+VA ELNPQILG DWP QLE   C+H
Sbjct: 300 PGMNRILPGRYIQKSRKPKYASVLDFRVAMELNPQILGEDWPIQLEKI-CLH 350

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224105687|ref|XP_002313900.1| predicted protein [Populus trichocarpa] gi|222850308|gb|EEE87855.1| predicted protein [Populus trichocarpa]

 Score =  331 bits (849), Expect = 2e-88,   Method: Compositional matrix adjust.
 Identities = 180/336 (53%), Positives = 225/336 (66%), Gaps = 19/336 (5%)

Query: 1   MPADRHFMRLDILEIKSHIERKLGAAKSDKYFSLLTRYLSLKISKSEFDRLCIGTIGREN 60
           M ++  + R+D LE+KS I +K+G  ++DKYF  LT+  SLKI+K EFD+LCI  IGREN
Sbjct: 1   MASNEMYSRIDTLELKSLILKKIGHQRADKYFDELTQLFSLKITKCEFDKLCIRIIGREN 60

Query: 61  VRLHNRLLRSIIQNACLSKTPPPKEPKVDGFERG-KVPNGYQRSCLQSLCKD-IPQSSRK 118
           + LHNRL+RSI++NACL K PPPK  +  G     K  NG+QR+ LQSL +D  P S RK
Sbjct: 61  IPLHNRLIRSILKNACLGKVPPPKGVRRAGSNLTVKTTNGHQRNYLQSLYRDAFPSSPRK 120

Query: 119 GMTPALRDCKLKDFPSPLGPRGKSHSIACQDSVPKIQEQLSTNELFSLGSRPP---GSVE 175
           G +P  RD K +D PSPLGP GK  S+AC++   + QEQ S  EL SLGSRPP    SVE
Sbjct: 121 GRSPVNRDRKFRDRPSPLGPLGKPQSMACEELNSRAQEQQSATELHSLGSRPPIEVASVE 180

Query: 176 DGEEVDQAAGSPSIYSRSPVKAPLGIPINGKGTPKLLHKSSTDAYYT-GICQNHGELPDA 234
           +GEEV+Q A SP + SRSPV AP GI +N  G+ K L   S  + Y    C N GELPD 
Sbjct: 181 EGEEVEQMAVSPGVQSRSPVTAPFGISLNPGGSRKALSNISIGSNYIPETCLNSGELPDT 240

Query: 235 YSLRKRLEKKLEMEGLKVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKH------- 287
            SLR RLE+KLEMEG+ VS+DC N+LN GLD ++KRLI+PC+ LAG+R   +        
Sbjct: 241 RSLRSRLERKLEMEGIGVSLDCVNVLNIGLDAYLKRLIEPCMALAGARCDSEQLKGANGQ 300

Query: 288 ------SSFSASILDFQVATELNPQILGNDWPSQLE 317
                  S +AS+LDF+VA E NPQILG DWP QLE
Sbjct: 301 YVKRQTESVNASMLDFRVAMESNPQILGEDWPVQLE 336

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224105691|ref|XP_002313901.1| predicted protein [Populus trichocarpa] gi|222850309|gb|EEE87856.1| predicted protein [Populus trichocarpa]

 Score =  331 bits (848), Expect = 4e-88,   Method: Compositional matrix adjust.
 Identities = 179/347 (51%), Positives = 224/347 (64%), Gaps = 30/347 (8%)

Query: 3   ADRHFMRLDILEIKSHIERKLGAAKSDKYFSLLTRYLSLKISKSEFDRLCIGTIGRENVR 62
           +++  MR++ LE+KS I +K+G  ++DKYF  LT  L+LKI+K EFD+  +G IGREN+ 
Sbjct: 4   SNQMSMRINTLELKSLIVKKIGRQRADKYFYQLTGLLNLKITKCEFDKFFVGIIGRENIP 63

Query: 63  LHNRLLRSIIQNACLSKTPPPKEPKVDGFERGKVPNGYQRSCLQSLCKD-IPQSSRKGMT 121
           LHNR ++SI++N C SK PP K  K  G     V NGYQ++ LQSL  D  P S RKG +
Sbjct: 64  LHNRFIQSILKNPCCSKVPPSKSAKRAG-SNLTVTNGYQKNSLQSLYGDAFPSSPRKGRS 122

Query: 122 PALRDCKLKDFPSPLGPRGKSHSIACQDSVPKIQEQLSTNELFSLGSRPP---GSVEDGE 178
           P  RDCK +D PSPLGP GK  S+ C++   + QEQ S  EL SLGSRPP    SVEDGE
Sbjct: 123 PVNRDCKFRDRPSPLGPLGKPQSVECEELNARGQEQQSATELLSLGSRPPVEVASVEDGE 182

Query: 179 EVDQAAGSPSIYSRSPVKAPLGIPINGKGTPKLLHKSSTDAYYTGICQNHGELPDAYSLR 238
           EVDQ AGSPS+ SRSPV APLGI +N      L + S  + +    C N GELPD  SLR
Sbjct: 183 EVDQMAGSPSVQSRSPVTAPLGISMNFGSRKALSNASLCNNHLKRTCLNSGELPDTRSLR 242

Query: 239 KRLEKKLEMEGLKVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKH----------- 287
            RLE+KLEMEG+  S+DC NLLNNGLD ++KRLI+PC+ LAGSR G ++           
Sbjct: 243 SRLEQKLEMEGISASLDCVNLLNNGLDAYLKRLIEPCMALAGSRHGKEYLKKASGQFIPG 302

Query: 288 --------------SSFSASILDFQVATELNPQILGNDWPSQLEIFS 320
                          S  AS+LDF+V+ E NPQILG DWP+QLE  S
Sbjct: 303 LNEMLPGKYMQRETKSIYASMLDFRVSMESNPQILGEDWPTQLEKIS 349

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356565509|ref|XP_003550982.1| PREDICTED: uncharacterized protein LOC100809982 [Glycine max]

 Score =  326 bits (836), Expect = 8e-87,   Method: Compositional matrix adjust.
 Identities = 186/327 (56%), Positives = 228/327 (69%), Gaps = 8/327 (2%)

Query: 1   MPADRHFMRLDILEIKSHIERKLGAAKSDKYFSLLTRYLSLKISKSEFDRLCIGTIGREN 60
           MPA R+F   D +E K  IER+LG+ K+ KYF+LL R+LS KISK EFDR+CI TIGREN
Sbjct: 40  MPAARYFSPADTIEQKLQIERRLGSVKTRKYFNLLERFLSFKISKHEFDRVCIATIGREN 99

Query: 61  VRLHNRLLRSIIQNACLSKTPPPKEPKVDGFERGKVPNGYQRSCLQSLCKDIPQSSRKGM 120
           V LHN  L+SI++ ACLSKT   +E KV+     K PNG   S LQ LCKD PQS RKG 
Sbjct: 100 VPLHNHFLKSILRKACLSKTAGSRESKVESSLNVKTPNGC--SNLQILCKDFPQSPRKGR 157

Query: 121 TPALRDCKLKDFPSPLGPRGKSHSIACQDSVPKIQEQLSTNELFSLGSRPPGSVEDGEEV 180
           TP LRD + +D PSPLGP GK++SI C+DSVPKI EQ S   L S GSR P SVEDGEEV
Sbjct: 158 TPNLRDRRSRDRPSPLGPNGKNNSIGCEDSVPKIHEQQSILNLQSAGSRLPLSVEDGEEV 217

Query: 181 DQAAGSPSIYSRSPVKAPLGIPI-NGKGTPKLLHKSSTDAYYTGICQNHGELPDAYSLRK 239
           DQ     +++ +SP++APL IP  N +  PK L +  +    +  CQ+  +LPD  SL K
Sbjct: 218 DQDYEILNLFKKSPIQAPLAIPTYNRRPQPKYLSQGLSSGTVSDTCQSIAQLPDTCSLTK 277

Query: 240 RLEKKLEMEGLKVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQV 299
           RLE+KLE+EGLK+S D A+LLNN LDV++KRLIKPCL+LA S+S +K  S S SI DF+ 
Sbjct: 278 RLEQKLEIEGLKISTDAASLLNNALDVYLKRLIKPCLDLAASKSVNK--SASVSISDFRT 335

Query: 300 ATELNPQILGNDWPSQLEIF---SCMH 323
           A ELNP ILG DWP  LE     +C+H
Sbjct: 336 AVELNPTILGEDWPLNLEKTEEAACVH 362

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224060715|ref|XP_002300258.1| predicted protein [Populus trichocarpa] gi|222847516|gb|EEE85063.1| predicted protein [Populus trichocarpa]

 Score =  325 bits (833), Expect = 2e-86,   Method: Compositional matrix adjust.
 Identities = 180/344 (52%), Positives = 221/344 (64%), Gaps = 29/344 (8%)

Query: 1   MPADRHFMRLDILEIKSHIERKLGAAKSDKYFSLLTRYLSLKISKSEFDRLCIGTIGREN 60
           M ++    R+D LE+KS I +K G  ++DKYF  LTR  SLKI+K EFD+ C+  IGREN
Sbjct: 1   MGSNEMNSRIDTLELKSLILKKFGHQRADKYFDQLTRLFSLKITKCEFDKFCLRIIGREN 60

Query: 61  VRLHNRLLRSIIQNACLSKTPPPKEPKVDGFERG------KVPNGYQRSCLQSLCKD-IP 113
           + LHN  +RSI++N CL K PP K     G ER       K  NGY+R+CLQSL ++  P
Sbjct: 61  ISLHNHFIRSILKNTCLGKVPPHK-----GVERAGSNLTVKTANGYKRNCLQSLYREAFP 115

Query: 114 QSSRKGMTPALRDCKLKDFPSPLGPRGKSHSIACQDSVPKIQEQLSTNELFSLGSRPP-- 171
            S RKG +P  RD K +D PSPLGP GK  S+AC++   + QEQ S  EL S GSRPP  
Sbjct: 116 SSPRKGRSPVSRDRKCRDRPSPLGPLGKPQSMACEELNSRAQEQQSATELLSTGSRPPIE 175

Query: 172 -GSVEDGEEVDQAAGSPSIYSRSPVKAPLGIPINGKGTPKLLHKSSTDAYYT-GICQNHG 229
             SVEDGEEV+Q A SP + SRSPV AP GI +N  G+ K L   S  + Y    C N G
Sbjct: 176 FASVEDGEEVEQMAVSPGVQSRSPVTAPYGILMNLGGSRKALSNISRGSNYIPETCLNSG 235

Query: 230 ELPDAYSLRKRLEKKLEMEGLKVSVDCANLLNNGLDVFMKRLIKPCLELAGSR------- 282
           ELPD  SLR  LE+KLEMEG+ VS+DC NLLNNGLDV++KRLI+PC+ LAGSR       
Sbjct: 236 ELPDTRSLRSHLEQKLEMEGIGVSLDCVNLLNNGLDVYLKRLIEPCMALAGSRCDNEQLK 295

Query: 283 ------SGHKHSSFSASILDFQVATELNPQILGNDWPSQLEIFS 320
                 +  +  S +AS+LDF+ A E NPQILG DWP QLE  S
Sbjct: 296 SASGEYAQRQRKSVNASMLDFRFAMESNPQILGEDWPVQLEKIS 339

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255573127|ref|XP_002527493.1| conserved hypothetical protein [Ricinus communis] gi|223533133|gb|EEF34891.1| conserved hypothetical protein [Ricinus communis]

 Score =  322 bits (826), Expect = 1e-85,   Method: Compositional matrix adjust.
 Identities = 174/351 (49%), Positives = 224/351 (63%), Gaps = 31/351 (8%)

Query: 1   MPADRHFMRLDILEIKSHIERKLGAAKSDKYFSLLTRYLSLKISKSEFDRLCIGTIGREN 60
           M +++++ R++ LE+K+ + +K+G  ++DKYF  LTR  +LK++K EFD+LC+  IGREN
Sbjct: 1   MLSNQNYTRINTLELKALLVKKIGHERADKYFDQLTRLFTLKVAKCEFDKLCVRIIGREN 60

Query: 61  VRLHNRLLRSIIQNACLSKTPPPKEPKVDGFERG-KVPNGYQRSCLQSLCKD-IPQSSRK 118
           V LHNRL+RSI++NACL+  PPPK  K  G     +  NGYQR+CLQSL  D  P S RK
Sbjct: 61  VPLHNRLIRSIVKNACLANVPPPKGIKRVGSSLNVRTANGYQRNCLQSLYGDAFPPSPRK 120

Query: 119 GMTPALRDCKLKDFPSPLGPRGKSHSIACQDSVPKIQEQLSTNELFSLGSRPP---GSVE 175
           G +P  RD K +D PSPLGP GK  S+ C++   + QEQ S  EL SLGSRPP    SVE
Sbjct: 121 GRSPVNRDRKFRDRPSPLGPLGKPQSMVCEELNSRAQEQQSATELLSLGSRPPAEVASVE 180

Query: 176 DGEEVDQAAGSPSIYSRSPVKAPLGIPINGKGTPKLLHKSST-DAYYTGICQNHGELPDA 234
           +GEEV+QAAGSP + SRSPV APLG+ +N  G  K +   S   ++    C + G LPD 
Sbjct: 181 EGEEVEQAAGSPCVQSRSPVTAPLGVSMNLGGARKAISNVSICSSHLRETCLSSGMLPDT 240

Query: 235 YSLRKRLEKKLEMEGLKVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKH------- 287
            SLR RLE+KLEME L VSVDC NLLNN LD ++K+LI+PC+ LA SR G  H       
Sbjct: 241 RSLRSRLERKLEMEDLSVSVDCVNLLNNALDSYLKKLIEPCMGLASSRCGRDHLRKDSDQ 300

Query: 288 ------------------SSFSASILDFQVATELNPQILGNDWPSQLEIFS 320
                              S  AS+LDF  A ++NPQILG DW + LE  S
Sbjct: 301 FAPGSNEILPGRYMQRPTESVYASMLDFHAAMQVNPQILGGDWATSLEKIS 351

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

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	328
TAIR|locus:2118944	342	AT4G33890 "AT4G33890" [Arabido	0.932	0.894	0.468	1.1e-66
TAIR|locus:2046693	407	AT2G24530 "AT2G24530" [Arabido	0.399	0.321	0.401	1.2e-45
TAIR|locus:2125279	379	AT4G31440 "AT4G31440" [Arabido	0.814	0.704	0.355	4.6e-40
TAIR|locus:2046956	291	AT2G14850 "AT2G14850" [Arabido	0.807	0.910	0.392	5.3e-40
TAIR|locus:2158237	287	AT5G67410 "AT5G67410" [Arabido	0.637	0.728	0.418	3.3e-31
DICTYBASE|DDB_G0292000	592	DDB_G0292000 [Dictyostelium di	0.243	0.135	0.296	0.00083

TAIR|locus:2118944 AT4G33890 "AT4G33890" [Arabidopsis thaliana (taxid:3702)]

 Score = 678 (243.7 bits), Expect = 1.1e-66, P = 1.1e-66
 Identities = 161/344 (46%), Positives = 223/344 (64%)

Query:     1 MPADRHFMRLDILEIKSHIERKLGAAKSDKYFSLLTRYLSLKISKSEFDRLCIGTIGREN 60
             M +++   RLD LEIK+ I R++G  +++ YF+ L R+ +LKI+KSEFD+LCI TIGR+N
Sbjct:     1 MGSNQGSSRLDTLEIKALIYREIGNQRAESYFNQLGRFFALKITKSEFDKLCIKTIGRQN 60

Query:    61 VRLHNRLLRSIIQNACLSKTPPPKEPKVDGFERGKVPNGYQRSCLQSLCKDIPQSSRKGM 120
             + LHNRL+RSII+NAC++K+PP  + K   F R    +  + S +Q L  D         
Sbjct:    61 IHLHNRLIRSIIKNACIAKSPPFIK-KGGSFVRFGNGDSKKNSQIQPLHGD------SAF 113

Query:   121 TPALRDC---KLKDFPSPLGPRGKSHSIAC--QDSVPKIQEQLSTNELFSLGSRPPG--- 172
             +P+ R C   KL+D PSPLGP GK HS+    ++S+ K Q   S  EL SLGSRPP    
Sbjct:   114 SPSTRKCRSRKLRDRPSPLGPLGKPHSLTTTNEESMSKAQ---SATELLSLGSRPPVEVV 170

Query:   173 SVEDGEEVDQ-AAGSPSIYSRSPVKAPLGIPI---NGKGTPKLLHKSS--TDAYYTGICQ 226
             SVE+GEEV+Q A GSPS+ SR P+ APLG+ +   NG  T K +   S  + ++    CQ
Sbjct:   171 SVEEGEEVEQIAGGSPSVQSRCPLTAPLGVSMSLRNG-ATRKSVSNVSMCSRSFNRETCQ 229

Query:   227 NHGELPDAYSLRKRLEKKLEMEGLKVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSG-- 284
             N+GELPD  +LR RLE++LEMEGLK+++D  +LLN+GLDVFM+RLI+PCL LA +R G  
Sbjct:   230 NNGELPDTRTLRSRLERRLEMEGLKITMDSVSLLNSGLDVFMRRLIEPCLSLANTRCGTD 289

Query:   285 ------HKHSSFS-----ASILDFQVATELNPQILGNDWPSQLE 317
                   ++++  S      S+ DF+   ELN +ILG DWP  +E
Sbjct:   290 RVREMNYQYTQQSRRLSYVSMSDFRAGMELNTEILGEDWPMHME 333

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2046693 AT2G24530 "AT2G24530" [Arabidopsis thaliana (taxid:3702)]

 Score = 248 (92.4 bits), Expect = 1.2e-45, Sum P(3) = 1.2e-45
 Identities = 59/147 (40%), Positives = 89/147 (60%)

Query:     9 RLDILEIKSHIERKLGAAKSDKYFSLLTRYLSLKISKSEFDRLCIGTIGRENVRLHNRLL 68
             R+ + E+K HI +K G  +S +YF  L R+LS K++KSEFD+ C+  +GREN+ LHN+L+
Sbjct:     8 RISLCELKEHIVKKTGVERSRRYFYYLGRFLSQKLTKSEFDKTCLRLLGRENLSLHNQLI 67

Query:    69 RSIIQNACLSKTPPPKEP-----KVDGFE-RGK--------VPNGYQRSCLQSLCKDIPQ 114
             RSI++NA ++K+PPP        K + F+ RG         +PN  Q   + S    +P 
Sbjct:    68 RSILRNATVAKSPPPDHEAGHSTKANAFQSRGDGLEQSGTLIPNHSQHEPVWSNGV-LPI 126

Query:   115 SSRKGMTPALRDCKLKDFPSPLGPRGK 141
             S RK +   +++ K +D PSPLG  GK
Sbjct:   127 SPRK-VRSGMQNRKSRDRPSPLGSNGK 152

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2125279 AT4G31440 "AT4G31440" [Arabidopsis thaliana (taxid:3702)]

 Score = 356 (130.4 bits), Expect = 4.6e-40, Sum P(2) = 4.6e-40
 Identities = 105/295 (35%), Positives = 157/295 (53%)

Query:     9 RLDILEIKSHIERKLGAAKSDKYFSLLTRYLSLKISKSEFDRLCIGTIGRENVRLHNRLL 68
             R+D+ E+K HI +K+G  +S +YF  L R+LS K++KSEFD+ C   +GREN+ LHN+L+
Sbjct:     8 RIDLAELKVHIVKKVGVERSTRYFYYLGRFLSQKLTKSEFDKSCFRLLGRENLSLHNKLI 67

Query:    69 RSIIQNACLSKTPP-------PKEP----KVDGFERGKVPN-GYQRSCLQSLCKDIPQSS 116
             RSI++NA L+K+PP       P +     K DG E  +  N  + R+ L +L   +    
Sbjct:    68 RSILRNASLAKSPPSVHQSGHPGKSLVLGKEDGPEESRSLNPDHIRNDL-ALSNGVLAKV 126

Query:   117 RKGMTPALRDCKLKDFPSPLGPRGK---SHSIACQDSVPKIQEQ--LSTNELFSLGSRPP 171
             R G      D  ++D P PLG  GK     + +     P  ++   L   E  ++  +  
Sbjct:   127 RPGTCD---DRTIRDKPCPLGSNGKVLGPFAYSRPGRYPDERDSAFLCPAEQKAVSGKDQ 183

Query:   172 GSVEDGEEVDQAAGSPSIYSRSPVKAPLGIPINGK--GTPKLLHKSSTDAYYTGICQNHG 229
              +     + D+A     I S  PV APLGIP      G  +     ST A     C + G
Sbjct:   184 VAAPISRD-DEA--QVRILSTPPVMAPLGIPFCSASVGGDRRTVPVSTSAAAIS-CYDSG 239

Query:   230 ELPDAYSLRKRLEKKLEMEGLK-VSVDCANLLNNGLDVFMKRLIKPCLELAGSRS 283
              L D   LRKR+E     +GL  VS +C+ +LNN LD+++K+L+K C++LAG+RS
Sbjct:   240 GLSDTEMLRKRMENIAVTQGLGGVSAECSIVLNNMLDLYLKKLMKSCVDLAGARS 294

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2046956 AT2G14850 "AT2G14850" [Arabidopsis thaliana (taxid:3702)]

 Score = 426 (155.0 bits), Expect = 5.3e-40, P = 5.3e-40
 Identities = 115/293 (39%), Positives = 158/293 (53%)

Query:    42 KISKSEFDRLCIGTIGRENVRLHNRLLRSIIQNACLSKTPPPKE-PKVDGFERGKVPNGY 100
             +++  E   L    IG +    +   L   + +  +SK+   K   K  G E   + N  
Sbjct:     9 RLNSLEIKALIYQKIGHQRADTYFDQLGKFLTSR-ISKSEFDKLCSKTVGRENISLHNRL 67

Query:   101 QRSCLQ--SLCKD----IPQSSRKG---MTPALRDC---KLKDFPSPLGPRGKSHSIACQ 148
              RS L+  S+ K      P+ S  G     P+ R C   K +D PSPLGP GK  S+   
Sbjct:    68 VRSILKNASVAKSPPPRYPKKSLYGDPVFPPSPRKCRSRKFRDRPSPLGPLGKPQSLTTT 127

Query:   149 DSVPKIQEQLSTNELFSLGSRPPGSVEDGEEVDQAAGSPSIYSRSPVKAPLGIPINGKGT 208
             +     + Q    E+ S        VEDGEEV+Q  GSPS+ SRSP+ APLG+  + K  
Sbjct:   128 NDESMSKAQRLPMEVVS--------VEDGEEVEQMTGSPSVQSRSPLTAPLGVSFHLKSK 179

Query:   209 PKLLHKSSTDAYYTGICQNHGELPDAYSLRKRLEKKLEMEGLKVSVDCANLLNNGLDVFM 268
              +    S+ +      CQ+ GELPD  +LR RLEKKLEMEG+K+S+D ANLLN GL+ +M
Sbjct:   180 ARF---STYNGINRETCQSSGELPDMITLRARLEKKLEMEGIKLSMDSANLLNRGLNAYM 236

Query:   269 KRLIKPCLELAGSRSGHKHSSFSASILDFQVATELNPQILGNDWPSQLEIFSC 321
             +RLI+PCL LA   S  K +  + S+LDF  A E+NP++LG +WP QLE   C
Sbjct:   237 RRLIEPCLSLA---SQQKRAVSNVSMLDFHAAMEVNPRVLGEEWPIQLEKICC 286

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2158237 AT5G67410 "AT5G67410" [Arabidopsis thaliana (taxid:3702)]

 Score = 343 (125.8 bits), Expect = 3.3e-31, P = 3.3e-31
 Identities = 98/234 (41%), Positives = 134/234 (57%)

Query:    98 NGYQRSCLQSLC--KDIPQSSRKGMTPALRDCKLKD--FPS-----PLGPR-GKSHSIAC 147
             N   R  L+++C  K +P   + G+    +  K  +  F S     P  PR G++     
Sbjct:    66 NALLRGILKNICLSKTLPPFVKNGVESDNKKKKQLNGAFQSLCKELPRSPRKGRTQRRLN 125

Query:   148 QDSVPKIQEQLSTNELFSLGSRPPGSVEDGEEVDQAAGSPSIYSRSPVKAPLGIPINGKG 207
             +D      + L T E+ S   R   S+E+ EEVDQ    P   S+ P++AP G+  N + 
Sbjct:   126 KDGNISKGKSLVT-EVVSSSGRQQWSMENVEEVDQLI--PCWRSQ-PIEAPFGV--NLRD 179

Query:   208 TPKLLHKSSTDAYYTGICQNHGELPDAYSLRKRLEKKLEMEGLKVSVDCANLLNNGLDVF 267
               K  H+  T       C + GELPD+ SL+K+LE  LE EGL+VSV  AN LN GLDVF
Sbjct:   180 VIKKQHRIDT------CCYSSGELPDSVSLKKKLEDDLE-EGLEVSVGFANSLNAGLDVF 232

Query:   268 MKRLIKPCLELAGSRSGHKHSSFSASILDFQVATELNPQILGNDWPSQLEIFSC 321
             +KRLIKPCLELA SRS +  +S ++S++DFQVA  LNP ILG DWP++LE  +C
Sbjct:   233 LKRLIKPCLELAASRSSN--ASSASSLVDFQVAMALNPSILGEDWPTKLEKIAC 284

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

DICTYBASE|DDB_G0292000 DDB_G0292000 [Dictyostelium discoideum (taxid:44689)]

 Score = 116 (45.9 bits), Expect = 0.00083, P = 0.00083
 Identities = 24/81 (29%), Positives = 43/81 (53%)

Query:     2 PADRHFMRLDILEIKSHIERKLGAAKSDKYFSLLTRYLSLKISKSEFDRLCIGTIGRENV 61
             P +    R+D++ +K  ++  L   +S+ Y+  + +YL  ++SK E D      +   N+
Sbjct:    26 PYETSLERIDLIPLKKQLDAVL-KDRSEDYWEWIRKYLCGRLSKRELDYYVTTNLNEPNL 84

Query:    62 RLHNRLLRSIIQNACLSKTPP 82
              LHN   +++I NA  SKT P
Sbjct:    85 HLHNTFFKAVIFNAFYSKTSP 105


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.317   0.135   0.401    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      328       328   0.00088  116 3  11 22  0.42    34
                                                     33  0.45    37


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  6
  No. of states in DFA:  602 (64 KB)
  Total size of DFA:  218 KB (2120 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  31.40u 0.09s 31.49t   Elapsed:  00:00:02
  Total cpu time:  31.40u 0.09s 31.49t   Elapsed:  00:00:02
  Start:  Thu May  9 16:49:29 2013   End:  Thu May  9 16:49:31 2013

GO:0070461 "SAGA-type complex" 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

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00019640001 SubName- Full=Chromosome chr7 scaffold_20, whole genome shotgun sequence; (307 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	328
pfam12767	210	pfam12767, SAGA-Tad1, Transcriptional regulator of	2e-45

>gnl|CDD|221761 pfam12767, SAGA-Tad1, Transcriptional regulator of RNA polII, SAGA, subunit

 Score =  153 bits (388), Expect = 2e-45
 Identities = 83/280 (29%), Positives = 118/280 (42%), Gaps = 71/280 (25%)

Query: 2   PADRHFMRLDILEIKSHIERKLGAAKSDKYFSLLTRYLSLKISKSEFDRLCIGTIGRENV 61
            A +   R+D+ E+KS + ++LGA +++KYF  L R+LS K+SK EFD+LC   +GREN+
Sbjct: 1   MAVKQAARVDLEELKSQLVKRLGAERAEKYFQHLKRFLSGKLSKEEFDKLCFRLLGRENI 60

Query: 62  RLHNRLLRSIIQNACLSKTPPPKEPKVDGFERGKVPNGYQRSCLQSLCKDIPQSSRKGMT 121
            LHN+L+ SI++NAC +K+PPP        +      G            +P S R   +
Sbjct: 61  PLHNQLILSILKNAC-AKSPPP------SSQAKTGNWGTTSGSPSDNGGALPVSGRASRS 113

Query: 122 PALRDCKLKDFPSPLGPRGKSHSIACQDSVPKIQEQLSTNELFSLGSRPPGSVEDGEEVD 181
                                          +    LS  E   L              +
Sbjct: 114 VKRLK--------------------------RELMGLSPRERGRLKKLTKKPQGKQSTGE 147

Query: 182 QAAGSPSIYSRSPVKAPLGIPINGKGTPKLLHKSSTDAYYTGICQNHGELPDAYSLRKRL 241
             +                                       +C   GELPD  SLRKR+
Sbjct: 148 SVS-------------------------------------LPLCYETGELPDTGSLRKRM 170

Query: 242 EKKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAG 280
           E+     GL  VSVDCA+LLN+GLD ++KRLIK C+EL  
Sbjct: 171 EQIAAENGLGGVSVDCADLLNSGLDAYLKRLIKSCIELVK 210

The yeast SAGA complex is a multifunctional coactivator that regulates transcription by RNA polymerase II. It is formed of five major modular subunits and shows a high degree of structural conservation to human TFTC and STAGA. The complex can also be conceived of as consisting of two histone-fold-containing core subunits, and this family is one of these. As a family it is likely to carry binding regions for interactions with a number of the other components of the complex. Length = 210

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	328
PF12767	252	SAGA-Tad1: Transcriptional regulator of RNA polII,	100.0
PF05236	264	TAF4: Transcription initiation factor TFIID compon	96.89
smart00803	65	TAF TATA box binding protein associated factor. TA	96.55
cd08045	212	TAF4 TATA Binding Protein (TBP) Associated Factor	96.37
PF02969	66	TAF: TATA box binding protein associated factor (T	95.42
smart00576	77	BTP Bromodomain transcription factors and PHD doma	95.34
cd00076	85	H4 Histone H4, one of the four histones, along wit	95.2
PLN00035	103	histone H4; Provisional	95.17
PTZ00015	102	histone H4; Provisional	95.07
PF00808	65	CBFD_NFYB_HMF: Histone-like transcription factor (	94.17
cd07981	72	TAF12 TATA Binding Protein (TBP) Associated Factor	93.44
PF07524	77	Bromo_TP: Bromodomain associated; InterPro: IPR006	93.24
COG2036	91	HHT1 Histones H3 and H4 [Chromatin structure and d	91.96
cd07979	117	TAF9 TATA Binding Protein (TBP) Associated Factor	91.84
PF00125	75	Histone: Core histone H2A/H2B/H3/H4 histone h2a si	91.78
smart00417	74	H4 Histone H4.	91.7
cd08050	343	TAF6 TATA Binding Protein (TBP) Associated Factor	91.28
PF03847	68	TFIID_20kDa: Transcription initiation factor TFIID	89.51
PF12174	70	RST: RCD1-SRO-TAF4 (RST) plant domain; InterPro: I	87.43
KOG3423	176	consensus Transcription initiation factor TFIID, s	87.13
PF03540	51	TFIID_30kDa: Transcription initiation factor TFIID	86.54
PF02269	93	TFIID-18kDa: Transcription initiation factor IID,	81.03

>PF12767 SAGA-Tad1: Transcriptional regulator of RNA polII, SAGA, subunit; InterPro: IPR024738 The yeast Spt-Ada-Gcn5-Acetyl (SAGA) transferase complex is a multifunctional coactivator involved in multiple cellular processes [], including regulation of transcription by RNA polymerase II [, ]

Probab=100.00  E-value=2.2e-53  Score=398.07  Aligned_cols=249  Identities=39%  Similarity=0.509  Sum_probs=178.8

Q ss_pred             CCCCCccccccHHHHHHHHHHHhCCccHHHHHHHHHHHHhccCCHHHHHHHHHhhcCCCcccccHHHHHHHHHhhhcCCC
Q 036514            1 MPADRHFMRLDILEIKSHIERKLGAAKSDKYFSLLTRYLSLKISKSEFDRLCIGTIGRENVRLHNRLLRSIIQNACLSKT   80 (328)
Q Consensus         1 m~~~~~~~RiDl~~lk~~L~~~LG~~~~~~Y~~~l~~fl~gklsk~Efd~~~~~~L~~e~i~LHN~lilsIl~Na~~~~~   80 (328)
                      |++ ++++||||.++|++|+++||+++|++||++|++||.|||||+|||++|+.+||+||+||||+||+|||+||+... 
T Consensus         1 ~~~-~~~~Ridl~~lk~~l~~~LG~~~~~~Y~~~l~~fl~~klsk~Efd~~~~~~L~~~~~~LHN~li~sIl~na~~~~-   78 (252)
T PF12767_consen    1 MSQ-QQNSRIDLEELKSQLQKRLGPDRWKKYFQSLKRFLSGKLSKEEFDKECRRILGRENVHLHNQLILSILKNALAKS-   78 (252)
T ss_pred             CCC-CcccccCHHHHHHHHHHHHChHHHHHHHHHHHHHHHhccCHHHHHHHHHHHhChhHHHHHHHHHHHHHHHHhhcC-
Confidence            555 899999999999999999999999999999999999999999999999999999999999999999999995554 


Q ss_pred             CCCCCCCCCCCcccccCCCccccccccccCCCCCCccCCCCccccccccc-CCCCCCCCCCCCCcccccCCchhh-Hhhh
Q 036514           81 PPPKEPKVDGFERGKVPNGYQRSCLQSLCKDIPQSSRKGMTPALRDCKLK-DFPSPLGPRGKSHSIACQDSVPKI-QEQL  158 (328)
Q Consensus        81 pp~~~~~~~~s~~~~~~~g~~~~~~q~l~~~~~~~prk~rs~~~rdrr~k-d~~~~lgp~gk~~s~~~~~~~~~~-q~~~  158 (328)
                      ||+..+.+.++..  ...+.......+..+.++.++++.++...+++.+. +.+++.+++++....  +.+.... ....
T Consensus        79 p~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~k~~~~~~~~~~r~r~~~~~~~--~~~~~~~~~~~~  154 (252)
T PF12767_consen   79 PPPSSASGPPSSV--KSWVKANGKPSSNQGAKPVSPRKSRSSRRLKRKVMSLPPRERGRLKKIETK--ESGKRQSPDEPS  154 (252)
T ss_pred             CCccCcccccccc--cccccccCCCcccccccCCCCccchhHHHHhhhhccCCccccccccccccc--ccccccCCCCcc
Confidence            5543332211100  00011111112233456777877777655666555 555555666654100  0000000 0000


Q ss_pred             hhhhhccCCCCCCCCccchhhhhhhcCCCCccCCCCccCCCCCCCCCCCCCcccccCCCCcccchhHhhhCCCCCHHhHH
Q 036514          159 STNELFSLGSRPPGSVEDGEEVDQAAGSPSIYSRSPVKAPLGIPINGKGTPKLLHKSSTDAYYTGICQNHGELPDAYSLR  238 (328)
Q Consensus       159 ~~~e~~~~~~~~p~sve~~ee~~q~~~~~~~~s~spv~aPlgip~~~~s~g~~~~~~~~~~~~~~~c~esgeLPDt~sL~  238 (328)
                      ++....+.+.....+++++++++|.  + ..|+++                      +.+.+..++|+++|+|||+++|+
T Consensus       155 ~~~~~~~~~~~~~~~~~~~e~~~~~--~-~~~s~~----------------------~~~~~~~~lc~es~~LPD~~~L~  209 (252)
T PF12767_consen  155 SLLQTRSKQPPEIPSVEDGEEVEQI--N-SNWSRS----------------------VSSGYQSPLCSESGELPDTQSLR  209 (252)
T ss_pred             ccccccccccccCCcccCccccccc--c-cccccc----------------------cccCCCCccHHHhCcCCCHHHHH
Confidence            0001111122223688999999866  3 566654                      12346788999999999999999


Q ss_pred             HHHHHHHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhh
Q 036514          239 KRLEKKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAG  280 (328)
Q Consensus       239 ~RM~~ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~  280 (328)
                      +||+.||||+|| ||+++||++||+|||+|||+||++||++||
T Consensus       210 ~Rm~~ia~e~GL~gvs~~~a~ll~~ale~~LK~lI~s~l~~~r  252 (252)
T PF12767_consen  210 KRMEQIAWEHGLGGVSDDCANLLNLALEVHLKNLIKSCLDLVR  252 (252)
T ss_pred             HHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcC
Confidence            999999999999 999999999999999999999999999986

It is formed of five major modular subunits and shows a high degree of structural conservation to human TFTC and STAGA []. This entry represents Ada1 (known as Tada1 in higher eukaryotes), one of the subunits that constitute the SAGA core. It also functions as a component of the SALSA and SLIK complexes. ; GO: 0070461 SAGA-type complex

>PF05236 TAF4: Transcription initiation factor TFIID component TAF4 family; InterPro: IPR007900 Accurate transcription initiation at protein-coding genes by RNA polymerase II requires the assembly of a multiprotein complex around the mRNA start site

Probab=96.89  E-value=0.0012  Score=62.56  Aligned_cols=62  Identities=23%  Similarity=0.319  Sum_probs=41.3

Q ss_pred             hHhhhCCCCCHHhHHHHHHHHHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCC
Q 036514          224 ICQNHGELPDAYSLRKRLEKKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHK  286 (328)
Q Consensus       224 ~c~esgeLPDt~sL~~RM~~ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~  286 (328)
                      .|.+ --|-++..|.+||..|+..+|+ .++.|.++||+.|++.||++||+.++.+++.|....
T Consensus        37 ~~~~-~~fL~~~~L~~~i~~i~~~~g~~~~~~d~l~llS~A~e~rLr~lie~~~~~s~hR~~~~   99 (264)
T PF05236_consen   37 SEKE-EPFLNPSPLQKRIQKIAKKHGLKSVDEDVLELLSLATEERLRNLIEKAIVLSRHRRDSS   99 (264)
T ss_dssp             --------S-HHHHHHHHHHHHHCTT--EE-TCHHHHHHHHHHHHHHHHHHHHH----------
T ss_pred             cccc-ccccCHHHHHHHHHHHHHHcCCcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccc
Confidence            3444 3377899999999999999999 999999999999999999999999999999888653

Transcription factor TFIID is one of the general factors involved in this process. Yeast TFIID comprises the TATA binding protein and 14 TBP-associated factors (TAFIIs), nine of which contain histone-fold domains (IPR007124 from INTERPRO). The C-terminal region of the TFIID-specific yeast TAF4 (yTAF4) containing the HFD shares strong sequence similarity with Drosophila (d)TAF4 and human TAF4. A structure/function analysis of yTAF4 demonstrates that the HFD, a short conserved C-terminal domain (CCTD), and the region separating them are all required for yTAF4 function. This region of similarity is found in Transcription initiation factor TFIID component TAF4 []. ; GO: 0006352 transcription initiation, DNA-dependent, 0005669 transcription factor TFIID complex; PDB: 1H3O_C.

>smart00803 TAF TATA box binding protein associated factor

Probab=96.55  E-value=0.011  Score=44.95  Aligned_cols=56  Identities=18%  Similarity=0.297  Sum_probs=49.2

Q ss_pred             HHHHHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHH
Q 036514          241 LEKKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVAT  301 (328)
Q Consensus       241 M~~ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~am  301 (328)
                      +..+|+..|. .|+.|++..|..-++.|+++|++.++.+++.     .++..++..|+..|+
T Consensus         8 i~ria~~~Gi~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~h-----akRktlt~~DI~~Al   64 (65)
T smart00803        8 IKDVAESLGIGNLSDEAAKLLAEDVEYRIKEIVQEALKFMRH-----SKRTTLTTSDIDSAL   64 (65)
T ss_pred             HHHHHHHCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----hCCCeecHHHHHHHh
Confidence            5678899999 8999999999999999999999999999874     235569999998886

TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold.

>cd08045 TAF4 TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex

Probab=96.37  E-value=0.014  Score=53.79  Aligned_cols=75  Identities=17%  Similarity=0.263  Sum_probs=60.2

Q ss_pred             hhCCCCCHHhHHHHHHHHHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCC-CCCccchHhhHHHHH
Q 036514          227 NHGELPDAYSLRKRLEKKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHK-HSSFSASILDFQVAT  301 (328)
Q Consensus       227 esgeLPDt~sL~~RM~~ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~-~~~~~~Sl~Df~~am  301 (328)
                      ...-|-+...|.++|..++.++|+ +++.|..++|+.|++.||++||+-.+.+++-|.... ....+.-..|.+..|
T Consensus        40 ~~~~fl~~~~l~~~~~~i~~~~g~~~~~~d~~~lis~a~e~rlr~li~k~~~~s~hR~~~~~~~~r~~~~sdvr~qL  116 (212)
T cd08045          40 KDPSFLNPSPLAKKIRKIAKKHGLKEVDEDVLDLISLALEERLRNLLEKLIEVSEHRVDSEKEDERYEITSDVRKQL  116 (212)
T ss_pred             chhhccCHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCceeecchHHHHH
Confidence            344577889999999999999999 999999999999999999999999999999886542 123333344555443

The TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryote. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypotheses are

>PF02969 TAF: TATA box binding protein associated factor (TAF); InterPro: IPR004823 The TATA box binding protein associated factor (TAF) is part of the transcription initiation factor TFIID multimeric protein complex

Probab=95.42  E-value=0.09  Score=40.31  Aligned_cols=56  Identities=16%  Similarity=0.242  Sum_probs=44.2

Q ss_pred             HHHHHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHH
Q 036514          241 LEKKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVAT  301 (328)
Q Consensus       241 M~~ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~am  301 (328)
                      +..+|+.-|+ .++.||+..|..=+++-||+||..++.+.+-     ..+..++..|+-.|+
T Consensus         9 vk~iAes~Gi~~l~de~a~~La~dveyrlreiiq~a~kfm~h-----skR~~Lt~~Di~~AL   65 (66)
T PF02969_consen    9 VKDIAESLGISNLSDEAAKALAEDVEYRLREIIQEALKFMRH-----SKRTKLTTDDINSAL   65 (66)
T ss_dssp             HHHHHHHTT---B-HHHHHHHHHHHHHHHHHHHHHHHHHHHH-----TT-SSB-HHHHHHHH
T ss_pred             HHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----hCCCCCCHHHHHHHh
Confidence            4568999999 9999999999999999999999999999873     124458899998886

TFIID plays a central role in mediating promoter responses to various activators and repressors. It binds tightly to TAFII-250 and directly interacts with TAFII-40. TFIID is composed of TATA binding protein (TBP)and a number of TBP-associated factors (TAFS). TAF proteins adopt a histone-like fold.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus; PDB: 1TAF_B.

>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins

Probab=95.34  E-value=0.15  Score=39.63  Aligned_cols=64  Identities=19%  Similarity=0.184  Sum_probs=53.5

Q ss_pred             hHHHHHHHHHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHhC
Q 036514          236 SLRKRLEKKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATELN  304 (328)
Q Consensus       236 sL~~RM~~ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amEln  304 (328)
                      .|+.=+.+||+..|. .+++.+.+.|-..++.|+.+|.+.+...+..-     ++...++.|+..||+-.
T Consensus         7 ll~~~Vaqil~~~Gf~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~a-----gR~~~~~~Dv~~Al~~~   71 (77)
T smart00576        7 LLRIAVAQILESAGFDSFQESALETLTDILQSYIQELGRTAHSYAELA-----GRTEPNLGDVVLALENL   71 (77)
T ss_pred             HHHHHHHHHHHHcCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHc-----CCCCCCHHHHHHHHHHh
Confidence            355558899999999 99999999999999999999999999998531     12335699999999753

subdomain of archael histone-like transcription factors

>cd00076 H4 Histone H4, one of the four histones, along with H2A, H2B and H3, which forms the eukaryotic nucleosome core; along with H3, it plays a central role in nucleosome formation; histones bind to DNA and wrap the genetic material into "beads on a string" in which DNA (the string) is wrapped around small blobs of histones (the beads) at regular intervals; play a role in the inheritance of specialized chromosome structures and the control of gene activity; defects in the establishment of proper chromosome structure by histones may activate or silence genes aberrantly and thus lead to disease; the sequence of histone H4 has remained almost invariant in more than 2 billion years of evolution

Probab=95.20  E-value=0.093  Score=42.14  Aligned_cols=61  Identities=11%  Similarity=0.205  Sum_probs=52.7

Q ss_pred             HHHHHHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHhCC
Q 036514          240 RLEKKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATELNP  305 (328)
Q Consensus       240 RM~~ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amElnP  305 (328)
                      =+..+|+-.|. -||.++.+-+...|+.||++|++-++.++..     .+...++..|...||+.-.
T Consensus        18 ~I~RLarr~GvkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~H-----a~RKTVt~~DV~~alkr~g   79 (85)
T cd00076          18 AIRRLARRGGVKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEH-----AKRKTVTAMDVVYALKRQG   79 (85)
T ss_pred             HHHHHHHHcCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHh-----cCCCcCcHHHHHHHHHHCC
Confidence            35678889999 8999999999999999999999999999885     3455699999999987543

>PLN00035 histone H4; Provisional

Probab=95.17  E-value=0.093  Score=43.62  Aligned_cols=59  Identities=12%  Similarity=0.186  Sum_probs=52.1

Q ss_pred             HHHHHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHhC
Q 036514          241 LEKKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATELN  304 (328)
Q Consensus       241 M~~ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amEln  304 (328)
                      +..+|+..|. -||.++.+-+...|+.||+.|++-++.++..     .....++..|...|++.-
T Consensus        35 IrRLARr~GvkRIS~~ay~elr~vle~~l~~I~~dav~ya~H-----A~RKTV~~~DV~~Alkr~   94 (103)
T PLN00035         35 IRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEH-----ARRKTVTAMDVVYALKRQ   94 (103)
T ss_pred             HHHHHHHcCcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHh-----cCCCcCcHHHHHHHHHHc
Confidence            5678889999 8999999999999999999999999999986     345569999999998754

>PTZ00015 histone H4; Provisional

Probab=95.07  E-value=0.12  Score=42.81  Aligned_cols=61  Identities=11%  Similarity=0.184  Sum_probs=52.7

Q ss_pred             HHHHHHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHhCC
Q 036514          240 RLEKKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATELNP  305 (328)
Q Consensus       240 RM~~ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amElnP  305 (328)
                      =+..+|+-.|. -||.++.+-+...|+.||++|++-++.++..-     ....++.+|...|+..--
T Consensus        35 ~IrRLarr~GvkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA-----~RKTVt~~DV~~AlKr~g   96 (102)
T PTZ00015         35 AIRRLARRGGVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYA-----RRKTVTAMDVVYALKRQG   96 (102)
T ss_pred             HHHHHHHHcCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-----CCCcccHHHHHHHHHhcC
Confidence            35678889999 89999999999999999999999999999863     355699999999987543

>PF00808 CBFD_NFYB_HMF: Histone-like transcription factor (CBF/NF-Y) and archaeal histone; InterPro: IPR003958 The CCAAT-binding factor (CBF) is a mammalian transcription factor that binds to a CCAAT motif in the promoters of a wide variety of genes, including type I collagen and albumin

Probab=94.17  E-value=0.3  Score=36.42  Aligned_cols=59  Identities=17%  Similarity=0.264  Sum_probs=47.9

Q ss_pred             HHHHHHHHHHh-CC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHH
Q 036514          238 RKRLEKKLEME-GL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVAT  301 (328)
Q Consensus       238 ~~RM~~ia~e~-GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~am  301 (328)
                      ..|+..|+.+. +. .|+.|++.+|+.+.+.|+..|.+.+.+.+...     +...|+-.|+..|+
T Consensus         5 ~a~vkri~k~~~~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~~-----~rkti~~~Dv~~Av   65 (65)
T PF00808_consen    5 LARVKRIMKSDPDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQRD-----KRKTITYEDVAKAV   65 (65)
T ss_dssp             HHHHHHHHHHTSTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHT-----TSSEE-HHHHHHHH
T ss_pred             hHHHHHHhccCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHc-----CCCccCHHHHHHHC
Confidence            35777788877 55 79999999999999999999999999998852     35579999998875

The factor is a heteromeric complex of A and B subunits, both of which are required for DNA-binding [, ]. The subunits can interact in the absence of DNA-binding, conserved regions in each being important in mediating this interaction. The A subunit can be split into 3 domains on the basis of sequence similarity, a non-conserved N-terminal 'A domain'; a highly-conserved central 'B domain' involved in DNA-binding; and a C-terminal 'C domain', which contains a number of glutamine and acidic residues involved in protein-protein interactions []. The A subunit shows striking similarity to the HAP3 subunit of the yeast CCAAT-binding heterotrimeric transcription factor [, ]. The Kluyveromyces lactis HAP3 protein has been predicted to contain a 4-cysteine zinc finger, which is thought to be present in similar HAP3 and CBF subunit A proteins, in which the third cysteine is replaced by a serine []. This domain is found in the CCAAT transcription factor and archaeal histones.; GO: 0043565 sequence-specific DNA binding, 0005622 intracellular; PDB: 1F1E_A 2BYM_D 2BYK_D 1HTA_A 1B67_A 1JFI_B 1KU5_B 1N1J_A 1BFM_A 1B6W_A ....

>cd07981 TAF12 TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex

Probab=93.44  E-value=0.3  Score=37.67  Aligned_cols=54  Identities=24%  Similarity=0.271  Sum_probs=47.5

Q ss_pred             CCCCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHhCCcc
Q 036514          249 GLKVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATELNPQI  307 (328)
Q Consensus       249 GLgVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amElnP~l  307 (328)
                      |..+++++.++|...+|.|+-++++.+..+|+-|..+     .+...|++.++|-+-.+
T Consensus        17 ~~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~-----tv~~~Di~l~l~r~~~~   70 (72)
T cd07981          17 REQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSD-----TLEVKDVQLHLERNWNI   70 (72)
T ss_pred             CCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCC-----CCCHHHHHHHHHHhcCC
Confidence            3479999999999999999999999999999976553     49999999999987654

The TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of the seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs function such as serving as activator-bind

>PF07524 Bromo_TP: Bromodomain associated; InterPro: IPR006565 This bromodomain is found in eukaryotic transcription factors and PHD domain containing proteins (IPR001965 from INTERPRO)

Probab=93.24  E-value=0.78  Score=35.41  Aligned_cols=64  Identities=19%  Similarity=0.243  Sum_probs=53.0

Q ss_pred             HhHHHHHHHHHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHh
Q 036514          235 YSLRKRLEKKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATEL  303 (328)
Q Consensus       235 ~sL~~RM~~ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amEl  303 (328)
                      ..|+.=+.+++...|. +++..+.+.|..-+..||.+|-+.+-..+..     .++...++.|+..||+-
T Consensus         6 ~~l~~~va~il~~~GF~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~-----~gRt~~~~~Dv~~al~~   70 (77)
T PF07524_consen    6 SLLRRSVAQILKHAGFDSASPSALDTLTDILQRYLQELGRTAKRYAEH-----AGRTEPNLQDVEQALEE   70 (77)
T ss_pred             HHHHHHHHHHHHHcCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----cCCCCCCHHHHHHHHHH
Confidence            3566777889999999 9999999999999999999999999888752     12334569999999864

The tandem PHD finger-bromodomain is found in many chromatin-associated proteins. It is involved in gene silencing by the human co-repressor KRAB-associated protein 1 (KAP1). The tandem PHD finger-bromodomain of KAP1 has a distinct structure that joins the two protein modules. The first helix, alpha(Z), of an atypical bromodomain forms the central hydrophobic core that anchors the other three helices of the bromodomain on one side and the zinc binding PHD finger on the other []. The Rap1 GTPase-activating protein, Sipa1, is modulated by the cellular bromodomain protein, Brd4. Brd4 belongs to the BET family and is a multifunctional protein involved in transcription, replication, the signal transduction pathway, and cell cycle progression. All of these functions are linked to its association with acetylated chromatin. It has tandem bromodomains []. The dysregulation of the Brd4-associated pathways may play an important role in breast cancer progression []. Bovine papillomavirus type 1 E2 also binds to chromosomes in a complex with Brd4. Interaction with Brd4 is additionally important for E2-mediated transcriptional regulation [, ].

>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]

Probab=91.96  E-value=0.6  Score=38.02  Aligned_cols=57  Identities=19%  Similarity=0.307  Sum_probs=48.3

Q ss_pred             HHHHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHh
Q 036514          242 EKKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATEL  303 (328)
Q Consensus       242 ~~ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amEl  303 (328)
                      ..++...|- .|+.+|.+.|+.+++.|+..|.+-..++|..     .++..|.-.|+..|+..
T Consensus        26 ~Ri~r~~~~~Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~h-----a~RKTV~~~DI~la~~~   83 (91)
T COG2036          26 RRILRKAGAERVSSSAIEELQEALEEYLEEIAEDAVELAEH-----AKRKTVKAEDIKLALKR   83 (91)
T ss_pred             HHHHHHHhHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----cCCCeecHHHHHHHHHH
Confidence            455666666 8999999999999999999999999999986     34567889999998853

>cd07979 TAF9 TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex

Probab=91.84  E-value=0.86  Score=38.51  Aligned_cols=66  Identities=9%  Similarity=0.039  Sum_probs=53.7

Q ss_pred             HHHHHHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHhCCc-cccC
Q 036514          240 RLEKKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATELNPQ-ILGN  310 (328)
Q Consensus       240 RM~~ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amElnP~-lLg~  310 (328)
                      -|..|+...|. .+++++++.|.--+..|..+|++-...+++-     .+...|+..|++.|++.-=. ..+.
T Consensus         6 ~v~~iLk~~Gv~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~h-----A~r~tV~~eDV~lAi~~r~~~~f~~   73 (117)
T cd07979           6 VIAAILKSMGITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEH-----AGKANIDADDVKLAIQSRVDYSFTS   73 (117)
T ss_pred             HHHHHHHHCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----cCCCCCCHHHHHHHHHHHhccCCCC
Confidence            35667778899 8999999999999999999999999999874     23567999999999765332 4444

The TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Human TAF9 has a paralogue gene (TAF9L) whi

>PF00125 Histone: Core histone H2A/H2B/H3/H4 histone h2a signature histone h2b signature histone h3 signature histone h4 signature; InterPro: IPR007125 The core histones together with some other DNA binding proteins appear to form a superfamily defined by a common fold and distant sequence similarities [, ]

Probab=91.78  E-value=0.6  Score=35.44  Aligned_cols=49  Identities=16%  Similarity=0.236  Sum_probs=44.2

Q ss_pred             CCCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHh
Q 036514          250 LKVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATEL  303 (328)
Q Consensus       250 LgVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amEl  303 (328)
                      +.++.++..+|+.++|.|+-+|++.+..++..     ++...|+-.|+..|+.+
T Consensus        26 ~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~-----~kR~tI~~~DI~~A~r~   74 (75)
T PF00125_consen   26 YRISSEALVALQSVLEYLLVEILEEAGNLARH-----AKRKTITPRDIQLAVRI   74 (75)
T ss_dssp             SEECHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----TTBSEEGHHHHHHHHHH
T ss_pred             cccccccchhhhhhhhhhhhhhhhHHHHHHhh-----cCCcEecHHHHHHHHhc
Confidence            57999999999999999999999999999986     44677999999999865

Some proteins contain local homology domains related to the histone fold [].; GO: 0003677 DNA binding; PDB: 2YFW_D 2YFV_B 1U35_H 2F8N_D 2PYO_D 2NQB_D 3AN2_C 3AZJ_C 3AV1_G 3AZM_G ....

>smart00417 H4 Histone H4

Probab=91.70  E-value=0.45  Score=37.31  Aligned_cols=55  Identities=11%  Similarity=0.193  Sum_probs=46.0

Q ss_pred             HHHHHHHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHH
Q 036514          239 KRLEKKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQ  298 (328)
Q Consensus       239 ~RM~~ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~  298 (328)
                      .=+..+|.-.|. -||.++.+-+...|+.||.+|++-++.++...     +...++..|..
T Consensus        17 ~~IrRLaRr~GvkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha-----~RKTV~~~DV~   72 (74)
T smart00417       17 PAIRRLARRGGVKRISGLIYDETRNVLKSFLENVVRDAVTYTEHA-----RRKTVTAMDVV   72 (74)
T ss_pred             HHHHHHHHHcCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-----CCCcccHHHhe
Confidence            346778889999 89999999999999999999999999999863     34457777753

>cd08050 TAF6 TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex

Probab=91.28  E-value=0.71  Score=45.67  Aligned_cols=58  Identities=17%  Similarity=0.236  Sum_probs=50.9

Q ss_pred             HHHHHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHh
Q 036514          241 LEKKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATEL  303 (328)
Q Consensus       241 M~~ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amEl  303 (328)
                      +..+|+..|. .|+.|++..|..-++.++++|++.++.+++-     .++..++..|+..|+++
T Consensus         5 i~~ia~~~Gi~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~h-----skR~~l~~~Di~~Al~~   63 (343)
T cd08050           5 IKLIAESLGIDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRH-----SKRRKLTTSDVNHALRL   63 (343)
T ss_pred             HHHHHHHcCCCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----hCCCcCCHHHHHHHHHH
Confidence            4578999999 8999999999999999999999999999873     22456899999999876

The TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs functions such as serving as

>PF03847 TFIID_20kDa: Transcription initiation factor TFIID subunit A; InterPro: IPR003228 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription []

Probab=89.51  E-value=1.3  Score=33.99  Aligned_cols=49  Identities=27%  Similarity=0.289  Sum_probs=40.5

Q ss_pred             CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHhC
Q 036514          251 KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATELN  304 (328)
Q Consensus       251 gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amEln  304 (328)
                      .+++++.++|..-.|.|+-+++.....+|+.|..     ..+.+.|+...+|-|
T Consensus        17 ~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s-----~tle~~Dv~~~Ler~   65 (68)
T PF03847_consen   17 KLDPDVEELLLELADDFVDDVVSFACRLAKHRKS-----STLEVKDVQLHLERN   65 (68)
T ss_dssp             ---HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT------SEE-HHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCC-----CCCCHHHHHHHHHhh
Confidence            7999999999999999999999999999999765     469999999998864

; GO: 0006352 transcription initiation, DNA-dependent, 0005669 transcription factor TFIID complex; PDB: 1H3O_B.

>PF12174 RST: RCD1-SRO-TAF4 (RST) plant domain; InterPro: IPR022003 This domain is found in many plant proteins including SROs and RCD1s; it is required for interaction with multiple plant transcription factors

Probab=87.43  E-value=2.4  Score=32.77  Aligned_cols=56  Identities=29%  Similarity=0.357  Sum_probs=45.9

Q ss_pred             ccHHHHHHHHHHHhCCccHHHHHHHHHHHHhccCCHHHHHHHHHhhcCCCcccccHHHHHHHH
Q 036514           10 LDILEIKSHIERKLGAAKSDKYFSLLTRYLSLKISKSEFDRLCIGTIGRENVRLHNRLLRSII   72 (328)
Q Consensus        10 iDl~~lk~~L~~~LG~~~~~~Y~~~l~~fl~gklsk~Efd~~~~~~L~~e~i~LHN~lilsIl   72 (328)
                      +=...|-..|.+.|++++...-..+-..|=.+||||+||-+..+.+.|       .++|.+++
T Consensus         9 ~~F~~L~~~l~~~l~~~~~~~l~~~Y~~~k~~kIsR~~fvr~lR~IVG-------D~lL~s~I   64 (70)
T PF12174_consen    9 MPFPMLFSALSKHLPPSKMDLLQKHYEEFKKKKISREEFVRKLRQIVG-------DQLLRSAI   64 (70)
T ss_pred             ccHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHH-------HHHHHHHH
Confidence            446678888999999888777777777888999999999999999999       34566666

>KOG3423 consensus Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]

Probab=87.13  E-value=2.4  Score=38.14  Aligned_cols=71  Identities=15%  Similarity=0.225  Sum_probs=59.2

Q ss_pred             CCCHHhHHHHHHHHHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCC---------CCCccchHhhHHHH
Q 036514          231 LPDAYSLRKRLEKKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHK---------HSSFSASILDFQVA  300 (328)
Q Consensus       231 LPDt~sL~~RM~~ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~---------~~~~~~Sl~Df~~a  300 (328)
                      +||.-..     -++...|+ .+++...-|+..|.+.|+-.|+..++...|.|.+..         ...+.++|.||.-|
T Consensus        87 IPDavt~-----~yL~~aGf~~~D~rv~RLvsLaAQKfvSDIa~DA~Q~~k~r~~~~~~~~k~~~kdkK~tLtmeDL~~A  161 (176)
T KOG3423|consen   87 IPDAVTD-----HYLKKAGFQTSDPRVKRLVSLAAQKFVSDIANDALQHSKIRTKTAIGKDKKQAKDKKYTLTMEDLSPA  161 (176)
T ss_pred             CcHHHHH-----HHHHhcCCCcCcHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccccccccceeeeHHHHHHH
Confidence            5665443     36778999 999999999999999999999999999999998421         57889999999999


Q ss_pred             HHhCCc
Q 036514          301 TELNPQ  306 (328)
Q Consensus       301 mElnP~  306 (328)
                      ++=...
T Consensus       162 L~EyGi  167 (176)
T KOG3423|consen  162 LAEYGI  167 (176)
T ss_pred             HHHhCc
Confidence            875433

>PF03540 TFIID_30kDa: Transcription initiation factor TFIID 23-30kDa subunit; InterPro: IPR003923 Transcription initiation factor TFIID is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors

Probab=86.54  E-value=2.6  Score=30.84  Aligned_cols=42  Identities=14%  Similarity=0.264  Sum_probs=38.0

Q ss_pred             HHHHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccC
Q 036514          242 EKKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRS  283 (328)
Q Consensus       242 ~~ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~  283 (328)
                      .-++...|+ ..++.++-|++.|.+.|+-+|+..++...+.|.
T Consensus         9 ~~yL~~~G~~~~D~rv~RLvSLaaQKFisdI~~dA~q~~k~r~   51 (51)
T PF03540_consen    9 DYYLERSGFQTSDPRVKRLVSLAAQKFISDIANDAMQYCKIRT   51 (51)
T ss_pred             HHHHHHCCCCCCCHhHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence            456788999 899999999999999999999999999988773

The complex includes TATA binding protein (TBP) and various TBP-associated factors (TAFS). TFIID a bona fide RNA polymerase II-specific TATA-binding protein-associated factor (TAF) and is essential for viability []. TFIID acts to nucleate the transcription complex, recruiting the rest of the factors through a direct interaction with TFIIB. The TBP subunit of TFIID is sufficient for TATA-element binding and TFIIB interaction, and can support basal transcription. The protein belongs to the TAF2H family.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus

>PF02269 TFIID-18kDa: Transcription initiation factor IID, 18kD subunit; InterPro: IPR003195 This family includes the Spt3 yeast transcription factors and the 18 kDa subunit from human transcription initiation factor IID (TFIID-18)

Probab=81.03  E-value=1.7  Score=35.15  Aligned_cols=55  Identities=16%  Similarity=0.259  Sum_probs=23.7

Q ss_pred             CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHhCCccccC
Q 036514          251 KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATELNPQILGN  310 (328)
Q Consensus       251 gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amElnP~lLg~  310 (328)
                      .-.+|++++|-.-|-.|+-.++..+...|..|.     +..+++.||.-+|--+|.-|+.
T Consensus        19 ~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg-----~~~i~~eDl~F~lR~D~~Kl~R   73 (93)
T PF02269_consen   19 EPLPETVDLVEDIVREYIIELCQEAMEVAQRRG-----SKKIKVEDLLFLLRKDPKKLAR   73 (93)
T ss_dssp             S--HHHHHHHHHHHHHHHHHHHHHHHC---------------------------------
T ss_pred             CCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccc-----cCcCcHHHHHHHHhcCHHHHHH
Confidence            467899999999999999999999999987753     4469999999999999987775

Determination of the crystal structure reveals an atypical histone fold [].; GO: 0006366 transcription from RNA polymerase II promoter; PDB: 1BH9_A 1BH8_A.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	328
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-04

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 40.6 bits (94), Expect = 6e-04
 Identities = 53/367 (14%), Positives = 103/367 (28%), Gaps = 108/367 (29%)

Query: 9   RLDILEIKSHIERKLGAAKSDKYF-SLLTRYL----SLKISKSEFDRLCIGTIGRENVRL 63
           +L I  I++ + R L   KS  Y   LL   L    + K   + F+  C           
Sbjct: 224 KLRIHSIQAELRRLL---KSKPYENCLLV--LLNVQNAKAWNA-FNLSC----------- 266

Query: 64  HNRLL-----RSIIQNACLSKT-PPPKEPKVDGFERGKVPNGYQRSCLQSLCKDIPQSSR 117
             ++L     + +      + T     +         +V        L    +D+P+   
Sbjct: 267 --KILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEV-KSLLLKYLDCRPQDLPREVL 323

Query: 118 KG------MTPALRDCKLKDFPSPLG----PRGKSHSIACQDSVPKIQEQLSTNEL---- 163
                   +        ++D  +             +   + S+      L   E     
Sbjct: 324 TTNPRRLSIIAES----IRDGLATWDNWKHVNCDKLTTIIESSL----NVLEPAEYRKMF 375

Query: 164 -----FSLGSRPPGSV-----EDGEEVDQAAGSPSIYSRSPVKAPLGIPINGKGTPKLLH 213
                F   +  P  +      D  + D       ++  S                 L+ 
Sbjct: 376 DRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYS-----------------LVE 418

Query: 214 KSSTDAYYTGICQNHGELPDAY-SLRKRLEKKLEMEGLKVSVDCANLLNNGLDVFMKRLI 272
           K   ++  +        +P  Y  L+ +LE +  +   +  VD  N+           LI
Sbjct: 419 KQPKESTIS--------IPSIYLELKVKLENEYALH--RSIVDHYNIPKT---FDSDDLI 465

Query: 273 KPCLE----------LAGSRSGHKHSSFSASILDFQ-VATELNPQILGNDWPSQLEIFSC 321
            P L+          L       + + F    LDF+ +  ++        W +   I + 
Sbjct: 466 PPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHD--STAWNASGSILNT 523

Query: 322 MHQ-KIY 327
           + Q K Y
Sbjct: 524 LQQLKFY 530

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	328
1h3o_A	75	Transcription initiation factor TFIID 135 kDa subu	97.52
1taf_B	70	TFIID TBP associated factor 62; transcription init	96.92
1id3_B	102	Histone H4; nucleosome core particle, chromatin, p	95.85
2hue_C	84	Histone H4; mini beta sheet, elongated beta sandwh	95.56
2yfw_B	103	Histone H4, H4; cell cycle, kinetochore, centromer	95.45
1tzy_D	103	Histone H4-VI; histone-fold, tetramer-dimer-dimer,	95.42
3b0b_B	107	CENP-S, centromere protein S; histone fold, DNA bi	95.22
1ku5_A	70	HPHA, archaeal histon; histone fold, DNA binding p	95.21
3b0c_T	111	CENP-T, centromere protein T; histone fold, DNA bi	94.87
1taf_A	68	TFIID TBP associated factor 42; transcription init	94.26
4dra_A	113	Centromere protein S; DNA binding complex, DNA dam	93.72
3v9r_A	90	MHF1, uncharacterized protein YOL086W-A; histone f	93.47
1b67_A	68	Protein (histone HMFA); DNA binding protein; 1.48A	92.43
3vh5_A	140	CENP-S; histone fold, chromosome segregation, DNA	91.99
1f1e_A	154	Histone fold protein; archaeal histone protein, DN	91.64
1n1j_B	97	NF-YC; histone-like PAIR, DNA binding protein; 1.6	90.74
1h3o_B	76	Transcription initiation factor TFIID 20/15 kDa su	88.97
4g92_C	119	HAPE; transcription factor, nucleosome, minor groo	88.36
2ly8_A	121	Budding yeast chaperone SCM3; centromere protein,	88.31
1n1j_A	93	NF-YB; histone-like PAIR, DNA binding protein; 1.6	87.71
3b0c_W	76	CENP-W, centromere protein W; histone fold, DNA bi	87.62
1f1e_A	154	Histone fold protein; archaeal histone protein, DN	85.56
1jfi_A	98	Transcription regulator NC2 alpha chain; histone,	85.04
2l5a_A	235	Histone H3-like centromeric protein CSE4, protein	82.96
2nqb_D	123	Histone H2B; nucleosome, NCP, chromatin, structura	82.6
1tzy_B	126	Histone H2B; histone-fold, tetramer-dimer-dimer, D	81.91

>1h3o_A Transcription initiation factor TFIID 135 kDa subunit; transcription/TBP-associated factors, TBP-associated factors; 2.3A {Homo sapiens} SCOP: a.22.1.3

Probab=97.52  E-value=0.00011  Score=56.44  Aligned_cols=55  Identities=13%  Similarity=0.172  Sum_probs=44.4

Q ss_pred             CCCHHhHHHHHHHHHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCC
Q 036514          231 LPDAYSLRKRLEKKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGH  285 (328)
Q Consensus       231 LPDt~sL~~RM~~ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~  285 (328)
                      |-....|.+||..|+..+|| .++.|++++++.|.+..|++||+-.+..|.-|.-.
T Consensus         2 fL~~~~Lqkri~~I~~k~gl~~~~~dv~~~iS~a~qeRLr~llekl~~~a~~R~~~   57 (75)
T 1h3o_A            2 FLLQAPLQRRILEIGKKHGITELHPDVVSYVSHATQQRLQNLVEKISETAQQKNFS   57 (75)
T ss_dssp             CSCHHHHHHHHHHHHHTTTCCEECTTHHHHHHHHHHHHHHHHHHHHHC--------
T ss_pred             ccccHHHHHHHHHHHHhcCCCcCChhHHHHhHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence            34677899999999999999 89999999999999999999999999998877643

>1taf_B TFIID TBP associated factor 62; transcription initiation, histone fold, complex (TWO transcr factors); 2.00A {Drosophila melanogaster} SCOP: a.22.1.3

Probab=96.92  E-value=0.003  Score=47.85  Aligned_cols=58  Identities=17%  Similarity=0.274  Sum_probs=51.4

Q ss_pred             HHHHHHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHH
Q 036514          240 RLEKKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATE  302 (328)
Q Consensus       240 RM~~ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amE  302 (328)
                      =+..+|+..|. .|+.||+..|..-++.++++|++.++.+++-     .++..++..|+..|+.
T Consensus        11 ~v~~iaes~Gi~~lsddaa~~LA~dvEyr~~eI~qeA~kfmrH-----akRk~Lt~~DI~~Alk   69 (70)
T 1taf_B           11 SMKVIAESIGVGSLSDDAAKELAEDVSIKLKRIVQDAAKFMNH-----AKRQKLSVRDIDMSLK   69 (70)
T ss_dssp             HHHHHHHHTTCCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----TTCSSBCHHHHHHHHC
T ss_pred             HHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----cCCCeecHHHHHHHHc
Confidence            36789999999 9999999999999999999999999999884     2355699999999875

>1id3_B Histone H4; nucleosome core particle, chromatin, protein/DNA interaction, nucleoprotein, supercoiled DNA; 3.10A {Saccharomyces cerevisiae} SCOP: a.22.1.1

Probab=95.85  E-value=0.023  Score=45.74  Aligned_cols=59  Identities=14%  Similarity=0.174  Sum_probs=52.3

Q ss_pred             HHHHHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHhC
Q 036514          241 LEKKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATELN  304 (328)
Q Consensus       241 M~~ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amEln  304 (328)
                      +..+|+..|. .||.++.+.|...|+.|+.+|++.++.++..     .....++..|+..||..+
T Consensus        34 I~Rlar~~Gv~rIS~da~~~l~~~le~fi~~I~~dA~~~a~H-----akRKTVt~~DV~~ALkr~   93 (102)
T 1id3_B           34 IRRLARRGGVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEH-----AKRKTVTSLDVVYALKRQ   93 (102)
T ss_dssp             HHHHHHHTTCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHH-----TTCSEECHHHHHHHHHHT
T ss_pred             HHHHHHHcCchhccHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----cCCCcCcHHHHHHHHHHc
Confidence            6677788899 8999999999999999999999999999985     345679999999999965

>2hue_C Histone H4; mini beta sheet, elongated beta sandwhich, DNA binding prote; 1.70A {Xenopus laevis} SCOP: a.22.1.1 PDB: 3nqj_B 1aoi_B 3kwq_B* 1hio_D 2yfv_B

Probab=95.56  E-value=0.026  Score=43.69  Aligned_cols=59  Identities=14%  Similarity=0.189  Sum_probs=52.0

Q ss_pred             HHHHHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHhC
Q 036514          241 LEKKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATELN  304 (328)
Q Consensus       241 M~~ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amEln  304 (328)
                      +..+|+..|. .||.++.+.|...|+.|+++|++.++.+++.     .++..++..|+..||...
T Consensus        16 I~Riar~~Gv~rIs~da~~~l~~~l~~~~~~I~~dA~~~a~h-----a~RKTvt~~DV~~Alk~~   75 (84)
T 2hue_C           16 IRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEH-----AKRKTVTAMDVVYALKRQ   75 (84)
T ss_dssp             HHHHHHHTTCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHH-----TTCSEECHHHHHHHTTTT
T ss_pred             HHHHHHHcCchhccHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----cCCCcCcHHHHHHHHHHc
Confidence            5577888899 8999999999999999999999999999885     345679999999999865

>2yfw_B Histone H4, H4; cell cycle, kinetochore, centromere, histone chaperone, BUDD; 2.60A {Kluyveromyces lactis nrrl y-1140}

Probab=95.45  E-value=0.045  Score=43.98  Aligned_cols=61  Identities=15%  Similarity=0.192  Sum_probs=53.7

Q ss_pred             HHHHHHHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHhC
Q 036514          239 KRLEKKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATELN  304 (328)
Q Consensus       239 ~RM~~ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amEln  304 (328)
                      ..+..+|+..|. .|+.++++.|...|+.|+.+|++-++..++.     .....|+..|+..||+-.
T Consensus        33 ~~I~Rlar~~G~~rIs~~a~~~l~~vle~~~~~V~~dA~~~a~h-----akRktvt~~DV~~Alr~~   94 (103)
T 2yfw_B           33 PAIRRLARRGGVKRISGLIYEEVRNVLKTFLESVIRDAVTYTEH-----AKRKTVTSLDVVYALKRQ   94 (103)
T ss_dssp             HHHHHHHHHTTCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHH-----TTCSEECHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----cCCCcCcHHHHHHHHHHc
Confidence            357778888899 8999999999999999999999999999885     345679999999999864

>1tzy_D Histone H4-VI; histone-fold, tetramer-dimer-dimer, DNA binding protein; 1.90A {Gallus gallus} SCOP: a.22.1.1 PDB: 1f66_B 1eqz_D 1hq3_D 1u35_B 2aro_D 2cv5_B* 2f8n_B 3nqu_B 3r45_B 3azg_B 3a6n_B 3an2_B 3av1_B 3av2_B 3ayw_B 3aze_B 3azf_B 3afa_B 3azh_B 3azk_B ...

Probab=95.42  E-value=0.047  Score=43.85  Aligned_cols=60  Identities=13%  Similarity=0.183  Sum_probs=53.7

Q ss_pred             HHHHHHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHhC
Q 036514          240 RLEKKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATELN  304 (328)
Q Consensus       240 RM~~ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amEln  304 (328)
                      .+..+|+..|. .|+.++++.|...|+.|+.+|++.++..++.     .....|+..|+..||+-.
T Consensus        34 ~I~Rlar~~G~~rIs~~a~~~l~~vle~~~~~V~~dA~~~a~h-----akRktIt~~DV~~Alr~~   94 (103)
T 1tzy_D           34 AIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEH-----AKRKTVTAMDVVYALKRQ   94 (103)
T ss_dssp             HHHHHHHHTTCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHH-----TTCSEECHHHHHHHHHHT
T ss_pred             HHHHHHHHcCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----cCCCcCCHHHHHHHHHHc
Confidence            67778888899 8999999999999999999999999999885     345679999999999975

>3b0b_B CENP-S, centromere protein S; histone fold, DNA binding, DNA, nucleus, DNA binding protein; 2.15A {Gallus gallus}

Probab=95.22  E-value=0.018  Score=46.97  Aligned_cols=69  Identities=6%  Similarity=-0.103  Sum_probs=59.6

Q ss_pred             HHHHHHHHHHHhCC----CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHhCCccccC
Q 036514          237 LRKRLEKKLEMEGL----KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATELNPQILGN  310 (328)
Q Consensus       237 L~~RM~~ia~e~GL----gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amElnP~lLg~  310 (328)
                      |+-.+..||.+.|.    .|++++++.|.-.+..|..+|.+-...+|+.     .++..|.+.|++.|+.-||++++.
T Consensus        21 l~~~V~rI~~~~g~~~~~~vs~~~i~aL~E~~~~~~~~ia~Da~~fA~H-----AgRkTI~~eDV~La~Rrn~~l~~~   93 (107)
T 3b0b_B           21 VHYTTGCLCQDVAEDKGVLFSKQTVAAISEITFRQCENFARDLEMFARH-----AKRSTITSEDVKLLARRSNSLLKY   93 (107)
T ss_dssp             HHHHHHHHHHHHHHHHTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----TTCSEECHHHHHHHTTTCHHHHHH
T ss_pred             HHHHHHHHHHHHhhhcCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHh-----cCcCcCCHHHHHHHHHhCHHHHHH
Confidence            44447788888876    5999999999999999999999999999885     346689999999999999999864

>1ku5_A HPHA, archaeal histon; histone fold, DNA binding protein; 2.30A {Pyrococcus horikoshii} SCOP: a.22.1.2

Probab=95.21  E-value=0.07  Score=39.66  Aligned_cols=58  Identities=19%  Similarity=0.324  Sum_probs=50.8

Q ss_pred             HHHHHHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHH
Q 036514          240 RLEKKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATE  302 (328)
Q Consensus       240 RM~~ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amE  302 (328)
                      .+..++++.|- .++.++.+.|..+++.|+.+|++-+...+..     .++..|+..|+..|++
T Consensus        11 ~v~Rl~r~~g~~ris~~a~~~l~e~~~~~~~~v~~dA~~~a~h-----akRkTI~~~DV~lA~~   69 (70)
T 1ku5_A           11 PVDRLIRKAGAERVSEQAAKVLAEYLEEYAIEIAKKAVEFARH-----AGRKTVKVEDIKLAIK   69 (70)
T ss_dssp             HHHHHHHHTTCSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHT-----TTCSEECHHHHHHHHT
T ss_pred             HHHHHHHHcCcceeCHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----cCCCcCCHHHHHHHHH
Confidence            66777778898 8999999999999999999999999999874     3456799999999986

>3b0c_T CENP-T, centromere protein T; histone fold, DNA binding, DNA binding protein; HET: CIT; 2.20A {Gallus gallus} PDB: 3b0d_T* 3vh5_T 3vh6_T

Probab=94.87  E-value=0.081  Score=43.15  Aligned_cols=62  Identities=6%  Similarity=0.063  Sum_probs=53.8

Q ss_pred             HHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHhCCccccC
Q 036514          244 KLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATELNPQILGN  310 (328)
Q Consensus       244 ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amElnP~lLg~  310 (328)
                      ++...|- .||.++.+.|...++.|+.++++-+..+++.     .++..|+..|+..||.-|+.+--.
T Consensus        16 i~r~~g~~rIS~~a~~~l~e~l~~f~~~v~~da~~~A~H-----A~RKTV~~eDV~lalrr~g~~~~~   78 (111)
T 3b0c_T           16 IFSHYVKTPVTRDAYKIVEKCSERYFKQISSDLEAYSQH-----AGRKTVEMADVELLMRRQGLVTDK   78 (111)
T ss_dssp             HHHHHHCSCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----TTCSEECHHHHHHHHHHTTSSBTT
T ss_pred             HHHHCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----cCCCcCCHHHHHHHHHHCCCcccc
Confidence            4555577 8999999999999999999999999999985     345679999999999999988643

>1taf_A TFIID TBP associated factor 42; transcription initiation, histone fold, complex (TWO transcr factors); 2.00A {Drosophila melanogaster} SCOP: a.22.1.3

Probab=94.26  E-value=0.22  Score=37.27  Aligned_cols=59  Identities=14%  Similarity=0.083  Sum_probs=52.7

Q ss_pred             HHHHHHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHh
Q 036514          240 RLEKKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATEL  303 (328)
Q Consensus       240 RM~~ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amEl  303 (328)
                      -|..|+...|. .+++++++.|.--+..|...|++-...+++-.     +...|+..|.+.|.+.
T Consensus         6 ~i~~iLk~~G~~~~~~~v~~~L~e~~~ry~~~il~dA~~~a~HA-----grktv~~eDVkLAi~~   65 (68)
T 1taf_A            6 VIMSILKELNVQEYEPRVVNQLLEFTFRYVTSILDDAKVYANHA-----RKKTIDLDDVRLATEV   65 (68)
T ss_dssp             HHHHHHHHTTCCCBCTHHHHHHHHHHHHHHHHHHHHHHHHHHHT-----TCSSBCHHHHHHHHHH
T ss_pred             HHHHHHHHCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHc-----CCCCCCHHHHHHHHHh
Confidence            46788889999 99999999999999999999999999999853     3467999999999875

>4dra_A Centromere protein S; DNA binding complex, DNA damage repair, histone-fold, DNA BI protein; 2.41A {Homo sapiens} PDB: 4drb_A

Probab=93.72  E-value=0.07  Score=43.85  Aligned_cols=69  Identities=10%  Similarity=-0.008  Sum_probs=58.9

Q ss_pred             hHHHHHHHHHHHhCC----CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHhCCcccc
Q 036514          236 SLRKRLEKKLEMEGL----KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATELNPQILG  309 (328)
Q Consensus       236 sL~~RM~~ia~e~GL----gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amElnP~lLg  309 (328)
                      .|+--+..|+.+.|.    .||+++++.|.-.+..|..+|-+-...+|+=     .++..|...|++.++.-||+|+.
T Consensus        28 al~y~V~rIvke~gaer~~~vS~~ai~aL~El~~~~~~~ia~Dl~~fAkH-----AgRkTI~~eDV~La~Rr~~~L~~  100 (113)
T 4dra_A           28 AVHYTVGCLCEEVALDKEMQFSKQTIAAISELTFRQCENFAKDLEMFARH-----AKRTTINTEDVKLLARRSNSLLK  100 (113)
T ss_dssp             HHHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----TTCSEECHHHHHHHTTTCHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHh-----cCCCccCHHHHHHHHHhCHHHHH
Confidence            355566788888876    4999999999999999999999999999873     34677999999999999999864

>3v9r_A MHF1, uncharacterized protein YOL086W-A; histone fold, fanconi anemia, DNA repair, DNA BI protein; 2.40A {Saccharomyces cerevisiae}

Probab=93.47  E-value=0.2  Score=39.51  Aligned_cols=69  Identities=14%  Similarity=0.079  Sum_probs=57.7

Q ss_pred             hHHHHHHHHHHHh----CCCCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHhCCcccc
Q 036514          236 SLRKRLEKKLEME----GLKVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATELNPQILG  309 (328)
Q Consensus       236 sL~~RM~~ia~e~----GLgVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amElnP~lLg  309 (328)
                      .|+--...||.++    |..||+++++.|.-.+..|+.+|.+-...+|+-     .++..|...|++.++.-||+|..
T Consensus        13 al~~~V~ki~~e~~~~~g~~vs~~~i~aL~e~~~~~~~~ia~Dl~~fA~H-----AgRkTI~~eDV~L~~Rrn~~L~~   85 (90)
T 3v9r_A           13 RLWIRVEERLQQVLSSEDIKYTPRFINSLLELAYLQLGEMGSDLQAFARH-----AGRGVVNKSDLMLYLRKQPDLQE   85 (90)
T ss_dssp             HHHHHHHHHHHHHSCSSCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----TTCSEECHHHHHHHTTTCHHHHH
T ss_pred             HHHHHHHHHHHHHHHhcCceeCHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----cCCCccCHHHHHHHHHhChHHHH
Confidence            3445567888888    345999999999999999999999999999873     34678999999999999998853

>1b67_A Protein (histone HMFA); DNA binding protein; 1.48A {Methanothermus fervidus} SCOP: a.22.1.2 PDB: 1hta_A 1a7w_A 1b6w_A 1bfm_A

Probab=92.43  E-value=0.46  Score=34.75  Aligned_cols=60  Identities=17%  Similarity=0.219  Sum_probs=49.0

Q ss_pred             HHHHHHHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHh
Q 036514          239 KRLEKKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATEL  303 (328)
Q Consensus       239 ~RM~~ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amEl  303 (328)
                      .++..++.+-|- .++.++...|..+++.|+-.|.+.+.+.+..     .++..|+-.|+..|++.
T Consensus         6 a~v~Ri~k~~~~~ris~~A~~~l~~a~e~fi~~l~~~A~~~a~~-----~kRkTI~~~Di~~A~~~   66 (68)
T 1b67_A            6 APIGRIIKNAGAERVSDDARIALAKVLEEMGEEIASEAVKLAKH-----AGRKTIKAEDIELARKM   66 (68)
T ss_dssp             HHHHHHHHHTTCSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----TTCSEECHHHHHHHGGG
T ss_pred             cHHHHHHhcCCcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----cCCCccCHHHHHHHHHh
Confidence            345555555566 8999999999999999999999999998875     34667999999999863

>3vh5_A CENP-S; histone fold, chromosome segregation, DNA binding, nucleus, binding protein; 2.40A {Gallus gallus} PDB: 3vh6_A

Probab=91.99  E-value=0.19  Score=42.74  Aligned_cols=69  Identities=6%  Similarity=-0.077  Sum_probs=58.0

Q ss_pred             hHHHHHHHHHHHhCC----CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHhCCcccc
Q 036514          236 SLRKRLEKKLEMEGL----KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATELNPQILG  309 (328)
Q Consensus       236 sL~~RM~~ia~e~GL----gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amElnP~lLg  309 (328)
                      .|+--...||.+.|.    .||++++..|.-.+..|+.+|-+-...+|+-     .++..|...|++.++.-||+|+.
T Consensus        20 Al~y~VgkIvee~~~~~~~~vS~~ai~aL~El~~~~~e~ia~DLe~FAkH-----AGRKTI~~eDVkLa~Rrn~~L~~   92 (140)
T 3vh5_A           20 AVHYTTGALAQDVAEDKGVLFSKQTVAAISEITFRQAENFARDLEMFARH-----AKRSTITSEDVKLLARRSNSLLK   92 (140)
T ss_dssp             HHHHHHHHHHHHHHHHHTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----TTCSEECHHHHHHHHTTSHHHHH
T ss_pred             HHHHHHHHHHHHHHHhcCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----cCCCccCHHHHHHHHHhCHHHHH
Confidence            345556677777755    5999999999999999999999999999873     34678999999999999999864

>1f1e_A Histone fold protein; archaeal histone protein, DNA binding protein; HET: MSE; 1.37A {Methanopyrus kandleri} SCOP: a.22.1.2

Probab=91.64  E-value=0.43  Score=41.09  Aligned_cols=61  Identities=18%  Similarity=0.177  Sum_probs=53.4

Q ss_pred             HHHHHHHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHhC
Q 036514          239 KRLEKKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATELN  304 (328)
Q Consensus       239 ~RM~~ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amEln  304 (328)
                      ..+..++.+.|- .||.++.+.|...|+.|+-+|.+...+++..     .++..|+-.|...||+.+
T Consensus        86 a~V~Ri~k~~g~~RVS~~A~~~l~~~le~f~~~I~~~A~~~a~h-----a~RKTIt~eDV~~Al~~~  147 (154)
T 1f1e_A           86 ATVRRILKRAGIERASSDAVDLYNKLICRATEELGEKAAEYADE-----DGRKTVQGEDVEKAITYS  147 (154)
T ss_dssp             HHHHHHHHHTTCCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----TTCSEECHHHHHHHHHHH
T ss_pred             cHHHHHHHHcCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----cCCCccCHHHHHHHHHhc
Confidence            456677777788 8999999999999999999999999999986     346679999999999875

>1n1j_B NF-YC; histone-like PAIR, DNA binding protein; 1.67A {Homo sapiens} SCOP: a.22.1.3

Probab=90.74  E-value=0.6  Score=36.84  Aligned_cols=64  Identities=14%  Similarity=0.161  Sum_probs=52.6

Q ss_pred             HHHHHHHHHHhCC--CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHhCCc
Q 036514          238 RKRLEKKLEMEGL--KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATELNPQ  306 (328)
Q Consensus       238 ~~RM~~ia~e~GL--gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amElnP~  306 (328)
                      -.|+-.|+...+=  .|+.++..++.-|++.|+..|.+.+.+.++..     +...|+-.|+..|++-+..
T Consensus        22 ~arIkrImK~~~~~~~is~eA~~~laka~E~Fi~~l~~~A~~~a~~~-----krktI~~~di~~Av~~~e~   87 (97)
T 1n1j_B           22 LARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDN-----KRRTLQRNDIAMAITKFDQ   87 (97)
T ss_dssp             HHHHHHHHTTSTTCCCBCTHHHHHHHHHHHHHHHHHHHHHHHHHHHT-----TCSEECHHHHHHHHTTCGG
T ss_pred             HHHHHHHHccCccccccChHHHHHHHHHHHHHHHHHHHHHHHHHHHc-----CCccCCHHHHHHHHhcCcH
Confidence            3577777776655  59999999999999999999999999888652     3567999999999987654

>1h3o_B Transcription initiation factor TFIID 20/15 kDa subunits; transcription/TBP-associated factors, TBP-associated factors; 2.3A {Homo sapiens} SCOP: a.22.1.3

Probab=88.97  E-value=1.7  Score=33.14  Aligned_cols=70  Identities=16%  Similarity=0.169  Sum_probs=55.6

Q ss_pred             hCCCCCHHhHHHHHHHHHHHhCCCCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHhC
Q 036514          228 HGELPDAYSLRKRLEKKLEMEGLKVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATELN  304 (328)
Q Consensus       228 sgeLPDt~sL~~RM~~ia~e~GLgVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amEln  304 (328)
                      ||.+-....|..-+.++.  -|..+++++-++|..-.|.|+.+++.....+|+.|..     ..+.+.|+...+|-|
T Consensus         2 s~~vl~k~~L~~Lv~~id--p~~~ld~~vee~ll~lADdFV~~V~~~ac~lAKhR~s-----~~le~kDvql~Ler~   71 (76)
T 1h3o_B            2 SHMVLTKKKLQDLVREVD--PNEQLDEDVEEMLLQIADDFIESVVTAACQLARHRKS-----STLEVKDVQLHLERQ   71 (76)
T ss_dssp             -CCSSCHHHHHHHHHHHC--SSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTC-----CEECHHHHHHHHHHH
T ss_pred             CcccccHHHHHHHHHhcC--CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC-----CCccHHHHHHHHHhh
Confidence            344555566666666663  3448999999999999999999999999999999765     458899999998865

>4g92_C HAPE; transcription factor, nucleosome, minor groove binding, CCAA complex, histone fold motif, specific binding to the ccaat- nucleus; HET: DNA; 1.80A {Aspergillus nidulans} PDB: 4g91_C*

Probab=88.36  E-value=1  Score=36.86  Aligned_cols=64  Identities=19%  Similarity=0.233  Sum_probs=51.2

Q ss_pred             HHHHHHHHH-hCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHhCCcc
Q 036514          239 KRLEKKLEM-EGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATELNPQI  307 (328)
Q Consensus       239 ~RM~~ia~e-~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amElnP~l  307 (328)
                      .|+..|+.. ... .|+.++.-++..|++.|+..|.+.+.+.++.+.     ...|+-.|+..|++-++.+
T Consensus        45 aRIkrImK~d~~~~~is~eA~v~la~a~E~Fi~~L~~~A~~~a~~~k-----rktI~~~di~~Av~~~e~~  110 (119)
T 4g92_C           45 ARIKKVMKADPEVKMISAEAPILFAKGCDVFITELTMRAWIHAEDNK-----RRTLQRSDIAAALSKSDMF  110 (119)
T ss_dssp             HHHHHHHHTSTTCCEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-----CSEECHHHHHHHHTTCGGG
T ss_pred             HHHHHHHhhCCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc-----cCccCHHHHHHHHhcCchh
Confidence            455666653 223 699999999999999999999999998887533     4569999999999887654

>2ly8_A Budding yeast chaperone SCM3; centromere protein, CENH3 variants, partially unfolded; NMR {Saccharomyces cerevisiae}

Probab=88.31  E-value=1  Score=37.35  Aligned_cols=53  Identities=15%  Similarity=0.159  Sum_probs=45.8

Q ss_pred             hCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHhCC
Q 036514          248 EGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATELNP  305 (328)
Q Consensus       248 ~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amElnP  305 (328)
                      .|. -||.++.+-+...|+.||.+||+.++.++..     .++..++..|...|+..-.
T Consensus        60 gGvkRIS~~iy~e~r~vl~~~l~~i~rdav~yaeh-----A~RKTVta~DV~~Alkr~G  113 (121)
T 2ly8_A           60 RGSKRISGLIYEEVRAVLKSFLESVIRDSVTYTEH-----AKRKTVTSLDVVYALKRQG  113 (121)
T ss_dssp             CCSSCCSSCHHHHHHHHHHHHHHHHHHHHHHHHHH-----TTCCCBCHHHHHHHHHHTT
T ss_pred             cCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHh-----cCCCcCcHHHHHHHHHhCC
Confidence            566 6999999999999999999999999999986     3455799999999987543

>1n1j_A NF-YB; histone-like PAIR, DNA binding protein; 1.67A {Homo sapiens} SCOP: a.22.1.3

Probab=87.71  E-value=2.3  Score=33.04  Aligned_cols=60  Identities=10%  Similarity=0.066  Sum_probs=50.3

Q ss_pred             HHHHHHHHHHhCC---CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHH
Q 036514          238 RKRLEKKLEMEGL---KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATE  302 (328)
Q Consensus       238 ~~RM~~ia~e~GL---gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amE  302 (328)
                      ..++..++.+.|=   .|+.|+..+|..+++.|+..|.+.+.+.+..     .++..|+-.|+..|++
T Consensus        11 ~a~i~ri~K~~~~~~~~is~dA~~~l~~a~e~Fi~~l~~~A~~~a~~-----~kRkTI~~~Dv~~Al~   73 (93)
T 1n1j_A           11 IANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQ-----EKRKTINGEDILFAMS   73 (93)
T ss_dssp             HHHHHHHHHHTSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----TTCSSBCHHHHHHHHH
T ss_pred             hhHHHHHHHHhCCccceeCHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----cCCCccCHHHHHHHHH
Confidence            4566777777753   6999999999999999999999999998874     2355799999999998

>3b0c_W CENP-W, centromere protein W; histone fold, DNA binding, DNA binding protein; HET: CIT; 2.20A {Gallus gallus} PDB: 3b0d_W* 3vh5_W 3vh6_W

Probab=87.62  E-value=1.9  Score=32.40  Aligned_cols=49  Identities=16%  Similarity=0.123  Sum_probs=43.5

Q ss_pred             CCCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHh
Q 036514          250 LKVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATEL  303 (328)
Q Consensus       250 LgVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amEl  303 (328)
                      .+||.|+.++|+.+++.|+..|-+...++++..     +...|+-.|+..|++.
T Consensus        21 ~~is~~A~~~i~~~~~~Fi~~la~eA~~~a~~~-----~rKTI~~~dI~~A~~~   69 (76)
T 3b0c_W           21 LRLAANTDLLVHLSFLLFLHRLAEEARTNAFEN-----KSKIIKPEHTIAAAKV   69 (76)
T ss_dssp             CEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHH-----TCSSBCHHHHHHHHHH
T ss_pred             CccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHc-----CCCCCCHHHHHHHHHH
Confidence            479999999999999999999999999998763     3557999999999974

>1f1e_A Histone fold protein; archaeal histone protein, DNA binding protein; HET: MSE; 1.37A {Methanopyrus kandleri} SCOP: a.22.1.2

Probab=85.56  E-value=1.8  Score=37.22  Aligned_cols=57  Identities=7%  Similarity=0.126  Sum_probs=49.2

Q ss_pred             HHHHHHHh-CC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHH
Q 036514          241 LEKKLEME-GL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATE  302 (328)
Q Consensus       241 M~~ia~e~-GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amE  302 (328)
                      +..++.+. |- .||.|+.+.|..+++.|+-.|.+...+++..     .++..|+-.|+..||.
T Consensus        10 V~Riik~~lg~~rVS~dA~~~l~~~l~~f~~~i~~~A~~~a~h-----a~RKTv~a~DV~~a~~   68 (154)
T 1f1e_A           10 IERIFRQGIGERRLSQDAKDTIYDFVPTMAEYVANAAKSVLDA-----SGKKTLMEEHLKALAD   68 (154)
T ss_dssp             HHHHHHTTSTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHT-----TTCSEECHHHHHHHHH
T ss_pred             HHHHHHhcCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----cCCCcCCHHHHHHHHH
Confidence            45666666 77 8999999999999999999999999999875     3467899999999994

>1jfi_A Transcription regulator NC2 alpha chain; histone, H2A/H2B, tata-DNA, transcription initiation, NC2, negative cofactor, structural genomics, PSI; 2.62A {Homo sapiens} SCOP: a.22.1.3

Probab=85.04  E-value=1  Score=35.66  Aligned_cols=63  Identities=19%  Similarity=0.379  Sum_probs=47.1

Q ss_pred             HHHHHHHHHhCC--CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHhCCc
Q 036514          239 KRLEKKLEMEGL--KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATELNPQ  306 (328)
Q Consensus       239 ~RM~~ia~e~GL--gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amElnP~  306 (328)
                      .|+-.|+...+=  -|+.+++-++.-++|.|+..|.+-+...++.+     +...|+-.|+..|++-+..
T Consensus        15 aRIkrimK~~~~~~~vs~~A~v~la~a~E~Fi~el~~~A~~~a~~~-----krktI~~~di~~av~~~e~   79 (98)
T 1jfi_A           15 ARIKKIMQTDEEIGKVAAAVPVIISRALELFLESLLKKACQVTQSR-----NAKTMTTSHLKQCIELEGD   79 (98)
T ss_dssp             HHHHHHHTTSTTCCCBCTTHHHHHHHHHHHHHHHHHHHHHHHHHTC--------CBCHHHHHTTCC----
T ss_pred             HHHHHHHHcCccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHc-----CCCeecHHHHHHHHhcCch
Confidence            466667665444  69999999999999999999999999988753     3456888999988876544

>2l5a_A Histone H3-like centromeric protein CSE4, protein histone H4; A single chain of CSE4+SCM3+H4, fusion protein; NMR {Saccharomyces cerevisiae}

Probab=82.96  E-value=1.2  Score=40.90  Aligned_cols=56  Identities=14%  Similarity=0.165  Sum_probs=48.4

Q ss_pred             HHHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHh
Q 036514          243 KKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATEL  303 (328)
Q Consensus       243 ~ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amEl  303 (328)
                      .+|+-.|. -||.++.+-+...|+.||++||+-++.++...     +...++..|...|+..
T Consensus       169 RlaRrgGVkRIS~~iyeelr~vLe~fle~IirdAv~yaeHA-----~RKTVta~DV~~ALKr  225 (235)
T 2l5a_A          169 EDGDKGGVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHA-----KRKTVTSLDVVYALKR  225 (235)
T ss_dssp             TTSCCTTCCTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHT-----TCCSCCHHHHHHHHHH
T ss_pred             HHhhcCCchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-----CCCcCcHHHHHHHHHh
Confidence            45677788 89999999999999999999999999999863     3456889999988864

>2nqb_D Histone H2B; nucleosome, NCP, chromatin, structural protein/DNA complex; 2.30A {Drosophila melanogaster} PDB: 2pyo_D*

Probab=82.60  E-value=2.2  Score=35.47  Aligned_cols=48  Identities=17%  Similarity=0.223  Sum_probs=44.3

Q ss_pred             CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHh
Q 036514          251 KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATEL  303 (328)
Q Consensus       251 gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amEl  303 (328)
                      |+|.++.++||+-++....+|......++++     +....|+-.|+.+|+.|
T Consensus        51 gISskAm~ImnSfvnDiferIA~EAs~La~~-----nkr~TitsreIqtAvrL   98 (123)
T 2nqb_D           51 GISSKAMSIMNSFVNDIFERIAAEASRLAHY-----NKRSTITSREIQTAVRL   98 (123)
T ss_dssp             EECHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----TTCCEECHHHHHHHHHH
T ss_pred             CcCHHHHHHHHHHHHHHHHHHHHHHHHHHHh-----cCCCcCCHHHHHHHHHH
Confidence            8999999999999999999999999999998     44678999999999976

>1tzy_B Histone H2B; histone-fold, tetramer-dimer-dimer, DNA binding protein; 1.90A {Gallus gallus} SCOP: a.22.1.1 PDB: 1eqz_B 1hq3_B 2aro_B 2hio_B 3c9k_B 3azg_D 3a6n_D 3an2_D 3av1_D 3av2_D 3ayw_D 3aze_D 3azf_D 3afa_D 3azh_D 3azi_D 3azj_D 3azk_D 3azl_D 3azm_D ...

Probab=81.91  E-value=2.4  Score=35.38  Aligned_cols=49  Identities=16%  Similarity=0.201  Sum_probs=44.7

Q ss_pred             CCCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHh
Q 036514          250 LKVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATEL  303 (328)
Q Consensus       250 LgVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amEl  303 (328)
                      .|+|.++.++||+-++....+|......++++     +....|+-.|+.+|+.|
T Consensus        53 ~gISskAm~ImnSfvnDiferIA~EAs~La~~-----nkr~TitsreIqtAvrL  101 (126)
T 1tzy_B           53 TGISSKAMGIMNSFVNDIFERIAGEASRLAHY-----NKRSTITSREIQTAVRL  101 (126)
T ss_dssp             CEECHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----TTCSEECHHHHHHHHHH
T ss_pred             CCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----cCCCCCCHHHHHHHHHH
Confidence            38999999999999999999999999999998     44678999999999976

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	328
d1h3oa_	50	TAF(II)-135, (TAF(II)-130, hTAF4), histone fold do	97.24
d1htaa_	68	Archaeal histone {Archaeon Methanothermus fervidus	96.87
d1ku5a_	66	Archaeal histone {Archaeon (Pyrococcus horikoshii)	96.81
d2huec1	82	Histone H4 {African clawed frog (Xenopus laevis) [	95.82
d1f1ea_	151	Archaeal histone {Archaeon Methanopyrus kandleri [	95.3
d1n1jb_	78	Nuclear transcription factor Y subunit gamma (Nf-Y	93.73
d1tafb_	70	TAF(II)62 {Fruit fly (Drosophila melanogaster) [Ta	93.37
d1jfia_	66	Negative cofactor 2, NC2, alpha chain {Human (Homo	93.12
d2byka1	72	Chrac-16 {Fruit fly (Drosophila melanogaster) [Tax	92.03
d1n1ja_	87	Nuclear transcription factor Y subunit beta (Nf-Yb	86.47
d1h3ob_	74	TAF(II)-20, (TAF(II)-15, hTAF12), histone fold dom	85.27
d2bykb1	89	Chrac-14 {Fruit fly (Drosophila melanogaster) [Tax	83.13

>d1h3oa_ a.22.1.3 (A:) TAF(II)-135, (TAF(II)-130, hTAF4), histone fold domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: TAF(II)-135, (TAF(II)-130, hTAF4), histone fold domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.24  E-value=0.00023  Score=48.66  Aligned_cols=44  Identities=11%  Similarity=0.200  Sum_probs=40.5

Q ss_pred             CCHHhHHHHHHHHHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHH
Q 036514          232 PDAYSLRKRLEKKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPC  275 (328)
Q Consensus       232 PDt~sL~~RM~~ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~  275 (328)
                      --..-|.+||..|+..+|| .+++|++.+++.|.+.=||+|++-.
T Consensus         3 L~~~~Lq~ri~~I~~k~Gl~e~~~dV~~lISHA~QeRLk~lvEKl   47 (50)
T d1h3oa_           3 LLQAPLQRRILEIGKKHGITELHPDVVSYVSHATQQRLQNLVEKI   47 (50)
T ss_dssp             SCHHHHHHHHHHHHHTTTCCEECTTHHHHHHHHHHHHHHHHHHHH
T ss_pred             CChHHHHHHHHHHHHHcCCCccCHHHHHHHHHHHHHHHHHHHHHH
Confidence            3467899999999999999 8999999999999999999999864

>d1htaa_ a.22.1.2 (A:) Archaeal histone {Archaeon Methanothermus fervidus, histone A [TaxId: 2180]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Archaeal histone
domain: Archaeal histone
species: Archaeon Methanothermus fervidus, histone A [TaxId: 2180]

Probab=96.87  E-value=0.0025  Score=45.47  Aligned_cols=61  Identities=16%  Similarity=0.202  Sum_probs=53.2

Q ss_pred             HHHHHHHHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHh
Q 036514          238 RKRLEKKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATEL  303 (328)
Q Consensus       238 ~~RM~~ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amEl  303 (328)
                      ..++..|+.+-|. .|+.|+.+++..+++.|++.|.+.+.+.+..     .++..|+..|+..|++.
T Consensus         6 ~a~I~ri~k~~~~~ris~ea~~~l~~~~e~fi~~l~~~a~~~a~~-----~kRkTi~~~DV~~Alk~   67 (68)
T d1htaa_           6 IAPIGRIIKNAGAERVSDDARIALAKVLEEMGEEIASEAVKLAKH-----AGRKTIKAEDIELARKM   67 (68)
T ss_dssp             HHHHHHHHHHTTCSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----TTCSSCCHHHHHHHHHT
T ss_pred             HHHHHHHHHHCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----hCCCcCCHHHHHHHHHh
Confidence            4567778888788 8999999999999999999999999999986     23667999999999974

>d1ku5a_ a.22.1.2 (A:) Archaeal histone {Archaeon (Pyrococcus horikoshii) [TaxId: 53953]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Archaeal histone
domain: Archaeal histone
species: Archaeon (Pyrococcus horikoshii) [TaxId: 53953]

Probab=96.81  E-value=0.0024  Score=45.43  Aligned_cols=60  Identities=18%  Similarity=0.299  Sum_probs=52.3

Q ss_pred             HHHHHHHHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHH
Q 036514          238 RKRLEKKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATE  302 (328)
Q Consensus       238 ~~RM~~ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amE  302 (328)
                      ..|+..|+.+.|- .|+.|+.+++..+++.|++.|.+...+.+...     ++..|+..|+..||+
T Consensus         5 ~a~I~rI~k~~~~~ris~ea~~~l~~a~e~Fi~~l~~~a~~~a~~~-----~RKTI~~~Dv~~Al~   65 (66)
T d1ku5a_           5 IAPVDRLIRKAGAERVSEQAAKVLAEYLEEYAIEIAKKAVEFARHA-----GRKTVKVEDIKLAIK   65 (66)
T ss_dssp             HHHHHHHHHHTTCSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-----TCSEECHHHHHHHHT
T ss_pred             HHHHHHHHHhCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc-----CCCCCCHHHHHHHHh
Confidence            4577778887766 89999999999999999999999999998763     466799999999986

>d2huec1 a.22.1.1 (C:20-101) Histone H4 {African clawed frog (Xenopus laevis) [TaxId: 8355]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Nucleosome core histones
domain: Histone H4
species: African clawed frog (Xenopus laevis) [TaxId: 8355]

Probab=95.82  E-value=0.0089  Score=44.50  Aligned_cols=59  Identities=14%  Similarity=0.189  Sum_probs=51.7

Q ss_pred             HHHHHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHhC
Q 036514          241 LEKKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATELN  304 (328)
Q Consensus       241 M~~ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amEln  304 (328)
                      +..+|+..|. .||.|+.+.|...++.||+.|+..++.++..     ..+..++..|+..||.-+
T Consensus        15 i~Riar~~Gv~ris~d~~~~l~~~l~~~l~~i~~~a~~~~~h-----akRKTvt~~DV~~Alkr~   74 (82)
T d2huec1          15 IRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEH-----AKRKTVTAMDVVYALKRQ   74 (82)
T ss_dssp             HHHHHHHTTCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHH-----TTCSEECHHHHHHHTTTT
T ss_pred             HHHHHHHcCcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----hCCCcCCHHHHHHHHHhc
Confidence            4467888999 8999999999999999999999999999874     346779999999999743

>d1f1ea_ a.22.1.2 (A:) Archaeal histone {Archaeon Methanopyrus kandleri [TaxId: 2320]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Archaeal histone
domain: Archaeal histone
species: Archaeon Methanopyrus kandleri [TaxId: 2320]

Probab=95.30  E-value=0.02  Score=47.02  Aligned_cols=61  Identities=18%  Similarity=0.177  Sum_probs=52.9

Q ss_pred             HHHHHHHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHhC
Q 036514          239 KRLEKKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATELN  304 (328)
Q Consensus       239 ~RM~~ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amEln  304 (328)
                      .++..++...|. -++.|+..+|+.+++.|+++|++.+...+..     .++..|+-.|+..|+..+
T Consensus        83 a~IkRi~k~~g~~ris~dA~~~l~~~~E~fi~~l~~~A~~~a~~-----~kRkTI~~~DI~~Av~~~  144 (151)
T d1f1ea_          83 ATVRRILKRAGIERASSDAVDLYNKLICRATEELGEKAAEYADE-----DGRKTVQGEDVEKAITYS  144 (151)
T ss_dssp             HHHHHHHHHTTCCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----TTCSEECHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----hCCCcCCHHHHHHHHHHc
Confidence            566777778899 7999999999999999999999999999886     335679999999998753

>d1n1jb_ a.22.1.3 (B:) Nuclear transcription factor Y subunit gamma (Nf-Yc2) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: Nuclear transcription factor Y subunit gamma (Nf-Yc2)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.73  E-value=0.079  Score=38.24  Aligned_cols=64  Identities=14%  Similarity=0.213  Sum_probs=50.8

Q ss_pred             HHHHHHHHHh-CC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHhCCcc
Q 036514          239 KRLEKKLEME-GL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATELNPQI  307 (328)
Q Consensus       239 ~RM~~ia~e~-GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amElnP~l  307 (328)
                      .|+..|+.+. .. .++.|+..++..|++.|+..|.+.+.+.++...     +..|+-.|+..|++-++..
T Consensus         4 srVkrImK~~~~~~~is~ea~~~i~~a~E~Fi~~l~~~A~~~a~~~~-----rkti~~~dl~~av~~~~~~   69 (78)
T d1n1jb_           4 ARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNK-----RRTLQRNDIAMAITKFDQF   69 (78)
T ss_dssp             HHHHHHHTTSTTCCCBCTHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-----CSEECHHHHHHHHTTCGGG
T ss_pred             HHHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHcC-----CCcCCHHHHHHHHhcCChh
Confidence            3455555422 22 699999999999999999999999999887533     4579999999999988753

>d1tafb_ a.22.1.3 (B:) TAF(II)62 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: TAF(II)62
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=93.37  E-value=0.15  Score=36.68  Aligned_cols=57  Identities=18%  Similarity=0.280  Sum_probs=49.5

Q ss_pred             HHHHHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHH
Q 036514          241 LEKKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATE  302 (328)
Q Consensus       241 M~~ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amE  302 (328)
                      +..+|+.-|+ .+++|+|..|..=++.=||+||...+.+-+-     ..+..++..|+.-|+-
T Consensus        12 ik~iAeS~Gi~~l~de~a~~LA~DveYRl~eiiQeA~KFMrh-----skR~~Ltt~Did~ALk   69 (70)
T d1tafb_          12 MKVIAESIGVGSLSDDAAKELAEDVSIKLKRIVQDAAKFMNH-----AKRQKLSVRDIDMSLK   69 (70)
T ss_dssp             HHHHHHHTTCCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----TTCSSBCHHHHHHHHC
T ss_pred             HHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----hccCcCcHHHHHHHHc
Confidence            5679999999 8999999999999999999999999998773     2345688999988874

>d1jfia_ a.22.1.3 (A:) Negative cofactor 2, NC2, alpha chain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: Negative cofactor 2, NC2, alpha chain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.12  E-value=0.052  Score=38.21  Aligned_cols=59  Identities=19%  Similarity=0.412  Sum_probs=45.7

Q ss_pred             HHHHHHHHHh-CC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHH
Q 036514          239 KRLEKKLEME-GL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATE  302 (328)
Q Consensus       239 ~RM~~ia~e~-GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amE  302 (328)
                      .|+..|+.+. .. .|+.|+..+|..|+|.|+..|.+.+.+.+...     +...|+-.|+..|+|
T Consensus         6 srVkkimk~~~~~~~is~~A~~~~~~a~E~Fi~~l~~~A~~~a~~~-----krktI~~~dl~~ai~   66 (66)
T d1jfia_           6 ARIKKIMQTDEEIGKVAAAVPVIISRALELFLESLLKKACQVTQSR-----NAKTMTTSHLKQCIE   66 (66)
T ss_dssp             HHHHHHHTTSTTCCCBCTTHHHHHHHHHHHHHHHHHHHHHHHHHTC--------CBCHHHHHTTCC
T ss_pred             HHHHHHHhcCCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-----CCCcCCHHHHHHHhC
Confidence            4666777633 33 79999999999999999999999999988752     245688899887654

>d2byka1 a.22.1.3 (A:29-100) Chrac-16 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: Chrac-16
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=92.03  E-value=0.2  Score=35.77  Aligned_cols=53  Identities=8%  Similarity=0.093  Sum_probs=43.8

Q ss_pred             CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHhCCcc
Q 036514          251 KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATELNPQI  307 (328)
Q Consensus       251 gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amElnP~l  307 (328)
                      .|+.++.-++..|+|-|++.|.+.+...+....+    ...++-.|+..|.+.++++
T Consensus         9 ~is~ea~~lvskAtElFi~~L~~~a~~~a~~~~~----~ktl~~~dl~~aV~~~~~f   61 (72)
T d2byka1           9 LITNEVLFLMTKCTELFVRHLAGAAYTEEFGQRP----GEALKYEHLSQVVNKNKNL   61 (72)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCC----SCEECHHHHHHHHHTCSTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccC----CccccHHHHHHHHccCchh
Confidence            4899999999999999999999988776643222    3469999999999999864

>d1n1ja_ a.22.1.3 (A:) Nuclear transcription factor Y subunit beta (Nf-Yb3) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: Nuclear transcription factor Y subunit beta (Nf-Yb3)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.47  E-value=1.7  Score=31.42  Aligned_cols=63  Identities=10%  Similarity=0.054  Sum_probs=51.0

Q ss_pred             HHHHHHHHHh--CC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHhCCc
Q 036514          239 KRLEKKLEME--GL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATELNPQ  306 (328)
Q Consensus       239 ~RM~~ia~e~--GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amElnP~  306 (328)
                      .|...|+.+.  +- .|+.|+..++..|.+.|+..|-+.+-+.+....     +..|+-.|+..|++-...
T Consensus         6 a~v~ri~K~~~p~~~~is~ea~~~i~~a~e~Fi~~lt~~A~~~a~~~~-----rKTI~~~dv~~Al~~~~~   71 (87)
T d1n1ja_           6 ANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEK-----RKTINGEDILFAMSTLGF   71 (87)
T ss_dssp             HHHHHHHHHTSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-----CSSBCHHHHHHHHHHTTC
T ss_pred             hHHHHHHHHhCCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-----CCCCCHHHHHHHHHHcCc
Confidence            4666777543  34 699999999999999999999999988877633     456999999999998653

>d1h3ob_ a.22.1.3 (B:) TAF(II)-20, (TAF(II)-15, hTAF12), histone fold domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: TAF(II)-20, (TAF(II)-15, hTAF12), histone fold domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.27  E-value=2  Score=30.83  Aligned_cols=49  Identities=20%  Similarity=0.294  Sum_probs=44.6

Q ss_pred             CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHhC
Q 036514          251 KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATELN  304 (328)
Q Consensus       251 gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amEln  304 (328)
                      .+++++.++|..-.|.|+-+++.....+|+.|..     ..+.+.|+...+|-|
T Consensus        21 ~ld~~vee~ll~iADdFV~~V~~~ac~lAKhR~s-----~~le~kDvql~LeR~   69 (74)
T d1h3ob_          21 QLDEDVEEMLLQIADDFIESVVTAACQLARHRKS-----STLEVKDVQLHLERQ   69 (74)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTC-----CEECHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC-----CCCcHHHHHHHHHhh
Confidence            8999999999999999999999999999999654     568999999998865

>d2bykb1 a.22.1.3 (B:11-99) Chrac-14 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: Chrac-14
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=83.13  E-value=1.3  Score=32.43  Aligned_cols=59  Identities=14%  Similarity=0.117  Sum_probs=46.6

Q ss_pred             HHHHHHHH---hCCCCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHh
Q 036514          240 RLEKKLEM---EGLKVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATEL  303 (328)
Q Consensus       240 RM~~ia~e---~GLgVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amEl  303 (328)
                      |...|+.+   .+..|+.|+..++..|.+.|+..|-..+.+.+....     ...|+-.|+..|++-
T Consensus         4 ~i~ri~K~~~p~~~~iskeA~~~i~~aae~FI~~lt~~A~~~a~~~~-----rKtI~~~dv~~Al~~   65 (89)
T d2bykb1           4 VIGRLIKEALPESASVSKEARAAIARAASVFAIFVTSSSTALAHKQN-----HKTITAKDILQTLTE   65 (89)
T ss_dssp             HHHHHHHHHSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-----CSSCCHHHHHHHHHH
T ss_pred             HHHHHHHHhCcccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC-----CCccCHHHHHHHHHH
Confidence            34444432   333799999999999999999999999988876533     457999999999985