Citrus Sinensis ID: 005668

---

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-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------610-------620-------630-------640-------650-------660-------670-------680----
Protein Sequence
MARERHGTTSQQQQQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEIRRRFTVKNGAESTSLVPLVDQLRQIRVQELRAEVQRRDVSIVSLELKVKRLEEEREKSMKPEADLESDRKAMPEIEAAVDGDGDSNRSFNESNSTTQKAETTNKKQNDDAEGEEEKEQKMKPEPDVENDPVQNRTESGPDREDRDWSSNGKLNENGNGTGNVKEETDEDNDKTASEGKVESVKNKTSAVGGLSESNELWDESKREGKQSSDVQSSASLSRNKRRRSGEEPYDEEVSPATKKVLAVKSEPLVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQEYAAAQELRTLVIKEMTDMLRKQQPIAVTKPKPKPKPEHHRQQPQPPPASLSKPNRGSTMVVCGKRSSIKAISKNAYGKKGDRKDREVEEKPKVNEKKVDSSFVGIEDKGIKKKRSQERSVSLRRNSRSSSRSGDVKHQFGGNELSSHDTLEAKTENKKENAVKKKKLGAASFLKRMKQNSPSEVMEDDDEEEDENDNDNDDDDSGDDSKDSKVEEEKKRRSVTRRDVNRVTRSSRGRGVREENRRRGVGRPPKRSASGAMSPPEKTSGKRGRDNGESEVGGGGRSRKRTRR
Secondary Structure (PSIPRED)
cccccccccccccccHHHHHHHHHHHHHHHHccccHHHHHHHHHHHccccccccHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHccccHHHHHHHHHHHHcccccccccccccccccccHHHccccccHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHcccHHHHHHHHccccccccccccccccccccccccccccccccccHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccHcccHHHHHHHHHHHHHcccccHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHcccccccccccccHccHHHHHHHHccccHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccEEEEcccccHHHcccHHcccccccccccccccccccccccHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHccccccccccccccccccccHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
marerhgttsqqqQQWGTLEELLLACAVnrhgtrswDSIAMEVQNrssalssltpqscrDKFNEIRRRFTVkngaestslvpLVDQLRQIRVQELRAEVQRRDVSIVSLELKVKRLEEEReksmkpeadlesdrkampeieaavdgdgdsnrsfnesnsttqkaettnkkqnddaegeeekeqkmkpepdvendpvqnrtesgpdredrdwssngklnengngtgnvkeetdedndktasegkvesvknktsavgglsesnelwdeskregkqssdvqssaslsrnkrrrsgeepydeevspATKKVLAVKSEPLVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQsrldrglysnCFQKFFRDLLLLFNNFVIFFRKSSQEYAAAQELRTLVIKEMTDMLRKqqpiavtkpkpkpkpehhrqqpqpppaslskpnrgstmvvcgkrssikaisknaygkkgdrkdreveekpkvnekkvdssfvgiedkgikkkrsQERSVslrrnsrsssrsgdvkhqfggnelsshdtleakTENKKENAVKKKKLGAASFLKRmkqnspsevmedddeeedendndnddddsgddskdskveeekkrrsvtrrdvnrvtrssrgrgvreenrrrgvgrppkrsasgamsppektsgkrgrdngesevggggrsrkrtrr
Flexible Loop (DISEMBL)
marerhgttsqqqqqwGTLEELLLACAVNRHGTRSWDSIAMEVQNrssalssltpqscrDKFNEIRRRFTvkngaestslvplvdqlRQIRVQElraevqrrdvsivslelkvkrleeereksmkpeadlesdrkaMPEIEaavdgdgdsnrsfnesnsttqkaettnkkqnddaegeeekeqkmkpepdvendpvqnrtesgpdredrdwssngklnengngtgnvkeetdedndktasegkvesvknktsavgglsesnelwdeskregkqssdvqssaslsrnkrrrsgeepydeevspatkkvlavkseplVRFLGmirshrlsshferrlrsqeserykklvrqhidlrtiqsrldrgLYSNCFQKFFRDLLLLFNNFVIFFRKSSQEYAAAQELRTLVIKEMTDMLRKQQPIAVTKPKPKPkpehhrqqpqpppaslskpnrGSTMVvcgkrssikaisknaygkkgdrkdreveekpkvnekkvdssfvgiedkgikkkrsqersvslrrnsrsssrsgdvkhqfggnelsshdtleaktenkkenavkkkklgaasflkrmkqnspsevmedddeeedendndnddddsgddskdskveeekkrrsvtrrdvnrvtrssrgrgvreenrrrgvgrppkrsasgamsppektsgkrgrdngesevggggrsrkrtrr
Low Complexity Region (SEG)
MARERHGTTSqqqqqWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEIRRRFTVKNGAESTSLVPLVDQLRQIRVQELRAEVQRRDVSIvslelkvkrleeereksMKPEADLESDRKAMPEIEAAVDGDGDSNRSFNESNSTTQKAETTNKKQNDDAegeeekeqkmkpePDVENDPVQNRTESGPDREDRDWSSNGKLNENGNGTGNVKEETDEDNDKTASEGKVESVKNKTSAVGGLSESNELWDESKREGKQssdvqssaslsRNKRRRSGEEPYDEEVSPATKKVLAVKSEPLVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKffrdllllfnnfviffRKSSQEYAAAQELRTLVIKEMTDMLRKQQPIAVTkpkpkpkpehhrqqpqpppASLSKPNRGSTMVVCGKRSSIKAISKNAYGKKGDRKDReveekpkvnekkvDSSFVGIEDKGIKKKRSQErsvslrrnsrsssrsGDVKHQFGGNELSSHDtleaktenkkenavkkkklGAASFLKRMKQNSPSEVMedddeeedendndnddddsgddskdskveeekKRRSVTRRDvnrvtrssrgrgvreenrrrgvgrPPKRSASGAMSPPEKTSGKRgrdngesevggggrsrkrtrr
Disordered region (IsUnstruct)
***************WGTLEELLLACAVNRHGTRSWDSIA************************IRRRFTVKNGAESTSLVPLVDQLRQIRVQELRAEVQRRDVSIVSLEL****************************************************************************************************************************************************************************************************LAVKSEPLVRFLGMIRSH*****************YKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQEYAAAQELRTLVIKEM************************************************************************************************************************************************************************************************************************************************************************************
Disordered Region (DISOPRED)
***************WGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEI************TSLVPLVDQLRQIRV*****************************************************************************************************************************************************************************************************************************PLVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQEYAAAQELRTLVIKEM************************************************************************************************************************************************************************************************************************************************************************************
Disordered Region (DISEMBL)
***************WGTLEELLLACAVNRHGTRSWDSIAMEV***********PQSCRDKFNEIRRRFTVKNGAESTSLVPLVDQLRQIRVQELRAEVQRRDVSIVSLELKVKRL******************KAMPEIEAAVDGDGD**************************************************************SSNGKLNENGNGTGN*****************************************************************************TKKVLAVKSEPLVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQEYAAAQELRTLVIKEMTDMLRKQQPIAV**********************************CGKRSSIKAISK*********************EKKVDSSFVGIEDKG***************************HQFGGNELSSHDTLEAKTENKKENAVKKKKLGAASFLKR********************************************************************************************************************
Disordered Region (DISPRO)
************QQQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEIRRRFTVKNGAESTSLVPLVDQLRQIRVQELRAEVQRRDVSIVSLELKVKRLEEE**********************************************************************************************************************************************************************************************VKSEPLVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQEYAAAQELRTLVIKEMTDMLRK************************************TM****************************************************************************************************************************************************************************************************************************************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MARERHGTTSQQQQQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEIRRRFTVKNGAESTSLVPLVDQLRQIRVQELRAEVQRRDVSIVSLELKVKRLEEEREKSMKPEADLESDRKAMPEIEAAVDGDGDSNRSFNESNSTTQKAETTNKKQNDDAEGEEEKEQKMKPEPDVENDPVQNRTESGPDREDRDWSSNGKLNENGNGTGNVKEETDEDNDKTASEGKVESVKNKTSAVGGLSESNELWDESKREGKQSSDVQSSASLSRNKRRRSGEEPYDEEVSPATKKVLAVKSEPLVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQEYAAAQELRTLVIKEMTDMLRKQQPIAVTKPKPKPKPEHHRQQPQPPPASLSKPNRGSTMVVCGKRSSIKAISKNAYGKKGDRKDREVEEKPKVNEKKVDSSFVGIEDKGIKKKRSQERSVSLRRNSRSSSRSGDVKHQFGGNELSSHDTLEAKTENKKENAVKKKKLGAASFLKRMKQNSPSEVMEDDDEEEDENDNDNDDDDSGDDSKDSKVEEEKKRRSVTRRDVNRVTRSSRGRGVREENRRRGVGRPPKRSASGAMSPPEKTSGKRGRDNGESEVGGGGRSRKRTRR
Positional Conservation
no confident homologs detected

---

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	684	2.2.26 [Sep-21-2011]
Q9H0E9	1235	Bromodomain-containing pr	yes	no	0.135	0.075	0.319	1e-07
Q8R3B7	951	Bromodomain-containing pr	no	no	0.131	0.094	0.263	0.0002
A8DZJ1	1441	Tyrosine-protein kinase B	N/A	no	0.173	0.082	0.268	0.0003

>sp|Q9H0E9|BRD8_HUMAN Bromodomain-containing protein 8 OS=Homo sapiens GN=BRD8 PE=1 SV=2

 Score = 59.3 bits (142), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 30/94 (31%), Positives = 53/94 (56%), Gaps = 1/94 (1%)

Query: 315  LVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFR 374
            L+    MI SHR SS F + +  +++  YK +V++ +DL +++  L +G      Q F R
Sbjct: 1112 LLPVWKMIASHRFSSPFLKPVSERQAPGYKDVVKRPMDLTSLKRNLSKGRIRTMAQ-FLR 1170

Query: 375  DLLLLFNNFVIFFRKSSQEYAAAQELRTLVIKEM 408
            DL+L+F N V++       Y  A E+R  V++++
Sbjct: 1171 DLMLMFQNAVMYNDSDHHVYHMAVEMRQEVLEQI 1204

May act as a coactivator during transcriptional activation by hormone-activated nuclear receptors (NR). Isoform 2 stimulates transcriptional activation by AR/DHTR, ESR1/NR3A1, RXRA/NR2B1 and THRB/ERBA2. At least isoform 1 and isoform 2 are components of the NuA4 histone acetyltransferase (HAT) complex which is involved in transcriptional activation of select genes principally by acetylation of nucleosomal histones H4 and H2A. This modification may both alter nucleosome - DNA interactions and promote interaction of the modified histones with other proteins which positively regulate transcription. This complex may be required for the activation of transcriptional programs associated with oncogene and proto-oncogene mediated growth induction, tumor suppressor mediated growth arrest and replicative senescence, apoptosis, and DNA repair. NuA4 may also play a direct role in DNA repair when recruited to sites of DNA damage.
Homo sapiens (taxid: 9606)

>sp|Q8R3B7|BRD8_MOUSE Bromodomain-containing protein 8 OS=Mus musculus GN=Brd8 PE=1 SV=2

 Score = 48.5 bits (114), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/91 (26%), Positives = 49/91 (53%), Gaps = 1/91 (1%)

Query: 325 HRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFV 384
           HR ++ F + +    +  Y  +V++ +DL TI+  ++ GL  +   +F RD++L+F N V
Sbjct: 799 HRYANVFLQPVTDDIAPGYHSIVQRPMDLSTIKKNIENGLIRST-AEFQRDIMLMFQNAV 857

Query: 385 IFFRKSSQEYAAAQELRTLVIKEMTDMLRKQ 415
           ++       Y  A E++  V++++   L  Q
Sbjct: 858 MYNSSDHDVYHMAVEMQRDVLEQIQQFLATQ 888

May act as a coactivator during transcriptional activation by hormone-activated nuclear receptors (NR). Stimulates transcriptional activation by AR/DHTR, ESR1/NR3A1, RXRA/NR2B1 and THRB/ERBA2. Component of the NuA4 histone acetyltransferase (HAT) complex which is involved in transcriptional activation of select genes principally by acetylation of nucleosomal histones H4 and H2A. This modification may both alter nucleosome - DNA interactions and promote interaction of the modified histones with other proteins which positively regulate transcription. This complex may be required for the activation of transcriptional programs associated with oncogene and proto-oncogene mediated growth induction, tumor suppressor mediated growth arrest and replicative senescence, apoptosis, and DNA repair. NuA4 may also play a direct role in DNA repair when recruited to sites of DNA damage.

Mus musculus (taxid: 10090)

>sp|A8DZJ1|BAZ1B_XENLA Tyrosine-protein kinase BAZ1B OS=Xenopus laevis GN=baz1b PE=2 SV=2

 Score = 47.8 bits (112), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 36/134 (26%), Positives = 59/134 (44%), Gaps = 15/134 (11%)

Query: 318  FLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLL 377
             L  +  +R S  F     + E E Y K+V   +D +T+QS+   G Y    Q+F  DL 
Sbjct: 1316 ILAKLIKYRFSWPFREPFNADEIEDYTKVVTTPMDFQTMQSKCSCGSYQT-VQEFLNDLK 1374

Query: 378  LLFNNFVIFFRKSSQEYAAAQELRTLVIKEMTDMLRKQQPIAVTKPKPKPKPEHHR--QQ 435
            L+F N  +++   S + +  ++          D+L K  P    + +       HR  Q 
Sbjct: 1375 LVFGNTELYYEAGSSQLSCLEKTEQCA----RDLLGKHLPAHTYQRR-------HRKHQS 1423

Query: 436  PQPPPASLSKPNRG 449
            P+P P + + P RG
Sbjct: 1424 PEPEPET-ANPGRG 1436

Atypical tyrosine-protein kinase that plays a central role in chromatin remodeling and acts as a transcription regulator. Involved in DNA damage response by phosphorylating 'Tyr-142' of histone H2AX (H2AXY142ph). H2AXY142ph plays a central role in DNA repair and acts as a mark that distinguishes between apoptotic and repair responses to genotoxic stress. Essential component of the WICH complex, a chromatin remodeling complex that mobilizes nucleosomes and reconfigures irregular chromatin to a regular nucleosomal array structure. The WICH complex regulates the transcription of various genes, has a role in RNA polymerase I and RNA polymerase III transcription, mediates the histone H2AX phosphorylation at 'Tyr-142', and is involved in the maintenance of chromatin structures during DNA replication processes. Also involved in vitamin D-coupled transcription regulation via its association with the WINAC complex, a chromatin-remodeling complex recruited by vitamin D receptor (VDR). In the WINAC complex, plays an essential role by targeting the complex to acetylated histones, an essential step for VDR-promoter association.

Xenopus laevis (taxid: 8355)

EC: 2

EC: .

EC: 7

EC: .

EC: 1

EC: 0

EC: .

EC: 2

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	684
255544738	674	DNA binding protein, putative [Ricinus c	0.919	0.933	0.544	1e-168
449448952	673	PREDICTED: uncharacterized protein LOC10	0.783	0.796	0.464	1e-112
225450325	686	PREDICTED: uncharacterized protein LOC10	0.852	0.849	0.394	4e-90
224073218	385	bromodomain protein [Populus trichocarpa	0.470	0.836	0.531	7e-85
449436657	703	PREDICTED: uncharacterized protein LOC10	0.884	0.860	0.368	2e-71
449519334	688	PREDICTED: uncharacterized protein LOC10	0.871	0.866	0.363	4e-71
297820594	629	predicted protein [Arabidopsis lyrata su	0.742	0.807	0.362	3e-65
356555278	746	PREDICTED: uncharacterized protein LOC10	0.757	0.694	0.360	1e-64
356528554	747	PREDICTED: uncharacterized protein LOC10	0.752	0.689	0.352	4e-64
224053014	251	hypothetical protein POPTRDRAFT_547688 [	0.321	0.876	0.575	7e-64

>gi|255544738|ref|XP_002513430.1| DNA binding protein, putative [Ricinus communis] gi|223547338|gb|EEF48833.1| DNA binding protein, putative [Ricinus communis]

 Score =  599 bits (1544), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 392/720 (54%), Positives = 491/720 (68%), Gaps = 91/720 (12%)

Query: 1   MARERHGTTSQQQQQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRD 60
           MAR+ H   +  Q  WGTLEELLLACAVNRHGT+SWDSIAMEVQNR+S L SLT Q+C+D
Sbjct: 10  MARQHHHQETSVQP-WGTLEELLLACAVNRHGTKSWDSIAMEVQNRTSTLPSLTSQNCKD 68

Query: 61  KFNEIRRRFTVKNGAESTSLVPLVDQLRQIRVQELRAEVQRRDVSIVSLELKVKRLEEER 120
           K+N+++RRF  +N   S     ++DQLR+IRV+ELR EVQRRDVSIVSLELKVKRLEEER
Sbjct: 69  KYNDLKRRFMSQNDTSS-----IIDQLRKIRVEELRREVQRRDVSIVSLELKVKRLEEER 123

Query: 121 EKSMKPEADLESDRKAMPEIEAAVDGDGDS-----NRSFNESNST-TQKAETTN-KKQND 173
           E+S K EADL S+RK      +   GD DS     +RSFNESNST  QKAETT  ++QND
Sbjct: 124 ERSFKEEADLISERKFSIAGNSTAGGD-DSVDERDSRSFNESNSTGQQKAETTMVRQQND 182

Query: 174 DAEGEEEKEQKMKPEP-DVENDPVQNRTESGPDREDRDWSSNGKLNENGNGTGNVKEETD 232
           D +    ++QK+K +P D EN   Q+   SG D         G  ++NGN          
Sbjct: 183 DVD----RQQKIKVKPNDSENKNEQDPVPSGSD--------PGGSHKNGN---------- 220

Query: 233 EDNDKTASEGKVESVKNKTSAVGGLSESNELWD---ESKRE-------GKQSSDVQSSAS 282
            D    A   K   +K   +  G   ESNE+ +   ESKRE        + +SDVQSS S
Sbjct: 221 -DKKPLAMVKKESEIKTSQTTGGFGGESNEVGESVGESKREERDKEKEKQNNSDVQSSIS 279

Query: 283 LSRNKRRR-------------SGEEPYD-EEVSPATKKVLAVKSEPLVRFLGMIRSHRLS 328
           LS+NK++R             SGEEP   +EVSPA      VKSEPLV+ LG+IRSHRL 
Sbjct: 280 LSQNKKKRRGSSGGGDRVGSSSGEEPEGGDEVSPA------VKSEPLVKLLGIIRSHRLG 333

Query: 329 SHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFR 388
           S FERRLRSQESERYK L+RQHIDL+TIQSRLD+G+YS+C QKFFRDLLLLFNN +IFFR
Sbjct: 334 STFERRLRSQESERYKNLIRQHIDLQTIQSRLDKGVYSSCIQKFFRDLLLLFNNAIIFFR 393

Query: 389 KSSQEYAAAQELRTLVIKEMTDMLRKQQPIAVTKPKPKPKPEHHRQQPQPPPASLSKPNR 448
           K+S E  AA ELR +V KEMT+ LRK +   VT      KPE     P+    S SKPN+
Sbjct: 394 KNSPENLAACELRAVVQKEMTEKLRKLKTEPVT-----AKPE-----PKQTAVSFSKPNK 443

Query: 449 -GSTMVVCGKRSSIKAISKNAYGKKGDRKDREVEEKPKVNEKKVDSSFVGIEDKGIKKKR 507
             ST+VVCGK +S KAI +N   KKGD+K+REVEEK K+NE+++D SFV IE+K I+KKR
Sbjct: 444 SSSTIVVCGKGNSKKAIPENDI-KKGDKKEREVEEKIKLNERQID-SFVKIEEKSIRKKR 501

Query: 508 SQERSVSLRRNSRSSSRSGDVKHQFGGNELSSHDTLEAKTENKKENAVKKKKLGAASFLK 567
           +++RS+S  R+S +S+++G+VKHQ+GGNELSSHD LE K E K + +  +KK GAASFLK
Sbjct: 502 TKDRSISNHRSSNTSNKNGEVKHQYGGNELSSHDALEMKVERKGKGSTARKKQGAASFLK 561

Query: 568 RMKQNSPSEVMEDDDEEEDENDNDNDDDDSGDDSKDSKVEEEKKRR--SVTRRDVNRVTR 625
           RMKQNSPSEV E+DDE+ D++++++  ++   + KDSK +EEK RR   +      RVTR
Sbjct: 562 RMKQNSPSEVPENDDEDYDDDNDNDSSEED--EKKDSKGKEEKGRRRGKIIDGMTERVTR 619

Query: 626 SSRGRGVREENR-RRGVGRPPKRSASGAMSPPEKTSGKRGRDNGESEVGGGGRSRKRTRR 684
           SSRGRG RE  R +RGVGRPP++ A    S     +GKRGR+NG SEV   GR+RKR++R
Sbjct: 620 SSRGRGARENGRGKRGVGRPPRKQAERGESGG--GTGKRGRENGGSEV---GRTRKRSKR 674

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449448952|ref|XP_004142229.1| PREDICTED: uncharacterized protein LOC101213195 [Cucumis sativus]

 Score =  412 bits (1060), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 290/625 (46%), Positives = 381/625 (60%), Gaps = 89/625 (14%)

Query: 14  QQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSS--ALSSLTPQSCRDKFNEIRRRFTV 71
           ++WGTLEELLLA AVNRHGT SW+S+AME+ NR S  + SSLTPQ CR+KF +++RRF  
Sbjct: 10  KRWGTLEELLLASAVNRHGTASWESVAMEIHNRCSHQSSSSLTPQDCRNKFYDLKRRFLS 69

Query: 72  KNGAES----TSLVPLVDQLRQIRVQELRAEVQRRDVSIVSLELKVKRLEEEREKS--MK 125
           +N  +S    T+L+P++D+LR+IRVQELR +V+RRDV IVSLE+KVKRLEEER++S    
Sbjct: 70  QNVLDSDSDPTTLMPMLDELRKIRVQELRRDVERRDVLIVSLEMKVKRLEEERDRSSNQS 129

Query: 126 PE-ADLESDRKAMPEIE----AAVDGDGDS--NRSFNESNSTTQKAETTNKKQNDDAEGE 178
           PE +DL++D KA   +     AA   D D   NRS NESNST++K +    +QN   E  
Sbjct: 130 PEGSDLDTD-KAKTNLHLQNPAASGDDSDDRENRSLNESNSTSKKDDV---RQNGVVEDN 185

Query: 179 EEKEQKMKPEPDVENDPVQNRTESGP----DREDRDWSSNGKLNENGNGTGNVKEETDED 234
                     P +E+  +    E+GP    D   R+WS        G       +   + 
Sbjct: 186 ----------PIIESVNMSKMEETGPPKTGDEPGREWS----FESAGQEPEPEPDPEAKP 231

Query: 235 NDKTASEGKV---ESVKNKTSAVGGLSESNELWD---ESKREGK-------QSSDVQSSA 281
             +  S G     E  +N  +    + +SNE W+   ESK++GK       QSSDVQSS 
Sbjct: 232 EREKKSSGGYKRREKERNWGNLKAAVVDSNEAWESVSESKQDGKEGAVSKQQSSDVQSSG 291

Query: 282 SLSRNKRRR--SGEEPYDEEVSPATKK--VLAVKSEPLVRFLGMIRSHRLSSHFERRLRS 337
           SLS+ KR R  SGEEP   EVSPA  K   LAVK+EPL++ L +IRSH+L S FERRLRS
Sbjct: 292 SLSQRKRCRNSSGEEP---EVSPAKPKPKALAVKTEPLLKLLDIIRSHQLGSTFERRLRS 348

Query: 338 QESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQEYAAA 397
           QES+RYK L+RQHIDLRTI+ R+ +G Y++   +FFRDLLLLFNN +IFF +SS E  AA
Sbjct: 349 QESDRYKNLIRQHIDLRTIRCRVVKGAYADSIHRFFRDLLLLFNNAIIFFHRSSPENGAA 408

Query: 398 QELRTLVIKEMTDMLRKQQPIAVTKPKPKPKPEHHRQQPQPPPASLSKPNRGSTMVVCGK 457
            +LR LV+K+M D + K QPI V K KPK + +          +  +     +T+V C K
Sbjct: 409 LKLRALVLKDMKDHIDKPQPI-VLKSKPKQETDLSLPS-----SKPTTKPSTTTIVGCRK 462

Query: 458 RSSIKAISKNAYGKKGDRKDREVEEKPKVNEKKVDSSFVGIEDKGIKKK--RSQER---- 511
           R S+         KK D+  R++E KPKV+    DSS + I +KG  KK   S+ER    
Sbjct: 463 RDSVATDC-----KKVDKNSRDIEVKPKVS----DSSEIKIYEKGTWKKGLNSKERLRPT 513

Query: 512 SVSLRRNS--------RSSSRSGDVKHQFGGNELSSHDTLEAKTENKKENAVKKKKLGAA 563
           S     NS         +S  +G+VKH++GGNELSSHD +E + E K+   V KKK GA 
Sbjct: 514 STPTPANSGQRSSRTSSTSKNNGEVKHEYGGNELSSHDGMEVRMEKKER--VTKKKQGAV 571

Query: 564 SFLKRMKQNSPSEVMEDD-DEEEDE 587
           SFLKRMKQNSP+E  E+D D  E+E
Sbjct: 572 SFLKRMKQNSPNEAAEEDGDASENE 596

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225450325|ref|XP_002268328.1| PREDICTED: uncharacterized protein LOC100263099 [Vitis vinifera] gi|147768907|emb|CAN75881.1| hypothetical protein VITISV_024454 [Vitis vinifera]

 Score =  338 bits (868), Expect = 4e-90,   Method: Compositional matrix adjust.
 Identities = 291/737 (39%), Positives = 390/737 (52%), Gaps = 154/737 (20%)

Query: 16  WGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLT-PQSCRDKFNEIRRRFTVK-- 72
           W T EELLLACAV RHG ++WDS+AME+Q RSS    LT  Q+C+ K+++++RRFT    
Sbjct: 32  WTTWEELLLACAVKRHGFQNWDSVAMEIQTRSSLPHLLTTAQNCQQKYHDLKRRFTATAK 91

Query: 73  -NGAES---------TSLVPLVDQLRQIRVQELRAEVQRRDVSIVSLELKVKRLEEEREK 122
            N AE+         T  +P +++LR++RV ELR EV R DVSI+SL+LKVKRLEEERE+
Sbjct: 92  DNDAETQSQNQVRDETDTIPWLEELRKLRVAELRNEVHRSDVSILSLQLKVKRLEEEREQ 151

Query: 123 S--------MKPEADLESDR---------------KAMPEIEAAVDGDGDS----NRSFN 155
           S        +KP+ D E                  K+ PE +A     G+     NRS N
Sbjct: 152 STKENDNDVVKPDLDDEVKEERSKDEVKEGDEVPEKSSPEGDAGKLISGEESDRENRSVN 211

Query: 156 ESNSTTQKAETTNKKQNDDAEGEEEKEQKMKPEPDVENDPVQNRTESG---PDREDRDWS 212
           ESNST  K E      N +   EE   +   PEP          TE G   PD    D  
Sbjct: 212 ESNSTGVKGE------NIETAVEEAARE---PEP----------TEPGSTKPDPVSSDSK 252

Query: 213 SNGKLNENGNGTGNVKEETDEDNDKTASEGKVESVKNKTSAVGGLSESNELWDESKREGK 272
             G+ + NG+   N  ++ D+                        SE  E    SK   K
Sbjct: 253 PVGEDSYNGSSEPNRAKKADDS-----------------------SELRESAAHSKDGTK 289

Query: 273 QSSDVQSSASLSRNKRRR---------SGEEPYDEEVSPATKKVLAVKSEPLVRFLGMIR 323
           +SSDVQSSASL+R ++RR         SG+EP  E VSPATK++  VKS+PLV FL +IR
Sbjct: 290 ESSDVQSSASLTRKRKRRRKKEISGSSSGDEPETEAVSPATKRI-CVKSQPLVSFLEIIR 348

Query: 324 SHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNF 383
           SH+ SS FERRL +QE+E YK +VRQH+DL +IQ++LD G YS+  + F+RDLLLLF N 
Sbjct: 349 SHKHSSLFERRLETQETEVYKSIVRQHVDLESIQTKLDDGTYSSSPRAFYRDLLLLFTNA 408

Query: 384 VIFFRKSSQEYAAAQELRTLVIKEMTDMLRKQQPIAVTKPKPKPKPEHHRQQPQPPP--- 440
           ++FF K+S E  AA ELR +V+ E    +RKQQP         P PE H   PQP P   
Sbjct: 409 IVFFPKASAEALAAGELRAMVLNE----VRKQQP---------PAPE-HLLLPQPKPELE 454

Query: 441 ---ASLSKPNRGSTMVVCGKRSSIKAISKNAYGKKGDRKDRE---VEEKPKVNEKKVDSS 494
              + L+K    + ++VC KRSSI A + +   K G+ +  E   V+ KP V E++   S
Sbjct: 455 RSDSLLAKQKSSAPIIVCRKRSSISAKASSFGVKAGESRSEEKPAVDIKPSVREEQ---S 511

Query: 495 FVGIEDKGIKKKRSQERSVSLRRNSRSSSRSGDV-KHQFGGNELSSHDTLEA-KTENKKE 552
            V    K   K++S     SLRR  +  +RSG++ K+Q       S D  E  K E KK 
Sbjct: 512 LV----KAGTKEKSTTGVRSLRRGGK--NRSGNLNKNQSTSTNHGSSDKGETPKAEKKKA 565

Query: 553 NA-VKKKKLGAASFLKRMKQNSPSEVMEDDDEEEDENDNDNDDDDSGDDSKDSKVEEEKK 611
           +A    KK GAA FLKR+K+NSP           D   +  +D  SG      + + ++ 
Sbjct: 566 DASASAKKRGAADFLKRIKKNSPM----------DMGKSTVNDTRSGRGGGGGEEKRKRN 615

Query: 612 RRSVTRRDVNRVTRSSRG--RGVREEN-RRRGVGRPPKRSASGAMSPPEKTSGKRGRDN- 667
            +   RRD  RV R S G  +G  E +  +R VGRPPK++A+         +GKRGR++ 
Sbjct: 616 EKGDGRRD--RVLRQSGGGKQGKDESSPSKRSVGRPPKKAAAD--------TGKRGRESG 665

Query: 668 GESEVGGGGRSRKRTRR 684
           GE E      S KR R+
Sbjct: 666 GEKEAAPAASSSKRARK 682

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224073218|ref|XP_002304028.1| bromodomain protein [Populus trichocarpa] gi|222841460|gb|EEE79007.1| bromodomain protein [Populus trichocarpa]

 Score =  321 bits (823), Expect = 7e-85,   Method: Compositional matrix adjust.
 Identities = 188/354 (53%), Positives = 251/354 (70%), Gaps = 32/354 (9%)

Query: 335 LRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQEY 394
           L+ +ESERYKKL+RQH+DL+ IQSRLD+G+YS CF+K F+DLL+L NN ++FFRK+S E 
Sbjct: 60  LKIKESERYKKLIRQHMDLQMIQSRLDKGVYSKCFKKLFKDLLILLNNAIVFFRKNSPEN 119

Query: 395 AAAQELRTLVIKEMTDMLRKQQPIAVTKPKPKPKPEHHRQQPQPPPASLSKPNRG-STMV 453
            AA ELR +V+KEM + L+K          PKPKP   +   +   AS SKPN+  STMV
Sbjct: 120 LAANELRAVVLKEMKEKLQK----------PKPKPVAVKPATEQYSASFSKPNKSTSTMV 169

Query: 454 VCGKRSSIKAISKNAYGKKGDRKDREVEEKPKVNEKKVDSSFVGIEDKGIKKKRSQERSV 513
            C K SSIKAIS+ A GKK D+KD E+EEKPK NEKK++ S V IE+KG+KKK ++ERSV
Sbjct: 170 ACSKHSSIKAISEGA-GKKDDKKDAEIEEKPKANEKKLEVSIVRIEEKGLKKKTTKERSV 228

Query: 514 SLRRNSRSSSRSGDVKHQFGGNELSSHDTLEAKTENKKENAVKKKKLGAASFLKRMKQNS 573
           S RRNSR+S+++G++KHQ+GGNELSSHD LE   + K+     +KKLGAASFLKRMKQNS
Sbjct: 229 SGRRNSRASNKNGEIKHQYGGNELSSHDALEITVDRKESTG--RKKLGAASFLKRMKQNS 286

Query: 574 PSEVMEDDDEEEDENDNDNDDDDSGDDSKDSKVEEEKKRRSVTRRDVNRVTRSSRGRGVR 633
           P +V E+DD++   +++++ D  + D         +K+RR    R   RVTRSS+GRG+ 
Sbjct: 287 PGQVTENDDDDSSSSEDESKDSKTVD---------KKRRRREADRITKRVTRSSKGRGLG 337

Query: 634 EENRRRGVGRPPKRSA-SGAMSPPEKTSGKRGRDNGESE--VGGGGRSRKRTRR 684
           E++R    GRPPK+   SG        +GKRGR++ +SE  VGG GR++KR+RR
Sbjct: 338 EDSRNIKRGRPPKKQMDSGG------GTGKRGREDDDSEVGVGGAGRAKKRSRR 385

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449436657|ref|XP_004136109.1| PREDICTED: uncharacterized protein LOC101208443 [Cucumis sativus]

 Score =  277 bits (708), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 281/763 (36%), Positives = 376/763 (49%), Gaps = 158/763 (20%)

Query: 11  QQQQQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLT-PQSCRDKFNEIRRRF 69
           Q    WGTLEELLLACAV RHG + W+S++ME+QNRSS    LT  ++C  KF +++RRF
Sbjct: 6   QITATWGTLEELLLACAVKRHGFKDWNSVSMELQNRSSLPPLLTTARNCELKFQDLKRRF 65

Query: 70  T------VKNGAEST------SLVPLVDQLRQIRVQELRAEVQRRDVSIVSLELKVKRLE 117
           T      V N   S       + +P VD+LR++RV ELR EVQR DVSI SL+LKVK+LE
Sbjct: 66  TSFQNDAVLNHNASGIADKLDTALPWVDELRKLRVAELRREVQRYDVSINSLQLKVKKLE 125

Query: 118 EEREKSM--------KPEADLES-------DRKAMPEIE------------AAVDGDGDS 150
           EERE+ +        KP+   ES       D+K   E +             AV G+ DS
Sbjct: 126 EEREQGVNDREASTGKPDLKTESRERRSENDKKHFGEPDHRSGPNGTVTKPPAVPGE-DS 184

Query: 151 NR---SFNESNSTTQKAETTNKKQNDDAEGEEEKEQKMKPEPDVEND--PVQNRTESGPD 205
           +R   S N+SNST  K+   N+K   +    E K       PD      P QNR  S P 
Sbjct: 185 DRENFSVNQSNSTGSKS--GNRKSTAEIAKSETK-------PDFAGSYRPEQNRGTSEP- 234

Query: 206 REDRDWSSNGKLNENGNGTGNVKEETDEDNDKTASEGKVESVKNKTSAVGGLSESNELWD 265
                    G  +++G+    VK  T + +         E+ K +T  V    +S+EL D
Sbjct: 235 --------AGPQSDDGSTDTVVKNPTCDIS---------ETKKKETQRV---DDSSELAD 274

Query: 266 -ESKREG-----KQSSDVQSSASLS-RNKRRR----------SGEEPYDEEVSPATKKVL 308
            E++  G     ++SS+VQSSASL+ R K +R          SG EP         ++ +
Sbjct: 275 SEAQSHGGGTTTRESSEVQSSASLTGRMKSKRLLRKEISGGSSGNEP---------RRSV 325

Query: 309 AVKSEPLVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNC 368
            +KS      L +IR+H+  S FE RL+SQE+E YK +VRQH+DL  +QS++  G YS+ 
Sbjct: 326 GIKSRRFDEVLQLIRAHKHGSLFESRLQSQETEEYKGMVRQHLDLEIVQSKITSGSYSSS 385

Query: 369 FQKFFRDLLLLFNNFVIFFRKSSQEYAAAQELRTLVIKEMTDMLRKQQPIAVTKPKPKPK 428
              F+RDLLLLFNN V FF KSS+E  AA ELR L+  EM   LR    IA T     P 
Sbjct: 386 NLAFYRDLLLLFNNVVTFFPKSSKEAVAACELRLLISNEMKKSLR----IAQT----DPL 437

Query: 429 PEHHRQQPQPPPAS-----------LSKPNRGSTMVVCGKRSSIKAISKNAYGKKGDRKD 477
           PE     P  P  S           L+K      +VVC KRS I   S    G+KG+R +
Sbjct: 438 PEVVDSSPTIPSRSKGPDLEGSQSLLAKQKSSVPIVVCRKRSKISNPSTTGVGEKGERSN 497

Query: 478 REVEEKPKVNEK---KVDSSFVGIEDKG----IKKK-----RSQERSVSLRRNSR--SSS 523
              +EKP  + K   K  S+ V  ED      +K+K     RS  RS     NS   SSS
Sbjct: 498 D--DEKPAADLKSSIKTASNLVEDEDTTKDSKVKEKPTTGARSMRRSNDSATNSSGPSSS 555

Query: 524 RSGDVKHQFGGNELSSHDTLEAKTENKK--ENAVKKKKLGAASFLKRMKQNSPSEVMEDD 581
           +  ++  ++   + SS +  E  T +KK  E    +KK  AA FLKR+KQNSP+E  + +
Sbjct: 556 KKQNITSRW---KPSSANETEIPTPDKKKSETVALEKKRSAADFLKRIKQNSPAETTKRN 612

Query: 582 DEEEDENDNDNDDDDSGDDSKDSKVEEEKKRRSVTRRDVNRVTRSSRGRGVREENRRRGV 641
                     N   +    S  SK E+ K+R S T +  N   R            +R V
Sbjct: 613 GRGGSSGGVSNATPEQKKGS--SKNEKGKERVSTTMKQSNDRKRPKED----ASPSKRSV 666

Query: 642 GRPPKRSASGAMSPPEKTSGKRGRDNGESEVGGGGRSRKRTRR 684
           GRPPK++A     PP  T  KR R+      GGG    KR R+
Sbjct: 667 GRPPKKAAEA--EPP--TPIKRARE------GGGKEPLKRPRK 699

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449519334|ref|XP_004166690.1| PREDICTED: uncharacterized protein LOC101228284 [Cucumis sativus]

 Score =  275 bits (704), Expect = 4e-71,   Method: Compositional matrix adjust.
 Identities = 275/757 (36%), Positives = 367/757 (48%), Gaps = 161/757 (21%)

Query: 11  QQQQQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLT-PQSCRDKFNEIRRRF 69
           Q    WGTLEELLLACAV RHG + W+S++ME+QNRSS    LT  ++C  KF +++RRF
Sbjct: 6   QITATWGTLEELLLACAVKRHGFKDWNSVSMELQNRSSLPPLLTTARNCELKFQDLKRRF 65

Query: 70  T------VKNGAEST------SLVPLVDQLRQIRVQELRAEVQRRDVSIVSLELKVKRLE 117
           T      V N   S       + +P VD+LR++RV ELR EVQR DVSI SL+LKVK+LE
Sbjct: 66  TSFQNDAVLNHNASGIADKLDTALPWVDELRKLRVAELRREVQRYDVSINSLQLKVKKLE 125

Query: 118 EEREKSM--------KPEADLES-------DRKAMPEIE------------AAVDGDGDS 150
           EERE+ +        KP+   ES       D+K   E +             AV G+ DS
Sbjct: 126 EEREQGVNDREASTGKPDLKTESRERRSENDKKHFGEPDHRSGPNGTVTKPPAVPGE-DS 184

Query: 151 NR---SFNESNSTTQKAETTNKKQNDDAEGEEEKEQKMKPEPDVEND--PVQNRTESGPD 205
           +R   S N+SNST  K+   N+K   +    E K       PD      P QNR  S P 
Sbjct: 185 DRENFSVNQSNSTGSKS--GNRKSTAEIAKSETK-------PDFAGSYRPEQNRGTSEP- 234

Query: 206 REDRDWSSNGKLNENGNGTGNVKEETDEDNDKTASEGKVESVKNKTSAVGGLSESNELWD 265
                    G  +++G+    VK  T +          +   K K ++ GG + + E   
Sbjct: 235 --------AGPQSDDGSTDTVVKNPTCD----------ISETKKKGNSHGGGTTTRE--- 273

Query: 266 ESKREGKQSSDVQSSASLS-RNKRRR----------SGEEPYDEEVSPATKKVLAVKSEP 314
                   SS+VQSSASL+ R K +R          SG EP         ++ + +KS  
Sbjct: 274 --------SSEVQSSASLTGRMKSKRLLRKEISGGSSGNEP---------RRSVGIKSRR 316

Query: 315 LVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFR 374
               L +IR+H+  S FE RL+SQE+E YK +VRQH+DL  +QS++  G YS+    F+R
Sbjct: 317 FDEVLQLIRAHKHGSLFESRLQSQETEEYKGMVRQHLDLEIVQSKITSGSYSSSNLAFYR 376

Query: 375 DLLLLFNNFVIFFRKSSQEYAAAQELRTLVIKEMTDMLRKQQPIAVTKPKPKPKPEHHRQ 434
           DLLLLFNN V FF KSS+E  AA ELR L+  EM   LR    IA T     P PE    
Sbjct: 377 DLLLLFNNMVTFFPKSSKEAVAACELRLLISNEMKKSLR----IAQT----DPLPEVVDS 428

Query: 435 QPQPPPAS-----------LSKPNRGSTMVVCGKRSSIKAISKNAYGKKGDRKDREVEEK 483
            P  P  S           L+K      +VVC KRS I   S    G+KG+R +   +EK
Sbjct: 429 SPTIPSRSKGPDLEGSQSLLAKQKSSVPIVVCRKRSKISNPSTTGVGEKGERSND--DEK 486

Query: 484 PKVNEK---KVDSSFVGIEDKG----IKKK-----RSQERSVSLRRNSR--SSSRSGDVK 529
           P  + K   K  S+ V  ED      +K+K     RS  RS     NS   SSS+  ++ 
Sbjct: 487 PAADLKSSIKTASNLVEDEDTTKDSKVKEKPTTGARSMRRSNDSATNSSGPSSSKKQNIT 546

Query: 530 HQFGGNELSSHDTLEAKTENKK--ENAVKKKKLGAASFLKRMKQNSPSEVMEDDDEEEDE 587
            ++   + SS +  E  T +KK  E    +KK  AA FLKR+KQNSP+E  + +      
Sbjct: 547 SRW---KPSSANETEIPTPDKKKSETVALEKKRSAADFLKRIKQNSPAETTKRNGRGGSS 603

Query: 588 NDNDNDDDDSGDDSKDSKVEEEKKRRSVTRRDVNRVTRSSRGRGVREENRRRGVGRPPKR 647
               N   +    S  SK ++ K+R S T +  N   R            +R VGRPPK+
Sbjct: 604 GGVSNATPEQKKGS--SKNDKGKERVSTTMKQSNDRKRPKED----ASPSKRSVGRPPKK 657

Query: 648 SASGAMSPPEKTSGKRGRDNGESEVGGGGRSRKRTRR 684
           +A     PP  T  KR R+      GGG    KR R+
Sbjct: 658 AAEA--EPP--TPIKRARE------GGGKEPLKRPRK 684

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297820594|ref|XP_002878180.1| predicted protein [Arabidopsis lyrata subsp. lyrata] gi|297324018|gb|EFH54439.1| predicted protein [Arabidopsis lyrata subsp. lyrata]

 Score =  256 bits (654), Expect = 3e-65,   Method: Compositional matrix adjust.
 Identities = 215/593 (36%), Positives = 311/593 (52%), Gaps = 85/593 (14%)

Query: 19  LEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEIRRRFT---VKNG- 74
           +EELLLACAV+RHGT SWDS+A E+  ++  + +LT   CR K+N+++RRF+   V  G 
Sbjct: 1   MEELLLACAVHRHGTDSWDSVASEIHKQNPTVRTLTAIDCRHKYNDLKRRFSRNLVSPGS 60

Query: 75  --------AESTSLVPLVDQLRQIRVQELRAEVQRRDVSIVSLELKVKRLEEEREKSMKP 126
                   A   S VP +++LR++RV ELR EV+R D+SI SL+LKVKRLE+EREKS+K 
Sbjct: 61  AEGEEDTLAAEISSVPWLEELRKLRVDELRREVERYDLSISSLQLKVKRLEDEREKSLKT 120

Query: 127 EADLESDRKAMPEIEAAVDGDGDSNRSFNESNSTTQKAETTNKKQNDD---AEGEEEKEQ 183
           E    SD   + E +         N S + +NS    AE TN    +D     G E+  +
Sbjct: 121 E---NSDLDKIAETK--------ENHSESGNNSGVPVAEPTNSPDPNDNSPGTGSEKTNK 169

Query: 184 KMKPEPDVENDPVQNRTESGPDREDRDWSSNGKLNENGNGTG-NVKEETD------EDND 236
            +K    V+ +P  NR +  P RED           +G G+  +V +E+D      E ND
Sbjct: 170 DVKIAEPVDEEP--NRIDEKPVRED-----------SGRGSCESVAKESDRAEPEREGND 216

Query: 237 KTASEGKVESVKNKTSAVGGLSESNELWDESKREG--KQSSDVQSSASLSRNKRRRSGEE 294
              S   VES+                 DESK E   K++SD QSSASL R K      +
Sbjct: 217 ---SPEFVESM-----------------DESKGEEDRKETSDGQSSASLPR-KETVDQHQ 255

Query: 295 PYDEEVSPATKKVLAVKSEPLVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLR 354
           P +E+ S    K+ A +S+PL+ F+ +++SH + SHF RRL+SQE+  Y +++RQHID  
Sbjct: 256 PGNEDQSLTVNKIPA-ESQPLIDFIEILQSHPIGSHFSRRLQSQETSEYDRIIRQHIDFE 314

Query: 355 TIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQEYAAAQELRTLVIKEMTDMLRK 414
            I+SR++ G Y     KFFRDLLLL NN  +F+ + S E+   ++L  L+ K+M+  + K
Sbjct: 315 MIRSRVEEGYYKTSRSKFFRDLLLLVNNVRVFYGEPSSEFNVTKQLYQLIKKQMSLKIPK 374

Query: 415 QQPIAVTKPKPKPKPEHHRQQPQPPPASLSKPNRGSTMVVCGKRSSIKAISKNAYGKKGD 474
           Q         P PK E      +    S  KP     ++ C KRSS+   S  +  +   
Sbjct: 375 QT-------LPTPKEESLVTSKEEVTVSSLKPTLSVPIIACRKRSSLAVRSSASVTETLK 427

Query: 475 RKDR---EVEEKPKVNEKKVDSSFVGIEDKGIKKKRSQERSVSLRRNSRSSSRSGDVKHQ 531
           +K +    V+EKP V+E++ D +    E   + KK ++  + S  +N  S++    +   
Sbjct: 428 KKTKVVPTVDEKP-VSEEEEDGTSDKDEKPIVSKKMTRGGAPSTAKNVGSTNVKTSLNAG 486

Query: 532 FGGNELSSHDTLEAK---TENKKENAV-KKKKLGAASFLKRMKQNSPSEVMED 580
                 SS+D+   K    E K  NA    KK  AASFLKRMK  S SE + D
Sbjct: 487 ISSKGRSSNDSSVPKKSVQEKKGNNASGGSKKQSAASFLKRMKGVSSSETVVD 539

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356555278|ref|XP_003545961.1| PREDICTED: uncharacterized protein LOC100779988 [Glycine max]

 Score =  254 bits (649), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 229/636 (36%), Positives = 321/636 (50%), Gaps = 118/636 (18%)

Query: 16  WGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEIRRRF------ 69
           WGT EELLLACAVNRHG + WD++AMEVQ+R++ L + T   C  KF+++ RRF      
Sbjct: 36  WGTWEELLLACAVNRHGFKDWDAVAMEVQSRTTRLLA-TAHHCEQKFDDLSRRFADQCND 94

Query: 70  ----TVKNG--AESTSLVPLVDQLRQIRVQELRAEVQRRDVSIVSLELKVKRLEEEREKS 123
               + +NG  A  +  VP +D+LR++RV ELR EVQR DVSI+SL+L+VKRLEEE+ K 
Sbjct: 95  DVPPSRQNGGAAAISDHVPWLDELRKLRVAELRREVQRSDVSILSLQLEVKRLEEEKTKE 154

Query: 124 ----------------MKPE-------ADLESDRKAMPEIEAAVDGD------GDS---- 150
                           ++PE        D      + PE   A + D      GD     
Sbjct: 155 KDGKDDKKPDLAVSGELRPENDKTGGEVDEAGPANSEPEERTANNTDKTLPTMGDESDRE 214

Query: 151 NRSFNESNSTTQKAETTNKKQNDDAEGEEEKEQKMKPEP----DVENDPVQNRTESGPDR 206
           N+S NESNST  + E T         G+ + +    P P     +E DPV          
Sbjct: 215 NQSVNESNSTGSRFEKT---------GDGDAKAGTGPAPVQTGSIEPDPVL--------- 256

Query: 207 EDRDWSSNGKLNENGNGTGNVKEETDEDNDKTASEGKVESVKNKTSAVGGLSESNELWDE 266
             R     G+ + NG+     K  T E +   + E KVE   N          S+EL D 
Sbjct: 257 --RKGKPVGEESNNGSYDALAKVPTCE-SVPPSEERKVEEDDN----------SSELHDS 303

Query: 267 SKREG----KQSSDVQSSASLSRNKRRRSGEEPYDE--EVSPATKKVLA-VKSEPLVRFL 319
               G    ++SS+VQSSASL+R ++ R  +E        SPA    LA VKSEPLV  L
Sbjct: 304 VAHSGEGGTRESSEVQSSASLTRKRKTRRRKEVSGGGGASSPAENDELATVKSEPLVGVL 363

Query: 320 GMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLL 379
            +I+ H  SS FERRL SQ+++RYK LV+Q +DL TIQ RL +G YS+C   FFRDLLLL
Sbjct: 364 ELIKGHEHSSLFERRLESQDTDRYKDLVKQPMDLETIQLRLQKGHYSSCTSAFFRDLLLL 423

Query: 380 FNNFVIFFRKSSQEYAAAQELRTLVIKEMTDMLRKQQPIAVTKPKPKPKPEHHRQQPQPP 439
           F N  +FF   + E    ++L  L   EM     K    A + P P+      +    PP
Sbjct: 424 FTNATVFFSHDTLESQVGRQLHRLATTEM-----KNHGQAQSDPIPR------KNDSLPP 472

Query: 440 PASLSKP------NRGS-TMVVCGKRSSIKAISKNA-YGKKG------DRKDR-EVEEKP 484
            ASL+KP      N+ S  ++VC KRSS+ A   +A +G+KG      D+K+R   + KP
Sbjct: 473 NASLAKPDSLISKNKASGPILVCRKRSSMLAKPSSATFGQKGDQPTFNDKKERPSSDAKP 532

Query: 485 KVNEKKVDSS---FVGIEDKGIKKKRSQERSVSLRRNSRSSSRSGDVKHQFGGNELSSHD 541
            +     D+        ++K +   RS  RS     N+ +   S +   + G +     +
Sbjct: 533 PMKPSSSDTDEEELPKAKEKPVTGARSLRRSYKNLNNNNNKKPSSNSTPKTGSSGNKPSE 592

Query: 542 TLEAKTENKKENAVKKKKLGAASFLKRMKQNSPSEV 577
           T++ + ++K E    KK+  AA FLKR+K+N+ +E 
Sbjct: 593 TVKPE-KSKAEGGPDKKRNAAADFLKRIKRNTSAEA 627

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356528554|ref|XP_003532866.1| PREDICTED: uncharacterized protein LOC100811021 [Glycine max]

 Score =  252 bits (644), Expect = 4e-64,   Method: Compositional matrix adjust.
 Identities = 228/647 (35%), Positives = 322/647 (49%), Gaps = 132/647 (20%)

Query: 14  QQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEIRRRFTVK- 72
           + WGT EELLLACAVNRHG   WD++AMEVQ+R++ L + T + C  KF+++ RRF V+ 
Sbjct: 31  EAWGTWEELLLACAVNRHGFTDWDAVAMEVQSRTTRLLA-TARHCEQKFHDLSRRFAVQC 89

Query: 73  ---------NGAES--TSLVPLVDQLRQIRVQELRAEVQRRDVSIVSLELKVKRLEEER- 120
                    NGA +  +  VP +D+LR++RV ELR +VQR DVSI+SL+L+VKRLEEE+ 
Sbjct: 90  NDDVPPPRQNGAAAAISDHVPWLDELRKLRVAELRRDVQRSDVSILSLQLEVKRLEEEKA 149

Query: 121 -EKSMK--------------PE-------------ADLESDRKAMPEIEAAVDGDGDS-- 150
            EK +K              PE             A+ E + +     +  +   GD   
Sbjct: 150 QEKDLKDDEKPDLAVSGELRPENDKTGGEVEEAGPANSEPEERTANNTDKTLPTTGDESD 209

Query: 151 --NRSFNESNSTTQKAETTNKKQNDDAEGEEEKEQKMKPEPDVENDPVQNRTESGPDRED 208
             N+S NESNST  + E T         G+ + +    P      DPV   ++  PD  +
Sbjct: 210 RENQSVNESNSTGSRFEKT---------GDGDAKTGTGP------DPVHTGSQE-PDPVE 253

Query: 209 RDWSSNGKLNENGNGTGNVKEETDEDNDKTASEG-KVESVKNKTSAVGGLSESNELWDES 267
           R     G+ + NG+     K  T E      SEG KVE             +S+EL D  
Sbjct: 254 RKGKPVGEESNNGSYDALAKVPTCES--VPPSEGRKVEED----------DDSSELHDSV 301

Query: 268 KREG----KQSSDVQSSASLSRNKRRRSGEE---PYDEEVSPATKKVLAVKSEPLVRFLG 320
              G    ++SS+VQSSASL R ++ R  +E     D        +   VKSEPLV  L 
Sbjct: 302 AHSGEGGTRESSEVQSSASLMRKRKTRRRKEVSGATDASCPAENDEAATVKSEPLVGVLE 361

Query: 321 MIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLF 380
           +I+ H  SS FERRL SQ+++RYK LV+Q +DL TIQ RL +G YS+C   FFRDLLLLF
Sbjct: 362 LIKGHEHSSLFERRLDSQDTDRYKDLVKQPMDLETIQLRLQKGHYSSCTSAFFRDLLLLF 421

Query: 381 NNFVIFFRKSSQEYAAAQELRTLVIKEMTDMLRKQQPIAVTKPKPKPKPEHHRQQPQPPP 440
            N  +FF   S E  A ++L  L   EM     K    A + P P+      +    PP 
Sbjct: 422 TNATVFFSHDSLESQAGRQLHRLATAEM-----KNHGQAQSDPIPR------KNDSLPPN 470

Query: 441 ASLSKP------NRGS-TMVVCGKRSSIKAISKNA-YGKKGDR----------------- 475
           A L+KP      N+ S  ++VC KRSS+ +   +A +G+KGD+                 
Sbjct: 471 APLAKPDSLLSKNKASGPILVCRKRSSMSSKPSSATFGQKGDQPVFNDKKERPSSDAKPP 530

Query: 476 -----KDREVEEKPKVNEKKVDSSFVGIEDKGIKKKRSQERSVSLRRNSRSSSRSGDVKH 530
                 D + EE PK  EK V  +      + +++      S S   N++  S     K 
Sbjct: 531 MKPSSSDTDEEELPKAKEKPVTGA------RSLRRSNKNLNSNSSNNNNKKPSSISTPKA 584

Query: 531 QFGGNELSSHDTLEAKTENKKENAVKKKKLGAASFLKRMKQNSPSEV 577
              GN+ S  +T++ + ++K E    KK+  AA FLKR+K+N+ +E 
Sbjct: 585 GSSGNKPS--ETVKPE-KSKAEGGADKKRSAAADFLKRIKRNTSAEA 628

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224053014|ref|XP_002297664.1| hypothetical protein POPTRDRAFT_547688 [Populus trichocarpa] gi|222844922|gb|EEE82469.1| hypothetical protein POPTRDRAFT_547688 [Populus trichocarpa]

 Score =  251 bits (642), Expect = 7e-64,   Method: Compositional matrix adjust.
 Identities = 137/238 (57%), Positives = 177/238 (74%), Gaps = 18/238 (7%)

Query: 346 LVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQEYAAAQELRTLVI 405
           +VRQH+DL+ IQSRL++G+YSNCFQKFF+DLL+L NN ++FFRK+S E  AA ELR +V+
Sbjct: 1   MVRQHMDLQMIQSRLNKGVYSNCFQKFFKDLLILLNNAIVFFRKNSPENLAANELRAVVL 60

Query: 406 KEMTDMLRKQQPIAVTKPKPKPKPEHHRQQPQPPPASLSKPNRGS--TMVVCGKRSSIKA 463
           KE+ + LRK +P  V     KP  E H        A+LS+PN+ S  T+V C K SS+KA
Sbjct: 61  KEVKEKLRKPKPQPVD---AKPATEQH-------SAALSRPNKSSSSTLVACCKHSSMKA 110

Query: 464 ISKNAYGKKGDRKDREVEEKPKVNEKKVDSSFVGIEDKGIKKKRSQERSVSLRRNSRSSS 523
           IS  A GKKGD+   E+E K KVNEKKV+ S   IE+KG+KKK ++ERSVS RRNS++S+
Sbjct: 111 ISGGA-GKKGDK---EMEGKHKVNEKKVEVSIDRIEEKGLKKKTTKERSVSGRRNSKTSN 166

Query: 524 RSGDVKHQFGGNELSSHDTLEAKTENKKENAVKKKKLGAASFLKRMKQNSPSEVMEDD 581
           ++G++KHQ+GGNELSSHD LE K + K+     +KK GAASFLKRMKQNSPS V E+D
Sbjct: 167 KNGEIKHQYGGNELSSHDALEIKVDRKEHTG--RKKQGAASFLKRMKQNSPSRVTEED 222

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

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	684
TAIR|locus:2060040	631	AT2G42150 [Arabidopsis thalian	0.154	0.167	0.445	4.7e-36
TAIR|locus:2101477	641	AT3G60110 [Arabidopsis thalian	0.296	0.316	0.324	2.5e-19
TAIR|locus:2050574	646	AT2G44430 [Arabidopsis thalian	0.356	0.377	0.287	3.1e-18
TAIR|locus:2095878	632	AT3G57980 [Arabidopsis thalian	0.321	0.348	0.305	1.7e-17
TAIR|locus:1006230673	475	BRD4 "AT1G61215" [Arabidopsis	0.216	0.311	0.284	1.7e-16

TAIR|locus:2060040 AT2G42150 [Arabidopsis thaliana (taxid:3702)]

 Score = 240 (89.5 bits), Expect = 4.7e-36, Sum P(3) = 4.7e-36
 Identities = 49/110 (44%), Positives = 69/110 (62%)

Query:     1 MARERHGTTSXXXXXWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRD 60
             MA+  +  T      W T EELLLACAV+RHGT SW+S++ E+Q  S  L SLT  +CR 
Sbjct:     1 MAKPENDVTLTEKQTWSTWEELLLACAVHRHGTESWNSVSAEIQKLSPNLCSLTASACRH 60

Query:    61 KFNEIRRRFT----VKNGAESTSLVPLVDQLRQIRVQELRAEVQRRDVSI 106
             K+ +++ RFT    V       S  P +++LR++RV ELR EV++ D+SI
Sbjct:    61 KYFDLKSRFTQELPVPESVAEISTAPWLEELRKLRVDELRREVEQYDLSI 110

GO:0003677 "DNA binding" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM;ISS

TAIR|locus:2101477 AT3G60110 [Arabidopsis thaliana (taxid:3702)]

 Score = 245 (91.3 bits), Expect = 2.5e-19, Sum P(2) = 2.5e-19
 Identities = 75/231 (32%), Positives = 112/231 (48%)

Query:    16 WGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEIRRRF--TVKN 73
             WGT EEL+L CAV RH    WDS+A EVQ RS +   ++  +CR K+ +++RRF  +V  
Sbjct:    52 WGTWEELVLTCAVKRHAFSDWDSVAKEVQARSRSSLIVSAVNCRLKYQDLKRRFQDSVDV 111

Query:    74 GAESTSL----------VPLVDQLRQIRVQELRAEVQRRD---VSIXXXXXXXXXXXXXX 120
             G E+T            +  ++QLR + + ELR EVQR D   +S+              
Sbjct:   112 GDENTEAAANEEDEVGEISWLEQLRSLHMAELRREVQRCDDSILSLQLKVKKLEEEKDGD 171

Query:   121 XXXMKPEADLESDR-KAMPEIEAAVDGDGDSNRSFNESNSTTQKAETTNKKQNDDAXXXX 179
                 KP  DL++D  K +       + D D NRS NESNST     + +K  + D     
Sbjct:   172 DGDNKP--DLKNDETKPVRVNRETTESDRDDNRSMNESNSTA----SVDKIADHDRLDGD 225

Query:   180 XXXXXXXXXPDVENDPVQNRTESGPDREDRDWSSNGKLNENG----NGTGN 226
                       + + DPV N+ E+ P+ E+R  S   +++ +G    +GT N
Sbjct:   226 KMVKANENSRNPDPDPV-NKAET-PEEEERTVSKRSEMSNSGELDESGTSN 274

GO:0003677 "DNA binding" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM

TAIR|locus:2050574 AT2G44430 [Arabidopsis thaliana (taxid:3702)]

 Score = 250 (93.1 bits), Expect = 3.1e-18, P = 3.1e-18
 Identities = 78/271 (28%), Positives = 117/271 (43%)

Query:     4 ERHGTTSXXXXXWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSL--TPQSCRDK 61
             +   T       WGT EELLLACAV RHG   WDS+A EV++RSS LS L  +   CR K
Sbjct:    38 DNSNTKKSQTQAWGTWEELLLACAVKRHGFGDWDSVATEVRSRSS-LSHLLASANDCRHK 96

Query:    62 FNEIRRRF----------TVKNGAESTSLV----PLVDQLRQIRVQELRAEVQRRDVSIX 107
             + +++RRF          TV+   E    V    P ++QLR +RV ELR EV+R D SI 
Sbjct:    97 YRDLKRRFHEQEKTDVTATVEEEEEEEERVGNNIPWLEQLRNLRVAELRREVERYDCSIL 156

Query:   108 XXXXXXXXXXXXXXXXMKPEADLESDRKAMPEIEAAVDGDGDSNRSFNESNSTTQKAETT 167
                              + + DLE++RK     E   + DG  +    ++ S  ++++  
Sbjct:   157 SLQLKVKKLEEEREVG-EEKPDLENERK-----EERSENDGSESEHREKAVSAAEESDRE 210

Query:   168 NKKQNDDAXXXXXXXXXXXXXPD---VENDPVQNRTESGPDREDRDWSSNGKLNENGNGT 224
             N+  N+                +      D   N     PD  ++D ++  +  E     
Sbjct:   211 NRSMNESNSTATAGEEERVCGDEPSQTREDDSGNDKNPDPDPVNKD-ATAAEEEEGSVSR 269

Query:   225 GNVKEETDEDNDKTASEGKVESVKNKTSAVG 255
             G+    +DE  +   SE K +  + K    G
Sbjct:   270 GSEASHSDELGESGTSESKWKRKRRKQGGAG 300

GO:0003677 "DNA binding" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM

TAIR|locus:2095878 AT3G57980 [Arabidopsis thaliana (taxid:3702)]

 Score = 237 (88.5 bits), Expect = 1.7e-17, Sum P(2) = 1.7e-17
 Identities = 76/249 (30%), Positives = 116/249 (46%)

Query:    19 LEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEIRRRFT---VKNGA 75
             +EELLLACAV+RHGT SWDS+A EV  ++S   +LT   CR K+N+++RRF+   V  G+
Sbjct:     1 MEELLLACAVHRHGTDSWDSVASEVHKQNSTFRTLTAIDCRHKYNDLKRRFSRNLVSPGS 60

Query:    76 --EST-----SLVPLVDQLRQIRVQELRAEVQRRDVSIXXXXXXXXXXXXXXXXXMKPE- 127
               E T     S VP +++LR++RV ELR EV+R D+SI                 +K E 
Sbjct:    61 ADEETLAAEISSVPWLEELRKLRVDELRREVERYDLSISSLQLKVKTLEDEREKSLKTEN 120

Query:   128 ADLESDRKAMPEIEAAVDGDGDSNRSFNESNSTTQKAETTNKKQNDDAXXXXXXXXXXXX 187
             +DL  DR A  +      G+       N     T+   + +   N               
Sbjct:   121 SDL--DRIAETKENHTESGN-------NSGVPVTELKNSPDPNDNSPGTGSENTNRAVKI 171

Query:   188 XPDVENDPVQNRTESGPDREDRDWSSNGKLNENGNGT-GNVKEETDEDNDKTASEGKVES 246
                V+ +P  NR   G D +++         ++G G+  +V +E+D    K       E 
Sbjct:   172 AEPVDEEP--NRI-GGEDNDEKP-----AREDSGRGSCESVAKESDRAEPKREGNDSPEL 223

Query:   247 VKNKTSAVG 255
             V++   + G
Sbjct:   224 VESMDESKG 232

GO:0003677 "DNA binding" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM

TAIR|locus:1006230673 BRD4 "AT1G61215" [Arabidopsis thaliana (taxid:3702)]

 Score = 145 (56.1 bits), Expect = 1.7e-16, Sum P(3) = 1.7e-16
 Identities = 47/165 (28%), Positives = 78/165 (47%)

Query:     9 TSXXXXXWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSL-TPQSCRDKFNEIRR 67
             T+     WGT EELLL  AV RHGT  W  +A E+  RS +L  + TP+ C+ K+ ++R+
Sbjct:     7 TTTMESDWGTWEELLLGGAVLRHGTGDWTVVADEL--RSHSLPEIFTPEICKAKYKDLRK 64

Query:    68 RFTVKNGAESTSLVPLVDQLRQIRVQELRAEVQRRDVSIXXXXXXXXXXXXXXXXXMKPE 127
             R+    G ++       ++L++ RV EL+A + + + SI                    +
Sbjct:    65 RYV---GCKAW-----FEELKKKRVAELKAALLKSEDSIGSLESKLQSLKSESNDECH-Q 115

Query:   128 ADLESDRKAMPEIEAAVDGDG-----DSNRSFNESNSTTQKAETT 167
              + +S R    E     +G G     D+++  +   S TQ+  TT
Sbjct:   116 NNYDSSRTLSLEPSPKSEGGGECTSKDTSKDLSSVGSFTQQELTT 160

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

---

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: BRD913 bromodomain protein (385 aa) (Populus trichocarpa)

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	684
smart00297	107	smart00297, BROMO, bromo domain	3e-17
cd04369	99	cd04369, Bromodomain, Bromodomain	2e-15
pfam00439	84	pfam00439, Bromodomain, Bromodomain	1e-12
cd05507	104	cd05507, Bromo_brd8_like, Bromodomain, brd8_like s	6e-09
cd05492	109	cd05492, Bromo_ZMYND11, Bromodomain; ZMYND11_like	7e-08
cd05502	109	cd05502, Bromo_tif1_like, Bromodomain; tif1_like s	1e-06
cd05522	104	cd05522, Bromo_Rsc1_2_II, Bromodomain, repeat II i	6e-06
smart00717	49	smart00717, SANT, SANT SWI3, ADA2, N-CoR and TFIII	6e-06
cd00167	45	cd00167, SANT, 'SWI3, ADA2, N-CoR and TFIIIB' DNA-	2e-05
pfam00249	47	pfam00249, Myb_DNA-binding, Myb-like DNA-binding d	2e-05
cd05509	101	cd05509, Bromo_gcn5_like, Bromodomain; Gcn5_like s	3e-05
cd05495	108	cd05495, Bromo_cbp_like, Bromodomain, cbp_like sub	1e-04
cd05498	102	cd05498, Bromo_Brdt_II_like, Bromodomain, Brdt_lik	2e-04
cd05524	113	cd05524, Bromo_polybromo_I, Bromodomain, polybromo	2e-04
PRK12678	672	PRK12678, PRK12678, transcription termination fact	9e-04
cd05505	97	cd05505, Bromo_WSTF_like, Bromodomain; Williams sy	0.001
cd05497	107	cd05497, Bromo_Brdt_I_like, Bromodomain, Brdt_like	0.001
PTZ00108	1388	PTZ00108, PTZ00108, DNA topoisomerase 2-like prote	0.001
cd05499	102	cd05499, Bromo_BDF1_2_II, Bromodomain	0.002
cd05503	97	cd05503, Bromo_BAZ2A_B_like, Bromodomain, BAZ2A/BA	0.002
cd05504	115	cd05504, Bromo_Acf1_like, Bromodomain; Acf1_like o	0.003
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	0.004
COG5076	371	COG5076, COG5076, Transcription factor involved in	0.004

>gnl|CDD|197636 smart00297, BROMO, bromo domain

 Score = 77.3 bits (191), Expect = 3e-17
 Identities = 28/100 (28%), Positives = 55/100 (55%), Gaps = 1/100 (1%)

Query: 312 SEPLVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQK 371
            E L   L  + SH LS  F + +  +E+  Y  ++++ +DL+TI+ +L+ G YS+  ++
Sbjct: 9   QELLKAVLDKLDSHPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSS-VEE 67

Query: 372 FFRDLLLLFNNFVIFFRKSSQEYAAAQELRTLVIKEMTDM 411
           F  D  L+F+N   +    S+ Y  A++L     K++ ++
Sbjct: 68  FVADFNLMFSNARTYNGPDSEVYKDAKKLEKFFEKKLREL 107

Length = 107

>gnl|CDD|99922 cd04369, Bromodomain, Bromodomain

 Score = 71.6 bits (176), Expect = 2e-15
 Identities = 25/96 (26%), Positives = 47/96 (48%), Gaps = 3/96 (3%)

Query: 315 LVRFLGMIRSH--RLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKF 372
           L   L  ++     LS  F   +  +E+  Y ++++  +DL TI+ +L  G Y +  ++F
Sbjct: 5   LRSLLDALKKLKRDLSEPFLEPVDPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKS-LEEF 63

Query: 373 FRDLLLLFNNFVIFFRKSSQEYAAAQELRTLVIKEM 408
             D+ L+F+N   +    S  Y  A++L  L  K +
Sbjct: 64  EADVRLIFSNAKTYNGPGSPIYKDAKKLEKLFEKLL 99

Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine. Length = 99

>gnl|CDD|215921 pfam00439, Bromodomain, Bromodomain

 Score = 63.6 bits (155), Expect = 1e-12
 Identities = 21/85 (24%), Positives = 45/85 (52%), Gaps = 1/85 (1%)

Query: 315 LVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFR 374
            +  L  +  H L+  F   +  +E   Y +++++ +DL TI+ +L  G Y +   +F +
Sbjct: 1   CLEILEDLMEHPLAEPFLEPVDPEEYPDYYEVIKEPMDLSTIRQKLKSGKYKS-LAEFLK 59

Query: 375 DLLLLFNNFVIFFRKSSQEYAAAQE 399
           D+ L+F+N + +  + S  Y  A++
Sbjct: 60  DVELIFSNAITYNGEDSDIYKDAKK 84

Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Length = 84

>gnl|CDD|99939 cd05507, Bromo_brd8_like, Bromodomain, brd8_like subgroup

 Score = 53.5 bits (129), Expect = 6e-09
 Identities = 23/88 (26%), Positives = 45/88 (51%), Gaps = 1/88 (1%)

Query: 321 MIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLF 380
            + SHR +S F + +    +  Y  +V + +DL TI+  ++ G       +F RD+LL+F
Sbjct: 14  TLASHRYASVFLKPVTEDIAPGYHSVVYRPMDLSTIKKNIENGTI-RSTAEFQRDVLLMF 72

Query: 381 NNFVIFFRKSSQEYAAAQELRTLVIKEM 408
            N +++       Y  A E++  V+ ++
Sbjct: 73  QNAIMYNSSDHDVYLMAVEMQREVMSQI 100

In mammals, brd8 (bromodomain containing 8) interacts with the thyroid hormone receptor in a ligand-dependent fashion and enhances thyroid hormone-dependent activation from thyroid response elements. Brd8 is thought to be a nuclear receptor coactivator. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Length = 104

>gnl|CDD|99924 cd05492, Bromo_ZMYND11, Bromodomain; ZMYND11_like sub-family

 Score = 50.8 bits (122), Expect = 7e-08
 Identities = 20/71 (28%), Positives = 41/71 (57%), Gaps = 1/71 (1%)

Query: 330 HFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRK 389
              +R ++ +  + ++L+  H+D+  IQ +++   Y++  ++F  D LLL +N  IF   
Sbjct: 26  VLNKRGKATKLPKRRRLIHTHLDVADIQEKINSEKYTS-LEEFKADALLLLHNTAIFHGA 84

Query: 390 SSQEYAAAQEL 400
            S++Y AA+ L
Sbjct: 85  DSEQYDAARWL 95

ZMYND11 or BS69 is a ubiquitously expressed nuclear protein that has been shown to associate with chromatin. It interacts with chromatin remodeling factors and might play a role in chromatin remodeling and gene expression. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Length = 109

>gnl|CDD|99934 cd05502, Bromo_tif1_like, Bromodomain; tif1_like subfamily

 Score = 47.3 bits (113), Expect = 1e-06
 Identities = 23/80 (28%), Positives = 37/80 (46%), Gaps = 5/80 (6%)

Query: 324 SHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGL---YSNCFQKFFRDLLLLF 380
            H LS  F     S     Y K+++  +DL  I+ +L       YS+  ++F  D+ L+F
Sbjct: 18  CHELSLPF-HEPVSPSVPNYYKIIKTPMDLSLIRKKLQPKSPQHYSSP-EEFVADVRLMF 75

Query: 381 NNFVIFFRKSSQEYAAAQEL 400
            N   F  + S+   A +EL
Sbjct: 76  KNCYKFNEEDSEVAQAGKEL 95

Tif1 (transcription intermediary factor 1) is a member of the tripartite motif (TRIM) protein family, which is characterized by a particular domain architecture. It functions by recruiting coactivators and/or corepressors to modulate transcription. Vertebrate Tif1-gamma, also labeled E3 ubiquitin-protein ligase TRIM33, plays a role in the control of hematopoiesis. Its homologue in Xenopus laevis, Ectodermin, has been shown to function in germ-layer specification and control of cell growth during embryogenesis. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Length = 109

>gnl|CDD|99953 cd05522, Bromo_Rsc1_2_II, Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi

 Score = 44.9 bits (107), Expect = 6e-06
 Identities = 25/89 (28%), Positives = 38/89 (42%), Gaps = 5/89 (5%)

Query: 323 RSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNN 382
               L+ HFE+         Y + +   I L  I+ ++ R  Y + F +F  DL L+F N
Sbjct: 20  NGRLLTLHFEKLPDKAREPEYYQEISNPISLDDIKKKVKRRKYKS-FDQFLNDLNLMFEN 78

Query: 383 FVIFFRKSSQEYAAAQELRTLVIKEMTDM 411
             ++    SQEY  A  L     KE   +
Sbjct: 79  AKLYNENDSQEYKDAVLLE----KEARLL 103

Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Length = 104

>gnl|CDD|197842 smart00717, SANT, SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains

 Score = 43.4 bits (103), Expect = 6e-06
 Identities = 14/53 (26%), Positives = 26/53 (49%), Gaps = 7/53 (13%)

Query: 16 WGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEIRRR 68
          W   E+ LL   V ++G  +W+ IA E+  R       T + CR+++  + + 
Sbjct: 4  WTEEEDELLIELVKKYGKNNWEKIAKELPGR-------TAEQCRERWRNLLKP 49

Length = 49

>gnl|CDD|238096 cd00167, SANT, 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains

 Score = 41.8 bits (99), Expect = 2e-05
 Identities = 16/50 (32%), Positives = 27/50 (54%), Gaps = 7/50 (14%)

Query: 16 WGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEI 65
          W   E+ LL  AV ++G  +W+ IA E+  R       TP+ CR+++  +
Sbjct: 2  WTEEEDELLLEAVKKYGKNNWEKIAKELPGR-------TPKQCRERWRNL 44

Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA. Length = 45

>gnl|CDD|215818 pfam00249, Myb_DNA-binding, Myb-like DNA-binding domain

 Score = 41.7 bits (99), Expect = 2e-05
 Identities = 15/48 (31%), Positives = 23/48 (47%), Gaps = 7/48 (14%)

Query: 16 WGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFN 63
          W   E+ LL  AV +HG  +W  IA  +  R       T   C++++N
Sbjct: 4  WTPEEDELLIEAVKKHGNGNWSKIAKHLPGR-------TDNQCKNRWN 44

This family contains the DNA binding domains from Myb proteins, as well as the SANT domain family. Length = 47

>gnl|CDD|99941 cd05509, Bromo_gcn5_like, Bromodomain; Gcn5_like subfamily

 Score = 42.9 bits (102), Expect = 3e-05
 Identities = 22/97 (22%), Positives = 53/97 (54%), Gaps = 1/97 (1%)

Query: 315 LVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFR 374
           L + L  +++H+ +  F   +  +E+  Y  ++++ +DL T++ +L+ G Y    ++F  
Sbjct: 6   LKKVLDSLKNHKSAWPFLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYV-TLEEFVA 64

Query: 375 DLLLLFNNFVIFFRKSSQEYAAAQELRTLVIKEMTDM 411
           DL L+F+N  ++    ++ Y  A +L     K++ ++
Sbjct: 65  DLKLIFDNCRLYNGPDTEYYKCANKLEKFFWKKLKEL 101

Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Length = 101

>gnl|CDD|99927 cd05495, Bromo_cbp_like, Bromodomain, cbp_like subfamily

 Score = 41.7 bits (98), Expect = 1e-04
 Identities = 21/66 (31%), Positives = 40/66 (60%), Gaps = 1/66 (1%)

Query: 343 YKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQEYAAAQELRT 402
           Y  +V+  +DL TI+ +LD G Y + +Q +  D+ L+F+N  ++ RK+S+ Y    +L  
Sbjct: 39  YFDIVKNPMDLSTIRRKLDTGQYQDPWQ-YVDDVWLMFDNAWLYNRKTSRVYKYCTKLAE 97

Query: 403 LVIKEM 408
           +  +E+
Sbjct: 98  VFEQEI 103

Cbp (CREB binding protein or CREBBP) is an acetyltransferase acting on histone, which gives a specific tag for transcriptional activation and also acetylates non-histone proteins. CREBBP binds specifically to phosphorylated CREB protein and augments the activity of phosphorylated CREB to activate transcription of cAMP-responsive genes. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Length = 108

>gnl|CDD|99930 cd05498, Bromo_Brdt_II_like, Bromodomain, Brdt_like subfamily, repeat II

 Score = 40.7 bits (96), Expect = 2e-04
 Identities = 17/59 (28%), Positives = 34/59 (57%), Gaps = 1/59 (1%)

Query: 343 YKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQEYAAAQELR 401
           Y  +++  +DL TI+ +LD   Y++  Q+F  D+ L+F+N   +       +A A++L+
Sbjct: 38  YHDIIKHPMDLSTIKKKLDNREYADA-QEFAADVRLMFSNCYKYNPPDHPVHAMARKLQ 95

Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Length = 102

>gnl|CDD|99954 cd05524, Bromo_polybromo_I, Bromodomain, polybromo repeat I

 Score = 40.8 bits (96), Expect = 2e-04
 Identities = 22/68 (32%), Positives = 31/68 (45%), Gaps = 2/68 (2%)

Query: 336 RSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQEYA 395
           R  E E Y ++V   IDL  IQ +L    Y +       D  LL NN   +++  S E+ 
Sbjct: 35  RRNEPE-YYEVVSNPIDLLKIQQKLKTEEYDD-VDDLTADFELLINNAKAYYKPDSPEHK 92

Query: 396 AAQELRTL 403
            A +L  L
Sbjct: 93  DACKLWEL 100

Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine. Length = 113

>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 42.2 bits (100), Expect = 9e-04
 Identities = 21/106 (19%), Positives = 37/106 (34%), Gaps = 9/106 (8%)

Query: 579 EDDDEEEDENDNDNDDDDSGDDSKDSKVEEEKKRRSVTRRDVNRVTRSSRGRGVREENRR 638
                + ++   + +  + G   +  +  +++ RR    +   R  R  R  G R   RR
Sbjct: 172 RRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRR 231

Query: 639 RGVGRPPKRSASGAMSPPEKTSGKRGRDNGESEVGGGGRSRKRTRR 684
           R   R  +                RG  +G+   G GGR  +R R 
Sbjct: 232 RRDRRDARGDD---------NREDRGDRDGDDGEGRGGRRGRRFRD 268

Length = 672

>gnl|CDD|99937 cd05505, Bromo_WSTF_like, Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like)

 Score = 38.7 bits (90), Expect = 0.001
 Identities = 24/73 (32%), Positives = 42/73 (57%), Gaps = 1/73 (1%)

Query: 319 LGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLL 378
           L  I  +R S  F   + + E+E YKK++   +DL+T+Q++   G YS+  Q+F  D+ L
Sbjct: 9   LSKILKYRFSWPFREPVTADEAEDYKKVITNPMDLQTMQTKCSCGSYSS-VQEFLDDMKL 67

Query: 379 LFNNFVIFFRKSS 391
           +F+N   ++   S
Sbjct: 68  VFSNAEKYYENGS 80

The Williams-Beuren syndrome deletion transcript 9 is a putative transcriptional regulator. WSTF was found to play a role in vitamin D-mediated transcription as part of two chromatin remodeling complexes, WINAC and WICH. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Length = 97

>gnl|CDD|99929 cd05497, Bromo_Brdt_I_like, Bromodomain, Brdt_like subfamily, repeat I

 Score = 38.6 bits (90), Expect = 0.001
 Identities = 18/69 (26%), Positives = 32/69 (46%), Gaps = 1/69 (1%)

Query: 343 YKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQEYAAAQELRT 402
           Y K+++  +DL TI+ RL    Y     +  +D   +F N  I+ +        AQ L  
Sbjct: 40  YHKIIKTPMDLGTIKKRL-ENNYYWSASECIQDFNTMFTNCYIYNKPGDDVVLMAQTLEK 98

Query: 403 LVIKEMTDM 411
           L ++++  M
Sbjct: 99  LFLQKLAQM 107

Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Length = 107

>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional

 Score = 42.0 bits (99), Expect = 0.001
 Identities = 36/154 (23%), Positives = 60/154 (38%), Gaps = 18/154 (11%)

Query: 457  KRSSIKAISKNAYGKKGDRKDREVEEKPKVNEKKVDSSFVGIEDKGIKKKRSQERSVSLR 516
            K     +   +    +    D   E KPK   K+V +  V        K+   E +   +
Sbjct: 1244 KSKKNNSSKSSEDNDEFSSDDLSKEGKPKNAPKRVSA--VQYSPPPPSKRPDGESNGGSK 1301

Query: 517  RNSRSSSRSGDVKHQFGGNELSSHDTLEAKTENKKENAVKKK-----KLGAAS----FLK 567
             +S +  +              S   L+ K +++K+ A KKK     K  +AS     L+
Sbjct: 1302 PSSPTKKKVKKRL-------EGSLAALKKKKKSEKKTARKKKSKTRVKQASASQSSRLLR 1354

Query: 568  RMKQNSPSEVMEDDDEEEDENDNDNDDDDSGDDS 601
            R ++       EDDD+ E ++  D DD+D  DD 
Sbjct: 1355 RPRKKKSDSSSEDDDDSEVDDSEDEDDEDDEDDD 1388

Length = 1388

>gnl|CDD|99931 cd05499, Bromo_BDF1_2_II, Bromodomain

 Score = 38.0 bits (89), Expect = 0.002
 Identities = 17/66 (25%), Positives = 33/66 (50%), Gaps = 1/66 (1%)

Query: 343 YKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQEYAAAQELRT 402
           Y  ++++ +DL TI  +L  G Y +  ++F RD+ L+F N   F  + +  Y    +L  
Sbjct: 38  YFSIIKKPMDLGTISKKLQNGQYQSA-KEFERDVRLIFKNCYTFNPEGTDVYMMGHQLEE 96

Query: 403 LVIKEM 408
           +   + 
Sbjct: 97  VFNDKW 102

BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Length = 102

>gnl|CDD|99935 cd05503, Bromo_BAZ2A_B_like, Bromodomain, BAZ2A/BAZ2B_like subfamily

 Score = 37.7 bits (88), Expect = 0.002
 Identities = 13/40 (32%), Positives = 27/40 (67%), Gaps = 1/40 (2%)

Query: 343 YKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNN 382
           Y+K++++ +D  TI+ +L+ G Y    ++F  D+ L+F+N
Sbjct: 33  YRKIIKKPMDFSTIREKLESGQYKTL-EEFAEDVRLVFDN 71

Bromo adjacent to zinc finger 2A (BAZ2A) and 2B (BAZ2B) were identified as a novel human bromodomain gene by cDNA library screening. BAZ2A is also known as Tip5 (Transcription termination factor I-interacting protein 5) and hWALp3. The proteins may play roles in transcriptional regulation. Human Tip5 is part of a complex termed NoRC (nucleolar remodeling complex), which induces nucleosome sliding and may play a role in the regulation of the rDNA locus. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Length = 97

>gnl|CDD|99936 cd05504, Bromo_Acf1_like, Bromodomain; Acf1_like or BAZ1A_like subfamily

 Score = 37.8 bits (88), Expect = 0.003
 Identities = 24/90 (26%), Positives = 45/90 (50%), Gaps = 1/90 (1%)

Query: 322 IRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFN 381
           I  H+ S  F R +   E   Y  ++++ +DL TI+ +L+ G Y    ++F  D+ L+F+
Sbjct: 24  IVKHKDSWPFLRPVSKIEVPDYYDIIKKPMDLGTIKEKLNMGEY-KLAEEFLSDIQLVFS 82

Query: 382 NFVIFFRKSSQEYAAAQELRTLVIKEMTDM 411
           N  ++  + +  Y A   L+   IK    +
Sbjct: 83  NCFLYNPEHTSVYKAGTRLQRFFIKRCRKL 112

Bromo adjacent to zinc finger 1A (BAZ1A) was identified as a novel human bromodomain gene by cDNA library screening. The Drosophila homologue, Acf1, is part of the CHRAC (chromatin accessibility complex) and regulates ISWI-induced nucleosome remodeling. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Length = 115

>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score = 40.0 bits (94), Expect = 0.004
 Identities = 28/157 (17%), Positives = 66/157 (42%), Gaps = 7/157 (4%)

Query: 457 KRSSIKAISKN-AYGKKGDRKDREVEEKPKVNEKKVDSSFVGIEDKGIKKKRSQERSVSL 515
           K+   K  +K+ + G     + +E  E  K   +++D   + +         + E  +  
Sbjct: 17  KKKLKKLAAKSKSKGFITKEEIKEALESKKKTPEQIDQVLIFLSGMVKDTDDATESDIPK 76

Query: 516 RRNSRSSSRSGDVKHQFGGNELSSHDTLEAKTENKKENAVKKKKLGAASFLKRMKQNSPS 575
           ++   ++  +          +    D L++  + +K+NA+ K           +   +  
Sbjct: 77  KKTKTAAKAAAAKA----PAKKKLKDELDSSKKAEKKNALDKDDDLNYVKDIDVLNQADD 132

Query: 576 E-VMEDDDEEEDENDNDNDDDDSGD-DSKDSKVEEEK 610
           +   +DDD+ +D++ +D+DDD+  D D  D  V++E 
Sbjct: 133 DDDDDDDDDLDDDDIDDDDDDEDDDEDDDDDDVDDED 169

Length = 509

>gnl|CDD|227408 COG5076, COG5076, Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription]

 Score = 39.8 bits (93), Expect = 0.004
 Identities = 43/173 (24%), Positives = 74/173 (42%), Gaps = 13/173 (7%)

Query: 265 DESKREGKQSSDVQSSASLSRNKRRRSGEEPYDEEVSPATKKVLAVKSEPLVRFLGMIRS 324
           +    E    S + +    S  KR+    E   +E+  A  K +A   + L    G    
Sbjct: 110 ESVTPESGLGSLLMAHLKTSVKKRKTPKIE---DELLYADNKAIAKFKKQLFLRDG---- 162

Query: 325 HRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFV 384
             LSS F      +E   Y ++++  +DL TIQ +L  G Y + F++F  DL L+F+N  
Sbjct: 163 RFLSSIFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKS-FEEFVSDLNLMFDNCK 221

Query: 385 IFFRKSSQEYAAAQELRTLVIKEMTDMLRKQQPIAVTKPKPKPKPEHHRQQPQ 437
           ++    S  Y  A+EL    +K +     ++ P  + +   KP  E   ++  
Sbjct: 222 LYNGPDSSVYVDAKELEKYFLKLI-----EEIPEEMLELSIKPGREEREERES 269

Length = 371

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	684
cd05507	104	Bromo_brd8_like Bromodomain, brd8_like subgroup. I	99.93
cd05497	107	Bromo_Brdt_I_like Bromodomain, Brdt_like subfamily	99.92
cd05495	108	Bromo_cbp_like Bromodomain, cbp_like subfamily. Cb	99.92
cd05505	97	Bromo_WSTF_like Bromodomain; Williams syndrome tra	99.92
cd05496	119	Bromo_WDR9_II Bromodomain; WDR9 repeat II_like sub	99.92
cd05504	115	Bromo_Acf1_like Bromodomain; Acf1_like or BAZ1A_li	99.91
cd05508	99	Bromo_RACK7 Bromodomain, RACK7_like subfamily. RAC	99.91
cd05503	97	Bromo_BAZ2A_B_like Bromodomain, BAZ2A/BAZ2B_like s	99.91
KOG1474	640	consensus Transcription initiation factor TFIID, s	99.91
cd05509	101	Bromo_gcn5_like Bromodomain; Gcn5_like subfamily.	99.91
cd05502	109	Bromo_tif1_like Bromodomain; tif1_like subfamily.	99.91
cd05510	112	Bromo_SPT7_like Bromodomain; SPT7_like subfamily.	99.9
cd05528	112	Bromo_AAA Bromodomain; sub-family co-occurring wit	99.9
cd05506	99	Bromo_plant1 Bromodomain, uncharacterized subfamil	99.9
cd05511	112	Bromo_TFIID Bromodomain, TFIID-like subfamily. Hum	99.9
cd05513	98	Bromo_brd7_like Bromodomain, brd7_like subgroup. T	99.9
cd05512	98	Bromo_brd1_like Bromodomain; brd1_like subfamily.	99.9
cd05516	107	Bromo_SNF2L2 Bromodomain, SNF2L2-like subfamily, s	99.89
cd05499	102	Bromo_BDF1_2_II Bromodomain. BDF1/BDF2 like subfam	99.89
cd05520	103	Bromo_polybromo_III Bromodomain, polybromo repeat	99.89
cd05500	103	Bromo_BDF1_2_I Bromodomain. BDF1/BDF2 like subfami	99.89
cd05498	102	Bromo_Brdt_II_like Bromodomain, Brdt_like subfamil	99.89
cd05524	113	Bromo_polybromo_I Bromodomain, polybromo repeat I.	99.88
cd05515	105	Bromo_polybromo_V Bromodomain, polybromo repeat V.	99.88
cd05519	103	Bromo_SNF2 Bromodomain, SNF2-like subfamily, speci	99.87
cd05501	102	Bromo_SP100C_like Bromodomain, SP100C_like subfami	99.87
smart00297	107	BROMO bromo domain.	99.87
cd05529	128	Bromo_WDR9_I_like Bromodomain; WDR9 repeat I_like	99.87
cd05518	103	Bromo_polybromo_IV Bromodomain, polybromo repeat I	99.86
cd05525	106	Bromo_ASH1 Bromodomain; ASH1_like sub-family. ASH1	99.86
cd05517	103	Bromo_polybromo_II Bromodomain, polybromo repeat I	99.85
cd04369	99	Bromodomain Bromodomain. Bromodomains are found in	99.84
cd05522	104	Bromo_Rsc1_2_II Bromodomain, repeat II in Rsc1/2_l	99.84
PF00439	84	Bromodomain: Bromodomain; InterPro: IPR001487 Brom	99.84
cd05521	106	Bromo_Rsc1_2_I Bromodomain, repeat I in Rsc1/2_lik	99.82
cd05492	109	Bromo_ZMYND11 Bromodomain; ZMYND11_like sub-family	99.81
cd05526	110	Bromo_polybromo_VI Bromodomain, polybromo repeat V	99.69
KOG1245	1404	consensus Chromatin remodeling complex WSTF-ISWI,	99.66
COG5076	371	Transcription factor involved in chromatin remodel	99.66
KOG1472	720	consensus Histone acetyltransferase SAGA/ADA, cata	99.49
cd05494	114	Bromodomain_1 Bromodomain; uncharacterized subfami	99.1
KOG0955	1051	consensus PHD finger protein BR140/LIN-49 [General	99.06
KOG0008	1563	consensus Transcription initiation factor TFIID, s	98.97
cd05491	119	Bromo_TBP7_like Bromodomain; TBP7_like subfamily,	98.83
KOG0008	1563	consensus Transcription initiation factor TFIID, s	98.77
KOG1827	629	consensus Chromatin remodeling complex RSC, subuni	98.76
KOG0386	1157	consensus Chromatin remodeling complex SWI/SNF, co	98.74
KOG1474	640	consensus Transcription initiation factor TFIID, s	98.54
KOG1472	720	consensus Histone acetyltransferase SAGA/ADA, cata	98.45
KOG1828	418	consensus IRF-2-binding protein CELTIX-1, contains	98.43
KOG1828	418	consensus IRF-2-binding protein CELTIX-1, contains	98.13
PF00249	48	Myb_DNA-binding: Myb-like DNA-binding domain; Inte	97.74
smart00717	49	SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-bindi	97.42
COG5076	371	Transcription factor involved in chromatin remodel	97.37
cd00167	45	SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding do	96.89
cd05493	131	Bromo_ALL-1 Bromodomain, ALL-1 like proteins. ALL-	96.18
PF13921	60	Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB:	95.8
TIGR02894	161	DNA_bind_RsfA transcription factor, RsfA family. I	93.67
PF13837	90	Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain;	91.71
KOG0049	939	consensus Transcription factor, Myb superfamily [T	90.05
KOG0644	1113	consensus Uncharacterized conserved protein, conta	89.23
COG5259	531	RSC8 RSC chromatin remodeling complex subunit RSC8	87.9
PLN03212	249	Transcription repressor MYB5; Provisional	87.34
KOG0732	1080	consensus AAA+-type ATPase containing the bromodom	85.9
KOG0457	438	consensus Histone acetyltransferase complex SAGA/A	85.65
PLN03091	459	hypothetical protein; Provisional	84.91
PRK13923	170	putative spore coat protein regulator protein YlbO	84.0
COG5114	432	Histone acetyltransferase complex SAGA/ADA, subuni	83.14
PLN03212	249	Transcription repressor MYB5; Provisional	80.26

>cd05507 Bromo_brd8_like Bromodomain, brd8_like subgroup

Probab=99.93  E-value=6.8e-26  Score=203.53  Aligned_cols=100  Identities=23%  Similarity=0.435  Sum_probs=96.3

Q ss_pred             CchHHHHHHHHHHhCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCCC
Q 005668          311 KSEPLVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKS  390 (684)
Q Consensus       311 kskpLl~ILe~L~~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~pd  390 (684)
                      ..+.|+.||+.|..|+.+++|..||+...+|+||++|++||||+||++||++|.|.++. +|.+||.|||+||++||+++
T Consensus         4 ~~~~~~~il~~l~~~~~a~~F~~pV~~~~~p~Y~~iIk~PmDL~tI~~kl~~~~Y~s~~-ef~~D~~li~~Na~~yN~~~   82 (104)
T cd05507           4 WKKAILLVYRTLASHRYASVFLKPVTEDIAPGYHSVVYRPMDLSTIKKNIENGTIRSTA-EFQRDVLLMFQNAIMYNSSD   82 (104)
T ss_pred             HHHHHHHHHHHHHcCCCCHhhcCCCCccccCCHHHHhCCCcCHHHHHHHHhcCCCCCHH-HHHHHHHHHHHHHHHHCCCC
Confidence            34789999999999999999999999999999999999999999999999999999998 99999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHHHHHHH
Q 005668          391 SQEYAAAQELRTLVIKEMTDM  411 (684)
Q Consensus       391 S~vykaA~eLr~lf~k~msk~  411 (684)
                      +.+|.+|..|+..|.+.|.+.
T Consensus        83 s~v~~~A~~l~~~~~~~~~~~  103 (104)
T cd05507          83 HDVYLMAVEMQREVMSQIQQL  103 (104)
T ss_pred             CHHHHHHHHHHHHHHHHhhcc
Confidence            999999999999999998764

In mammals, brd8 (bromodomain containing 8) interacts with the thyroid hormone receptor in a ligand-dependent fashion and enhances thyroid hormone-dependent activation from thyroid response elements. Brd8 is thought to be a nuclear receptor coactivator. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

>cd05497 Bromo_Brdt_I_like Bromodomain, Brdt_like subfamily, repeat I

Probab=99.92  E-value=1.5e-25  Score=202.62  Aligned_cols=95  Identities=22%  Similarity=0.416  Sum_probs=91.1

Q ss_pred             HHHHHHHHHhCcCCcccccccCcc--ccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCCCCH
Q 005668          315 LVRFLGMIRSHRLSSHFERRLRSQ--ESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQ  392 (684)
Q Consensus       315 Ll~ILe~L~~hk~a~pF~~PVD~q--e~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~pdS~  392 (684)
                      |..||+.|..|+.+++|..|||..  ++|+||+||++||||+||+.||+++.|.++. +|..||.|||.||+.||+++|.
T Consensus        10 ~~~il~~l~~~~~s~~F~~PVd~~~~~~pdY~~iIk~PmDL~tI~~kL~~~~Y~s~~-ef~~D~~li~~Na~~yN~~~s~   88 (107)
T cd05497          10 LKVVLKALWKHKFAWPFQQPVDAVKLNLPDYHKIIKTPMDLGTIKKRLENNYYWSAS-ECIQDFNTMFTNCYIYNKPGDD   88 (107)
T ss_pred             HHHHHHHHHhCCcCccccCCCCcccccCCcHHHHHcCcccHHHHHHHHcCCCCCCHH-HHHHHHHHHHHHHHHHCCCCCH
Confidence            457789999999999999999986  7999999999999999999999999999998 9999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHH
Q 005668          393 EYAAAQELRTLVIKEMTD  410 (684)
Q Consensus       393 vykaA~eLr~lf~k~msk  410 (684)
                      +|.+|..|+.+|.++|.+
T Consensus        89 i~~~A~~l~~~f~~~l~~  106 (107)
T cd05497          89 VVLMAQTLEKLFLQKLAQ  106 (107)
T ss_pred             HHHHHHHHHHHHHHHHHc
Confidence            999999999999999876

Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

>cd05495 Bromo_cbp_like Bromodomain, cbp_like subfamily

Probab=99.92  E-value=3.5e-25  Score=200.45  Aligned_cols=100  Identities=24%  Similarity=0.450  Sum_probs=96.0

Q ss_pred             chHHHHHHHHHHhC-cCCcccccccCcc--ccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCC
Q 005668          312 SEPLVRFLGMIRSH-RLSSHFERRLRSQ--ESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFR  388 (684)
Q Consensus       312 skpLl~ILe~L~~h-k~a~pF~~PVD~q--e~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~  388 (684)
                      .+.|+.||+.|+.+ +.+++|..||++.  ++|+||++|++||||+||++||++|.|.++. +|..||.|||+||+.||+
T Consensus         5 ~~~~~~il~~l~~~~~~s~~F~~PV~~~~~~~pdY~~iIk~PmDL~tI~~kL~~~~Y~s~~-ef~~D~~li~~Na~~yN~   83 (108)
T cd05495           5 RQALMPTLEKLYKQDPESLPFRQPVDPKLLGIPDYFDIVKNPMDLSTIRRKLDTGQYQDPW-QYVDDVWLMFDNAWLYNR   83 (108)
T ss_pred             HHHHHHHHHHHHHcCcccchhcCCCCccccCCCcHHHHhCCCCCHHHHHHHHhcCCCCCHH-HHHHHHHHHHHHHHHHCC
Confidence            36799999999999 9999999999986  7999999999999999999999999999998 999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHh
Q 005668          389 KSSQEYAAAQELRTLVIKEMTDML  412 (684)
Q Consensus       389 pdS~vykaA~eLr~lf~k~msk~l  412 (684)
                      ++|.+|.+|..|+.+|+++|..++
T Consensus        84 ~~s~i~~~a~~l~~~F~~~~~~~~  107 (108)
T cd05495          84 KTSRVYKYCTKLAEVFEQEIDPVM  107 (108)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHh
Confidence            999999999999999999998876

Cbp (CREB binding protein or CREBBP) is an acetyltransferase acting on histone, which gives a specific tag for transcriptional activation and also acetylates non-histone proteins. CREBBP binds specifically to phosphorylated CREB protein and augments the activity of phosphorylated CREB to activate transcription of cAMP-responsive genes. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

>cd05505 Bromo_WSTF_like Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like)

Probab=99.92  E-value=2.4e-25  Score=198.37  Aligned_cols=96  Identities=24%  Similarity=0.409  Sum_probs=92.4

Q ss_pred             chHHHHHHHHHHhCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCCCC
Q 005668          312 SEPLVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSS  391 (684)
Q Consensus       312 skpLl~ILe~L~~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~pdS  391 (684)
                      .+.|..||+.|+.|+.+++|..||+...+|+||++|++||||+||+.||+++.|.++. +|.+||.|||.||++||+++|
T Consensus         2 ~~~c~~il~~l~~~~~s~~F~~pv~~~~~pdY~~iIk~PmDL~tI~~kl~~~~Y~s~~-ef~~D~~li~~Na~~yN~~~s   80 (97)
T cd05505           2 LQKCEEILSKILKYRFSWPFREPVTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQ-EFLDDMKLVFSNAEKYYENGS   80 (97)
T ss_pred             HHHHHHHHHHHHhCCCcccccCCCChhhcccHHHHcCCcCCHHHHHHHHcCCCCCCHH-HHHHHHHHHHHHHHHHCCCCC
Confidence            3679999999999999999999999999999999999999999999999999999998 999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHH
Q 005668          392 QEYAAAQELRTLVIKEM  408 (684)
Q Consensus       392 ~vykaA~eLr~lf~k~m  408 (684)
                      .+|.+|..|+++|...+
T Consensus        81 ~i~~~a~~le~~f~~~~   97 (97)
T cd05505          81 YVLSCMRKTEQCCVNLL   97 (97)
T ss_pred             HHHHHHHHHHHHHHHhC
Confidence            99999999999998753

The Williams-Beuren syndrome deletion transcript 9 is a putative transcriptional regulator. WSTF was found to play a role in vitamin D-mediated transcription as part of two chromatin remodeling complexes, WINAC and WICH. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

>cd05496 Bromo_WDR9_II Bromodomain; WDR9 repeat II_like subfamily

Probab=99.92  E-value=4.8e-25  Score=203.31  Aligned_cols=104  Identities=17%  Similarity=0.314  Sum_probs=99.3

Q ss_pred             CchHHHHHHHHHHhCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCC-
Q 005668          311 KSEPLVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRK-  389 (684)
Q Consensus       311 kskpLl~ILe~L~~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~p-  389 (684)
                      .-+.|..||+.|+.|+.+++|..||+...+|+||+||++||||+||+.||.+|.|.++. +|..||.|||.||+.||++ 
T Consensus         6 w~~~c~~il~~l~~~~~s~~F~~PVd~~~~pdY~~iIk~PmDL~tIk~kL~~~~Y~~~~-ef~~D~~lif~Na~~yN~~~   84 (119)
T cd05496           6 WKKQCKELVNLMWDCEDSEPFRQPVDLLKYPDYRDIIDTPMDLGTVKETLFGGNYDDPM-EFAKDVRLIFSNSKSYTPNK   84 (119)
T ss_pred             HHHHHHHHHHHHHhCCccccccCCCChhhcCcHHHHhCCcccHHHHHHHHhCCCCCCHH-HHHHHHHHHHHHHHHHCCCC
Confidence            44789999999999999999999999999999999999999999999999999999998 9999999999999999985 


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHhhhc
Q 005668          390 SSQEYAAAQELRTLVIKEMTDMLRKQ  415 (684)
Q Consensus       390 dS~vykaA~eLr~lf~k~msk~l~k~  415 (684)
                      ++.+|.+|..|+.+|.++|.+++...
T Consensus        85 ~s~i~~~a~~L~~~F~~~~~~l~~~~  110 (119)
T cd05496          85 RSRIYSMTLRLSALFEEHIKKIISDW  110 (119)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            89999999999999999999998753

WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

>cd05504 Bromo_Acf1_like Bromodomain; Acf1_like or BAZ1A_like subfamily

Probab=99.91  E-value=1.2e-24  Score=199.03  Aligned_cols=101  Identities=26%  Similarity=0.433  Sum_probs=97.3

Q ss_pred             cCchHHHHHHHHHHhCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCC
Q 005668          310 VKSEPLVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRK  389 (684)
Q Consensus       310 ~kskpLl~ILe~L~~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~p  389 (684)
                      .....|..||+.|..++.+++|..||+...+|+||++|++||||+||++||+.|.|.++. +|..||.|||+||++||++
T Consensus        12 ~~~~~c~~il~~l~~~~~s~~F~~pvd~~~~pdY~~vI~~PmDL~tI~~kL~~~~Y~s~~-~f~~Dv~LI~~Na~~yN~~   90 (115)
T cd05504          12 LNLSALEQLLVEIVKHKDSWPFLRPVSKIEVPDYYDIIKKPMDLGTIKEKLNMGEYKLAE-EFLSDIQLVFSNCFLYNPE   90 (115)
T ss_pred             HHHHHHHHHHHHHHhCCCchhhcCCCCccccccHHHHhcCcccHHHHHHHHccCCCCCHH-HHHHHHHHHHHHHHHHCCC
Confidence            445789999999999999999999999999999999999999999999999999999998 9999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHH
Q 005668          390 SSQEYAAAQELRTLVIKEMTDM  411 (684)
Q Consensus       390 dS~vykaA~eLr~lf~k~msk~  411 (684)
                      +|.+|.+|..|+.+|.++|.++
T Consensus        91 ~s~i~~~A~~l~~~f~~~~~~~  112 (115)
T cd05504          91 HTSVYKAGTRLQRFFIKRCRKL  112 (115)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHh
Confidence            9999999999999999999875

Bromo adjacent to zinc finger 1A (BAZ1A) was identified as a novel human bromodomain gene by cDNA library screening. The Drosophila homologue, Acf1, is part of the CHRAC (chromatin accessibility complex) and regulates ISWI-induced nucleosome remodeling. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

>cd05508 Bromo_RACK7 Bromodomain, RACK7_like subfamily

Probab=99.91  E-value=1.5e-24  Score=194.13  Aligned_cols=94  Identities=18%  Similarity=0.265  Sum_probs=89.2

Q ss_pred             hHHHHHHHHHHhCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCCCCH
Q 005668          313 EPLVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQ  392 (684)
Q Consensus       313 kpLl~ILe~L~~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~pdS~  392 (684)
                      ..|..+|+.|+ |+.+++|..||+...+|+||.+|++||||+||++||++|.|.++. +|.+||.|||.||++||+++|.
T Consensus         6 ~~L~~~~~~~~-~~~s~~F~~PV~~~~~pdY~~iIk~PmDL~tI~~kl~~~~Y~s~~-ef~~Dv~LI~~Na~~YN~~~s~   83 (99)
T cd05508           6 KLLKFALERMK-QPGAEPFLKPVDLEQFPDYAQYVFKPMDLSTLEKNVRKKAYGSTD-AFLADAKWILHNAIIYNGGDHK   83 (99)
T ss_pred             HHHHHHHHHHh-CcCcchhcCCCChhhCCCHHHHcCCCCCHHHHHHHHhcCCCCCHH-HHHHHHHHHHHHHHHHCCCCCH
Confidence            45777888888 999999999999999999999999999999999999999999998 9999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHH
Q 005668          393 EYAAAQELRTLVIKEM  408 (684)
Q Consensus       393 vykaA~eLr~lf~k~m  408 (684)
                      +|.+|..|..+|...|
T Consensus        84 i~~~A~~l~~~~~~e~   99 (99)
T cd05508          84 LTQAAKAIVKICEQEM   99 (99)
T ss_pred             HHHHHHHHHHHHHhhC
Confidence            9999999999987754

RACK7 (also called human protein kinase C-binding protein) was identified as a potential tumor suppressor genes, it shares domain architecture with BS69/ZMYND11; both have been implicated in the regulation of cellular proliferation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

>cd05503 Bromo_BAZ2A_B_like Bromodomain, BAZ2A/BAZ2B_like subfamily

Probab=99.91  E-value=2.3e-24  Score=191.11  Aligned_cols=95  Identities=22%  Similarity=0.367  Sum_probs=92.0

Q ss_pred             hHHHHHHHHHHhCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCCCCH
Q 005668          313 EPLVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQ  392 (684)
Q Consensus       313 kpLl~ILe~L~~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~pdS~  392 (684)
                      ..|..||+.|..|+.+++|..||+...+|+||++|++||||+||+.||++|.|.++. +|..||.|||.||+.||++++.
T Consensus         3 ~~c~~il~~l~~~~~~~~F~~pv~~~~~p~Y~~iIk~PmdL~tI~~kl~~~~Y~s~~-ef~~D~~li~~Na~~yN~~~s~   81 (97)
T cd05503           3 ALCETILDEMEAHEDAWPFLEPVNTKLVPGYRKIIKKPMDFSTIREKLESGQYKTLE-EFAEDVRLVFDNCETFNEDDSE   81 (97)
T ss_pred             HHHHHHHHHHHcCCCchhhcCCCCccccCCHHHHhCCCCCHHHHHHHHccCCCCCHH-HHHHHHHHHHHHHHHHCCCCCH
Confidence            568999999999999999999999999999999999999999999999999999998 9999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHH
Q 005668          393 EYAAAQELRTLVIKEM  408 (684)
Q Consensus       393 vykaA~eLr~lf~k~m  408 (684)
                      +|.+|..|+++|.++|
T Consensus        82 i~~~a~~l~~~f~~~~   97 (97)
T cd05503          82 VGRAGHNMRKFFEKRW   97 (97)
T ss_pred             HHHHHHHHHHHHHHhC
Confidence            9999999999998764

Bromo adjacent to zinc finger 2A (BAZ2A) and 2B (BAZ2B) were identified as a novel human bromodomain gene by cDNA library screening. BAZ2A is also known as Tip5 (Transcription termination factor I-interacting protein 5) and hWALp3. The proteins may play roles in transcriptional regulation. Human Tip5 is part of a complex termed NoRC (nucleolar remodeling complex), which induces nucleosome sliding and may play a role in the regulation of the rDNA locus. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

>KOG1474 consensus Transcription initiation factor TFIID, subunit BDF1 and related bromodomain proteins [Transcription]

Probab=99.91  E-value=1.4e-24  Score=246.44  Aligned_cols=106  Identities=21%  Similarity=0.353  Sum_probs=100.7

Q ss_pred             cccCchHHHHHHHHHHhCcCCcccccccCcc--ccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhh
Q 005668          308 LAVKSEPLVRFLGMIRSHRLSSHFERRLRSQ--ESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVI  385 (684)
Q Consensus       308 ~~~kskpLl~ILe~L~~hk~a~pF~~PVD~q--e~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~  385 (684)
                      .......|..||..|+.|+++|||..|||..  .+||||+||++||||+||+.||+++.|.++. +|++||+|||+|||+
T Consensus       220 ~~~~lk~C~~iLk~l~~~k~awpF~~PVD~v~LgLpDY~~IIK~PMDLgTIK~kL~~~~Y~~~~-eF~~DVRL~F~Ncm~  298 (640)
T KOG1474|consen  220 TVELLKQCLSILKRLMKHKHAWPFNEPVDVVKLGLPDYHDIIKHPMDLGTIKKKLEKGEYKSAE-EFAADVRLTFDNCMT  298 (640)
T ss_pred             cHHHHHHHHHHHHHHHhccCCCCcCCCcCHHhcCCcchhhhcCCCccHHHHHhhhcccccCCHH-HHHHHHHHHHHHHHh
Confidence            3445588999999999999999999999986  8999999999999999999999999999998 999999999999999


Q ss_pred             hCCCCCHHHHHHHHHHHHHHHHHHHHhhh
Q 005668          386 FFRKSSQEYAAAQELRTLVIKEMTDMLRK  414 (684)
Q Consensus       386 FN~pdS~vykaA~eLr~lf~k~msk~l~k  414 (684)
                      ||+++++||.||..|+.+|+.+|..+...
T Consensus       299 YNp~g~dV~~Ma~~L~~~Fe~rw~~~~~~  327 (640)
T KOG1474|consen  299 YNPEGSDVYAMAKKLQEVFEERWASMPLE  327 (640)
T ss_pred             cCCCCCHHHHHHHHHHHHHHHHHhhcccc
Confidence            99999999999999999999999998765

>cd05509 Bromo_gcn5_like Bromodomain; Gcn5_like subfamily

Probab=99.91  E-value=4e-24  Score=189.85  Aligned_cols=97  Identities=23%  Similarity=0.485  Sum_probs=94.3

Q ss_pred             hHHHHHHHHHHhCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCCCCH
Q 005668          313 EPLVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQ  392 (684)
Q Consensus       313 kpLl~ILe~L~~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~pdS~  392 (684)
                      ..|..||+.|..|+.+++|..||+...+|+||++|++||||.||+.||..+.|.++. +|..||.|||.||+.||+++|.
T Consensus         4 ~~~~~il~~l~~~~~a~~F~~pv~~~~~p~Y~~~I~~PmdL~tI~~kl~~~~Y~s~~-~f~~Dv~li~~Na~~yN~~~s~   82 (101)
T cd05509           4 TQLKKVLDSLKNHKSAWPFLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLE-EFVADLKLIFDNCRLYNGPDTE   82 (101)
T ss_pred             HHHHHHHHHHHhCCCchhhcCCCChhhcCCHHHHhcCCCCHHHHHHHHhcCCCCCHH-HHHHHHHHHHHHHHHHCCCCCH
Confidence            468999999999999999999999999999999999999999999999999999998 9999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHH
Q 005668          393 EYAAAQELRTLVIKEMTD  410 (684)
Q Consensus       393 vykaA~eLr~lf~k~msk  410 (684)
                      +|.+|..|+.+|++.|.+
T Consensus        83 ~~~~a~~l~~~f~~~~~~  100 (101)
T cd05509          83 YYKCANKLEKFFWKKLKE  100 (101)
T ss_pred             HHHHHHHHHHHHHHHHhh
Confidence            999999999999999876

Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

>cd05502 Bromo_tif1_like Bromodomain; tif1_like subfamily

Probab=99.91  E-value=5.4e-24  Score=192.20  Aligned_cols=100  Identities=25%  Similarity=0.385  Sum_probs=96.6

Q ss_pred             chHHHHHHHHHHhCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhC---CCccCcHHHHHHHHHHHHHHHhhhCC
Q 005668          312 SEPLVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDR---GLYSNCFQKFFRDLLLLFNNFVIFFR  388 (684)
Q Consensus       312 skpLl~ILe~L~~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~---g~YsSi~~EF~rDL~LMF~NA~~FN~  388 (684)
                      .+.|..||..|..|+.+++|..||+. .+|+||++|++||||+||++||+.   +.|.++. +|.+||.|||+||+.||+
T Consensus         6 ~~~c~~il~~l~~~~~s~~F~~pv~~-~~p~Y~~iI~~PmdL~tI~~kL~~~~~~~Y~s~~-~f~~D~~li~~Na~~yN~   83 (109)
T cd05502           6 QRKCERLLLELYCHELSLPFHEPVSP-SVPNYYKIIKTPMDLSLIRKKLQPKSPQHYSSPE-EFVADVRLMFKNCYKFNE   83 (109)
T ss_pred             HHHHHHHHHHHHhCCCChhhcCCCCC-CCCCHHHHCCCCccHHHHHHHHhcCCCCCCCCHH-HHHHHHHHHHHHHHHHCC
Confidence            46799999999999999999999998 899999999999999999999998   6999998 999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHhh
Q 005668          389 KSSQEYAAAQELRTLVIKEMTDMLR  413 (684)
Q Consensus       389 pdS~vykaA~eLr~lf~k~msk~l~  413 (684)
                      ++|.++.+|..|+.+|.+.|.+++|
T Consensus        84 ~~s~i~~~a~~l~~~f~~~~~~~~p  108 (109)
T cd05502          84 EDSEVAQAGKELELFFEEQLKEILP  108 (109)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHCc
Confidence            9999999999999999999999986

Tif1 (transcription intermediary factor 1) is a member of the tripartite motif (TRIM) protein family, which is characterized by a particular domain architecture. It functions by recruiting coactivators and/or corepressors to modulate transcription. Vertebrate Tif1-gamma, also labeled E3 ubiquitin-protein ligase TRIM33, plays a role in the control of hematopoiesis. Its homologue in Xenopus laevis, Ectodermin, has been shown to function in germ-layer specification and control of cell growth during embryogenesis. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

>cd05510 Bromo_SPT7_like Bromodomain; SPT7_like subfamily

Probab=99.90  E-value=8.6e-24  Score=192.98  Aligned_cols=99  Identities=19%  Similarity=0.312  Sum_probs=93.7

Q ss_pred             hHHHHHHHHHHhC-cCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCCCC
Q 005668          313 EPLVRFLGMIRSH-RLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSS  391 (684)
Q Consensus       313 kpLl~ILe~L~~h-k~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~pdS  391 (684)
                      +.|..||+.|+.| +++++|..||+...+|+||++|++||||+||++||.++.|.++. +|.+||.|||+||+.||++++
T Consensus        10 ~~~~~il~~l~~~~~~s~~F~~pv~~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~-ef~~D~~Li~~N~~~yN~~~s   88 (112)
T cd05510          10 ESLDKVLNELKTYTEHSTPFLTKVSKREAPDYYDIIKKPMDLGTMLKKLKNLQYKSKA-EFVDDLNLIWKNCLLYNSDPS   88 (112)
T ss_pred             HHHHHHHHHHHhcCccccchhcCCChhhcCCHHHHhcCccCHHHHHHHHhCCCCCCHH-HHHHHHHHHHHHHHHHCCCCC
Confidence            5799999999999 99999999999999999999999999999999999999999998 999999999999999999865


Q ss_pred             -HHHHHHHHHHHHHHHHHHHHh
Q 005668          392 -QEYAAAQELRTLVIKEMTDML  412 (684)
Q Consensus       392 -~vykaA~eLr~lf~k~msk~l  412 (684)
                       .+|.+|..|+++|.+.|..+.
T Consensus        89 ~~~~~~A~~l~~~~~~~~~~~~  110 (112)
T cd05510          89 HPLRRHANFMKKKAEHLLKLIP  110 (112)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCC
Confidence             788999999999999988753

SPT7 is a yeast protein that functions as a component of the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA, and SLIK. SAGA is involved in the RNA polymerase II-dependent transcriptional regulation of about 10% of all yeast genes. The SPT7 bromodomain has been shown to weakly interact with acetylated histone H3, but not H4. The human representative of this subfamily is cat eye syndrome critical region protein 2 (CECR2). Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

>cd05528 Bromo_AAA Bromodomain; sub-family co-occurring with AAA domains

Probab=99.90  E-value=9e-24  Score=192.75  Aligned_cols=100  Identities=24%  Similarity=0.305  Sum_probs=95.6

Q ss_pred             hHHHHHHHHHHhCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCCC--
Q 005668          313 EPLVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKS--  390 (684)
Q Consensus       313 kpLl~ILe~L~~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~pd--  390 (684)
                      .-|..||+.|+.|+.+++|..||+...+|+||++|++||||.||+.||+++.|.++. +|..||.|||+||+.||+++  
T Consensus         6 ~~L~~il~~l~~~~~~~~F~~pv~~~~~pdY~~vI~~PmdL~tI~~kl~~~~Y~s~~-ef~~Dv~li~~Na~~yN~~~s~   84 (112)
T cd05528           6 LFLRDVLKRLASDKRFNAFTKPVDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAK-DFLKDIDLIVTNALEYNPDRDP   84 (112)
T ss_pred             HHHHHHHHHHHhCCCchhhcCCCCccccCcHHHHHcCCCCHHHHHHHHcCCCcCCHH-HHHHHHHHHHHHHHHHCCCCCc
Confidence            358899999999999999999999999999999999999999999999999999998 99999999999999999995  


Q ss_pred             --CHHHHHHHHHHHHHHHHHHHHhh
Q 005668          391 --SQEYAAAQELRTLVIKEMTDMLR  413 (684)
Q Consensus       391 --S~vykaA~eLr~lf~k~msk~l~  413 (684)
                        +.++.+|..|+++|.+++.+.+|
T Consensus        85 ~~s~i~~~A~~L~~~~~~~~~~~~~  109 (112)
T cd05528          85 ADKLIRSRACELRDEVHAMIEAELD  109 (112)
T ss_pred             cccHHHHHHHHHHHHHHHHHHhcCC
Confidence              69999999999999999998874

Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. The structure(2DKW) in this alignment is an uncharacterized protein predicted from analysis of cDNA clones from human fetal liver

>cd05506 Bromo_plant1 Bromodomain, uncharacterized subfamily specific to plants

Probab=99.90  E-value=1.3e-23  Score=185.78  Aligned_cols=95  Identities=20%  Similarity=0.297  Sum_probs=91.0

Q ss_pred             hHHHHHHHHHHhCcCCcccccccCcc--ccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCCC
Q 005668          313 EPLVRFLGMIRSHRLSSHFERRLRSQ--ESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKS  390 (684)
Q Consensus       313 kpLl~ILe~L~~hk~a~pF~~PVD~q--e~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~pd  390 (684)
                      +.|..||+.|+.|+.+++|..||+..  .+|+||++|++||||+||+.||+++.|.++. +|..||.|||.||+.||+++
T Consensus         3 ~~c~~il~~l~~~~~~~~F~~pv~~~~~~~p~Y~~~I~~P~dl~tI~~kL~~~~Y~s~~-ef~~D~~li~~Na~~yn~~~   81 (99)
T cd05506           3 KQCGTLLRKLMKHKWGWVFNAPVDVVALGLPDYFDIIKKPMDLGTVKKKLEKGEYSSPE-EFAADVRLTFANAMRYNPPG   81 (99)
T ss_pred             HHHHHHHHHHHhCCCCccccCCCCccccCCCCHHHHHcCCCCHHHHHHHHhcCCCCCHH-HHHHHHHHHHHHHHHHCCCC
Confidence            46899999999999999999999976  7999999999999999999999999999998 99999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHHHH
Q 005668          391 SQEYAAAQELRTLVIKEM  408 (684)
Q Consensus       391 S~vykaA~eLr~lf~k~m  408 (684)
                      |.+|.+|..|+.+|++++
T Consensus        82 s~i~~~a~~l~~~fe~~w   99 (99)
T cd05506          82 NDVHTMAKELLKIFETRW   99 (99)
T ss_pred             CHHHHHHHHHHHHHHHhC
Confidence            999999999999998763

Might function as a global transcription factor. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

>cd05511 Bromo_TFIID Bromodomain, TFIID-like subfamily

Probab=99.90  E-value=2e-23  Score=190.14  Aligned_cols=100  Identities=20%  Similarity=0.316  Sum_probs=96.5

Q ss_pred             HHHHHHHHHHhCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCCCCHH
Q 005668          314 PLVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQE  393 (684)
Q Consensus       314 pLl~ILe~L~~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~pdS~v  393 (684)
                      -|..||+.|+.|+.+++|..||++..+|+||++|++||||+||++||.++.|.++. +|.+||.|||.||+.||+++|.+
T Consensus         4 ~l~~ii~~l~~~~~s~~F~~pv~~~~~p~Y~~~I~~PmdL~tI~~kl~~~~Y~s~~-ef~~Dv~li~~Na~~yN~~~s~i   82 (112)
T cd05511           4 ILDEIVNELKNLPDSWPFHTPVNKKKVPDYYKIIKRPMDLQTIRKKISKHKYQSRE-EFLEDIELIVDNSVLYNGPDSVY   82 (112)
T ss_pred             HHHHHHHHHHhCCCchhhcCCCChhhcccHHHHhcCCCCHHHHHHHHhcCCCCCHH-HHHHHHHHHHHHHHHHCCCCCHH
Confidence            47889999999999999999999999999999999999999999999999999998 99999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhhh
Q 005668          394 YAAAQELRTLVIKEMTDMLRK  414 (684)
Q Consensus       394 ykaA~eLr~lf~k~msk~l~k  414 (684)
                      |.+|..|+.+|...|..+..+
T Consensus        83 ~~~A~~l~~~~~~~~~~~~~~  103 (112)
T cd05511          83 TKKAKEMLELAEELLAEREEK  103 (112)
T ss_pred             HHHHHHHHHHHHHHHHHhHHH
Confidence            999999999999999988654

Human TAFII250 (or TAF250) is the largest subunit of TFIID, a large multi-domain complex, which initiates the assembly of the transcription machinery. TAFII250 contains two bromodomains that specifically bind to acetylated histone H4. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

>cd05513 Bromo_brd7_like Bromodomain, brd7_like subgroup

Probab=99.90  E-value=1.5e-23  Score=187.42  Aligned_cols=93  Identities=16%  Similarity=0.301  Sum_probs=88.1

Q ss_pred             hHHHHHHHHHHhCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCCCCH
Q 005668          313 EPLVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQ  392 (684)
Q Consensus       313 kpLl~ILe~L~~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~pdS~  392 (684)
                      +.|..||+.|..++.+++|..||+...+|+||++|++||||+||++||+++.|.++. +|..||.|||.||+.||+++|.
T Consensus         4 ~~l~~il~~l~~~~~~~~F~~PV~~~~~pdY~~vIk~PmDL~tI~~kl~~~~Y~s~~-~f~~D~~li~~Na~~yN~~~s~   82 (98)
T cd05513           4 KALEQLIRQLQRKDPHGFFAFPVTDFIAPGYSSIIKHPMDFSTMKEKIKNNDYQSIE-EFKDDFKLMCENAMKYNKPDTI   82 (98)
T ss_pred             HHHHHHHHHHHcCCccccccCcCCccccccHHHHHcCccCHHHHHHHHhCCCCCCHH-HHHHHHHHHHHHHHHHCCCCCH
Confidence            457889999999999999999999989999999999999999999999999999998 9999999999999999999999


Q ss_pred             HHHHHHHHHHHHHH
Q 005668          393 EYAAAQELRTLVIK  406 (684)
Q Consensus       393 vykaA~eLr~lf~k  406 (684)
                      +|.+|..|.+...+
T Consensus        83 ~~~~A~~L~~~~~~   96 (98)
T cd05513          83 YYKAAKKLLHSGMK   96 (98)
T ss_pred             HHHHHHHHHHhhhh
Confidence            99999999876543

The BRD7 gene encodes a nuclear protein that has been shown to inhibit cell growth and the progression of the cell cycle by regulating cell-cycle genes at the transcriptional level. BRD7 has been identified as a gene involved in nasopharyngeal carcinoma. The protein interacts with acetylated histone H3 via its bromodomain. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

>cd05512 Bromo_brd1_like Bromodomain; brd1_like subfamily

Probab=99.90  E-value=1.4e-23  Score=187.26  Aligned_cols=90  Identities=23%  Similarity=0.332  Sum_probs=87.0

Q ss_pred             hHHHHHHHHHHhCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCCCCH
Q 005668          313 EPLVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQ  392 (684)
Q Consensus       313 kpLl~ILe~L~~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~pdS~  392 (684)
                      ..|..+|+.|..|+.+++|..||+...+|+||++|++||||+||++||.++.|.++. +|..||.|||.||+.||+++|.
T Consensus         4 ~~l~~il~~l~~~~~~~~F~~pVd~~~~pdY~~iIk~PmDL~tI~~kl~~~~Y~s~~-ef~~D~~li~~Na~~yN~~~s~   82 (98)
T cd05512           4 VLLRKTLDQLQEKDTAEIFSEPVDLSEVPDYLDHIKQPMDFSTMRKKLESQRYRTLE-DFEADFNLIINNCLAYNAKDTI   82 (98)
T ss_pred             HHHHHHHHHHHhCCCchhhcCCCCccccCCHHHHhcCCcCHHHHHHHHhCCCCCCHH-HHHHHHHHHHHHHHHHCCCCCH
Confidence            468899999999999999999999999999999999999999999999999999998 9999999999999999999999


Q ss_pred             HHHHHHHHHHH
Q 005668          393 EYAAAQELRTL  403 (684)
Q Consensus       393 vykaA~eLr~l  403 (684)
                      +|.+|..|+..
T Consensus        83 ~~~~A~~l~~~   93 (98)
T cd05512          83 FYRAAVRLRDQ   93 (98)
T ss_pred             HHHHHHHHHHh
Confidence            99999999874

BRD1 is a mammalian gene which encodes for a nuclear protein assumed to be a transcriptional regulator. BRD1 has been implicated with brain development and susceptibility to schizophrenia and bipolar affective disorder. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

>cd05516 Bromo_SNF2L2 Bromodomain, SNF2L2-like subfamily, specific to animals

Probab=99.89  E-value=2e-23  Score=188.64  Aligned_cols=97  Identities=18%  Similarity=0.286  Sum_probs=92.8

Q ss_pred             hHHHHHHHHHHhCcC------CcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhh
Q 005668          313 EPLVRFLGMIRSHRL------SSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIF  386 (684)
Q Consensus       313 kpLl~ILe~L~~hk~------a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~F  386 (684)
                      +.|..||+.|..+..      +++|..||+...+|+||++|++||||+||+.||.+|.|.++. +|..||.|||.||+.|
T Consensus         4 ~~~~~il~~v~~~~d~~g~~~s~~F~~~p~~~~~pdYy~iI~~Pmdl~tI~~kl~~~~Y~s~~-ef~~D~~li~~Na~~y   82 (107)
T cd05516           4 KKMNKIVDVVIKYKDSDGRQLAEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLE-DLEKDVMLLCQNAQTF   82 (107)
T ss_pred             HHHHHHHHHHHhhhCcCCCEeeHHhhcCCCcccCCCHHHHcCCCCCHHHHHHHHccCCCCCHH-HHHHHHHHHHHHHHHH
Confidence            578899999988876      899999999999999999999999999999999999999998 9999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHH
Q 005668          387 FRKSSQEYAAAQELRTLVIKEMTD  410 (684)
Q Consensus       387 N~pdS~vykaA~eLr~lf~k~msk  410 (684)
                      |+++|.+|.+|..|+.+|...|++
T Consensus        83 N~~~s~i~~~a~~l~~~f~~~~~~  106 (107)
T cd05516          83 NLEGSLIYEDSIVLQSVFKSARQK  106 (107)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHhc
Confidence            999999999999999999999875

SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone receptors to boost transcriptional activation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

>cd05499 Bromo_BDF1_2_II Bromodomain

Probab=99.89  E-value=2.3e-23  Score=185.74  Aligned_cols=96  Identities=20%  Similarity=0.315  Sum_probs=90.6

Q ss_pred             chHHHHHHHHHHh---CcCCcccccccCcc--ccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhh
Q 005668          312 SEPLVRFLGMIRS---HRLSSHFERRLRSQ--ESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIF  386 (684)
Q Consensus       312 skpLl~ILe~L~~---hk~a~pF~~PVD~q--e~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~F  386 (684)
                      .+.|..||+.|..   ++.+++|..||++.  .+|+||++|++||||+||+.||+++.|.++. +|..||+|||.||+.|
T Consensus         2 ~~~c~~Il~~l~~~~~~~~s~~F~~pvd~~~~~~pdY~~~I~~P~dL~~I~~kl~~~~Y~s~~-ef~~D~~li~~N~~~y   80 (102)
T cd05499           2 LKFCEEVLKELMKPKHSAYNWPFLDPVDPVALNIPNYFSIIKKPMDLGTISKKLQNGQYQSAK-EFERDVRLIFKNCYTF   80 (102)
T ss_pred             hHHHHHHHHHHHcccCCcccchhcCCCCccccCCCCHHHHhcCCCCHHHHHHHHcCCCCCCHH-HHHHHHHHHHHHHHHH
Confidence            3578899999987   46799999999987  9999999999999999999999999999998 9999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHH
Q 005668          387 FRKSSQEYAAAQELRTLVIKEM  408 (684)
Q Consensus       387 N~pdS~vykaA~eLr~lf~k~m  408 (684)
                      |+++|.+|.+|..|+.+|+++|
T Consensus        81 n~~~s~~~~~a~~l~~~fe~~~  102 (102)
T cd05499          81 NPEGTDVYMMGHQLEEVFNDKW  102 (102)
T ss_pred             CCCCCHHHHHHHHHHHHHHHhC
Confidence            9999999999999999998864

BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

>cd05520 Bromo_polybromo_III Bromodomain, polybromo repeat III

Probab=99.89  E-value=2e-23  Score=187.71  Aligned_cols=95  Identities=26%  Similarity=0.410  Sum_probs=90.3

Q ss_pred             chHHHHHHHHHHhCc------CCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhh
Q 005668          312 SEPLVRFLGMIRSHR------LSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVI  385 (684)
Q Consensus       312 skpLl~ILe~L~~hk------~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~  385 (684)
                      ++||..||+.|+.+.      .+++|..||+...+|+||++|++||||+||+.||.++.|.++. +|..||.|||.||+.
T Consensus         2 ~~~~~~l~~~i~~~~~~~g~~~s~pF~~~p~~~~~PdYy~iI~~PmdL~tI~~kl~~~~Y~s~~-~f~~D~~lm~~Na~~   80 (103)
T cd05520           2 SNPLWQLYDTIRNARNNQGQLLAEPFLKLPSKRKYPDYYQEIKNPISLQQIRTKLKNGEYETLE-ELEADLNLMFENAKR   80 (103)
T ss_pred             CchHHHHHHHHHhhcCCCCCCccHhhhcCCCcccCCCHHHHcCCCcCHHHHHHHHccCCCCCHH-HHHHHHHHHHHHHHH
Confidence            689999999998664      6899999999999999999999999999999999999999998 999999999999999


Q ss_pred             hCCCCCHHHHHHHHHHHHHHHH
Q 005668          386 FFRKSSQEYAAAQELRTLVIKE  407 (684)
Q Consensus       386 FN~pdS~vykaA~eLr~lf~k~  407 (684)
                      ||+++|.+|.+|..|+.+|..+
T Consensus        81 yN~~~s~i~~~A~~L~~~f~~~  102 (103)
T cd05520          81 YNVPNSRIYKDAEKLQKLMQAK  102 (103)
T ss_pred             HCCCCCHHHHHHHHHHHHHHHh
Confidence            9999999999999999999764

Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.

>cd05500 Bromo_BDF1_2_I Bromodomain

Probab=99.89  E-value=3.2e-23  Score=185.47  Aligned_cols=96  Identities=17%  Similarity=0.294  Sum_probs=92.0

Q ss_pred             chHHHHHHHHHHhCcCCcccccccCcc--ccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCC
Q 005668          312 SEPLVRFLGMIRSHRLSSHFERRLRSQ--ESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRK  389 (684)
Q Consensus       312 skpLl~ILe~L~~hk~a~pF~~PVD~q--e~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~p  389 (684)
                      .+.|+.||+.|..++.+++|..||++.  .+|+||++|++||||+||+.||.++.|.++. +|..||.|||.||+.||++
T Consensus         6 ~~~~~~ii~~l~~~~~a~~F~~pv~~~~~~~p~Y~~~I~~P~dL~tI~~kl~~~~Y~s~~-~f~~D~~li~~Na~~yN~~   84 (103)
T cd05500           6 HKFLLSSIRSLKRLKDARPFLVPVDPVKLNIPHYPTIIKKPMDLGTIERKLKSNVYTSVE-EFTADFNLMVDNCLTFNGP   84 (103)
T ss_pred             HHHHHHHHHHHHcCCCChhhcCCCCcccccCCCHHHHhcCCCCHHHHHHHHhcCCCCCHH-HHHHHHHHHHHHHHHHCCC
Confidence            367999999999999999999999975  7999999999999999999999999999998 9999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHHHHH
Q 005668          390 SSQEYAAAQELRTLVIKEM  408 (684)
Q Consensus       390 dS~vykaA~eLr~lf~k~m  408 (684)
                      +|.++.+|..|+..|++.|
T Consensus        85 ~s~~~~~A~~l~~~fe~~~  103 (103)
T cd05500          85 EHPVSQMGKRLQAAFEKHL  103 (103)
T ss_pred             CCHHHHHHHHHHHHHHHhC
Confidence            9999999999999998864

BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

>cd05498 Bromo_Brdt_II_like Bromodomain, Brdt_like subfamily, repeat II

Probab=99.89  E-value=4.3e-23  Score=183.55  Aligned_cols=95  Identities=20%  Similarity=0.306  Sum_probs=90.7

Q ss_pred             hHHHHHHHHHHhC---cCCcccccccCcc--ccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhC
Q 005668          313 EPLVRFLGMIRSH---RLSSHFERRLRSQ--ESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFF  387 (684)
Q Consensus       313 kpLl~ILe~L~~h---k~a~pF~~PVD~q--e~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN  387 (684)
                      +.|..||+.|..+   +.+++|..||+..  .+|+||++|++||||+||+.||.++.|.++. +|..||+|||.||+.||
T Consensus         3 ~~c~~il~~l~~~~~~~~a~~F~~pv~~~~~~~p~Y~~~I~~Pmdl~~I~~kl~~~~Y~s~~-ef~~D~~li~~Na~~yn   81 (102)
T cd05498           3 KFCSGILKELFSKKHKAYAWPFYKPVDPEALGLHDYHDIIKHPMDLSTIKKKLDNREYADAQ-EFAADVRLMFSNCYKYN   81 (102)
T ss_pred             hHHHHHHHHHHhCCCccccCcccCcCCccccCCCcHHHHccCCCcHHHHHHHHccCCCCCHH-HHHHHHHHHHHHHHHHC
Confidence            5689999999999   8999999999986  6999999999999999999999999999998 99999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHHH
Q 005668          388 RKSSQEYAAAQELRTLVIKEM  408 (684)
Q Consensus       388 ~pdS~vykaA~eLr~lf~k~m  408 (684)
                      +++|.+|.+|..|+++|++++
T Consensus        82 ~~~s~i~~~a~~l~~~fe~~~  102 (102)
T cd05498          82 PPDHPVHAMARKLQDVFEDRW  102 (102)
T ss_pred             CCCCHHHHHHHHHHHHHHHhC
Confidence            999999999999999998764

Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

>cd05524 Bromo_polybromo_I Bromodomain, polybromo repeat I

Probab=99.88  E-value=1.7e-22  Score=184.47  Aligned_cols=101  Identities=25%  Similarity=0.346  Sum_probs=94.2

Q ss_pred             hHHHHHHHHHHh------CcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhh
Q 005668          313 EPLVRFLGMIRS------HRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIF  386 (684)
Q Consensus       313 kpLl~ILe~L~~------hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~F  386 (684)
                      +.|..||+.|+.      ++.+.+|.++++...+|+||++|++||||+||++||.++.|.++. +|..||.|||+||+.|
T Consensus         5 ~~c~~il~~l~~~~~~~g~~l~~~F~~~p~~~~~PdYy~iI~~Pmdl~tI~~kl~~~~Y~s~~-~f~~D~~lm~~Na~~y   83 (113)
T cd05524           5 AVCQELYDTIRNYKSEDGRILCESFIRVPKRRNEPEYYEVVSNPIDLLKIQQKLKTEEYDDVD-DLTADFELLINNAKAY   83 (113)
T ss_pred             HHHHHHHHHHHhhcccCCCchhHHHhcCCCcccCCCHHHHhCCccCHHHHHHHhCcCCCCCHH-HHHHHHHHHHHHHHHH
Confidence            568899999985      455679999999999999999999999999999999999999998 9999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHhhh
Q 005668          387 FRKSSQEYAAAQELRTLVIKEMTDMLRK  414 (684)
Q Consensus       387 N~pdS~vykaA~eLr~lf~k~msk~l~k  414 (684)
                      |+++|.+|.+|..|+++|.+.+.++++.
T Consensus        84 N~~~s~~~~~A~~L~~~f~~~~~~~~~~  111 (113)
T cd05524          84 YKPDSPEHKDACKLWELFLSARNEVLSG  111 (113)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHhhcc
Confidence            9999999999999999999999888753

Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.

>cd05515 Bromo_polybromo_V Bromodomain, polybromo repeat V

Probab=99.88  E-value=2.1e-22  Score=181.31  Aligned_cols=95  Identities=23%  Similarity=0.413  Sum_probs=88.3

Q ss_pred             hHHHHHHHHHHh------CcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhh
Q 005668          313 EPLVRFLGMIRS------HRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIF  386 (684)
Q Consensus       313 kpLl~ILe~L~~------hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~F  386 (684)
                      +.|..||+.|..      |+.+++|..||+..++|+||++|++||||+||++||.++.|.++. +|..||.|||.||+.|
T Consensus         3 ~~~~~~~~~i~~~~d~~~~~~a~~F~~~p~~~~~pdYy~iIk~PmdL~tI~~kl~~~~Y~s~~-ef~~D~~l~~~Na~~y   81 (105)
T cd05515           3 QKLWELYNAVKNYTDGRGRRLSLIFMRLPSKSEYPDYYDVIKKPIDMEKIRSKIEGNQYQSLD-DMVSDFVLMFDNACKY   81 (105)
T ss_pred             HHHHHHHHHHHHhhCcCCCcccHHhccCCCcccCCcHHHHcCCCcCHHHHHHHHccCCCCCHH-HHHHHHHHHHHHHHHH
Confidence            567788888875      456899999999999999999999999999999999999999998 9999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHH
Q 005668          387 FRKSSQEYAAAQELRTLVIKEM  408 (684)
Q Consensus       387 N~pdS~vykaA~eLr~lf~k~m  408 (684)
                      |+++|.+|.+|..|+.+|....
T Consensus        82 N~~~s~i~~~A~~L~~~~~~~~  103 (105)
T cd05515          82 NEPDSQIYKDALTLQKVLLETK  103 (105)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHH
Confidence            9999999999999999998764

Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.

>cd05519 Bromo_SNF2 Bromodomain, SNF2-like subfamily, specific to fungi

Probab=99.87  E-value=2.3e-22  Score=179.93  Aligned_cols=94  Identities=20%  Similarity=0.354  Sum_probs=88.6

Q ss_pred             hHHHHHHHHHH------hCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhh
Q 005668          313 EPLVRFLGMIR------SHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIF  386 (684)
Q Consensus       313 kpLl~ILe~L~------~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~F  386 (684)
                      +.|..||+.|.      .++.+++|..|++...+|+||++|++||||+||++||+.+.|.++. +|..||.|||.||+.|
T Consensus         3 ~~~~~i~~~v~~~~~~~~~~~~~~F~~~p~~~~~pdYy~iIk~Pmdl~~I~~kl~~~~Y~s~~-~f~~D~~li~~Na~~y   81 (103)
T cd05519           3 AAMLEIYDAVLNCEDETGRKLSELFLEKPSKKLYPDYYVIIKRPIALDQIKRRIEGRAYKSLE-EFLEDFHLMFANARTY   81 (103)
T ss_pred             HHHHHHHHHHHHhcCcCCCchhHHhcCCCCCCCCcCHHHHcCCCcCHHHHHHHHccCCCCCHH-HHHHHHHHHHHHHHHH
Confidence            46888999988      4556999999999999999999999999999999999999999998 9999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHHH
Q 005668          387 FRKSSQEYAAAQELRTLVIKE  407 (684)
Q Consensus       387 N~pdS~vykaA~eLr~lf~k~  407 (684)
                      |+++|.+|.+|..|+.+|...
T Consensus        82 n~~~s~i~~~A~~l~~~f~~~  102 (103)
T cd05519          82 NQEGSIVYEDAVEMEKAFKKK  102 (103)
T ss_pred             CCCCCHHHHHHHHHHHHHHHh
Confidence            999999999999999999865

SNF2 is a yeast protein involved in transcriptional activation, it is the catalytic component of the SWI/SNF ATP-dependent chromatin remodeling complex. The protein is essential for the regulation of gene expression (both positive and negative) of a large number of genes. The SWI/SNF complex changes chromatin structure by altering DNA-histone contacts within the nucleosome, which results in a re-positioning of the nucleosome and facilitates or represses the binding of gene-specific transcription factors. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

>cd05501 Bromo_SP100C_like Bromodomain, SP100C_like subfamily

Probab=99.87  E-value=3.9e-22  Score=179.92  Aligned_cols=97  Identities=18%  Similarity=0.262  Sum_probs=91.2

Q ss_pred             chHHHHHHHHHHhCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCCCC
Q 005668          312 SEPLVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSS  391 (684)
Q Consensus       312 skpLl~ILe~L~~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~pdS  391 (684)
                      ...|-.||-.|+.++.+++|..+  +..+|+||++|++||||+||+.||.++.|.++. +|.+||+|||+||+.||+++ 
T Consensus         4 l~~ce~il~~l~~~~~s~~f~~~--p~~~pdY~~iIk~PMDL~tI~~kL~~~~Y~s~~-ef~~D~~Lif~N~~~yN~~~-   79 (102)
T cd05501           4 LLKCEFLLLKVYCMSKSGFFISK--PYYIRDYCQGIKEPMWLNKVKERLNERVYHTVE-GFVRDMRLIFHNHKLFYKDD-   79 (102)
T ss_pred             HHHHHHHHHHHHhCcccccccCC--CCCCCchHHHcCCCCCHHHHHHHHcCCCCCCHH-HHHHHHHHHHHHHHHHcCCC-
Confidence            45688999999999999999763  458999999999999999999999999999998 99999999999999999999 


Q ss_pred             HHHHHHHHHHHHHHHHHHHHh
Q 005668          392 QEYAAAQELRTLVIKEMTDML  412 (684)
Q Consensus       392 ~vykaA~eLr~lf~k~msk~l  412 (684)
                      .+|.+|..|+..|++.|..++
T Consensus        80 ~~~~~a~~L~~~Fek~~~~~f  100 (102)
T cd05501          80 DFGQVGITLEKKFEKNFKEVF  100 (102)
T ss_pred             HHHHHHHHHHHHHHHHHHHHh
Confidence            999999999999999999876

The SP100C protein is a splice variant of SP100, a major component of PML-SP100 nuclear bodies (NBs), which are poorly understood. It is covalently modified by SUMO-1 and may play a role in processes at the chromatin level. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

>smart00297 BROMO bromo domain

Probab=99.87  E-value=5.3e-22  Score=175.16  Aligned_cols=97  Identities=29%  Similarity=0.492  Sum_probs=93.0

Q ss_pred             hHHHHHHHHHHhCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCCCCH
Q 005668          313 EPLVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQ  392 (684)
Q Consensus       313 kpLl~ILe~L~~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~pdS~  392 (684)
                      ..|..|++.|..|+.+++|..||+...+|+||.+|.+||||.||++||+++.|.++. +|..||.|||.||+.||++++.
T Consensus        10 ~~~~~i~~~~~~~~~~~~F~~~~~~~~~p~Y~~~i~~P~dl~~I~~kl~~~~Y~s~~-ef~~D~~li~~Na~~~n~~~s~   88 (107)
T smart00297       10 SLLKAVLDKLDSHRLSWPFLKPVDRKEAPDYYDIIKKPMDLSTIKKKLENGKYSSVE-EFVADVQLMFSNAKTYNGPDSE   88 (107)
T ss_pred             HHHHHHHHHHHhCccchhhccCCChhhccCHHHHhcCCCCHHHHHHHHhcCCCCCHH-HHHHHHHHHHHHHHHHCCCCCH
Confidence            457888888999999999999999999999999999999999999999999999998 9999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHH
Q 005668          393 EYAAAQELRTLVIKEMTD  410 (684)
Q Consensus       393 vykaA~eLr~lf~k~msk  410 (684)
                      +|.+|..|+.+|...|.+
T Consensus        89 ~~~~a~~l~~~f~~~~~~  106 (107)
T smart00297       89 VYKDAKKLEKFFEKKLRE  106 (107)
T ss_pred             HHHHHHHHHHHHHHHHhh
Confidence            999999999999999875

>cd05529 Bromo_WDR9_I_like Bromodomain; WDR9 repeat I_like subfamily

Probab=99.87  E-value=5.3e-22  Score=184.76  Aligned_cols=98  Identities=22%  Similarity=0.276  Sum_probs=93.4

Q ss_pred             CchHHHHHHHHHH---hCcCCcccccccCcc-ccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhh
Q 005668          311 KSEPLVRFLGMIR---SHRLSSHFERRLRSQ-ESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIF  386 (684)
Q Consensus       311 kskpLl~ILe~L~---~hk~a~pF~~PVD~q-e~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~F  386 (684)
                      ....|+.+|..|.   .++.+++|..||+.. .+|+||++|++||||+||++||.++.|.++. +|..||.|||.||+.|
T Consensus        25 ~~~~i~~~l~~l~~~~~~~~~~~F~~pv~~~~~~p~Y~~iI~~PmdL~tI~~kl~~~~Y~s~~-~f~~Dv~Li~~Na~~y  103 (128)
T cd05529          25 ERERLISGLDKLLLSLQLEIAEYFEYPVDLRAWYPDYWNRVPVPMDLETIRSRLENRYYRSLE-ALRHDVRLILSNAETF  103 (128)
T ss_pred             HHHHHHHHHHHHHhcccCcccccccCCCCccccCCcHHHHcCCCCCHHHHHHHHhcCCCCCHH-HHHHHHHHHHHHHHHH
Confidence            3466889999999   999999999999999 9999999999999999999999999999998 9999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHH
Q 005668          387 FRKSSQEYAAAQELRTLVIKEMT  409 (684)
Q Consensus       387 N~pdS~vykaA~eLr~lf~k~ms  409 (684)
                      |+++|.+|.+|..|+.+|...|.
T Consensus       104 N~~~s~i~~~A~~l~~~~~~~l~  126 (128)
T cd05529         104 NEPNSEIAKKAKRLSDWLLRILS  126 (128)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHhc
Confidence            99999999999999999998875

WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

>cd05518 Bromo_polybromo_IV Bromodomain, polybromo repeat IV

Probab=99.86  E-value=9.1e-22  Score=177.15  Aligned_cols=94  Identities=21%  Similarity=0.370  Sum_probs=86.2

Q ss_pred             hHHHHHHHHHHh------CcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhh
Q 005668          313 EPLVRFLGMIRS------HRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIF  386 (684)
Q Consensus       313 kpLl~ILe~L~~------hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~F  386 (684)
                      +.|..|++.|..      +..+.+|..+|+...+|+||++|++||||.||+.||.++.|.++. +|..||.|||.||+.|
T Consensus         3 ~~~~~l~~~v~~~~d~~gr~~~~~F~~~p~~~~~pdYy~iIk~Pmdl~tI~~kl~~~~Y~s~~-ef~~D~~li~~Na~~y   81 (103)
T cd05518           3 KRMLALFLYVLEYREGSGRRLCDLFMEKPSKKDYPDYYKIILEPIDLKTIEHNIRNDKYATEE-ELMDDFKLMFRNARHY   81 (103)
T ss_pred             HHHHHHHHHHHHhhccCCCcccHHHhcCCCcccCccHHHHcCCCcCHHHHHHHHCCCCCCCHH-HHHHHHHHHHHHHHHH
Confidence            456677777654      467899999999999999999999999999999999999999998 9999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHHH
Q 005668          387 FRKSSQEYAAAQELRTLVIKE  407 (684)
Q Consensus       387 N~pdS~vykaA~eLr~lf~k~  407 (684)
                      |+++|.+|.+|..|+.+|.++
T Consensus        82 N~~~s~i~~~A~~le~~~~~~  102 (103)
T cd05518          82 NEEGSQVYEDANILEKVLKEK  102 (103)
T ss_pred             CCCCCHHHHHHHHHHHHHHhc
Confidence            999999999999999998753

Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.

>cd05525 Bromo_ASH1 Bromodomain; ASH1_like sub-family

Probab=99.86  E-value=1.1e-21  Score=177.57  Aligned_cols=94  Identities=20%  Similarity=0.258  Sum_probs=87.2

Q ss_pred             hHHHHHHHHHHhC------cCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhh
Q 005668          313 EPLVRFLGMIRSH------RLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIF  386 (684)
Q Consensus       313 kpLl~ILe~L~~h------k~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~F  386 (684)
                      +.|..||+.|...      ..+++|.++++...+|+||++|++||||.||+.||.+|.|.++. +|..||.|||.||+.|
T Consensus         5 ~~l~~i~~~i~~~kd~~g~~~s~~F~~lp~k~~~pdYy~~I~~P~dL~tI~~kl~~~~Y~s~~-ef~~D~~l~f~Na~~y   83 (106)
T cd05525           5 QVLKEICDAIITYKDSNGQSLAIPFINLPSKKKNPDYYERITDPVDLSTIEKQILTGYYKTPE-AFDSDMLKVFRNAEKY   83 (106)
T ss_pred             HHHHHHHHHHHHhhccCCCcccHhhccCCCcccCCchhhhCCCCcCHHHHHHHHcCCCCCCHH-HHHHHHHHHHHHHHHH
Confidence            4577888888754      45799999999999999999999999999999999999999998 9999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHHH
Q 005668          387 FRKSSQEYAAAQELRTLVIKE  407 (684)
Q Consensus       387 N~pdS~vykaA~eLr~lf~k~  407 (684)
                      |+++|.+|.+|..|+++|.+.
T Consensus        84 n~~~S~i~~~A~~L~~~f~~~  104 (106)
T cd05525          84 YGRKSPIGRDVCRLRKAYYQA  104 (106)
T ss_pred             CCCCCHHHHHHHHHHHHHHHc
Confidence            999999999999999999763

ASH1 (absent, small, or homeotic 1) is a member of the trithorax-group in Drosophila melanogaster, an epigenetic transcriptional regulator of HOX genes. Drosophila ASH1 has been shown to methylate specific lysines in histones H3 and H4. Mammalian ASH1 has been shown to methylate histone H3. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

>cd05517 Bromo_polybromo_II Bromodomain, polybromo repeat II

Probab=99.85  E-value=1.8e-21  Score=175.13  Aligned_cols=93  Identities=24%  Similarity=0.365  Sum_probs=86.7

Q ss_pred             hHHHHHHHHHHhC------cCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhh
Q 005668          313 EPLVRFLGMIRSH------RLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIF  386 (684)
Q Consensus       313 kpLl~ILe~L~~h------k~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~F  386 (684)
                      +.|..||+.|..+      +.+++|..+++...+|+||++|++||||.||++||..+.|.++. +|..||.|||.||+.|
T Consensus         3 ~~~~~l~~~i~~~~d~~gr~~~~~F~~lp~~~~~pdYy~vI~~PmdL~tI~~kl~~~~Y~s~~-~f~~D~~lm~~Na~~y   81 (103)
T cd05517           3 QILEQLLEAVMTATDPSGRLISELFQKLPSKVLYPDYYAVIKEPIDLKTIAQRIQSGYYKSIE-DMEKDLDLMVKNAKTF   81 (103)
T ss_pred             HHHHHHHHHHHHhhCcCCCChhHHHhcCCCCCCCCCHHHHcCCCcCHHHHHHHHCcCCCCCHH-HHHHHHHHHHHHHHHH
Confidence            4577888888765      45799999999999999999999999999999999999999998 9999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHH
Q 005668          387 FRKSSQEYAAAQELRTLVIK  406 (684)
Q Consensus       387 N~pdS~vykaA~eLr~lf~k  406 (684)
                      |+++|.+|.+|..|+.+|..
T Consensus        82 N~~~s~i~~~A~~l~~~f~~  101 (103)
T cd05517          82 NEPGSQVYKDANAIKKIFTA  101 (103)
T ss_pred             CCCCCHHHHHHHHHHHHHHh
Confidence            99999999999999999975

Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.

>cd04369 Bromodomain Bromodomain

Probab=99.84  E-value=5.9e-21  Score=162.34  Aligned_cols=94  Identities=27%  Similarity=0.412  Sum_probs=90.4

Q ss_pred             hHHHHHHHHHHhC--cCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCCC
Q 005668          313 EPLVRFLGMIRSH--RLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKS  390 (684)
Q Consensus       313 kpLl~ILe~L~~h--k~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~pd  390 (684)
                      ..|..|++.|..+  +.+++|..||+...+|+||.+|++||||.+|+.||..+.|.++. +|..||.|||.||+.||+++
T Consensus         3 ~~~~~i~~~l~~~~~~~~~~F~~~~~~~~~~~Y~~~i~~P~~l~~I~~kl~~~~Y~s~~-~f~~D~~li~~Na~~~n~~~   81 (99)
T cd04369           3 KKLRSLLDALKKLKRDLSEPFLEPVDPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSLE-EFEADVRLIFSNAKTYNGPG   81 (99)
T ss_pred             HHHHHHHHHHHhhcccccHHHhcCCChhcCCCHHHHHhCcccHHHHHHHHhcCCCCCHH-HHHHHHHHHHHHHHHHCCCC
Confidence            4688899999999  99999999999999999999999999999999999999999998 99999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHHH
Q 005668          391 SQEYAAAQELRTLVIKE  407 (684)
Q Consensus       391 S~vykaA~eLr~lf~k~  407 (684)
                      +.+|.+|..|+.+|...
T Consensus        82 ~~~~~~a~~l~~~~~~~   98 (99)
T cd04369          82 SPIYKDAKKLEKLFEKL   98 (99)
T ss_pred             CHHHHHHHHHHHHHHHh
Confidence            99999999999999875

Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.

>cd05522 Bromo_Rsc1_2_II Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi

Probab=99.84  E-value=6.7e-21  Score=171.43  Aligned_cols=93  Identities=26%  Similarity=0.366  Sum_probs=85.2

Q ss_pred             HHHHHHHHHHh------CcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhC
Q 005668          314 PLVRFLGMIRS------HRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFF  387 (684)
Q Consensus       314 pLl~ILe~L~~------hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN  387 (684)
                      .|..||+.|..      ++.+++|..+++...+|+||++|++||||+||+.||..+.|.++. +|..||.|||.||+.||
T Consensus         5 ~~~~i~~~v~~~~d~~g~~l~~~F~~~p~~~~~pdYy~~I~~Pmdl~tI~~kl~~~~Y~s~~-~f~~D~~li~~Na~~yn   83 (104)
T cd05522           5 RIKNILKGLRKERDENGRLLTLHFEKLPDKAREPEYYQEISNPISLDDIKKKVKRRKYKSFD-QFLNDLNLMFENAKLYN   83 (104)
T ss_pred             HHHHHHHHHHHHhCcCCCcccHHHhcCCCccccCcHHHHhCCCcCHHHHHHHHccCCCCCHH-HHHHHHHHHHHHHHHHC
Confidence            45556666654      578999999999999999999999999999999999999999998 99999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHH
Q 005668          388 RKSSQEYAAAQELRTLVIKE  407 (684)
Q Consensus       388 ~pdS~vykaA~eLr~lf~k~  407 (684)
                      ++++.+|.+|..|+..|...
T Consensus        84 ~~~s~i~~~A~~l~~~f~~l  103 (104)
T cd05522          84 ENDSQEYKDAVLLEKEARLL  103 (104)
T ss_pred             CCCCHHHHHHHHHHHHHHHh
Confidence            99999999999999999763

Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

>PF00439 Bromodomain: Bromodomain; InterPro: IPR001487 Bromodomains are found in a variety of mammalian, invertebrate and yeast DNA-binding proteins []

Probab=99.84  E-value=8.3e-21  Score=160.86  Aligned_cols=84  Identities=27%  Similarity=0.445  Sum_probs=79.6

Q ss_pred             HHHHHHHHHhCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCCCCHHH
Q 005668          315 LVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQEY  394 (684)
Q Consensus       315 Ll~ILe~L~~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~pdS~vy  394 (684)
                      |..||+.|..|+.+++|..||+...+|+|+++|++||||.||+.||++|.|.++. +|..||.|||.||+.||+++|.+|
T Consensus         1 C~~il~~l~~~~~~~~F~~~~~~~~~p~y~~~i~~P~dL~~I~~kl~~~~Y~s~~-~f~~Dv~~i~~Na~~yn~~~s~~~   79 (84)
T PF00439_consen    1 CREILEELMKHPISSPFSKPVDPKEYPDYYEIIKNPMDLSTIRKKLENGKYKSIE-EFEADVRLIFQNARRYNPPDSPIY   79 (84)
T ss_dssp             HHHHHHHHHTSTTGGGGSSSTHTTTSTTHHHHSSSS--HHHHHHHHHTTSSSSHH-HHHHHHHHHHHHHHHHSCTTSHHH
T ss_pred             CHHHHHHHHcCCCchhhcCCCChhhCCCHHHHHhhccchhhhhHHhhccchhhHH-HHHHHHHHHHHHHHHHCCCcCHHH
Confidence            6789999999999999999999999999999999999999999999999999998 999999999999999999999999


Q ss_pred             HHHHH
Q 005668          395 AAAQE  399 (684)
Q Consensus       395 kaA~e  399 (684)
                      .+|.+
T Consensus        80 ~~A~~   84 (84)
T PF00439_consen   80 KAAEK   84 (84)
T ss_dssp             HHHHH
T ss_pred             HHhcC
Confidence            99974

Bromodomains can interact with acetylated lysine []. In some proteins, the classical bromodomain has diverged to such an extent that parts of the region are either missing or contain an insertion (e.g., mammalian protein HRX, Caenorhabditis elegans hypothetical protein ZK783.4, yeast protein YTA7). The bromodomain may occur as a single copy, or in duplicate. The precise function of the domain is unclear, but it may be involved in protein-protein interactions and may play a role in assembly or activity of multi-component complexes involved in transcriptional activation [].; GO: 0005515 protein binding; PDB: 3P1C_A 4A9K_B 3SVH_A 3P1E_B 3P1F_A 1JSP_B 2L85_A 3P1D_B 3DWY_B 2D82_A ....

>cd05521 Bromo_Rsc1_2_I Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi

Probab=99.82  E-value=3.7e-20  Score=167.74  Aligned_cols=94  Identities=21%  Similarity=0.285  Sum_probs=86.1

Q ss_pred             hHHHHHHHHHHhC------cCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhh
Q 005668          313 EPLVRFLGMIRSH------RLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIF  386 (684)
Q Consensus       313 kpLl~ILe~L~~h------k~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~F  386 (684)
                      +.|..||+.|+..      +.+.+|..+++...+|+||++|++||||+||++||..  |.++. +|..||.|||.||+.|
T Consensus         4 ~~~~~l~~~i~~~~~~~g~~~~~~F~~lp~~~~~pdYy~iI~~PmdL~tI~~kl~~--Y~s~~-ef~~D~~li~~Na~~y   80 (106)
T cd05521           4 KKLKPLYDGIYTLKEENGIEIHPIFNVLPLRKDYPDYYKIIKNPLSLNTVKKRLPH--YTNAQ-EFVNDLAQIPWNARLY   80 (106)
T ss_pred             HHHHHHHHHHHhhcCcCCCCchHhhhcCCccccCccHHHHhcCCCCHHHHHHHHHc--CCCHH-HHHHHHHHHHHHHHHH
Confidence            4678888888754      4467999999999999999999999999999999998  99998 9999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHH
Q 005668          387 FRKSSQEYAAAQELRTLVIKEMT  409 (684)
Q Consensus       387 N~pdS~vykaA~eLr~lf~k~ms  409 (684)
                      |+++|.+|.+|..|+.+|.+.|.
T Consensus        81 N~~~s~i~~~A~~le~~~~~~~~  103 (106)
T cd05521          81 NTKGSVIYKYALILEKYINDVII  103 (106)
T ss_pred             cCCCCHHHHHHHHHHHHHHHhhc
Confidence            99999999999999999988763

Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

>cd05492 Bromo_ZMYND11 Bromodomain; ZMYND11_like sub-family

Probab=99.81  E-value=8.7e-20  Score=166.44  Aligned_cols=96  Identities=22%  Similarity=0.352  Sum_probs=86.3

Q ss_pred             HHHHHHHHHh-CcCCcccccccCc-----cccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCC
Q 005668          315 LVRFLGMIRS-HRLSSHFERRLRS-----QESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFR  388 (684)
Q Consensus       315 Ll~ILe~L~~-hk~a~pF~~PVD~-----qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~  388 (684)
                      |-.++..++. -+-++||+.||.+     ..+|+||.+|++||||+||++||++|.|.++. ||.+||.|||+||++||+
T Consensus         5 L~f~~~~~k~~lp~~~~~~~~v~~~~~~~~~~pdY~~iIk~PmDL~tI~~kl~~~~Y~s~~-ef~~Dv~LI~~N~~~yNg   83 (109)
T cd05492           5 LKFIVSRMKSWLPPDTTNRAIVLNKRGKATKLPKRRRLIHTHLDVADIQEKINSEKYTSLE-EFKADALLLLHNTAIFHG   83 (109)
T ss_pred             HHHHHHHHHhcCcccccccccccccCchhccCCCHHHHhCCCCcHHHHHHHHHcCCCCCHH-HHHHHHHHHHHHHHHHCC
Confidence            4556667766 4668999999963     25999999999999999999999999999998 999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHH
Q 005668          389 KSSQEYAAAQELRTLVIKEMTDM  411 (684)
Q Consensus       389 pdS~vykaA~eLr~lf~k~msk~  411 (684)
                      ++|.+|.+|..|.+.+...|.++
T Consensus        84 ~~s~~~~~A~~l~~d~~~el~Ei  106 (109)
T cd05492          84 ADSEQYDAARWLYRDTCHDLREL  106 (109)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999888888765

ZMYND11 or BS69 is a ubiquitously expressed nuclear protein that has been shown to associate with chromatin. It interacts with chromatin remodeling factors and might play a role in chromatin remodeling and gene expression. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

>cd05526 Bromo_polybromo_VI Bromodomain, polybromo repeat VI

Probab=99.69  E-value=9.8e-17  Score=146.85  Aligned_cols=97  Identities=21%  Similarity=0.250  Sum_probs=87.8

Q ss_pred             hHHHHHHHHHHhCc------CCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhh
Q 005668          313 EPLVRFLGMIRSHR------LSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIF  386 (684)
Q Consensus       313 kpLl~ILe~L~~hk------~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~F  386 (684)
                      +.|..|++.|+.|.      .+.+|.+.+.  ..++||.+|+.||||.+|++||.+|.|.++. +|..||.|||+||..|
T Consensus         6 ~~l~~l~~~V~~~~D~~Gr~~s~~f~~LP~--~~~~~~~~ik~Pi~l~~Ik~ki~~~~Y~~ld-~~~~D~~lmf~NAr~y   82 (110)
T cd05526           6 ELLATLFVSVMNHQDEEGRCYSDSLAELPE--LAVDGVGPKKIPLTLDIIKRNVDKGRYRRLD-KFQEDMFEVLERARRL   82 (110)
T ss_pred             HHHHHHHHHHHhccCCCCCCchHHHHHCCC--cccCchhhhcCCccHHHHHHHHHcCCcCcHH-HHHHHHHHHHHHHHHh
Confidence            46888999999886      4788988887  4578889999999999999999999999999 9999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHh
Q 005668          387 FRKSSQEYAAAQELRTLVIKEMTDML  412 (684)
Q Consensus       387 N~pdS~vykaA~eLr~lf~k~msk~l  412 (684)
                      |.++|.+|.+|.+|+.+|.+.-.++.
T Consensus        83 N~~~S~iy~dA~eLq~~f~~~rd~~~  108 (110)
T cd05526          83 SRTDSEIYEDAVELQQFFIKIRDELC  108 (110)
T ss_pred             CcccCHHHHHHHHHHHHHHHHHHHHh
Confidence            99999999999999999998766553

Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.

>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]

Probab=99.66  E-value=7.4e-17  Score=195.34  Aligned_cols=97  Identities=23%  Similarity=0.357  Sum_probs=93.8

Q ss_pred             HHHHHHHHHhCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCCCCHHH
Q 005668          315 LVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQEY  394 (684)
Q Consensus       315 Ll~ILe~L~~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~pdS~vy  394 (684)
                      |..||..|..|..+|||+.||+...+|+||+||++||||.||+.||..|.|.+.. +|..||.|||.||.+||.+ +.++
T Consensus      1306 ~e~il~e~~~~~~awPFlepVn~~~vp~Y~~IIk~Pmdl~tir~k~~~~~Y~~~e-ef~~Di~lvf~Nc~~yN~~-s~i~ 1383 (1404)
T KOG1245|consen 1306 CEDILHELVVHKAAWPFLEPVNPKEVPDYYDIIKKPMDLSTIREKLSKGIYPSPE-EFATDIELVFDNCETYNED-SEIG 1383 (1404)
T ss_pred             HHHHHHHHHHhhhcchhhccCChhhcccHHHHhcChhHHHHHHHHHhcccCCCHH-HHHHHHHHHHHHHHHhccc-hhhh
Confidence            8899999999999999999999999999999999999999999999999999998 9999999999999999999 9999


Q ss_pred             HHHHHHHHHHHHHHHHHhh
Q 005668          395 AAAQELRTLVIKEMTDMLR  413 (684)
Q Consensus       395 kaA~eLr~lf~k~msk~l~  413 (684)
                      .+...|+.+|++.+...++
T Consensus      1384 ~ag~~l~~ff~~~~~~~~~ 1402 (1404)
T KOG1245|consen 1384 RAGTCLRRFFHKRWRKKFP 1402 (1404)
T ss_pred             hhcchHHHHHHHHHHhhcC
Confidence            9999999999997777664

>COG5076 Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription]

Probab=99.66  E-value=9.2e-17  Score=171.97  Aligned_cols=90  Identities=29%  Similarity=0.442  Sum_probs=85.9

Q ss_pred             hCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHH
Q 005668          324 SHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQEYAAAQELRTL  403 (684)
Q Consensus       324 ~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~pdS~vykaA~eLr~l  403 (684)
                      .+...++|..+|+...+|+||.||+.||||.||+++|..+.|.++. +|..||+|||+||..||.+++.+|.+|..|+..
T Consensus       162 ~~~~s~~F~~~p~k~~~PdYy~iIk~Pm~L~~i~kkl~~~~Y~s~e-ef~~D~~lM~~N~~~yN~~~s~v~~~a~~l~~~  240 (371)
T COG5076         162 GRFLSSIFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFE-EFVSDLNLMFDNCKLYNGPDSSVYVDAKELEKY  240 (371)
T ss_pred             ccccccccccCCccccCCChheeecchhhHHHHHHHHHhhhhhhHH-HHHHHHHHHHHhhhhccCCCcchhhhhHHHHHH
Confidence            4567899999999999999999999999999999999999999998 999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhh
Q 005668          404 VIKEMTDMLRK  414 (684)
Q Consensus       404 f~k~msk~l~k  414 (684)
                      |...|..+...
T Consensus       241 ~~~~i~~~~~~  251 (371)
T COG5076         241 FLKLIEEIPEE  251 (371)
T ss_pred             HHHHHHhcccc
Confidence            99999987754

>KOG1472 consensus Histone acetyltransferase SAGA/ADA, catalytic subunit PCAF/GCN5 and related proteins [Chromatin structure and dynamics; Transcription]

Probab=99.49  E-value=1.6e-14  Score=164.80  Aligned_cols=100  Identities=22%  Similarity=0.442  Sum_probs=95.6

Q ss_pred             HHHHHHHHHHhCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCCCCHH
Q 005668          314 PLVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQE  393 (684)
Q Consensus       314 pLl~ILe~L~~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~pdS~v  393 (684)
                      .+..||..|..|.++|||.+||+..++|+||++|++||||.||+.+|..+.|..+. .|.+|+.+||+||.+||+.++.+
T Consensus       610 ~~~~il~~l~~h~~awPf~~Pv~~~e~pdyy~~I~~pmDl~tM~~~l~~~~y~~~~-~f~ad~~~vf~ncr~yn~~~~~y  688 (720)
T KOG1472|consen  610 AIQNILDQLQNHGDAWPFLKPVNKKEVPDYYDVIKHPMDLRTMQNRLKDNQYTEVE-LFMADVVRVFANCRMYNGSDTQY  688 (720)
T ss_pred             HHHhHHhhhhcCCccCCccCccccccCCcHHHHhcccccHHHHhhhccccchhhHH-HHHHHHHHHHhhhhccCCccchh
Confidence            36678899999999999999999999999999999999999999999999999998 99999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhhh
Q 005668          394 YAAAQELRTLVIKEMTDMLRK  414 (684)
Q Consensus       394 ykaA~eLr~lf~k~msk~l~k  414 (684)
                      |+.|..|..+|...|...+..
T Consensus       689 ~k~~~~le~~~~~k~~~~i~~  709 (720)
T KOG1472|consen  689 YKCAQALEKFFLFKLNELILR  709 (720)
T ss_pred             eecccchhhhhcchhhhhhhh
Confidence            999999999999999888654

>cd05494 Bromodomain_1 Bromodomain; uncharacterized subfamily

Probab=99.10  E-value=5.5e-11  Score=109.45  Aligned_cols=77  Identities=9%  Similarity=-0.013  Sum_probs=59.8

Q ss_pred             hHHHHHHHHHHhCcCCcccccccCc--cccchhhhhhcCCCCHHHHHHHHhCCCccC------cHHHHHHHHHHHHHHHh
Q 005668          313 EPLVRFLGMIRSHRLSSHFERRLRS--QESERYKKLVRQHIDLRTIQSRLDRGLYSN------CFQKFFRDLLLLFNNFV  384 (684)
Q Consensus       313 kpLl~ILe~L~~hk~a~pF~~PVD~--qe~PdYyeIIK~PMDLsTIKkKLe~g~YsS------i~~EF~rDL~LMF~NA~  384 (684)
                      +.|+.+|..+..|+.+|||..||++  ..+|+||++|++||||+||+.+|..+.|..      ....+..++..++.||.
T Consensus         6 ~~~l~~l~~~~~~~~~~pF~~PVd~~~~~~pdY~~iIK~PMDL~ti~~kl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   85 (114)
T cd05494           6 ERVLRELKRHRRNEDAWPFLEPVNPPRRGAPDYRDVIKRPMSFGTKVNNIVETGARDLEDLQIVQEDPADKQIDDEGRRS   85 (114)
T ss_pred             HHHHHHHHHhhhCCCCCCcCCCCCchhcCCCChhhhcCCCCChHHHHHHHHccccccccccccccccccccccccccccC
Confidence            4577777777888899999999999  799999999999999999999999874422      22245556666666666


Q ss_pred             hhCCC
Q 005668          385 IFFRK  389 (684)
Q Consensus       385 ~FN~p  389 (684)
                      -||..
T Consensus        86 ~~~~~   90 (114)
T cd05494          86 PSNIY   90 (114)
T ss_pred             ccccc
Confidence            55553

Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.

>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]

Probab=99.06  E-value=1.7e-10  Score=136.90  Aligned_cols=100  Identities=22%  Similarity=0.347  Sum_probs=93.7

Q ss_pred             hHHHHHHHHHHhCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCCCCH
Q 005668          313 EPLVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQ  392 (684)
Q Consensus       313 kpLl~ILe~L~~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~pdS~  392 (684)
                      +.|..+|+.|...+...+|..|||..++|+|.+||++||||.||+.++.++.|.++. +|..|+.||+.||+.||..++.
T Consensus       568 kLl~~~l~~lq~kD~~gif~~pvd~~e~pdy~~iik~pmd~~t~~~kl~s~~y~tle-~ieed~~l~~~nc~~yn~~dtv  646 (1051)
T KOG0955|consen  568 KLLQKSLDKLQKKDSYGIFAEPVDPSELPDYIDIIKKPMDFFTMRLKLESGAYSTLE-PIEEDVNLIVSNCMEYNAKDTV  646 (1051)
T ss_pred             HHHHHHHHHhhcccccCceeeccChhhcccHHHHhcCccchhhhhhhccccchhhhh-HHHHhHhHhHhHHHHhhccCee
Confidence            445578888888999999999999999999999999999999999999999999998 9999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHhh
Q 005668          393 EYAAAQELRTLVIKEMTDMLR  413 (684)
Q Consensus       393 vykaA~eLr~lf~k~msk~l~  413 (684)
                      +|.+|..|++++...+.+...
T Consensus       647 ~~r~av~~~e~~~~~~~~ark  667 (1051)
T KOG0955|consen  647 YYRAAVRLRELIKKDFRNARK  667 (1051)
T ss_pred             hHhhhHHHHhhhhhHHHhccc
Confidence            999999999999888877664

>KOG0008 consensus Transcription initiation factor TFIID, subunit TAF1 [Transcription]

Probab=98.97  E-value=5.3e-10  Score=133.07  Aligned_cols=93  Identities=17%  Similarity=0.270  Sum_probs=83.6

Q ss_pred             HHHHhCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHH
Q 005668          320 GMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQEYAAAQE  399 (684)
Q Consensus       320 e~L~~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~pdS~vykaA~e  399 (684)
                      ..+..-+.+|+|+.||+...+|+||.+|++||||.||.+++..+.|.+.. ||++|+.||+.||..||+..+.+...|.+
T Consensus      1392 s~~~~ipes~~f~~~v~~k~~~~yy~kik~pmdl~~i~~n~~~~~y~s~~-e~l~dv~~i~~n~~~~ng~e~~y~~k~~k 1470 (1563)
T KOG0008|consen 1392 SQMKEIPESWPFHEPVNKKRVPDYYKKIKNPMDLETILKNIPPHKYDSRS-EFLDDVNLIYVNSVEYNGAESAYTKKARK 1470 (1563)
T ss_pred             HHHHhcchhcccccccchhhchHHHHHhcChhhHHHHhhcCCccccccHH-HHhhhhHhhcccceeecCccccccHHHHH
Confidence            34556688999999999999999999999999999999999999999998 99999999999999999999999999988


Q ss_pred             HHHHHHHHHHHHhh
Q 005668          400 LRTLVIKEMTDMLR  413 (684)
Q Consensus       400 Lr~lf~k~msk~l~  413 (684)
                      +-.+....|.+.+.
T Consensus      1471 ~~ev~~~~~~e~~~ 1484 (1563)
T KOG0008|consen 1471 IGEVGLANLLEYIE 1484 (1563)
T ss_pred             HHHHHHHHHHHHHH
Confidence            87777666655443

>cd05491 Bromo_TBP7_like Bromodomain; TBP7_like subfamily, limited to fungi

Probab=98.83  E-value=5e-09  Score=97.54  Aligned_cols=42  Identities=24%  Similarity=0.371  Sum_probs=39.7

Q ss_pred             CCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCCCC
Q 005668          349 QHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSS  391 (684)
Q Consensus       349 ~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~pdS  391 (684)
                      .||||+||++||.+|+|.++. +|++||.|||.||..||.++.
T Consensus        63 y~MDL~tIe~RL~ng~Y~tp~-~F~~DiklI~~Nc~~ynd~dr  104 (119)
T cd05491          63 YNMDLDTIEERLWNGYYATPK-DFLKDIKRIVRDAKTIGDRER  104 (119)
T ss_pred             eccCHHHHHHHHhcCCCCCHH-HHHHHHHHHHHHHHHhCCHHH
Confidence            589999999999999999998 999999999999999998743

TBP7, or TAT-binding protein homolog 7, is a yeast protein of unknown function that contains AAA-superfamily ATP-ase domains and a bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.

>KOG0008 consensus Transcription initiation factor TFIID, subunit TAF1 [Transcription]

Probab=98.77  E-value=8.9e-09  Score=122.95  Aligned_cols=105  Identities=17%  Similarity=0.246  Sum_probs=94.6

Q ss_pred             cccCchHHHHHHHHHHhCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhC
Q 005668          308 LAVKSEPLVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFF  387 (684)
Q Consensus       308 ~~~kskpLl~ILe~L~~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN  387 (684)
                      .++.+..|..|++.+...++..+|..||+..++++||.||..||||.||++.|....|.+-. .|+.|+.|||.|..+||
T Consensus      1259 ~V~~ss~l~~i~n~~~~~~~t~~f~~Pv~~k~v~dyy~vi~~P~~lq~~kk~v~kr~y~~r~-~fle~~~~~~~ns~~yn 1337 (1563)
T KOG0008|consen 1259 SVSLSSILETIINQARSSPNTYPFPTPVNAKEVKDYYRVITPPMDLQTQKKLVRKRLYESRE-HFLEELPLIVSNSTKYN 1337 (1563)
T ss_pred             eeecccchHHHHHHHhcCCCCcCCCCccchhhccchhhccCCCcchHHHHHHHHHHHHHHHH-HHHHHhHHHhhchhhhc
Confidence            45555667888899999999999999999999999999999999999999999999999998 99999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHhh
Q 005668          388 RKSSQEYAAAQELRTLVIKEMTDMLR  413 (684)
Q Consensus       388 ~pdS~vykaA~eLr~lf~k~msk~l~  413 (684)
                      ++.+.+..++..|..+....|...-.
T Consensus      1338 g~~~~~t~~~q~mls~~~~~~~eked 1363 (1563)
T KOG0008|consen 1338 GPLASLTRQQQSMLSLCFEKLKEKED 1363 (1563)
T ss_pred             CchHHHHHHHHHHHHHHHHhhchhHH
Confidence            99999999999888777666654433

>KOG1827 consensus Chromatin remodeling complex RSC, subunit RSC1/Polybromo and related proteins [Chromatin structure and dynamics; Transcription]

Probab=98.76  E-value=2.5e-08  Score=113.43  Aligned_cols=95  Identities=24%  Similarity=0.337  Sum_probs=85.8

Q ss_pred             hHHHHHHHHHHhCc------CCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhh
Q 005668          313 EPLVRFLGMIRSHR------LSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIF  386 (684)
Q Consensus       313 kpLl~ILe~L~~hk------~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~F  386 (684)
                      ..+..||..|+.+.      ....|.+..+....|.||.+|-+||.|..|++||..+.|.++. .|+.|++|||.||..|
T Consensus        55 ~~f~~il~~~~~~~d~~gk~~~d~feklp~~~~~p~yy~~i~~pisl~~ik~kv~k~~y~~~~-~f~~D~~lm~ena~~~  133 (629)
T KOG1827|consen   55 PKFKTILASLLDLKDDEGKQLFDKFEKLPSRKEFPEYYYVIQQPISLDQIKRKVKKGRYKRLS-FFQLDFLLMTENARLY  133 (629)
T ss_pred             HHHHHHHHHHHhhccccCcccchhHhhccccccCCCcceeecCcccHHHHHHHHHhcccccHH-HHHHHHHHHHHHHHHh
Confidence            44666666666553      4678999999999999999999999999999999999999999 9999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHH
Q 005668          387 FRKSSQEYAAAQELRTLVIKEM  408 (684)
Q Consensus       387 N~pdS~vykaA~eLr~lf~k~m  408 (684)
                      |.+++.+|.++..|...|....
T Consensus       134 n~~ds~~~~~s~~l~~~~~~~~  155 (629)
T KOG1827|consen  134 NRPDSLIYKDSGELEKYFISLE  155 (629)
T ss_pred             cCcchhhhhhhhhhhcchhhhh
Confidence            9999999999999999988755

>KOG0386 consensus Chromatin remodeling complex SWI/SNF, component SWI2 and related ATPases (DNA/RNA helicase superfamily) [Chromatin structure and dynamics; Transcription]

Probab=98.74  E-value=1.1e-08  Score=119.90  Aligned_cols=101  Identities=18%  Similarity=0.327  Sum_probs=92.8

Q ss_pred             hHHHHHHHHHHhC------cCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhh
Q 005668          313 EPLVRFLGMIRSH------RLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIF  386 (684)
Q Consensus       313 kpLl~ILe~L~~h------k~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~F  386 (684)
                      .++..|+.....+      .....|........+|+||.||+.||+|..|.++|.++.|.++. ++..||.+||+||.+|
T Consensus      1027 ~~~~~i~~~~~~~~~~~~r~~~~~~~~~~s~k~~~d~~~~i~~~~~~~~~~~~i~~~~~~~~~-~~~~~~~~~~~na~~~ 1105 (1157)
T KOG0386|consen 1027 KQALKIASTSIKYKDSAGRELSEVFLKLPSRKEYPDYYEIIKKPVAIDKIKKRIENHKYNSLK-ELEKDFMLLFNNARTY 1105 (1157)
T ss_pred             HHHHHHHHHHHhcccccccccchhcccCcccccccchHHHhcchhhHHHHhhhccccccchHH-HHHHHHHhhcchhhhh
Confidence            6788888887744      45789999999999999999999999999999999999999998 9999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHhhh
Q 005668          387 FRKSSQEYAAAQELRTLVIKEMTDMLRK  414 (684)
Q Consensus       387 N~pdS~vykaA~eLr~lf~k~msk~l~k  414 (684)
                      |..+|.+|..|..|+.+|......+...
T Consensus      1106 ~~egs~~y~d~~~l~~~~~~~~~~~~~~ 1133 (1157)
T KOG0386|consen 1106 NEEGSRVYEDAIVLQSVFKSARQEISKE 1133 (1157)
T ss_pred             ccCCceechhHHHHHHHHhhhHHHHhcc
Confidence            9999999999999999999888887743

>KOG1474 consensus Transcription initiation factor TFIID, subunit BDF1 and related bromodomain proteins [Transcription]

Probab=98.54  E-value=1.8e-08  Score=115.96  Aligned_cols=93  Identities=20%  Similarity=0.341  Sum_probs=85.9

Q ss_pred             HHHhCcCCcccccccCcc--ccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCCCCHHHHHHH
Q 005668          321 MIRSHRLSSHFERRLRSQ--ESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQEYAAAQ  398 (684)
Q Consensus       321 ~L~~hk~a~pF~~PVD~q--e~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~pdS~vykaA~  398 (684)
                      .+..|.++|+|..||+..  ..|+||.+|++|||+.||..+|++.+|.+.. +..+||..+|.||+.||...-.++.++.
T Consensus         3 ~~~~~~~~~~f~~~v~~v~l~~~~~~~~~~~~~d~~~~~~~~e~n~~~~~~-~~~~~f~~~~sn~~~~~~~~~~v~~~~~   81 (640)
T KOG1474|consen    3 EARKHKLAWPFLEPVDAVALNLPAYYEIIKRPMDIGTIEKRVENNYYFSAS-ECIADFKTKFSNCYLFNDSGDDVVRMKQ   81 (640)
T ss_pred             ccccccccccccCccchhhccchhhhcccCCCCCchhhhhhhccCccccHh-hhhhhccccccchhcccCCccchhhccc
Confidence            345789999999999964  7899999999999999999999998899997 9999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhhh
Q 005668          399 ELRTLVIKEMTDMLRK  414 (684)
Q Consensus       399 eLr~lf~k~msk~l~k  414 (684)
                      .+..+|.+.+......
T Consensus        82 ~~~~~~~~~~~~~~~~   97 (640)
T KOG1474|consen   82 SLEKLFPKKLRSMPSD   97 (640)
T ss_pred             cchhhccccccccccc
Confidence            9999998888777765

>KOG1472 consensus Histone acetyltransferase SAGA/ADA, catalytic subunit PCAF/GCN5 and related proteins [Chromatin structure and dynamics; Transcription]

Probab=98.45  E-value=1.2e-07  Score=109.48  Aligned_cols=72  Identities=21%  Similarity=0.403  Sum_probs=67.1

Q ss_pred             hCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCCCCHHHHH
Q 005668          324 SHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQEYAA  396 (684)
Q Consensus       324 ~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~pdS~vyka  396 (684)
                      .+.++++|..+|+...+|+||.||+-||||.|+-.++..+.|.+.. +|..||.+||.||..||...+.....
T Consensus       300 ~~~~s~~~~~kvs~~~a~~y~~i~k~pmdl~t~~~k~~~~~y~~~~-~fv~d~~~~~~n~~~~n~ee~~~~~~  371 (720)
T KOG1472|consen  300 RTEHSTPFLEKVSKEDAPNYYQIIKAPMDLSTELKKLKSGPYCSKE-EFVNDLMLIWRNCEKYNSEESHGLIE  371 (720)
T ss_pred             ccccccccccCCChhhCcchHHhhhcchHHHHHHHHhccccccchh-HHHHHHHHHHhcchhhccccchhhhh
Confidence            4899999999999999999999999999999999999999999998 99999999999999999987654433

>KOG1828 consensus IRF-2-binding protein CELTIX-1, contains BROMO domain [Transcription]

Probab=98.43  E-value=4.5e-08  Score=105.62  Aligned_cols=98  Identities=17%  Similarity=0.150  Sum_probs=88.1

Q ss_pred             HHHHHHHHHhCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCCCCHHH
Q 005668          315 LVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQEY  394 (684)
Q Consensus       315 Ll~ILe~L~~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~pdS~vy  394 (684)
                      +-.+|..+.....-..|..||...-.|+|.+||..|||+.||+.+|+-+.|.++. +|..|..||++||++||-..+.++
T Consensus        24 ~ehhlrkl~sKdp~q~fafplt~~map~y~~iis~Pmd~~t~r~kidd~~yl~L~-~m~~d~kl~~~na~~yn~~~Tv~~  102 (418)
T KOG1828|consen   24 AEHHLRKLPSKDPKQKFAFPLTDKMAPNYLEIISEPMDRITKRSKIDDTRYLVLS-QMEFDRKLPDGNATLYNLHPTVPI  102 (418)
T ss_pred             HHHHHHhccccChhhhhccccchhhccchHhhhhcccccccccccCCCccceech-hhhhhhcccccchhhhhcCCcccc
Confidence            4456666667777888999999999999999999999999999999999999998 999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHhh
Q 005668          395 AAAQELRTLVIKEMTDMLR  413 (684)
Q Consensus       395 kaA~eLr~lf~k~msk~l~  413 (684)
                      .+|..|..+....+...+.
T Consensus       103 ~aaKrL~~v~~~~~qe~~l  121 (418)
T KOG1828|consen  103 VAAKRLCPVRLGMTQERLL  121 (418)
T ss_pred             ccccccchhhcchhhHHHH
Confidence            9999999887776665554

>KOG1828 consensus IRF-2-binding protein CELTIX-1, contains BROMO domain [Transcription]

Probab=98.13  E-value=1.7e-06  Score=93.70  Aligned_cols=89  Identities=12%  Similarity=0.052  Sum_probs=78.1

Q ss_pred             chHHHHHH-HHHHhCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCCC
Q 005668          312 SEPLVRFL-GMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKS  390 (684)
Q Consensus       312 skpLl~IL-e~L~~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~pd  390 (684)
                      .+.|+.+. .++.......+|..++....+|.|.-+|++|+|+.|+..++.++.|.| . +|..|+.|||.||++||.+.
T Consensus       209 ~~~l~~~q~~kl~~~~p~~~lnyg~tas~aP~YSm~Ik~~~~~~Tygdk~~andy~S-~-~f~~D~kl~~l~amT~gehs  286 (418)
T KOG1828|consen  209 GQQLQTLQEDKLNRVDPVAYLNYGPTASFAPGYSMTITEVEPPGTYGDKSSANDYES-L-SFTQDRKLIALKAVTNGEHS  286 (418)
T ss_pred             cHHHHHHHHHHhcccCchhhhcccchhhhcccccccccccCCCcchhhhhhhhhhhh-h-hhhcccchhhHHHHhcCCcc
Confidence            34444443 456666678899999999999999999999999999999999999999 5 99999999999999999999


Q ss_pred             CHHHHHHHHHHH
Q 005668          391 SQEYAAAQELRT  402 (684)
Q Consensus       391 S~vykaA~eLr~  402 (684)
                      ..+|..|..+..
T Consensus       287 k~yyelank~lh  298 (418)
T KOG1828|consen  287 KSYYELANKQLH  298 (418)
T ss_pred             hHHHHHHHhhhh
Confidence            999999987654

>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins

Probab=97.74  E-value=4.5e-05  Score=59.66  Aligned_cols=46  Identities=26%  Similarity=0.567  Sum_probs=39.7

Q ss_pred             ccchhhHHHHHHHHHhhccCCCchHHHHHHHhhcCCCCCCCHHHHHHHHHHH
Q 005668           14 QQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEI   65 (684)
Q Consensus        14 ~~WGTwEELLLacAV~RHGt~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~l   65 (684)
                      +.|..-|+.+|.-||..||..+|+.||..|-      ...|+..|+.+|..|
T Consensus         2 ~~Wt~eE~~~l~~~v~~~g~~~W~~Ia~~~~------~~Rt~~qc~~~~~~~   47 (48)
T PF00249_consen    2 GPWTEEEDEKLLEAVKKYGKDNWKKIAKRMP------GGRTAKQCRSRYQNL   47 (48)
T ss_dssp             -SS-HHHHHHHHHHHHHSTTTHHHHHHHHHS------SSSTHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHhCCcHHHHHHHHcC------CCCCHHHHHHHHHhh
Confidence            4699999999999999999999999999998      234579999999876

These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....

>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains

Probab=97.42  E-value=0.00022  Score=53.32  Aligned_cols=48  Identities=31%  Similarity=0.690  Sum_probs=42.2

Q ss_pred             ccchhhHHHHHHHHHhhccCCCchHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhh
Q 005668           14 QQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEIRRR   68 (684)
Q Consensus        14 ~~WGTwEELLLacAV~RHGt~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~l~~R   68 (684)
                      ..|..-|+.+|..+|..||..+|..||..|..|       |+..|+.+|..|.++
T Consensus         2 ~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~r-------t~~~~~~~~~~~~~~   49 (49)
T smart00717        2 GEWTEEEDELLIELVKKYGKNNWEKIAKELPGR-------TAEQCRERWNNLLKP   49 (49)
T ss_pred             CCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCC-------CHHHHHHHHHHHcCC
Confidence            469999999999999999999999999998744       679999999987653

>COG5076 Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription]

Probab=97.37  E-value=5.3e-05  Score=82.05  Aligned_cols=94  Identities=27%  Similarity=0.366  Sum_probs=86.6

Q ss_pred             HHHHHHhCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCCCCHHHHHH
Q 005668          318 FLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQEYAAA  397 (684)
Q Consensus       318 ILe~L~~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~pdS~vykaA  397 (684)
                      ++..+..+..+|+|..++.....|+|+++|..+|++.|++-+|..+.|.... +|.+|..++|.||..||.....++..+
T Consensus       271 ~i~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~  349 (371)
T COG5076         271 LITNSQAHVGAWPFLRPVSDEEVPDYYKDIRDPMDLSTKELKLRNNYYRPEE-TFVRDAKLFFDNCVMYNGEVTDYYKNA  349 (371)
T ss_pred             cccccccccccccccccCCcccccchhhhhhcccccccchhhhhcccCCCcc-ccccccchhhhcccccchhhhhhhhhc
Confidence            3344467888999999999999999999999999999999999999999996 999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHh
Q 005668          398 QELRTLVIKEMTDML  412 (684)
Q Consensus       398 ~eLr~lf~k~msk~l  412 (684)
                      ..+..+|...+....
T Consensus       350 ~~~~~~~~~~~~~~~  364 (371)
T COG5076         350 NVLEDFVIKKTRLIR  364 (371)
T ss_pred             cchhhhHhhhhhhhh
Confidence            999999988877654

>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains

Probab=96.89  E-value=0.0012  Score=48.63  Aligned_cols=44  Identities=36%  Similarity=0.800  Sum_probs=39.1

Q ss_pred             cchhhHHHHHHHHHhhccCCCchHHHHHHHhhcCCCCCCCHHHHHHHHHHH
Q 005668           15 QWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEI   65 (684)
Q Consensus        15 ~WGTwEELLLacAV~RHGt~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~l   65 (684)
                      .|..-|+-+|-.+|..||..+|+.||..|..|       |+..|+.+|..|
T Consensus         1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~r-------s~~~~~~~~~~~   44 (45)
T cd00167           1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGR-------TPKQCRERWRNL   44 (45)
T ss_pred             CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCC-------CHHHHHHHHHHh
Confidence            48889999999999999999999999998765       578999999765

Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.

>cd05493 Bromo_ALL-1 Bromodomain, ALL-1 like proteins

Probab=96.18  E-value=0.0074  Score=57.78  Aligned_cols=65  Identities=17%  Similarity=0.284  Sum_probs=56.2

Q ss_pred             CCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHHHHHHHhhhc
Q 005668          350 HIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQEYAAAQELRTLVIKEMTDMLRKQ  415 (684)
Q Consensus       350 PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~pdS~vykaA~eLr~lf~k~msk~l~k~  415 (684)
                      |.||.-+++||+.|.|.++. +|.+||..|++=++.--+....+-.+-..+..+|.+.|.+.++-+
T Consensus        59 p~dL~~V~kkl~~G~Y~sv~-~F~~DvvkIiqa~l~~e~~~pe~~ka~s~~Ksf~ik~me~vf~Wf  123 (131)
T cd05493          59 PLDLEAVGKKLEAGFYTSVL-DFSDDIVKIIQAALNSEGGQPEIKKANSMAKSFFIKLMESVFPWF  123 (131)
T ss_pred             cccHHHHHHHHhccceehHH-HHHHHHHHHHHHHHhhccCCccccCcchHHHHHHHHHHHHhcccc
Confidence            88999999999999999998 999999999998887766666666666678889999999988753

ALL-1 is a vertebrate homologue of Drosophila trithorax and is often affected in chromosomal rearrangements that are linked to acute leukemias, such as acute lymphocytic leukemia (ALL). Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.

>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A

Probab=95.80  E-value=0.0086  Score=48.41  Aligned_cols=48  Identities=33%  Similarity=0.731  Sum_probs=37.4

Q ss_pred             chhhHHHHHHHHHhhccCCCchHHHHHHHhhcCCCCCCCHHHHHHHHHH-HHhhhcC
Q 005668           16 WGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNE-IRRRFTV   71 (684)
Q Consensus        16 WGTwEELLLacAV~RHGt~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~-l~~R~~~   71 (684)
                      |.-=|+-+|.-+|..||. +|..||..|-.|       |+..|+.||.. |+..++.
T Consensus         1 WT~eEd~~L~~~~~~~g~-~W~~Ia~~l~~R-------t~~~~~~r~~~~l~~~~~~   49 (60)
T PF13921_consen    1 WTKEEDELLLELVKKYGN-DWKKIAEHLGNR-------TPKQCRNRWRNHLRPKISR   49 (60)
T ss_dssp             S-HHHHHHHHHHHHHHTS--HHHHHHHSTTS--------HHHHHHHHHHTTSTTSTS
T ss_pred             CCHHHHHHHHHHHHHHCc-CHHHHHHHHCcC-------CHHHHHHHHHHHCcccccC
Confidence            566688999999999995 899999988434       57999999999 8765554

...

>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family

Probab=93.67  E-value=0.1  Score=51.64  Aligned_cols=101  Identities=28%  Similarity=0.426  Sum_probs=65.2

Q ss_pred             cccchhhHHHHHHHHHhhcc----C--CCchHHHHHHHhhcCCCCCCCHHHHHHHHHHH-HhhhcCCC----------C-
Q 005668           13 QQQWGTLEELLLACAVNRHG----T--RSWDSIAMEVQNRSSALSSLTPQSCRDKFNEI-RRRFTVKN----------G-   74 (684)
Q Consensus        13 ~~~WGTwEELLLacAV~RHG----t--~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~l-~~R~~~~~----------~-   74 (684)
                      ...|..=|.||||..|+||=    |  ++++-|+.-| +|       |+..|+.+|+-. +.+|....          + 
T Consensus         4 QDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L-~R-------TsAACGFRWNs~VRkqY~~~i~~AKkqRk~~~~   75 (161)
T TIGR02894         4 QDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRAL-NR-------TAAACGFRWNAYVRKQYEEAIELAKKQRKELKR   75 (161)
T ss_pred             ccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHH-cc-------cHHHhcchHHHHHHHHHHHHHHHHHHHHhcccc
Confidence            45799999999999999993    2  4677777554 34       556666665542 33454320          0 


Q ss_pred             --C--CcCCccchHHHHHHH--HHHHHHHHHHhhccchhhHHHHHHHHHHHHh
Q 005668           75 --A--ESTSLVPLVDQLRQI--RVQELRAEVQRRDVSIVSLELKVKRLEEERE  121 (684)
Q Consensus        75 --~--~~~~~~~W~EELRKl--RVAELRRever~d~SIgSLqsKvk~L~eere  121 (684)
                        .  .-.+++..|..|...  .+..|+-|.++-..-+-.||.+++.|+.+-+
T Consensus        76 ~~~~ltl~~vI~fLq~l~~~~~~~~~~~~e~~~l~~e~~~l~~~~e~Le~e~~  128 (161)
T TIGR02894        76 EAGSLTLQDVISFLQNLKTTNPSDQALQKENERLKNQNESLQKRNEELEKELE  128 (161)
T ss_pred             CcccCCHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence              0  123456667666654  4566777777777777788888888887754

In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.

>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A

Probab=91.71  E-value=0.21  Score=42.88  Aligned_cols=71  Identities=24%  Similarity=0.486  Sum_probs=41.1

Q ss_pred             cchhhHHHHHHHHHhhcc-------------CCCchHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhhhcCCCCCC--cCC
Q 005668           15 QWGTLEELLLACAVNRHG-------------TRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEIRRRFTVKNGAE--STS   79 (684)
Q Consensus        15 ~WGTwEELLLacAV~RHG-------------t~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~l~~R~~~~~~~~--~~~   79 (684)
                      .|..=|-++|.-++.-|.             ..-|..||.+|+.+-.   ..|+..|+.||..|.++|-.-....  ...
T Consensus         3 ~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~---~rt~~qc~~Kw~~L~~~Yk~~k~~~~~~~~   79 (90)
T PF13837_consen    3 NWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGY---NRTPEQCRNKWKNLKKKYKKIKDRNKKSGS   79 (90)
T ss_dssp             SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC-------HHHHHHHHHHHHHHHHCSSSSSS----
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCC---CCCHHHHHHHHHHHHHHHHHHHhcCCCCCC
Confidence            466666666665555421             1269999999998743   4699999999999999998754321  112


Q ss_pred             ccchHHHHH
Q 005668           80 LVPLVDQLR   88 (684)
Q Consensus        80 ~~~W~EELR   88 (684)
                      .-+||++|-
T Consensus        80 ~w~~f~~md   88 (90)
T PF13837_consen   80 SWPYFDEMD   88 (90)
T ss_dssp             S---TT---
T ss_pred             cCcCHHHHh
Confidence            335677663

>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]

Probab=90.05  E-value=0.29  Score=57.24  Aligned_cols=52  Identities=35%  Similarity=0.800  Sum_probs=44.6

Q ss_pred             cccchhhHHHHHHHHHhhccCCCchHHHHHHHhhcCCCCCCCHHHHHHHHH-HHHhhhcC
Q 005668           13 QQQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFN-EIRRRFTV   71 (684)
Q Consensus        13 ~~~WGTwEELLLacAV~RHGt~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~-~l~~R~~~   71 (684)
                      .+.|.|=|..+|.|||.|+|..+|--|-.+|=.|+-       .-||.+|. .|++|--.
T Consensus       360 hg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vPnRSd-------sQcR~RY~nvL~~s~K~  412 (939)
T KOG0049|consen  360 HGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVPNRSD-------SQCRERYTNVLNRSAKV  412 (939)
T ss_pred             CCCCCCHHHHHHHHHHHHhCccchhhHHHhcCCccH-------HHHHHHHHHHHHHhhcc
Confidence            468999999999999999999999999999888864       68999996 46766543

>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]

Probab=89.23  E-value=0.3  Score=58.54  Aligned_cols=63  Identities=17%  Similarity=0.252  Sum_probs=53.9

Q ss_pred             hhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHHHH
Q 005668          345 KLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQEYAAAQELRTLVIKEM  408 (684)
Q Consensus       345 eIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~pdS~vykaA~eLr~lf~k~m  408 (684)
                      .----|..|..|+.+|++.+|.++. .|.+|+-.|..||-+|++.+-.+...+..|..+|...+
T Consensus      1048 ~~fpvpls~evi~~rlEn~yYrs~e-~~~hdvs~mlsnae~~fg~~~~~~~ki~~l~~~~~~Tl 1110 (1113)
T KOG0644|consen 1048 NRFPVPLSLEVIRSRLENNYYRSQE-ALRHDVSVMLSNAETFFGRNKNVAIKISFLSPWFDRTL 1110 (1113)
T ss_pred             CCCCCcccHHHHHHHHHhhhhhhhH-hhhcchhhhhcccceeecccccHHHHhhhcchhhhhhc
Confidence            3345688999999999999999998 99999999999999999999877777777777765443

>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]

Probab=87.90  E-value=0.35  Score=54.73  Aligned_cols=46  Identities=26%  Similarity=0.575  Sum_probs=40.4

Q ss_pred             ccccchhhHHHHHHHHHhhccCCCchHHHHHHHhhcCCCCCCCHHHHHHHHHHH
Q 005668           12 QQQQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEI   65 (684)
Q Consensus        12 ~~~~WGTwEELLLacAV~RHGt~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~l   65 (684)
                      ....|.-=|+|||.-+|-+.| ++|+.||.-|++++       ++.|-.+|-.|
T Consensus       278 ~dk~WS~qE~~LLLEGIe~yg-DdW~kVA~HVgtKt-------~EqCIl~FL~L  323 (531)
T COG5259         278 RDKNWSRQELLLLLEGIEMYG-DDWDKVARHVGTKT-------KEQCILHFLQL  323 (531)
T ss_pred             ccccccHHHHHHHHHHHHHhh-hhHHHHHHHhCCCC-------HHHHHHHHHcC
Confidence            345799999999999999998 68999999999876       59999999766

>PLN03212 Transcription repressor MYB5; Provisional

Probab=87.34  E-value=0.61  Score=49.16  Aligned_cols=46  Identities=20%  Similarity=0.442  Sum_probs=37.6

Q ss_pred             cccchhhHHHHHHHHHhhccCCCchHHHHHHHhhcCCCCCCCHHHHHHHHHH
Q 005668           13 QQQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNE   64 (684)
Q Consensus        13 ~~~WGTwEELLLacAV~RHGt~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~   64 (684)
                      ...|..=|.=+|.-+|.+||..+|..||..+-      ...|+..|+.||..
T Consensus        25 Rg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g------~gRT~KQCReRW~N   70 (249)
T PLN03212         25 RGPWTVEEDEILVSFIKKEGEGRWRSLPKRAG------LLRCGKSCRLRWMN   70 (249)
T ss_pred             CCCCCHHHHHHHHHHHHHhCcccHHHHHHhhh------cCCCcchHHHHHHH
Confidence            45688888888889999999999999997763      12467999999974

>KOG0732 consensus AAA+-type ATPase containing the bromodomain [Posttranslational modification, protein turnover, chaperones]

Probab=85.90  E-value=0.37  Score=59.27  Aligned_cols=65  Identities=14%  Similarity=0.116  Sum_probs=58.5

Q ss_pred             CcCCcccccccCccc-----cchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHH--HHHHHHHHHhhhCCCC
Q 005668          325 HRLSSHFERRLRSQE-----SERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFR--DLLLLFNNFVIFFRKS  390 (684)
Q Consensus       325 hk~a~pF~~PVD~qe-----~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~r--DL~LMF~NA~~FN~pd  390 (684)
                      ++....|..|++...     +++|-.+|.++||+...-.++..+.|.++. +|..  ++.|||.|++.||+..
T Consensus       530 ~R~~~~~s~Pl~~~~~~ll~~~~~~~~iq~~~~va~~~~k~~e~~~~~v~-~~e~~~~i~lic~~~lli~~~~  601 (1080)
T KOG0732|consen  530 RRSSVIFSRPLSTYLKPLLPFQDALEDIQGLMDVASSMAKIEEHLKLLVR-SFESNFAIRLICRPRLLINGGK  601 (1080)
T ss_pred             CccccCCCCCCCcceecccchHHHHHHhhcchhHHhhhhhHHHHhHHHHH-hhhcccchhhhcCcHHhcCCCc
Confidence            345778999999652     569999999999999999999999999997 9999  9999999999999976

>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]

Probab=85.65  E-value=1.1  Score=50.49  Aligned_cols=50  Identities=22%  Similarity=0.496  Sum_probs=43.5

Q ss_pred             CcccccccchhhHHHHHHHHHhhccCCCchHHHHHHHhhcCCCCCCCHHHHHHHHHH
Q 005668            8 TTSQQQQQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNE   64 (684)
Q Consensus         8 ~~~~~~~~WGTwEELLLacAV~RHGt~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~   64 (684)
                      +-+-+...|+--|||||.-|+.=.|+++|.-||.=|=+++       .+.|+.-|.-
T Consensus        67 s~~i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIGtKt-------keeck~hy~k  116 (438)
T KOG0457|consen   67 SFPILDPSWTADEEILLLEAAETYGFGNWQDIADHIGTKT-------KEECKEHYLK  116 (438)
T ss_pred             CCCCCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcccc-------hHHHHHHHHH
Confidence            3456778999999999999999999999999998887654       6999998864

>PLN03091 hypothetical protein; Provisional

Probab=84.91  E-value=0.92  Score=51.30  Aligned_cols=45  Identities=20%  Similarity=0.404  Sum_probs=37.7

Q ss_pred             cccchhhHHHHHHHHHhhccCCCchHHHHHHHhhcCCCCCCCHHHHHHHHH
Q 005668           13 QQQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFN   63 (684)
Q Consensus        13 ~~~WGTwEELLLacAV~RHGt~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~   63 (684)
                      ...|..-|.=+|--+|..||..+|..||..+-      ...|+..|+.||.
T Consensus        14 Kg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g------~gRT~KQCRERW~   58 (459)
T PLN03091         14 KGLWSPEEDEKLLRHITKYGHGCWSSVPKQAG------LQRCGKSCRLRWI   58 (459)
T ss_pred             CCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhc------cCcCcchHhHHHH
Confidence            45699999999999999999999999997653      1346789999986

>PRK13923 putative spore coat protein regulator protein YlbO; Provisional

Probab=84.00  E-value=4.1  Score=41.00  Aligned_cols=56  Identities=23%  Similarity=0.336  Sum_probs=36.8

Q ss_pred             cccchhhHHHHHHHHHhhccCCCchHHHH-HHHhhcCCCCCCCHHHHHHHHH-HHHhhhcC
Q 005668           13 QQQWGTLEELLLACAVNRHGTRSWDSIAM-EVQNRSSALSSLTPQSCRDKFN-EIRRRFTV   71 (684)
Q Consensus        13 ~~~WGTwEELLLacAV~RHGt~~WdsVA~-e~~~r~~~~~~~t~~~C~~k~~-~l~~R~~~   71 (684)
                      ...|..=++||||..|+||+.-.=.-+++ |.-... +  .-|+..|..+|+ -|..+|-.
T Consensus         5 qdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~-L--~rt~aac~fRwNs~vrk~Yee   62 (170)
T PRK13923          5 QDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDA-L--KRTAAACGFRWNSVVRKQYQE   62 (170)
T ss_pred             hhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHH-H--hhhHHHHHhHHHHHHHHHHHH
Confidence            45799999999999999999866444443 111110 0  237899999994 34445543

>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]

Probab=83.14  E-value=1.4  Score=48.16  Aligned_cols=47  Identities=26%  Similarity=0.531  Sum_probs=41.6

Q ss_pred             cccccchhhHHHHHHHHHhhccCCCchHHHHHHHhhcCCCCCCCHHHHHHHHHH
Q 005668           11 QQQQQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNE   64 (684)
Q Consensus        11 ~~~~~WGTwEELLLacAV~RHGt~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~   64 (684)
                      -+.+.||--|||||.-+.---|-++|.-||.=|-+|.-       +.|+..|-.
T Consensus        61 I~~e~WgadEEllli~~~~TlGlGNW~dIadyiGsr~k-------ee~k~HylK  107 (432)
T COG5114          61 IGEEGWGADEELLLIECLDTLGLGNWEDIADYIGSRAK-------EEIKSHYLK  107 (432)
T ss_pred             ccCCCcCchHHHHHHHHHHhcCCCcHHHHHHHHhhhhh-------HHHHHHHHH
Confidence            56789999999999999999999999999999988864       889877743

>PLN03212 Transcription repressor MYB5; Provisional

Probab=80.26  E-value=1.9  Score=45.63  Aligned_cols=49  Identities=20%  Similarity=0.239  Sum_probs=39.0

Q ss_pred             cccchhhHHHHHHHHHhhccCCCchHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhhh
Q 005668           13 QQQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEIRRRF   69 (684)
Q Consensus        13 ~~~WGTwEELLLacAV~RHGt~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~l~~R~   69 (684)
                      ...|..-|+.||..+|..||. .|..||..|--||       ...|+-+|..+-+++
T Consensus        78 kgpWT~EED~lLlel~~~~Gn-KWs~IAk~LpGRT-------DnqIKNRWns~LrK~  126 (249)
T PLN03212         78 RGGITSDEEDLILRLHRLLGN-RWSLIAGRIPGRT-------DNEIKNYWNTHLRKK  126 (249)
T ss_pred             cCCCChHHHHHHHHHHHhccc-cHHHHHhhcCCCC-------HHHHHHHHHHHHhHH
Confidence            356777799999999999996 5999999886665       589998887655443

---

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	684
3mqm_A	126	Probable histone-lysine N-methyltransferase ASH1L;	4e-11
3iu5_A	116	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	6e-11
3tlp_A	150	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	2e-10
4alg_A	154	Bromodomain-containing protein 2; signaling protei	5e-10
3k2j_A	130	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	7e-10
3mb4_A	124	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	7e-10
2r0y_A	311	Chromatin structure-remodeling complex protein RSC	2e-09
3rcw_A	135	Bromodomain-containing protein 1; transcription, s	2e-09
3ljw_A	120	Protein polybromo-1; alpha helix, alternative spli	2e-09
3iu6_A	147	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	4e-09
2dat_A	123	Possible global transcription activator SNF2L2; br	5e-09
2ri7_A	174	Nucleosome-remodeling factor subunit BPTF; zinc fi	8e-09
2grc_A	129	Probable global transcription activator SNF2L4; br	1e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-06
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	3e-08
3aad_A	292	Transcription initiation factor TFIID subunit 1; p	3e-08
3aad_A	292	Transcription initiation factor TFIID subunit 1; p	3e-06
3d7c_A	112	General control of amino acid synthesis protein 5;	8e-08
2r10_A	361	Chromatin structure-remodeling complex protein RSC	1e-07
2d9e_A	121	Peregrin; four-helix bundle, transcription activat	2e-07
2i7k_A	117	Bromodomain-containing protein 7; helix, LEFT-hand	2e-07
3g0l_A	117	Hwalp4, bromodomain adjacent to zinc finger domain	3e-07
2oss_A	127	HUNK1 protein, bromodomain-containing protein 4; B	6e-07
3uv5_A	265	Transcription initiation factor TFIID subunit 1; t	7e-07
3uv5_A	265	Transcription initiation factor TFIID subunit 1; t	2e-06
3nxb_A	116	CAT eye syndrome critical region protein 2; struct	8e-07
1e6i_A	121	Transcriptional activator GCN5; gene regulation, b	9e-07
3hme_A	123	Bromodomain-containing protein 9; BRD9, bromodomai	2e-06
3p1f_A	119	CREB-binding protein; structural genomics consorti	4e-06
3uv4_A	158	Second bromodomain of human transcription initiat	4e-06
3jvl_A	120	Bromodomain-containing protein 4; alpha helical, N	7e-06
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	1e-05
3fkm_X	166	Signaling protein; bromodomain, malaria, structura	1e-05
2yyn_A	135	Transcription intermediary factor 1-alpha; bromo d	1e-05
2ouo_A	130	HUNK1 protein, bromodomain-containing protein 4; B	2e-05
3q2e_A	123	Bromodomain and WD repeat-containing protein 1; st	1e-04
1x41_A	60	Transcriptional adaptor 2-like, isoform B; transcr	2e-04
1guu_A	52	C-MYB, MYB proto-oncogene protein; transcription,	6e-04
3mb3_A	135	PH-interacting protein; PHIP, pleckstrin homology	8e-04

>3mqm_A Probable histone-lysine N-methyltransferase ASH1L; KIAA1420, absent small and homeotic disks prote homolog, lysine N-methyltransferase 2H, KMT2H; 2.54A {Homo sapiens} Length = 126

 Score = 59.7 bits (145), Expect = 4e-11
 Identities = 17/94 (18%), Positives = 36/94 (38%), Gaps = 1/94 (1%)

Query: 325 HRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFV 384
             L++        +++  Y + +   +DL TI+ ++  G Y    + F  D+L +F N  
Sbjct: 30  QALAAPLLNLPPKKKNADYYEKISDPLDLITIEKQILTGYYKT-VEAFDADMLKVFRNAE 88

Query: 385 IFFRKSSQEYAAAQELRTLVIKEMTDMLRKQQPI 418
            ++ + S        LR        +   +   I
Sbjct: 89  KYYGRKSPVGRDVCRLRKAYYNARHEASAQIDEI 122

>3iu5_A Protein polybromo-1; PB1, polybromo 1 isoform 1, BAF180, polybromo0ID, PBRM1, BRG associated factor 180, structural genomics, SGC; 1.63A {Homo sapiens} Length = 116

 Score = 58.9 bits (143), Expect = 6e-11
 Identities = 27/92 (29%), Positives = 43/92 (46%), Gaps = 1/92 (1%)

Query: 325 HRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFV 384
             L   F R  + +    Y ++V Q IDL  IQ +L    Y +       D  LLFNN  
Sbjct: 26  RLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDD-VNLLTADFQLLFNNAK 84

Query: 385 IFFRKSSQEYAAAQELRTLVIKEMTDMLRKQQ 416
            +++  S EY AA +L  L ++   + ++K +
Sbjct: 85  SYYKPDSPEYKAACKLWDLYLRTRNEFVQKGE 116

>3tlp_A Protein polybromo-1; PB1, polybromo 1 isoform 1, BAF180, polybromo-1D, PBRM1, BRG associated factor 180, structural genomics consortium, SGC; 2.13A {Homo sapiens} Length = 150

 Score = 58.7 bits (142), Expect = 2e-10
 Identities = 27/153 (17%), Positives = 59/153 (38%), Gaps = 9/153 (5%)

Query: 274 SSDVQSSASLSRNKRRRSGEEPYDEEVSPATKKVLAVKSEPLVRFLGMIRSHRLSSHFER 333
            S + S+ S + + +R+S +    + +      VL  +              RL   F  
Sbjct: 3   DSMISSATSDTGSAKRKSKKNIRKQRMKILFNVVLEAREP--------GSGRRLCDLFMV 54

Query: 334 RLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQE 393
           +   ++   Y K++ + +DL+ I+  +    Y+   +    D+ L+F N   +  + SQ 
Sbjct: 55  KPSKKDYPDYYKIILEPMDLKIIEHNIRNDKYAG-EEGMIEDMKLMFRNARHYNEEGSQV 113

Query: 394 YAAAQELRTLVIKEMTDMLRKQQPIAVTKPKPK 426
           Y  A  L  L+ ++  ++        +  P   
Sbjct: 114 YNDAHILEKLLKEKRKELGPLPDDDDMASPAEN 146

>4alg_A Bromodomain-containing protein 2; signaling protein, inhibitor, histone, epigenetic reader; HET: 1GH; 1.60A {Homo sapiens} PDB: 4a9e_A 4a9h_A* 4a9i_A* 4a9j_A* 4a9m_A* 4a9n_A* 4a9o_A* 4a9p_A* 4a9f_A* 4alh_A* 4akn_A* 2yek_A* 2ydw_A* 2yw5_A Length = 154

 Score = 57.4 bits (139), Expect = 5e-10
 Identities = 32/154 (20%), Positives = 65/154 (42%), Gaps = 9/154 (5%)

Query: 281 ASLSRNKRRRSGEEPYDEEVSPATKKVLAVKSEPLVRFLGMI----RSHRLSSHFERRLR 336
            S   +    SG  P    +S   K      +  L     ++      H+ +  F + + 
Sbjct: 1   GSSHHHHHHSSGLVPRGSHMSNPKKP--GRVTNQLQYLHKVVMKALWKHQFAWPFRQPVD 58

Query: 337 SQESE--RYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQEY 394
           + +     Y K+++Q +D+ TI+ RL+   Y     +  +D   +F N  I+ + +    
Sbjct: 59  AVKLGLPDYHKIIKQPMDMGTIKRRLENNYYWAA-SECMQDFNTMFTNCYIYNKPTDDIV 117

Query: 395 AAAQELRTLVIKEMTDMLRKQQPIAVTKPKPKPK 428
             AQ L  + ++++  M +++Q + VT PK   K
Sbjct: 118 LMAQTLEKIFLQKVASMPQEEQELVVTIPKNSHK 151

>3k2j_A Protein polybromo-1; PB1, polybromo 1 isoform 1, BAF180, polybromo01D, PBRM1, BRG associated factor 180, structural genomics consortium, SGC; 2.20A {Homo sapiens} Length = 130

 Score = 56.6 bits (137), Expect = 7e-10
 Identities = 21/129 (16%), Positives = 49/129 (37%), Gaps = 6/129 (4%)

Query: 288 RRRSGEEPYDEEVSPATKKVLAVKSEPLVRFLGMIRSHRLSSHFERRLRSQESERYKKLV 347
              SG +   E +   + ++        VR     +   ++  F      ++   Y + +
Sbjct: 6   HHSSGVDLGTENLYFQSMQLYDT-----VRSCRNNQGQLIAEPFYHLPSKKKYPDYYQQI 60

Query: 348 RQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQEYAAAQELRTLVIKE 407
           +  I L+ I+++L    Y         DL L+F N   +   +S  Y    +L+ ++  +
Sbjct: 61  KMPISLQQIRTKLKNQEYET-LDHLECDLNLMFENAKRYNVPNSAIYKRVLKLQQVMQAK 119

Query: 408 MTDMLRKQQ 416
             ++ R+  
Sbjct: 120 KKELARRDD 128

>3mb4_A Protein polybromo-1; PB1, polybromo 1 isoform 1, BAF180, polybromo-1D, PBRM1, BRG associated factor 180, structural genomics consortium, SGC; 1.66A {Homo sapiens} PDB: 3g0j_A 2yqd_A Length = 124

 Score = 56.2 bits (136), Expect = 7e-10
 Identities = 24/119 (20%), Positives = 48/119 (40%), Gaps = 7/119 (5%)

Query: 299 EVSPATKKVLAVKSEPLVRFLGMIRS------HRLSSHFERRLRSQESERYKKLVRQHID 352
            +SP   K +    + L      +++       RLS+ F R     E   Y   +++ +D
Sbjct: 4   GISPKKSKYMTPMQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPMD 63

Query: 353 LRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQEYAAAQELRTLVIKEMTDM 411
           +  I+S +    Y +       D +++FNN   +    S  Y  A  L  ++++   D+
Sbjct: 64  MEKIRSHMMANKYQD-IDSMVEDFVMMFNNACTYNEPESLIYKDALVLHKVLLETRRDL 121

>2r0y_A Chromatin structure-remodeling complex protein RSC4; bromodomain, chromatin, remodeler, RSC, acetylation, transcription, chromatin regulator, nucleus, phosphorylation; HET: ALY; 1.75A {Saccharomyces cerevisiae} PDB: 2r0s_A Length = 311

 Score = 58.6 bits (141), Expect = 2e-09
 Identities = 28/158 (17%), Positives = 52/158 (32%), Gaps = 1/158 (0%)

Query: 294 EPYDEEVSPATKKVLAVKSEPLVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDL 353
             Y  ++  AT+K +            +    +LS  F   +   E   Y ++V   + L
Sbjct: 147 LHYLNKLVDATEKKINQALLGASSPKNLDDKVKLSEPFMELVDKDELPEYYEIVHSPMAL 206

Query: 354 RTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQEYAAAQELRTLVIKEMTDMLR 413
             ++  L+ G YS     F  D+LL+F N  IF   S+  Y  A  L       +     
Sbjct: 207 SIVKQNLEIGQYSK-IYDFIIDMLLVFQNAHIFNDPSALIYKDATTLTNYFNYLIQKEFF 265

Query: 414 KQQPIAVTKPKPKPKPEHHRQQPQPPPASLSKPNRGST 451
            +      + +   + +    +             G+ 
Sbjct: 266 PELQDLNERGEINLEFDKFEFENYLAIGGGGPAAAGAL 303

>3rcw_A Bromodomain-containing protein 1; transcription, structural genomics, structural consortium, SGC; 2.21A {Homo sapiens} Length = 135

 Score = 55.1 bits (133), Expect = 2e-09
 Identities = 24/116 (20%), Positives = 47/116 (40%), Gaps = 1/116 (0%)

Query: 315 LVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFR 374
           L   L  ++    +  F + +  +E   Y   ++  +D  T++ RL+   Y N   +F  
Sbjct: 18  LRSVLDQLQDKDPARIFAQPVSLKEVPDYLDHIKHPMDFATMRKRLEAQGYKN-LHEFEE 76

Query: 375 DLLLLFNNFVIFFRKSSQEYAAAQELRTLVIKEMTDMLRKQQPIAVTKPKPKPKPE 430
           D  L+ +N + +  + +  Y AA  LR      +    R+   I + +      PE
Sbjct: 77  DFDLIIDNCMKYNARDTVFYRAAVRLRDQGGVVLRQARREVDSIGLEEASGMHLPE 132

>3ljw_A Protein polybromo-1; alpha helix, alternative splicing, bromodomain, chromatin RE DNA-binding, nucleus, phosphoprotein, transcription; 1.50A {Homo sapiens} PDB: 2ktb_B* 3hmf_A Length = 120

 Score = 54.7 bits (132), Expect = 2e-09
 Identities = 16/69 (23%), Positives = 33/69 (47%), Gaps = 1/69 (1%)

Query: 343 YKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQEYAAAQELRT 402
           Y  ++++ IDL+TI  R+  G Y +      +D+ LL  N   +    SQ +  A  ++ 
Sbjct: 47  YYAIIKEPIDLKTIAQRIQNGSYKS-IHAMAKDIDLLAKNAKTYNEPGSQVFKDANSIKK 105

Query: 403 LVIKEMTDM 411
           +   +  ++
Sbjct: 106 IFYMKKAEI 114

>3iu6_A Protein polybromo-1; PB1, polybromo 1 isoform 1, BAF180, polybromo0ID, PBRM1, BRG associated factor 180, structural genomics, SGC; HET: OCS; 1.79A {Homo sapiens} Length = 147

 Score = 54.9 bits (132), Expect = 4e-09
 Identities = 13/82 (15%), Positives = 27/82 (32%), Gaps = 1/82 (1%)

Query: 351 IDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQEYAAAQELRTLVIKEMTD 410
           +    I+  ++   Y      F   +  +        R  S+ Y  A EL+   IK   +
Sbjct: 50  LTFDIIRKNVENNRYRR-LDLFQEHMFEVLERARRMNRTDSEIYEDAVELQQFFIKIRDE 108

Query: 411 MLRKQQPIAVTKPKPKPKPEHH 432
           + +  + +         K  H+
Sbjct: 109 LCKNGEILLSPALSYTTKHLHN 130

>2dat_A Possible global transcription activator SNF2L2; bromodomain, all alpha protein, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 123

 Score = 53.5 bits (129), Expect = 5e-09
 Identities = 20/87 (22%), Positives = 40/87 (45%), Gaps = 1/87 (1%)

Query: 325 HRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFV 384
            +LS  F +    +E   Y +L+R+ +D + I+ R+    Y +      +D++LL +N  
Sbjct: 34  RQLSEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRS-LGDLEKDVMLLCHNAQ 92

Query: 385 IFFRKSSQEYAAAQELRTLVIKEMTDM 411
            F  + SQ Y  +  L+++        
Sbjct: 93  TFNLEGSQIYEDSIVLQSVFKSARQSG 119

>2ri7_A Nucleosome-remodeling factor subunit BPTF; zinc finger, alpha-helical bundle, dimethyl-lysine, bromodom chromatin regulator, metal-binding, nucleus; HET: MLY; 1.45A {Homo sapiens} PDB: 2fsa_A* 2f6n_A 2f6j_A* 3qzv_A* 3uv2_A* 3qzt_A* 3qzs_A* 2fui_A 2fuu_A* Length = 174

 Score = 54.5 bits (131), Expect = 8e-09
 Identities = 20/97 (20%), Positives = 48/97 (49%), Gaps = 1/97 (1%)

Query: 315 LVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFR 374
           L R L  +++H+++  F   +   ++  Y  ++++ +DL T++ R+ R  Y     +F  
Sbjct: 77  LKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEK-LTEFVA 135

Query: 375 DLLLLFNNFVIFFRKSSQEYAAAQELRTLVIKEMTDM 411
           D+  +F+N   +    S  Y  A+ L +  ++++   
Sbjct: 136 DMTKIFDNCRYYNPSDSPFYQCAEVLESFFVQKLKGF 172

>2grc_A Probable global transcription activator SNF2L4; bromodomain, BRG1, chromatin remodelling, acely-lysine binding, protein-protein interactions; 1.50A {Homo sapiens} PDB: 3uvd_A 2h60_A Length = 129

 Score = 52.8 bits (127), Expect = 1e-08
 Identities = 19/105 (18%), Positives = 45/105 (42%), Gaps = 1/105 (0%)

Query: 315 LVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFR 374
           ++++       +LS  F +    +E   Y +L+R+ +D + I+ R+    Y +      +
Sbjct: 23  VIKYKDSSSGRQLSEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRS-LNDLEK 81

Query: 375 DLLLLFNNFVIFFRKSSQEYAAAQELRTLVIKEMTDMLRKQQPIA 419
           D++LL  N   F  + S  Y  +  L+++       + ++     
Sbjct: 82  DVMLLCQNAQTFNLEGSLIYEDSIVLQSVFTSVRQKIEKEDDSEG 126

>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 = 56.8 bits (136), Expect = 2e-08
 Identities = 70/452 (15%), Positives = 130/452 (28%), Gaps = 126/452 (27%)

Query: 228 KEETD----EDNDKTASEGKVESVKNKTS-----AVGGLSESNE--LWDESKREGKQSSD 276
           KEE D      +  + +     ++ +K        V  +   N   L    K E +Q S 
Sbjct: 48  KEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSM 107

Query: 277 VQSSASLSRNKRRRSGEE--PYD----EEVSPATKKVLAVKSEPLVRFLGM--------- 321
           +       R++     +    Y+    +      + +L ++    V   G+         
Sbjct: 108 MTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVA 167

Query: 322 ---IRSHRLSSHFE--------RRLRSQES--ERYKKLVRQ-------------HIDLRT 355
                S+++    +        +   S E+  E  +KL+ Q             +I LR 
Sbjct: 168 LDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRI 227

Query: 356 --IQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQEYAAAQEL--RTLVI---KEM 408
             IQ+ L R L S   + +   LL+L N  V      + +   A  L  + L+    K++
Sbjct: 228 HSIQAELRRLLKS---KPYENCLLVLLN--V-----QNAKAWNAFNLSCKILLTTRFKQV 277

Query: 409 TDML---RKQQPIAVTKPKPKPKPE---------HHRQQPQPPPASLSKPNRGSTMVVCG 456
           TD L                    E           R Q  P     + P       +  
Sbjct: 278 TDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNP-----RRL-- 330

Query: 457 KRSSIKAISKNAYGKKGDRKDREVEEKPKVNEKKVD---SSFVGIEDKGIKKKRSQERSV 513
             S I    +       D      +    VN  K+     S + + +    +K     SV
Sbjct: 331 --SIIAESIR-------DGLAT-WDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSV 380

Query: 514 SLRRNSR-----------------------SSSRSGDVKHQFGGNELSSHD-TLEAKTEN 549
               ++                           +   V+ Q   + +S     LE K + 
Sbjct: 381 -FPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKL 439

Query: 550 KKENAVKKKKLGAASFLKRMKQNSPSEVMEDD 581
           + E A+ +  +   +  K    +       D 
Sbjct: 440 ENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQ 471

>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 = 56.4 bits (135), Expect = 2e-08
 Identities = 50/464 (10%), Positives = 129/464 (27%), Gaps = 121/464 (26%)

Query: 51  SSLTPQSCRDKFNEIRRRF-------TVKNGAESTSLVPLVDQLRQIRVQELRAEVQRRD 103
           + +    C     +++ +         +KN     +++ ++ +L         +      
Sbjct: 164 TWVALDVCLSY--KVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSS 221

Query: 104 ---VSIVSLELKVKRLEEEREKSMKPEA-----DLESDRKAMPEIEAAVDGD-------G 148
              + I S++ +++RL + +             ++++      +   A +          
Sbjct: 222 NIKLRIHSIQAELRRLLKSK---PYENCLLVLLNVQN-----AKAWNAFNLSCKILLTTR 273

Query: 149 DSNRSFNESNSTTQKAETTNKKQNDDAEGEEEKEQK--------MK----PEPDVENDP- 195
               +   S +TT     T+   +  +      E K         +    P   +  +P 
Sbjct: 274 FKQVTDFLSAATT-----THISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPR 328

Query: 196 ----VQNRTESGPDREDRDW--SSNGKLNENGNGTGNVK---EETDEDNDKTASEGKV-- 244
               +      G    D  W   +  KL         ++      +    +   +     
Sbjct: 329 RLSIIAESIRDGLATWDN-WKHVNCDKLTTI------IESSLNVLEPAEYRKMFDRLSVF 381

Query: 245 -ESVKNKTSAVGGLSESNELWDESKREGKQSSDVQSSASLSRNKR---RRSGEEPY---- 296
             S  +  + +  LS    +W +  +      DV    +         ++  E       
Sbjct: 382 PPSA-HIPTIL--LSL---IWFDVIKS-----DVMVVVNKLHKYSLVEKQPKESTISIPS 430

Query: 297 ---DEEVSPATKKVL---------AVKSEPLVRFL-----GMIRSHRLSSHFERRLRSQE 339
              + +V    +  L           K+      +         SH +  H +     + 
Sbjct: 431 IYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSH-IGHHLKNIEHPER 489

Query: 340 SERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQEYAAAQE 399
              ++ +    +D R ++ ++     +        + L     +  +   +  +Y     
Sbjct: 490 MTLFRMV---FLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVN 546

Query: 400 -----LRT----LVIKEMTDMLRKQQPIAVTKPKPKPKPEHHRQ 434
                L      L+  + TD+LR    IA+         E H+Q
Sbjct: 547 AILDFLPKIEENLICSKYTDLLR----IALMAEDEAIFEEAHKQ 586

>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 = 51.0 bits (121), Expect = 1e-06
 Identities = 76/510 (14%), Positives = 147/510 (28%), Gaps = 159/510 (31%)

Query: 36  WDSIAMEVQNRSSALSSLTPQSCRDKFNEIRRRFTVKNGAESTSLVPLVDQLRQIR--VQ 93
              I  E   R  ++ +      RD+     + F   N       V  +    ++R  + 
Sbjct: 95  MSPIKTE--QRQPSMMTRMYIEQRDRLYNDNQVFAKYN-------VSRLQPYLKLRQALL 145

Query: 94  ELRAEVQRRDVSIV--------SLELKVKRLEEEREKSM-------------KPEADLES 132
           ELR     ++V I          + L V     + +  M              PE  LE 
Sbjct: 146 ELRPA---KNVLIDGVLGSGKTWVALDVCL-SYKVQCKMDFKIFWLNLKNCNSPETVLEM 201

Query: 133 DRKAMPEIEAAVDGDGDSNRSFNESNSTTQKAETTNKKQNDDAEGEEEKEQKMKPEP--- 189
            +K + +I        D N +    +S+  K            + E  +  K KP     
Sbjct: 202 LQKLLYQI--------DPNWTSRSDHSSNIKLRI------HSIQAELRRLLKSKPYENCL 247

Query: 190 ----DVEN----DPVQNR------TESGPDREDRDWSSNGKLNENGNGTGNVKEETDEDN 235
               +V+N    +           T        R       L+            + + +
Sbjct: 248 LVLLNVQNAKAWNAFNLSCKILLTT--------RFKQVTDFLSAA-----TTTHISLDHH 294

Query: 236 DKTASEGKVES-----VKNKTS-----AVGG-----------LSESNELWDESKREG--K 272
             T +  +V+S     +  +        +             + +    WD  K     K
Sbjct: 295 SMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDK 354

Query: 273 QSSDVQSS-ASLSRNKRRRSGEE----PYDEEVSPATKKVL---AVKSEP------LVRF 318
            ++ ++SS   L   + R+  +     P    +      ++    +KS+       L ++
Sbjct: 355 LTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKY 414

Query: 319 LGMIRSHRLSSHFE-----RRLRSQESERY---KKLVRQHIDLRTIQS------RLDRGL 364
             ++      S          L+ +    Y   + +V  +   +T  S       LD+  
Sbjct: 415 -SLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYF 473

Query: 365 YS-------NCFQ----KFFRDLLLLFNNFVIFFRKSSQEYAAAQELRTLVIKEMTDMLR 413
           YS       N         FR + L F     F  +  +  + A      ++  +   L+
Sbjct: 474 YSHIGHHLKNIEHPERMTLFRMVFLDFR----FLEQKIRHDSTAWNASGSILNTLQQ-LK 528

Query: 414 KQQP-IAVTKPKPK----------PKPEHH 432
             +P I    PK +          PK E +
Sbjct: 529 FYKPYICDNDPKYERLVNAILDFLPKIEEN 558

>3o36_A Transcription intermediary factor 1-alpha; TRIM24, PHD finger, bromodomain, H4K16 acetylation, breast C transcription-protein binding complex; HET: ALY; 1.70A {Homo sapiens} PDB: 3o33_A* 3o34_A* 3o35_A* 3o37_A Length = 184

 Score = 53.1 bits (127), Expect = 3e-08
 Identities = 25/100 (25%), Positives = 42/100 (42%), Gaps = 4/100 (4%)

Query: 315 LVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRL--DRGLYSNCFQKF 372
             R L  +  H +S  F +         Y K+++  +DL TI+ RL  D  +YS   + F
Sbjct: 86  CERLLLFLYCHEMSLAF-QDPVPLTVPDYYKIIKNPMDLSTIKKRLQEDYSMYSKP-EDF 143

Query: 373 FRDLLLLFNNFVIFFRKSSQEYAAAQELRTLVIKEMTDML 412
             D  L+F N   F    S+   A  +L     + + ++ 
Sbjct: 144 VADFRLIFQNCAEFNEPDSEVANAGIKLENYFEELLKNLY 183

>3aad_A Transcription initiation factor TFIID subunit 1; protein-protein complex, bromodomain, transcription, transcr regulation, chromatin regulator, transcription-C complex; 3.30A {Homo sapiens} Length = 292

 Score = 54.6 bits (131), Expect = 3e-08
 Identities = 25/172 (14%), Positives = 64/172 (37%), Gaps = 8/172 (4%)

Query: 281 ASLSRNKRRRSGEEPYDEEVSPATKKVLAVKSEPLVRF-------LGMIRSHRLSSHFER 333
             L   K+RR G   + + ++   K +   +++P+V         +  +R    +  F  
Sbjct: 11  QQLPPKKKRRVGTTVHCDYLNRPHKSIHRRRTDPMVTLSSILESIINDMRDLPNTYPFHT 70

Query: 334 RLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQE 393
            + ++  + Y K++ + +DL+T++  + + LY +  ++F   L L+  N   +       
Sbjct: 71  PVNAKVVKDYYKIITRPMDLQTLRENVRKRLYPS-REEFREHLELIVKNSATYNGPKHSL 129

Query: 394 YAAAQELRTLVIKEMTDMLRKQQPIAVTKPKPKPKPEHHRQQPQPPPASLSK 445
              +Q +  L  +++ +   K   +           +              K
Sbjct: 130 TQISQSMLDLCDEKLKEKEDKLARLEKAINPLLDDDDQVAFSFILDNIVTQK 181

>3aad_A Transcription initiation factor TFIID subunit 1; protein-protein complex, bromodomain, transcription, transcr regulation, chromatin regulator, transcription-C complex; 3.30A {Homo sapiens} Length = 292

 Score = 48.5 bits (115), Expect = 3e-06
 Identities = 21/108 (19%), Positives = 42/108 (38%), Gaps = 1/108 (0%)

Query: 322 IRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFN 381
           + +   S  F   +  +    Y K++   +DL TI+  + +  Y +  + F  D+ L+  
Sbjct: 182 MMAVPDSWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQS-RESFLDDVNLILA 240

Query: 382 NFVIFFRKSSQEYAAAQELRTLVIKEMTDMLRKQQPIAVTKPKPKPKP 429
           N V +    SQ    AQE+  +  + +T+       +       K   
Sbjct: 241 NSVKYNGPESQYTKTAQEIVNVCYQTLTEYDEHLTQLEKDICTAKEAA 288

>3d7c_A General control of amino acid synthesis protein 5; GCN5, bromodomain, structural genomics consortium, SGC, HOST-virus interaction, nucleus; 2.06A {Homo sapiens} SCOP: a.29.2.1 PDB: 1f68_A 1jm4_B* 1n72_A 1wug_A* 1wum_A* 1zs5_A* 2rnw_A* 2rnx_A* 3gg3_A Length = 112

 Score = 50.0 bits (120), Expect = 8e-08
 Identities = 23/97 (23%), Positives = 40/97 (41%), Gaps = 1/97 (1%)

Query: 315 LVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFR 374
           L   L  I+SH  +  F   ++  E+  Y +++R  IDL+T+  RL    Y    + F  
Sbjct: 12  LKNLLAQIKSHPSAWPFMEPVKKSEAPDYYEVIRFPIDLKTMTERLRSRYYVT-RKLFVA 70

Query: 375 DLLLLFNNFVIFFRKSSQEYAAAQELRTLVIKEMTDM 411
           DL  +  N   +    S+    A  L      ++ + 
Sbjct: 71  DLQRVIANCREYNPPDSEYCRCASALEKFFYFKLKEG 107

>2r10_A Chromatin structure-remodeling complex protein RSC4, linker, histone H3; bromodomain, remodeler, acetylation, transcription; HET: ALY; 2.20A {Saccharomyces cerevisiae} PDB: 2r0v_A* Length = 361

 Score = 53.3 bits (127), Expect = 1e-07
 Identities = 28/158 (17%), Positives = 52/158 (32%), Gaps = 1/158 (0%)

Query: 294 EPYDEEVSPATKKVLAVKSEPLVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDL 353
             Y  ++  AT+K +            +    +LS  F   +   E   Y ++V   + L
Sbjct: 197 LHYLNKLVDATEKKINQALLGASSPKNLDDKVKLSEPFMELVDKDELPEYYEIVHSPMAL 256

Query: 354 RTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQEYAAAQELRTLVIKEMTDMLR 413
             ++  L+ G YS     F  D+LL+F N  IF   S+  Y  A  L       +     
Sbjct: 257 SIVKQNLEIGQYSK-IYDFIIDMLLVFQNAHIFNDPSALIYKDATTLTNYFNYLIQKEFF 315

Query: 414 KQQPIAVTKPKPKPKPEHHRQQPQPPPASLSKPNRGST 451
            +      + +   + +    +             G+ 
Sbjct: 316 PELQDLNERGEINLEFDKFEFENYLAIGGGGPAAAGAL 353

>2d9e_A Peregrin; four-helix bundle, transcription activator, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 121

 Score = 49.3 bits (118), Expect = 2e-07
 Identities = 23/106 (21%), Positives = 43/106 (40%), Gaps = 4/106 (3%)

Query: 315 LVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFR 374
           L + L  ++     + F   +   E   Y   +++ +D  T++  L+   Y N F  F  
Sbjct: 12  LRKTLEQLQEKDTGNIFSEPVPLSEVPDYLDHIKKPMDFFTMKQNLEAYRYLN-FDDFEE 70

Query: 375 DLLLLFNNFVIFFRKSSQEYAAAQELRTL---VIKEMTDMLRKQQP 417
           D  L+ +N + +  K +  Y AA  LR     V+++      K   
Sbjct: 71  DFNLIVSNCLKYNAKDTIFYRAAVRLREQGGAVLRQARRQAEKMGS 116

>2i7k_A Bromodomain-containing protein 7; helix, LEFT-handed four-helix bundle, transcription; NMR {Homo sapiens} Length = 117

 Score = 48.9 bits (117), Expect = 2e-07
 Identities = 15/100 (15%), Positives = 45/100 (45%), Gaps = 1/100 (1%)

Query: 315 LVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFR 374
           L + +  ++    S+ F   +    +  Y  +++  +D  T++ ++    Y +  ++   
Sbjct: 13  LNQLMRQLQRKDPSAFFSFPVTDFIAPGYSMIIKHPMDFSTMKEKIKNNDYQS-IEELKD 71

Query: 375 DLLLLFNNFVIFFRKSSQEYAAAQELRTLVIKEMTDMLRK 414
           +  L+  N +I+ +  +  Y AA++L    +K ++    +
Sbjct: 72  NFKLMCTNAMIYNKPETIYYKAAKKLLHSGMKILSQERLE 111

>3g0l_A Hwalp4, bromodomain adjacent to zinc finger domain protei; BAZB2, KIAA1 WALP4, structural genomics consortium, SGC, transcription; 2.03A {Homo sapiens} PDB: 3q2f_A* 2e7o_A Length = 117

 Score = 48.8 bits (117), Expect = 3e-07
 Identities = 26/107 (24%), Positives = 45/107 (42%), Gaps = 5/107 (4%)

Query: 311 KSEPLVRFLGMI----RSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYS 366
                +    MI     +H  +  F   +  +    YKK++++ +D  TI+ +L  G Y 
Sbjct: 10  DDSKDLALCSMILTEMETHEDAWPFLLPVNLKLVPGYKKVIKKPMDFSTIREKLSSGQYP 69

Query: 367 NCFQKFFRDLLLLFNNFVIFFRKSSQEYAAAQELRTLVIKEMTDMLR 413
           N  + F  D+ L+F+N   F    S    A   +R    K+ TD  +
Sbjct: 70  NL-ETFALDVRLVFDNCETFNEDDSDIGRAGHNMRKYFEKKWTDTFK 115

>2oss_A HUNK1 protein, bromodomain-containing protein 4; BRD4, structural genomics consortium, SGC, signaling protein; 1.35A {Homo sapiens} PDB: 2yel_A* 3mxf_A* 3p5o_A* 3svf_A* 3svg_A* 3u5j_A* 3u5k_A* 3u5l_A* 3uvw_A* 3uvx_A* 3uvy_A* 3uw9_A* 3zyu_A* 4a9l_A* 4e96_A* 3jvj_A 3jvk_A* 3muk_A* 3mul_A* 2nxb_A ... Length = 127

 Score = 48.1 bits (115), Expect = 6e-07
 Identities = 17/69 (24%), Positives = 36/69 (52%), Gaps = 1/69 (1%)

Query: 343 YKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQEYAAAQELRT 402
           Y K+++  +D+ TI+ RL+   Y N  Q+  +D   +F N  I+ +        A+ L  
Sbjct: 56  YYKIIKTPMDMGTIKKRLENNYYWNA-QECIQDFNTMFTNCYIYNKPGDDIVLMAEALEK 114

Query: 403 LVIKEMTDM 411
           L ++++ ++
Sbjct: 115 LFLQKINEL 123

>3uv5_A Transcription initiation factor TFIID subunit 1; tandem bromodomain, TAF1, cell cycle gene 1 protein, TBP-ASS factor 250 kDa; 2.03A {Homo sapiens} PDB: 1eqf_A Length = 265

 Score = 50.3 bits (120), Expect = 7e-07
 Identities = 23/164 (14%), Positives = 55/164 (33%), Gaps = 16/164 (9%)

Query: 282 SLSRNKRRRSGEEPYDEEVSPATKKVLAVKSEPLVRFLGMIRSHRLSSHFERRLRSQESE 341
           S+S ++RR                      S  L   +  +R    +  F   + ++  +
Sbjct: 1   SMSIHRRRTDPMVTL---------------SSILESIINDMRDLPNTYPFHTPVNAKVVK 45

Query: 342 RYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQEYAAAQELR 401
            Y K++ + +DL+T++  + + LY +  ++F   L L+  N   +          +Q + 
Sbjct: 46  DYYKIITRPMDLQTLRENVRKRLYPS-REEFREHLELIVKNSATYNGPKHSLTQISQSML 104

Query: 402 TLVIKEMTDMLRKQQPIAVTKPKPKPKPEHHRQQPQPPPASLSK 445
            L  +++ +   K   +           +              K
Sbjct: 105 DLCDEKLKEKEDKLARLEKAINPLLDDDDQVAFSFILDNIVTQK 148

>3uv5_A Transcription initiation factor TFIID subunit 1; tandem bromodomain, TAF1, cell cycle gene 1 protein, TBP-ASS factor 250 kDa; 2.03A {Homo sapiens} PDB: 1eqf_A Length = 265

 Score = 48.8 bits (116), Expect = 2e-06
 Identities = 19/88 (21%), Positives = 36/88 (40%), Gaps = 1/88 (1%)

Query: 343 YKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQEYAAAQELRT 402
           Y K++   +DL TI+  + +  Y +  + F  D+ L+  N V +    SQ    AQE+  
Sbjct: 170 YYKVIVNPMDLETIRKNISKHKYQS-RESFLDDVNLILANSVKYNGPESQYTKTAQEIVN 228

Query: 403 LVIKEMTDMLRKQQPIAVTKPKPKPKPE 430
           +  + +T+       +       K    
Sbjct: 229 VCYQTLTEYDEHLTQLEKDICTAKEAAL 256

>3nxb_A CAT eye syndrome critical region protein 2; structural genomics consortium, SGC, CECR2, CAT eye syndrome chromosome region candidate 2, bromodomain; 1.83A {Homo sapiens} Length = 116

 Score = 47.3 bits (113), Expect = 8e-07
 Identities = 18/94 (19%), Positives = 47/94 (50%), Gaps = 1/94 (1%)

Query: 315 LVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFR 374
           + + L ++++H+ S  F   +    +  Y ++++  +D+ +++ +L+ GLY    ++F  
Sbjct: 21  MYKVLDVVKAHKDSWPFLEPVDESYAPNYYQIIKAPMDISSMEKKLNGGLYCT-KEEFVN 79

Query: 375 DLLLLFNNFVIFFRKSSQEYAAAQELRTLVIKEM 408
           D+  +F N   +  +SS+    +  L     + M
Sbjct: 80  DMKTMFRNCRKYNGESSEYTKMSDNLERCFHRAM 113

>1e6i_A Transcriptional activator GCN5; gene regulation, bromodomain, histone binding, N-acetyl lysine; HET: ALY; 1.87A {Saccharomyces cerevisiae} SCOP: a.29.2.1 Length = 121

 Score = 47.3 bits (113), Expect = 9e-07
 Identities = 19/97 (19%), Positives = 46/97 (47%), Gaps = 1/97 (1%)

Query: 315 LVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFR 374
           +   L  +++H  +  F + +  +E   Y   +++ +DL T++ +L+   Y    + F  
Sbjct: 18  IQNILTELQNHAAAWPFLQPVNKEEVPDYYDFIKEPMDLSTMEIKLESNKYQK-MEDFIY 76

Query: 375 DLLLLFNNFVIFFRKSSQEYAAAQELRTLVIKEMTDM 411
           D  L+FNN  ++  +++  Y  A  L      ++ ++
Sbjct: 77  DARLVFNNCRMYNGENTSYYKYANRLEKFFNNKVKEI 113

>3hme_A Bromodomain-containing protein 9; BRD9, bromodomain containing 9 isoform 1, LAVS3040, rhabdomyosarcoma antigen MU-RMS-40.8; 2.23A {Homo sapiens} Length = 123

 Score = 46.6 bits (111), Expect = 2e-06
 Identities = 18/109 (16%), Positives = 46/109 (42%), Gaps = 5/109 (4%)

Query: 315 LVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFR 374
           L  FL  ++       F   +    +  Y  +++  +D  T++ ++    Y +   +F  
Sbjct: 18  LEHFLRQLQRKDPHGFFAFPVTDAIAPGYSMIIKHPMDFGTMKDKIVANEYKS-VTEFKA 76

Query: 375 DLLLLFNNFVIFFRKSSQEYAAAQELRTLVIKEMTDMLRKQQPIAVTKP 423
           D  L+ +N + + R  +  Y  A+++          M+ K++ +A+ + 
Sbjct: 77  DFKLMCDNAMTYNRPDTVYYKLAKKIL----HAGFKMMSKERLLALKRS 121

>3p1f_A CREB-binding protein; structural genomics consortium, SGC, CBP, crebbp, CREB bindi protein isoform A, KAT3A, RSTS, RST, bromodomain, transcrip; HET: 3PF; 1.63A {Homo sapiens} PDB: 3dwy_A 3p1d_A 3p1c_A 3p1e_A* 3svh_A* 4a9k_A* 1jsp_B* 2d82_A* 2l84_A* 2l85_A* 2rny_A* 3i3j_A Length = 119

 Score = 45.4 bits (108), Expect = 4e-06
 Identities = 22/72 (30%), Positives = 42/72 (58%), Gaps = 1/72 (1%)

Query: 343 YKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQEYAAAQELRT 402
           Y  +V+  +DL TI+ +LD G Y   +Q +  D+ L+FNN  ++ RK+S+ Y    +L  
Sbjct: 47  YFDIVKNPMDLSTIKRKLDTGQYQEPWQ-YVDDVWLMFNNAWLYNRKTSRVYKFCSKLAE 105

Query: 403 LVIKEMTDMLRK 414
           +  +E+  +++ 
Sbjct: 106 VFEQEIDPVMQS 117

>3uv4_A Second bromodomain of human transcription initiat TFIID subunit 1 (TAF1); structural genomics consortium, SGC; 1.89A {Homo sapiens} PDB: 3hmh_A Length = 158

 Score = 46.4 bits (110), Expect = 4e-06
 Identities = 21/92 (22%), Positives = 40/92 (43%), Gaps = 5/92 (5%)

Query: 343 YKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQEYAAAQELRT 402
           Y K++   +DL TI+  + +  Y +  + F  D+ L+  N V +    SQ    AQE+  
Sbjct: 63  YYKVIVNPMDLETIRKNISKHKYQS-RESFLDDVNLILANSVKYNGPESQYTKTAQEIVN 121

Query: 403 LVIKEMTDMLRK----QQPIAVTKPKPKPKPE 430
           +  + +T+        ++ I   K     + E
Sbjct: 122 VCYQTLTEYDEHLTQLEKDICTAKEAALEEAE 153

>3jvl_A Bromodomain-containing protein 4; alpha helical, N-acetyl lysine binding domain, signaling protein; 1.20A {Mus musculus} PDB: 3jvm_A 2dww_A 2i8n_A 3oni_A* 2dvv_A* 2e3k_A* 2g4a_A 3s92_A* 2oo1_A* 2e7n_A 2wp1_A* Length = 120

 Score = 44.6 bits (106), Expect = 7e-06
 Identities = 17/69 (24%), Positives = 36/69 (52%), Gaps = 1/69 (1%)

Query: 343 YKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQEYAAAQELRT 402
           Y  +++  +D+ TI+S+L+   Y +  Q+F  D+ L+F+N   +     +  A A++L+ 
Sbjct: 47  YCDIIKHPMDMSTIKSKLESREYRDA-QEFGADVRLMFSNCYKYNPPDHEVVAMARKLQD 105

Query: 403 LVIKEMTDM 411
           +       M
Sbjct: 106 VFEMRFAKM 114

>3lqh_A Histone-lysine N-methyltransferase MLL; PHD finger, bromodomain, leukemia, apoptosis, chromati regulator, DNA-binding, isopeptide bond; 1.72A {Homo sapiens} PDB: 3lqi_A* 3lqj_A* 2kyu_A Length = 183

 Score = 45.4 bits (106), Expect = 1e-05
 Identities = 14/89 (15%), Positives = 37/89 (41%), Gaps = 2/89 (2%)

Query: 321 MIRSHRLSSHFERRLRSQESERYKKL-VRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLL 379
                 L       L S+ +    +   +Q +DL  ++ ++D+G Y++   +F  D++ +
Sbjct: 74  KELQISLKQVLTALLNSRTTSHLLRYRQQQPLDLEGVKRKMDQGNYTSV-LEFSDDIVKI 132

Query: 380 FNNFVIFFRKSSQEYAAAQELRTLVIKEM 408
               +       +   A   +++  I++M
Sbjct: 133 IQAAINSDGGQPEIKKANSMVKSFFIRQM 161

>3fkm_X Signaling protein; bromodomain, malaria, structural genomics, structural genomi consortium, SGC; 2.50A {Plasmodium falciparum 3D7} Length = 166

 Score = 44.8 bits (106), Expect = 1e-05
 Identities = 15/104 (14%), Positives = 41/104 (39%), Gaps = 4/104 (3%)

Query: 343 YKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQEYAAAQELRT 402
           Y  +++  +    I+++L +G Y+   + F +D+ L+F+N  ++   +S      + + T
Sbjct: 56  YYDVIKNPMSFSCIKTKLKKGQYAYPSE-FVKDVQLIFDNCSLYNTSNSVVAITGKNIET 114

Query: 403 LVIKEMTDMLRKQQPIAVTKPKPKPKPEHHRQQPQPPPASLSKP 446
               ++  M        + K K         ++     +   + 
Sbjct: 115 YFNNQLIVM---GYNNFILKEKKINDMLKLVEEENIKWSKEKED 155

>2yyn_A Transcription intermediary factor 1-alpha; bromo domain, structural genomics, NPPSFA; 2.50A {Homo sapiens} Length = 135

 Score = 44.3 bits (105), Expect = 1e-05
 Identities = 23/88 (26%), Positives = 39/88 (44%), Gaps = 8/88 (9%)

Query: 343 YKKLVRQHIDLRTIQSRL--DRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQEYAAAQEL 400
           Y K+++  +DL TI+ RL  D  +YS     F  D  L+F N   F    S+   A  +L
Sbjct: 52  YYKIIKNPMDLSTIKKRLQEDYSMYSKPED-FVADFRLIFQNCAEFNEPDSEVANAGIKL 110

Query: 401 RTLVIKEMTDMLRKQQPIAVTKPKPKPK 428
                + + ++  +++      PK  P 
Sbjct: 111 ENYFEELLKNLYPEKR-----FPKSGPS 133

>2ouo_A HUNK1 protein, bromodomain-containing protein 4; BRD4, structural genomics consortium, SGC, signaling protein; 1.89A {Homo sapiens} PDB: 2yem_A* Length = 130

 Score = 43.9 bits (104), Expect = 2e-05
 Identities = 17/69 (24%), Positives = 36/69 (52%), Gaps = 1/69 (1%)

Query: 343 YKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQEYAAAQELRT 402
           Y  +++  +D+ TI+S+L+   Y +  Q+F  D+ L+F+N   +     +  A A++L+ 
Sbjct: 60  YCDIIKHPMDMSTIKSKLEAREYRD-AQEFGADVRLMFSNCYKYNPPDHEVVAMARKLQD 118

Query: 403 LVIKEMTDM 411
           +       M
Sbjct: 119 VFEMRFAKM 127

>3q2e_A Bromodomain and WD repeat-containing protein 1; structural genomics consortium, SGC, cell cycle progression, signal transduction, apoptosis; 1.74A {Homo sapiens} Length = 123

 Score = 41.6 bits (98), Expect = 1e-04
 Identities = 18/73 (24%), Positives = 36/73 (49%), Gaps = 2/73 (2%)

Query: 343 YKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIF-FRKSSQEYAAAQELR 401
           Y+ ++   +D  T++  LD G Y +  + F +D+ L+F+N   +   K S+ Y+    L 
Sbjct: 43  YRDIIDTPMDFGTVRETLDAGNYDSPLE-FCKDIRLIFSNAKAYTPNKRSKIYSMTLRLS 101

Query: 402 TLVIKEMTDMLRK 414
            L  ++M  +   
Sbjct: 102 ALFEEKMKKISSD 114

>1x41_A Transcriptional adaptor 2-like, isoform B; transcriptional adaptor protein2, transcriptional activation, MYB domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 60

 Score = 38.9 bits (91), Expect = 2e-04
 Identities = 12/57 (21%), Positives = 22/57 (38%), Gaps = 7/57 (12%)

Query: 8  TTSQQQQQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNE 64
          + S     W   EE+ L  AV   G  +W  +A ++  +       T + C   + +
Sbjct: 3  SGSSGDPSWTAQEEMALLEAVMDCGFGNWQDVANQMCTK-------TKEECEKHYMK 52

>1guu_A C-MYB, MYB proto-oncogene protein; transcription, transcription regulation, DNA binding, ION bindi proto-oncogene, nuclear protein, activator; 1.6A {Mus musculus} SCOP: a.4.1.3 PDB: 1mbe_A 1mbf_A Length = 52

 Score = 37.2 bits (87), Expect = 6e-04
 Identities = 13/46 (28%), Positives = 19/46 (41%), Gaps = 7/46 (15%)

Query: 15 QWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRD 60
          +W   E+  L   V ++GT  W  IA  + NR       T   C+ 
Sbjct: 5  RWTREEDEKLKKLVEQNGTDDWKVIANYLPNR-------TDVQCQH 43

>3mb3_A PH-interacting protein; PHIP, pleckstrin homology domain interacting protein, DCAF14 DDB1 and CUL4 associated factor 14, SGC; 2.25A {Homo sapiens} Length = 135

 Score = 39.3 bits (92), Expect = 8e-04
 Identities = 15/73 (20%), Positives = 36/73 (49%), Gaps = 2/73 (2%)

Query: 343 YKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIF-FRKSSQEYAAAQELR 401
           Y+ ++   +D  T++  L+ G Y +  +   +D+ L+F+N   +   K S+ Y+ +  L 
Sbjct: 54  YRDIIDTPMDFATVRETLEAGNYESPME-LCKDVRLIFSNSKAYTPSKRSRIYSMSLRLS 112

Query: 402 TLVIKEMTDMLRK 414
               + ++ +L  
Sbjct: 113 AFFEEHISSVLSD 125

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	684
3g0l_A	117	Hwalp4, bromodomain adjacent to zinc finger domain	99.93
3d7c_A	112	General control of amino acid synthesis protein 5;	99.93
3nxb_A	116	CAT eye syndrome critical region protein 2; struct	99.93
1e6i_A	121	Transcriptional activator GCN5; gene regulation, b	99.93
2d9e_A	121	Peregrin; four-helix bundle, transcription activat	99.92
2dat_A	123	Possible global transcription activator SNF2L2; br	99.92
3mb3_A	135	PH-interacting protein; PHIP, pleckstrin homology	99.92
2yyn_A	135	Transcription intermediary factor 1-alpha; bromo d	99.92
3p1f_A	119	CREB-binding protein; structural genomics consorti	99.92
3q2e_A	123	Bromodomain and WD repeat-containing protein 1; st	99.92
2i7k_A	117	Bromodomain-containing protein 7; helix, LEFT-hand	99.92
2oss_A	127	HUNK1 protein, bromodomain-containing protein 4; B	99.92
4alg_A	154	Bromodomain-containing protein 2; signaling protei	99.92
3iu5_A	116	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.92
3mb4_A	124	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.92
2ouo_A	130	HUNK1 protein, bromodomain-containing protein 4; B	99.92
2grc_A	129	Probable global transcription activator SNF2L4; br	99.91
3rcw_A	135	Bromodomain-containing protein 1; transcription, s	99.91
3hme_A	123	Bromodomain-containing protein 9; BRD9, bromodomai	99.91
3mqm_A	126	Probable histone-lysine N-methyltransferase ASH1L;	99.91
3k2j_A	130	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.91
3ljw_A	120	Protein polybromo-1; alpha helix, alternative spli	99.91
3jvl_A	120	Bromodomain-containing protein 4; alpha helical, N	99.91
3fkm_X	166	Signaling protein; bromodomain, malaria, structura	99.9
2ri7_A	174	Nucleosome-remodeling factor subunit BPTF; zinc fi	99.9
3uv4_A	158	Second bromodomain of human transcription initiat	99.9
3tlp_A	150	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.89
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	99.89
3dai_A	130	ATPase family AAA domain-containing protein 2; anc	99.89
3u5n_A	207	E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b	99.87
3uv5_A	265	Transcription initiation factor TFIID subunit 1; t	99.86
2ro1_A	189	Transcription intermediary factor 1-beta; KAP, TIF	99.86
2dkw_A	131	Hypothetical protein KIAA1240; bromodomain-like, f	99.86
3uv5_A	265	Transcription initiation factor TFIID subunit 1; t	99.85
3aad_A	292	Transcription initiation factor TFIID subunit 1; p	99.84
3aad_A	292	Transcription initiation factor TFIID subunit 1; p	99.84
2r0y_A	311	Chromatin structure-remodeling complex protein RSC	99.83
2r10_A	361	Chromatin structure-remodeling complex protein RSC	99.83
2r10_A	361	Chromatin structure-remodeling complex protein RSC	99.77
2r0y_A	311	Chromatin structure-remodeling complex protein RSC	99.75
3iu6_A	147	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.67
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	99.48
2elk_A	58	SPCC24B10.08C protein; hypothetical protein, struc	97.55
1x41_A	60	Transcriptional adaptor 2-like, isoform B; transcr	97.32
1w0t_A	53	Telomeric repeat binding factor 1; telomere, DNA-b	97.27
3sjm_A	64	Telomeric repeat-binding factor 2; human telomeric	97.2
1guu_A	52	C-MYB, MYB proto-oncogene protein; transcription,	97.08
2yus_A	79	SWI/SNF-related matrix-associated actin- dependent	97.01
2d9a_A	60	B-MYB, MYB-related protein B; DNA binding, structu	96.84
1gvd_A	52	MYB proto-oncogene protein; transcription, transcr	96.69
1ity_A	69	TRF1; helix-turn-helix, telomeres, DNA binding, MY	96.65
2dim_A	70	Cell division cycle 5-like protein; MYB_DNA-bindin	96.56
2cu7_A	72	KIAA1915 protein; nuclear protein, SANT domain, DN	96.38
2llk_A	73	Cyclin-D-binding MYB-like transcription factor 1;	96.08
2din_A	66	Cell division cycle 5-like protein; MYB_DNA-bindin	95.93
2k9n_A	107	MYB24; R2R3 domain, DNA-binding, nucleus, DNA bind	95.77
2ltp_A	89	Nuclear receptor corepressor 2; SMRT, TRAC, SGC, s	94.74
2ckx_A	83	NGTRF1, telomere binding protein TBP1; nuclear pro	95.73
2k9n_A	107	MYB24; R2R3 domain, DNA-binding, nucleus, DNA bind	95.7
2yum_A	75	ZZZ3 protein, zinc finger ZZ-type-containing prote	95.62
2roh_A	122	RTBP1, telomere binding protein-1; plant, nucleus,	95.45
2cqr_A	73	RSGI RUH-043, DNAJ homolog subfamily C member 1; m	95.26
1gv2_A	105	C-MYB, MYB proto-oncogene protein; transcription,	95.19
3osg_A	126	MYB21; transcription-DNA complex, MYB2, R2R3 domai	95.11
3zqc_A	131	MYB3; transcription-DNA complex, DNA-binding prote	95.07
2juh_A	121	Telomere binding protein TBP1; helix, nucleus, nuc	95.03
2aje_A	105	Telomere repeat-binding protein; DNA-binding, Trp,	94.85
3osg_A	126	MYB21; transcription-DNA complex, MYB2, R2R3 domai	94.72
1gv2_A	105	C-MYB, MYB proto-oncogene protein; transcription,	94.57
2iw5_B	235	Protein corest, REST corepressor 1; oxidoreductase	94.37
1h8a_C	128	AMV V-MYB, MYB transforming protein; transcription	94.37
2cjj_A	93	Radialis; plant development, DNA-binding protein,	94.04
1h8a_C	128	AMV V-MYB, MYB transforming protein; transcription	92.75
1h89_C	159	C-MYB, MYB proto-oncogene protein; transcription/D	92.67
1h89_C	159	C-MYB, MYB proto-oncogene protein; transcription/D	92.51
2eqr_A	61	N-COR1, N-COR, nuclear receptor corepressor 1; SAN	91.89
2ebi_A	86	DNA binding protein GT-1; DNA-binding domain, phos	91.87
1wgx_A	73	KIAA1903 protein; MYB DNA-binding domain, human cD	91.72
2cqq_A	72	RSGI RUH-037, DNAJ homolog subfamily C member 1; m	91.61
3zqc_A	131	MYB3; transcription-DNA complex, DNA-binding prote	91.18
2xag_B	482	REST corepressor 1; amine oxidase, chromatin regul	84.44

>3g0l_A Hwalp4, bromodomain adjacent to zinc finger domain protei; BAZB2, KIAA1 WALP4, structural genomics consortium, SGC, transcription; 2.03A {Homo sapiens} PDB: 3q2f_A* 2e7o_A

Probab=99.93  E-value=6.8e-26  Score=204.71  Aligned_cols=101  Identities=25%  Similarity=0.332  Sum_probs=98.0

Q ss_pred             chHHHHHHHHHHhCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCCCC
Q 005668          312 SEPLVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSS  391 (684)
Q Consensus       312 skpLl~ILe~L~~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~pdS  391 (684)
                      .+.|..||+.|..|+.+++|..||+...+|+||++|++||||+||+.||+++.|.++. +|..||.|||.||++||+++|
T Consensus        15 ~~~c~~il~~l~~~~~s~~F~~pv~~~~~pdY~~~I~~Pmdl~tI~~kl~~~~Y~~~~-~f~~D~~li~~Na~~yN~~~s   93 (117)
T 3g0l_A           15 LALCSMILTEMETHEDAWPFLLPVNLKLVPGYKKVIKKPMDFSTIREKLSSGQYPNLE-TFALDVRLVFDNCETFNEDDS   93 (117)
T ss_dssp             HHHHHHHHHHHHTSTTCGGGSSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCCSHH-HHHHHHHHHHHHHHHHSCSSS
T ss_pred             HHHHHHHHHHHHhCCCchhhcCcCChhhcCChHHHcCCCCCHHHHHHHHhCCCCCCHH-HHHHHHHHHHHHHHHHCCCCC
Confidence            4679999999999999999999999999999999999999999999999999999998 999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHhh
Q 005668          392 QEYAAAQELRTLVIKEMTDMLR  413 (684)
Q Consensus       392 ~vykaA~eLr~lf~k~msk~l~  413 (684)
                      .+|.+|..|+.+|++.|.+++.
T Consensus        94 ~~~~~A~~L~~~f~~~~~~~~~  115 (117)
T 3g0l_A           94 DIGRAGHNMRKYFEKKWTDTFK  115 (117)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHc
Confidence            9999999999999999998874

>3d7c_A General control of amino acid synthesis protein 5; GCN5, bromodomain, structural genomics consortium, SGC, HOST-virus interaction, nucleus; 2.06A {Homo sapiens} SCOP: a.29.2.1 PDB: 1f68_A 1jm4_B* 1n72_A 1wug_A* 1wum_A* 1zs5_A* 2rnw_A* 2rnx_A* 3gg3_A

Probab=99.93  E-value=7.1e-26  Score=203.37  Aligned_cols=99  Identities=23%  Similarity=0.298  Sum_probs=95.6

Q ss_pred             hHHHHHHHHHHhCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCCCCH
Q 005668          313 EPLVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQ  392 (684)
Q Consensus       313 kpLl~ILe~L~~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~pdS~  392 (684)
                      ..|..||+.|..|+.+++|..||+...+|+||++|++||||+||+.||++|.|.++. +|.+||.|||.||++||+++|.
T Consensus        10 ~~~~~il~~l~~~~~~~~F~~pvd~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~-~f~~Dv~li~~Na~~yN~~~s~   88 (112)
T 3d7c_A           10 TTLKNLLAQIKSHPSAWPFMEPVKKSEAPDYYEVIRFPIDLKTMTERLRSRYYVTRK-LFVADLQRVIANCREYNPPDSE   88 (112)
T ss_dssp             HHHHHHHHHHHHSGGGGGGSSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCCSHH-HHHHHHHHHHHHHHHHSCTTSH
T ss_pred             HHHHHHHHHHHcCCCchhhcCCCCcccccCHHHHccCCcCHHHHHHHHcCCCCcCHH-HHHHHHHHHHHHHHHHCCCCCH
Confidence            568999999999999999999999999999999999999999999999999999998 9999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHh
Q 005668          393 EYAAAQELRTLVIKEMTDML  412 (684)
Q Consensus       393 vykaA~eLr~lf~k~msk~l  412 (684)
                      +|.+|..|+.+|.+.|.++.
T Consensus        89 ~~~~A~~L~~~f~~~~~~~~  108 (112)
T 3d7c_A           89 YCRCASALEKFFYFKLKEGG  108 (112)
T ss_dssp             HHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHCC
Confidence            99999999999999998753

>3nxb_A CAT eye syndrome critical region protein 2; structural genomics consortium, SGC, CECR2, CAT eye syndrome chromosome region candidate 2, bromodomain; 1.83A {Homo sapiens} SCOP: a.29.2.0

Probab=99.93  E-value=7.7e-26  Score=204.07  Aligned_cols=99  Identities=18%  Similarity=0.353  Sum_probs=95.4

Q ss_pred             chHHHHHHHHHHhCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCCCC
Q 005668          312 SEPLVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSS  391 (684)
Q Consensus       312 skpLl~ILe~L~~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~pdS  391 (684)
                      .+.|..||+.|..|+.+++|..||+...+|+||++|++||||+||+.||+++.|.++. +|..||.|||.||++||+++|
T Consensus        18 ~~~~~~il~~l~~~~~s~~F~~pv~~~~~pdY~~~I~~Pmdl~tI~~kl~~~~Y~~~~-~f~~D~~li~~Na~~yN~~~s   96 (116)
T 3nxb_A           18 FTAMYKVLDVVKAHKDSWPFLEPVDESYAPNYYQIIKAPMDISSMEKKLNGGLYCTKE-EFVNDMKTMFRNCRKYNGESS   96 (116)
T ss_dssp             HHHHHHHHHHHHHSTTCGGGSSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCSSHH-HHHHHHHHHHHHHHHHHCTTC
T ss_pred             HHHHHHHHHHHHhCCCcHhhcCcCChhhccChHHHcCCCCCHHHHHHHHcCCCCCCHH-HHHHHHHHHHHHHHHHCCCCC
Confidence            4789999999999999999999999999999999999999999999999999999998 999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHH
Q 005668          392 QEYAAAQELRTLVIKEMTDM  411 (684)
Q Consensus       392 ~vykaA~eLr~lf~k~msk~  411 (684)
                      .+|.+|..|+.+|++.|.++
T Consensus        97 ~~~~~A~~L~~~f~~~~~kh  116 (116)
T 3nxb_A           97 EYTKMSDNLERCFHRAMMKH  116 (116)
T ss_dssp             HHHHHHHHHHHHHHHHHHC-
T ss_pred             HHHHHHHHHHHHHHHHHhhC
Confidence            99999999999999998753

>1e6i_A Transcriptional activator GCN5; gene regulation, bromodomain, histone binding, N-acetyl lysine; HET: ALY; 1.87A {Saccharomyces cerevisiae} SCOP: a.29.2.1

Probab=99.93  E-value=1.3e-25  Score=204.80  Aligned_cols=100  Identities=19%  Similarity=0.375  Sum_probs=96.5

Q ss_pred             chHHHHHHHHHHhCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCCCC
Q 005668          312 SEPLVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSS  391 (684)
Q Consensus       312 skpLl~ILe~L~~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~pdS  391 (684)
                      ...|..||+.|..|+.+++|..||+...+|+||++|++||||+||+.||++|.|.++. +|.+||+|||+||++||+++|
T Consensus        15 ~~~~~~il~~l~~~~~a~~F~~pvd~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~-~f~~D~~li~~Na~~yN~~~s   93 (121)
T 1e6i_A           15 DAAIQNILTELQNHAAAWPFLQPVNKEEVPDYYDFIKEPMDLSTMEIKLESNKYQKME-DFIYDARLVFNNCRMYNGENT   93 (121)
T ss_dssp             HHHHHHHHHHHHHSTTCGGGSSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCSSHH-HHHHHHHHHHHHHHHHSCTTS
T ss_pred             HHHHHHHHHHHHcCCCchhhCCCCChhhCcCHHHHcCCCCCHHHHHHHHhcCCCCCHH-HHHHHHHHHHHHHHHHCCCCC
Confidence            3679999999999999999999999999999999999999999999999999999998 999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHh
Q 005668          392 QEYAAAQELRTLVIKEMTDML  412 (684)
Q Consensus       392 ~vykaA~eLr~lf~k~msk~l  412 (684)
                      .+|.+|..|+.+|.+.|..+.
T Consensus        94 ~i~~~A~~L~~~f~~~~~~~p  114 (121)
T 1e6i_A           94 SYYKYANRLEKFFNNKVKEIP  114 (121)
T ss_dssp             HHHHHHHHHHHHHHHHHHTSG
T ss_pred             HHHHHHHHHHHHHHHHHHHcc
Confidence            999999999999999998754

>2d9e_A Peregrin; four-helix bundle, transcription activator, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.92  E-value=1.9e-25  Score=203.87  Aligned_cols=100  Identities=21%  Similarity=0.233  Sum_probs=96.0

Q ss_pred             hHHHHHHHHHHhCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCCCCH
Q 005668          313 EPLVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQ  392 (684)
Q Consensus       313 kpLl~ILe~L~~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~pdS~  392 (684)
                      ..|..||+.|..|+.+++|..||+...+|+||++|++||||.||+.||+++.|.++. +|.+||+|||.||++||+++|.
T Consensus        10 ~~l~~il~~l~~~~~~~~F~~pv~~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~-ef~~D~~li~~Na~~yN~~~s~   88 (121)
T 2d9e_A           10 ILLRKTLEQLQEKDTGNIFSEPVPLSEVPDYLDHIKKPMDFFTMKQNLEAYRYLNFD-DFEEDFNLIVSNCLKYNAKDTI   88 (121)
T ss_dssp             HHHHHHHHHHHHHCSSCSSSSCCCTTTCTTHHHHCSSCCCHHHHHHHHHTTCCCSHH-HHHHHHHHHHHHHHHHSCTTSH
T ss_pred             HHHHHHHHHHHcCCccHhhCCcCCccccCCHHHHcCCCcCHHHHHHHHhcCCCCCHH-HHHHHHHHHHHHHHHHCCCCCH
Confidence            568999999999999999999999999999999999999999999999999999998 9999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHhh
Q 005668          393 EYAAAQELRTLVIKEMTDMLR  413 (684)
Q Consensus       393 vykaA~eLr~lf~k~msk~l~  413 (684)
                      +|.+|..|+.+|...|.+...
T Consensus        89 ~~~~A~~L~~~~~~~l~~~~~  109 (121)
T 2d9e_A           89 FYRAAVRLREQGGAVLRQARR  109 (121)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999988877654

>2dat_A Possible global transcription activator SNF2L2; bromodomain, all alpha protein, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.92  E-value=1.6e-25  Score=204.58  Aligned_cols=100  Identities=20%  Similarity=0.294  Sum_probs=94.9

Q ss_pred             chHHHHHHHHHHhCc------CCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhh
Q 005668          312 SEPLVRFLGMIRSHR------LSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVI  385 (684)
Q Consensus       312 skpLl~ILe~L~~hk------~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~  385 (684)
                      .+.|..||+.|+.++      .+++|..||+...+|+||++|++||||.||++||+++.|.++. +|.+||+|||.||++
T Consensus        15 ~~~~~~il~~l~~~~d~~g~~~s~~F~~pv~~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~-~f~~D~~li~~Na~~   93 (123)
T 2dat_A           15 TKQMNAIIDTVINYKDSSGRQLSEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLG-DLEKDVMLLCHNAQT   93 (123)
T ss_dssp             HHHHHHHHHHHHHCBCSSSCBSGGGGTSCCCTTTSCHHHHHCSSCCCHHHHHHHHTTTCCCSHH-HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhhcccCCeeeHHhcCCCCcccCCCHHHHcCCCCCHHHHHHHHhCCCCCCHH-HHHHHHHHHHHHHHH
Confidence            367999999999886      6999999999999999999999999999999999999999998 999999999999999


Q ss_pred             hCCCCCHHHHHHHHHHHHHHHHHHHHh
Q 005668          386 FFRKSSQEYAAAQELRTLVIKEMTDML  412 (684)
Q Consensus       386 FN~pdS~vykaA~eLr~lf~k~msk~l  412 (684)
                      ||+++|.+|.+|..|+.+|++.|++++
T Consensus        94 yN~~~s~i~~~A~~L~~~f~~~~~~~p  120 (123)
T 2dat_A           94 FNLEGSQIYEDSIVLQSVFKSARQSGP  120 (123)
T ss_dssp             HSCTTSHHHHHHHHHHHHHHHHHHSSS
T ss_pred             HCCCCCHHHHHHHHHHHHHHHHHHHcC
Confidence            999999999999999999999988655

>3mb3_A PH-interacting protein; PHIP, pleckstrin homology domain interacting protein, DCAF14 DDB1 and CUL4 associated factor 14, SGC; 2.25A {Homo sapiens}

Probab=99.92  E-value=2.5e-25  Score=205.73  Aligned_cols=103  Identities=18%  Similarity=0.343  Sum_probs=99.4

Q ss_pred             CchHHHHHHHHHHhCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCC-
Q 005668          311 KSEPLVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRK-  389 (684)
Q Consensus       311 kskpLl~ILe~L~~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~p-  389 (684)
                      ..+.|..||+.|..|+.+++|..||+...+|+||++|++||||.||+.||.+|.|.++. +|..||.|||.||++||++ 
T Consensus        22 l~~~~~~il~~l~~~~~s~~F~~pv~~~~~pdY~~iI~~Pmdl~tI~~kl~~~~Y~~~~-~f~~D~~li~~Na~~yN~~~  100 (135)
T 3mb3_A           22 WKKQCEELLNLIFQCEDSEPFRQPVDLLEYPDYRDIIDTPMDFATVRETLEAGNYESPM-ELCKDVRLIFSNSKAYTPSK  100 (135)
T ss_dssp             HHHHHHHHHHHHHHSGGGGGGSSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCSSHH-HHHHHHHHHHHHHHHHSCCT
T ss_pred             HHHHHHHHHHHHHhCCCChhhcCCCChhhCCCHHHHhCCCcCHHHHHHHHhCCCCCCHH-HHHHHHHHHHHHHHHHCCCC
Confidence            34679999999999999999999999999999999999999999999999999999998 9999999999999999998 


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHhhh
Q 005668          390 SSQEYAAAQELRTLVIKEMTDMLRK  414 (684)
Q Consensus       390 dS~vykaA~eLr~lf~k~msk~l~k  414 (684)
                      +|.+|.+|..|+.+|++.|..+++.
T Consensus       101 ~s~i~~~A~~L~~~f~~~~~~~~~~  125 (135)
T 3mb3_A          101 RSRIYSMSLRLSAFFEEHISSVLSD  125 (135)
T ss_dssp             TCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            8999999999999999999999876

>2yyn_A Transcription intermediary factor 1-alpha; bromo domain, structural genomics, NPPSFA; 2.50A {Homo sapiens}

Probab=99.92  E-value=2.6e-25  Score=206.42  Aligned_cols=103  Identities=23%  Similarity=0.378  Sum_probs=98.2

Q ss_pred             cCchHHHHHHHHHHhCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhC--CCccCcHHHHHHHHHHHHHHHhhhC
Q 005668          310 VKSEPLVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDR--GLYSNCFQKFFRDLLLLFNNFVIFF  387 (684)
Q Consensus       310 ~kskpLl~ILe~L~~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~--g~YsSi~~EF~rDL~LMF~NA~~FN  387 (684)
                      ...+.|..||..|+.|+.+++|..||+. .+|+||+||++||||.||+.||++  +.|.++. +|.+||+|||+||++||
T Consensus        20 ~~~~~c~~il~~L~~~~~s~~F~~Pv~~-~~pdY~~iIk~PmDL~tI~~kL~~~~~~Y~s~~-ef~~Dv~Lif~Na~~yN   97 (135)
T 2yyn_A           20 IDKRKCERLLLFLYCHEMSLAFQDPVPL-TVPDYYKIIKNPMDLSTIKKRLQEDYSMYSKPE-DFVADFRLIFQNCAEFN   97 (135)
T ss_dssp             HHHHHHHHHHHHHHTSGGGGGGSSCCCT-TSTTHHHHCSSCCCHHHHHHHHHSSSCCCSSHH-HHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHHhCccchhhcCCCcc-cCCCHHHHcCCCCCHHHHHHHHhccccCCCCHH-HHHHHHHHHHHHHHHHC
Confidence            3446799999999999999999999997 799999999999999999999998  5899998 99999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHhhh
Q 005668          388 RKSSQEYAAAQELRTLVIKEMTDMLRK  414 (684)
Q Consensus       388 ~pdS~vykaA~eLr~lf~k~msk~l~k  414 (684)
                      +++|.+|.+|..|+.+|++.|.++++.
T Consensus        98 ~~~s~i~~~A~~L~~~f~~~~~~~~~~  124 (135)
T 2yyn_A           98 EPDSEVANAGIKLENYFEELLKNLYPE  124 (135)
T ss_dssp             CTTSHHHHHHHHHHHHHHHHHHHHSSS
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHhccc
Confidence            999999999999999999999999976

>3p1f_A CREB-binding protein; structural genomics consortium, SGC, CBP, crebbp, CREB bindi protein isoform A, KAT3A, RSTS, RST, bromodomain, transcrip; HET: 3PF; 1.63A {Homo sapiens} SCOP: a.29.2.1 PDB: 3dwy_A 3p1d_A 3p1c_A 3p1e_A* 3svh_A* 4a9k_A* 1jsp_B* 2d82_A* 2l84_A* 2l85_A* 2rny_A* 3i3j_A

Probab=99.92  E-value=3.4e-25  Score=200.65  Aligned_cols=101  Identities=26%  Similarity=0.455  Sum_probs=96.1

Q ss_pred             hHHHHHHHHHHh-CcCCcccccccCcc--ccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCC
Q 005668          313 EPLVRFLGMIRS-HRLSSHFERRLRSQ--ESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRK  389 (684)
Q Consensus       313 kpLl~ILe~L~~-hk~a~pF~~PVD~q--e~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~p  389 (684)
                      +.|+.+|+.|.. ++.+++|..||++.  ++|+||++|++||||+||+.||++|.|.++. +|..||.|||.||++||++
T Consensus        14 ~~l~~~l~~l~~~~~~s~~F~~pv~~~~~~~pdY~~iI~~Pmdl~tI~~kl~~~~Y~~~~-~f~~D~~li~~Na~~yN~~   92 (119)
T 3p1f_A           14 QALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPW-QYVDDVWLMFNNAWLYNRK   92 (119)
T ss_dssp             HHHHHHHHHHHTCTTTTGGGSSCCCHHHHTCTTHHHHCSSCCCHHHHHHHHHTTCCSSHH-HHHHHHHHHHHHHHHHSCT
T ss_pred             HHHHHHHHHHHHhCCCCchhcCCCCchhccCCCHHHHhcCCCCHHHHHHHHhcCCCCCHH-HHHHHHHHHHHHHHHHCCC
Confidence            568889999877 78999999999987  7999999999999999999999999999998 9999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHhhh
Q 005668          390 SSQEYAAAQELRTLVIKEMTDMLRK  414 (684)
Q Consensus       390 dS~vykaA~eLr~lf~k~msk~l~k  414 (684)
                      +|.+|.+|..|+.+|++.|..++..
T Consensus        93 ~s~i~~~A~~L~~~f~~~~~~~~~~  117 (119)
T 3p1f_A           93 TSRVYKFCSKLAEVFEQEIDPVMQS  117 (119)
T ss_dssp             TSHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHh
Confidence            9999999999999999999998864

>3q2e_A Bromodomain and WD repeat-containing protein 1; structural genomics consortium, SGC, cell cycle progression, signal transduction, apoptosis; 1.74A {Homo sapiens}

Probab=99.92  E-value=3.6e-25  Score=201.97  Aligned_cols=104  Identities=20%  Similarity=0.364  Sum_probs=99.9

Q ss_pred             chHHHHHHHHHHhCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCC-C
Q 005668          312 SEPLVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRK-S  390 (684)
Q Consensus       312 skpLl~ILe~L~~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~p-d  390 (684)
                      .+.|..||+.|..|+.+++|..||+...+|+||++|++||||.||+.||.++.|.++. +|..||.|||.||++||++ +
T Consensus        12 ~~~c~~il~~l~~~~~s~~F~~pv~~~~~pdY~~~I~~PmdL~tI~~kl~~~~Y~~~~-~f~~D~~li~~Na~~yN~~~~   90 (123)
T 3q2e_A           12 KKQCKELVNLIFQCEDSEPFRQPVDLVEYPDYRDIIDTPMDFGTVRETLDAGNYDSPL-EFCKDIRLIFSNAKAYTPNKR   90 (123)
T ss_dssp             HHHHHHHHHHHHTSGGGGGGSSCCCTTTCTTHHHHCSSCCCHHHHHHHHHTTCCSSHH-HHHHHHHHHHHHHHHHSCCTT
T ss_pred             HHHHHHHHHHHHhCCCcHhhcCCCChhhcCCHHHHcCCCCCHHHHHHHHhcCCCCCHH-HHHHHHHHHHHHHHHHCCCCC
Confidence            3679999999999999999999999999999999999999999999999999999998 9999999999999999996 9


Q ss_pred             CHHHHHHHHHHHHHHHHHHHHhhhcC
Q 005668          391 SQEYAAAQELRTLVIKEMTDMLRKQQ  416 (684)
Q Consensus       391 S~vykaA~eLr~lf~k~msk~l~k~~  416 (684)
                      |.+|.+|..|+.+|.+.|.++++.+.
T Consensus        91 s~i~~~A~~L~~~f~~~~~~~~~~~~  116 (123)
T 3q2e_A           91 SKIYSMTLRLSALFEEKMKKISSDFK  116 (123)
T ss_dssp             SHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999998744

>2i7k_A Bromodomain-containing protein 7; helix, LEFT-handed four-helix bundle, transcription; NMR {Homo sapiens}

Probab=99.92  E-value=3.6e-25  Score=201.31  Aligned_cols=101  Identities=16%  Similarity=0.275  Sum_probs=96.7

Q ss_pred             hHHHHHHHHHHhCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCCCCH
Q 005668          313 EPLVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQ  392 (684)
Q Consensus       313 kpLl~ILe~L~~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~pdS~  392 (684)
                      ..|..||+.|..++.+++|..||+...+|+||+||++||||+||++||.+|.|.++. +|.+||+|||+||++||+++|.
T Consensus        11 ~~l~~il~~L~~~~~~~~F~~PVd~~~~pdY~~iIk~PMDL~tI~~kl~~~~Y~s~~-ef~~Dv~Li~~Na~~yN~~~s~   89 (117)
T 2i7k_A           11 EALNQLMRQLQRKDPSAFFSFPVTDFIAPGYSMIIKHPMDFSTMKEKIKNNDYQSIE-ELKDNFKLMCTNAMIYNKPETI   89 (117)
T ss_dssp             HHHHHHHHHHHTSSGGGTSSSCCCTTTSSSHHHHCSCCCCHHHHHHHHTTTSCCSHH-HHHHHHHHHHHHHHHTSCSSSS
T ss_pred             HHHHHHHHHHHhCcccHHhcCCCCccccCCHHHHhCCCCCHHHHHHHHHcCCCCCHH-HHHHHHHHHHHHHHHHCCCCCH
Confidence            568889999999999999999999999999999999999999999999999999998 9999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHhhh
Q 005668          393 EYAAAQELRTLVIKEMTDMLRK  414 (684)
Q Consensus       393 vykaA~eLr~lf~k~msk~l~k  414 (684)
                      +|.+|..|++.|.+.+...+-+
T Consensus        90 i~~~A~~L~~~f~~~~~~~~~~  111 (117)
T 2i7k_A           90 YYKAAKKLLHSGMKILSQERLE  111 (117)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTCS
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999988743

>2oss_A HUNK1 protein, bromodomain-containing protein 4; BRD4, structural genomics consortium, SGC, signaling protein; 1.35A {Homo sapiens} PDB: 2yel_A* 3mxf_A* 3p5o_A* 3svf_A* 3svg_A* 3u5j_A* 3u5k_A* 3u5l_A* 3uvw_A* 3uvx_A* 3uvy_A* 3uw9_A* 3zyu_A* 4a9l_A* 4e96_A* 3jvj_A 3jvk_A* 3muk_A* 3mul_A* 2nxb_A ...

Probab=99.92  E-value=2.8e-25  Score=204.29  Aligned_cols=97  Identities=21%  Similarity=0.400  Sum_probs=91.9

Q ss_pred             HHHHHHHHHhCcCCcccccccCcc--ccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCCCCH
Q 005668          315 LVRFLGMIRSHRLSSHFERRLRSQ--ESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQ  392 (684)
Q Consensus       315 Ll~ILe~L~~hk~a~pF~~PVD~q--e~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~pdS~  392 (684)
                      |..||+.|..|+.+++|..||+..  .+|+||+||++||||+||+.||++|.|.++. +|.+||+|||+||++||+++|.
T Consensus        26 ~~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~-ef~~D~~li~~Na~~yN~~~s~  104 (127)
T 2oss_A           26 LRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLENNYYWNAQ-ECIQDFNTMFTNCYIYNKPGDD  104 (127)
T ss_dssp             HHTHHHHHHTSTTCGGGSSCCCTTTTTCTTHHHHCSSCCCHHHHHHHHHTTCCSSHH-HHHHHHHHHHHHHHHHSCTTCH
T ss_pred             HHHHHHHHHhCccchhhcCCCChhhccCccHHHHcCCCCCHHHHHHHHHcCCCCCHH-HHHHHHHHHHHHHHHHCCCCCH
Confidence            445889999999999999999975  8999999999999999999999999999998 9999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHh
Q 005668          393 EYAAAQELRTLVIKEMTDML  412 (684)
Q Consensus       393 vykaA~eLr~lf~k~msk~l  412 (684)
                      +|.+|..|+.+|++.|.++.
T Consensus       105 i~~~A~~L~~~f~~~~~~lp  124 (127)
T 2oss_A          105 IVLMAEALEKLFLQKINELP  124 (127)
T ss_dssp             HHHHHHHHHHHHHHHHTTCC
T ss_pred             HHHHHHHHHHHHHHHHHHCC
Confidence            99999999999999987654

>4alg_A Bromodomain-containing protein 2; signaling protein, inhibitor, histone, epigenetic reader; HET: 1GH; 1.60A {Homo sapiens} PDB: 4a9e_A 4a9h_A* 4a9i_A* 4a9j_A* 4a9m_A* 4a9n_A* 4a9o_A* 4a9p_A* 4a9f_A* 4alh_A* 4akn_A* 2yek_A* 2ydw_A* 2yw5_A

Probab=99.92  E-value=3.3e-25  Score=210.16  Aligned_cols=99  Identities=19%  Similarity=0.371  Sum_probs=93.4

Q ss_pred             HHHHHHHHHhCcCCcccccccCcc--ccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCCCCH
Q 005668          315 LVRFLGMIRSHRLSSHFERRLRSQ--ESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQ  392 (684)
Q Consensus       315 Ll~ILe~L~~hk~a~pF~~PVD~q--e~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~pdS~  392 (684)
                      |..||+.|..|+.+|+|..||+..  .+|+||+||++||||.||+.||+++.|.++. +|+.||+|||.||++||++++.
T Consensus        37 ~~~il~~l~~~~~a~~F~~PVd~~~~~~PdY~~iIk~PMDL~tI~~kl~~~~Y~s~~-ef~~Dv~Lif~Na~~YN~~~s~  115 (154)
T 4alg_A           37 HKVVMKALWKHQFAWPFRQPVDAVKLGLPDYHKIIKQPMDMGTIKRRLENNYYWAAS-ECMQDFNTMFTNCYIYNKPTDD  115 (154)
T ss_dssp             HHTHHHHHHTSTTCGGGSSCCCTTTTTCTTHHHHCSSCCCHHHHHHHHHTTCCSSHH-HHHHHHHHHHHHHHHHSCTTSH
T ss_pred             HHHHHHHHHhCcCchhhcCCCChhhccCCCHHHHcCCCCCHHHHHHHHhcCCCCCHH-HHHHHHHHHHHHHHHHCCCCCH
Confidence            445678999999999999999987  7999999999999999999999999999998 9999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHhhh
Q 005668          393 EYAAAQELRTLVIKEMTDMLRK  414 (684)
Q Consensus       393 vykaA~eLr~lf~k~msk~l~k  414 (684)
                      +|.+|..|+.+|.+.|.++...
T Consensus       116 i~~~A~~L~~~f~~~~~~l~~~  137 (154)
T 4alg_A          116 IVLMAQTLEKIFLQKVASMPQE  137 (154)
T ss_dssp             HHHHHHHHHHHHHHHHTTSCSS
T ss_pred             HHHHHHHHHHHHHHHHHHCCch
Confidence            9999999999999999887654

>3iu5_A Protein polybromo-1; PB1, polybromo 1 isoform 1, BAF180, polybromo0ID, PBRM1, BRG associated factor 180, structural genomics, SGC; 1.63A {Homo sapiens}

Probab=99.92  E-value=6.4e-25  Score=198.29  Aligned_cols=102  Identities=28%  Similarity=0.400  Sum_probs=96.8

Q ss_pred             chHHHHHHHHHHhC------cCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhh
Q 005668          312 SEPLVRFLGMIRSH------RLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVI  385 (684)
Q Consensus       312 skpLl~ILe~L~~h------k~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~  385 (684)
                      .+.|..||+.|..+      +.+++|..||+...+|+||++|++||||+||+.||+++.|.++. +|..||.|||.||+.
T Consensus         7 ~~~c~~il~~l~~~~d~~g~~~s~~F~~p~~~~~~pdY~~iI~~PmdL~tI~~kl~~~~Y~s~~-~f~~D~~li~~Na~~   85 (116)
T 3iu5_A            7 IAVCHELYNTIRDYKDEQGRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVN-LLTADFQLLFNNAKS   85 (116)
T ss_dssp             HHHHHHHHHHHHHCBCTTCCBGGGGGSSCCCGGGCHHHHHHCSSCCCHHHHHHHHHTTCCCSHH-HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhccCCCeeeHHhcCCCCcccCCCHHHHhCCCCCHHHHHHHHHcCCCCCHH-HHHHHHHHHHHHHHH
Confidence            46799999999987      45999999999999999999999999999999999999999998 999999999999999


Q ss_pred             hCCCCCHHHHHHHHHHHHHHHHHHHHhhh
Q 005668          386 FFRKSSQEYAAAQELRTLVIKEMTDMLRK  414 (684)
Q Consensus       386 FN~pdS~vykaA~eLr~lf~k~msk~l~k  414 (684)
                      ||+++|.+|.+|..|+++|.+.|.++..+
T Consensus        86 yN~~~s~~~~~A~~L~~~f~~~~~~l~~~  114 (116)
T 3iu5_A           86 YYKPDSPEYKAACKLWDLYLRTRNEFVQK  114 (116)
T ss_dssp             HSCTTSHHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             HCCCCCHHHHHHHHHHHHHHHHHHHHHhc
Confidence            99999999999999999999999998753

>3mb4_A Protein polybromo-1; PB1, polybromo 1 isoform 1, BAF180, polybromo-1D, PBRM1, BRG associated factor 180, structural genomics consortium, SGC; 1.66A {Homo sapiens} PDB: 3g0j_A 2yqd_A

Probab=99.92  E-value=5.2e-25  Score=201.19  Aligned_cols=100  Identities=21%  Similarity=0.343  Sum_probs=95.0

Q ss_pred             chHHHHHHHHHHh------CcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhh
Q 005668          312 SEPLVRFLGMIRS------HRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVI  385 (684)
Q Consensus       312 skpLl~ILe~L~~------hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~  385 (684)
                      .+.|..||+.|..      |+.+++|..||+...+|+||++|++||||+||+.||+++.|.++. +|..||+|||.||++
T Consensus        17 ~~~~~~il~~l~~~~d~~g~~~s~~F~~pv~~~~~pdY~~iI~~PmdL~tI~~kl~~~~Y~~~~-~f~~D~~li~~Na~~   95 (124)
T 3mb4_A           17 QQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDID-SMVEDFVMMFNNACT   95 (124)
T ss_dssp             HHHHHHHHHHHHHCBCTTSCBGGGGGSCCCCTTTCHHHHHHCSSCCCHHHHHHHHHTTCCCSHH-HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhHhcccCCcccHHhhcCCCccccCCHHHHcCCCCCHHHHHHHHHcCCCCCHH-HHHHHHHHHHHHHHH
Confidence            3679999999987      667899999999999999999999999999999999999999998 999999999999999


Q ss_pred             hCCCCCHHHHHHHHHHHHHHHHHHHHh
Q 005668          386 FFRKSSQEYAAAQELRTLVIKEMTDML  412 (684)
Q Consensus       386 FN~pdS~vykaA~eLr~lf~k~msk~l  412 (684)
                      ||+++|.+|.+|..|+.+|.+.+.++.
T Consensus        96 yN~~~s~i~~~A~~L~~~f~~~~~~l~  122 (124)
T 3mb4_A           96 YNEPESLIYKDALVLHKVLLETRRDLE  122 (124)
T ss_dssp             HSCTTSHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HCCCCCHHHHHHHHHHHHHHHHHHHHh
Confidence            999999999999999999999998764

>2ouo_A HUNK1 protein, bromodomain-containing protein 4; BRD4, structural genomics consortium, SGC, signaling protein; 1.89A {Homo sapiens} PDB: 2yem_A*

Probab=99.92  E-value=2.7e-25  Score=205.16  Aligned_cols=101  Identities=18%  Similarity=0.274  Sum_probs=94.7

Q ss_pred             CchHHHHHHHHHHhCcC---CcccccccCcc--ccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhh
Q 005668          311 KSEPLVRFLGMIRSHRL---SSHFERRLRSQ--ESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVI  385 (684)
Q Consensus       311 kskpLl~ILe~L~~hk~---a~pF~~PVD~q--e~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~  385 (684)
                      ..+.|..||+.|..+++   +|+|..|||..  .+|+||+||++||||+||+.||.+|.|.++. +|.+||+|||.||++
T Consensus        23 ~l~~c~~il~~L~~~~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PmDL~tI~~kl~~~~Y~s~~-ef~~Dv~li~~Na~~  101 (130)
T 2ouo_A           23 QLKCCSGILKEMFAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLEAREYRDAQ-EFGADVRLMFSNCYK  101 (130)
T ss_dssp             HHHHHHHHHHHHTSGGGHHHHGGGSSCCCTTSTTCTTHHHHCSSCCCHHHHHHHHHTTCCSSHH-HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCcchhHHHhcCCCChhhccCCcHHHHcCCCCCHHHHHHHHHcCCCCCHH-HHHHHHHHHHHHHHH
Confidence            34679999999998875   89999999986  5999999999999999999999999999998 999999999999999


Q ss_pred             hCCCCCHHHHHHHHHHHHHHHHHHHHh
Q 005668          386 FFRKSSQEYAAAQELRTLVIKEMTDML  412 (684)
Q Consensus       386 FN~pdS~vykaA~eLr~lf~k~msk~l  412 (684)
                      ||+++|.+|.+|..|+.+|++.|.++.
T Consensus       102 yN~~~s~i~~~A~~L~~~f~~~~~~lp  128 (130)
T 2ouo_A          102 YNPPDHEVVAMARKLQDVFEMRFAKMP  128 (130)
T ss_dssp             HSCTTSHHHHHHHHHHHHHHHHHHTSC
T ss_pred             HcCCCCHHHHHHHHHHHHHHHHHHHCC
Confidence            999999999999999999999998764

>2grc_A Probable global transcription activator SNF2L4; bromodomain, BRG1, chromatin remodelling, acely-lysine binding, protein-protein interactions; 1.50A {Homo sapiens} PDB: 3uvd_A 2h60_A

Probab=99.91  E-value=7.6e-25  Score=201.70  Aligned_cols=102  Identities=19%  Similarity=0.314  Sum_probs=97.0

Q ss_pred             chHHHHHHHHHHhCc-------CCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHh
Q 005668          312 SEPLVRFLGMIRSHR-------LSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFV  384 (684)
Q Consensus       312 skpLl~ILe~L~~hk-------~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~  384 (684)
                      .+.|..||+.|..++       .+++|..||+...+|+||+||++||||+||++||.++.|.++. +|.+||+|||.||+
T Consensus        13 ~~~~~~il~~l~~~~d~~~~~~~s~~F~~pv~~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~-~f~~Dv~Li~~Na~   91 (129)
T 2grc_A           13 TKKMKKIVDAVIKYKDSSSGRQLSEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLN-DLEKDVMLLCQNAQ   91 (129)
T ss_dssp             HHHHHHHHHHHHHCBCTTTCCBGGGGGSSCCCTTTCHHHHHHCSSCCCHHHHHHHHHTTCCCSHH-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcccccccCeeeHHhcCCCCcccCCCHHHHcCCCCCHHHHHHHHhcCCCCCHH-HHHHHHHHHHHHHH
Confidence            467999999999875       5899999999999999999999999999999999999999998 99999999999999


Q ss_pred             hhCCCCCHHHHHHHHHHHHHHHHHHHHhhh
Q 005668          385 IFFRKSSQEYAAAQELRTLVIKEMTDMLRK  414 (684)
Q Consensus       385 ~FN~pdS~vykaA~eLr~lf~k~msk~l~k  414 (684)
                      +||+++|.+|.+|..|+.+|.+.+.++...
T Consensus        92 ~yN~~~s~i~~~A~~L~~~f~~~~~~l~~~  121 (129)
T 2grc_A           92 TFNLEGSLIYEDSIVLQSVFTSVRQKIEKE  121 (129)
T ss_dssp             HHSCTTSHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHCCCCCHHHHHHHHHHHHHHHHHHHccCC
Confidence            999999999999999999999999988865

>3rcw_A Bromodomain-containing protein 1; transcription, structural genomics, structural consortium, SGC; 2.21A {Homo sapiens}

Probab=99.91  E-value=1.4e-24  Score=200.72  Aligned_cols=101  Identities=21%  Similarity=0.290  Sum_probs=96.7

Q ss_pred             hHHHHHHHHHHhCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCCCCH
Q 005668          313 EPLVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQ  392 (684)
Q Consensus       313 kpLl~ILe~L~~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~pdS~  392 (684)
                      ..|..||+.|..|+.+++|..||+...+|+||++|++||||.||+.||+++.|.++. +|..||.|||.||++||+++|.
T Consensus        16 ~~l~~il~~l~~~~~~~~F~~pv~~~~~pdY~~iI~~PmdL~tI~~kl~~~~Y~~~~-~f~~D~~li~~Na~~yN~~~s~   94 (135)
T 3rcw_A           16 VLLRSVLDQLQDKDPARIFAQPVSLKEVPDYLDHIKHPMDFATMRKRLEAQGYKNLH-EFEEDFDLIIDNCMKYNARDTV   94 (135)
T ss_dssp             HHHHHHHHHHHHTCTTCSSSSCCCTTTCTTHHHHCSSCCCHHHHHHHHHTTCCSSHH-HHHHHHHHHHHHHHHHSCTTSH
T ss_pred             HHHHHHHHHHHhCCcchhhcCCCChhhcCCHHHHhCCCCCHHHHHHHHhcCCCCCHH-HHHHHHHHHHHHHHHHCCCCCH
Confidence            568889999999999999999999999999999999999999999999999999998 9999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHhhh
Q 005668          393 EYAAAQELRTLVIKEMTDMLRK  414 (684)
Q Consensus       393 vykaA~eLr~lf~k~msk~l~k  414 (684)
                      +|.+|..|+.+|.+.|.+....
T Consensus        95 ~~~~A~~L~~~~~~~~~~~~~~  116 (135)
T 3rcw_A           95 FYRAAVRLRDQGGVVLRQARRE  116 (135)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999887653

>3hme_A Bromodomain-containing protein 9; BRD9, bromodomain containing 9 isoform 1, LAVS3040, rhabdomyosarcoma antigen MU-RMS-40.8; 2.23A {Homo sapiens}

Probab=99.91  E-value=9.3e-25  Score=199.65  Aligned_cols=99  Identities=17%  Similarity=0.293  Sum_probs=95.1

Q ss_pred             hHHHHHHHHHHhCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCCCCH
Q 005668          313 EPLVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQ  392 (684)
Q Consensus       313 kpLl~ILe~L~~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~pdS~  392 (684)
                      +.|..||+.|..++.+++|..||+...+|+||++|++||||+||+.||++|.|.++. +|..||.|||.||++||+++|.
T Consensus        16 ~~l~~il~~l~~~~~~~~F~~pv~~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~~~~-~f~~D~~li~~Na~~yN~~~s~   94 (123)
T 3hme_A           16 QLLEHFLRQLQRKDPHGFFAFPVTDAIAPGYSMIIKHPMDFGTMKDKIVANEYKSVT-EFKADFKLMCDNAMTYNRPDTV   94 (123)
T ss_dssp             HHHHHHHHHHHTTCTTCSSSSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCCSHH-HHHHHHHHHHHHHHHHSCTTSH
T ss_pred             HHHHHHHHHHHhCCccHhhcCCCChhhccCHHHHCCCCCCHHHHHHHhccCCCCCHH-HHHHHHHHHHHHHHHHCCCCCH
Confidence            569999999999999999999999999999999999999999999999999999998 9999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHh
Q 005668          393 EYAAAQELRTLVIKEMTDML  412 (684)
Q Consensus       393 vykaA~eLr~lf~k~msk~l  412 (684)
                      +|.+|..|++.|.+.|.+..
T Consensus        95 ~~~~A~~L~~~~~~~~~~~~  114 (123)
T 3hme_A           95 YYKLAKKILHAGFKMMSKER  114 (123)
T ss_dssp             HHHHHHHHHHHHHHHTCHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999987654

>3mqm_A Probable histone-lysine N-methyltransferase ASH1L; KIAA1420, absent small and homeotic disks prote homolog, lysine N-methyltransferase 2H, KMT2H; 2.54A {Homo sapiens}

Probab=99.91  E-value=1.1e-24  Score=199.22  Aligned_cols=101  Identities=18%  Similarity=0.223  Sum_probs=95.1

Q ss_pred             hHHHHHHHHHHhCc------CCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhh
Q 005668          313 EPLVRFLGMIRSHR------LSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIF  386 (684)
Q Consensus       313 kpLl~ILe~L~~hk------~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~F  386 (684)
                      +.|..||+.|..+.      .+++|..||+...+|+||++|++||||+||++||.++.|.++. +|.+||.|||.||+.|
T Consensus        12 ~~~~~i~~~l~~~~d~~g~~~s~~F~~pv~~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~-~f~~D~~li~~Na~~y   90 (126)
T 3mqm_A           12 QIFKEICDGIISYKDSSRQALAAPLLNLPPKKKNADYYEKISDPLDLITIEKQILTGYYKTVE-AFDADMLKVFRNAEKY   90 (126)
T ss_dssp             HHHHHHHHHHHHCBCTTCCBTTGGGSSCCCGGGCTTHHHHCSSCCCHHHHHHHHHHTCCCSHH-HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCcCCCChhHHhcCCCCcccCCCHHHHcCCCCCHHHHHHHHHcCCCCCHH-HHHHHHHHHHHHHHHH
Confidence            46788888888764      5999999999999999999999999999999999999999998 9999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHhhh
Q 005668          387 FRKSSQEYAAAQELRTLVIKEMTDMLRK  414 (684)
Q Consensus       387 N~pdS~vykaA~eLr~lf~k~msk~l~k  414 (684)
                      |+++|.+|.+|..|+.+|.+.+.+..+.
T Consensus        91 N~~~s~~~~~A~~L~~~f~~~~~~~~~~  118 (126)
T 3mqm_A           91 YGRKSPVGRDVCRLRKAYYNARHEASAQ  118 (126)
T ss_dssp             HCTTSHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999988765

>3k2j_A Protein polybromo-1; PB1, polybromo 1 isoform 1, BAF180, polybromo01D, PBRM1, BRG associated factor 180, structural genomics consortium, SGC; 2.20A {Homo sapiens}

Probab=99.91  E-value=2e-24  Score=199.63  Aligned_cols=102  Identities=19%  Similarity=0.277  Sum_probs=96.1

Q ss_pred             chHHHHHHHHHHhCc------CCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhh
Q 005668          312 SEPLVRFLGMIRSHR------LSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVI  385 (684)
Q Consensus       312 skpLl~ILe~L~~hk------~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~  385 (684)
                      ...|..||+.|....      .+++|..||+...+|+||++|++||||+||+.||+++.|.++. +|..||+|||.||++
T Consensus        19 ~~~~~~l~~~l~~~~d~~g~~~s~~F~~pv~~~~~PdY~~iIk~PMdL~tI~~kL~~~~Y~s~~-ef~~Dv~Lif~Na~~   97 (130)
T 3k2j_A           19 YFQSMQLYDTVRSCRNNQGQLIAEPFYHLPSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLD-HLECDLNLMFENAKR   97 (130)
T ss_dssp             HHHHHHHHHHHHTCBCSSSCBTTGGGSSCCCTTTCHHHHHHCSSCCCHHHHHHHHHTTCCSSHH-HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhcccCCCccHhhcCCCChhhCccHHHHcCCCCCHHHHHHHHhcCCCCCHH-HHHHHHHHHHHHHHH
Confidence            367888888888654      4999999999999999999999999999999999999999998 999999999999999


Q ss_pred             hCCCCCHHHHHHHHHHHHHHHHHHHHhhh
Q 005668          386 FFRKSSQEYAAAQELRTLVIKEMTDMLRK  414 (684)
Q Consensus       386 FN~pdS~vykaA~eLr~lf~k~msk~l~k  414 (684)
                      ||+++|.+|.+|..|+.+|.+.|.++...
T Consensus        98 yN~~~s~i~~~A~~L~~~f~~~~~~l~~~  126 (130)
T 3k2j_A           98 YNVPNSAIYKRVLKLQQVMQAKKKELARR  126 (130)
T ss_dssp             HSCTTSHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HCCCCCHHHHHHHHHHHHHHHHHHHHHhc
Confidence            99999999999999999999999998865

>3ljw_A Protein polybromo-1; alpha helix, alternative splicing, bromodomain, chromatin RE DNA-binding, nucleus, phosphoprotein, transcription; 1.50A {Homo sapiens} PDB: 2ktb_B* 3hmf_A

Probab=99.91  E-value=1.7e-24  Score=196.70  Aligned_cols=101  Identities=22%  Similarity=0.339  Sum_probs=95.7

Q ss_pred             hHHHHHHHHHHhCcC------CcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhh
Q 005668          313 EPLVRFLGMIRSHRL------SSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIF  386 (684)
Q Consensus       313 kpLl~ILe~L~~hk~------a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~F  386 (684)
                      +.|..||+.|..+..      +++|..||+...+|+||++|++||||+||+.||.++.|.++. +|..||+|||.||++|
T Consensus        11 ~~~~~ll~~l~~~~d~~g~~~s~~F~~~~~~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~-~f~~D~~li~~Na~~y   89 (120)
T 3ljw_A           11 EILEQLLEAIVVATNPSGRLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIH-AMAKDIDLLAKNAKTY   89 (120)
T ss_dssp             HHHHHHHHHHHHCBCTTSCBTTGGGSSCCCTTTCHHHHHHCSSCCCHHHHHHHHHHTCCCSHH-HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccCcCCCcccHHhcCCCCcccCCChHHHcCCCCCHHHHHHHHccCCCCCHH-HHHHHHHHHHHHHHHH
Confidence            568888999987776      999999999999999999999999999999999999999998 9999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHhhh
Q 005668          387 FRKSSQEYAAAQELRTLVIKEMTDMLRK  414 (684)
Q Consensus       387 N~pdS~vykaA~eLr~lf~k~msk~l~k  414 (684)
                      |+++|.+|.+|..|+.+|.+.|.++...
T Consensus        90 N~~~s~~~~~A~~L~~~f~~~~~~i~~~  117 (120)
T 3ljw_A           90 NEPGSQVFKDANSIKKIFYMKKAEIEHH  117 (120)
T ss_dssp             SCTTSHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHhhhc
Confidence            9999999999999999999999997653

>3jvl_A Bromodomain-containing protein 4; alpha helical, N-acetyl lysine binding domain, signaling protein; 1.20A {Mus musculus} PDB: 3jvm_A 2dww_A 2i8n_A 3oni_A* 2dvv_A* 2e3k_A* 2g4a_A 3s92_A* 2oo1_A* 2e7n_A 2wp1_A*

Probab=99.91  E-value=5e-25  Score=199.85  Aligned_cols=104  Identities=17%  Similarity=0.267  Sum_probs=96.5

Q ss_pred             cCchHHHHHHHHHHhCcC---CcccccccCccc--cchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHh
Q 005668          310 VKSEPLVRFLGMIRSHRL---SSHFERRLRSQE--SERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFV  384 (684)
Q Consensus       310 ~kskpLl~ILe~L~~hk~---a~pF~~PVD~qe--~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~  384 (684)
                      ...+.|..||..|..++.   +|+|..||+...  +|+||++|++||||+||+.||+++.|.++. +|..||.|||.||+
T Consensus         9 ~~l~~c~~il~~l~~~~~~~~a~~F~~pvd~~~~~~pdY~~iI~~Pmdl~tI~~kl~~~~Y~~~~-~f~~D~~li~~Na~   87 (120)
T 3jvl_A            9 EQLKCCSGILKEMFAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLESREYRDAQ-EFGADVRLMFSNCY   87 (120)
T ss_dssp             HHHHHHHHHHHHHTSGGGHHHHGGGSSCCCHHHHTCTTHHHHCSSCCCHHHHHHHHHTTCCCSHH-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCcCccccchhcCCCCchhcCCCCHHHHcCCCCCHHHHHHHHccCCCCCHH-HHHHHHHHHHHHHH
Confidence            334678999999998887   999999999986  999999999999999999999999999998 99999999999999


Q ss_pred             hhCCCCCHHHHHHHHHHHHHHHHHHHHhhh
Q 005668          385 IFFRKSSQEYAAAQELRTLVIKEMTDMLRK  414 (684)
Q Consensus       385 ~FN~pdS~vykaA~eLr~lf~k~msk~l~k  414 (684)
                      +||+++|.+|.+|..|+.+|.+.|.++...
T Consensus        88 ~yN~~~s~~~~~A~~L~~~f~~~~~~~p~~  117 (120)
T 3jvl_A           88 KYNPPDHEVVAMARKLQDVFEMRFAKMPDE  117 (120)
T ss_dssp             HHSCTTSHHHHHHHHHHHHHHHHHTTCCC-
T ss_pred             HHCCCCCHHHHHHHHHHHHHHHHHHHCcCC
Confidence            999999999999999999999999877643

>3fkm_X Signaling protein; bromodomain, malaria, structural genomics, structural genomi consortium, SGC; 2.50A {Plasmodium falciparum 3D7}

Probab=99.90  E-value=3.3e-24  Score=205.54  Aligned_cols=101  Identities=15%  Similarity=0.270  Sum_probs=94.0

Q ss_pred             CchHHHHHHHHHHhCcCCcccccccCcc--ccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCC
Q 005668          311 KSEPLVRFLGMIRSHRLSSHFERRLRSQ--ESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFR  388 (684)
Q Consensus       311 kskpLl~ILe~L~~hk~a~pF~~PVD~q--e~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~  388 (684)
                      ....|..||..|+.++.+++|..||++.  .+|+||+||++||||+||+.||.++.|.++. +|..||+|||.||++||+
T Consensus        22 ~~~~~~~il~~L~~~~~s~~F~~PVd~~~~~~pdY~~iIk~PmDL~tI~~kL~~~~Y~s~~-ef~~Dv~Lif~Na~~yN~  100 (166)
T 3fkm_X           22 WYLLANQLILSLSKYEGGHIFEKLVDAKKQNCPDYYDVIKNPMSFSCIKTKLKKGQYAYPS-EFVKDVQLIFDNCSLYNT  100 (166)
T ss_dssp             HHHHHHHHHHHHTTSTTGGGGSSCCC-----CCCGGGCCSSCCCHHHHHHHHHHTCCCSHH-HHHHHHHHHHHHHHHSSC
T ss_pred             HHHHHHHHHHHHHhCCCChhhcCCCChhhccCCCHHHhcCCCCCHHHHHHHHcCCCCCCHH-HHHHHHHHHHHHHHHHCC
Confidence            3467899999999999999999999975  6999999999999999999999999999998 999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHh
Q 005668          389 KSSQEYAAAQELRTLVIKEMTDML  412 (684)
Q Consensus       389 pdS~vykaA~eLr~lf~k~msk~l  412 (684)
                      ++|.+|.+|..|+.+|.+.|.++.
T Consensus       101 ~~s~i~~~A~~L~~~f~~~l~~~~  124 (166)
T 3fkm_X          101 SNSVVAITGKNIETYFNNQLIVMG  124 (166)
T ss_dssp             TTSHHHHHHHHHHHHHHHHHHHTT
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHcc
Confidence            999999999999999999998865

>2ri7_A Nucleosome-remodeling factor subunit BPTF; zinc finger, alpha-helical bundle, dimethyl-lysine, bromodom chromatin regulator, metal-binding, nucleus; HET: MLY; 1.45A {Homo sapiens} PDB: 2fsa_A* 2f6n_A 2f6j_A* 3qzv_A* 3uv2_A* 3qzt_A* 3qzs_A* 2fui_A 2fuu_A*

Probab=99.90  E-value=2.8e-24  Score=204.93  Aligned_cols=100  Identities=21%  Similarity=0.439  Sum_probs=95.6

Q ss_pred             CchHHHHHHHHHHhCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCCC
Q 005668          311 KSEPLVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKS  390 (684)
Q Consensus       311 kskpLl~ILe~L~~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~pd  390 (684)
                      ..+.|..||..|..|+.+++|..||+...+|+||++|++||||+||++||+++.|.++. +|.+||+|||+||++||+++
T Consensus        73 ~~~~l~~il~~l~~~~~~~~F~~pv~~~~~pdY~~~I~~PmdL~tI~~kl~~~~Y~s~~-~f~~D~~li~~Na~~yN~~~  151 (174)
T 2ri7_A           73 DYEGLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLT-EFVADMTKIFDNCRYYNPSD  151 (174)
T ss_dssp             HHHHHHHHHHHHHTSGGGTTTSSCCCTTTCHHHHHHCSSCCCHHHHHHHHHTTCCCBHH-HHHHHHHHHHHHHHHHSCTT
T ss_pred             HHHHHHHHHHHHHhhhhhhhhhcCCCcccCCchHHHhCCcCCHHHHHHHHHcCCCCCHH-HHHHHHHHHHHHHHHHCCCC
Confidence            34679999999999999999999999999999999999999999999999999999998 99999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHHHHHHH
Q 005668          391 SQEYAAAQELRTLVIKEMTDM  411 (684)
Q Consensus       391 S~vykaA~eLr~lf~k~msk~  411 (684)
                      |.+|.+|..|+.+|.++|.++
T Consensus       152 s~~~~~A~~L~~~f~~~~~~~  172 (174)
T 2ri7_A          152 SPFYQCAEVLESFFVQKLKGF  172 (174)
T ss_dssp             SHHHHHHHHHHHHHHHHTTTC
T ss_pred             CHHHHHHHHHHHHHHHHHHhc
Confidence            999999999999999988653

>3uv4_A Second bromodomain of human transcription initiat TFIID subunit 1 (TAF1); structural genomics consortium, SGC; 1.89A {Homo sapiens} PDB: 3hmh_A

Probab=99.90  E-value=9.9e-24  Score=201.07  Aligned_cols=100  Identities=21%  Similarity=0.259  Sum_probs=91.7

Q ss_pred             HHHHHHHH-----HHhCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCC
Q 005668          314 PLVRFLGM-----IRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFR  388 (684)
Q Consensus       314 pLl~ILe~-----L~~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~  388 (684)
                      .|..||+.     |..++.+|+|..||+...+|+||+||++||||.||+.||.++.|.++. +|..||.|||.||++||+
T Consensus        29 ~l~~iL~~i~~~kl~~~~~s~~F~~PVd~~~~PdY~~iIk~PMDL~tI~~kl~~~~Y~s~~-ef~~Dv~Lif~Na~~yN~  107 (158)
T 3uv4_A           29 AFSFILDNIVTQKMMAVPDSWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRE-SFLDDVNLILANSVKYNG  107 (158)
T ss_dssp             HHHHHHHHHHHHTTTTSTTCGGGTSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCSSHH-HHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHcCCCchhhcCcCChhhcccHHHHcCCccCHHHHHHHHHcCCCCCHH-HHHHHHHHHHHHHHHHCC
Confidence            45555555     456889999999999999999999999999999999999999999998 999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHhhh
Q 005668          389 KSSQEYAAAQELRTLVIKEMTDMLRK  414 (684)
Q Consensus       389 pdS~vykaA~eLr~lf~k~msk~l~k  414 (684)
                      ++|.+|.+|..|..+|.+.|.++...
T Consensus       108 ~~s~i~~~A~~L~~~~~~~l~e~~~~  133 (158)
T 3uv4_A          108 PESQYTKTAQEIVNVCYQTLTEYDEH  133 (158)
T ss_dssp             TTCHHHHHHHHHHHHHHHHHHHTHHH
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999887653

>3tlp_A Protein polybromo-1; PB1, polybromo 1 isoform 1, BAF180, polybromo-1D, PBRM1, BRG associated factor 180, structural genomics consortium, SGC; 2.13A {Homo sapiens}

Probab=99.89  E-value=1.9e-23  Score=196.27  Aligned_cols=102  Identities=18%  Similarity=0.288  Sum_probs=95.7

Q ss_pred             chHHHHHHHHHHhCcC-------CcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHh
Q 005668          312 SEPLVRFLGMIRSHRL-------SSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFV  384 (684)
Q Consensus       312 skpLl~ILe~L~~hk~-------a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~  384 (684)
                      .+.|..||+.|..+..       +++|..||+...+|+||++|++||||.||+.||+++.|.++. +|+.||.|||.||+
T Consensus        26 ~~~~k~ll~~l~~~~~~~~~~~~~~~F~~~~~~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~-ef~~D~~li~~Na~  104 (150)
T 3tlp_A           26 KQRMKILFNVVLEAREPGSGRRLCDLFMVKPSKKDYPDYYKIILEPMDLKIIEHNIRNDKYAGEE-GMIEDMKLMFRNAR  104 (150)
T ss_dssp             HHHHHHHHHHHHHCBCTTTCCBGGGGGSSCCCTTTCHHHHHHCSSCCCHHHHHHHHHTTCCSSHH-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhcccCCcccHHhcCCCchhhCcCHHHHhCCCCCHHHHHHHHhcCCCCCHH-HHHHHHHHHHHHHH
Confidence            4678888888876554       999999999999999999999999999999999999999998 99999999999999


Q ss_pred             hhCCCCCHHHHHHHHHHHHHHHHHHHHhhh
Q 005668          385 IFFRKSSQEYAAAQELRTLVIKEMTDMLRK  414 (684)
Q Consensus       385 ~FN~pdS~vykaA~eLr~lf~k~msk~l~k  414 (684)
                      +||+++|.+|.+|..|+.+|.+.|.++.+.
T Consensus       105 ~yN~~~s~i~~~A~~L~~~f~~~~~~l~~~  134 (150)
T 3tlp_A          105 HYNEEGSQVYNDAHILEKLLKEKRKELGPL  134 (150)
T ss_dssp             HHSCTTSHHHHHHHHHHHHHHHHHHHHCCC
T ss_pred             HHCCCCCHHHHHHHHHHHHHHHHHHHccCC
Confidence            999999999999999999999999998854

>3o36_A Transcription intermediary factor 1-alpha; TRIM24, PHD finger, bromodomain, H4K16 acetylation, breast C transcription-protein binding complex; HET: ALY; 1.70A {Homo sapiens} PDB: 3o33_A* 3o34_A* 3o35_A* 3o37_A

Probab=99.89  E-value=2.4e-23  Score=200.87  Aligned_cols=102  Identities=24%  Similarity=0.378  Sum_probs=96.4

Q ss_pred             cCchHHHHHHHHHHhCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhC--CCccCcHHHHHHHHHHHHHHHhhhC
Q 005668          310 VKSEPLVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDR--GLYSNCFQKFFRDLLLLFNNFVIFF  387 (684)
Q Consensus       310 ~kskpLl~ILe~L~~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~--g~YsSi~~EF~rDL~LMF~NA~~FN  387 (684)
                      ...+.|..||..|+.|+.+++|..||+. .+|+||+||++||||+||++||++  +.|.++. +|.+||+|||.||++||
T Consensus        81 ~~~~~c~~il~~l~~~~~s~~F~~Pv~~-~~pdY~~iIk~PmdL~tI~~kl~~~~~~Y~s~~-ef~~Dv~li~~Na~~yN  158 (184)
T 3o36_A           81 IDKRKCERLLLFLYCHEMSLAFQDPVPL-TVPDYYKIIKNPMDLSTIKKRLQEDYSMYSKPE-DFVADFRLIFQNCAEFN  158 (184)
T ss_dssp             HHHHHHHHHHHHHHHSTTCHHHHSCCCT-TSTTHHHHCSSCCCHHHHHHHHHSTTCSCCSHH-HHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHHhchhhhhhcccccc-CCCchhhhcCCCCCHHHHHHHHHhcCCCCCCHH-HHHHHHHHHHHHHHHHC
Confidence            3446799999999999999999999995 499999999999999999999998  7899998 99999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHhh
Q 005668          388 RKSSQEYAAAQELRTLVIKEMTDMLR  413 (684)
Q Consensus       388 ~pdS~vykaA~eLr~lf~k~msk~l~  413 (684)
                      +++|.+|.+|..|+.+|++.|.+++|
T Consensus       159 ~~~s~v~~~a~~L~~~f~~~~~~~~P  184 (184)
T 3o36_A          159 EPDSEVANAGIKLENYFEELLKNLYP  184 (184)
T ss_dssp             CTTCHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHhCc
Confidence            99999999999999999999999874

>3dai_A ATPase family AAA domain-containing protein 2; ancca, AAA+ nuclear coregulator cancer-associated Pro2000 protein, two AAA DOMA containing protein; 1.95A {Homo sapiens} PDB: 3lxj_A

Probab=99.89  E-value=3.4e-23  Score=190.77  Aligned_cols=99  Identities=18%  Similarity=0.243  Sum_probs=91.3

Q ss_pred             hHHHHHHHHHHhCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCCCCH
Q 005668          313 EPLVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQ  392 (684)
Q Consensus       313 kpLl~ILe~L~~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~pdS~  392 (684)
                      ..|..||+.|..|+.+++|..||+...+|+||++|++||||+||+.||.+|.|.++. +|..||.|||.||++||+++|+
T Consensus        13 ~~l~~il~~l~~~~~~~~F~~pv~~~~~pdY~~iI~~PmdL~tI~~kl~~~~Y~~~~-~f~~D~~li~~Na~~yN~~~s~   91 (130)
T 3dai_A           13 IFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVK-DYLRDIDLICSNALEYNPDRDP   91 (130)
T ss_dssp             HHHHHHHHHHHTSGGGGGGSSCCCTTTCTTHHHHCSSCCCHHHHHHHHHTTCCSSHH-HHHHHHHHHHHHHHHHCCSSSH
T ss_pred             HHHHHHHHHHHcCCccHhhcCCCChhhcCCHHHHcCCCCCHHHHHHHHhCCCCCCHH-HHHHHHHHHHHHHHHHCCCCCh
Confidence            458888999999999999999999999999999999999999999999999999998 9999999999999999999987


Q ss_pred             H----HHHHHHHHHHHHHHHHHHh
Q 005668          393 E----YAAAQELRTLVIKEMTDML  412 (684)
Q Consensus       393 v----ykaA~eLr~lf~k~msk~l  412 (684)
                      +    +.+|..|++.+...|...+
T Consensus        92 ~~~~i~~~A~~L~~~~~~~i~~el  115 (130)
T 3dai_A           92 GDRLIRHRACALRDTAYAIIKEEL  115 (130)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHh
Confidence            6    7788888888888886444

>3u5n_A E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, bromodomain, TGF-beta, epigenetics, methylation, K9ME3, K14AC, transcription; HET: M3L ALY; 1.95A {Homo sapiens} PDB: 3u5m_A* 3u5o_A* 3u5p_A*

Probab=99.87  E-value=3.5e-22  Score=196.44  Aligned_cols=102  Identities=22%  Similarity=0.354  Sum_probs=97.5

Q ss_pred             CchHHHHHHHHHHhCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhC---CCccCcHHHHHHHHHHHHHHHhhhC
Q 005668          311 KSEPLVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDR---GLYSNCFQKFFRDLLLLFNNFVIFF  387 (684)
Q Consensus       311 kskpLl~ILe~L~~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~---g~YsSi~~EF~rDL~LMF~NA~~FN  387 (684)
                      ....|..||..|+.|+.+++|..||+. .+|+||+||++||||.||++||++   +.|.++. +|.+||+|||.||++||
T Consensus        82 ~~~~c~~il~~l~~~~~s~~F~~Pv~~-~~pdY~~iIk~PmdL~tI~~kl~~~~~~~Y~s~~-~f~~Dv~li~~Na~~yN  159 (207)
T 3u5n_A           82 DQRKCERLLLYLYCHELSIEFQEPVPA-SIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPD-DFVADVRLIFKNCERFN  159 (207)
T ss_dssp             HHHHHHHHHHHHHTSTTCGGGSSCCCT-TSTTHHHHCSSCCCHHHHHHHHSTTSTTCCSSHH-HHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccchhhhhccCCh-hhccHhHHhCCccCHHHHHHHHhcccCCCcCCHH-HHHHHHHHHHHHHHHHC
Confidence            346789999999999999999999987 799999999999999999999997   7999998 99999999999999999


Q ss_pred             C-----------------CCCHHHHHHHHHHHHHHHHHHHHhhh
Q 005668          388 R-----------------KSSQEYAAAQELRTLVIKEMTDMLRK  414 (684)
Q Consensus       388 ~-----------------pdS~vykaA~eLr~lf~k~msk~l~k  414 (684)
                      +                 +++.++.+|..|+.+|+.+|.++++.
T Consensus       160 ~~~s~v~~~A~~l~~~~~~~s~i~~~a~~L~~~fe~~~~~~~p~  203 (207)
T 3u5n_A          160 EMMKVVQVYADTQEINLKADSEVAQAGKAVALYFEDKLTEIYSD  203 (207)
T ss_dssp             HHHHHHC----------CCCCHHHHHHHHHHHHHHHHHHHHSTT
T ss_pred             CCcchHHHHHHHHHhcccccCHHHHHHHHHHHHHHHHHHHhCCC
Confidence            9                 99999999999999999999999986

>3uv5_A Transcription initiation factor TFIID subunit 1; tandem bromodomain, TAF1, cell cycle gene 1 protein, TBP-ASS factor 250 kDa; 2.03A {Homo sapiens} PDB: 1eqf_A

Probab=99.86  E-value=5.9e-22  Score=201.58  Aligned_cols=103  Identities=17%  Similarity=0.251  Sum_probs=98.2

Q ss_pred             CchHHHHHHHHHHhCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCCC
Q 005668          311 KSEPLVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKS  390 (684)
Q Consensus       311 kskpLl~ILe~L~~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~pd  390 (684)
                      -...|..||+.|..|+.+++|..||+...+|+||++|++||||+||+.||.+|.|.++. +|..||.|||+||++||+++
T Consensus        15 l~~~l~~il~~l~~~~~~~~F~~pv~~~~~pdY~~iI~~PmdL~tI~~kl~~~~Y~~~~-~f~~D~~li~~Na~~yN~~~   93 (265)
T 3uv5_A           15 LSSILESIINDMRDLPNTYPFHTPVNAKVVKDYYKIITRPMDLQTLRENVRKRLYPSRE-EFREHLELIVKNSATYNGPK   93 (265)
T ss_dssp             HHHHHHHHHHHHHTSTTCGGGTSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCSSHH-HHHHHHHHHHHHHHHHHCTT
T ss_pred             HHHHHHHHHHHHHcCCCchhhhCCCChhhcCCHHHHhCCCCcHHHHHHHHHcCCCCCHH-HHHHHHHHHHhhhhhcCCCC
Confidence            34679999999999999999999999999999999999999999999999999999998 99999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHHHHHHHhhh
Q 005668          391 SQEYAAAQELRTLVIKEMTDMLRK  414 (684)
Q Consensus       391 S~vykaA~eLr~lf~k~msk~l~k  414 (684)
                      |.+|.+|..|+.+|...|.+...+
T Consensus        94 s~i~~~A~~l~~~~~~~~~~~~~~  117 (265)
T 3uv5_A           94 HSLTQISQSMLDLCDEKLKEKEDK  117 (265)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHTHHH
T ss_pred             ChHHHHHHHHHHHHHHHHHHHhhh
Confidence            999999999999999999887654

>2ro1_A Transcription intermediary factor 1-beta; KAP, TIF, PHD finger, bromodomain, SUMO, acetylation, alternative splicing, metal-binding, nucleus; NMR {Homo sapiens}

Probab=99.86  E-value=2.6e-22  Score=195.81  Aligned_cols=97  Identities=18%  Similarity=0.227  Sum_probs=92.1

Q ss_pred             chHHHHHHHHHHhCcCCcccccccCccccchhhhhhc--CCCCHHHHHHHHhCC---CccCcHHHHHHHHHHHHHHHhhh
Q 005668          312 SEPLVRFLGMIRSHRLSSHFERRLRSQESERYKKLVR--QHIDLRTIQSRLDRG---LYSNCFQKFFRDLLLLFNNFVIF  386 (684)
Q Consensus       312 skpLl~ILe~L~~hk~a~pF~~PVD~qe~PdYyeIIK--~PMDLsTIKkKLe~g---~YsSi~~EF~rDL~LMF~NA~~F  386 (684)
                      ...|..||..|+.|+.+|||..||+    |+||.||+  +||||+||++||+++   .|.++. +|.+||+|||+||++|
T Consensus        78 ~~~c~~iL~~l~~~~~s~pF~~pV~----~~Yy~iIk~~~PMDL~tIk~kL~~~~~~~Y~s~~-eF~~Dv~Lif~N~~~y  152 (189)
T 2ro1_A           78 QRKCERVLLALFCHEPCRPLHQLAT----DSTFSLDQPGGTLDLTLIRARLQEKLSPPYSSPQ-EFAQDVGRMFKQFNKL  152 (189)
T ss_dssp             HHHHHHHHHHHHHSTTHHHHHSCSC----CTTCSSSCSSCCCCHHHHHHHHHTSSSSCCSCHH-HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhcccCccchhhcCCCC----hhhhccccCCCcccHHHHHHHHhcCCCcccCCHH-HHHHHHHHHHHHHHHH
Confidence            3568999999999999999999999    68999998  899999999999999   999998 9999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHhhh
Q 005668          387 FRKSSQEYAAAQELRTLVIKEMTDMLRK  414 (684)
Q Consensus       387 N~pdS~vykaA~eLr~lf~k~msk~l~k  414 (684)
                      | +++.+|.+|..|+.+|+++|.++++.
T Consensus       153 N-~~s~~~~~a~~L~~~Fe~~~~~~~~~  179 (189)
T 2ro1_A          153 T-EDKADVQSIIGLQRFFETRMNEAFGD  179 (189)
T ss_dssp             C-CSSCSSHHHHHHHHHHHHHHHHHTTT
T ss_pred             C-CCCHHHHHHHHHHHHHHHHHHHhcCc
Confidence            9 58889999999999999999999976

>2dkw_A Hypothetical protein KIAA1240; bromodomain-like, five-helix, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.86  E-value=6.1e-22  Score=183.55  Aligned_cols=95  Identities=16%  Similarity=0.235  Sum_probs=88.6

Q ss_pred             hHHHHHHHHHHhCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCCCCH
Q 005668          313 EPLVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQ  392 (684)
Q Consensus       313 kpLl~ILe~L~~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~pdS~  392 (684)
                      ..|..||+.|..|+.+++|..|     +|+||+||++||||+||+.||.++.|.++. +|..||.|||+||++||+++|+
T Consensus        15 ~~~~~il~~l~~~~~~~~F~~P-----~pdY~~iIk~PmDL~tI~~kl~~~~Y~s~~-~f~~D~~Li~~Na~~yN~~~s~   88 (131)
T 2dkw_A           15 LFLRDVTKRLATDKRFNIFSKP-----VSDYLEVIKEPMDLSTVITKIDKHNYLTAK-DFLKDIDLICSNALEYNPDKDP   88 (131)
T ss_dssp             HHHHHHHHHHHHSGGGCTTSSC-----CSSCTTSCSSCCCHHHHHHHHHTTCCCSSH-HHHHHHHHHHHHHHHSCCCSST
T ss_pred             HHHHHHHHHHHhCccchhhcCc-----CccHHhHcCCCcCHHHHHHHHcCCCCCCHH-HHHHHHHHHHHHHHHHCCCCCh
Confidence            4588899999999999999999     899999999999999999999999999998 9999999999999999999985


Q ss_pred             ----HHHHHHHHHHHHHHHHHHHhh
Q 005668          393 ----EYAAAQELRTLVIKEMTDMLR  413 (684)
Q Consensus       393 ----vykaA~eLr~lf~k~msk~l~  413 (684)
                          +|.+|..|++.|...|...+.
T Consensus        89 ~~~~i~~~A~~L~~~~~~~l~~~l~  113 (131)
T 2dkw_A           89 GDKIIRHRACTLKDTAHAIIAAELD  113 (131)
T ss_dssp             THHHHHHHHHHHHHHHHHHHHHHSC
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHH
Confidence                578999999999998876664

>3uv5_A Transcription initiation factor TFIID subunit 1; tandem bromodomain, TAF1, cell cycle gene 1 protein, TBP-ASS factor 250 kDa; 2.03A {Homo sapiens} PDB: 1eqf_A

Probab=99.85  E-value=1.7e-21  Score=198.21  Aligned_cols=92  Identities=22%  Similarity=0.277  Sum_probs=88.2

Q ss_pred             HHhCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHH
Q 005668          322 IRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQEYAAAQELR  401 (684)
Q Consensus       322 L~~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~pdS~vykaA~eLr  401 (684)
                      |..|+.+++|..||+...+|+||++|++||||.||+.||.+|.|.++. +|..||.|||.||++||+++|.+|.+|..|+
T Consensus       149 l~~~~~~~~F~~pv~~~~~pdY~~iIk~Pmdl~tI~~kl~~~~Y~~~~-~f~~D~~lif~Na~~yN~~~s~~~~~A~~l~  227 (265)
T 3uv5_A          149 MMAVPDSWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRE-SFLDDVNLILANSVKYNGPESQYTKTAQEIV  227 (265)
T ss_dssp             TTTSTTCGGGTSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCSSHH-HHHHHHHHHHHHHHHHTCTTCHHHHHHHHHH
T ss_pred             HHhhhhhHHHhCCCChhHhCcHHHHhCCcccHHHHHHHHhcCCCCCHH-HHHHHHHHHHHHHHHHCCCCCHHHHHHHHHH
Confidence            667899999999999999999999999999999999999999999998 9999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhhh
Q 005668          402 TLVIKEMTDMLRK  414 (684)
Q Consensus       402 ~lf~k~msk~l~k  414 (684)
                      .+|.+.|..+...
T Consensus       228 ~~~~~~~~~~~~~  240 (265)
T 3uv5_A          228 NVCYQTLTEYDEH  240 (265)
T ss_dssp             HHHHHHHHHTHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999887654

>3aad_A Transcription initiation factor TFIID subunit 1; protein-protein complex, bromodomain, transcription, transcr regulation, chromatin regulator, transcription-C complex; 3.30A {Homo sapiens}

Probab=99.84  E-value=1.5e-21  Score=201.50  Aligned_cols=100  Identities=17%  Similarity=0.255  Sum_probs=95.0

Q ss_pred             chHHHHHHHHHHhCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCCCC
Q 005668          312 SEPLVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSS  391 (684)
Q Consensus       312 skpLl~ILe~L~~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~pdS  391 (684)
                      ...|..||+.|..|+.+++|..||+...+|+||+||++||||+||++||+++.|.++. +|..||.|||+||++||+++|
T Consensus        49 ~~~~~~il~~l~~~~~a~~F~~pV~~~~~pdY~~iIk~PmDL~tIk~kl~~~~Y~s~~-~f~~D~~li~~Na~~yN~~~s  127 (292)
T 3aad_A           49 SSILESIINDMRDLPNTYPFHTPVNAKVVKDYYKIITRPMDLQTLRENVRKRLYPSRE-EFREHLELIVKNSATYNGPKH  127 (292)
T ss_dssp             HHHHHHHHHHHSSSTTCGGGSSSCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCSSHH-HHHHHHHHHHHHHHHHTCSSS
T ss_pred             HHHHHHHHHHHHhCCcchhhcCCCCchhcccHHHHcCCcCCHHHHHHHhhCCCcCCHH-HHHHHHHHHHHHHHHHcCCch
Confidence            4678899999999999999999999999999999999999999999999999999998 999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHh
Q 005668          392 QEYAAAQELRTLVIKEMTDML  412 (684)
Q Consensus       392 ~vykaA~eLr~lf~k~msk~l  412 (684)
                      .+|.+|..|+.+|.+.|.+..
T Consensus       128 ~i~~~A~~L~~~~~~~~~~~~  148 (292)
T 3aad_A          128 SLTQISQSMLDLCDEKLKEKE  148 (292)
T ss_dssp             HHHHHHTHHHHTTTTTGGGSH
T ss_pred             HHHHHHHHHHHHHHhhhhcch
Confidence            999999999999988876643

>3aad_A Transcription initiation factor TFIID subunit 1; protein-protein complex, bromodomain, transcription, transcr regulation, chromatin regulator, transcription-C complex; 3.30A {Homo sapiens}

Probab=99.84  E-value=4.2e-21  Score=198.16  Aligned_cols=92  Identities=22%  Similarity=0.270  Sum_probs=88.0

Q ss_pred             HHHhCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHH
Q 005668          321 MIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQEYAAAQEL  400 (684)
Q Consensus       321 ~L~~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~pdS~vykaA~eL  400 (684)
                      .|+.++.+++|..||+...+|+||+||++||||+||+.||.+|.|.++. +|..||.|||.||++||+++|.+|.+|..|
T Consensus       181 ~l~~~~~s~~F~~pvd~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~-~f~~D~~Li~~Na~~yN~~~s~i~~~A~~L  259 (292)
T 3aad_A          181 KMMAVPDSWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRE-SFLDDVNLILANSVKYNGPESQYTKTAQEI  259 (292)
T ss_dssp             TGGGSTTCGGGTSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCSSHH-HHHHHHHHHHHHHHHHHCTTSHHHHHHHHH
T ss_pred             hhhcCcchhHHHhcccccccccHHHHcCCcCCHHHHHHHHhcCCCCCHH-HHHHHHHHHHHHHHHHCCCCCHHHHHHHHH
Confidence            3678899999999999999999999999999999999999999999998 999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhh
Q 005668          401 RTLVIKEMTDMLR  413 (684)
Q Consensus       401 r~lf~k~msk~l~  413 (684)
                      +.+|.+.|..+..
T Consensus       260 ~~~~~~~~~~~~~  272 (292)
T 3aad_A          260 VNVCYQTLTEYDE  272 (292)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999987754

>2r0y_A Chromatin structure-remodeling complex protein RSC4; bromodomain, chromatin, remodeler, RSC, acetylation, transcription, chromatin regulator, nucleus, phosphorylation; HET: ALY; 1.75A {Saccharomyces cerevisiae} PDB: 2r0s_A

Probab=99.83  E-value=5.6e-21  Score=199.23  Aligned_cols=87  Identities=26%  Similarity=0.401  Sum_probs=84.7

Q ss_pred             hCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHH
Q 005668          324 SHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQEYAAAQELRTL  403 (684)
Q Consensus       324 ~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~pdS~vykaA~eLr~l  403 (684)
                      .|+.+++|..||+...+|+||+||++||||+||++||+++.|.++. +|..||+|||+||++||+++|.+|.+|..|+.+
T Consensus       177 ~~~~s~~F~~pvd~~~~PdY~~iIk~PMDL~tI~~kl~~~~Y~s~~-ef~~Dv~Lif~N~~~yN~~~s~i~~~A~~L~~~  255 (311)
T 2r0y_A          177 KVKLSEPFMELVDKDELPEYYEIVHSPMALSIVKQNLEIGQYSKIY-DFIIDMLLVFQNAHIFNDPSALIYKDATTLTNY  255 (311)
T ss_dssp             SSCTTGGGSSCCCTTTCHHHHHHCSSCCCHHHHHHHHHHTCCCBHH-HHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHHH
T ss_pred             CCccHHHHhCCCChhhcccHHHHhCCccCHHHHHHHHHcCCCCCHH-HHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHH
Confidence            5789999999999999999999999999999999999999999998 999999999999999999999999999999999


Q ss_pred             HHHHHHHH
Q 005668          404 VIKEMTDM  411 (684)
Q Consensus       404 f~k~msk~  411 (684)
                      |.+.|.+.
T Consensus       256 f~~~~~~~  263 (311)
T 2r0y_A          256 FNYLIQKE  263 (311)
T ss_dssp             HHHHHHHT
T ss_pred             HHHHHHHh
Confidence            99999884

>2r10_A Chromatin structure-remodeling complex protein RSC4, linker, histone H3; bromodomain, remodeler, acetylation, transcription; HET: ALY; 2.20A {Saccharomyces cerevisiae} PDB: 2r0v_A*

Probab=99.83  E-value=5.9e-21  Score=202.36  Aligned_cols=87  Identities=26%  Similarity=0.401  Sum_probs=84.3

Q ss_pred             hCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHH
Q 005668          324 SHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQEYAAAQELRTL  403 (684)
Q Consensus       324 ~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~pdS~vykaA~eLr~l  403 (684)
                      .|+.+|+|..||+...+|+||+||++||||.||+.||+++.|.++. +|..||+|||+||++||+++|.+|.+|..|+.+
T Consensus       227 ~~~~s~~F~~pvd~~~~PdY~~iIk~PmDL~tI~~kl~~~~Y~s~~-ef~~Dv~Lif~N~~~yN~~~s~i~~~A~~L~~~  305 (361)
T 2r10_A          227 KVKLSEPFMELVDKDELPEYYEIVHSPMALSIVKQNLEIGQYSKIY-DFIIDMLLVFQNAHIFNDPSALIYKDATTLTNY  305 (361)
T ss_dssp             SSCTTGGGSSCCCTTTCTHHHHHCSSCCCHHHHHHHHHHTCCCBHH-HHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHHH
T ss_pred             CCcchhcccCCCChhhcccHHHHhcCcccHHHHHHHHhcCCCCCHH-HHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHH
Confidence            4678999999999999999999999999999999999999999998 999999999999999999999999999999999


Q ss_pred             HHHHHHHH
Q 005668          404 VIKEMTDM  411 (684)
Q Consensus       404 f~k~msk~  411 (684)
                      |+..|.+.
T Consensus       306 f~~~~~~~  313 (361)
T 2r10_A          306 FNYLIQKE  313 (361)
T ss_dssp             HHHHHHHT
T ss_pred             HHHHHHHh
Confidence            99999884

>2r10_A Chromatin structure-remodeling complex protein RSC4, linker, histone H3; bromodomain, remodeler, acetylation, transcription; HET: ALY; 2.20A {Saccharomyces cerevisiae} PDB: 2r0v_A*

Probab=99.77  E-value=3.5e-19  Score=188.84  Aligned_cols=95  Identities=17%  Similarity=0.141  Sum_probs=83.7

Q ss_pred             HHHHHHHHHHh--CcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCcc-CcHHHHHHHHHHHHHHHhhhCCCC
Q 005668          314 PLVRFLGMIRS--HRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYS-NCFQKFFRDLLLLFNNFVIFFRKS  390 (684)
Q Consensus       314 pLl~ILe~L~~--hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~Ys-Si~~EF~rDL~LMF~NA~~FN~pd  390 (684)
                      .|..+|+.|..  ..++++|..||+...+|+||+||++||||+||+.||  +.|. ++. +|..||.|||+||++||+++
T Consensus        82 ~~~~~l~~l~~~~~~~~~~F~~p~~~~~~PdY~~iIk~Pmdl~tI~~kl--~~y~~~~~-~f~~D~~li~~Na~~yN~~~  158 (361)
T 2r10_A           82 FISFTLDVLIDKYKDIFKDFIKLPSRKFHPQYYYKIQQPMSINEIKSRD--YEYEDGPS-NFLLDVELLTKNCQAYNEYD  158 (361)
T ss_dssp             HHHHHHHHHHHHTHHHHGGGSSCCCTTTCTTHHHHCSSCCCHHHHHTSC--CCSTTHHH-HHHHHHHHHHHHHHHHBCSS
T ss_pred             HHHHHHHHHHHcCCcccHHhcCCCCcccCCChHhhcCCCcCHHHHHHHh--hccCCCHH-HHHHHHHHHHHHHhhcCCCC
Confidence            34555666643  346899999999999999999999999999999999  4444 787 99999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHHHHHHH
Q 005668          391 SQEYAAAQELRTLVIKEMTDM  411 (684)
Q Consensus       391 S~vykaA~eLr~lf~k~msk~  411 (684)
                      |.||.+|..|+.+|.++|.+.
T Consensus       159 s~i~~~a~~l~~~~~~~~~k~  179 (361)
T 2r10_A          159 SLIVKNSMQVVMLIEFEVLKA  179 (361)
T ss_dssp             SHHHHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHhhc
Confidence            999999999999999998865

>2r0y_A Chromatin structure-remodeling complex protein RSC4; bromodomain, chromatin, remodeler, RSC, acetylation, transcription, chromatin regulator, nucleus, phosphorylation; HET: ALY; 1.75A {Saccharomyces cerevisiae} PDB: 2r0s_A

Probab=99.75  E-value=9.7e-19  Score=182.43  Aligned_cols=93  Identities=17%  Similarity=0.147  Sum_probs=82.1

Q ss_pred             HHHHHHHHh--CcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCcc-CcHHHHHHHHHHHHHHHhhhCCCCCH
Q 005668          316 VRFLGMIRS--HRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYS-NCFQKFFRDLLLLFNNFVIFFRKSSQ  392 (684)
Q Consensus       316 l~ILe~L~~--hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~Ys-Si~~EF~rDL~LMF~NA~~FN~pdS~  392 (684)
                      ..+|..+..  +.++++|..||+...+|+||+||++||||+||++||  ..|. ++. +|..||.|||+||++||+++|.
T Consensus        34 ~~~L~~~~~~~r~~~~~F~~p~~~~~~PdY~~iIk~PmDL~tI~~kl--~~y~~s~~-~f~~D~~li~~Na~~yN~~~s~  110 (311)
T 2r0y_A           34 SFTLDVLIDKYKDIFKDFIKLPSRKFHPQYYYKIQQPMSINEIKSRD--YEYEDGPS-NFLLDVELLTKNCQAYNEYDSL  110 (311)
T ss_dssp             HHHHHHHHHHSHHHHGGGSSCCCTTTCHHHHHHCSSCCCHHHHHHSC--CCSTTHHH-HHHHHHHHHHHHHHHHSCTTSH
T ss_pred             HHHHHHHHHcCCchhHHhcCCCCcccCCChHHHcCCCCCHHHHHHHH--hcccCCHH-HHHHHHHHHHHHHHHccCCCCH
Confidence            334444443  347899999999999999999999999999999999  4555 787 9999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHH
Q 005668          393 EYAAAQELRTLVIKEMTDM  411 (684)
Q Consensus       393 vykaA~eLr~lf~k~msk~  411 (684)
                      +|.+|..|+.+|.++|.+.
T Consensus       111 i~~~A~~l~~~~~~~~~k~  129 (311)
T 2r0y_A          111 IVKNSMQVVMLIEFEVLKA  129 (311)
T ss_dssp             HHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhhc
Confidence            9999999999999998875

>3iu6_A Protein polybromo-1; PB1, polybromo 1 isoform 1, BAF180, polybromo0ID, PBRM1, BRG associated factor 180, structural genomics, SGC; HET: OCS; 1.79A {Homo sapiens}

Probab=99.67  E-value=2.3e-16  Score=149.49  Aligned_cols=97  Identities=15%  Similarity=0.248  Sum_probs=89.8

Q ss_pred             hHHHHHHHHHHhCc------CCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhh
Q 005668          313 EPLVRFLGMIRSHR------LSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIF  386 (684)
Q Consensus       313 kpLl~ILe~L~~hk------~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~F  386 (684)
                      ..|..||+.|..+.      .+.+|...++..  |+||.  ++||||.+|++||..|.|.++. +|..||.|||+||.+|
T Consensus        10 ~~l~~l~~~v~~~~De~GR~lsd~F~~LPsk~--pdYY~--k~Pi~l~~Ikkri~~~~Y~sld-~f~~D~~lmf~NAr~y   84 (147)
T 3iu6_A           10 ELIHNLFVSVMSHQDDEGRCYSDSLAEIPAVD--PNFPN--KPPLTFDIIRKNVENNRYRRLD-LFQEHMFEVLERARRM   84 (147)
T ss_dssp             HHHHHHHHHHHTCBCTTSCBGGGGGTTCCSSC--TTSTT--SCCCCHHHHHHHHHTTCCCCHH-HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhcCCCCCcchHHHhHCCCCC--ccccC--CCCcCHHHHHHHHhcCCCCCHH-HHHHHHHHHHHHHHHh
Confidence            45778888888775      478999998876  78998  9999999999999999999999 9999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHhhh
Q 005668          387 FRKSSQEYAAAQELRTLVIKEMTDMLRK  414 (684)
Q Consensus       387 N~pdS~vykaA~eLr~lf~k~msk~l~k  414 (684)
                      |.++|.||.+|..|+.+|...+.++...
T Consensus        85 N~e~S~IyeDAv~Lq~~f~~~r~eL~~~  112 (147)
T 3iu6_A           85 NRTDSEIYEDAVELQQFFIKIRDELCKN  112 (147)
T ss_dssp             SCTTSHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHhhC
Confidence            9999999999999999999999998876

>3lqh_A Histone-lysine N-methyltransferase MLL; PHD finger, bromodomain, leukemia, apoptosis, chromati regulator, DNA-binding, isopeptide bond; 1.72A {Homo sapiens} PDB: 3lqi_A* 3lqj_A* 2kyu_A

Probab=99.48  E-value=2.9e-14  Score=139.28  Aligned_cols=90  Identities=19%  Similarity=0.314  Sum_probs=82.4

Q ss_pred             HHHHHHHHHhCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCCCCHHH
Q 005668          315 LVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQEY  394 (684)
Q Consensus       315 Ll~ILe~L~~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~pdS~vy  394 (684)
                      |..||..|..|+.++||...           .++.||||.||++||+.|.|.++. +|..||.|||.||+.||.+++.+.
T Consensus        80 l~~vl~~L~~~~~s~~~~~y-----------~~k~PmDL~~i~kKl~~~~Y~s~~-eF~~Dv~lIf~n~~~~~~~~~e~~  147 (183)
T 3lqh_A           80 LKQVLTALLNSRTTSHLLRY-----------RQQQPLDLEGVKRKMDQGNYTSVL-EFSDDIVKIIQAAINSDGGQPEIK  147 (183)
T ss_dssp             HHHHHHHHHTCHHHHHHHTC-----------CC--CCSHHHHHHHHHTTCCCCHH-HHHHHHHHHHHHHHHHSCCCHHHH
T ss_pred             HHHHHHHHHhccccHhhhhh-----------hhcCCccHHHHHHHHhcCCCCCHH-HHHHHHHHHHHHHhhccCCChhhh
Confidence            78899999999999999873           259999999999999999999998 999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHhhhcC
Q 005668          395 AAAQELRTLVIKEMTDMLRKQQ  416 (684)
Q Consensus       395 kaA~eLr~lf~k~msk~l~k~~  416 (684)
                      .++..|+.+|.+.|.+++|-+-
T Consensus       148 ~ag~~l~~~f~~~l~~vfpwf~  169 (183)
T 3lqh_A          148 KANSMVKSFFIRQMERVFPWFS  169 (183)
T ss_dssp             HHHHHHHHHHHHHHHHHCTTSC
T ss_pred             hhhhHHHHHHHHHHHHHCCCCC
Confidence            9999999999999999998644

>2elk_A SPCC24B10.08C protein; hypothetical protein, structural genomics, NPPSFA; NMR {Schizosaccharomyces pombe}

Probab=97.55  E-value=0.0001  Score=59.22  Aligned_cols=47  Identities=38%  Similarity=0.636  Sum_probs=41.3

Q ss_pred             ccccchhhHHHHHHHHHhhccCCCchHHHHHHH-hhcCCCCCCCHHHHHHHHHHH
Q 005668           12 QQQQWGTLEELLLACAVNRHGTRSWDSIAMEVQ-NRSSALSSLTPQSCRDKFNEI   65 (684)
Q Consensus        12 ~~~~WGTwEELLLacAV~RHGt~~WdsVA~e~~-~r~~~~~~~t~~~C~~k~~~l   65 (684)
                      ....|..-|+++|.-||..||..+|..||..|. .|       |+..|+.+|..+
T Consensus         8 ~~~~WT~eED~~L~~~v~~~G~~~W~~IA~~~~~~R-------t~~qcr~r~~~~   55 (58)
T 2elk_A            8 FDENWGADEELLLIDACETLGLGNWADIADYVGNAR-------TKEECRDHYLKT   55 (58)
T ss_dssp             CCCCCCHHHHHHHHHHHHHTTTTCHHHHHHHHCSSC-------CHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHHHCcCCHHHHHHHHCCCC-------CHHHHHHHHHHH
Confidence            356799999999999999999999999999997 56       479999999754

>1x41_A Transcriptional adaptor 2-like, isoform B; transcriptional adaptor protein2, transcriptional activation, MYB domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=97.32  E-value=0.00024  Score=57.26  Aligned_cols=47  Identities=21%  Similarity=0.491  Sum_probs=41.3

Q ss_pred             ccccchhhHHHHHHHHHhhccCCCchHHHHHHHhhcCCCCCCCHHHHHHHHHHH
Q 005668           12 QQQQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEI   65 (684)
Q Consensus        12 ~~~~WGTwEELLLacAV~RHGt~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~l   65 (684)
                      ....|..=|+.+|.-||..||..+|..||..|..|+       +..|+.+|..+
T Consensus         7 ~~~~WT~eED~~L~~~v~~~G~~~W~~Ia~~~~~Rt-------~~qcr~r~~~~   53 (60)
T 1x41_A            7 GDPSWTAQEEMALLEAVMDCGFGNWQDVANQMCTKT-------KEECEKHYMKY   53 (60)
T ss_dssp             CCSSSCHHHHHHHHHHHHHTCTTCHHHHHHHHTTSC-------HHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHHHCcCcHHHHHHHhCCCC-------HHHHHHHHHHH
Confidence            346799999999999999999999999999997664       68999999754

>1w0t_A Telomeric repeat binding factor 1; telomere, DNA-binding protein, homeodomain, mitosis, cell cycle; 2.00A {Homo sapiens} SCOP: a.4.1.4 PDB: 1ba5_A

Probab=97.27  E-value=0.00021  Score=56.03  Aligned_cols=49  Identities=20%  Similarity=0.443  Sum_probs=42.0

Q ss_pred             ccchhhHHHHHHHHHhhccCCCchHHHHHHHhhcCCCCCCCHHHHHHHHHHHHh
Q 005668           14 QQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEIRR   67 (684)
Q Consensus        14 ~~WGTwEELLLacAV~RHGt~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~l~~   67 (684)
                      ..|..=|+.+|..+|..||+.+|..||..|.     ....|+..|+.+|..|.+
T Consensus         3 ~~WT~eEd~~L~~~v~~~G~~~W~~Ia~~~~-----~~~Rt~~qcr~Rw~~~~k   51 (53)
T 1w0t_A            3 QAWLWEEDKNLRSGVRKYGEGNWSKILLHYK-----FNNRTSVMLKDRWRTMKK   51 (53)
T ss_dssp             CCCCHHHHHHHHHHHHHHCTTCHHHHHHHSC-----CSSCCHHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHHHHHCcCCHHHHHHHcC-----CCCCCHHHHHHHHHHHHc
Confidence            4688889999999999999999999999874     113578999999998865

>3sjm_A Telomeric repeat-binding factor 2; human telomeric repeat binding protein 2, telomere, telomeri homeodomain proteins amino acid sequence; HET: DNA; 1.35A {Homo sapiens} PDB: 1xg1_A 1vfc_A 1vf9_A 1w0u_A

Probab=97.20  E-value=0.00035  Score=57.43  Aligned_cols=51  Identities=20%  Similarity=0.470  Sum_probs=43.1

Q ss_pred             ccccchhhHHHHHHHHHhhccCCCchHHHHHHHhhcCCCCCCCHHHHHHHHHHHHh
Q 005668           12 QQQQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEIRR   67 (684)
Q Consensus        12 ~~~~WGTwEELLLacAV~RHGt~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~l~~   67 (684)
                      -...|..-|+-+|.-+|.+||..+|..||..+-     ....|+..|+.||+-|.+
T Consensus        10 kk~~WT~eED~~L~~~V~~~G~~~W~~Ia~~~~-----~~~Rt~~qcr~Rw~nl~k   60 (64)
T 3sjm_A           10 KKQKWTVEESEWVKAGVQKYGEGNWAAISKNYP-----FVNRTAVMIKDRWRTMKR   60 (64)
T ss_dssp             CCCCCCHHHHHHHHHHHHHHCTTCHHHHHHHSC-----CSSCCHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHccCCCchHHHHhhcC-----CCCCCHHHHHHHHHHHhc
Confidence            456899999999999999999999999998742     124588999999998864

>1guu_A C-MYB, MYB proto-oncogene protein; transcription, transcription regulation, DNA binding, ION bindi proto-oncogene, nuclear protein, activator; 1.6A {Mus musculus} SCOP: a.4.1.3 PDB: 1mbe_A 1mbf_A

Probab=97.08  E-value=0.00037  Score=54.17  Aligned_cols=45  Identities=29%  Similarity=0.589  Sum_probs=39.5

Q ss_pred             ccchhhHHHHHHHHHhhccCCCchHHHHHHHhhcCCCCCCCHHHHHHHHHHH
Q 005668           14 QQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEI   65 (684)
Q Consensus        14 ~~WGTwEELLLacAV~RHGt~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~l   65 (684)
                      ..|..=|+.+|.-+|..||..+|..||..|..|       |+..|+.+|..+
T Consensus         4 ~~Wt~eED~~L~~~v~~~G~~~W~~Ia~~~~~R-------t~~qcr~Rw~~~   48 (52)
T 1guu_A            4 TRWTREEDEKLKKLVEQNGTDDWKVIANYLPNR-------TDVQCQHRWQKV   48 (52)
T ss_dssp             CCCCHHHHHHHHHHHHHHCSSCHHHHHHTSTTC-------CHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHhCCCCHHHHHHHcCCC-------CHHHHHHHHHHH
Confidence            578888999999999999999999999887544       679999999865

>2yus_A SWI/SNF-related matrix-associated actin- dependent regulator of chromatin subfamily...; SWI/SNF complex 155 kDa subunit, BRG1-associated factor 155; NMR {Homo sapiens}

Probab=97.01  E-value=0.00033  Score=59.92  Aligned_cols=48  Identities=23%  Similarity=0.478  Sum_probs=41.9

Q ss_pred             ccccccchhhHHHHHHHHHhhccCCCchHHHHHHHhhcCCCCCCCHHHHHHHHHHH
Q 005668           10 SQQQQQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEI   65 (684)
Q Consensus        10 ~~~~~~WGTwEELLLacAV~RHGt~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~l   65 (684)
                      ......|..=|+++|.-||..|| .+|..||..|..||       +..|+.+|..|
T Consensus        15 ~~~~~~WT~eEd~~Ll~~v~~~G-~~W~~IA~~v~~RT-------~~qcr~r~~~~   62 (79)
T 2yus_A           15 ASAGREWTEQETLLLLEALEMYK-DDWNKVSEHVGSRT-------QDECILHFLRL   62 (79)
T ss_dssp             SCCSCCCCHHHHHHHHHHHHHSS-SCHHHHHHHHSSCC-------HHHHHHHHTTS
T ss_pred             cccCCCcCHHHHHHHHHHHHHhC-CCHHHHHHHcCCCC-------HHHHHHHHHHh
Confidence            34567899999999999999999 99999999997665       69999999754

>2d9a_A B-MYB, MYB-related protein B; DNA binding, structural genomics, unknown function, NPPSFA; NMR {Mus musculus}

Probab=96.84  E-value=0.00073  Score=54.07  Aligned_cols=47  Identities=26%  Similarity=0.533  Sum_probs=40.7

Q ss_pred             ccccchhhHHHHHHHHHhhccCCCchHHHHHHHhhcCCCCCCCHHHHHHHHHHH
Q 005668           12 QQQQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEI   65 (684)
Q Consensus        12 ~~~~WGTwEELLLacAV~RHGt~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~l   65 (684)
                      ....|.--|+.+|.-+|..||+.+|..||..|..|       |+..|+.+|..+
T Consensus         7 ~k~~Wt~eED~~L~~~v~~~G~~~W~~Ia~~~~~R-------t~~qcr~Rw~~~   53 (60)
T 2d9a_A            7 GKVKWTHEEDEQLRALVRQFGQQDWKFLASHFPNR-------TDQQCQYRWLRV   53 (60)
T ss_dssp             CCSCCCHHHHHHHHHHHHHTCTTCHHHHHHHCSSS-------CHHHHHHHHHHT
T ss_pred             CCCCCCHHHHHHHHHHHHHhCCCCHHHHHHHccCC-------CHHHHHHHHHHH
Confidence            34679999999999999999999999999987544       579999999864

>1gvd_A MYB proto-oncogene protein; transcription, transcription regulation, C-MYB, DNA binding, ION binding, nuclear protein; 1.45A {Mus musculus} SCOP: a.4.1.3 PDB: 1gv5_A 1mbg_A 1mbh_A

Probab=96.69  E-value=0.0008  Score=52.36  Aligned_cols=44  Identities=25%  Similarity=0.599  Sum_probs=38.5

Q ss_pred             ccchhhHHHHHHHHHhhccCCCchHHHHHHHhhcCCCCCCCHHHHHHHHHH
Q 005668           14 QQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNE   64 (684)
Q Consensus        14 ~~WGTwEELLLacAV~RHGt~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~   64 (684)
                      ..|..=|+.+|.-+|..||..+|..||..|..|       |+..|+.+|..
T Consensus         4 ~~Wt~eED~~L~~~v~~~G~~~W~~Ia~~~~~R-------t~~qcr~Rw~~   47 (52)
T 1gvd_A            4 GPWTKEEDQRLIKLVQKYGPKRWSVIAKHLKGR-------IGKQCRERWHN   47 (52)
T ss_dssp             CSCCHHHHHHHHHHHHHHCTTCHHHHHTTSTTC-------CHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHCcChHHHHHHHcCCC-------CHHHHHHHHHH
Confidence            578888999999999999999999999876544       67999999975

>1ity_A TRF1; helix-turn-helix, telomeres, DNA binding, MYB domain, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Homo sapiens} SCOP: a.4.1.4 PDB: 1iv6_A

Probab=96.65  E-value=0.0015  Score=53.77  Aligned_cols=53  Identities=19%  Similarity=0.394  Sum_probs=44.2

Q ss_pred             ccccchhhHHHHHHHHHhhccCCCchHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhhh
Q 005668           12 QQQQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEIRRRF   69 (684)
Q Consensus        12 ~~~~WGTwEELLLacAV~RHGt~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~l~~R~   69 (684)
                      ....|..=|+.+|..+|..||+..|..||..|.     ....|+..|+.+|..+.+.-
T Consensus         9 ~r~~WT~eED~~L~~~v~~~G~~~W~~Ia~~~~-----~~~Rt~~qcr~Rw~~~l~p~   61 (69)
T 1ity_A            9 KRQAWLWEEDKNLRSGVRKYGEGNWSKILLHYK-----FNNRTSVMLKDRWRTMKKLK   61 (69)
T ss_dssp             SCCCCCHHHHHHHHHHHHHHCSSCHHHHHHHSC-----CSSCCHHHHHHHHHHHHHTS
T ss_pred             CCCCCCHHHHHHHHHHHHHHCCCcHHHHHHHcC-----cCCCCHHHHHHHHHHHcCCC
Confidence            346799999999999999999999999999874     11457899999999886653

>2dim_A Cell division cycle 5-like protein; MYB_DNA-binding domain, cell cycle, DNA binding, spliceosome, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=96.56  E-value=0.0018  Score=53.40  Aligned_cols=46  Identities=24%  Similarity=0.562  Sum_probs=39.9

Q ss_pred             cccchhhHHHHHHHHHhhccCCCchHHHHHHHhhcCCCCCCCHHHHHHHHHHH
Q 005668           13 QQQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEI   65 (684)
Q Consensus        13 ~~~WGTwEELLLacAV~RHGt~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~l   65 (684)
                      ...|.-=|+.+|..+|..||+.+|..||..|..|       |+..|+.+|..+
T Consensus         9 ~~~Wt~eED~~L~~~v~~~G~~~W~~Ia~~l~~R-------t~~qcr~Rw~~~   54 (70)
T 2dim_A            9 GGVWRNTEDEILKAAVMKYGKNQWSRIASLLHRK-------SAKQCKARWYEW   54 (70)
T ss_dssp             TCCCCHHHHHHHHHHHHHTCSSCHHHHHHHSTTC-------CHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHhcCC-------CHHHHHHHHHHH
Confidence            3578888999999999999999999999988644       579999999763

>2cu7_A KIAA1915 protein; nuclear protein, SANT domain, DNA binding, regulation of transcription, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.3

Probab=96.38  E-value=0.0032  Score=52.29  Aligned_cols=52  Identities=13%  Similarity=0.263  Sum_probs=45.2

Q ss_pred             ccccchhhHHHHHHHHHhhccCCCchHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhhhcC
Q 005668           12 QQQQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEIRRRFTV   71 (684)
Q Consensus        12 ~~~~WGTwEELLLacAV~RHGt~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~l~~R~~~   71 (684)
                      ....|.--|+.+|.-||..||. +|..||..|..|+       +..|+.+|..+.++..-
T Consensus         8 ~~~~WT~eEd~~l~~~~~~~G~-~W~~Ia~~~~~Rt-------~~q~k~r~~~~l~~~~~   59 (72)
T 2cu7_A            8 YSVKWTIEEKELFEQGLAKFGR-RWTKISKLIGSRT-------VLQVKSYARQYFKNKVK   59 (72)
T ss_dssp             CCCCCCHHHHHHHHHHHHHTCS-CHHHHHHHHSSSC-------HHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCHHHHHHHHHHHHHHCc-CHHHHHHHcCCCC-------HHHHHHHHHHHHHHHHh
Confidence            4568999999999999999999 9999999887775       68999999988777644

>2llk_A Cyclin-D-binding MYB-like transcription factor 1; helix bundle, SGC, structural genomics consortium, NESG, NOR structural genomics consortium; NMR {Homo sapiens}

Probab=96.08  E-value=0.0036  Score=53.02  Aligned_cols=49  Identities=20%  Similarity=0.325  Sum_probs=43.4

Q ss_pred             cccchhhHHHHHHHHHhhccCCCchHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhhhc
Q 005668           13 QQQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEIRRRFT   70 (684)
Q Consensus        13 ~~~WGTwEELLLacAV~RHGt~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~l~~R~~   70 (684)
                      ...|.-=|+.+|.-+|..||.. |..||..| .||       +..|+.+|.-|++.+.
T Consensus        23 k~~wT~EED~~L~~l~~~~G~k-W~~IA~~l-gRt-------~~q~knRw~~L~~~~~   71 (73)
T 2llk_A           23 VGKYTPEEIEKLKELRIKHGND-WATIGAAL-GRS-------ASSVKDRCRLMKDTCN   71 (73)
T ss_dssp             CCSSCHHHHHHHHHHHHHHSSC-HHHHHHHH-TSC-------HHHHHHHHHHCSCCCS
T ss_pred             CCCCCHHHHHHHHHHHHHHCCC-HHHHHHHh-CCC-------HHHHHHHHHHHHHHcc
Confidence            4678888999999999999987 99999999 886       5899999999987654

>2din_A Cell division cycle 5-like protein; MYB_DNA-binding domain, cell cycle, DNA binding, spliceosome, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=95.93  E-value=0.0098  Score=48.39  Aligned_cols=48  Identities=23%  Similarity=0.416  Sum_probs=41.2

Q ss_pred             cccchhhHHHHHHHHHhhccCCCchHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhhh
Q 005668           13 QQQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEIRRRF   69 (684)
Q Consensus        13 ~~~WGTwEELLLacAV~RHGt~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~l~~R~   69 (684)
                      ...|.-=|+.+|..+|..||. .|..||. +-.|       |+..|+.+|..|-+.-
T Consensus         9 k~~WT~eED~~L~~~~~~~g~-~W~~Ia~-~~gR-------t~~qcr~Rw~~~l~~~   56 (66)
T 2din_A            9 KTEWSREEEEKLLHLAKLMPT-QWRTIAP-IIGR-------TAAQCLEHYEFLLDKA   56 (66)
T ss_dssp             CCCCCHHHHHHHHHHHHHCTT-CHHHHHH-HHSS-------CHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHcCC-CHHHHhc-ccCc-------CHHHHHHHHHHHhChH
Confidence            457999999999999999999 9999999 7655       5799999999886554

>2k9n_A MYB24; R2R3 domain, DNA-binding, nucleus, DNA binding protein; NMR {Trichomonas vaginalis} PDB: 2kdz_A

Probab=95.77  E-value=0.008  Score=53.16  Aligned_cols=44  Identities=30%  Similarity=0.593  Sum_probs=38.6

Q ss_pred             ccchhhHHHHHHHHHhhccCCCchHHHHHHHhhcCCCCCCCHHHHHHHHHH
Q 005668           14 QQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNE   64 (684)
Q Consensus        14 ~~WGTwEELLLacAV~RHGt~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~   64 (684)
                      ..|..=|+-+|.-+|..||+.+|..||..|-.|       |+..|+.+|..
T Consensus         2 ~~Wt~eED~~L~~~v~~~g~~~W~~Ia~~~~~R-------t~~qcr~Rw~~   45 (107)
T 2k9n_A            2 VKFTEEEDLKLQQLVMRYGAKDWIRISQLMITR-------NPRQCRERWNN   45 (107)
T ss_dssp             CSSCHHHHHHHHHHHHHHCSSCHHHHHHHTTTS-------CHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHCCCCHHHHhhhcCCC-------CHHHHHHHHHH
Confidence            468888999999999999999999999988655       57999999975

>2ltp_A Nuclear receptor corepressor 2; SMRT, TRAC, SGC, structural genomics consortium, NESG, north structural genomics consortium; NMR {Homo sapiens}

Probab=94.74  E-value=0.0017  Score=56.46  Aligned_cols=52  Identities=21%  Similarity=0.397  Sum_probs=45.2

Q ss_pred             ccccchhhHHHHHHHHHhhccCCCchHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhhhcC
Q 005668           12 QQQQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEIRRRFTV   71 (684)
Q Consensus        12 ~~~~WGTwEELLLacAV~RHGt~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~l~~R~~~   71 (684)
                      ....|.--|+.||.-+|..||. +|..||.-|..||       ...|+.+|..+.+|+.-
T Consensus        15 ~~~~WT~eEd~~l~~~~~~~G~-~W~~IA~~l~gRt-------~~q~k~r~~~~lrk~~l   66 (89)
T 2ltp_A           15 YFQGWTEEEMGTAKKGLLEHGR-NWSAIARMVGSKT-------VSQCKNFYFNYKKRQNL   66 (89)
Confidence            4567999999999999999999 7999999988776       47999999988888753

>2ckx_A NGTRF1, telomere binding protein TBP1; nuclear protein; 1.9A {Nicotiana tabacum} SCOP: a.4.1.3 PDB: 2qhb_A

Probab=95.73  E-value=0.0077  Score=52.09  Aligned_cols=52  Identities=21%  Similarity=0.270  Sum_probs=42.6

Q ss_pred             cchhhHHHHHHHHHhhccCCCchHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhhh
Q 005668           15 QWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEIRRRF   69 (684)
Q Consensus        15 ~WGTwEELLLacAV~RHGt~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~l~~R~   69 (684)
                      .|..=|+.+|.-+|.+||.+.|..|+..--   ......|...|+.||+-|.++-
T Consensus         2 ~WT~eEd~~L~~gv~k~G~g~W~~I~~~~~---~~~~~RT~~~lKdrWrnllk~~   53 (83)
T 2ckx_A            2 PFSVAEVEALVEAVEHLGTGRWRDVKMRAF---DNADHRTYVDLKDKWKTLVHTA   53 (83)
T ss_dssp             CCCHHHHHHHHHHHHHHCSSCHHHHHHHHC---TTCTTSCHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHCCCCcHHHHHhhc---cccCCCCHHHHHHHHHHHHHhc
Confidence            588889999999999999999999998531   1123568999999999988643

>2k9n_A MYB24; R2R3 domain, DNA-binding, nucleus, DNA binding protein; NMR {Trichomonas vaginalis} PDB: 2kdz_A

Probab=95.70  E-value=0.0093  Score=52.74  Aligned_cols=51  Identities=25%  Similarity=0.483  Sum_probs=44.3

Q ss_pred             cccchhhHHHHHHHHHhhccCCCchHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhhhcC
Q 005668           13 QQQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEIRRRFTV   71 (684)
Q Consensus        13 ~~~WGTwEELLLacAV~RHGt~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~l~~R~~~   71 (684)
                      ...|.--|+.+|.-+|..||. .|..||..|..||       +..|+.+|..|.++..-
T Consensus        53 ~~~WT~eEd~~L~~~~~~~G~-~W~~Ia~~l~gRt-------~~~~k~rw~~l~r~~~~  103 (107)
T 2k9n_A           53 TDPWSPEEDMLLDQKYAEYGP-KWNKISKFLKNRS-------DNNIRNRWMMIARHRAK  103 (107)
T ss_dssp             TCCCCHHHHHHHHHHHHHTCS-CHHHHHHHHSSSC-------HHHHHHHHHHHHHHHHS
T ss_pred             ccccCHHHHHHHHHHHHHhCc-CHHHHHHHCCCCC-------HHHHHHHHHHHHhhHHH
Confidence            468988899999999999997 7999999886654       68999999999988643

>2yum_A ZZZ3 protein, zinc finger ZZ-type-containing protein 3; transcription, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=95.62  E-value=0.0077  Score=50.13  Aligned_cols=49  Identities=22%  Similarity=0.323  Sum_probs=41.1

Q ss_pred             ccccchhhHHHHHHHHHhhccC-----CCchHHHHHHHhhcCCCCCCCHHHHHHHHHHHHh
Q 005668           12 QQQQWGTLEELLLACAVNRHGT-----RSWDSIAMEVQNRSSALSSLTPQSCRDKFNEIRR   67 (684)
Q Consensus        12 ~~~~WGTwEELLLacAV~RHGt-----~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~l~~   67 (684)
                      ....|.-=|+.+|--||..||.     .+|..||..|..||       +..|+.+|+.+-.
T Consensus         7 ~~~~WT~eEd~~L~~~v~~~g~~~~~~~~W~~IA~~~~~Rt-------~~qcr~r~~~~l~   60 (75)
T 2yum_A            7 GNQLWTVEEQKKLEQLLIKYPPEEVESRRWQKIADELGNRT-------AKQVASQVQKYFI   60 (75)
T ss_dssp             CSSCCCHHHHHHHHHHHHHSCCCSCHHHHHHHHHHHHSSSC-------HHHHHHHHHHHHG
T ss_pred             CCCCCCHHHHHHHHHHHHHhCCCCCCcccHHHHHHHhCCCC-------HHHHHHHHHHHHH
Confidence            3467998999999999999997     88999999997665       6899999944433

>2roh_A RTBP1, telomere binding protein-1; plant, nucleus, DNA binding protein; NMR {Oryza sativa}

Probab=95.45  E-value=0.024  Score=52.44  Aligned_cols=56  Identities=20%  Similarity=0.288  Sum_probs=46.8

Q ss_pred             cccccchhhHHHHHHHHHhhccCCCchHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhhh
Q 005668           11 QQQQQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEIRRRF   69 (684)
Q Consensus        11 ~~~~~WGTwEELLLacAV~RHGt~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~l~~R~   69 (684)
                      -....|..-|+-+|.-+|.+||.+.|..|+..+-.   .....|...|+.||+.|.+.-
T Consensus        29 r~r~~WT~EEd~~L~~gV~k~G~g~W~~I~~~~~~---~~~~RT~vdlKdRWrnllk~~   84 (122)
T 2roh_A           29 RIRRPFTVAEVELLVEAVEHLGTGRWRDVKFRAFE---NVHHRTYVDLKDKWKTLVHTA   84 (122)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHSSSCHHHHHHHHHS---SSCCCCHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHHCCCChHHHHHHhcc---ccCCCCHHHHHHHHHHHHhhc
Confidence            45678999999999999999999999999986541   224568999999999998754

>2cqr_A RSGI RUH-043, DNAJ homolog subfamily C member 1; membrane protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.3

Probab=95.26  E-value=0.0061  Score=51.53  Aligned_cols=53  Identities=19%  Similarity=0.396  Sum_probs=44.5

Q ss_pred             cccccchhhHHHHHHHHHhhcc---CCCchHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhhhc
Q 005668           11 QQQQQWGTLEELLLACAVNRHG---TRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEIRRRFT   70 (684)
Q Consensus        11 ~~~~~WGTwEELLLacAV~RHG---t~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~l~~R~~   70 (684)
                      .....|.--|+.+|--||..||   ...|..||..|-.       -|+..|+.+|..|.+-++
T Consensus        16 ~~~~~WT~eEd~~L~~al~~~g~~~~~rW~~IA~~vpG-------RT~~qcr~Ry~~L~~d~~   71 (73)
T 2cqr_A           16 SAEEPWTQNQQKLLELALQQYPRGSSDCWDKIARCVPS-------KSKEDCIARYKLLVSGPS   71 (73)
T ss_dssp             CSSCCCCHHHHHHHHHHHHHSCSSSHHHHHHHGGGCSS-------SCHHHHHHHHHHHHSSCC
T ss_pred             cCCCCCCHHHHHHHHHHHHHcCCCCCchHHHHHHHcCC-------CCHHHHHHHHHHHHHccc
Confidence            4556799999999999999999   4689999977643       568999999999977654

>1gv2_A C-MYB, MYB proto-oncogene protein; transcription, DNA binding, ION binding; 1.68A {Mus musculus} SCOP: a.4.1.3 a.4.1.3 PDB: 1mse_C* 1msf_C* 1a5j_A 1idy_A 1idz_A 1mbj_A 1mbk_A

Probab=95.19  E-value=0.0089  Score=52.34  Aligned_cols=46  Identities=22%  Similarity=0.552  Sum_probs=39.1

Q ss_pred             cccchhhHHHHHHHHHhhccCCCchHHHHHHHhhcCCCCCCCHHHHHHHHHHH
Q 005668           13 QQQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEI   65 (684)
Q Consensus        13 ~~~WGTwEELLLacAV~RHGt~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~l   65 (684)
                      ...|..=|+-+|.-+|..||..+|..||..|-.|       |+..|+.+|..+
T Consensus         4 k~~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~R-------t~~qcr~Rw~~~   49 (105)
T 1gv2_A            4 KGPWTKEEDQRVIKLVQKYGPKRWSVIAKHLKGR-------IGKQCRERWHNH   49 (105)
T ss_dssp             CSCCCHHHHHHHHHHHHHHCTTCHHHHHTTSTTC-------CHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHHHhCCCcHHHHhhhhcCC-------CHHHHHHHHHhc
Confidence            3578888999999999999999999999876544       679999999763

>3osg_A MYB21; transcription-DNA complex, MYB2, R2R3 domain, DNA binding PR transcription factor; 2.00A {Trichomonas vaginalis} PDB: 3osf_A

Probab=95.11  E-value=0.013  Score=53.39  Aligned_cols=47  Identities=32%  Similarity=0.668  Sum_probs=39.9

Q ss_pred             cccccchhhHHHHHHHHHhhccCCCchHHHHHHHhhcCCCCCCCHHHHHHHHHHH
Q 005668           11 QQQQQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEI   65 (684)
Q Consensus        11 ~~~~~WGTwEELLLacAV~RHGt~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~l   65 (684)
                      .-...|..=|+-+|.-||..||+ +|..||..|-.|       |+..|+.+|...
T Consensus         9 ~kk~~WT~eED~~L~~~v~~~G~-~W~~Ia~~~~~R-------t~~qcr~Rw~~~   55 (126)
T 3osg_A            9 AKKQKFTPEEDEMLKRAVAQHGS-DWKMIAATFPNR-------NARQCRDRWKNY   55 (126)
T ss_dssp             CSSCCCCHHHHHHHHHHHHHHTT-CHHHHHHTCTTC-------CHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHhCC-CHHHHHHHcCCC-------CHHHHHHHHhhh
Confidence            34567999999999999999999 999999876554       578999999864

>3zqc_A MYB3; transcription-DNA complex, DNA-binding protein, nucleus; 2.90A {Trichomonas vaginalis}

Probab=95.07  E-value=0.0094  Score=54.53  Aligned_cols=46  Identities=24%  Similarity=0.537  Sum_probs=38.9

Q ss_pred             cccchhhHHHHHHHHHhhccCCCchHHHHHHHhhcCCCCCCCHHHHHHHHHHH
Q 005668           13 QQQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEI   65 (684)
Q Consensus        13 ~~~WGTwEELLLacAV~RHGt~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~l   65 (684)
                      .+.|..=|+-+|.-+|..||+.+|..||..|-.|       |+..|+.+|...
T Consensus         2 Kg~Wt~eED~~L~~~v~~~g~~~W~~Ia~~~~~R-------t~~qcr~Rw~~~   47 (131)
T 3zqc_A            2 KGPFTEAEDDLIREYVKENGPQNWPRITSFLPNR-------SPKQCRERWFNH   47 (131)
T ss_dssp             CSSCCHHHHHHHHHHHHHHCSCCGGGGTTSCTTS-------CHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHhCcCCHHHHHHHHCCC-------CHHHHHHHHhhc
Confidence            3568888999999999999999999999877554       579999999653

>2juh_A Telomere binding protein TBP1; helix, nucleus, nuclear protein; NMR {Nicotiana glutinosa}

Probab=95.03  E-value=0.023  Score=52.48  Aligned_cols=56  Identities=20%  Similarity=0.276  Sum_probs=46.5

Q ss_pred             cccccchhhHHHHHHHHHhhccCCCchHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhhh
Q 005668           11 QQQQQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEIRRRF   69 (684)
Q Consensus        11 ~~~~~WGTwEELLLacAV~RHGt~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~l~~R~   69 (684)
                      -.-..|..-|+-+|.-+|.+||...|..||..+-.   .....|...|+.||+.|.+.-
T Consensus        15 r~r~~WT~EEd~~L~~gV~k~G~G~W~~Ia~~~~~---~f~~RT~v~lKdRWrnllk~~   70 (121)
T 2juh_A           15 RIRRPFSVAEVEALVEAVEHLGTGRWRDVKMRAFD---NADHRTYVDLKDKWKTLVHTA   70 (121)
T ss_dssp             CSSCCCCHHHHHHHHHHHHHHGGGCHHHHHHHHCS---CCSSCCSHHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHhcc---ccCCCCHHHHHHHHHHHHhhh
Confidence            34568999999999999999999999999988732   123568899999999998753

>2aje_A Telomere repeat-binding protein; DNA-binding, Trp, MYB motif, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: a.4.1.3

Probab=94.85  E-value=0.019  Score=51.75  Aligned_cols=57  Identities=18%  Similarity=0.257  Sum_probs=45.9

Q ss_pred             ccccchhhHHHHHHHHHhhccCCCchHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhhhcC
Q 005668           12 QQQQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEIRRRFTV   71 (684)
Q Consensus        12 ~~~~WGTwEELLLacAV~RHGt~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~l~~R~~~   71 (684)
                      ....|..-|+-+|..+|.+||...|..|+..+-   ......|...|+.||+.|.++-+-
T Consensus        12 ~r~~WT~EEd~~L~~gV~k~G~g~W~~I~~~~~---~~f~~RT~v~lKdrWrnllk~~~~   68 (105)
T 2aje_A           12 IRRPFSVAEVEALVQAVEKLGTGRWRDVKLCAF---EDADHRTYVDLKDKWKTLVHTAKI   68 (105)
T ss_dssp             CCCSCCHHHHHHHHHHHHHHCSSSHHHHHSSSS---SSTTCCCHHHHHHHHHHHHHTTTC
T ss_pred             CCCCCCHHHHHHHHHHHHHhCCCChHHHHHHhc---cccCCCCHHHHHHHHHHHHhhccC
Confidence            456899999999999999999999999986431   012356999999999999976543

>3osg_A MYB21; transcription-DNA complex, MYB2, R2R3 domain, DNA binding PR transcription factor; 2.00A {Trichomonas vaginalis} PDB: 3osf_A

Probab=94.72  E-value=0.016  Score=52.70  Aligned_cols=52  Identities=23%  Similarity=0.461  Sum_probs=43.9

Q ss_pred             cccchhhHHHHHHHHHhhccCCCchHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhhhcCC
Q 005668           13 QQQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEIRRRFTVK   72 (684)
Q Consensus        13 ~~~WGTwEELLLacAV~RHGt~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~l~~R~~~~   72 (684)
                      ...|.-=|+.+|.-+|..|| ..|..||..|..|       |...|+.+|..|.+++.-.
T Consensus        62 ~~~WT~eEd~~L~~~v~~~G-~~W~~Ia~~l~gR-------t~~~~k~rw~~l~~k~~~p  113 (126)
T 3osg_A           62 HTPWTAEEDALLVQKIQEYG-RQWAIIAKFFPGR-------TDIHIKNRWVTISNKLGIP  113 (126)
T ss_dssp             CSCCCHHHHHHHHHHHHHHC-SCHHHHHTTSTTC-------CHHHHHHHHHHHHHHTTC-
T ss_pred             cccCCHHHHHHHHHHHHHHC-cCHHHHHHHcCCC-------CHHHHHHHHHHHHHhcCCC
Confidence            45799999999999999999 5799999765544       5799999999999998654

>1gv2_A C-MYB, MYB proto-oncogene protein; transcription, DNA binding, ION binding; 1.68A {Mus musculus} SCOP: a.4.1.3 a.4.1.3 PDB: 1mse_C* 1msf_C* 1a5j_A 1idy_A 1idz_A 1mbj_A 1mbk_A

Probab=94.57  E-value=0.014  Score=51.03  Aligned_cols=49  Identities=24%  Similarity=0.465  Sum_probs=40.6

Q ss_pred             ccccchhhHHHHHHHHHhhccCCCchHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhh
Q 005668           12 QQQQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEIRRR   68 (684)
Q Consensus        12 ~~~~WGTwEELLLacAV~RHGt~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~l~~R   68 (684)
                      ....|.--|+.+|.-||..||. .|..||..|..       .|+..|+.+|..|.+|
T Consensus        55 ~~~~Wt~eEd~~L~~~~~~~G~-~W~~Ia~~l~g-------Rt~~~~k~rw~~~~~~  103 (105)
T 1gv2_A           55 KKTSWTEEEDRIIYQAHKRLGN-RWAEIAKLLPG-------RTDNAIKNHWNSTMRR  103 (105)
T ss_dssp             CCCCCCHHHHHHHHHHHHHHSS-CHHHHHTTCTT-------CCHHHHHHHHHHHTC-
T ss_pred             cccCCCHHHHHHHHHHHHHhCC-CHHHHHHHcCC-------CCHHHHHHHHHHHHhc
Confidence            3467988899999999999996 79999975543       5679999999998776

>2iw5_B Protein corest, REST corepressor 1; oxidoreductase-transcription regulator complex, oxidoreductase/repressor complex, histone demethylase, FAD; HET: FAD; 2.57A {Homo sapiens} SCOP: a.4.1.3 PDB: 2uxn_B* 2uxx_B* 2y48_B* 2v1d_B* 2x0l_B*

Probab=94.37  E-value=0.032  Score=56.50  Aligned_cols=52  Identities=31%  Similarity=0.536  Sum_probs=46.0

Q ss_pred             cccccchhhHHHHHHHHHhhccCCCchHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhhhc
Q 005668           11 QQQQQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEIRRRFT   70 (684)
Q Consensus        11 ~~~~~WGTwEELLLacAV~RHGt~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~l~~R~~   70 (684)
                      .....|..-|.+|+-.|+..|| .+|..||.-|.+||       ...|+..|...++||.
T Consensus       131 k~s~~WTeEE~~lFleAl~kYG-KDW~~IAk~VgTKT-------~~QcKnfY~~~kKRln  182 (235)
T 2iw5_B          131 KCNARWTTEEQLLAVQAIRKYG-RDFQAISDVIGNKS-------VVQVKNFFVNYRRRFN  182 (235)
T ss_dssp             CCCSSCCHHHHHHHHHHHHHHS-SCHHHHHHHHSSCC-------HHHHHHHHHHTTTTTT
T ss_pred             ccCCCCCHHHHHHHHHHHHHHC-cCHHHHHHHcCCCC-------HHHHHHHHHHHHHHhh
Confidence            4677999999999999999999 58999999998776       5899999988888884

>1h8a_C AMV V-MYB, MYB transforming protein; transcription/DNA; 2.23A {Avian myeloblastosis virus} SCOP: a.4.1.3 a.4.1.3

Probab=94.37  E-value=0.022  Score=51.70  Aligned_cols=46  Identities=22%  Similarity=0.585  Sum_probs=39.7

Q ss_pred             ccccchhhHHHHHHHHHhhccCCCchHHHHHHHhhcCCCCCCCHHHHHHHHHH
Q 005668           12 QQQQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNE   64 (684)
Q Consensus        12 ~~~~WGTwEELLLacAV~RHGt~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~   64 (684)
                      ....|..=|+-+|.-+|..||..+|..||..|-.|       |+..|+.+|..
T Consensus        26 ~k~~Wt~eED~~L~~~v~~~g~~~W~~Ia~~l~~R-------t~~qcr~Rw~~   71 (128)
T 1h8a_C           26 NKGPWTKEEDQRVIEHVQKYGPKRWSDIAKHLKGR-------IGKQCRERWHN   71 (128)
T ss_dssp             CCSCCCHHHHHHHHHHHHHTCSCCHHHHHHHSSSC-------CHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHhcCC-------cHHHHHHHHHH
Confidence            34678888999999999999999999999987544       57899999985

>2cjj_A Radialis; plant development, DNA-binding protein, MYB transcription FA DNA-binding, nuclear protein, floral asymmetry; 1.9A {Antirrhinum majus} SCOP: a.4.1.3

Probab=94.04  E-value=0.037  Score=48.83  Aligned_cols=51  Identities=18%  Similarity=0.418  Sum_probs=42.7

Q ss_pred             ccccchhhHHHHHHHHHhhcc---CCCchHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhhh
Q 005668           12 QQQQWGTLEELLLACAVNRHG---TRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEIRRRF   69 (684)
Q Consensus        12 ~~~~WGTwEELLLacAV~RHG---t~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~l~~R~   69 (684)
                      ....|..=|+.+|-.||..||   ...|..||..|-.|       |+..|+.+|..|....
T Consensus         7 ~~~~WT~eEd~~L~~al~~~~~~~~~rW~~IA~~vpGR-------T~~q~k~ry~~l~~dv   60 (93)
T 2cjj_A            7 SGRPWSAKENKAFERALAVYDKDTPDRWANVARAVEGR-------TPEEVKKHYEILVEDI   60 (93)
T ss_dssp             -CCSCCHHHHHHHHHHHHHSCTTCTTHHHHHHHHSTTC-------CHHHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHHcCCCCCchHHHHHHHcCCC-------CHHHHHHHHHHHHHHH
Confidence            346799999999999999998   56799999988655       5799999999997653

>1h8a_C AMV V-MYB, MYB transforming protein; transcription/DNA; 2.23A {Avian myeloblastosis virus} SCOP: a.4.1.3 a.4.1.3

Probab=92.75  E-value=0.03  Score=50.81  Aligned_cols=48  Identities=27%  Similarity=0.520  Sum_probs=40.7

Q ss_pred             cccchhhHHHHHHHHHhhccCCCchHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhh
Q 005668           13 QQQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEIRRR   68 (684)
Q Consensus        13 ~~~WGTwEELLLacAV~RHGt~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~l~~R   68 (684)
                      ...|.-=|+.+|.-+|..||. .|..||..|..|       |+..|+.+|..|.+|
T Consensus        79 ~~~WT~eEd~~L~~~~~~~G~-~W~~Ia~~l~gR-------t~~~~k~r~~~~~~~  126 (128)
T 1h8a_C           79 KTSWTEEEDRIIYQAHKRLGN-RWAEIAKLLPGR-------TDNAVKNHWNSTMRR  126 (128)
T ss_dssp             CSCCCHHHHHHHHHHHHHHCS-CHHHHGGGSTTC-------CHHHHHHHHHTTTTC
T ss_pred             cccCCHHHHHHHHHHHHHHCc-CHHHHHHHCCCC-------CHHHHHHHHHHHHhc
Confidence            467988899999999999996 799999765444       679999999988765

>1h89_C C-MYB, MYB proto-oncogene protein; transcription/DNA; 2.45A {Mus musculus} SCOP: a.4.1.3 a.4.1.3 a.4.1.3 PDB: 1h88_C

Probab=92.67  E-value=0.027  Score=52.84  Aligned_cols=45  Identities=27%  Similarity=0.570  Sum_probs=6.9

Q ss_pred             cccchhhHHHHHHHHHhhccCCCchHHHHHHHhhcCCCCCCCHHHHHHHHHH
Q 005668           13 QQQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNE   64 (684)
Q Consensus        13 ~~~WGTwEELLLacAV~RHGt~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~   64 (684)
                      ...|..=|+-+|.-+|..||+.+|..||..|-.|+       +..|+.+|..
T Consensus         6 k~~Wt~eED~~L~~~v~~~g~~~W~~Ia~~l~~Rt-------~~qcr~Rw~~   50 (159)
T 1h89_C            6 KTRWTREEDEKLKKLVEQNGTDDWKVIANYLPNRT-------DVQCQHRWQK   50 (159)
T ss_dssp             --------------------------------------------CHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHHHhCCCCHHHHHHHcCCCC-------HHHHHHHHHH
Confidence            45688889999999999999999999999887665       5789999974

>1h89_C C-MYB, MYB proto-oncogene protein; transcription/DNA; 2.45A {Mus musculus} SCOP: a.4.1.3 a.4.1.3 a.4.1.3 PDB: 1h88_C

Probab=92.51  E-value=0.058  Score=50.60  Aligned_cols=47  Identities=21%  Similarity=0.527  Sum_probs=40.1

Q ss_pred             ccccchhhHHHHHHHHHhhccCCCchHHHHHHHhhcCCCCCCCHHHHHHHHHHH
Q 005668           12 QQQQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEI   65 (684)
Q Consensus        12 ~~~~WGTwEELLLacAV~RHGt~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~l   65 (684)
                      ....|..=|+-+|.-+|..||..+|..||..|..|       |+..|+.+|..+
T Consensus        57 ~~~~Wt~eEd~~L~~~v~~~g~~~W~~Ia~~l~~R-------t~~qcr~Rw~~~  103 (159)
T 1h89_C           57 IKGPWTKEEDQRVIKLVQKYGPKRWSVIAKHLKGR-------IGKQCRERWHNH  103 (159)
T ss_dssp             CCSCCCHHHHHHHHHHHHHHCSCCHHHHHHTSTTC-------CHHHHHHHHHHT
T ss_pred             CCCCCChHHHHHHHHHHHHhCcccHHHHHHHcCCC-------CHHHHHHHHHHH
Confidence            35689888999999999999999999999877544       579999999753

>2eqr_A N-COR1, N-COR, nuclear receptor corepressor 1; SANT domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=91.89  E-value=0.12  Score=41.73  Aligned_cols=48  Identities=17%  Similarity=0.256  Sum_probs=40.3

Q ss_pred             cccccchhhHHHHHHHHHhhccCCCchHHHHHHHhhcCCCCCCCHHHHHHHHHHHH
Q 005668           11 QQQQQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEIR   66 (684)
Q Consensus        11 ~~~~~WGTwEELLLacAV~RHGt~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~l~   66 (684)
                      +....|..=|.-||-.|+..|| .+|..||.-|..|+       +..|...|-.-+
T Consensus        10 ~~~~~WT~eE~~~F~~~~~~~g-k~w~~Ia~~l~~rt-------~~~~v~~Yy~~K   57 (61)
T 2eqr_A           10 QFMNVWTDHEKEIFKDKFIQHP-KNFGLIASYLERKS-------VPDCVLYYYLTK   57 (61)
T ss_dssp             SCCCSCCHHHHHHHHHHHHHST-TCHHHHHHHCTTSC-------HHHHHHHHHHHT
T ss_pred             ccCCCCCHHHHHHHHHHHHHhC-CCHHHHHHHcCCCC-------HHHHHHHHHHhc
Confidence            5678999999999999999999 69999997776655       578999886544

>2ebi_A DNA binding protein GT-1; DNA-binding domain, phosphorylation; HET: DNA; NMR {Arabidopsis thaliana} PDB: 2jmw_A*

Probab=91.87  E-value=0.13  Score=43.75  Aligned_cols=56  Identities=18%  Similarity=0.408  Sum_probs=42.1

Q ss_pred             ccchhhHHHHHHHHHhhcc---------CCCchHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhhhcCC
Q 005668           14 QQWGTLEELLLACAVNRHG---------TRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEIRRRFTVK   72 (684)
Q Consensus        14 ~~WGTwEELLLacAV~RHG---------t~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~l~~R~~~~   72 (684)
                      ..|+-=|=+||.-+..=|-         ..-|..||..|+..--   ..|+.-|+.||..|+++|-.-
T Consensus         5 ~~Wt~~Et~~Li~~~~e~~~~f~~~~~~~~~W~~Ia~~m~~~G~---~rs~~qC~~K~~nL~k~Yk~~   69 (86)
T 2ebi_A            5 ETWVQDETRSLIMFRRGMDGLFNTSKSNKHLWEQISSKMREKGF---DRSPDMCTDKWRNLLKEFKKA   69 (86)
T ss_dssp             CCCCHHHHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHC---CCCHHHHHHHHHHHHHHHCSC
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHccccchHHHHHHHHHHHHcCC---CCCHHHHHHHHHHHHHHHHHH
Confidence            4576666666666553222         2379999999998753   579999999999999999863

>1wgx_A KIAA1903 protein; MYB DNA-binding domain, human cDNA, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: a.4.1.3

Probab=91.72  E-value=0.11  Score=44.02  Aligned_cols=53  Identities=28%  Similarity=0.510  Sum_probs=42.9

Q ss_pred             cccchhhHHHHHHHHHhhccC---CCchHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhhhcCC
Q 005668           13 QQQWGTLEELLLACAVNRHGT---RSWDSIAMEVQNRSSALSSLTPQSCRDKFNEIRRRFTVK   72 (684)
Q Consensus        13 ~~~WGTwEELLLacAV~RHGt---~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~l~~R~~~~   72 (684)
                      ...|.-=|+.+|=.|+.-++.   ..|+.||.-|-.|+       ++.|+.+|..|.+=|..+
T Consensus         8 ~~~WT~eE~k~fe~ALa~~~~~tp~rWe~IA~~V~gKT-------~eE~~~hY~~l~~~~~s~   63 (73)
T 1wgx_A            8 DKEWNEKELQKLHCAFASLPKHKPGFWSEVAAAVGSRS-------PEECQRKYMENPRGKGSQ   63 (73)
T ss_dssp             SSCCCHHHHHHHHHHHHHSCSSSSSHHHHHHHHTTTSC-------HHHHHHHHHHSSSSSCCC
T ss_pred             CCCCCHHHHHHHHHHHHHCCCCCccHHHHHHHHcCCCC-------HHHHHHHHHHHHhccccc
Confidence            457988899999888876654   56999998887665       799999999998777654

>2cqq_A RSGI RUH-037, DNAJ homolog subfamily C member 1; membrane protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.3

Probab=91.61  E-value=0.23  Score=41.71  Aligned_cols=51  Identities=16%  Similarity=0.326  Sum_probs=43.0

Q ss_pred             cccccchhhHHHHHHHHHhhccC---CCchHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhhh
Q 005668           11 QQQQQWGTLEELLLACAVNRHGT---RSWDSIAMEVQNRSSALSSLTPQSCRDKFNEIRRRF   69 (684)
Q Consensus        11 ~~~~~WGTwEELLLacAV~RHGt---~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~l~~R~   69 (684)
                      .....|..=|.-+|-.||..|+.   .-|..||..| .|       |+..|+.+|..|+.-+
T Consensus         6 ~~~~~WT~eE~k~fe~al~~~p~~t~~RW~~IA~~l-gR-------t~~eV~~~y~~L~~d~   59 (72)
T 2cqq_A            6 SGAPEWTEEDLSQLTRSMVKFPGGTPGRWEKIAHEL-GR-------SVTDVTTKAKQLKDSV   59 (72)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHSCTTCTTHHHHHHHHH-TS-------CHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCCcHHHHHHHHh-CC-------CHHHHHHHHHHHHHhc
Confidence            34567998899999999999983   5599999998 44       6899999999998875

>3zqc_A MYB3; transcription-DNA complex, DNA-binding protein, nucleus; 2.90A {Trichomonas vaginalis}

Probab=91.18  E-value=0.076  Score=48.47  Aligned_cols=51  Identities=20%  Similarity=0.428  Sum_probs=40.4

Q ss_pred             cccchhhHHHHHHHHHhhccCCCchHHHHHHHhhcCCCCCCCHHHHHHHHHHHH-hhhcC
Q 005668           13 QQQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEIR-RRFTV   71 (684)
Q Consensus        13 ~~~WGTwEELLLacAV~RHGt~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~l~-~R~~~   71 (684)
                      ...|.-=|+.+|..+|..||. .|..||..|..|       |...|+.+|..+- +++..
T Consensus        54 ~~~Wt~eEd~~L~~~~~~~G~-~W~~Ia~~l~gR-------t~~~~k~rw~~~l~~~~~~  105 (131)
T 3zqc_A           54 KHAWTPEEDETIFRNYLKLGS-KWSVIAKLIPGR-------TDNAIKNRWNSSISKRIST  105 (131)
T ss_dssp             CSCCCHHHHHHHHHHHHHSCS-CHHHHTTTSTTC-------CHHHHHHHHHHTTGGGCCC
T ss_pred             CCCCCHHHHHHHHHHHHHHCc-CHHHHHHHcCCC-------CHHHHHHHHHHHHHHHhhc
Confidence            357888899999999999995 699999765544       5789999997654 55544

>2xag_B REST corepressor 1; amine oxidase, chromatin regulator, histone inhibitor binding, methylation, nucleosome core, oxidoreductase; HET: FAD TCF; 3.10A {Homo sapiens} PDB: 2xaf_B* 2xah_B* 2xaj_B* 2xaq_B* 2xas_B*

Probab=84.44  E-value=0.64  Score=51.60  Aligned_cols=52  Identities=29%  Similarity=0.505  Sum_probs=44.8

Q ss_pred             cccccchhhHHHHHHHHHhhccCCCchHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhhhc
Q 005668           11 QQQQQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEIRRRFT   70 (684)
Q Consensus        11 ~~~~~WGTwEELLLacAV~RHGt~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~l~~R~~   70 (684)
                      .....|..=|-+|+--||..||- +|..||.-|.+|+       +..|+.-|..-++||.
T Consensus       378 ~~~~~WT~eE~~~f~~al~~yGk-dw~~IA~~VgTKT-------~~Qvk~fy~~~kkr~~  429 (482)
T 2xag_B          378 KCNARWTTEEQLLAVQAIRKYGR-DFQAISDVIGNKS-------VVQVKNFFVNYRRRFN  429 (482)
T ss_dssp             CCCSCCCHHHHHHHHHHHHHHTT-CHHHHHHHHSSCC-------HHHHHHHHHHTTTTTT
T ss_pred             ccCCCCCHHHHHHHHHHHHHHCc-CHHHHHHHhCCCC-------HHHHHHHHHHHHHHhC
Confidence            46789999999999999999996 9999999988876       5899999987677763

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	684
d1e6ia_	111	a.29.2.1 (A:) GCN5 {Baker's yeast (Saccharomyces c	5e-11
d1wuma1	118	a.29.2.1 (A:715-832) P300/CAF histone acetyltransf	4e-10
d3dwya1	114	a.29.2.1 (A:1084-1197) CREB-binding protein, CBP {	1e-09
d1eqfa2	128	a.29.2.1 (A:1498-1625) TAFII250 double bromodomain	7e-08
d1guua_	50	a.4.1.3 (A:) c-Myb, DNA-binding domain {Mouse (Mus	0.003

>d1e6ia_ a.29.2.1 (A:) GCN5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 111

class: All alpha proteins
fold: Bromodomain-like
superfamily: Bromodomain
family: Bromodomain
domain: GCN5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 58.0 bits (140), Expect = 5e-11
 Identities = 19/97 (19%), Positives = 45/97 (46%), Gaps = 1/97 (1%)

Query: 315 LVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFR 374
           +   L  +++H  +  F + +  +E   Y   +++ +DL T++ +L+   Y      F  
Sbjct: 8   IQNILTELQNHAAAWPFLQPVNKEEVPDYYDFIKEPMDLSTMEIKLESNKYQKMED-FIY 66

Query: 375 DLLLLFNNFVIFFRKSSQEYAAAQELRTLVIKEMTDM 411
           D  L+FNN  ++  +++  Y  A  L      ++ ++
Sbjct: 67  DARLVFNNCRMYNGENTSYYKYANRLEKFFNNKVKEI 103

>d1wuma1 a.29.2.1 (A:715-832) P300/CAF histone acetyltransferase bromodomain {Human (Homo sapiens) [TaxId: 9606]} Length = 118

class: All alpha proteins
fold: Bromodomain-like
superfamily: Bromodomain
family: Bromodomain
domain: P300/CAF histone acetyltransferase bromodomain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.8 bits (134), Expect = 4e-10
 Identities = 23/99 (23%), Positives = 43/99 (43%), Gaps = 1/99 (1%)

Query: 313 EPLVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKF 372
             L   L  ++SH+ +  F   ++  E+  Y +++R  +DL+T+  RL    Y    + F
Sbjct: 16  STLKSILQQVKSHQSAWPFMEPVKRTEAPGYYEVIRFPMDLKTMSERLKNRYYV-SKKLF 74

Query: 373 FRDLLLLFNNFVIFFRKSSQEYAAAQELRTLVIKEMTDM 411
             DL  +F N   +    S+ Y  A  L      ++ + 
Sbjct: 75  MADLQRVFTNCKEYNPPESEYYKCANILEKFFFSKIKEA 113

>d3dwya1 a.29.2.1 (A:1084-1197) CREB-binding protein, CBP {Human (Homo sapiens) [TaxId: 9606]} Length = 114

class: All alpha proteins
fold: Bromodomain-like
superfamily: Bromodomain
family: Bromodomain
domain: CREB-binding protein, CBP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.8 bits (129), Expect = 1e-09
 Identities = 21/72 (29%), Positives = 41/72 (56%), Gaps = 1/72 (1%)

Query: 343 YKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQEYAAAQELRT 402
           Y  +V+  +DL TI+ +LD G Y     ++  D+ L+FNN  ++ RK+S+ Y    +L  
Sbjct: 42  YFDIVKNPMDLSTIKRKLDTGQY-QEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAE 100

Query: 403 LVIKEMTDMLRK 414
           +  +E+  +++ 
Sbjct: 101 VFEQEIDPVMQS 112

>d1eqfa2 a.29.2.1 (A:1498-1625) TAFII250 double bromodomain module {Human (Homo sapiens) [TaxId: 9606]} Length = 128

class: All alpha proteins
fold: Bromodomain-like
superfamily: Bromodomain
family: Bromodomain
domain: TAFII250 double bromodomain module
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.6 bits (118), Expect = 7e-08
 Identities = 20/93 (21%), Positives = 39/93 (41%), Gaps = 1/93 (1%)

Query: 322 IRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFN 381
           + +   S  F   +  +    Y K++   +DL TI+  + +  Y    + F  D+ L+  
Sbjct: 22  MMAVPDSWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQ-SRESFLDDVNLILA 80

Query: 382 NFVIFFRKSSQEYAAAQELRTLVIKEMTDMLRK 414
           N V +    SQ    AQE+  +  + +T+    
Sbjct: 81  NSVKYNGPESQYTKTAQEIVNVCYQTLTEYDEH 113

>d1guua_ a.4.1.3 (A:) c-Myb, DNA-binding domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 50

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Myb/SANT domain
domain: c-Myb, DNA-binding domain
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 34.0 bits (78), Expect = 0.003
 Identities = 13/50 (26%), Positives = 21/50 (42%), Gaps = 7/50 (14%)

Query: 14 QQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFN 63
           +W   E+  L   V ++GT  W  IA  + NR       T   C+ ++ 
Sbjct: 2  TRWTREEDEKLKKLVEQNGTDDWKVIANYLPNR-------TDVQCQHRWQ 44

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	684
d3d7ca1	102	GCN5 {Human (Homo sapiens) [TaxId: 9606]}	99.93
d1e6ia_	111	GCN5 {Baker's yeast (Saccharomyces cerevisiae) [Ta	99.92
d1wuma1	118	P300/CAF histone acetyltransferase bromodomain {Hu	99.92
d3dwya1	114	CREB-binding protein, CBP {Human (Homo sapiens) [T	99.91
d1eqfa1	139	TAFII250 double bromodomain module {Human (Homo sa	99.91
d1eqfa2	128	TAFII250 double bromodomain module {Human (Homo sa	99.91
d1x41a1	47	Transcriptional adaptor 2-like, TADA2L, isoform b	97.92
d1w0ua_	55	Telomeric repeat binding factor 2, TRF2 {Human (Ho	97.53
d1w0ta_	52	DNA-binding domain of human telomeric protein, hTR	97.31
d2cjja1	63	Radialis {Garden snapdragon (Antirrhinum majus) [T	97.14
d1gvda_	52	c-Myb, DNA-binding domain {Mouse (Mus musculus) [T	97.1
d2iw5b1	65	REST corepressor 1, CoREST {Human (Homo sapiens) [	96.9
d1guua_	50	c-Myb, DNA-binding domain {Mouse (Mus musculus) [T	96.9
d2ckxa1	83	Telomere binding protein TBP1 {Tobacco (Nicotiana	96.88
d2cqra1	60	DnaJ homolog subfamily C member 1 {Human (Homo sap	96.51
d2cu7a1	65	MYSM1 (KIAA1915) {Human (Homo sapiens) [TaxId: 960	96.5
d1gv2a2	47	c-Myb, DNA-binding domain {Mouse (Mus musculus) [T	95.98
d1xc5a1	68	Nuclear receptor corepressor 2 {Human (Homo sapien	95.87
d1ug2a_	95	2610100b20rik gene product {Mouse (Mus musculus) [	91.46
d1igna1	86	DNA-binding domain of rap1 {Baker's yeast (Sacchar	88.63
d2cqqa1	59	DnaJ homolog subfamily C member 1 {Human (Homo sap	80.35

>d3d7ca1 a.29.2.1 (A:731-832) GCN5 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Bromodomain-like
superfamily: Bromodomain
family: Bromodomain
domain: GCN5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.93  E-value=3.9e-26  Score=200.34  Aligned_cols=97  Identities=24%  Similarity=0.331  Sum_probs=93.8

Q ss_pred             hHHHHHHHHHHhCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCCCCH
Q 005668          313 EPLVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQ  392 (684)
Q Consensus       313 kpLl~ILe~L~~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~pdS~  392 (684)
                      ..|..||..|..|+.+++|..||+...+|+||++|++||||.||++||.++.|.++. +|.+||.|||.||+.||+++|.
T Consensus         5 ~~l~~il~~l~~~~~s~~F~~pv~~~~~pdY~~~I~~PmdL~tI~~kl~~~~Y~s~~-~f~~D~~li~~Na~~yN~~~s~   83 (102)
T d3d7ca1           5 TTLKNLLAQIKSHPSAWPFMEPVKKSEAPDYYEVIRFPIDLKTMTERLRSRYYVTRK-LFVADLQRVIANCREYNPPDSE   83 (102)
T ss_dssp             HHHHHHHHHHHHSGGGGGGSSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCCSHH-HHHHHHHHHHHHHHHHSCTTSH
T ss_pred             HHHHHHHHHHHhCCCCCccCCCCChhhCcCHHHHcCCccCHHHHHHHhccCccCCHH-HHHHHHHHHHHHHHHHCCCCCH
Confidence            468899999999999999999999999999999999999999999999999999998 9999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHH
Q 005668          393 EYAAAQELRTLVIKEMTD  410 (684)
Q Consensus       393 vykaA~eLr~lf~k~msk  410 (684)
                      +|.+|..|+++|.++|++
T Consensus        84 ~~~~A~~l~~~f~~~~ke  101 (102)
T d3d7ca1          84 YCRCASALEKFFYFKLKE  101 (102)
T ss_dssp             HHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhc
Confidence            999999999999998875

>d1e6ia_ a.29.2.1 (A:) GCN5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: Bromodomain-like
superfamily: Bromodomain
family: Bromodomain
domain: GCN5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.92  E-value=7.3e-26  Score=201.31  Aligned_cols=98  Identities=19%  Similarity=0.389  Sum_probs=95.4

Q ss_pred             hHHHHHHHHHHhCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCCCCH
Q 005668          313 EPLVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQ  392 (684)
Q Consensus       313 kpLl~ILe~L~~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~pdS~  392 (684)
                      +.|..||+.|..|++++||..||+...+|+||++|++||||+||++||.+|.|.++. +|..||.|||.||+.||+++|.
T Consensus         6 ~~l~~il~~l~~~~~a~pF~~pvd~~~~pdY~~vI~~PmdL~tI~~kl~~~~Y~s~~-~f~~Dv~li~~Na~~yN~~~s~   84 (111)
T d1e6ia_           6 AAIQNILTELQNHAAAWPFLQPVNKEEVPDYYDFIKEPMDLSTMEIKLESNKYQKME-DFIYDARLVFNNCRMYNGENTS   84 (111)
T ss_dssp             HHHHHHHHHHHHSTTCGGGSSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCSSHH-HHHHHHHHHHHHHHHHSCTTSH
T ss_pred             HHHHHHHHHHHhCCCChhhcCCCCchhCcCHHHHcCCchhHHHHHHHHHccccchHH-HHHHHHHHHHHHHHHHCCCCCH
Confidence            679999999999999999999999999999999999999999999999999999998 9999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHH
Q 005668          393 EYAAAQELRTLVIKEMTDM  411 (684)
Q Consensus       393 vykaA~eLr~lf~k~msk~  411 (684)
                      +|.+|..|+.+|.++|.++
T Consensus        85 i~~~A~~l~~~f~~~~~~i  103 (111)
T d1e6ia_          85 YYKYANRLEKFFNNKVKEI  103 (111)
T ss_dssp             HHHHHHHHHHHHHHHHHTS
T ss_pred             HHHHHHHHHHHHHHHHHHh
Confidence            9999999999999999764

>d1wuma1 a.29.2.1 (A:715-832) P300/CAF histone acetyltransferase bromodomain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Bromodomain-like
superfamily: Bromodomain
family: Bromodomain
domain: P300/CAF histone acetyltransferase bromodomain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.92  E-value=2.3e-25  Score=200.19  Aligned_cols=98  Identities=23%  Similarity=0.382  Sum_probs=94.8

Q ss_pred             hHHHHHHHHHHhCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCCCCH
Q 005668          313 EPLVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQ  392 (684)
Q Consensus       313 kpLl~ILe~L~~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~pdS~  392 (684)
                      ..|..||+.|..|+.+++|..||+...+|+||++|++||||.||++||.+|.|.++. +|.+||.|||.||+.||+++|.
T Consensus        16 ~~l~~il~~l~~~~~a~~F~~pv~~~~~pdY~~iI~~PmdL~~I~~kl~~~~Y~s~~-ef~~Dv~li~~Na~~yn~~~s~   94 (118)
T d1wuma1          16 STLKSILQQVKSHQSAWPFMEPVKRTEAPGYYEVIRFPMDLKTMSERLKNRYYVSKK-LFMADLQRVFTNCKEYNPPESE   94 (118)
T ss_dssp             HHHHHHHHHHHHSSSCHHHHSCCCSSSSSSCTTTCSSCCCHHHHHHHHTTTCCCSSH-HHHHHHHHHHHHHHHHSCTTSS
T ss_pred             HHHHHHHHHHHhCCCcCcccCCCChhhCcCHHHHcCChhhHHHHHHHhcccccCchH-HHHHHHHHHHHHHHHHCCCCCH
Confidence            568899999999999999999999999999999999999999999999999999998 9999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHH
Q 005668          393 EYAAAQELRTLVIKEMTDM  411 (684)
Q Consensus       393 vykaA~eLr~lf~k~msk~  411 (684)
                      +|.+|..|+.+|.++|.+.
T Consensus        95 ~~~~A~~l~~~f~~~~~e~  113 (118)
T d1wuma1          95 YYKCANILEKFFFSKIKEA  113 (118)
T ss_dssp             HHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHc
Confidence            9999999999999999774

>d3dwya1 a.29.2.1 (A:1084-1197) CREB-binding protein, CBP {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Bromodomain-like
superfamily: Bromodomain
family: Bromodomain
domain: CREB-binding protein, CBP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.91  E-value=5.1e-25  Score=196.64  Aligned_cols=102  Identities=25%  Similarity=0.448  Sum_probs=96.6

Q ss_pred             hHHHHHHHHHHhC-cCCcccccccCcc--ccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCC
Q 005668          313 EPLVRFLGMIRSH-RLSSHFERRLRSQ--ESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRK  389 (684)
Q Consensus       313 kpLl~ILe~L~~h-k~a~pF~~PVD~q--e~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~p  389 (684)
                      +.|+.+|+.|+.+ +.+++|..||++.  .+|+||++|++||||.||++||.+|.|.++. +|.+||.|||+||+.||++
T Consensus         9 ~~l~~~l~~l~~~~p~a~pF~~pvd~~~~~~pdY~~iI~~PmdL~tI~~kl~~~~Y~s~~-ef~~Dv~li~~Na~~yN~~   87 (114)
T d3dwya1           9 QALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPW-QYVDDVWLMFNNAWLYNRK   87 (114)
T ss_dssp             HHHHHHHHHHHTCTTTTGGGSSCCCHHHHTCTTHHHHCSSCCCHHHHHHHHHTTCCSSHH-HHHHHHHHHHHHHHHHSCT
T ss_pred             HHHHHHHHHHHhcCcCCCccCCCCChhhccCCCHHHHcCCCCCHHHHHHHHHcCccccHH-HHHHHHHHHHHHHHHHCCC
Confidence            5688999999877 6999999999976  7999999999999999999999999999998 9999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHhhhc
Q 005668          390 SSQEYAAAQELRTLVIKEMTDMLRKQ  415 (684)
Q Consensus       390 dS~vykaA~eLr~lf~k~msk~l~k~  415 (684)
                      +|.+|.+|..|+.+|.++|..+++.+
T Consensus        88 ~s~~~~~A~~L~~~f~~~~~~i~~~~  113 (114)
T d3dwya1          88 TSRVYKFCSKLAEVFEQEIDPVMQSL  113 (114)
T ss_dssp             TSHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            99999999999999999999988753

>d1eqfa1 a.29.2.1 (A:1359-1497) TAFII250 double bromodomain module {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Bromodomain-like
superfamily: Bromodomain
family: Bromodomain
domain: TAFII250 double bromodomain module
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.91  E-value=7e-25  Score=202.23  Aligned_cols=100  Identities=16%  Similarity=0.247  Sum_probs=95.7

Q ss_pred             hHHHHHHHHHHhCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCCCCH
Q 005668          313 EPLVRFLGMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQ  392 (684)
Q Consensus       313 kpLl~ILe~L~~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~pdS~  392 (684)
                      ..|..||+.|..++.+++|..||+...+|+||++|++||||.||+.||.++.|.++. +|..||.|||+||++||+++|.
T Consensus        29 ~~l~~il~~l~~~~~s~pF~~Pvd~~~~pdY~~iI~~PmdL~tI~~kl~~~~Y~s~~-~f~~D~~li~~Na~~yN~~~s~  107 (139)
T d1eqfa1          29 SILESIINDMRDLPNTYPFHTPVNAKVVKDYYKIITRPMDLQTLRENVRKRLYPSRE-EFREHLELIVKNSATYNGPKHS  107 (139)
T ss_dssp             HHHHHHHHHHHTSTTCGGGTSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCSSHH-HHHHHHHHHHHHHHHHTCTTSH
T ss_pred             HHHHHHHHHHHcCCCchhhhCCCChhhccCHHHHcCChhhHHHHHHHHHcCCcCCHH-HHHHHHHHHHHHHHHHCCCCCH
Confidence            568888999999999999999999999999999999999999999999999999998 9999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHhh
Q 005668          393 EYAAAQELRTLVIKEMTDMLR  413 (684)
Q Consensus       393 vykaA~eLr~lf~k~msk~l~  413 (684)
                      +|.+|..|+.+|.+.|.++..
T Consensus       108 i~~~A~~L~~~~~~~~~~~~~  128 (139)
T d1eqfa1         108 LTQISQSMLDLCDEKLKEKED  128 (139)
T ss_dssp             HHHHHHHHHHHHHHHHHHTHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999987654

>d1eqfa2 a.29.2.1 (A:1498-1625) TAFII250 double bromodomain module {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Bromodomain-like
superfamily: Bromodomain
family: Bromodomain
domain: TAFII250 double bromodomain module
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.91  E-value=7.7e-25  Score=199.61  Aligned_cols=93  Identities=22%  Similarity=0.264  Sum_probs=87.8

Q ss_pred             HHHHhCcCCcccccccCccccchhhhhhcCCCCHHHHHHHHhCCCccCcHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHH
Q 005668          320 GMIRSHRLSSHFERRLRSQESERYKKLVRQHIDLRTIQSRLDRGLYSNCFQKFFRDLLLLFNNFVIFFRKSSQEYAAAQE  399 (684)
Q Consensus       320 e~L~~hk~a~pF~~PVD~qe~PdYyeIIK~PMDLsTIKkKLe~g~YsSi~~EF~rDL~LMF~NA~~FN~pdS~vykaA~e  399 (684)
                      +.|..++.+|||..||+...+|+||++|++||||+||+.||.+|.|.++. +|..||.|||.||+.||+++|.+|.+|..
T Consensus        20 ~~~~~~p~a~pF~~pVd~~~~PdY~~vIk~PmDL~tI~~kl~~~~Y~s~~-ef~~Dv~li~~Na~~yN~~~s~i~~~A~~   98 (128)
T d1eqfa2          20 QKMMAVPDSWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRE-SFLDDVNLILANSVKYNGPESQYTKTAQE   98 (128)
T ss_dssp             HTTTTSTTCGGGTSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCSSHH-HHHHHHHHHHHHHHHHHCTTCHHHHHHHH
T ss_pred             HHHHcCCCCChhcCCCCcccCcCHHHHcCCcccHHHHHHHHHhhccccHH-HHHHHHHHHHHHHHHHCCCCCHHHHHHHH
Confidence            44567789999999999999999999999999999999999999999998 99999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhh
Q 005668          400 LRTLVIKEMTDMLR  413 (684)
Q Consensus       400 Lr~lf~k~msk~l~  413 (684)
                      |..+|.+.|.++..
T Consensus        99 L~~~~~~~l~~~~~  112 (128)
T d1eqfa2          99 IVNVCYQTLTEYDE  112 (128)
T ss_dssp             HHHHHHHHHHHTHH
T ss_pred             HHHHHHHHHHHhHH
Confidence            99999999887643

>d1x41a1 a.4.1.1 (A:8-54) Transcriptional adaptor 2-like, TADA2L, isoform b {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Transcriptional adaptor 2-like, TADA2L, isoform b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.92  E-value=4.6e-06  Score=62.97  Aligned_cols=43  Identities=23%  Similarity=0.544  Sum_probs=39.6

Q ss_pred             cchhhHHHHHHHHHhhccCCCchHHHHHHHhhcCCCCCCCHHHHHHHHHH
Q 005668           15 QWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNE   64 (684)
Q Consensus        15 ~WGTwEELLLacAV~RHGt~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~   64 (684)
                      .|..-|+.+|.-||..||+.+|..||..|..||       +..|+.+|..
T Consensus         3 ~Wt~eEd~~L~~~v~~~G~~nW~~Ia~~~~~Rt-------~~Qcr~r~~~   45 (47)
T d1x41a1           3 SWTAQEEMALLEAVMDCGFGNWQDVANQMCTKT-------KEECEKHYMK   45 (47)
T ss_dssp             SSCHHHHHHHHHHHHHTCTTCHHHHHHHHTTSC-------HHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHCCccHHHHHHHcCCCC-------HHHHHHHHHH
Confidence            499999999999999999999999999998875       7999999974

>d1w0ua_ a.4.1.4 (A:) Telomeric repeat binding factor 2, TRF2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: DNA-binding domain of telomeric protein
domain: Telomeric repeat binding factor 2, TRF2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.53  E-value=4.1e-05  Score=59.27  Aligned_cols=49  Identities=20%  Similarity=0.469  Sum_probs=41.8

Q ss_pred             ccchhhHHHHHHHHHhhccCCCchHHHHHHHhhcCCCCCCCHHHHHHHHHHHHh
Q 005668           14 QQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEIRR   67 (684)
Q Consensus        14 ~~WGTwEELLLacAV~RHGt~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~l~~   67 (684)
                      ..|...|+.+|..+|.+||+.+|..||.++.     ....|+..|+.||+.|..
T Consensus         3 ~~WT~eEd~~L~~~V~~~G~~~W~~I~~~~~-----~~~Rt~~q~k~Rwrn~~k   51 (55)
T d1w0ua_           3 QKWTVEESEWVKAGVQKYGEGNWAAISKNYP-----FVNRTAVMIKDRWRTMKR   51 (55)
T ss_dssp             CCCCHHHHHHHHHHHHHHCTTCHHHHHHHSC-----CSSCCHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHhCCChHHHHHhhcC-----CCCcCHHHHHHHHHHHhc
Confidence            4799999999999999999999999998742     124689999999998764

>d1w0ta_ a.4.1.4 (A:) DNA-binding domain of human telomeric protein, hTRF1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: DNA-binding domain of telomeric protein
domain: DNA-binding domain of human telomeric protein, hTRF1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.31  E-value=0.00013  Score=55.90  Aligned_cols=49  Identities=20%  Similarity=0.443  Sum_probs=41.3

Q ss_pred             ccchhhHHHHHHHHHhhccCCCchHHHHHHHhhcCCCCCCCHHHHHHHHHHHHh
Q 005668           14 QQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEIRR   67 (684)
Q Consensus        14 ~~WGTwEELLLacAV~RHGt~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~l~~   67 (684)
                      ..|.+=|+-+|.-+|..||..+|..||.++-     ....|+..|+.||+.|++
T Consensus         3 ~~WT~eED~~L~~~v~~~G~~~W~~I~~~~~-----~~~Rt~~q~r~Rw~nl~K   51 (52)
T d1w0ta_           3 QAWLWEEDKNLRSGVRKYGEGNWSKILLHYK-----FNNRTSVMLKDRWRTMKK   51 (52)
T ss_dssp             CCCCHHHHHHHHHHHHHHCTTCHHHHHHHSC-----CSSCCHHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHHHHHCCCCHHHHHhhcC-----CCCCCHHHHHHHHHHHHC
Confidence            4698999999999999999999999997531     124689999999998864

>d2cjja1 a.4.1.3 (A:8-70) Radialis {Garden snapdragon (Antirrhinum majus) [TaxId: 4151]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Myb/SANT domain
domain: Radialis
species: Garden snapdragon (Antirrhinum majus) [TaxId: 4151]

Probab=97.14  E-value=0.0002  Score=56.50  Aligned_cols=49  Identities=16%  Similarity=0.432  Sum_probs=43.5

Q ss_pred             cccchhhHHHHHHHHHhhccCCC---chHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhh
Q 005668           13 QQQWGTLEELLLACAVNRHGTRS---WDSIAMEVQNRSSALSSLTPQSCRDKFNEIRRR   68 (684)
Q Consensus        13 ~~~WGTwEELLLacAV~RHGt~~---WdsVA~e~~~r~~~~~~~t~~~C~~k~~~l~~R   68 (684)
                      |..|..=|+.+|..||..||..+   |..||..|..||       +..|+.+|..|...
T Consensus         1 G~~WT~eEd~~L~~~v~~~~~~~~~~W~~Ia~~l~gRt-------~~qc~~r~~~L~~d   52 (63)
T d2cjja1           1 GRPWSAKENKAFERALAVYDKDTPDRWANVARAVEGRT-------PEEVKKHYEILVED   52 (63)
T ss_dssp             CCSCCHHHHHHHHHHHHHSCTTCTTHHHHHHHHSTTCC-------HHHHHHHHHHHHHH
T ss_pred             CcCCCHHHHHHHHHHHHHHCCCCchHHHHHHHHcCCCC-------HHHHHHHHHHHHHH
Confidence            45799999999999999999986   999999998776       69999999988764

>d1gvda_ a.4.1.3 (A:) c-Myb, DNA-binding domain {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Myb/SANT domain
domain: c-Myb, DNA-binding domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.10  E-value=0.00012  Score=56.04  Aligned_cols=44  Identities=25%  Similarity=0.599  Sum_probs=38.9

Q ss_pred             ccchhhHHHHHHHHHhhccCCCchHHHHHHHhhcCCCCCCCHHHHHHHHHH
Q 005668           14 QQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNE   64 (684)
Q Consensus        14 ~~WGTwEELLLacAV~RHGt~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~   64 (684)
                      ..|.--|+-+|.-+|..||+.+|..||..|..|       |+..|+.+|..
T Consensus         4 g~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~R-------t~~qc~~Rw~~   47 (52)
T d1gvda_           4 GPWTKEEDQRLIKLVQKYGPKRWSVIAKHLKGR-------IGKQCRERWHN   47 (52)
T ss_dssp             CSCCHHHHHHHHHHHHHHCTTCHHHHHTTSTTC-------CHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCC-------CHHHHHHHHHh
Confidence            568889999999999999999999999887655       57999999975

>d2iw5b1 a.4.1.3 (B:376-440) REST corepressor 1, CoREST {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Myb/SANT domain
domain: REST corepressor 1, CoREST
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.90  E-value=0.00029  Score=55.65  Aligned_cols=50  Identities=32%  Similarity=0.563  Sum_probs=44.4

Q ss_pred             cccchhhHHHHHHHHHhhccCCCchHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhhhc
Q 005668           13 QQQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEIRRRFT   70 (684)
Q Consensus        13 ~~~WGTwEELLLacAV~RHGt~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~l~~R~~   70 (684)
                      ...|..-|..+|..||..|| .+|..||..|..||       +..|+.+|..+++||.
T Consensus         5 ~~~WT~eE~~~f~~~~~~~G-~~w~~Ia~~~~~kt-------~~q~~~~y~~~~k~~~   54 (65)
T d2iw5b1           5 NARWTTEEQLLAVQAIRKYG-RDFQAISDVIGNKS-------VVQVKNFFVNYRRRFN   54 (65)
T ss_dssp             CSSCCHHHHHHHHHHHHHHS-SCHHHHHHHHSSCC-------HHHHHHHHHHTTTTTT
T ss_pred             CCCCCHHHHHHHHHHHHHhC-chHHHHHHHcCCCC-------HHHHHHHHHHHHhhcC
Confidence            35699999999999999999 56999999997765       6999999999998875

>d1guua_ a.4.1.3 (A:) c-Myb, DNA-binding domain {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Myb/SANT domain
domain: c-Myb, DNA-binding domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.90  E-value=0.00032  Score=53.03  Aligned_cols=44  Identities=30%  Similarity=0.579  Sum_probs=38.4

Q ss_pred             ccchhhHHHHHHHHHhhccCCCchHHHHHHHhhcCCCCCCCHHHHHHHHHH
Q 005668           14 QQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNE   64 (684)
Q Consensus        14 ~~WGTwEELLLacAV~RHGt~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~   64 (684)
                      ..|..=|+.+|.-+|.+||..+|..||..|..|       |+..|+.+|..
T Consensus         2 ~~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~R-------t~~qcr~Rw~~   45 (50)
T d1guua_           2 TRWTREEDEKLKKLVEQNGTDDWKVIANYLPNR-------TDVQCQHRWQK   45 (50)
T ss_dssp             CCCCHHHHHHHHHHHHHHCSSCHHHHHHTSTTC-------CHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCC-------CHHHHHHHHHh
Confidence            358888999999999999999999999987655       47899999975

>d2ckxa1 a.4.1.3 (A:578-660) Telomere binding protein TBP1 {Tobacco (Nicotiana tabacum) [TaxId: 4097]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Myb/SANT domain
domain: Telomere binding protein TBP1
species: Tobacco (Nicotiana tabacum) [TaxId: 4097]

Probab=96.88  E-value=0.00071  Score=56.09  Aligned_cols=50  Identities=22%  Similarity=0.297  Sum_probs=41.9

Q ss_pred             cchhhHHHHHHHHHhhccCCCchHHHHHHHhhcCCCCCCCHHHHHHHHHHHHh
Q 005668           15 QWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEIRR   67 (684)
Q Consensus        15 ~WGTwEELLLacAV~RHGt~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~l~~   67 (684)
                      .|..-|+-+|.-+|.+||+.+|..||..+-   +.....|+..|+.||+.|.+
T Consensus         2 ~WT~eEd~~L~~~V~~~G~~~W~~I~~~~~---~~~~~Rt~~qck~RWrn~l~   51 (83)
T d2ckxa1           2 PFSVAEVEALVEAVEHLGTGRWRDVKMRAF---DNADHRTYVDLKDKWKTLVH   51 (83)
T ss_dssp             CCCHHHHHHHHHHHHHHCSSCHHHHHHHHC---TTCTTSCHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHCcccHHHHHHHHH---hhccCCCHHHHHHHHHHHhh
Confidence            588999999999999999999999998763   22335699999999988764

>d2cqra1 a.4.1.3 (A:7-66) DnaJ homolog subfamily C member 1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Myb/SANT domain
domain: DnaJ homolog subfamily C member 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.51  E-value=0.00069  Score=52.74  Aligned_cols=49  Identities=22%  Similarity=0.494  Sum_probs=41.7

Q ss_pred             ccccccchhhHHHHHHHHHhhccCCC---chHHHHHHHhhcCCCCCCCHHHHHHHHHHH
Q 005668           10 SQQQQQWGTLEELLLACAVNRHGTRS---WDSIAMEVQNRSSALSSLTPQSCRDKFNEI   65 (684)
Q Consensus        10 ~~~~~~WGTwEELLLacAV~RHGt~~---WdsVA~e~~~r~~~~~~~t~~~C~~k~~~l   65 (684)
                      ......|..=|..||..||.-||..+   |..||..|-.|       |+..|+.+|..|
T Consensus         9 ~~~~~~WT~eEd~~L~~~v~~~~~~~~~~W~~IA~~l~~R-------t~~qc~~R~~~L   60 (60)
T d2cqra1           9 RSAEEPWTQNQQKLLELALQQYPRGSSDCWDKIARCVPSK-------SKEDCIARYKLL   60 (60)
T ss_dssp             TCSSCCCCHHHHHHHHHHHHHSCSSSHHHHHHHGGGCSSS-------CHHHHHHHHHHH
T ss_pred             CcCCCCcCHHHHHHHHHHHHHcCCccchHHHHHHHHcCCC-------CHHHHHHHHHHC
Confidence            34456799999999999999999975   99999877655       579999999876

>d2cu7a1 a.4.1.3 (A:8-72) MYSM1 (KIAA1915) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Myb/SANT domain
domain: MYSM1 (KIAA1915)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.50  E-value=0.0011  Score=51.86  Aligned_cols=49  Identities=16%  Similarity=0.333  Sum_probs=41.5

Q ss_pred             ccchhhHHHHHHHHHhhccCCCchHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhhhc
Q 005668           14 QQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEIRRRFT   70 (684)
Q Consensus        14 ~~WGTwEELLLacAV~RHGt~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~l~~R~~   70 (684)
                      ..|..=|+.+|..||..|| .+|..||..|..||       +..|+.+|..+.++-.
T Consensus         3 ~~WT~eEd~~l~~~~~~~G-~~W~~Ia~~~~~Rt-------~~q~k~ry~~~~~~~~   51 (65)
T d2cu7a1           3 VKWTIEEKELFEQGLAKFG-RRWTKISKLIGSRT-------VLQVKSYARQYFKNKV   51 (65)
T ss_dssp             CCCCHHHHHHHHHHHHHTC-SCHHHHHHHHSSSC-------HHHHHHHHHHHHHHHS
T ss_pred             CCCCHHHHHHHHHHHHHhc-chHHHHHHHcCCCC-------HHHHHHHHHHHHHHHH
Confidence            4599999999999999999 59999999987665       6899999987665543

>d1gv2a2 a.4.1.3 (A:144-190) c-Myb, DNA-binding domain {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Myb/SANT domain
domain: c-Myb, DNA-binding domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.98  E-value=0.0014  Score=49.09  Aligned_cols=46  Identities=24%  Similarity=0.440  Sum_probs=38.7

Q ss_pred             ccchhhHHHHHHHHHhhccCCCchHHHHHHHhhcCCCCCCCHHHHHHHHHHHHh
Q 005668           14 QQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEIRR   67 (684)
Q Consensus        14 ~~WGTwEELLLacAV~RHGt~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~l~~   67 (684)
                      ..|..-|+.+|..+|..||. .|..||.-|-       ..|...|+.+|..+.|
T Consensus         2 ~~WT~eED~~L~~~v~~~G~-~W~~Ia~~~~-------gRt~~~~knr~~~~lr   47 (47)
T d1gv2a2           2 TSWTEEEDRIIYQAHKRLGN-RWAEIAKLLP-------GRTDNAIKNHWNSTMR   47 (47)
T ss_dssp             CCCCHHHHHHHHHHHHHHSS-CHHHHHTTCT-------TCCHHHHHHHHHHHTC
T ss_pred             CCCCHHHHHHHHHHHHHHhh-HHHHHHhHcC-------CCCHHHHHHHHHHHcC
Confidence            46888999999999999998 6999997554       4567999999998753

>d1xc5a1 a.4.1.3 (A:413-480) Nuclear receptor corepressor 2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Myb/SANT domain
domain: Nuclear receptor corepressor 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.87  E-value=0.0019  Score=51.27  Aligned_cols=50  Identities=14%  Similarity=0.232  Sum_probs=42.2

Q ss_pred             cccccchhhHHHHHHHHHhhccCCCchHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhh
Q 005668           11 QQQQQWGTLEELLLACAVNRHGTRSWDSIAMEVQNRSSALSSLTPQSCRDKFNEIRRR   68 (684)
Q Consensus        11 ~~~~~WGTwEELLLacAV~RHGt~~WdsVA~e~~~r~~~~~~~t~~~C~~k~~~l~~R   68 (684)
                      .....|.--|.-+|..||.-||. +|..||..|..||       ...|+..|..++++
T Consensus        15 ~~~~~WT~eE~~~f~~~~~~~G~-~w~~Ia~~~~~rt-------~~q~~~~yy~~kk~   64 (68)
T d1xc5a1          15 QVMNMWSEQEKETFREKFMQHPK-NFGLIASFLERKT-------VAECVLYYYLTKKN   64 (68)
T ss_dssp             TTTTCCCTTTHHHHHHHHHHTTS-CSSSHHHHTTTSC-------HHHHHHHHHHHTTT
T ss_pred             cCCCCCCHHHHHHHHHHHHHHCC-cHHHHHHHcCCCC-------HHHHHHHHHHHHCc
Confidence            34467999999999999999996 8999999987776       58999999876553

>d1ug2a_ a.4.1.3 (A:) 2610100b20rik gene product {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Myb/SANT domain
domain: 2610100b20rik gene product
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=91.46  E-value=0.14  Score=43.41  Aligned_cols=58  Identities=14%  Similarity=0.379  Sum_probs=48.7

Q ss_pred             cccccchhhHHHHHHHHHhhccCCC--chHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhhhcCCCCC
Q 005668           11 QQQQQWGTLEELLLACAVNRHGTRS--WDSIAMEVQNRSSALSSLTPQSCRDKFNEIRRRFTVKNGA   75 (684)
Q Consensus        11 ~~~~~WGTwEELLLacAV~RHGt~~--WdsVA~e~~~r~~~~~~~t~~~C~~k~~~l~~R~~~~~~~   75 (684)
                      ....-|.==|.-+|.-.+.+||+..  |..||.-|..|+       +..|+.||..|-+.|...|.+
T Consensus        31 ~~~~~WTrEEDriIL~~~q~~G~~~~tw~~Ia~~L~~Rs-------~~qvr~Rf~~Lm~lf~~~~e~   90 (95)
T d1ug2a_          31 EKVVLWTREADRVILTMCQEQGAQPHTFSVISQQLGNKT-------PVEVSHRFRELMQLFHTACES   90 (95)
T ss_dssp             CCCSSSCHHHHHHHHHHHHHTTSCTTTHHHHHHHHSSCC-------HHHHHHHHHHHHHHHHHCSSS
T ss_pred             CccCCcCHHHHHHHHHHHHHcCCcHHHHHHHHHHcCCCC-------HHHHHHHHHHHHHHHHHhhcc
Confidence            3455576668888889999999755  999999998887       589999999999999987754

>d1igna1 a.4.1.6 (A:360-445) DNA-binding domain of rap1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: DNA-binding domain of rap1
domain: DNA-binding domain of rap1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=88.63  E-value=0.086  Score=43.71  Aligned_cols=49  Identities=27%  Similarity=0.408  Sum_probs=38.9

Q ss_pred             ccchhhHHHHHHHHHhhccCCC-----chHHHHHHHhhcCCCCCCCHHHHHHHHHH-HHhhh
Q 005668           14 QQWGTLEELLLACAVNRHGTRS-----WDSIAMEVQNRSSALSSLTPQSCRDKFNE-IRRRF   69 (684)
Q Consensus        14 ~~WGTwEELLLacAV~RHGt~~-----WdsVA~e~~~r~~~~~~~t~~~C~~k~~~-l~~R~   69 (684)
                      ..|..=|.-+|.-+|..||+..     |..||..|-.       .|+..|+.+|.. |.-+.
T Consensus         2 ~~WT~eED~~L~~~v~~~g~~~~~~~~W~~IA~~lpg-------Rt~~qcr~Rw~~~L~p~l   56 (86)
T d1igna1           2 ASFTDEEDEFILDVVRKNPTRRTTHTLYDEISHYVPN-------HTGNSIRHRFRVYLSKRL   56 (86)
T ss_dssp             CCCCHHHHHHHHHHHHTSGGGTTCSHHHHHHTTTSTT-------SCHHHHHHHHHHTTGGGC
T ss_pred             CCCCHHHHHHHHHHHHHhCcCcCCccCHHHHHHHcCC-------CCHHHHHHHHHHHcCccc
Confidence            3577779999999999999874     9999966544       457999999984 55544

>d2cqqa1 a.4.1.3 (A:8-66) DnaJ homolog subfamily C member 1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Myb/SANT domain
domain: DnaJ homolog subfamily C member 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.35  E-value=1  Score=34.83  Aligned_cols=48  Identities=23%  Similarity=0.458  Sum_probs=38.7

Q ss_pred             cchhhHHHHHHHHHhhc--cCCC-chHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhhhc
Q 005668           15 QWGTLEELLLACAVNRH--GTRS-WDSIAMEVQNRSSALSSLTPQSCRDKFNEIRRRFT   70 (684)
Q Consensus        15 ~WGTwEELLLacAV~RH--Gt~~-WdsVA~e~~~r~~~~~~~t~~~C~~k~~~l~~R~~   70 (684)
                      -|..=|--||--|+..|  ||.+ |+.||..| .|       |+..|..+|..|+.=+.
T Consensus         3 eWT~ee~~~le~Al~~~P~gt~~RW~~IA~~v-gk-------t~~ev~~~~k~l~e~~~   53 (59)
T d2cqqa1           3 EWTEEDLSQLTRSMVKFPGGTPGRWEKIAHEL-GR-------SVTDVTTKAKQLKDSVT   53 (59)
T ss_dssp             CCCHHHHHHHHHHHHHSCTTCTTHHHHHHHHH-TS-------CHHHHHHHHHHHHHSCC
T ss_pred             CCCHHHHHHHHHHHHHCCCCCcHHHHHHHHHH-CC-------CHHHHHHHHHHHHHhcc
Confidence            47777888899999888  4445 99999999 55       47999999999986553