Psyllid ID: psy8542

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180--
Protein Sequence
MANVNSQSSTSKLPRDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHARDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQLSGSFAKPPPRESKGSGQAGAMGSNAHNKAPLTKGAMKTVPQARNQNAQSNVQVI
Secondary Structure (PSIPRED)
cccccccccccccccHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHcccccccHHHcccccHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccHHHHHHHHHHHHcccccEccHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHcccccEccHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccEcHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHccccccccccccccccccEccccccccc
Coil and Loop (DISEMBL)
manvnsqsstsklprDAQVIVNMFQeagiknydprCVQQMLEFVNNYTTTILEDSRVYANHARDAQVIVNMFQeagiknydprCVQQMLEFVNNYTTTILEDSRVYANhakkktvdVEDIKLAITNqlsgsfakpppreskgsgqagamgsnahnkapltkgamktvpqarnqnaqsnvqvi
Flexible Loop (DISEMBL)
manvnsqsstsklprdAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHARDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAkkktvdveDIKLAITnqlsgsfakpppRESKGSGQAGAMGSNAHNKAPLTKGAMKTvpqarnqnaqsnvqvi
Low Complexity Region (SEG)
MANVNSQSSTSKLPRDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHARDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQLSGSFAKPPPRESKGSGQAGAMGSNAHNKAPLTKGAMKTVPQARNQNAQSNVQVI
Disordered region (IsUnstruct)
*****************QVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHARDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITN********************************************************
Disordered Region (DISOPRED)
*******************IVNMFQEAGIKNYDPRCVQQMLEFVN********************QVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQLS*********************************AMKTVPQARNQNAQSNVQVI
Disordered Region (DISEMBL)
*************PRDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHARDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQLSGS******************GSNAHNKAPLTKGAMKTVPQARN**********
Disordered Region (DISPRO)
***********KLPRDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHARDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQLSGSFAKPPPRESKGSGQAGAMGSNAHNKAPLTKGAMKTVPQARNQNAQSNV***
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MANVNSQSSTSKLPRDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHARDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQLSGSFAKPPPRESKGSGQAGAMGSNAHNKAPLTKGAMKTVPQARNQNAQSNVQVI
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	182	2.2.26 [Sep-21-2011]
Q62880	258	Transcription initiation	yes	N/A	0.439	0.310	0.487	2e-19
Q6NZA9	249	Transcription initiation	no	N/A	0.439	0.321	0.487	5e-19
Q17QQ4	264	Transcription initiation	yes	N/A	0.423	0.291	0.480	1e-18
Q16594	264	Transcription initiation	yes	N/A	0.423	0.291	0.480	1e-18
Q5BKE0	264	Transcription initiation	no	N/A	0.423	0.291	0.480	1e-18
Q8VI33	264	Transcription initiation	no	N/A	0.423	0.291	0.480	1e-18
Q5R7P7	251	Transcription initiation	no	N/A	0.439	0.318	0.475	4e-18
Q9HBM6	251	Transcription initiation	no	N/A	0.439	0.318	0.475	4e-18
Q27272	278	Transcription initiation	yes	N/A	0.401	0.262	0.493	6e-17
Q8SSI9	137	Transcription initiation	yes	N/A	0.423	0.562	0.376	3e-12

>sp|Q62880|TAF9B_RAT Transcription initiation factor TFIID subunit 9B OS=Rattus norvegicus GN=Taf9b PE=2 SV=2

 Score = 95.1 bits (235), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 39/80 (48%), Positives = 57/80 (71%)

Query: 60  NHARDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVED 119
           N  RDA V+  + ++ GI +Y+PR + QMLEF   Y TTIL+D+++Y++HAKK TVD +D
Sbjct: 11  NAPRDALVMAQILKDMGITDYEPRVINQMLEFAFRYVTTILDDAKIYSSHAKKPTVDADD 70

Query: 120 IKLAITNQLSGSFAKPPPRE 139
           ++LAI  +   SF  PPPR+
Sbjct: 71  VRLAIQCRADQSFTSPPPRD 90

Essential for cell viability. TAF9 and TAF9L are involved in transcriptional activation as well as repression of distinct but overlapping sets of genes. May have a role in gene regulation associated with apoptosis. TAFs are components of the transcription factor IID (TFIID) complex, the TBP-free TAFII complex (TFTC), the PCAF histone acetylase complex and the STAGA transcription coactivator-HAT complex. TFIID or TFTC are essential for the regulation of RNA polymerase II-mediated transcription.
Rattus norvegicus (taxid: 10116)

>sp|Q6NZA9|TAF9B_MOUSE Transcription initiation factor TFIID subunit 9B OS=Mus musculus GN=Taf9b PE=1 SV=2

 Score = 94.0 bits (232), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 39/80 (48%), Positives = 56/80 (70%)

Query: 60  NHARDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVED 119
           N  RDA V+  + ++ GI  Y+PR + QMLEF   Y TTIL+D+++Y++HAKK TVD +D
Sbjct: 11  NAPRDALVMAQILKDMGITEYEPRVINQMLEFAFRYVTTILDDAKIYSSHAKKPTVDADD 70

Query: 120 IKLAITNQLSGSFAKPPPRE 139
           ++LAI  +   SF  PPPR+
Sbjct: 71  VRLAIQCRADQSFTSPPPRD 90

Essential for cell viability. TAF9 and TAF9B are involved in transcriptional activation as well as repression of distinct but overlapping sets of genes. May have a role in gene regulation associated with apoptosis. TAFs are components of the transcription factor IID (TFIID) complex, the TBP-free TAFII complex (TFTC), the PCAF histone acetylase complex and the STAGA transcription coactivator-HAT complex. TFIID or TFTC are essential for the regulation of RNA polymerase II-mediated transcription.

Mus musculus (taxid: 10090)

>sp|Q17QQ4|TAF9_BOVIN Transcription initiation factor TFIID subunit 9 OS=Bos taurus GN=TAF9 PE=2 SV=1

 Score = 92.8 bits (229), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 37/77 (48%), Positives = 56/77 (72%)

Query: 63  RDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKL 122
           +DAQ++  + ++ GI  Y+PR + QMLEF   Y TTIL+D+++Y++HAKK TVD +D++L
Sbjct: 14  KDAQMMAQILKDMGITEYEPRVINQMLEFAFRYVTTILDDAKIYSSHAKKATVDADDVRL 73

Query: 123 AITNQLSGSFAKPPPRE 139
           AI  +   SF  PPPR+
Sbjct: 74  AIQCRADQSFTSPPPRD 90

Essential for cell viability. TAF9 and TAF9B are involved in transcriptional activation as well as repression of distinct but overlapping sets of genes. May have a role in gene regulation associated with apoptosis. TAFs are components of the transcription factor IID (TFIID) complex, the TBP-free TAFII complex (TFTC), the PCAF histone acetylase complex and the STAGA transcription coactivator-HAT complex. TFIID or TFTC are essential for the regulation of RNA polymerase II-mediated transcription.

Bos taurus (taxid: 9913)

>sp|Q16594|TAF9_HUMAN Transcription initiation factor TFIID subunit 9 OS=Homo sapiens GN=TAF9 PE=1 SV=1

 Score = 92.8 bits (229), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 37/77 (48%), Positives = 56/77 (72%)

Query: 63  RDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKL 122
           +DAQ++  + ++ GI  Y+PR + QMLEF   Y TTIL+D+++Y++HAKK TVD +D++L
Sbjct: 14  KDAQMMAQILKDMGITEYEPRVINQMLEFAFRYVTTILDDAKIYSSHAKKATVDADDVRL 73

Query: 123 AITNQLSGSFAKPPPRE 139
           AI  +   SF  PPPR+
Sbjct: 74  AIQCRADQSFTSPPPRD 90

Essential for cell viability. TAF9 and TAF9B are involved in transcriptional activation as well as repression of distinct but overlapping sets of genes. May have a role in gene regulation associated with apoptosis. TAFs are components of the transcription factor IID (TFIID) complex, the TBP-free TAFII complex (TFTC), the PCAF histone acetylase complex and the STAGA transcription coactivator-HAT complex. TFIID or TFTC are essential for the regulation of RNA polymerase II-mediated transcription.

Homo sapiens (taxid: 9606)

>sp|Q5BKE0|TAF9_RAT Transcription initiation factor TFIID subunit 9 OS=Rattus norvegicus GN=Taf9 PE=2 SV=1

 Score = 92.8 bits (229), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 37/77 (48%), Positives = 56/77 (72%)

Query: 63  RDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKL 122
           +DAQ++  + ++ GI  Y+PR + QMLEF   Y TTIL+D+++Y++HAKK TVD +D++L
Sbjct: 14  KDAQMMAQILKDMGITEYEPRVINQMLEFAFRYVTTILDDAKIYSSHAKKPTVDADDVRL 73

Query: 123 AITNQLSGSFAKPPPRE 139
           AI  +   SF  PPPR+
Sbjct: 74  AIQCRADQSFTSPPPRD 90

Essential for cell viability. TAF9 and TAF9B are involved in transcriptional activation as well as repression of distinct but overlapping sets of genes. May have a role in gene regulation associated with apoptosis. TAFs are components of the transcription factor IID (TFIID) complex, the TBP-free TAFII complex (TFTC), the PCAF histone acetylase complex and the STAGA transcription coactivator-HAT complex. TFIID or TFTC are essential for the regulation of RNA polymerase II-mediated transcription.

Rattus norvegicus (taxid: 10116)

>sp|Q8VI33|TAF9_MOUSE Transcription initiation factor TFIID subunit 9 OS=Mus musculus GN=Taf9 PE=2 SV=1

 Score = 92.4 bits (228), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 37/77 (48%), Positives = 56/77 (72%)

Query: 63  RDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKL 122
           +DAQ++  + ++ GI  Y+PR + QMLEF   Y TTIL+D+++Y++HAKK TVD +D++L
Sbjct: 14  KDAQMMAQILKDMGITEYEPRVINQMLEFAFRYVTTILDDAKIYSSHAKKATVDADDVRL 73

Query: 123 AITNQLSGSFAKPPPRE 139
           AI  +   SF  PPPR+
Sbjct: 74  AIQCRADQSFTSPPPRD 90

Essential for cell viability. TAF9 and TAF9B are involved in transcriptional activation as well as repression of distinct but overlapping sets of genes. May have a role in gene regulation associated with apoptosis. TAFs are components of the transcription factor IID (TFIID) complex, the TBP-free TAFII complex (TFTC), the PCAF histone acetylase complex and the STAGA transcription coactivator-HAT complex. TFIID or TFTC are essential for the regulation of RNA polymerase II-mediated transcription.

Mus musculus (taxid: 10090)

>sp|Q5R7P7|TAF9B_PONAB Transcription initiation factor TFIID subunit 9B OS=Pongo abelii GN=TAF9B PE=2 SV=1

 Score = 90.9 bits (224), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 38/80 (47%), Positives = 55/80 (68%)

Query: 60  NHARDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVED 119
           N  RDA V+  + ++ GI  Y+PR + QMLEF   Y TTIL+D+++Y++HAKK  VD +D
Sbjct: 11  NAPRDALVMAQILKDMGITEYEPRVINQMLEFAFRYVTTILDDAKIYSSHAKKPNVDADD 70

Query: 120 IKLAITNQLSGSFAKPPPRE 139
           ++LAI  +   SF  PPPR+
Sbjct: 71  VRLAIQCRADQSFTSPPPRD 90

Essential for cell viability. TAF9 and TAF9B are involved in transcriptional activation as well as repression of distinct but overlapping sets of genes. May have a role in gene regulation associated with apoptosis. TAFs are components of the transcription factor IID (TFIID) complex, the TBP-free TAFII complex (TFTC), the PCAF histone acetylase complex and the STAGA transcription coactivator-HAT complex. TFIID or TFTC are essential for the regulation of RNA polymerase II-mediated transcription.

Pongo abelii (taxid: 9601)

>sp|Q9HBM6|TAF9B_HUMAN Transcription initiation factor TFIID subunit 9B OS=Homo sapiens GN=TAF9B PE=1 SV=1

 Score = 90.9 bits (224), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 38/80 (47%), Positives = 55/80 (68%)

Query: 60  NHARDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVED 119
           N  RDA V+  + ++ GI  Y+PR + QMLEF   Y TTIL+D+++Y++HAKK  VD +D
Sbjct: 11  NAPRDALVMAQILKDMGITEYEPRVINQMLEFAFRYVTTILDDAKIYSSHAKKPNVDADD 70

Query: 120 IKLAITNQLSGSFAKPPPRE 139
           ++LAI  +   SF  PPPR+
Sbjct: 71  VRLAIQCRADQSFTSPPPRD 90

Essential for cell viability. TAF9 and TAF9B are involved in transcriptional activation as well as repression of distinct but overlapping sets of genes. May have a role in gene regulation associated with apoptosis. TAFs are components of the transcription factor IID (TFIID) complex, the TBP-free TAFII complex (TFTC), the PCAF histone acetylase complex and the STAGA transcription coactivator-HAT complex. TFIID or TFTC are essential for the regulation of RNA polymerase II-mediated transcription.

Homo sapiens (taxid: 9606)

>sp|Q27272|TAF9_DROME Transcription initiation factor TFIID subunit 9 OS=Drosophila melanogaster GN=e(y)1 PE=1 SV=1

 Score = 87.0 bits (214), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 36/73 (49%), Positives = 54/73 (73%)

Query: 63  RDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKL 122
           +DAQVI+++ +E  ++ Y+PR V Q+LEF   Y T IL+D++VYANHA+KKT+D++D++L
Sbjct: 20  KDAQVIMSILKELNVQEYEPRVVNQLLEFTFRYVTCILDDAKVYANHARKKTIDLDDVRL 79

Query: 123 AITNQLSGSFAKP 135
           A    L  SF  P
Sbjct: 80  ATEVTLDKSFTGP 92

TFIID is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors.

Drosophila melanogaster (taxid: 7227)

>sp|Q8SSI9|TAF9_ENCCU Transcription initiation factor TFIID subunit 9 OS=Encephalitozoon cuniculi (strain GB-M1) GN=TAF9 PE=1 SV=1

 Score = 71.2 bits (173), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 29/77 (37%), Positives = 48/77 (62%)

Query: 63  RDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKL 122
           RDA+VI  + +  GI+  +P+ + Q+LEF   YTT +LED+ ++A H  +  +   D+KL
Sbjct: 10  RDAKVISVILRSLGIEECEPKVIIQLLEFAYRYTTDVLEDALLFAKHTGRTHITTSDVKL 69

Query: 123 AITNQLSGSFAKPPPRE 139
           A+  ++   F  PPPR+
Sbjct: 70  ALQTKVGRHFVPPPPRQ 86

Functions as a component of the DNA-binding general transcription factor complex TFIID. May also function as a component of transcription regulatory histone acetyl transferase (HAT) complexes such as SAGA. Binding of TFIID to a promoter (with or without TATA element) is the initial step in preinitiation complex (PIC) formation. TFIID plays a key role in the regulation of gene expression by RNA polymerase II through different activities such as transcription activator interaction, core promoter recognition and selectivity, TFIIA and TFIIB interaction, chromatin modification, facilitation of DNA opening and initiation of transcription.

Encephalitozoon cuniculi (strain GB-M1) (taxid: 284813)

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	182
357613265	235	tbp-associated factor [Danaus plexippus]	0.423	0.327	0.545	2e-20
47221429	243	unnamed protein product [Tetraodon nigro	0.423	0.316	0.532	3e-19
432900534	244	PREDICTED: transcription initiation fact	0.423	0.315	0.532	4e-19
410929830	247	PREDICTED: transcription initiation fact	0.423	0.311	0.532	4e-19
307211901	245	Transcription initiation factor TFIID su	0.384	0.285	0.519	4e-19
156538134	231	PREDICTED: transcription initiation fact	0.384	0.303	0.519	5e-19
307167619	237	Transcription initiation factor TFIID su	0.373	0.286	0.519	5e-19
383862445	244	PREDICTED: transcription initiation fact	0.384	0.286	0.506	6e-19
380029236	266	PREDICTED: transcription initiation fact	0.384	0.263	0.506	6e-19
380029234	243	PREDICTED: transcription initiation fact	0.384	0.288	0.506	6e-19

>gi|357613265|gb|EHJ68411.1| tbp-associated factor [Danaus plexippus]

 Score =  103 bits (258), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 42/77 (54%), Positives = 61/77 (79%)

Query: 63  RDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKL 122
           +DAQVI+++ +E GI +Y+PR + Q+LEF   Y T++LED+RV+ANHAKKK +D++D++L
Sbjct: 18  KDAQVIMSIMKEIGITDYEPRVLNQLLEFTYRYVTSVLEDARVFANHAKKKNIDLDDVRL 77

Query: 123 AITNQLSGSFAKPPPRE 139
           A+  QL  SF  PPPRE
Sbjct: 78  AVQMQLDKSFTSPPPRE 94

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|47221429|emb|CAF97347.1| unnamed protein product [Tetraodon nigroviridis]

 Score =  100 bits (248), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 41/77 (53%), Positives = 57/77 (74%)

Query: 63  RDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKL 122
           +DAQV++ + ++ GI  Y+PR + QMLEF   Y TTI+ED+++YA HAKK TVD +DIKL
Sbjct: 9   KDAQVMIQILKDMGITEYEPRVINQMLEFTYRYVTTIIEDAKIYATHAKKSTVDADDIKL 68

Query: 123 AITNQLSGSFAKPPPRE 139
           AI  ++  SF  PPPR+
Sbjct: 69  AIQCRMDQSFTSPPPRD 85

Source: Tetraodon nigroviridis

Species: Tetraodon nigroviridis

Genus: Tetraodon

Family: Tetraodontidae

Order: Tetraodontiformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|432900534|ref|XP_004076704.1| PREDICTED: transcription initiation factor TFIID subunit 9-like [Oryzias latipes]

 Score =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 41/77 (53%), Positives = 57/77 (74%)

Query: 63  RDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKL 122
           +DAQV++ + ++ GI  Y+PR + QMLEF   Y TTI+ED+++YA HAKK TVD +DIKL
Sbjct: 9   KDAQVMIQILKDMGITEYEPRVINQMLEFTYRYVTTIIEDAKIYATHAKKSTVDADDIKL 68

Query: 123 AITNQLSGSFAKPPPRE 139
           AI  ++  SF  PPPR+
Sbjct: 69  AIQCRMDQSFTSPPPRD 85

Source: Oryzias latipes

Species: Oryzias latipes

Genus: Oryzias

Family: Adrianichthyidae

Order: Beloniformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|410929830|ref|XP_003978302.1| PREDICTED: transcription initiation factor TFIID subunit 9-like [Takifugu rubripes]

 Score = 99.8 bits (247), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 41/77 (53%), Positives = 57/77 (74%)

Query: 63  RDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKL 122
           +DAQV++ + ++ GI  Y+PR + QMLEF   Y TTI+ED+++YA HAKK TVD +DIKL
Sbjct: 9   KDAQVMIQILKDMGITEYEPRVINQMLEFTYRYVTTIIEDAKIYATHAKKSTVDADDIKL 68

Query: 123 AITNQLSGSFAKPPPRE 139
           AI  ++  SF  PPPR+
Sbjct: 69  AIQCRMDQSFTSPPPRD 85

Source: Takifugu rubripes

Species: Takifugu rubripes

Genus: Takifugu

Family: Tetraodontidae

Order: Tetraodontiformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|307211901|gb|EFN87828.1| Transcription initiation factor TFIID subunit 9 [Harpegnathos saltator]

 Score = 99.8 bits (247), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 40/77 (51%), Positives = 60/77 (77%)

Query: 63  RDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKL 122
           +DAQVI+++ ++ GI +Y+P+ + Q+LEF   Y T IL+DSRVYANHAKKK +D++D++L
Sbjct: 16  KDAQVIMSIMKDMGITDYEPKVINQLLEFTYRYVTCILDDSRVYANHAKKKFIDLDDVRL 75

Query: 123 AITNQLSGSFAKPPPRE 139
           A+  QL  +F  PPPR+
Sbjct: 76  AVKMQLERTFTNPPPRD 92

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|156538134|ref|XP_001608253.1| PREDICTED: transcription initiation factor TFIID subunit 9-like [Nasonia vitripennis]

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 40/77 (51%), Positives = 60/77 (77%)

Query: 63  RDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKL 122
           +DAQVIV++ ++ GI +Y+P+ + Q+LEF   Y T IL+DS+VYANH+KKK +D++D++L
Sbjct: 16  KDAQVIVSIMKDMGIADYEPKVINQLLEFTYRYVTCILDDSKVYANHSKKKFIDLDDVRL 75

Query: 123 AITNQLSGSFAKPPPRE 139
           A+  +L  SF  PPPRE
Sbjct: 76  AVKMELEKSFTNPPPRE 92

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307167619|gb|EFN61153.1| Transcription initiation factor TFIID subunit 9 [Camponotus floridanus]

 Score = 99.4 bits (246), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 40/77 (51%), Positives = 60/77 (77%)

Query: 63  RDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKL 122
           +DAQVI+++ ++ GI +Y+P+ + Q+LEF   Y T IL+DSR+YANHAKKK +D++D++L
Sbjct: 9   KDAQVIMSIMKDMGITDYEPKVINQLLEFTYRYVTCILDDSRIYANHAKKKFIDLDDVRL 68

Query: 123 AITNQLSGSFAKPPPRE 139
           A+  QL  SF  PPPR+
Sbjct: 69  AVKMQLERSFTNPPPRD 85

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383862445|ref|XP_003706694.1| PREDICTED: transcription initiation factor TFIID subunit 9-like [Megachile rotundata]

 Score = 99.4 bits (246), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 39/77 (50%), Positives = 60/77 (77%)

Query: 63  RDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKL 122
           +DAQVI+++ ++ GI +Y+P+ + Q+LEF   Y T IL+DSR+YANHAKKK +D++D++L
Sbjct: 16  KDAQVIMSIMKDMGISDYEPKVINQLLEFTYRYVTCILDDSRIYANHAKKKFIDLDDVRL 75

Query: 123 AITNQLSGSFAKPPPRE 139
           A+  QL  +F  PPPR+
Sbjct: 76  AVKMQLERTFTNPPPRD 92

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380029236|ref|XP_003698285.1| PREDICTED: transcription initiation factor TFIID subunit 9-like isoform 2 [Apis florea]

 Score = 99.4 bits (246), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 39/77 (50%), Positives = 60/77 (77%)

Query: 63  RDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKL 122
           +DAQVI+++ ++ GI +Y+P+ + Q+LEF   Y T IL+DSR+YANHAKKK +D++D++L
Sbjct: 16  KDAQVIMSIMKDMGITDYEPKVINQLLEFTYRYVTCILDDSRIYANHAKKKFIDLDDVRL 75

Query: 123 AITNQLSGSFAKPPPRE 139
           A+  QL  +F  PPPR+
Sbjct: 76  AVKMQLERTFTNPPPRD 92

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380029234|ref|XP_003698284.1| PREDICTED: transcription initiation factor TFIID subunit 9-like isoform 1 [Apis florea]

 Score = 99.4 bits (246), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 39/77 (50%), Positives = 60/77 (77%)

Query: 63  RDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKL 122
           +DAQVI+++ ++ GI +Y+P+ + Q+LEF   Y T IL+DSR+YANHAKKK +D++D++L
Sbjct: 16  KDAQVIMSIMKDMGITDYEPKVINQLLEFTYRYVTCILDDSRIYANHAKKKFIDLDDVRL 75

Query: 123 AITNQLSGSFAKPPPRE 139
           A+  QL  +F  PPPR+
Sbjct: 76  AVKMQLERTFTNPPPRD 92

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

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	182
UNIPROTKB|E1BU14	255	TAF9 "Uncharacterized protein"	0.423	0.301	0.493	2.8e-18
ZFIN|ZDB-GENE-030131-204	248	taf9 "TAF9 RNA polymerase II,	0.423	0.310	0.506	2.8e-18
RGD|621116	258	Taf9b "TAF9B RNA polymerase II	0.439	0.310	0.487	3.6e-18
MGI|MGI:3039562	249	Taf9b "TAF9B RNA polymerase II	0.439	0.321	0.487	4.6e-18
UNIPROTKB|Q17QQ4	264	TAF9 "Transcription initiation	0.423	0.291	0.480	7.5e-18
UNIPROTKB|E2R911	265	TAF9 "Uncharacterized protein"	0.423	0.290	0.480	7.5e-18
UNIPROTKB|D6RGK3	136	TAF9 "Transcription initiation	0.423	0.566	0.480	7.5e-18
UNIPROTKB|D6RHW1	102	TAF9 "Transcription initiation	0.423	0.754	0.480	7.5e-18
UNIPROTKB|D6RIE8	198	TAF9 "Transcription initiation	0.423	0.388	0.480	7.5e-18
UNIPROTKB|D6RIV9	166	TAF9 "Transcription initiation	0.423	0.463	0.480	7.5e-18

UNIPROTKB|E1BU14 TAF9 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 221 (82.9 bits), Expect = 2.8e-18, P = 2.8e-18
 Identities = 38/77 (49%), Positives = 56/77 (72%)

Query:    63 RDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKL 122
             +DAQV+  + ++ GI  Y+PR + QMLEF   Y TTILED+++Y++HAKK +VD +D++L
Sbjct:    14 KDAQVMAQILKDMGITEYEPRVINQMLEFAYRYVTTILEDAKIYSSHAKKSSVDADDVRL 73

Query:   123 AITNQLSGSFAKPPPRE 139
             AI  +   SF  PPPR+
Sbjct:    74 AIQCRTDQSFTSPPPRD 90

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IEA

ZFIN|ZDB-GENE-030131-204 taf9 "TAF9 RNA polymerase II, TATA box binding protein (TBP)-associated factor" [Danio rerio (taxid:7955)]

 Score = 221 (82.9 bits), Expect = 2.8e-18, P = 2.8e-18
 Identities = 39/77 (50%), Positives = 57/77 (74%)

Query:    63 RDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKL 122
             +DAQV++ + ++ GI  Y+PR V QMLEF   Y TTI+ED+++Y+ HAKK +VD +DI+L
Sbjct:     9 KDAQVMMQILKDMGITEYEPRVVNQMLEFTYRYVTTIIEDAKIYSAHAKKSSVDADDIRL 68

Query:   123 AITNQLSGSFAKPPPRE 139
             AI  ++  SF  PPPR+
Sbjct:    69 AIQCRVDQSFTSPPPRD 85

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA

RGD|621116 Taf9b "TAF9B RNA polymerase II, TATA box binding protein (TBP)-associated factor" [Rattus norvegicus (taxid:10116)]

 Score = 220 (82.5 bits), Expect = 3.6e-18, P = 3.6e-18
 Identities = 39/80 (48%), Positives = 57/80 (71%)

Query:    60 NHARDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVED 119
             N  RDA V+  + ++ GI +Y+PR + QMLEF   Y TTIL+D+++Y++HAKK TVD +D
Sbjct:    11 NAPRDALVMAQILKDMGITDYEPRVINQMLEFAFRYVTTILDDAKIYSSHAKKPTVDADD 70

Query:   120 IKLAITNQLSGSFAKPPPRE 139
             ++LAI  +   SF  PPPR+
Sbjct:    71 VRLAIQCRADQSFTSPPPRD 90

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IEA;ISO

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0005669 "transcription factor TFIID complex" evidence=IEA;ISO

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA

GO:0012501 "programmed cell death" evidence=IEP

GO:0014070 "response to organic cyclic compound" evidence=IEP

GO:0030307 "positive regulation of cell growth" evidence=IEA;ISO

GO:0033276 "transcription factor TFTC complex" evidence=IEA;ISO

GO:0043066 "negative regulation of apoptotic process" evidence=IEA;ISO

GO:0046982 "protein heterodimerization activity" evidence=IEA

MGI|MGI:3039562 Taf9b "TAF9B RNA polymerase II, TATA box binding protein (TBP)-associated factor" [Mus musculus (taxid:10090)]

 Score = 219 (82.2 bits), Expect = 4.6e-18, P = 4.6e-18
 Identities = 39/80 (48%), Positives = 56/80 (70%)

Query:    60 NHARDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVED 119
             N  RDA V+  + ++ GI  Y+PR + QMLEF   Y TTIL+D+++Y++HAKK TVD +D
Sbjct:    11 NAPRDALVMAQILKDMGITEYEPRVINQMLEFAFRYVTTILDDAKIYSSHAKKPTVDADD 70

Query:   120 IKLAITNQLSGSFAKPPPRE 139
             ++LAI  +   SF  PPPR+
Sbjct:    71 VRLAIQCRADQSFTSPPPRD 90

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=ISO

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=IEA

GO:0005669 "transcription factor TFIID complex" evidence=ISO

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

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA

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

GO:0030307 "positive regulation of cell growth" evidence=ISO

GO:0033276 "transcription factor TFTC complex" evidence=ISO

GO:0043066 "negative regulation of apoptotic process" evidence=ISO

GO:0046982 "protein heterodimerization activity" evidence=IEA

UNIPROTKB|Q17QQ4 TAF9 "Transcription initiation factor TFIID subunit 9" [Bos taurus (taxid:9913)]

 Score = 217 (81.4 bits), Expect = 7.5e-18, P = 7.5e-18
 Identities = 37/77 (48%), Positives = 56/77 (72%)

Query:    63 RDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKL 122
             +DAQ++  + ++ GI  Y+PR + QMLEF   Y TTIL+D+++Y++HAKK TVD +D++L
Sbjct:    14 KDAQMMAQILKDMGITEYEPRVINQMLEFAFRYVTTILDDAKIYSSHAKKATVDADDVRL 73

Query:   123 AITNQLSGSFAKPPPRE 139
             AI  +   SF  PPPR+
Sbjct:    74 AIQCRADQSFTSPPPRD 90

GO:0071339 "MLL1 complex" evidence=ISS

GO:0070761 "pre-snoRNP complex" evidence=IEA

GO:0070742 "C2H2 zinc finger domain binding" evidence=IEA

GO:0070555 "response to interleukin-1" evidence=IEA

GO:0060760 "positive regulation of response to cytokine stimulus" evidence=IEA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0044212 "transcription regulatory region DNA binding" evidence=IEA

GO:0043966 "histone H3 acetylation" evidence=IEA

GO:0043066 "negative regulation of apoptotic process" evidence=IEA

GO:0033613 "activating transcription factor binding" evidence=IEA

GO:0033276 "transcription factor TFTC complex" evidence=IEA

GO:0032435 "negative regulation of proteasomal ubiquitin-dependent protein catabolic process" evidence=IEA

GO:0030914 "STAGA complex" evidence=IEA

GO:0030307 "positive regulation of cell growth" evidence=IEA

GO:0005669 "transcription factor TFIID complex" evidence=IEA

GO:0004402 "histone acetyltransferase activity" evidence=IEA

GO:0003713 "transcription coactivator activity" evidence=IEA

GO:0002039 "p53 binding" evidence=IEA

GO:0000125 "PCAF complex" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA

UNIPROTKB|E2R911 TAF9 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 217 (81.4 bits), Expect = 7.5e-18, P = 7.5e-18
 Identities = 37/77 (48%), Positives = 56/77 (72%)

Query:    63 RDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKL 122
             +DAQ++  + ++ GI  Y+PR + QMLEF   Y TTIL+D+++Y++HAKK TVD +D++L
Sbjct:    14 KDAQMMAQILKDMGITEYEPRVINQMLEFAFRYVTTILDDAKIYSSHAKKATVDADDVRL 73

Query:   123 AITNQLSGSFAKPPPRE 139
             AI  +   SF  PPPR+
Sbjct:    74 AIQCRADQSFTSPPPRD 90

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA

UNIPROTKB|D6RGK3 TAF9 "Transcription initiation factor TFIID subunit 9" [Homo sapiens (taxid:9606)]

 Score = 217 (81.4 bits), Expect = 7.5e-18, P = 7.5e-18
 Identities = 37/77 (48%), Positives = 56/77 (72%)

Query:    63 RDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKL 122
             +DAQ++  + ++ GI  Y+PR + QMLEF   Y TTIL+D+++Y++HAKK TVD +D++L
Sbjct:    14 KDAQMMAQILKDMGITEYEPRVINQMLEFAFRYVTTILDDAKIYSSHAKKATVDADDVRL 73

Query:   123 AITNQLSGSFAKPPPRE 139
             AI  +   SF  PPPR+
Sbjct:    74 AIQCRADQSFTSPPPRD 90

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

UNIPROTKB|D6RHW1 TAF9 "Transcription initiation factor TFIID subunit 9" [Homo sapiens (taxid:9606)]

 Score = 217 (81.4 bits), Expect = 7.5e-18, P = 7.5e-18
 Identities = 37/77 (48%), Positives = 56/77 (72%)

Query:    63 RDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKL 122
             +DAQ++  + ++ GI  Y+PR + QMLEF   Y TTIL+D+++Y++HAKK TVD +D++L
Sbjct:    14 KDAQMMAQILKDMGITEYEPRVINQMLEFAFRYVTTILDDAKIYSSHAKKATVDADDVRL 73

Query:   123 AITNQLSGSFAKPPPRE 139
             AI  +   SF  PPPR+
Sbjct:    74 AIQCRADQSFTSPPPRD 90

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

UNIPROTKB|D6RIE8 TAF9 "Transcription initiation factor TFIID subunit 9" [Homo sapiens (taxid:9606)]

 Score = 217 (81.4 bits), Expect = 7.5e-18, P = 7.5e-18
 Identities = 37/77 (48%), Positives = 56/77 (72%)

Query:    63 RDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKL 122
             +DAQ++  + ++ GI  Y+PR + QMLEF   Y TTIL+D+++Y++HAKK TVD +D++L
Sbjct:    14 KDAQMMAQILKDMGITEYEPRVINQMLEFAFRYVTTILDDAKIYSSHAKKATVDADDVRL 73

Query:   123 AITNQLSGSFAKPPPRE 139
             AI  +   SF  PPPR+
Sbjct:    74 AIQCRADQSFTSPPPRD 90

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

UNIPROTKB|D6RIV9 TAF9 "Transcription initiation factor TFIID subunit 9" [Homo sapiens (taxid:9606)]

 Score = 217 (81.4 bits), Expect = 7.5e-18, P = 7.5e-18
 Identities = 37/77 (48%), Positives = 56/77 (72%)

Query:    63 RDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKL 122
             +DAQ++  + ++ GI  Y+PR + QMLEF   Y TTIL+D+++Y++HAKK TVD +D++L
Sbjct:    14 KDAQMMAQILKDMGITEYEPRVINQMLEFAFRYVTTILDDAKIYSSHAKKATVDADDVRL 73

Query:   123 AITNQLSGSFAKPPPRE 139
             AI  +   SF  PPPR+
Sbjct:    74 AIQCRADQSFTSPPPRD 90

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	182
cd07979	117	cd07979, TAF9, TATA Binding Protein (TBP) Associat	4e-30
pfam02291	129	pfam02291, TFIID-31kDa, Transcription initiation f	1e-25
COG5094	145	COG5094, TAF9, Transcription initiation factor TFI	1e-15
COG2036	91	COG2036, HHT1, Histones H3 and H4 [Chromatin struc	5e-07
pfam00125	75	pfam00125, Histone, Core histone H2A/H2B/H3/H4	1e-06
cd07981	72	cd07981, TAF12, TATA Binding Protein (TBP) Associa	7e-04
cd00076	85	cd00076, H4, Histone H4, one of the four histones,	8e-04

>gnl|CDD|173963 cd07979, TAF9, TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex

 Score =  106 bits (266), Expect = 4e-30
 Identities = 36/77 (46%), Positives = 54/77 (70%)

Query: 63  RDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKL 122
           RDA+VI  + +  GI  Y+PR + Q+LEF   YTT +L+D++VY+ HA K  +D +D+KL
Sbjct: 2   RDARVIAAILKSMGITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKL 61

Query: 123 AITNQLSGSFAKPPPRE 139
           AI +++  SF  PPPR+
Sbjct: 62  AIQSRVDYSFTSPPPRD 78

The TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Human TAF9 has a paralogue gene (TAF9L) which has a redundant function. Several hypotheses are proposed for TAF function such as serving as activator-binding sites, in core-promoter recognition or a role in essential catalytic activity. It has been shown that TAF9 interacts directly with different transcription factors such as p53, herpes simplex virus activator vp16 and the basal transcription factor TFIIB. Each TAF, with the help of a specific activator, is required only for expression of subset of genes and are not universally involved for transcription as are GTFs. In yeast and human cells, TAFs have been found as components of other complexes besides TFIID. TAF9 is a component of TFIID in multiple organisms as well as different TBP-free TAF complexes containing the GCN5-type histone acetyltransferase. Several TAFs interact via histone-fold (HFD) motifs; HFD is the interaction motif involved in heterodimerization of the core histones and their assembly into nucleosome octamers. The minimal HFD contains three alpha-helices linked by two loops and is found in core histones, TAFS and many other transcription factors. TFIID has a histone octamer-like substructure. TFIID has a histone octamer-like substructure. TAF9 is a shared subunit of both, histone acetyltransferase complex (SAGA) and TFIID complexes. TAF9 domain interacts with TAF6 to form a novel histone-like heterodimer that is structurally related to the histone H3 and H4 oligomer. Length = 117

>gnl|CDD|111209 pfam02291, TFIID-31kDa, Transcription initiation factor IID, 31kD subunit

 Score = 95.3 bits (237), Expect = 1e-25
 Identities = 37/77 (48%), Positives = 57/77 (74%)

Query: 63  RDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKL 122
           +DA++I ++ +E GI+ Y+PR V Q+L+F + YT  IL+D++VY+ HA+K  +D ED++L
Sbjct: 13  KDARLIHSILKELGIQEYEPRVVLQLLDFAHRYTQKILQDAKVYSRHARKANIDAEDVRL 72

Query: 123 AITNQLSGSFAKPPPRE 139
           AI  +L  SF  PPPRE
Sbjct: 73  AIAARLDVSFTGPPPRE 89

This family represents the N-terminus of the 31kD subunit (42kD in drosophila) of transcription initiation factor IID (TAFII31). TAFII31 binds to p53, and is an essential requirement for p53 mediated transcription activation. Length = 129

>gnl|CDD|227425 COG5094, TAF9, Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]

 Score = 70.0 bits (171), Expect = 1e-15
 Identities = 31/80 (38%), Positives = 50/80 (62%), Gaps = 3/80 (3%)

Query: 63  RDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKK---KTVDVED 119
           RD ++I  + +  GI+ Y+P+   Q+LEF + YT  +LED+ VYA H  +    T+ VED
Sbjct: 15  RDVRLIHLILRSLGIEEYEPKVPLQLLEFAHRYTQDVLEDALVYAKHTGRGHIATLGVED 74

Query: 120 IKLAITNQLSGSFAKPPPRE 139
           ++LA+  ++   F  PPP+E
Sbjct: 75  VRLALATKVGRHFVPPPPKE 94

Length = 145

>gnl|CDD|224947 COG2036, HHT1, Histones H3 and H4 [Chromatin structure and dynamics]

 Score = 45.4 bits (108), Expect = 5e-07
 Identities = 20/51 (39%), Positives = 27/51 (52%), Gaps = 3/51 (5%)

Query: 84  CVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQLSGSFAK 134
            +Q+ LE    Y   I ED+   A HAK+KTV  EDIKLA+       + +
Sbjct: 44  ELQEALE---EYLEEIAEDAVELAEHAKRKTVKAEDIKLALKRLGRRIYGE 91

Length = 91

>gnl|CDD|201020 pfam00125, Histone, Core histone H2A/H2B/H3/H4

 Score = 44.1 bits (105), Expect = 1e-06
 Identities = 15/45 (33%), Positives = 25/45 (55%)

Query: 83  RCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQ 127
           +    + E + +    ILED+ + A HAK+KT+   DI+LA+   
Sbjct: 31  KAPVALQEALEDLLEEILEDAGLLARHAKRKTITPRDIQLAVRLD 75

Length = 75

>gnl|CDD|173964 cd07981, TAF12, TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex

 Score = 36.4 bits (85), Expect = 7e-04
 Identities = 11/40 (27%), Positives = 24/40 (60%)

Query: 88  MLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQ 127
           +LE  +++   ++ED+   A H K  T++V+D++L +   
Sbjct: 28  LLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLERN 67

The TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of the seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs function such as serving as activator-binding sites, core-promoter recognition or a role in essential catalytic activity. These TAFs, with the help of specific activators, are required only for expression of a subset of genes and are not universally involved for transcription as are GTFs. In yeast and human cells, TAFs have been found as components of other complexes besides TFIID. Several TAFs interact via histone-fold (HFD) motifs; the HFD is the interaction motif involved in heterodimerization of the core histones and their assembly into nucleosome octamers. The minimal HFD contains three alpha-helices linked by two loops and is found in core histones, TAFs and many other transcription factors. TFIID has a histone octamer-like substructure. TAF12 domain interacts with TAF4 and makes a novel histone-like heterodimer that binds DNA and has a core promoter function of a subset of genes. Length = 72

>gnl|CDD|238031 cd00076, H4, Histone H4, one of the four histones, along with H2A, H2B and H3, which forms the eukaryotic nucleosome core; along with H3, it plays a central role in nucleosome formation; histones bind to DNA and wrap the genetic material into "beads on a string" in which DNA (the string) is wrapped around small blobs of histones (the beads) at regular intervals; play a role in the inheritance of specialized chromosome structures and the control of gene activity; defects in the establishment of proper chromosome structure by histones may activate or silence genes aberrantly and thus lead to disease; the sequence of histone H4 has remained almost invariant in more than 2 billion years of evolution

 Score = 36.7 bits (85), Expect = 8e-04
 Identities = 15/60 (25%), Positives = 28/60 (46%)

Query: 68  IVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQ 127
           I  + +  G+K        ++   + +Y   ++ D+  Y  HAK+KTV   D+  A+  Q
Sbjct: 19  IRRLARRGGVKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQ 78

Length = 85

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	182
KOG3334|consensus	148		100.0
PF02291	129	TFIID-31kDa: Transcription initiation factor IID,	100.0
COG5094	145	TAF9 Transcription initiation factor TFIID, subuni	100.0
cd07979	117	TAF9 TATA Binding Protein (TBP) Associated Factor	100.0
cd07979	117	TAF9 TATA Binding Protein (TBP) Associated Factor	99.76
PLN00035	103	histone H4; Provisional	99.56
cd00076	85	H4 Histone H4, one of the four histones, along wit	99.56
PTZ00015	102	histone H4; Provisional	99.54
smart00417	74	H4 Histone H4.	99.44
smart00803	65	TAF TATA box binding protein associated factor. TA	99.4
COG2036	91	HHT1 Histones H3 and H4 [Chromatin structure and d	99.37
PF02291	129	TFIID-31kDa: Transcription initiation factor IID,	99.33
KOG3334|consensus	148		99.31
smart00576	77	BTP Bromodomain transcription factors and PHD doma	99.2
COG5094	145	TAF9 Transcription initiation factor TFIID, subuni	99.05
KOG3467|consensus	103		98.95
cd07981	72	TAF12 TATA Binding Protein (TBP) Associated Factor	98.91
PF07524	77	Bromo_TP: Bromodomain associated; InterPro: IPR006	98.74
PF15630	76	CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C	98.69
cd08050	343	TAF6 TATA Binding Protein (TBP) Associated Factor	98.68
PF00125	75	Histone: Core histone H2A/H2B/H3/H4 histone h2a si	98.55
PF02969	66	TAF: TATA box binding protein associated factor (T	98.39
smart00428	105	H3 Histone H3.	98.35
cd00074	115	H2A Histone 2A; H2A is a subunit of the nucleosome	98.26
PF00808	65	CBFD_NFYB_HMF: Histone-like transcription factor (	98.24
PLN00161	135	histone H3; Provisional	97.62
PLN00160	97	histone H3; Provisional	97.6
PTZ00018	136	histone H3; Provisional	97.58
PLN00121	136	histone H3; Provisional	97.5
PF15511	414	CENP-T: Centromere kinetochore component CENP-T; P	97.48
PF03847	68	TFIID_20kDa: Transcription initiation factor TFIID	97.29
PF07524	77	Bromo_TP: Bromodomain associated; InterPro: IPR006	97.21
KOG4336|consensus	323		97.07
smart00576	77	BTP Bromodomain transcription factors and PHD doma	97.01
KOG1142|consensus	258		96.98
KOG2549|consensus	576		96.7
KOG2389|consensus	353		96.54
smart00414	106	H2A Histone 2A.	95.96
PF02269	93	TFIID-18kDa: Transcription initiation factor IID,	95.73
KOG3423|consensus	176		95.58
PLN00154	136	histone H2A; Provisional	95.5
PF03540	51	TFIID_30kDa: Transcription initiation factor TFIID	95.26
PF13654	509	AAA_32: AAA domain; PDB: 3K1J_B.	95.02
KOG0869|consensus	168		94.98
PTZ00017	134	histone H2A; Provisional	94.59
KOG1745|consensus	137		93.8
PLN00157	132	histone H2A; Provisional	93.16
cd07978	92	TAF13 The TATA Binding Protein (TBP) Associated Fa	93.03
KOG0870|consensus	172		92.9
COG5095	450	TAF6 Transcription initiation factor TFIID, subuni	92.9
PLN00156	139	histone H2AX; Provisional	92.51
KOG1756|consensus	131		92.29
PLN00153	129	histone H2A; Provisional	92.02
PTZ00252	134	histone H2A; Provisional	91.34
PF03540	51	TFIID_30kDa: Transcription initiation factor TFIID	91.25
PF15630	76	CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C	91.23
smart00427	89	H2B Histone H2B.	91.17
COG5262	132	HTA1 Histone H2A [Chromatin structure and dynamics	90.97
COG5208	286	HAP5 CCAAT-binding factor, subunit C [Transcriptio	90.43
PLN00158	116	histone H2B; Provisional	89.51
TIGR00764	608	lon_rel lon-related putative ATP-dependent proteas	89.18
PTZ00463	117	histone H2B; Provisional	89.07
PRK00411	394	cdc6 cell division control protein 6; Reviewed	88.99
cd08048	85	TAF11 TATA Binding Protein (TBP) Associated Factor	86.47
cd08045	212	TAF4 TATA Binding Protein (TBP) Associated Factor	85.61
smart00803	65	TAF TATA box binding protein associated factor. TA	84.59
PF02969	66	TAF: TATA box binding protein associated factor (T	83.52
KOG1744|consensus	127		83.49
PRK13406	584	bchD magnesium chelatase subunit D; Provisional	82.92
cd00076	85	H4 Histone H4, one of the four histones, along wit	82.73
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	80.16
PF05236	264	TAF4: Transcription initiation factor TFIID compon	80.03

>KOG3334|consensus

Probab=100.00  E-value=2e-50  Score=320.18  Aligned_cols=120  Identities=42%  Similarity=0.693  Sum_probs=114.9

Q ss_pred             CCCCCCCchHHHHHHHHHHcCCCccChHHHHHHHHHHHhhhcccccccHhhhhhhhhHHHHHHHHHhcCCcccChHHHHH
Q psy8542           8 SSTSKLPRDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHARDAQVIVNMFQEAGIKNYDPRCVQQ   87 (182)
Q Consensus         8 ~~~~~~prda~~i~~il~~~gi~~yep~v~~qll~f~yryt~~vL~DA~vys~hardaqlI~rIlk~~Gv~r~sp~v~~q   87 (182)
                      ++++..||||++|++||+||||+|||||||+||||||||||++||+||.+|                             
T Consensus         7 ~~~~~~pkDa~~i~~iL~s~GI~eyEprVi~qlLefa~rYtt~vL~DA~vy-----------------------------   57 (148)
T KOG3334|consen    7 SGTKGVPKDARVIASILKSLGIQEYEPRVINQLLEFAYRYTTTVLDDAKVY-----------------------------   57 (148)
T ss_pred             CcccCCcHHHHHHHHHHHHcCccccChHHHHHHHHHHHHHHHHHHHHHHHH-----------------------------
Confidence            577899999999999999999999999999999999999999999998888                             


Q ss_pred             HHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhcCCCCCCCCChhhhhccccccCCcccccCCCCC---CCCC
Q psy8542          88 MLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQLSGSFAKPPPRESKGSGQAGAMGSNAHNKAPLT---KGAM  164 (182)
Q Consensus        88 Lle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~~~~F~~pppke~Ll~lA~~~~~~~~~N~~pLP---~~~g  164 (182)
                                         |+||++++|++|||+|||+++++++|++|||||+|+++|      ++||+.|||   +.||
T Consensus        58 -------------------s~HA~ka~i~~eDVrlA~~~~~~~sf~~pPpRe~lL~lA------~~rN~~pLp~i~~~~g  112 (148)
T KOG3334|consen   58 -------------------SSHAKKATIDAEDVRLAIQMRVDHSFTPPPPREFLLELA------AERNSKPLPQIRAGPG  112 (148)
T ss_pred             -------------------HHhccCCCCcHHHHHHHHHHHhccccCCCCchHHHHHHH------HhhccCCCCcccCCCC
Confidence                               667889999999999999999999999999999999999      899999999   5899


Q ss_pred             ccCCccccccccccccc
Q psy8542         165 KTVPQARNQNAQSNVQV  181 (182)
Q Consensus       165 irlP~e~~~~~~~n~~~  181 (182)
                      +||||++.|++|+||++
T Consensus       113 ~rLPpdryclt~~n~~l  129 (148)
T KOG3334|consen  113 LRLPPDRYCLTQPNYVL  129 (148)
T ss_pred             ccCChhHHHhcCcccee
Confidence            99999999999999986

>PF02291 TFIID-31kDa: Transcription initiation factor IID, 31kD subunit; InterPro: IPR003162 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription []

Probab=100.00  E-value=1e-50  Score=318.71  Aligned_cols=122  Identities=39%  Similarity=0.649  Sum_probs=55.7

Q ss_pred             CCCCCCCCCchHHHHHHHHHHcCCCccChHHHHHHHHHHHhhhcccccccHhhhhhhhhHHHHHHHHHhcCCcccChHHH
Q psy8542           6 SQSSTSKLPRDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHARDAQVIVNMFQEAGIKNYDPRCV   85 (182)
Q Consensus         6 ~~~~~~~~prda~~i~~il~~~gi~~yep~v~~qll~f~yryt~~vL~DA~vys~hardaqlI~rIlk~~Gv~r~sp~v~   85 (182)
                      ..++.+.+||||++|++||+||||++|||||++|||||+||||++||+||.+|                           
T Consensus         4 ~~~~~~~~PrDa~~i~~iL~~~Gv~~yeprVv~qLLEfayRYt~~vL~DA~~y---------------------------   56 (129)
T PF02291_consen    4 IDSQSKSLPRDARVIHLILKSMGVTEYEPRVVNQLLEFAYRYTSDVLEDAQVY---------------------------   56 (129)
T ss_dssp             ---------HHHHHHHHHHHHTT---B-THHHHHHHHHHHHHHHHHHHHHHHH---------------------------
T ss_pred             cCCCCccCChHHHHHHHHHHHcCCcccCHHHHHHHHHHHHHHHHHHHHHHHHH---------------------------
Confidence            34566789999999999999999999999999999999999988888777776                           


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhcCCCCCCCCChhhhhccccccCCcccccCCCCC---CC
Q psy8542          86 QQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQLSGSFAKPPPRESKGSGQAGAMGSNAHNKAPLT---KG  162 (182)
Q Consensus        86 ~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~~~~F~~pppke~Ll~lA~~~~~~~~~N~~pLP---~~  162 (182)
                                           |+||||++|+++||||||++|.+++|++|||||+|+++|      +++|++|||   +.
T Consensus        57 ---------------------a~hA~~~~i~~~DVrLAi~~r~~~~f~~pppre~llelA------~e~N~~PLP~i~~~  109 (129)
T PF02291_consen   57 ---------------------ADHAGRSTIDADDVRLAIQSRLDHSFTQPPPREFLLELA------REKNSIPLPPIPPK  109 (129)
T ss_dssp             ---------------------HHHTT-SSB-HHHHHHHHHHT--------------------------------------
T ss_pred             ---------------------HHhcccccCChHHHHHHHHHHHhhhccCCCChHHHHHHH------HHhcCCCCCCCCCC
Confidence                                 778999999999999999999999999999999999999      899999999   47


Q ss_pred             CCccCCccccccccccccc
Q psy8542         163 AMKTVPQARNQNAQSNVQV  181 (182)
Q Consensus       163 ~girlP~e~~~~~~~n~~~  181 (182)
                      ||+|||||++||+++||++
T Consensus       110 ~GirLPpe~~cLt~~Ny~l  128 (129)
T PF02291_consen  110 FGIRLPPERYCLTAPNYQL  128 (129)
T ss_dssp             -------------------
T ss_pred             CCCCCCchhccccCCCCcC
Confidence            9999999999999999987

TAFII-31 protein is a transcriptional coactivator of the p53 protein [].; GO: 0006352 transcription initiation, DNA-dependent; PDB: 1TAF_A.

>COG5094 TAF9 Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]

Probab=100.00  E-value=1.2e-45  Score=287.73  Aligned_cols=114  Identities=32%  Similarity=0.579  Sum_probs=107.1

Q ss_pred             CchHHHHHHHHHHcCCCccChHHHHHHHHHHHhhhcccccccHhhhhhhhhHHHHHHHHHhcCCcccChHHHHHHHHHHH
Q psy8542          14 PRDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHARDAQVIVNMFQEAGIKNYDPRCVQQMLEFVN   93 (182)
Q Consensus        14 prda~~i~~il~~~gi~~yep~v~~qll~f~yryt~~vL~DA~vys~hardaqlI~rIlk~~Gv~r~sp~v~~qLle~~~   93 (182)
                      |||+|+||+||+|+||++|||.||.||||||||||++||+||.+|                                   
T Consensus        14 PrDvrlihliL~Slgi~~ye~~VplQLl~FAhRYTq~vl~Dalvy-----------------------------------   58 (145)
T COG5094          14 PRDVRLIHLILRSLGIEEYEPKVPLQLLEFAHRYTQDVLEDALVY-----------------------------------   58 (145)
T ss_pred             CcchhHHHHHHHhcCchhhCccchHHHHHHHHHHHHHHHHHHHHH-----------------------------------
Confidence            999999999999999999999999999999999999999888888                                   


Q ss_pred             HHHHHHHHHHHHHhhhcCC---CCCCHHHHHHHHHHhcCCCCCCCCChhhhhccccccCCcccccCCCCC---CCCCccC
Q psy8542          94 NYTTTILEDSRVYANHAKK---KTVDVEDIKLAITNQLSGSFAKPPPRESKGSGQAGAMGSNAHNKAPLT---KGAMKTV  167 (182)
Q Consensus        94 ry~~~Vl~dA~~yA~HAgR---ktI~~eDVrLAI~~r~~~~F~~pppke~Ll~lA~~~~~~~~~N~~pLP---~~~girl  167 (182)
                                   |+|+||   .++.++|||||++++.+++|.+|||||+|+|+|      .|||++|||   ++||+||
T Consensus        59 -------------a~htgrg~~a~l~veDvrLA~at~v~~~F~pppPke~llela------~erN~KpLpq~~g~~g~Rl  119 (145)
T COG5094          59 -------------AKHTGRGHIATLGVEDVRLALATKVGRHFVPPPPKEYLLELA------TERNSKPLPQPDGENGIRL  119 (145)
T ss_pred             -------------HHhcCCCccCcccHHHHHHHHHHHhcCCcCCCChHHHHHHHH------HHhcCCCCCccCCccceec
Confidence                         455555   467889999999999999999999999999999      799999999   6999999


Q ss_pred             Cccccccccccccc
Q psy8542         168 PQARNQNAQSNVQV  181 (182)
Q Consensus       168 P~e~~~~~~~n~~~  181 (182)
                      |||.+||+|.||-|
T Consensus       120 PPekycLt~~~w~v  133 (145)
T COG5094         120 PPEKYCLTNLDWEV  133 (145)
T ss_pred             CcHHhhhcccchhh
Confidence            99999999999976

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

Probab=100.00  E-value=1.9e-41  Score=261.98  Aligned_cols=114  Identities=37%  Similarity=0.649  Sum_probs=111.6

Q ss_pred             hhhHHHHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhcCCCCCCCCChhhh
Q psy8542          62 ARDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQLSGSFAKPPPRESK  141 (182)
Q Consensus        62 ardaqlI~rIlk~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~~~~F~~pppke~L  141 (182)
                      |+|+++|.+||+++|+++|+|+|+++|+||+|||+.+|++||..||+||||+||+++||+|||++|++|+|++|||||+|
T Consensus         1 p~d~~~v~~iLk~~Gv~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~~~f~~~p~~~~l   80 (117)
T cd07979           1 PRDARVIAAILKSMGITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVDYSFTSPPPRDFL   80 (117)
T ss_pred             ChHHHHHHHHHHHCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhccCCCCCCcHHHH
Confidence            78999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hccccccCCcccccCCCCC---CCCCccCCccccccccccccc
Q psy8542         142 GSGQAGAMGSNAHNKAPLT---KGAMKTVPQARNQNAQSNVQV  181 (182)
Q Consensus       142 l~lA~~~~~~~~~N~~pLP---~~~girlP~e~~~~~~~n~~~  181 (182)
                      +++|      .++|++|||   +.||+|||||++||++.||++
T Consensus        81 ~~~a------~~~N~~pLP~~~~~~g~~LPp~~~~l~~~n~~~  117 (117)
T cd07979          81 LELA------REKNSIPLPPIPPSCGLRLPPERYCLTAPNYRL  117 (117)
T ss_pred             HHHH------HHhccCCCCCCCCCCCccCCCHHHcccccCccC
Confidence            9999      899999999   489999999999999999985

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

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

Probab=99.76  E-value=9.2e-19  Score=135.44  Aligned_cols=78  Identities=37%  Similarity=0.621  Sum_probs=60.6

Q ss_pred             CchHHHHHHHHHHcCCCccChHHHHHHHHHHHhhhcccccccHhhhhhhhh----HHHHHHHHHhcCC-cccChHHHHHH
Q psy8542          14 PRDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHARD----AQVIVNMFQEAGI-KNYDPRCVQQM   88 (182)
Q Consensus        14 prda~~i~~il~~~gi~~yep~v~~qll~f~yryt~~vL~DA~vys~hard----aqlI~rIlk~~Gv-~r~sp~v~~qL   88 (182)
                      |||+++|+.||++|||++|||+|++|||||+|||+.+||+||..|++|+++    +.-|+..++..+- ...++.-.+.|
T Consensus         1 p~d~~~v~~iLk~~Gv~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~~~f~~~p~~~~l   80 (117)
T cd07979           1 PRDARVIAAILKSMGITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVDYSFTSPPPRDFL   80 (117)
T ss_pred             ChHHHHHHHHHHHCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhccCCCCCCcHHHH
Confidence            899999999999999999999999999999999999999999999999973    2333333333332 33334444555


Q ss_pred             HHH
Q psy8542          89 LEF   91 (182)
Q Consensus        89 le~   91 (182)
                      ++.
T Consensus        81 ~~~   83 (117)
T cd07979          81 LEL   83 (117)
T ss_pred             HHH
Confidence            554

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

>PLN00035 histone H4; Provisional

Probab=99.56  E-value=1.8e-14  Score=109.73  Aligned_cols=68  Identities=21%  Similarity=0.351  Sum_probs=63.7

Q ss_pred             HHHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHh--cCCCCC
Q psy8542          66 QVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQ--LSGSFA  133 (182)
Q Consensus        66 qlI~rIlk~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r--~~~~F~  133 (182)
                      ..|+||++++|++|+|.+++.++.++++.|..+|++||+.||+||+||||+++||.+|++.+  .-|.|.
T Consensus        33 ~~IrRLARr~GvkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~g~~lyGf~  102 (103)
T PLN00035         33 PAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYGFG  102 (103)
T ss_pred             HHHHHHHHHcCcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHcCCcCCCCC
Confidence            47999999999999999999999999999999999999999999999999999999999875  446664

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

Probab=99.56  E-value=1.7e-14  Score=106.37  Aligned_cols=64  Identities=23%  Similarity=0.407  Sum_probs=61.3

Q ss_pred             HHHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhcC
Q psy8542          66 QVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQLS  129 (182)
Q Consensus        66 qlI~rIlk~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~~  129 (182)
                      ..|+||++++|++++|.+++.++.+.++.|..+|++||+.||+|||||||+++||.+|++.++.
T Consensus        17 ~~I~RLarr~GvkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr~g~   80 (85)
T cd00076          17 PAIRRLARRGGVKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQGR   80 (85)
T ss_pred             HHHHHHHHHcCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHCCC
Confidence            4799999999999999999999999999999999999999999999999999999999987654

>PTZ00015 histone H4; Provisional

Probab=99.54  E-value=3e-14  Score=108.32  Aligned_cols=64  Identities=20%  Similarity=0.344  Sum_probs=61.2

Q ss_pred             HHHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhcC
Q psy8542          66 QVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQLS  129 (182)
Q Consensus        66 qlI~rIlk~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~~  129 (182)
                      ..|+||+++.|++|+|.+++.++.++++.|..+|++||+.||+||+||||+++||.+|++.+..
T Consensus        34 ~~IrRLarr~GvkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr~g~   97 (102)
T PTZ00015         34 GAIRRLARRGGVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQGR   97 (102)
T ss_pred             HHHHHHHHHcCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcCC
Confidence            4799999999999999999999999999999999999999999999999999999999987644

>smart00417 H4 Histone H4

Probab=99.44  E-value=1.7e-13  Score=98.82  Aligned_cols=58  Identities=21%  Similarity=0.395  Sum_probs=55.7

Q ss_pred             HHHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHH
Q psy8542          66 QVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLA  123 (182)
Q Consensus        66 qlI~rIlk~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLA  123 (182)
                      ..|+||++++|++|+|.+++.++.++++.|..+|+.||+.|++|||||||+++||..|
T Consensus        17 ~~IrRLaRr~GvkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~a   74 (74)
T smart00417       17 PAIRRLARRGGVKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVYA   74 (74)
T ss_pred             HHHHHHHHHcCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHheeC
Confidence            3799999999999999999999999999999999999999999999999999999764

>smart00803 TAF TATA box binding protein associated factor

Probab=99.40  E-value=9.6e-13  Score=92.42  Aligned_cols=60  Identities=22%  Similarity=0.352  Sum_probs=57.7

Q ss_pred             HHHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHH
Q psy8542          66 QVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAIT  125 (182)
Q Consensus        66 qlI~rIlk~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~  125 (182)
                      ..|++|+++.|++++|+++...|.+.++.+..+|+++|+.|++|+||+|++.+||.+|++
T Consensus         6 ~~i~ria~~~Gi~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Alk   65 (65)
T smart00803        6 ETIKDVAESLGIGNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR   65 (65)
T ss_pred             HHHHHHHHHCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHhC
Confidence            468999999999999999999999999999999999999999999999999999999974

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

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

Probab=99.37  E-value=1.4e-12  Score=97.36  Aligned_cols=64  Identities=31%  Similarity=0.469  Sum_probs=61.1

Q ss_pred             HHHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhcC
Q psy8542          66 QVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQLS  129 (182)
Q Consensus        66 qlI~rIlk~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~~  129 (182)
                      ..+.||+++.|.+++|..+...|.+.++.|+.+|.++|..+|.|||||||+.+||++|++.+.-
T Consensus        23 apv~Ri~r~~~~~Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~~~~~   86 (91)
T COG2036          23 APVRRILRKAGAERVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKRLGR   86 (91)
T ss_pred             hHHHHHHHHHhHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHHHhcc
Confidence            3799999999999999999999999999999999999999999999999999999999987754

>PF02291 TFIID-31kDa: Transcription initiation factor IID, 31kD subunit; InterPro: IPR003162 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription []

Probab=99.33  E-value=1.9e-12  Score=102.12  Aligned_cols=93  Identities=26%  Similarity=0.388  Sum_probs=42.0

Q ss_pred             hhhhhhhHHHHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhcCCCCCCCCC
Q psy8542          58 YANHARDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQLSGSFAKPPP  137 (182)
Q Consensus        58 ys~hardaqlI~rIlk~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~~~~F~~ppp  137 (182)
                      -+..|+|+++|+.||+++||++|+|+|++|||||+|||+++||+||   ..+|               .-.+...  ...
T Consensus         8 ~~~~PrDa~~i~~iL~~~Gv~~yeprVv~qLLEfayRYt~~vL~DA---~~ya---------------~hA~~~~--i~~   67 (129)
T PF02291_consen    8 SKSLPRDARVIHLILKSMGVTEYEPRVVNQLLEFAYRYTSDVLEDA---QVYA---------------DHAGRST--IDA   67 (129)
T ss_dssp             -----HHHHHHHHHHHHTT---B-THHHHHHHHHHHHHHHHHHHHH---HHHH---------------HHTT-SS--B-H
T ss_pred             CccCChHHHHHHHHHHHcCCcccCHHHHHHHHHHHHHHHHHHHHHH---HHHH---------------Hhccccc--CCh
Confidence            3467999999999999999999999999999999999999999999   2222               1111111  112


Q ss_pred             hhhhhccccccCCcccccCCCCCCCCCccCCccccc
Q psy8542         138 RESKGSGQAGAMGSNAHNKAPLTKGAMKTVPQARNQ  173 (182)
Q Consensus       138 ke~Ll~lA~~~~~~~~~N~~pLP~~~girlP~e~~~  173 (182)
                      -|.-+..+   +........|.|.++.+.+-.|+|.
T Consensus        68 ~DVrLAi~---~r~~~~f~~pppre~llelA~e~N~  100 (129)
T PF02291_consen   68 DDVRLAIQ---SRLDHSFTQPPPREFLLELAREKNS  100 (129)
T ss_dssp             HHHHHHHH---HT-----------------------
T ss_pred             HHHHHHHH---HHHhhhccCCCChHHHHHHHHHhcC
Confidence            23333332   1123445567778999999888887

TAFII-31 protein is a transcriptional coactivator of the p53 protein [].; GO: 0006352 transcription initiation, DNA-dependent; PDB: 1TAF_A.

>KOG3334|consensus

Probab=99.31  E-value=2.5e-12  Score=102.84  Aligned_cols=92  Identities=27%  Similarity=0.399  Sum_probs=70.1

Q ss_pred             hhhhhhHHHHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhcCCCCCCCCCh
Q psy8542          59 ANHARDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQLSGSFAKPPPR  138 (182)
Q Consensus        59 s~hardaqlI~rIlk~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~~~~F~~pppk  138 (182)
                      ..+|+|+++|..||+++||++|+|+|++|||||+||||+.||+||                     +--..|.-..+-.-
T Consensus        10 ~~~pkDa~~i~~iL~s~GI~eyEprVi~qlLefa~rYtt~vL~DA---------------------~vys~HA~ka~i~~   68 (148)
T KOG3334|consen   10 KGVPKDARVIASILKSLGIQEYEPRVINQLLEFAYRYTTTVLDDA---------------------KVYSSHAKKATIDA   68 (148)
T ss_pred             cCCcHHHHHHHHHHHHcCccccChHHHHHHHHHHHHHHHHHHHHH---------------------HHHHHhccCCCCcH
Confidence            478999999999999999999999999999999999999999998                     22222233444555


Q ss_pred             hhhhccccccCCcccccCCCCCCCCCccCCccccc
Q psy8542         139 ESKGSGQAGAMGSNAHNKAPLTKGAMKTVPQARNQ  173 (182)
Q Consensus       139 e~Ll~lA~~~~~~~~~N~~pLP~~~girlP~e~~~  173 (182)
                      |.+. +| -+|..+.....|.|.++...|-.|||+
T Consensus        69 eDVr-lA-~~~~~~~sf~~pPpRe~lL~lA~~rN~  101 (148)
T KOG3334|consen   69 EDVR-LA-IQMRVDHSFTPPPPREFLLELAAERNS  101 (148)
T ss_pred             HHHH-HH-HHHHhccccCCCCchHHHHHHHHhhcc
Confidence            5442 22 234455566667778888888888886

>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins

Probab=99.20  E-value=9.7e-11  Score=84.05  Aligned_cols=62  Identities=16%  Similarity=0.412  Sum_probs=59.5

Q ss_pred             HHHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHh
Q psy8542          66 QVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQ  127 (182)
Q Consensus        66 qlI~rIlk~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r  127 (182)
                      ..|.+|++..|+++++|.+.+.|.|.+++|..++++.+..||+|+||++++..||++|++..
T Consensus        10 ~~Vaqil~~~Gf~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~~   71 (77)
T smart00576       10 IAVAQILESAGFDSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALENL   71 (77)
T ss_pred             HHHHHHHHHcCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence            57899999999999999999999999999999999999999999999999999999999754

subdomain of archael histone-like transcription factors

>COG5094 TAF9 Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]

Probab=99.05  E-value=1.5e-10  Score=91.02  Aligned_cols=95  Identities=25%  Similarity=0.375  Sum_probs=68.5

Q ss_pred             hhhhHHHHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHH-hcCCCCCCCCC-h
Q psy8542          61 HARDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITN-QLSGSFAKPPP-R  138 (182)
Q Consensus        61 hardaqlI~rIlk~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~-r~~~~F~~ppp-k  138 (182)
                      -|+|+++|+.||++.|++.|++.|+.|||||+||||.+|++||                ...|=-+ |++  .. +.. -
T Consensus        13 gPrDvrlihliL~Slgi~~ye~~VplQLl~FAhRYTq~vl~Da----------------lvya~htgrg~--~a-~l~ve   73 (145)
T COG5094          13 GPRDVRLIHLILRSLGIEEYEPKVPLQLLEFAHRYTQDVLEDA----------------LVYAKHTGRGH--IA-TLGVE   73 (145)
T ss_pred             CCcchhHHHHHHHhcCchhhCccchHHHHHHHHHHHHHHHHHH----------------HHHHHhcCCCc--cC-cccHH
Confidence            4999999999999999999999999999999999999999998                1111111 222  22 222 4


Q ss_pred             hhhhccccccCCcccccCCCCCCCCCccCCccccc--cccc
Q psy8542         139 ESKGSGQAGAMGSNAHNKAPLTKGAMKTVPQARNQ--NAQS  177 (182)
Q Consensus       139 e~Ll~lA~~~~~~~~~N~~pLP~~~girlP~e~~~--~~~~  177 (182)
                      |.=+.+|+   ..+....-|-|+++...|..|||.  |-|+
T Consensus        74 DvrLA~at---~v~~~F~pppPke~llela~erN~KpLpq~  111 (145)
T COG5094          74 DVRLALAT---KVGRHFVPPPPKEYLLELATERNSKPLPQP  111 (145)
T ss_pred             HHHHHHHH---HhcCCcCCCChHHHHHHHHHHhcCCCCCcc
Confidence            45556651   224445556667899999999987  5443

>KOG3467|consensus

Probab=98.95  E-value=3.3e-09  Score=79.08  Aligned_cols=67  Identities=22%  Similarity=0.347  Sum_probs=61.8

Q ss_pred             HHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhc--CCCCC
Q psy8542          67 VIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQL--SGSFA  133 (182)
Q Consensus        67 lI~rIlk~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~--~~~F~  133 (182)
                      .|++|.+..||+|++.-++++....+..|..+++.+|..|++||+||||++.||..+++...  -|.|.
T Consensus        34 aIRRlARr~GVkRi~G~~yeE~~~~~k~fl~n~i~~A~~yt~HAKRKTvT~~dvv~~LKR~G~~~~g~~  102 (103)
T KOG3467|consen   34 AIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFG  102 (103)
T ss_pred             HHHHHHHhcCcchhchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhceeeHHHHHHHHHHcCceeeccC
Confidence            69999999999999999999999999999999999999999999999999999999998653  34553

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

Probab=98.91  E-value=1.4e-08  Score=72.30  Aligned_cols=62  Identities=23%  Similarity=0.450  Sum_probs=54.0

Q ss_pred             HHHHHhc-CCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhcCC
Q psy8542          69 VNMFQEA-GIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQLSG  130 (182)
Q Consensus        69 ~rIlk~~-Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~~~  130 (182)
                      ..++++. +-.++++++...|.++++.|+.+|+++|..+|.|+||+||+++||+++++..-+.
T Consensus         8 ~~lv~~id~~~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~r~~~~   70 (72)
T cd07981           8 QELLKEIDPREQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLERNWNI   70 (72)
T ss_pred             HHHHHhhCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhcCC
Confidence            3444432 4589999999999999999999999999999999999999999999999875443

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

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

Probab=98.74  E-value=7.6e-08  Score=68.61  Aligned_cols=63  Identities=16%  Similarity=0.420  Sum_probs=59.8

Q ss_pred             HHHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhc
Q psy8542          66 QVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQL  128 (182)
Q Consensus        66 qlI~rIlk~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~  128 (182)
                      ++|..|++..|++..++.+.+.|.|++.+|..++.+.+..||+|+||...+..||.+|++.-+
T Consensus        10 ~~va~il~~~GF~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~~g   72 (77)
T PF07524_consen   10 RSVAQILKHAGFDSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALEEMG   72 (77)
T ss_pred             HHHHHHHHHcCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhC
Confidence            678999999999999999999999999999999999999999999999999999999997543

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

>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C

Probab=98.69  E-value=3.9e-08  Score=71.24  Aligned_cols=58  Identities=21%  Similarity=0.437  Sum_probs=48.3

Q ss_pred             HHHHHHhcCCc---ccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHH
Q psy8542          68 IVNMFQEAGIK---NYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAIT  125 (182)
Q Consensus        68 I~rIlk~~Gv~---r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~  125 (182)
                      +.+|..+.+-+   .++|.++..|.|.+|+++..+.+|-..||.||||+||+.+||+|..+
T Consensus        11 v~ki~ee~~~~~~~~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~R   71 (76)
T PF15630_consen   11 VGKIVEEEAKEKGVEVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLAR   71 (76)
T ss_dssp             HHHHHHHCCCCTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTT
T ss_pred             HHHHHHHHHhccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhh
Confidence            56666665433   49999999999999999999999999999999999999999999864

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

Probab=98.68  E-value=9.3e-08  Score=85.55  Aligned_cols=69  Identities=17%  Similarity=0.279  Sum_probs=63.2

Q ss_pred             HHHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHh---cCCCCCC
Q psy8542          66 QVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQ---LSGSFAK  134 (182)
Q Consensus        66 qlI~rIlk~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r---~~~~F~~  134 (182)
                      ..|+.|+++.|++++++++...|.+.++.++.+|+++|..++.|+||+|++.+||.+|++.+   ..|.|..
T Consensus         3 ~~i~~ia~~~Gi~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~~~n~eplyG~~~   74 (343)
T cd08050           3 ESIKLIAESLGIDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALRLRNVEPLYGFSS   74 (343)
T ss_pred             hHHHHHHHHcCCCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHHhCCCcccCCCC
Confidence            45788999999999999999999999999999999999999999999999999999999987   3356543

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

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

Probab=98.55  E-value=3.2e-07  Score=64.35  Aligned_cols=61  Identities=25%  Similarity=0.329  Sum_probs=53.5

Q ss_pred             HHHHHHHHhcCCc-ccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHH
Q psy8542          66 QVIVNMFQEAGIK-NYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITN  126 (182)
Q Consensus        66 qlI~rIlk~~Gv~-r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~  126 (182)
                      ++.+.|..+.+.. +++..+...|..+++-|+.+++++|..+|.|++|+||+..||++|++.
T Consensus        13 r~~r~i~~~~~~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~kR~tI~~~DI~~A~r~   74 (75)
T PF00125_consen   13 RLLREIGEEILSKYRISSEALVALQSVLEYLLVEILEEAGNLARHAKRKTITPRDIQLAVRI   74 (75)
T ss_dssp             HHHHHHHHTTSSSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBSEEGHHHHHHHHHH
T ss_pred             eeeehhhcccccccccccccchhhhhhhhhhhhhhhhHHHHHHhhcCCcEecHHHHHHHHhc
Confidence            3445555555554 999999999999999999999999999999999999999999999974

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

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

Probab=98.39  E-value=2.3e-06  Score=60.55  Aligned_cols=60  Identities=18%  Similarity=0.364  Sum_probs=50.9

Q ss_pred             HHHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHH
Q psy8542          66 QVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAIT  125 (182)
Q Consensus        66 qlI~rIlk~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~  125 (182)
                      ..|+.+..+.|+...++++...|.+-++.-..+|+++|..+..|++|++++.+||..|++
T Consensus         7 esvk~iAes~Gi~~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~ALr   66 (66)
T PF02969_consen    7 ESVKDIAESLGISNLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDDINSALR   66 (66)
T ss_dssp             HHHHHHHHHTT---B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred             HHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence            468889999999999999999999999999999999999999999999999999999984

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

>smart00428 H3 Histone H3

Probab=98.35  E-value=2.8e-06  Score=65.11  Aligned_cols=65  Identities=22%  Similarity=0.293  Sum_probs=58.0

Q ss_pred             HHHHHHHHHhcC---CcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhcC
Q psy8542          65 AQVIVNMFQEAG---IKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQLS  129 (182)
Q Consensus        65 aqlI~rIlk~~G---v~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~~  129 (182)
                      .++++.|..+..   -=++++++...|-|.++.|..++.+||...|.||+|.||...|++||..-|+.
T Consensus        36 ~RLVREI~~~~~~~~~~R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~kDi~La~rir~~  103 (105)
T smart00428       36 QRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQLARRIRGE  103 (105)
T ss_pred             HHHHHHHHHHcCCCCCceeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHhhHHHHHHHhcc
Confidence            478888888753   23899999999999999999999999999999999999999999999876653

>cd00074 H2A Histone 2A; H2A is a subunit of the nucleosome

Probab=98.26  E-value=2.7e-06  Score=66.07  Aligned_cols=61  Identities=18%  Similarity=0.187  Sum_probs=57.9

Q ss_pred             HHHHHHHHh-cCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHH
Q psy8542          66 QVIVNMFQE-AGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITN  126 (182)
Q Consensus        66 qlI~rIlk~-~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~  126 (182)
                      .-|+++|++ .++.|++..+...|...+|.++.||++-|..+|.|+++++|+.+||.+||..
T Consensus        24 ~ri~R~Lk~~~~a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi~n   85 (115)
T cd00074          24 GRIHRYLKKGRYAERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVRN   85 (115)
T ss_pred             HHHHHHHHcCccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHHhc
Confidence            468899997 7999999999999999999999999999999999999999999999999975

The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins.

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

Probab=98.24  E-value=4.8e-06  Score=57.38  Aligned_cols=58  Identities=14%  Similarity=0.302  Sum_probs=52.8

Q ss_pred             HHHHHHHhc-CCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHH
Q psy8542          67 VIVNMFQEA-GIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAI  124 (182)
Q Consensus        67 lI~rIlk~~-Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI  124 (182)
                      .|.+|++.. ++.+++.++...+-..++.|+..++++|...|.+.||+||+.+||..|+
T Consensus         7 ~vkri~k~~~~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~~~rkti~~~Dv~~Av   65 (65)
T PF00808_consen    7 RVKRIMKSDPDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQRDKRKTITYEDVAKAV   65 (65)
T ss_dssp             HHHHHHHHTSTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEE-HHHHHHHH
T ss_pred             HHHHHhccCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHC
Confidence            478899876 8889999999999999999999999999999999999999999999886

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

>PLN00161 histone H3; Provisional

Probab=97.62  E-value=0.0003  Score=56.19  Aligned_cols=65  Identities=20%  Similarity=0.266  Sum_probs=58.6

Q ss_pred             HHHHHHHHHhcC--CcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhcC
Q psy8542          65 AQVIVNMFQEAG--IKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQLS  129 (182)
Q Consensus        65 aqlI~rIlk~~G--v~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~~  129 (182)
                      .++|+.|..+..  -=++.+.++..|-|.+|.|..++.+||...|-||+|.||...|++||..-|..
T Consensus        62 ~RLVREI~~~~~~~~~Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kDm~La~rirg~  128 (135)
T PLN00161         62 ARLVREISNEMLREPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLARRIRGP  128 (135)
T ss_pred             HHHHHHHHHhcCCCCcEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhhHHHHHHhccc
Confidence            478999988753  35899999999999999999999999999999999999999999999877655

>PLN00160 histone H3; Provisional

Probab=97.60  E-value=0.00033  Score=53.12  Aligned_cols=65  Identities=20%  Similarity=0.237  Sum_probs=57.8

Q ss_pred             HHHHHHHHHhc--CCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhcC
Q psy8542          65 AQVIVNMFQEA--GIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQLS  129 (182)
Q Consensus        65 aqlI~rIlk~~--Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~~  129 (182)
                      .++++.|..+.  +--++.+.+...|-|.+|.|..++.+|+...|-||+|.||...|++||-.-|+.
T Consensus        28 ~RLVREI~~~~~~~~~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl~~kD~~L~~rirg~   94 (97)
T PLN00160         28 ARLVREIQMEMSREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIMPKDMQLARRIRGQ   94 (97)
T ss_pred             HHHHHHHHHHcCCCCcEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcccccchhhHHHHHHhhcc
Confidence            46888888765  235899999999999999999999999999999999999999999999876654

>PTZ00018 histone H3; Provisional

Probab=97.58  E-value=0.00031  Score=56.14  Aligned_cols=65  Identities=23%  Similarity=0.296  Sum_probs=57.4

Q ss_pred             HHHHHHHHHhcC-CcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhcC
Q psy8542          65 AQVIVNMFQEAG-IKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQLS  129 (182)
Q Consensus        65 aqlI~rIlk~~G-v~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~~  129 (182)
                      .++|+.|..+.+ -=++.+.++..|-|.+|.|...+.+|+...|-||+|-||...|++||-.-|+.
T Consensus        69 ~RLVREI~~~~~~~~rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~rirg~  134 (136)
T PTZ00018         69 QRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE  134 (136)
T ss_pred             HHHHHHHHHHcCCcceeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchhhHHHHHHhccc
Confidence            468888887642 23899999999999999999999999999999999999999999999876654

>PLN00121 histone H3; Provisional

Probab=97.50  E-value=0.00046  Score=55.20  Aligned_cols=65  Identities=23%  Similarity=0.296  Sum_probs=57.4

Q ss_pred             HHHHHHHHHhcC-CcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhcC
Q psy8542          65 AQVIVNMFQEAG-IKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQLS  129 (182)
Q Consensus        65 aqlI~rIlk~~G-v~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~~  129 (182)
                      .++|+.|..+.+ -=++.+.++..|-|.+|.|..++.+|+...|-||+|-||...|++||-.-|+.
T Consensus        69 ~RLVREI~~~~~~~~Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~rirg~  134 (136)
T PLN00121         69 QRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE  134 (136)
T ss_pred             HHHHHHHHHHhCccceeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhHHHHHHhccc
Confidence            478888887642 23899999999999999999999999999999999999999999999866654

>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T

Probab=97.48  E-value=0.0002  Score=65.87  Aligned_cols=42  Identities=21%  Similarity=0.347  Sum_probs=36.9

Q ss_pred             cccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHH
Q psy8542          78 KNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVED  119 (182)
Q Consensus        78 ~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eD  119 (182)
                      ..++.++...|......|-..+..|-.+||+|||||||+.+|
T Consensus       373 ~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIdesD  414 (414)
T PF15511_consen  373 MKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDESD  414 (414)
T ss_dssp             S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHH
T ss_pred             CccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCCCC
Confidence            479999999999999999999999999999999999999987

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

Probab=97.29  E-value=0.00073  Score=47.92  Aligned_cols=59  Identities=19%  Similarity=0.407  Sum_probs=45.8

Q ss_pred             HHHHHhc-CCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHh
Q psy8542          69 VNMFQEA-GIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQ  127 (182)
Q Consensus        69 ~rIlk~~-Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r  127 (182)
                      ..++++. .-...+|+|-..|++++..|+.+|+..|..+|.|.|..||+..||++.++..
T Consensus         6 ~~Lv~~iDp~~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~tle~~Dv~~~Ler~   65 (68)
T PF03847_consen    6 QELVKQIDPNEKLDPDVEELLLELADDFVDDVVSFACRLAKHRKSSTLEVKDVQLHLERN   65 (68)
T ss_dssp             HHHHHCC-SS----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHHHH
T ss_pred             HHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHHHhh
Confidence            3444443 3346899999999999999999999999999999999999999999998753

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

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

Probab=97.21  E-value=0.00062  Score=48.36  Aligned_cols=60  Identities=20%  Similarity=0.463  Sum_probs=55.0

Q ss_pred             HHHHHHHHHcCCCccChHHHHHHHHHHHhhhcccccccHhhhhhhhhH----HHHHHHHHhcCC
Q psy8542          18 QVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHARDA----QVIVNMFQEAGI   77 (182)
Q Consensus        18 ~~i~~il~~~gi~~yep~v~~qll~f~yryt~~vL~DA~vys~harda----qlI~rIlk~~Gv   77 (182)
                      +++..||++.|.+..+|.++..|-|...+|...+...+..|++|+++.    .-+...+.++|+
T Consensus        10 ~~va~il~~~GF~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~~gi   73 (77)
T PF07524_consen   10 RSVAQILKHAGFDSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALEEMGI   73 (77)
T ss_pred             HHHHHHHHHcCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCC
Confidence            678999999999999999999999999999999999999999999855    456688888988

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

>KOG4336|consensus

Probab=97.07  E-value=0.0021  Score=57.50  Aligned_cols=63  Identities=19%  Similarity=0.344  Sum_probs=60.0

Q ss_pred             hhHHHHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHH
Q psy8542          63 RDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAIT  125 (182)
Q Consensus        63 rdaqlI~rIlk~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~  125 (182)
                      -.+.+|..|+++.|+..++.-+.+.|++....|..+|.+.+.-|++|+||...+..||.+.+-
T Consensus         6 vl~~VV~~Ll~~~gfd~is~~aletlvell~~yi~eigrq~~n~celagRT~pT~~Dv~l~Li   68 (323)
T KOG4336|consen    6 VLAPVVSNLLKTKGFDSISNAALETLVELLQSYIREIGRQLHNYCELAGRTIPTQGDVKLTLI   68 (323)
T ss_pred             HHHHHHHHHHHHhCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHH
Confidence            356899999999999999999999999999999999999999999999999999999999885

>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins

Probab=97.01  E-value=0.0018  Score=46.31  Aligned_cols=61  Identities=15%  Similarity=0.375  Sum_probs=53.9

Q ss_pred             HHHHHHHHHcCCCccChHHHHHHHHHHHhhhcccccccHhhhhhhhhH----HHHHHHHHhcCCc
Q psy8542          18 QVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHARDA----QVIVNMFQEAGIK   78 (182)
Q Consensus        18 ~~i~~il~~~gi~~yep~v~~qll~f~yryt~~vL~DA~vys~harda----qlI~rIlk~~Gv~   78 (182)
                      +.|..||+..|.+..+|.++.-|.|...||-..+.+.+..|++|+++.    .-|..-+.++|+.
T Consensus        10 ~~Vaqil~~~Gf~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~~gi~   74 (77)
T smart00576       10 IAVAQILESAGFDSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALENLGIS   74 (77)
T ss_pred             HHHHHHHHHcCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCcc
Confidence            468899999999999999999999999999999999999999998744    4566777778873

subdomain of archael histone-like transcription factors

>KOG1142|consensus

Probab=96.98  E-value=0.0013  Score=57.41  Aligned_cols=59  Identities=25%  Similarity=0.451  Sum_probs=53.8

Q ss_pred             cCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhcCCCCC
Q psy8542          75 AGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQLSGSFA  133 (182)
Q Consensus        75 ~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~~~~F~  133 (182)
                      -|=+-.+++|.+.|+|+|..|+.+|..-|..+|+|.+.+||++-||+|.++..-+..|-
T Consensus       168 d~~~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIqLhLEr~~Nm~iP  226 (258)
T KOG1142|consen  168 DGTTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQLHLERNFNMEIP  226 (258)
T ss_pred             cCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhheeeeeeccccccCC
Confidence            46667899999999999999999999999999999999999999999999987776653

>KOG2549|consensus

Probab=96.70  E-value=0.0073  Score=57.79  Aligned_cols=70  Identities=19%  Similarity=0.290  Sum_probs=62.5

Q ss_pred             HHHHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHh---cCCCCCC
Q psy8542          65 AQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQ---LSGSFAK  134 (182)
Q Consensus        65 aqlI~rIlk~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r---~~~~F~~  134 (182)
                      ...++-++.+.|++..++++...|-+-.+.-+.||.+||..+-.|++|.+.+.+||..|++.+   ..|.|..
T Consensus        14 ~Es~k~vAEslGi~nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr~~nVep~yg~~s   86 (576)
T KOG2549|consen   14 KESVKVVAESLGITNLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALRSLNVEPLYGFGA   86 (576)
T ss_pred             HHHHHHHHHHhCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHhhcccccccCccc
Confidence            345777889999999999999999999999999999999999999999999999999999986   3456643

>KOG2389|consensus

Probab=96.54  E-value=0.011  Score=53.78  Aligned_cols=63  Identities=16%  Similarity=0.316  Sum_probs=59.6

Q ss_pred             HHHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhc
Q psy8542          66 QVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQL  128 (182)
Q Consensus        66 qlI~rIlk~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~  128 (182)
                      ..+.+|..+.|...+..-+.+-|-+++-+|+.++.+.|..|+++|||....+-||.+|++...
T Consensus        33 ~avaQIcqslg~~~~~~sale~Ltd~~~qyvQ~lgk~a~~~~n~anR~epnl~Div~Al~dls   95 (353)
T KOG2389|consen   33 VAVAQICQSLGYSSTQNSALETLTDVLQQYVQNLGKTAHRYSNLANRTEPNLFDIVLALQDLS   95 (353)
T ss_pred             HHHHHHHHhcCCcccccHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCccHHHHHHHHHHhh
Confidence            367889999999999999999999999999999999999999999999999999999999763

>smart00414 H2A Histone 2A

Probab=95.96  E-value=0.022  Score=43.72  Aligned_cols=60  Identities=20%  Similarity=0.247  Sum_probs=54.8

Q ss_pred             HHHHHHHhcC-CcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHH
Q psy8542          67 VIVNMFQEAG-IKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITN  126 (182)
Q Consensus        67 lI~rIlk~~G-v~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~  126 (182)
                      -|+++|++.. ..|++..+..-|...+|..+.||++-|...|...+++.|+..++.+||..
T Consensus        14 Ri~r~Lk~~~~~~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~k~~rItp~hi~lAi~n   74 (106)
T smart00414       14 RIHRLLRKGTYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRITPRHLQLAIRN   74 (106)
T ss_pred             HHHHHHHcCccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHHHhhhccC
Confidence            4788888763 77999999999999999999999999999999999999999999999974

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

Probab=95.73  E-value=0.014  Score=43.52  Aligned_cols=58  Identities=17%  Similarity=0.286  Sum_probs=28.3

Q ss_pred             HHHHHhc-CCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHH
Q psy8542          69 VNMFQEA-GIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITN  126 (182)
Q Consensus        69 ~rIlk~~-Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~  126 (182)
                      ..|+-.. .+....++.+..+-|++..|+.+++..|...|...|++.|+.+|+..+++.
T Consensus         8 ~~mMy~fGD~~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR~   66 (93)
T PF02269_consen    8 RQMMYGFGDVEEPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLRK   66 (93)
T ss_dssp             HHHHHCTTS-SS--HHHHHHHHHHHHHHHHHHHHHHHC---------------------
T ss_pred             HHHHHHcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHhc
Confidence            3444444 446788999999999999999999999999999999999999999999973

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

>KOG3423|consensus

Probab=95.58  E-value=0.061  Score=44.63  Aligned_cols=62  Identities=21%  Similarity=0.285  Sum_probs=53.1

Q ss_pred             HHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcC--------------CCCCCHHHHHHHHHHhc
Q psy8542          67 VIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAK--------------KKTVDVEDIKLAITNQL  128 (182)
Q Consensus        67 lI~rIlk~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAg--------------RktI~~eDVrLAI~~r~  128 (182)
                      ++.-.|+.+|+...++|++..+-=.+.+|+++|+.||..|++-.+              |-|++++|+.-|++.-+
T Consensus        91 vt~~yL~~aGf~~~D~rv~RLvsLaAQKfvSDIa~DA~Q~~k~r~~~~~~~~k~~~kdkK~tLtmeDL~~AL~EyG  166 (176)
T KOG3423|consen   91 VTDHYLKKAGFQTSDPRVKRLVSLAAQKFVSDIANDALQHSKIRTKTAIGKDKKQAKDKKYTLTMEDLSPALAEYG  166 (176)
T ss_pred             HHHHHHHhcCCCcCcHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccccccccceeeeHHHHHHHHHHhC
Confidence            345579999999999999999999999999999999999998443              22789999999997544

>PLN00154 histone H2A; Provisional

Probab=95.50  E-value=0.042  Score=44.05  Aligned_cols=60  Identities=15%  Similarity=0.128  Sum_probs=55.9

Q ss_pred             HHHHHHHhcC--CcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHH
Q psy8542          67 VIVNMFQEAG--IKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITN  126 (182)
Q Consensus        67 lI~rIlk~~G--v~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~  126 (182)
                      -|+++|++..  ..|++..++.-|-.++|..+.|||+-|-..|...+++.|+-..|.+||..
T Consensus        43 Ri~r~Lk~g~~~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lAIrn  104 (136)
T PLN00154         43 RIHRQLKQRVSAHGRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRG  104 (136)
T ss_pred             HHHHHHHhhhhhccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhhccC
Confidence            5889999875  67999999999999999999999999999999999999999999999963

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

Probab=95.26  E-value=0.092  Score=35.53  Aligned_cols=44  Identities=18%  Similarity=0.329  Sum_probs=40.6

Q ss_pred             HHHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q psy8542          66 QVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANH  109 (182)
Q Consensus        66 qlI~rIlk~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~H  109 (182)
                      .++.-+|++.|++.-++++...+-=.+.+|.++|+.||..|++.
T Consensus         6 ~v~~~yL~~~G~~~~D~rv~RLvSLaaQKFisdI~~dA~q~~k~   49 (51)
T PF03540_consen    6 EVTDYYLERSGFQTSDPRVKRLVSLAAQKFISDIANDAMQYCKI   49 (51)
T ss_pred             HHHHHHHHHCCCCCCCHhHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            36778999999999999999999999999999999999999874

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

>PF13654 AAA_32: AAA domain; PDB: 3K1J_B

Probab=95.02  E-value=0.11  Score=49.38  Aligned_cols=64  Identities=20%  Similarity=0.463  Sum_probs=53.8

Q ss_pred             HHHHHHHHHhcCCcccChHHHHHHHHHHHH-----------HHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhc
Q psy8542          65 AQVIVNMFQEAGIKNYDPRCVQQMLEFVNN-----------YTTTILEDSRVYANHAKKKTVDVEDIKLAITNQL  128 (182)
Q Consensus        65 aqlI~rIlk~~Gv~r~sp~v~~qLle~~~r-----------y~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~  128 (182)
                      ++.|..+.++.|...++..++..|++++-|           ...+++.+|-.+|...|++.|+.+||+.||+.|.
T Consensus       433 ~~~i~~~~~~~~L~~~~~~Av~~li~~~~R~~q~kLsl~~~~l~~ll~EA~~~A~~~~~~~I~~~~V~~Ai~~r~  507 (509)
T PF13654_consen  433 ARFIASICQKEGLPPFDRSAVARLIEYSARLDQDKLSLRFSWLADLLREANYWARKEGAKVITAEHVEQAIEERR  507 (509)
T ss_dssp             HHHHHHHHHHHSS--BBHHHHHHHHHHHHHCC-SEEE--HHHHHHHHHHHHHHHHHCT-SSB-HHHHHHHHHH--
T ss_pred             HHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHhCCEeCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHccc
Confidence            457888889999999999999999999988           5789999999999999999999999999999874

>KOG0869|consensus

Probab=94.98  E-value=0.12  Score=42.48  Aligned_cols=76  Identities=12%  Similarity=0.135  Sum_probs=58.6

Q ss_pred             HHHHHHhc--CCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhcCCCCCCCCChhhhhcc
Q psy8542          68 IVNMFQEA--GIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQLSGSFAKPPPRESKGSG  144 (182)
Q Consensus        68 I~rIlk~~--Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~~~~F~~pppke~Ll~l  144 (182)
                      |.||+|+.  .---++.++.+.+-|-+-.|++=|..+|..-+..-+||||+.|||.+|+...+ +.-..-|-|-||..+
T Consensus        38 V~RIMK~~lP~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~tLG-Fe~Y~eplkiyL~kY  115 (168)
T KOG0869|consen   38 VSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMSTLG-FENYAEPLKIYLQKY  115 (168)
T ss_pred             HHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHHHcC-cHhHHHHHHHHHHHH
Confidence            45555542  11238899999999999999999999999999999999999999999996544 333334566677665

>PTZ00017 histone H2A; Provisional

Probab=94.59  E-value=0.081  Score=42.31  Aligned_cols=60  Identities=22%  Similarity=0.222  Sum_probs=54.6

Q ss_pred             HHHHHHHhc-CCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHH
Q psy8542          67 VIVNMFQEA-GIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITN  126 (182)
Q Consensus        67 lI~rIlk~~-Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~  126 (182)
                      -|+++|++. -..|++..++.-|-..+|..+.|||+-|...|...+++.|+..+|.+||..
T Consensus        32 Ri~R~Lk~g~~a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lAI~n   92 (134)
T PTZ00017         32 RVHRYLKKGRYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIRN   92 (134)
T ss_pred             HHHHHHhccchhccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhhccC
Confidence            578888764 567999999999999999999999999999999999999999999999973

>KOG1745|consensus

Probab=93.80  E-value=0.034  Score=44.61  Aligned_cols=64  Identities=22%  Similarity=0.308  Sum_probs=53.4

Q ss_pred             HHHHHHHHhc-CCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhcC
Q psy8542          66 QVIVNMFQEA-GIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQLS  129 (182)
Q Consensus        66 qlI~rIlk~~-Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~~  129 (182)
                      ++++.|..+. -.=++...++..|-|.++.|..++.+|+...|-||+|-||.-.||.||.+.++.
T Consensus        71 Rlvrei~q~f~~dLrfqs~Ai~ALQeA~EayLv~LfEdtnlcAihAkRVTimpkdiQlArrirg~  135 (137)
T KOG1745|consen   71 RLVREIAQDFKTDLRFQSSAIAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE  135 (137)
T ss_pred             HHhHHHHhcccccceehHHHHHHHHHHHHHHHHHhccccchhhhccceeEecccceehhhhcccC
Confidence            4555444432 223688999999999999999999999999999999999999999999987764

>PLN00157 histone H2A; Provisional

Probab=93.16  E-value=0.2  Score=39.95  Aligned_cols=60  Identities=17%  Similarity=0.163  Sum_probs=54.4

Q ss_pred             HHHHHHHhc-CCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHH
Q psy8542          67 VIVNMFQEA-GIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITN  126 (182)
Q Consensus        67 lI~rIlk~~-Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~  126 (182)
                      -|++.|++. -..|++..++.-|-..+|.-+.|||+-|...|...+++.|+...|.+||..
T Consensus        31 Ri~R~Lk~g~~a~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~n   91 (132)
T PLN00157         31 RIARYLKAGKYATRVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKSRIVPRHIQLAVRN   91 (132)
T ss_pred             HHHHHHhcCchhhhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHhhcccC
Confidence            578888773 467899999999999999999999999999999999999999999999974

>cd07978 TAF13 The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex

Probab=93.03  E-value=0.86  Score=33.98  Aligned_cols=57  Identities=23%  Similarity=0.355  Sum_probs=48.1

Q ss_pred             HHHHHHhcC-CcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHH
Q psy8542          68 IVNMFQEAG-IKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAIT  125 (182)
Q Consensus        68 I~rIlk~~G-v~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~  125 (182)
                      |..|+-..| +....++.+..+=|....|..+++..|...|. .++..|+.||+..+|+
T Consensus         8 i~~mmy~~GD~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~-~r~~k~~~eD~~FliR   65 (92)
T cd07978           8 IRQMMYGFGDVQNPLPETVDLLEDIVVEYIIELCHKAAEVAQ-RRRGKVKVEDLIFLLR   65 (92)
T ss_pred             HHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCCCCHHHHHHHHh
Confidence            445555444 45788899999999999999999999999998 7777889999999996

The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Several hy

>KOG0870|consensus

Probab=92.90  E-value=0.49  Score=39.24  Aligned_cols=62  Identities=16%  Similarity=0.202  Sum_probs=52.6

Q ss_pred             ccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhcCCCCCCCCChhhh
Q psy8542          79 NYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQLSGSFAKPPPRESK  141 (182)
Q Consensus        79 r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~~~~F~~pppke~L  141 (182)
                      .++-++...+-.-|-=|+.-+..-|..+|...+|||++++||.-|+.-...-.|.+| -|+-|
T Consensus        30 sisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL~Eiefs~f~~p-lk~~L   91 (172)
T KOG0870|consen   30 SISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALDEIEFSSFVNP-LKSAL   91 (172)
T ss_pred             cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHHHhchHHHhhH-HHHHH
Confidence            477888888888888899999999999999999999999999999998887778755 34444

>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]

Probab=92.90  E-value=0.58  Score=42.88  Aligned_cols=75  Identities=13%  Similarity=0.274  Sum_probs=63.5

Q ss_pred             HHHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHh---cCCCCCCCCChhh
Q psy8542          66 QVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQ---LSGSFAKPPPRES  140 (182)
Q Consensus        66 qlI~rIlk~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r---~~~~F~~pppke~  140 (182)
                      ..++-...+.|+....+++...|.--++--+.+|.++|..+-.|.+|..++.+||-.|+.++   .-|.|.+.-|-+|
T Consensus         9 et~KdvAeslGi~Ni~Dd~l~alamDlEYRI~ev~qea~KFmvhSKRtvLt~dDis~ALr~lNVePLyGyd~~r~l~f   86 (450)
T COG5095           9 ETLKDVAESLGISNIDDDALRALAMDLEYRIKEVCQEASKFMVHSKRTVLTIDDISYALRSLNVEPLYGYDPSRPLQF   86 (450)
T ss_pred             HHHHHHHHHcCCcccccHHHHHHHHhHHHHHHHHHHHHHHHhhcccceeeeHHhHHHHHHhcCCCcccCCCCCcchhH
Confidence            34666778899999999999999888888899999999999999999999999999999986   3467776544444

>PLN00156 histone H2AX; Provisional

Probab=92.51  E-value=0.36  Score=38.91  Aligned_cols=60  Identities=17%  Similarity=0.178  Sum_probs=54.3

Q ss_pred             HHHHHHHhc-CCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHH
Q psy8542          67 VIVNMFQEA-GIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITN  126 (182)
Q Consensus        67 lI~rIlk~~-Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~  126 (182)
                      -|+|.|++. -..|++..++.-|-..+|.-+.|||+-|...|...+++.|+...|.+||..
T Consensus        34 Ri~R~Lk~g~ya~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~RItPrHi~lAIrn   94 (139)
T PLN00156         34 RIARFLKAGKYAERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRN   94 (139)
T ss_pred             HHHHHHhcCChhhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHhhccC
Confidence            578888774 467999999999999999999999999999999999999999999999974

>KOG1756|consensus

Probab=92.29  E-value=0.42  Score=38.09  Aligned_cols=59  Identities=19%  Similarity=0.188  Sum_probs=55.4

Q ss_pred             HHHHHHHh-cCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHH
Q psy8542          67 VIVNMFQE-AGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAIT  125 (182)
Q Consensus        67 lI~rIlk~-~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~  125 (182)
                      -|+++|++ ..+.|++..++..|-..++.-+.+|++-|-..|...+++.|+-.-|++||.
T Consensus        32 ri~r~Lr~~~~~~ri~~gapV~laavLeYL~Aeile~agnaardnkk~ri~PrH~~lAI~   91 (131)
T KOG1756|consen   32 RIHRLLRKGRYAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRITPRHLQLAIR   91 (131)
T ss_pred             HHHHHHHccchhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccccChHHHHHHHh
Confidence            57888887 688899999999999999999999999999999999999999999999997

>PLN00153 histone H2A; Provisional

Probab=92.02  E-value=0.39  Score=38.20  Aligned_cols=60  Identities=20%  Similarity=0.192  Sum_probs=54.0

Q ss_pred             HHHHHHHh-cCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHH
Q psy8542          67 VIVNMFQE-AGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITN  126 (182)
Q Consensus        67 lI~rIlk~-~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~  126 (182)
                      -|++.|++ .-..|++..++.-|-..++.-+.|||+-|...|...+++.|+...|.+||..
T Consensus        29 Ri~R~Lr~g~~a~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~n   89 (129)
T PLN00153         29 RIARYLKKGKYAERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIVPRHIQLAIRN   89 (129)
T ss_pred             HHHHHHhcCchhhccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHhhccC
Confidence            57788876 4567899999999999999999999999999999999999999999999974

>PTZ00252 histone H2A; Provisional

Probab=91.34  E-value=0.64  Score=37.24  Aligned_cols=60  Identities=17%  Similarity=0.192  Sum_probs=52.0

Q ss_pred             HHHHHHHhcC-CcccChHHHHHHHHHHHHHHHHHHHHHHHHhhh--cCCCCCCHHHHHHHHHH
Q psy8542          67 VIVNMFQEAG-IKNYDPRCVQQMLEFVNNYTTTILEDSRVYANH--AKKKTVDVEDIKLAITN  126 (182)
Q Consensus        67 lI~rIlk~~G-v~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~H--AgRktI~~eDVrLAI~~  126 (182)
                      -|++.|++.. ..|++..++.-|-.++|.-+.|||+-|...|..  .+++.|+-..|.|||..
T Consensus        30 Ri~R~Lr~g~ya~RIga~ApVYLAAVLEYLtaEVLELAgnaa~d~~~kk~RItPrHi~lAIrN   92 (134)
T PTZ00252         30 RVGSLLRRGQYARRIGASGAVYMAAVLEYLTAELLELSVKAAAQQAKKPKRLTPRTVTLAVRH   92 (134)
T ss_pred             HHHHHHHcCCcccccCCccHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccccHHHHHhhccC
Confidence            5778888765 679999999999999999999999999998864  45679999999999974

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

Probab=91.25  E-value=0.35  Score=32.72  Aligned_cols=44  Identities=18%  Similarity=0.329  Sum_probs=40.7

Q ss_pred             HHHHHHHHHcCCCccChHHHHHHHHHHHhhhcccccccHhhhhh
Q psy8542          18 QVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANH   61 (182)
Q Consensus        18 ~~i~~il~~~gi~~yep~v~~qll~f~yryt~~vL~DA~vys~h   61 (182)
                      .++.-+|+..|++.=+|||...+==.+.+|.++|+.||..|+..
T Consensus         6 ~v~~~yL~~~G~~~~D~rv~RLvSLaaQKFisdI~~dA~q~~k~   49 (51)
T PF03540_consen    6 EVTDYYLERSGFQTSDPRVKRLVSLAAQKFISDIANDAMQYCKI   49 (51)
T ss_pred             HHHHHHHHHCCCCCCCHhHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            47888999999999999999999999999999999999999753

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

>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C

Probab=91.23  E-value=0.28  Score=35.48  Aligned_cols=46  Identities=17%  Similarity=0.357  Sum_probs=36.3

Q ss_pred             HHHHHHHcCCC---ccChHHHHHHHHHHHhhhcccccccHhhhhhhhhH
Q psy8542          20 IVNMFQEAGIK---NYDPRCVQQMLEFVNNYTTTILEDSRVYANHARDA   65 (182)
Q Consensus        20 i~~il~~~gi~---~yep~v~~qll~f~yryt~~vL~DA~vys~harda   65 (182)
                      +..|..+.+..   ++.|.+|..|.|+.|+|...+=.|-..|+.||+..
T Consensus        11 v~ki~ee~~~~~~~~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~   59 (76)
T PF15630_consen   11 VGKIVEEEAKEKGVEVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRS   59 (76)
T ss_dssp             HHHHHHHCCCCTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-S
T ss_pred             HHHHHHHHHhccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Confidence            34455555433   49999999999999999999999999999999843

>smart00427 H2B Histone H2B

Probab=91.17  E-value=2  Score=32.15  Aligned_cols=49  Identities=24%  Similarity=0.307  Sum_probs=43.4

Q ss_pred             cChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhc
Q psy8542          80 YDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQL  128 (182)
Q Consensus        80 ~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~  128 (182)
                      ++.++..-+.-|.......|+.+|..++.+.+|+||+..+|+.|++-.+
T Consensus        20 iS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvrl~L   68 (89)
T smart00427       20 ISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLIL   68 (89)
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHHc
Confidence            5667777788888889999999999999999999999999999997655

>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]

Probab=90.97  E-value=0.62  Score=36.83  Aligned_cols=61  Identities=16%  Similarity=0.128  Sum_probs=56.4

Q ss_pred             HHHHHHHHH-hcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHH
Q psy8542          65 AQVIVNMFQ-EAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAIT  125 (182)
Q Consensus        65 aqlI~rIlk-~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~  125 (182)
                      +--|+++|+ ..+..|++..+..-+-..++..+.||++-|...|...+++.|.---+.+||.
T Consensus        29 vgrvkr~lk~~~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlAIr   90 (132)
T COG5262          29 VGRVKRLLKKGNYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAIR   90 (132)
T ss_pred             HHHHHHHHHcCccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHHhc
Confidence            346889998 6788899999999999999999999999999999999999999999999996

>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]

Probab=90.43  E-value=0.58  Score=40.67  Aligned_cols=92  Identities=12%  Similarity=0.173  Sum_probs=71.9

Q ss_pred             HHHHHhhhccccccc-HhhhhhhhhHHHHHHHHH-hcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHH
Q psy8542          41 LEFVNNYTTTILEDS-RVYANHARDAQVIVNMFQ-EAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVE  118 (182)
Q Consensus        41 l~f~yryt~~vL~DA-~vys~hardaqlI~rIlk-~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~e  118 (182)
                      .+||+.-...+-.+. ..+..|----.-|++++| +-||+-++.+++..+...++.|+.++.-.|-..|+..+|.|+...
T Consensus        87 ~ryWq~ti~~~e~~~q~~~k~h~LPlARIkkvMKtdedVkMisaEaPvlFak~~EiFI~ELTmRAW~~ae~NkRRtLQks  166 (286)
T COG5208          87 SRYWQQTIKAAEEERQILLKDHNLPLARIKKVMKTDEDVKMISAEAPVLFAKITEIFIEELTMRAWINAEENKRRTLQKS  166 (286)
T ss_pred             HHHHHHHHHHHHHhHHHHHHhccCcHHHHHHHHhcccchhheecccchHHHHHHHHHHHHHHHHHHHHHhHhhhhHHHHH
Confidence            345544433333333 445555433445777777 789999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhcCCCC
Q psy8542         119 DIKLAITNQLSGSF  132 (182)
Q Consensus       119 DVrLAI~~r~~~~F  132 (182)
                      ||-.|+++--.|.|
T Consensus       167 Dia~Av~kSeMfDF  180 (286)
T COG5208         167 DIAAAVKKSEMFDF  180 (286)
T ss_pred             HHHHHHHHHHHHhH
Confidence            99999998776655

>PLN00158 histone H2B; Provisional

Probab=89.51  E-value=1.8  Score=33.87  Aligned_cols=58  Identities=26%  Similarity=0.385  Sum_probs=48.2

Q ss_pred             HHHHHHh----cCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhc
Q psy8542          68 IVNMFQE----AGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQL  128 (182)
Q Consensus        68 I~rIlk~----~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~  128 (182)
                      |.++|+.    .|+   +..+..-+.-|.......|+.+|..++.+.+|+||+..+|+.|+.-.+
T Consensus        33 I~kVLKQVhPd~gI---S~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvrLvL   94 (116)
T PLN00158         33 IYKVLKQVHPDTGI---SSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRLIL   94 (116)
T ss_pred             HHHHHHHhCCCCCc---cHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHhc
Confidence            4455553    554   677777788899999999999999999999999999999999997654

>TIGR00764 lon_rel lon-related putative ATP-dependent protease

Probab=89.18  E-value=2  Score=41.65  Aligned_cols=62  Identities=13%  Similarity=0.137  Sum_probs=50.8

Q ss_pred             HHHHHHHHhc-CCcccChHHHHHHHHHHH-------------HHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHh
Q psy8542          66 QVIVNMFQEA-GIKNYDPRCVQQMLEFVN-------------NYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQ  127 (182)
Q Consensus        66 qlI~rIlk~~-Gv~r~sp~v~~qLle~~~-------------ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r  127 (182)
                      +.+.+.+++. ....++++++..|.+++.             |-..++++.|..+|...|+..|+.+||+.|++.+
T Consensus       316 ~~i~~~~~r~G~l~~~s~~Av~~Li~~~~R~ag~r~~lsl~~R~L~~llR~A~~iA~~~~~~~I~~ehV~~Ai~~~  391 (608)
T TIGR00764       316 QFVAQEVKKDGRIPHFTRDAVEEIVREAQRRAGRKDHLTLRLRELGGLVRAAGDIAKSSGKVYVTAEHVLKAKKLA  391 (608)
T ss_pred             HHHHHHHHHhCCCCcCCHHHHHHHHHHHHHHHhcccccCCCHHHHHHHHHHHHHHHHhcCCceecHHHHHHHHHHH
Confidence            4555555556 477899999999998776             5677899999888988899999999999999865

Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.

>PTZ00463 histone H2B; Provisional

Probab=89.07  E-value=1.9  Score=33.80  Aligned_cols=58  Identities=19%  Similarity=0.344  Sum_probs=48.5

Q ss_pred             HHHHHH----hcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhc
Q psy8542          68 IVNMFQ----EAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQL  128 (182)
Q Consensus        68 I~rIlk----~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~  128 (182)
                      |.++|+    +.|+   |..+..-+.-|.......|+.+|..++.+.+|.||+..+|+.|+.-.+
T Consensus        34 I~KVLKqVhPd~gI---S~kaM~ImnSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvrLlL   95 (117)
T PTZ00463         34 IFKVLKQVHPDTGI---SRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIRLVL   95 (117)
T ss_pred             HHHHHHhhCCCCCc---cHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHhhcc
Confidence            445554    3554   777888888899999999999999999999999999999999997655

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=88.99  E-value=2.7  Score=37.19  Aligned_cols=66  Identities=15%  Similarity=0.296  Sum_probs=50.8

Q ss_pred             hhhHHHHHHHHHh---cCC--cccChHHHHHHHHHH------HHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHh
Q psy8542          62 ARDAQVIVNMFQE---AGI--KNYDPRCVQQMLEFV------NNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQ  127 (182)
Q Consensus        62 ardaqlI~rIlk~---~Gv--~r~sp~v~~qLle~~------~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r  127 (182)
                      |.+..-+..|++.   .|.  ..+++++...+.+.+      .|++-+++..|..+|...|+.+|+.+||+.|++..
T Consensus       206 py~~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~~~  282 (394)
T PRK00411        206 PYTADEIFDILKDRVEEGFYPGVVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYEKS  282 (394)
T ss_pred             CCCHHHHHHHHHHHHHhhcccCCCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHH
Confidence            4455545555442   232  358899999998888      67778889999999999999999999999999864

>cd08048 TAF11 TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex

Probab=86.47  E-value=6.8  Score=28.79  Aligned_cols=61  Identities=11%  Similarity=0.149  Sum_probs=52.0

Q ss_pred             HHHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCC---CCCCHHHHHHHHHH
Q psy8542          66 QVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKK---KTVDVEDIKLAITN  126 (182)
Q Consensus        66 qlI~rIlk~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgR---ktI~~eDVrLAI~~  126 (182)
                      ..+++|+...--..+++.++.-+--+++-|++++.+.|...-+.-|.   ..|.-+.|+.|...
T Consensus        20 ~~iKr~~~~~~~~~v~~~v~i~v~glaKvFVGeivE~A~~V~~~~~~~~~~Pl~P~HireA~rr   83 (85)
T cd08048          20 AAIKRLIQSVTGQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGEANTGPLQPRHLREAYRR   83 (85)
T ss_pred             HHHHHHHHHHcCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCCcHHHHHHHHH
Confidence            45777777654489999999999999999999999999999887665   78999999998754

The TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypothes

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

Probab=85.61  E-value=4.6  Score=33.81  Aligned_cols=62  Identities=15%  Similarity=0.176  Sum_probs=51.6

Q ss_pred             hHHHHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCC------CCCCHHHHHHHHH
Q psy8542          64 DAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKK------KTVDVEDIKLAIT  125 (182)
Q Consensus        64 daqlI~rIlk~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgR------ktI~~eDVrLAI~  125 (182)
                      =.+-|.+|++..|++.++++++..|...++.|...++.+....|+|.-.      ..+-..||+--+.
T Consensus        50 l~~~~~~i~~~~g~~~~~~d~~~lis~a~e~rlr~li~k~~~~s~hR~~~~~~~~r~~~~sdvr~qL~  117 (212)
T cd08045          50 LAKKIRKIAKKHGLKEVDEDVLDLISLALEERLRNLLEKLIEVSEHRVDSEKEDERYEITSDVRKQLR  117 (212)
T ss_pred             HHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCceeecchHHHHHH
Confidence            3457899999999999999999999999999999999999999999732      2344566665554

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

>smart00803 TAF TATA box binding protein associated factor

Probab=84.59  E-value=1.4  Score=30.79  Aligned_cols=47  Identities=17%  Similarity=0.299  Sum_probs=40.0

Q ss_pred             HHHHHHHHcCCCccChHHHHHHHHHHHhhhcccccccHhhhhhhhhH
Q psy8542          19 VIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHARDA   65 (182)
Q Consensus        19 ~i~~il~~~gi~~yep~v~~qll~f~yryt~~vL~DA~vys~harda   65 (182)
                      .|..|.++.||+.-.+.+...|-+..=-|-.+|++||..|..|++..
T Consensus         7 ~i~ria~~~Gi~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRk   53 (65)
T smart00803        7 TIKDVAESLGIGNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRT   53 (65)
T ss_pred             HHHHHHHHCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC
Confidence            47889999999999999988887765555688999999999999853

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

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

Probab=83.52  E-value=0.85  Score=32.19  Aligned_cols=48  Identities=10%  Similarity=0.332  Sum_probs=37.0

Q ss_pred             HHHHHHHHHcCCCccChHHHHHHH-HHHHhhhcccccccHhhhhhhhhHH
Q psy8542          18 QVIVNMFQEAGIKNYDPRCVQQML-EFVNNYTTTILEDSRVYANHARDAQ   66 (182)
Q Consensus        18 ~~i~~il~~~gi~~yep~v~~qll-~f~yryt~~vL~DA~vys~hardaq   66 (182)
                      ..|..+-.|+||+.-.+.+...|- |..||- .+|++||..|..|.++.+
T Consensus         7 esvk~iAes~Gi~~l~de~a~~La~dveyrl-reiiq~a~kfm~hskR~~   55 (66)
T PF02969_consen    7 ESVKDIAESLGISNLSDEAAKALAEDVEYRL-REIIQEALKFMRHSKRTK   55 (66)
T ss_dssp             HHHHHHHHHTT---B-HHHHHHHHHHHHHHH-HHHHHHHHHHHHHTT-SS
T ss_pred             HHHHHHHHHcCCCCCCHHHHHHHHHHHHHHH-HHHHHHHHHHHHHhCCCC
Confidence            468889999999999999988874 678887 899999999999998654

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

>KOG1744|consensus

Probab=83.49  E-value=4.4  Score=32.22  Aligned_cols=49  Identities=22%  Similarity=0.309  Sum_probs=41.4

Q ss_pred             cChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhc
Q psy8542          80 YDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQL  128 (182)
Q Consensus        80 ~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~  128 (182)
                      ++..+..-+.-|.+.....|+.+|-.+|.+.||.||+-.+|+.|+.-.+
T Consensus        56 is~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~rLll  104 (127)
T KOG1744|consen   56 ISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVRLLL  104 (127)
T ss_pred             cCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHHHhC
Confidence            5566666677777888888999999999999999999999999997544

>PRK13406 bchD magnesium chelatase subunit D; Provisional

Probab=82.92  E-value=4.5  Score=39.18  Aligned_cols=95  Identities=17%  Similarity=0.105  Sum_probs=60.6

Q ss_pred             ccChHHHHHHHH-HHHhhhcccccccHhhhhhhhhHHHHHHHHHhcCCcccChHHHHHHHHHHHHHH-------HHHHHH
Q psy8542          31 NYDPRCVQQMLE-FVNNYTTTILEDSRVYANHARDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYT-------TTILED  102 (182)
Q Consensus        31 ~yep~v~~qll~-f~yryt~~vL~DA~vys~hardaqlI~rIlk~~Gv~r~sp~v~~qLle~~~ry~-------~~Vl~d  102 (182)
                      +|+.+...+||| |.....-.-+.+...-. -..+..-|....+..+--.+++.++..+++.+.++.       .-+++-
T Consensus       147 ~~~~~L~~~lLDRf~l~v~v~~~~~~~~~~-~~~~~~~I~~AR~rl~~v~v~~~~l~~i~~~~~~~gv~S~Ra~i~llra  225 (584)
T PRK13406        147 EEDERAPAALADRLAFHLDLDGLALRDARE-IPIDADDIAAARARLPAVGPPPEAIAALCAAAAALGIASLRAPLLALRA  225 (584)
T ss_pred             hcccCCCHHhHhheEEEEEcCCCChHHhcc-cCCCHHHHHHHHHHHccCCCCHHHHHHHHHHHHHhCCCCcCHHHHHHHH
Confidence            677778888887 33333332222221111 111112222222233445688888888888777765       478899


Q ss_pred             HHHHhhhcCCCCCCHHHHHHHHHH
Q psy8542         103 SRVYANHAKKKTVDVEDIKLAITN  126 (182)
Q Consensus       103 A~~yA~HAgRktI~~eDVrLAI~~  126 (182)
                      |..+|.-.||..|+.+||+.|+.-
T Consensus       226 ARa~AaL~Gr~~V~~~dv~~Aa~l  249 (584)
T PRK13406        226 ARAAAALAGRTAVEEEDLALAARL  249 (584)
T ss_pred             HHHHHHHcCCCCCCHHHHHHHHHH
Confidence            999999999999999999999884

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

Probab=82.73  E-value=3.6  Score=30.37  Aligned_cols=65  Identities=17%  Similarity=0.364  Sum_probs=53.1

Q ss_pred             CCchHHHHHHHHHHcCCCccChHHHHHHHHHHHhhhcccccccHhhhhhhh----hHHHHHHHHHhcCCcc
Q psy8542          13 LPRDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAR----DAQVIVNMFQEAGIKN   79 (182)
Q Consensus        13 ~prda~~i~~il~~~gi~~yep~v~~qll~f~yryt~~vL~DA~vys~har----daqlI~rIlk~~Gv~r   79 (182)
                      +|+-  .|.-|.+.-|+.--...+-.-+.+..=-|-.+|+.|+..|++|++    ++.-|...++..|-+-
T Consensus        14 i~k~--~I~RLarr~GvkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr~g~~~   82 (85)
T cd00076          14 ITKP--AIRRLARRGGVKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTL   82 (85)
T ss_pred             CCHH--HHHHHHHHcCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHCCCCc
Confidence            4543  588899999999888888888888777888999999999999998    4467788888888543

>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily

Probab=80.16  E-value=8.9  Score=31.80  Aligned_cols=60  Identities=13%  Similarity=0.218  Sum_probs=46.5

Q ss_pred             HHHHHHHhcCC---cccChHHHHHHHHHHHH---HHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHH
Q psy8542          67 VIVNMFQEAGI---KNYDPRCVQQMLEFVNN---YTTTILEDSRVYANHAKKKTVDVEDIKLAITN  126 (182)
Q Consensus        67 lI~rIlk~~Gv---~r~sp~v~~qLle~~~r---y~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~  126 (182)
                      .+...++..|.   ..+++++...+.+.+.-   ++..++..+...|--.|.++|+.++|+.++..
T Consensus       200 ~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~p~~i~~l~~~~~~~a~~~~~~~i~~~~v~~~~~~  265 (269)
T TIGR03015       200 YIEHRLERAGNRDAPVFSEGAFDAIHRFSRGIPRLINILCDRLLLSAFLEEKREIGGEEVREVIAE  265 (269)
T ss_pred             HHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCcccHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence            44455556664   35889999988888774   67777888877777778899999999999975

Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.

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

Probab=80.03  E-value=3  Score=35.95  Aligned_cols=60  Identities=13%  Similarity=0.230  Sum_probs=33.6

Q ss_pred             HHHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCC------CCCHHHHHHHHH
Q psy8542          66 QVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKK------TVDVEDIKLAIT  125 (182)
Q Consensus        66 qlI~rIlk~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRk------tI~~eDVrLAI~  125 (182)
                      +-|.+|.+..|...++++++..|--.++.|..+|+++++.+|.|.-..      .....||+..+.
T Consensus        51 ~~i~~i~~~~g~~~~~~d~l~llS~A~e~rLr~lie~~~~~s~hR~~~~~~~~~~~~~sdv~~qlr  116 (264)
T PF05236_consen   51 KRIQKIAKKHGLKSVDEDVLELLSLATEERLRNLIEKAIVLSRHRRDSSKSDPRYEIRSDVRKQLR  116 (264)
T ss_dssp             HHHHHHHHCTT--EE-TCHHHHHHHHHHHHHHHHHHHHH---------------------------
T ss_pred             HHHHHHHHHcCCcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccCCCcccccchHHHHHHH
Confidence            457788889999999999999999999999999999999999986432      223556665554

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	182
1taf_A	68	Drosophila Tbp Associated Factors Dtafii42DTAFII62		3e-16
1ku5_A	70	Crystal Structure Of Recombinant Histone Hpha From		2e-04

>pdb|1TAF|A Chain A, Drosophila Tbp Associated Factors Dtafii42DTAFII62 HETEROTETRAMER Length = 68

Iteration: 1
 Score = 81.3 bits (199), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 32/61 (52%), Positives = 51/61 (83%)
Query: 63  RDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKL 122
           +DAQVI+++ +E  ++ Y+PR V Q+LEF   Y T+IL+D++VYANHA+KKT+D++D++L
Sbjct: 2   KDAQVIMSILKELNVQEYEPRVVNQLLEFTFRYVTSILDDAKVYANHARKKTIDLDDVRL 61
Query: 123 A 123
           A
Sbjct: 62  A 62

>pdb|1KU5|A Chain A, Crystal Structure Of Recombinant Histone Hpha From Hyperthermophilic Archaeon Pyrococcus Horikoshii Ot3 Length = 70

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 19/57 (33%), Positives = 33/57 (57%)
Query: 70  NMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITN 126
            + ++AG +    +  + + E++  Y   I + +  +A HA +KTV VEDIKLAI +
Sbjct: 14  RLIRKAGAERVSEQAAKVLAEYLEEYAIEIAKKAVEFARHAGRKTVKVEDIKLAIKS 70

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	182
1taf_A	68	TFIID TBP associated factor 42; transcription init	7e-25
1taf_A	68	TFIID TBP associated factor 42; transcription init	7e-18
1ku5_A	70	HPHA, archaeal histon; histone fold, DNA binding p	1e-06
3b0c_T	111	CENP-T, centromere protein T; histone fold, DNA bi	3e-06
1tzy_D	103	Histone H4-VI; histone-fold, tetramer-dimer-dimer,	3e-06
1id3_B	102	Histone H4; nucleosome core particle, chromatin, p	3e-06
1b67_A	68	Protein (histone HMFA); DNA binding protein; 1.48A	9e-06
3v9r_A	90	MHF1, uncharacterized protein YOL086W-A; histone f	1e-05
2hue_C	84	Histone H4; mini beta sheet, elongated beta sandwh	1e-05
2yfw_B	103	Histone H4, H4; cell cycle, kinetochore, centromer	1e-05
4dra_A	113	Centromere protein S; DNA binding complex, DNA dam	2e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-04
3nqj_A	82	Histone H3-like centromeric protein A; alpha helix	1e-04
3b0b_B	107	CENP-S, centromere protein S; histone fold, DNA bi	2e-04
3nqu_A	140	Histone H3-like centromeric protein A; alpha helix	3e-04
3vh5_A	140	CENP-S; histone fold, chromosome segregation, DNA	4e-04
2hue_B	77	Histone H3; mini beta sheet, elongated beta sandwh	9e-04

>1taf_A TFIID TBP associated factor 42; transcription initiation, histone fold, complex (TWO transcr factors); 2.00A {Drosophila melanogaster} SCOP: a.22.1.3 Length = 68

 Score = 90.7 bits (225), Expect = 7e-25
 Identities = 33/66 (50%), Positives = 52/66 (78%)

Query: 63  RDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKL 122
           +DAQVI+++ +E  ++ Y+PR V Q+LEF   Y T+IL+D++VYANHA+KKT+D++D++L
Sbjct: 2   KDAQVIMSILKELNVQEYEPRVVNQLLEFTFRYVTSILDDAKVYANHARKKTIDLDDVRL 61

Query: 123 AITNQL 128
           A    L
Sbjct: 62  ATEVTL 67

>1taf_A TFIID TBP associated factor 42; transcription initiation, histone fold, complex (TWO transcr factors); 2.00A {Drosophila melanogaster} SCOP: a.22.1.3 Length = 68

 Score = 73.0 bits (179), Expect = 7e-18
 Identities = 27/57 (47%), Positives = 43/57 (75%)

Query: 14 PRDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHARDAQVIVN 70
          P+DAQVI+++ +E  ++ Y+PR V Q+LEF   Y T+IL+D++VYANHAR   + ++
Sbjct: 1  PKDAQVIMSILKELNVQEYEPRVVNQLLEFTFRYVTSILDDAKVYANHARKKTIDLD 57

>1ku5_A HPHA, archaeal histon; histone fold, DNA binding protein; 2.30A {Pyrococcus horikoshii} SCOP: a.22.1.2 Length = 70

 Score = 43.5 bits (103), Expect = 1e-06
 Identities = 19/59 (32%), Positives = 34/59 (57%)

Query: 68  IVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITN 126
           +  + ++AG +    +  + + E++  Y   I + +  +A HA +KTV VEDIKLAI +
Sbjct: 12  VDRLIRKAGAERVSEQAAKVLAEYLEEYAIEIAKKAVEFARHAGRKTVKVEDIKLAIKS 70

>3b0c_T CENP-T, centromere protein T; histone fold, DNA binding, DNA binding protein; HET: CIT; 2.20A {Gallus gallus} PDB: 3b0d_T* 3vh5_T 3vh6_T Length = 111

 Score = 43.4 bits (102), Expect = 3e-06
 Identities = 14/61 (22%), Positives = 26/61 (42%)

Query: 67  VIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITN 126
           +I  +F             + + +    Y   I  D   Y+ HA +KTV++ D++L +  
Sbjct: 12  LIKQIFSHYVKTPVTRDAYKIVEKCSERYFKQISSDLEAYSQHAGRKTVEMADVELLMRR 71

Query: 127 Q 127
           Q
Sbjct: 72  Q 72

>1tzy_D Histone H4-VI; histone-fold, tetramer-dimer-dimer, DNA binding protein; 1.90A {Gallus gallus} SCOP: a.22.1.1 PDB: 1f66_B 1eqz_D 1hq3_D 1u35_B 2aro_D 2cv5_B* 2f8n_B 3nqu_B 3r45_B 3azg_B 3a6n_B 3an2_B 3av1_B 3av2_B 3ayw_B 3aze_B 3azf_B 3afa_B 3azh_B 3azk_B ... Length = 103

 Score = 43.0 bits (101), Expect = 3e-06
 Identities = 14/61 (22%), Positives = 27/61 (44%)

Query: 67  VIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITN 126
            I  + +  G+K       ++    +  +   ++ D+  Y  HAK+KTV   D+  A+  
Sbjct: 34  AIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKR 93

Query: 127 Q 127
           Q
Sbjct: 94  Q 94

>1id3_B Histone H4; nucleosome core particle, chromatin, protein/DNA interaction, nucleoprotein, supercoiled DNA; 3.10A {Saccharomyces cerevisiae} SCOP: a.22.1.1 Length = 102

 Score = 43.1 bits (101), Expect = 3e-06
 Identities = 15/61 (24%), Positives = 30/61 (49%)

Query: 67  VIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITN 126
            I  + +  G+K       +++   + ++  +++ DS  Y  HAK+KTV   D+  A+  
Sbjct: 33  AIRRLARRGGVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKR 92

Query: 127 Q 127
           Q
Sbjct: 93  Q 93

>1b67_A Protein (histone HMFA); DNA binding protein; 1.48A {Methanothermus fervidus} SCOP: a.22.1.2 PDB: 1hta_A 1a7w_A 1b6w_A 1bfm_A Length = 68

 Score = 40.8 bits (96), Expect = 9e-06
 Identities = 13/41 (31%), Positives = 21/41 (51%), Gaps = 3/41 (7%)

Query: 84  CVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAI 124
            + ++LE        I  ++   A HA +KT+  EDI+LA 
Sbjct: 27  ALAKVLE---EMGEEIASEAVKLAKHAGRKTIKAEDIELAR 64

>3v9r_A MHF1, uncharacterized protein YOL086W-A; histone fold, fanconi anemia, DNA repair, DNA BI protein; 2.40A {Saccharomyces cerevisiae} Length = 90

 Score = 41.5 bits (97), Expect = 1e-05
 Identities = 13/59 (22%), Positives = 23/59 (38%), Gaps = 3/59 (5%)

Query: 67  VIVNMFQEAGIK---NYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKL 122
            +    Q+        Y PR +  +LE        +  D + +A HA +  V+  D+ L
Sbjct: 17  RVEERLQQVLSSEDIKYTPRFINSLLELAYLQLGEMGSDLQAFARHAGRGVVNKSDLML 75

>2hue_C Histone H4; mini beta sheet, elongated beta sandwhich, DNA binding prote; 1.70A {Xenopus laevis} SCOP: a.22.1.1 PDB: 3nqj_B 1aoi_B 3kwq_B* 1hio_D 2yfv_B Length = 84

 Score = 41.3 bits (97), Expect = 1e-05
 Identities = 13/53 (24%), Positives = 24/53 (45%)

Query: 75  AGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQ 127
            G+K       ++    +  +   ++ D+  Y  HAK+KTV   D+  A+  Q
Sbjct: 23  GGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQ 75

>2yfw_B Histone H4, H4; cell cycle, kinetochore, centromere, histone chaperone, BUDD; 2.60A {Kluyveromyces lactis nrrl y-1140} Length = 103

 Score = 41.6 bits (97), Expect = 1e-05
 Identities = 14/60 (23%), Positives = 29/60 (48%)

Query: 68  IVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQ 127
           I  + +  G+K       +++   +  +  +++ D+  Y  HAK+KTV   D+  A+  Q
Sbjct: 35  IRRLARRGGVKRISGLIYEEVRNVLKTFLESVIRDAVTYTEHAKRKTVTSLDVVYALKRQ 94

>4dra_A Centromere protein S; DNA binding complex, DNA damage repair, histone-fold, DNA BI protein; 2.41A {Homo sapiens} PDB: 4drb_A Length = 113

 Score = 40.8 bits (95), Expect = 2e-05
 Identities = 11/56 (19%), Positives = 23/56 (41%)

Query: 68  IVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLA 123
           +           +  + +  + E          +D  ++A HAK+ T++ ED+KL 
Sbjct: 36  LCEEVALDKEMQFSKQTIAAISELTFRQCENFAKDLEMFARHAKRTTINTEDVKLL 91

>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 = 41.0 bits (95), Expect = 1e-04
 Identities = 26/157 (16%), Positives = 52/157 (33%), Gaps = 40/157 (25%)

Query: 15  RDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHARDAQV------- 67
           +D   I+++F++A + N+D + VQ M + +   +   ++   +  +    +         
Sbjct: 19  KD---ILSVFEDAFVDNFDCKDVQDMPKSI--LSKEEIDH--IIMSKDAVSGTLRLFWTL 71

Query: 68  ------IVNMFQEAGI-KNYD-------PRCVQQMLEFV--NNYTTTILEDSRVYANHAK 111
                 +V  F E  +  NY            Q  +           +  D++V+A    
Sbjct: 72  LSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFA---- 127

Query: 112 KKTVDVEDIKLAITNQLSGSFAKPPPRES----KGSG 144
           K  V      L +   L     +P          GSG
Sbjct: 128 KYNVSRLQPYLKLRQALLE--LRPAKNVLIDGVLGSG 162

>3nqj_A Histone H3-like centromeric protein A; alpha helix, histone fold, centromere, DNA binding protein; 2.10A {Homo sapiens} Length = 82

 Score = 38.1 bits (88), Expect = 1e-04
 Identities = 12/56 (21%), Positives = 25/56 (44%)

Query: 68  IVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLA 123
           I   F      N+  + +  + E    +   + ED+ +   HA + T+  +D++LA
Sbjct: 16  ICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRVTLFPKDVQLA 71

>3b0b_B CENP-S, centromere protein S; histone fold, DNA binding, DNA, nucleus, DNA binding protein; 2.15A {Gallus gallus} Length = 107

 Score = 38.5 bits (89), Expect = 2e-04
 Identities = 13/55 (23%), Positives = 22/55 (40%)

Query: 68  IVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKL 122
           +     E     +  + V  + E           D  ++A HAK+ T+  ED+KL
Sbjct: 28  LCQDVAEDKGVLFSKQTVAAISEITFRQCENFARDLEMFARHAKRSTITSEDVKL 82

>3nqu_A Histone H3-like centromeric protein A; alpha helix, histone fold, centromere, DNA binding protein; 2.50A {Homo sapiens} PDB: 3an2_A Length = 140

 Score = 38.0 bits (87), Expect = 3e-04
 Identities = 12/56 (21%), Positives = 25/56 (44%)

Query: 68  IVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLA 123
           I   F      N+  + +  + E    +   + ED+ +   HA + T+  +D++LA
Sbjct: 74  ICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRVTLFPKDVQLA 129

>3vh5_A CENP-S; histone fold, chromosome segregation, DNA binding, nucleus, binding protein; 2.40A {Gallus gallus} PDB: 3vh6_A Length = 140

 Score = 37.8 bits (87), Expect = 4e-04
 Identities = 17/101 (16%), Positives = 33/101 (32%), Gaps = 10/101 (9%)

Query: 68  IVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKL----- 122
           +     E     +  + V  + E           D  ++A HAK+ T+  ED+KL     
Sbjct: 28  LAQDVAEDKGVLFSKQTVAAISEITFRQAENFARDLEMFARHAKRSTITSEDVKLLARRS 87

Query: 123 -----AITNQLSGSFAKPPPRESKGSGQAGAMGSNAHNKAP 158
                 IT +     +    ++ K   ++ A       +  
Sbjct: 88  NSLLKYITQKSDELASSNMEQKEKKKKKSSAAKGRKTEENE 128

>2hue_B Histone H3; mini beta sheet, elongated beta sandwhich, DNA binding prote; 1.70A {Xenopus laevis} Length = 77

 Score = 35.6 bits (82), Expect = 9e-04
 Identities = 14/45 (31%), Positives = 23/45 (51%)

Query: 79  NYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLA 123
            +    V  + E    Y   + ED+ + A HAK+ T+  +DI+LA
Sbjct: 25  RFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLA 69

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	182
1taf_A	68	TFIID TBP associated factor 42; transcription init	99.93
1taf_A	68	TFIID TBP associated factor 42; transcription init	99.8
3b0c_T	111	CENP-T, centromere protein T; histone fold, DNA bi	99.67
1ku5_A	70	HPHA, archaeal histon; histone fold, DNA binding p	99.64
2ly8_A	121	Budding yeast chaperone SCM3; centromere protein,	99.59
2hue_C	84	Histone H4; mini beta sheet, elongated beta sandwh	99.52
1id3_B	102	Histone H4; nucleosome core particle, chromatin, p	99.5
2yfw_B	103	Histone H4, H4; cell cycle, kinetochore, centromer	99.48
1tzy_D	103	Histone H4-VI; histone-fold, tetramer-dimer-dimer,	99.47
3b0b_B	107	CENP-S, centromere protein S; histone fold, DNA bi	99.45
4dra_A	113	Centromere protein S; DNA binding complex, DNA dam	99.4
3v9r_A	90	MHF1, uncharacterized protein YOL086W-A; histone f	99.37
1f1e_A	154	Histone fold protein; archaeal histone protein, DN	99.36
2l5a_A	235	Histone H3-like centromeric protein CSE4, protein	99.31
1taf_B	70	TFIID TBP associated factor 62; transcription init	99.26
3vh5_A	140	CENP-S; histone fold, chromosome segregation, DNA	99.19
1f1e_A	154	Histone fold protein; archaeal histone protein, DN	99.11
1b67_A	68	Protein (histone HMFA); DNA binding protein; 1.48A	99.0
1n1j_A	93	NF-YB; histone-like PAIR, DNA binding protein; 1.6	98.7
2hue_B	77	Histone H3; mini beta sheet, elongated beta sandwh	98.65
3nqj_A	82	Histone H3-like centromeric protein A; alpha helix	98.64
3b0c_W	76	CENP-W, centromere protein W; histone fold, DNA bi	98.54
3nqu_A	140	Histone H3-like centromeric protein A; alpha helix	98.4
1tzy_C	136	Histone H3; histone-fold, tetramer-dimer-dimer, DN	98.37
3r45_A	156	Histone H3-like centromeric protein A; histone fol	98.37
2yfv_A	100	Histone H3-like centromeric protein CSE4; cell cyc	98.35
2nqb_C	123	Histone H2A; nucleosome, NCP, chromatin, structura	98.33
2f8n_G	120	Core histone macro-H2A.1; nucleosome, NCP, macroh2	98.32
2byk_B	128	Chrac-14; nucleosome sliding, histone fold, DNA-bi	98.3
1tzy_A	129	Histone H2A-IV; histone-fold, tetramer-dimer-dimer	98.29
1n1j_B	97	NF-YC; histone-like PAIR, DNA binding protein; 1.6	98.27
2f8n_K	149	Histone H2A type 1; nucleosome, NCP, macroh2A, his	98.24
1jfi_B	179	DR1 protein, transcription regulator NC2 beta chai	98.22
1id3_C	131	Histone H2A.1; nucleosome core particle, chromatin	98.21
4g92_C	119	HAPE; transcription factor, nucleosome, minor groo	98.21
1f66_C	128	Histone H2A.Z; nucleosome, chromatin, histone vari	98.16
1ku5_A	70	HPHA, archaeal histon; histone fold, DNA binding p	98.15
1jfi_A	98	Transcription regulator NC2 alpha chain; histone,	98.05
3b0b_B	107	CENP-S, centromere protein S; histone fold, DNA bi	97.99
2jss_A	192	Chimera of histone H2B.1 and histone H2A.Z; histon	97.98
4dra_A	113	Centromere protein S; DNA binding complex, DNA dam	97.57
3v9r_A	90	MHF1, uncharacterized protein YOL086W-A; histone f	97.49
2nqb_D	123	Histone H2B; nucleosome, NCP, chromatin, structura	97.44
1tzy_B	126	Histone H2B; histone-fold, tetramer-dimer-dimer, D	97.34
3vh5_A	140	CENP-S; histone fold, chromosome segregation, DNA	97.33
3b0c_T	111	CENP-T, centromere protein T; histone fold, DNA bi	97.16
1h3o_B	76	Transcription initiation factor TFIID 20/15 kDa su	97.13
2jss_A	192	Chimera of histone H2B.1 and histone H2A.Z; histon	97.01
2byk_A	140	Chrac-16; nucleosome sliding, histone fold, DNA-bi	97.0
2l5a_A	235	Histone H3-like centromeric protein CSE4, protein	96.71
2hue_C	84	Histone H4; mini beta sheet, elongated beta sandwh	96.15
1id3_B	102	Histone H4; nucleosome core particle, chromatin, p	95.85
2yfw_B	103	Histone H4, H4; cell cycle, kinetochore, centromer	95.81
1tzy_D	103	Histone H4-VI; histone-fold, tetramer-dimer-dimer,	95.69
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	92.2
2ly8_A	121	Budding yeast chaperone SCM3; centromere protein,	90.08
4dra_E	84	Centromere protein X; DNA binding complex, DNA dam	89.02
3bos_A	242	Putative DNA replication factor; P-loop containing	88.68
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	88.04
1taf_B	70	TFIID TBP associated factor 62; transcription init	86.67
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	85.84
3b0b_C	81	CENP-X, centromere protein X; histone fold, DNA bi	85.21
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	84.13
1bh9_B	89	TAFII28; histone fold, tata binding protein, trans	83.19
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	82.08
1h3o_A	75	Transcription initiation factor TFIID 135 kDa subu	81.27
3ksy_A	1049	SOS-1, SON of sevenless homolog 1; RAS, RAS activa	80.67

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

Probab=99.93  E-value=2.8e-26  Score=161.62  Aligned_cols=68  Identities=49%  Similarity=0.884  Sum_probs=66.1

Q ss_pred             hhhHHHHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhcC
Q psy8542          62 ARDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQLS  129 (182)
Q Consensus        62 ardaqlI~rIlk~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~~  129 (182)
                      |+|+++|.+||+++|+++|||+|+.||+||+|||+.+|++||..||+||||+||+++||+|||++|++
T Consensus         1 Prda~~i~~iLk~~G~~~~~~~v~~~L~e~~~ry~~~il~dA~~~a~HAgrktv~~eDVkLAi~~~~~   68 (68)
T 1taf_A            1 PKDAQVIMSILKELNVQEYEPRVVNQLLEFTFRYVTSILDDAKVYANHARKKTIDLDDVRLATEVTLD   68 (68)
T ss_dssp             CHHHHHHHHHHHHTTCCCBCTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHTC-
T ss_pred             CchhHHHHHHHHHCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhccC
Confidence            79999999999999999999999999999999999999999999999999999999999999999864

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

Probab=99.80  E-value=3.7e-20  Score=130.32  Aligned_cols=51  Identities=53%  Similarity=0.983  Sum_probs=49.9

Q ss_pred             CchHHHHHHHHHHcCCCccChHHHHHHHHHHHhhhcccccccHhhhhhhhh
Q psy8542          14 PRDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHARD   64 (182)
Q Consensus        14 prda~~i~~il~~~gi~~yep~v~~qll~f~yryt~~vL~DA~vys~hard   64 (182)
                      |||+++|+.||++|||++|+|+|++|||||+|||+++||+||..||+||+.
T Consensus         1 Prda~~i~~iLk~~G~~~~~~~v~~~L~e~~~ry~~~il~dA~~~a~HAgr   51 (68)
T 1taf_A            1 PKDAQVIMSILKELNVQEYEPRVVNQLLEFTFRYVTSILDDAKVYANHARK   51 (68)
T ss_dssp             CHHHHHHHHHHHHTTCCCBCTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTC
T ss_pred             CchhHHHHHHHHHCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCC
Confidence            999999999999999999999999999999999999999999999999973

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

Probab=99.67  E-value=1.3e-16  Score=121.39  Aligned_cols=89  Identities=21%  Similarity=0.203  Sum_probs=74.8

Q ss_pred             HHHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhcCCCCCCC--------CC
Q psy8542          66 QVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQLSGSFAKP--------PP  137 (182)
Q Consensus        66 qlI~rIlk~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~~~~F~~p--------pp  137 (182)
                      ..|++|+++.|+.++|++++.+|.++++.|+..|++||..||+|||||||+++||++|++....-.|..|        +|
T Consensus        11 a~I~Ri~r~~g~~rIS~~a~~~l~e~l~~f~~~v~~da~~~A~HA~RKTV~~eDV~lalrr~g~~~~~~~l~~l~~~~lp   90 (111)
T 3b0c_T           11 SLIKQIFSHYVKTPVTRDAYKIVEKCSERYFKQISSDLEAYSQHAGRKTVEMADVELLMRRQGLVTDKMPLHVLVERHLP   90 (111)
T ss_dssp             HHHHHHHHHHHCSCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHTTSSBTTBCHHHHHHHHSC
T ss_pred             HHHHHHHHHCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHHCCCccccccHHHHHHHhCc
Confidence            3799999999999999999999999999999999999999999999999999999999999999999999        99


Q ss_pred             hhhhhccccccCCcccccCC
Q psy8542         138 RESKGSGQAGAMGSNAHNKA  157 (182)
Q Consensus       138 ke~Ll~lA~~~~~~~~~N~~  157 (182)
                      +|.+..+-   ......|++
T Consensus        91 ~E~~~~l~---~~a~~~n~~  107 (111)
T 3b0c_T           91 LEYRKLLI---PIAVSGNKV  107 (111)
T ss_dssp             HHHHHHHC---CC-------
T ss_pred             HHHHHHhc---cccccCCcc
Confidence            99555442   111566654

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

Probab=99.64  E-value=3.1e-16  Score=109.64  Aligned_cols=59  Identities=32%  Similarity=0.543  Sum_probs=57.8

Q ss_pred             HHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHH
Q psy8542          67 VIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAIT  125 (182)
Q Consensus        67 lI~rIlk~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~  125 (182)
                      .|.||++++|+.++|++++.+|.|++++|+.+|++||..||+||||+||+.+||++|++
T Consensus        11 ~v~Rl~r~~g~~ris~~a~~~l~e~~~~~~~~v~~dA~~~a~hakRkTI~~~DV~lA~~   69 (70)
T 1ku5_A           11 PVDRLIRKAGAERVSEQAAKVLAEYLEEYAIEIAKKAVEFARHAGRKTVKVEDIKLAIK   69 (70)
T ss_dssp             HHHHHHHHTTCSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHT
T ss_pred             HHHHHHHHcCcceeCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHH
Confidence            79999999999999999999999999999999999999999999999999999999986

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

Probab=99.59  E-value=5.2e-15  Score=114.39  Aligned_cols=107  Identities=21%  Similarity=0.317  Sum_probs=97.2

Q ss_pred             HHHHHHHHHHcC----CCccChHHHHHHHHHHHhhhcccccccHhhhhhhhhHHHHHHHHHhcCCcccChHHHHHHHHHH
Q psy8542          17 AQVIVNMFQEAG----IKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHARDAQVIVNMFQEAGIKNYDPRCVQQMLEFV   92 (182)
Q Consensus        17 a~~i~~il~~~g----i~~yep~v~~qll~f~yryt~~vL~DA~vys~hardaqlI~rIlk~~Gv~r~sp~v~~qLle~~   92 (182)
                      .|++..|..+..    ---|++..+.-|=|-+=-|-.+.++|+...+-|+          ..+||+|+|.+++.++.+.+
T Consensus         8 ~RLVREI~~~~~~~~~~lRfq~~Al~ALQeAsEayLV~lFEd~nlcaiHA----------~~gGvkRIS~~iy~e~r~vl   77 (121)
T 2ly8_A            8 ARLVKEVTDEFTTKDQDLRWQSMAIMALQEASEAYLVGLLEHTNLLALHL----------VPRGSKRISGLIYEEVRAVL   77 (121)
T ss_dssp             HHHHHHHHHHHTTCCSSCCBCHHHHHHHHHHHHHHHHHHHHHHHHHTTTC----------CCCCSSCCSSCHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCCCCccccHHHHHHHHHHHHHHHHHHHHHHhHHHHcC----------CccCccchhHHHHHHHHHHH
Confidence            577888877763    3469999999999999999999999999999999          67899999999999999999


Q ss_pred             HHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHh--cCCCCC
Q psy8542          93 NNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQ--LSGSFA  133 (182)
Q Consensus        93 ~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r--~~~~F~  133 (182)
                      +.|..+|++||+.|++|||||||+++||.+|++.+  .-|.|.
T Consensus        78 ~~~l~~i~rdav~yaehA~RKTVta~DV~~Alkr~G~~lygf~  120 (121)
T 2ly8_A           78 KSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQGRTLYGFG  120 (121)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCCCBCHHHHHHHHHHTTCGGGGCC
T ss_pred             HHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHhCCCcCCCCC
Confidence            99999999999999999999999999999999975  447765

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

Probab=99.52  E-value=1e-14  Score=105.58  Aligned_cols=67  Identities=22%  Similarity=0.362  Sum_probs=62.0

Q ss_pred             HHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHh--cCCCCC
Q psy8542          67 VIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQ--LSGSFA  133 (182)
Q Consensus        67 lI~rIlk~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r--~~~~F~  133 (182)
                      .|++|+++.|++++|++++.+|.+.++.|+.+|++||..|++|||||||+++||.+|++.+  ..|.|.
T Consensus        15 ~I~Riar~~Gv~rIs~da~~~l~~~l~~~~~~I~~dA~~~a~ha~RKTvt~~DV~~Alk~~g~~lYgf~   83 (84)
T 2hue_C           15 AIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFG   83 (84)
T ss_dssp             HHHHHHHHTTCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTTTCEEEESCC
T ss_pred             HHHHHHHHcCchhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHHHHHHcCCCCCCCC
Confidence            5899999999999999999999999999999999999999999999999999999999865  335553

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

Probab=99.50  E-value=4e-14  Score=106.20  Aligned_cols=80  Identities=24%  Similarity=0.342  Sum_probs=66.6

Q ss_pred             cccccccHhhhhhhhhHHHHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhc
Q psy8542          49 TTILEDSRVYANHARDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQL  128 (182)
Q Consensus        49 ~~vL~DA~vys~hardaqlI~rIlk~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~  128 (182)
                      ..+|.|...+  .|..  .|++|+++.|++++|++++.+|.+.++.|+.+|++||..|++||+|+||+++||.+|++.+.
T Consensus        19 ~k~~r~~i~~--ip~~--~I~Rlar~~Gv~rIS~da~~~l~~~le~fi~~I~~dA~~~a~HakRKTVt~~DV~~ALkr~g   94 (102)
T 1id3_B           19 RKILRDNIQG--ITKP--AIRRLARRGGVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQG   94 (102)
T ss_dssp             -----CCGGG--SCHH--HHHHHHHHTTCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHTT
T ss_pred             HHHHHhccCC--CCHH--HHHHHHHHcCchhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHHHHHHcC
Confidence            4566777665  3443  59999999999999999999999999999999999999999999999999999999999763


Q ss_pred             --CCCC
Q psy8542         129 --SGSF  132 (182)
Q Consensus       129 --~~~F  132 (182)
                        .|.|
T Consensus        95 ~~lYGf  100 (102)
T 1id3_B           95 RTLYGF  100 (102)
T ss_dssp             CCEESS
T ss_pred             CCCCCC
Confidence              3555

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

Probab=99.48  E-value=6.9e-14  Score=104.80  Aligned_cols=80  Identities=23%  Similarity=0.352  Sum_probs=61.6

Q ss_pred             ccccccHhhhhhhhhHHHHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhcC
Q psy8542          50 TILEDSRVYANHARDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQLS  129 (182)
Q Consensus        50 ~vL~DA~vys~hardaqlI~rIlk~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~~  129 (182)
                      .+|.|+..+  .|.  ..|++|+++.|++++|++++.+|.++++.|+.+|++||..||+|++|+||+.+||.+|++....
T Consensus        21 ~~~r~~~~g--ip~--~~I~Rlar~~G~~rIs~~a~~~l~~vle~~~~~V~~dA~~~a~hakRktvt~~DV~~Alr~~g~   96 (103)
T 2yfw_B           21 KILRDNIQG--ITK--PAIRRLARRGGVKRISGLIYEEVRNVLKTFLESVIRDAVTYTEHAKRKTVTSLDVVYALKRQGR   96 (103)
T ss_dssp             -----------CCH--HHHHHHHHHTTCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHHC-
T ss_pred             hhhhhhhcc--CCH--HHHHHHHHHcCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHHHHHHcCC
Confidence            455555555  343  3599999999999999999999999999999999999999999999999999999999997643


Q ss_pred             --CCCC
Q psy8542         130 --GSFA  133 (182)
Q Consensus       130 --~~F~  133 (182)
                        |.|.
T Consensus        97 ~lYGf~  102 (103)
T 2yfw_B           97 TLYGFG  102 (103)
T ss_dssp             ------
T ss_pred             CCcCCC
Confidence              6663

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

Probab=99.47  E-value=8.4e-14  Score=104.26  Aligned_cols=81  Identities=21%  Similarity=0.318  Sum_probs=70.3

Q ss_pred             cccccccHhhhhhhhhHHHHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhc
Q psy8542          49 TTILEDSRVYANHARDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQL  128 (182)
Q Consensus        49 ~~vL~DA~vys~hardaqlI~rIlk~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~  128 (182)
                      ..++.|+..+  .|..  .|++|+++.|+++++++++.+|.++++.|+.+|++||..||+|++|+||+.+||.+|++...
T Consensus        20 ~k~~r~~~~g--ip~~--~I~Rlar~~G~~rIs~~a~~~l~~vle~~~~~V~~dA~~~a~hakRktIt~~DV~~Alr~~g   95 (103)
T 1tzy_D           20 RKVLRDNIQG--ITKP--AIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQG   95 (103)
T ss_dssp             -CCCCCGGGG--SCHH--HHHHHHHHTTCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHTT
T ss_pred             ccchhhhccc--CCHH--HHHHHHHHcCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHHcC
Confidence            3566666665  4443  59999999999999999999999999999999999999999999999999999999999764


Q ss_pred             C--CCCC
Q psy8542         129 S--GSFA  133 (182)
Q Consensus       129 ~--~~F~  133 (182)
                      .  |.|.
T Consensus        96 ~~lYGf~  102 (103)
T 1tzy_D           96 RTLYGFG  102 (103)
T ss_dssp             CEEESCC
T ss_pred             CCCcCCC
Confidence            3  6664

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

Probab=99.45  E-value=5e-14  Score=106.82  Aligned_cols=60  Identities=22%  Similarity=0.294  Sum_probs=55.6

Q ss_pred             HHHHHHHhcCC---cccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHH
Q psy8542          67 VIVNMFQEAGI---KNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITN  126 (182)
Q Consensus        67 lI~rIlk~~Gv---~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~  126 (182)
                      .|.+|.++.|.   .+|||+++.+|.|++++|+.+|++|+..||.|||||||+.+||+||++.
T Consensus        24 ~V~rI~~~~g~~~~~~vs~~~i~aL~E~~~~~~~~ia~Da~~fA~HAgRkTI~~eDV~La~Rr   86 (107)
T 3b0b_B           24 TTGCLCQDVAEDKGVLFSKQTVAAISEITFRQCENFARDLEMFARHAKRSTITSEDVKLLARR   86 (107)
T ss_dssp             HHHHHHHHHHHHHTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTT
T ss_pred             HHHHHHHHHhhhcCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcCcCCHHHHHHHHHh
Confidence            47777877777   6899999999999999999999999999999999999999999999964

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

Probab=99.40  E-value=1.6e-13  Score=104.86  Aligned_cols=60  Identities=20%  Similarity=0.403  Sum_probs=57.1

Q ss_pred             HHHHHHHhcCCcc---cChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHH
Q psy8542          67 VIVNMFQEAGIKN---YDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITN  126 (182)
Q Consensus        67 lI~rIlk~~Gv~r---~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~  126 (182)
                      .|.+|+++.|.++   +||+++.+|.|++++|+.++++|+..||+|||||||+.+||+|+++.
T Consensus        32 ~V~rIvke~gaer~~~vS~~ai~aL~El~~~~~~~ia~Dl~~fAkHAgRkTI~~eDV~La~Rr   94 (113)
T 4dra_A           32 TVGCLCEEVALDKEMQFSKQTIAAISELTFRQCENFAKDLEMFARHAKRTTINTEDVKLLARR   94 (113)
T ss_dssp             HHHHHHHHHHHHHTCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHcCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHh
Confidence            5888999988888   99999999999999999999999999999999999999999999964

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

Probab=99.37  E-value=5.1e-13  Score=98.45  Aligned_cols=60  Identities=22%  Similarity=0.403  Sum_probs=53.0

Q ss_pred             HHHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHH
Q psy8542          66 QVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITN  126 (182)
Q Consensus        66 qlI~rIlk~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~  126 (182)
                      +++...+++.|+ .+||+++.+|.|++|+|+.++++|+..||+|||||||+.+||+|+++.
T Consensus        20 ki~~e~~~~~g~-~vs~~~i~aL~e~~~~~~~~ia~Dl~~fA~HAgRkTI~~eDV~L~~Rr   79 (90)
T 3v9r_A           20 ERLQQVLSSEDI-KYTPRFINSLLELAYLQLGEMGSDLQAFARHAGRGVVNKSDLMLYLRK   79 (90)
T ss_dssp             HHHHHHSCSSCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTT
T ss_pred             HHHHHHHHhcCc-eeCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHh
Confidence            445555555676 599999999999999999999999999999999999999999999864

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

Probab=99.36  E-value=4.7e-12  Score=101.36  Aligned_cols=110  Identities=19%  Similarity=0.328  Sum_probs=97.3

Q ss_pred             HHHHHHHHc-CCCccChHHHHHHHHHHHhhhcccccccHhhhhhhh-------hH----------------------HHH
Q psy8542          19 VIVNMFQEA-GIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAR-------DA----------------------QVI   68 (182)
Q Consensus        19 ~i~~il~~~-gi~~yep~v~~qll~f~yryt~~vL~DA~vys~har-------da----------------------qlI   68 (182)
                      .|.-|++.- |..--....-.-|-+..=-|...+..+|..|+.|++       |.                      ..|
T Consensus         9 ~V~Riik~~lg~~rVS~dA~~~l~~~l~~f~~~i~~~A~~~a~ha~RKTv~a~DV~~a~~~lg~~~v~d~~~l~lP~a~V   88 (154)
T 1f1e_A            9 AIERIFRQGIGERRLSQDAKDTIYDFVPTMAEYVANAAKSVLDASGKKTLMEEHLKALADVLMVEGVEDYDGELFGRATV   88 (154)
T ss_dssp             HHHHHHHTTSTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHHHHTCTTSTTCCSCCCCHHHH
T ss_pred             HHHHHHHhcCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHhcccccCCccccccCCccHH
Confidence            456677776 887777777778888888888899999999999976       33                      159


Q ss_pred             HHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhc
Q psy8542          69 VNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQL  128 (182)
Q Consensus        69 ~rIlk~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~  128 (182)
                      .||+++.|+.++|.+++..|.+.++.|+..|+++|..||+|+|||||+.+||.+|++...
T Consensus        89 ~Ri~k~~g~~RVS~~A~~~l~~~le~f~~~I~~~A~~~a~ha~RKTIt~eDV~~Al~~~~  148 (154)
T 1f1e_A           89 RRILKRAGIERASSDAVDLYNKLICRATEELGEKAAEYADEDGRKTVQGEDVEKAITYSM  148 (154)
T ss_dssp             HHHHHHTTCCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHHS
T ss_pred             HHHHHHcCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHhcC
Confidence            999999999999999999999999999999999999999999999999999999998754

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

Probab=99.31  E-value=7.5e-13  Score=112.09  Aligned_cols=66  Identities=23%  Similarity=0.321  Sum_probs=61.2

Q ss_pred             HHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHh--cCCCCC
Q psy8542          68 IVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQ--LSGSFA  133 (182)
Q Consensus        68 I~rIlk~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r--~~~~F~  133 (182)
                      +.||++++||+|+|..++.++.+.++.|..+|++||+.|++|||||||+++||.+|++..  .-|.|.
T Consensus       167 ~~RlaRrgGVkRIS~~iyeelr~vLe~fle~IirdAv~yaeHA~RKTVta~DV~~ALKr~gr~lYGf~  234 (235)
T 2l5a_A          167 DEEDGDKGGVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQGRTLYGFG  234 (235)
T ss_dssp             CCTTSCCTTCCTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHTTCC
T ss_pred             HHHHhhcCCchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHhcCCccccCC
Confidence            348889999999999999999999999999999999999999999999999999999964  557775

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

Probab=99.26  E-value=1.8e-11  Score=86.45  Aligned_cols=60  Identities=20%  Similarity=0.386  Sum_probs=58.1

Q ss_pred             HHHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHH
Q psy8542          66 QVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAIT  125 (182)
Q Consensus        66 qlI~rIlk~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~  125 (182)
                      ..|.+|+++.|++++++++...|.+-++.++.+|+++|..++.|+||+|++.+||.+|++
T Consensus        10 ~~v~~iaes~Gi~~lsddaa~~LA~dvEyr~~eI~qeA~kfmrHakRk~Lt~~DI~~Alk   69 (70)
T 1taf_B           10 ESMKVIAESIGVGSLSDDAAKELAEDVSIKLKRIVQDAAKFMNHAKRQKLSVRDIDMSLK   69 (70)
T ss_dssp             HHHHHHHHHTTCCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHC
T ss_pred             HHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHc
Confidence            468999999999999999999999999999999999999999999999999999999984

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

Probab=99.19  E-value=1.4e-11  Score=97.18  Aligned_cols=59  Identities=22%  Similarity=0.405  Sum_probs=51.1

Q ss_pred             HHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHH
Q psy8542          67 VIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITN  126 (182)
Q Consensus        67 lI~rIlk~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~  126 (182)
                      ++.....+.|++ +||+++.+|.|++|+|+.++++|+..||.||||+||+.+||+|+++.
T Consensus        28 Ivee~~~~~~~~-vS~~ai~aL~El~~~~~e~ia~DLe~FAkHAGRKTI~~eDVkLa~Rr   86 (140)
T 3vh5_A           28 LAQDVAEDKGVL-FSKQTVAAISEITFRQAENFARDLEMFARHAKRSTITSEDVKLLARR   86 (140)
T ss_dssp             HHHHHHHHHTCE-ECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHTT
T ss_pred             HHHHHHHhcCCC-cCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHh
Confidence            333333444543 99999999999999999999999999999999999999999999974

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

Probab=99.11  E-value=1.4e-10  Score=92.74  Aligned_cols=63  Identities=16%  Similarity=0.275  Sum_probs=60.2

Q ss_pred             HHHHHHHHhc-CCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhc
Q psy8542          66 QVIVNMFQEA-GIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQL  128 (182)
Q Consensus        66 qlI~rIlk~~-Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~  128 (182)
                      ..|.||+|++ |+.++|.++...|.+.++.|+..|.++|..+|+|+|||||+++||+.|...++
T Consensus         8 a~V~Riik~~lg~~rVS~dA~~~l~~~l~~f~~~i~~~A~~~a~ha~RKTv~a~DV~~a~~~lg   71 (154)
T 1f1e_A            8 AAIERIFRQGIGERRLSQDAKDTIYDFVPTMAEYVANAAKSVLDASGKKTLMEEHLKALADVLM   71 (154)
T ss_dssp             HHHHHHHHTTSTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHHHHT
T ss_pred             cHHHHHHHhcCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHhcc
Confidence            4689999999 99999999999999999999999999999999999999999999999997764

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

Probab=99.00  E-value=7.6e-10  Score=76.31  Aligned_cols=60  Identities=23%  Similarity=0.311  Sum_probs=57.0

Q ss_pred             HHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHH
Q psy8542          67 VIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITN  126 (182)
Q Consensus        67 lI~rIlk~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~  126 (182)
                      .+.||+++.|..+++.+++..|.+.++.|+..+.+||..+|.|+||+||+.+||.+|++.
T Consensus         7 ~v~Ri~k~~~~~ris~~A~~~l~~a~e~fi~~l~~~A~~~a~~~kRkTI~~~Di~~A~~~   66 (68)
T 1b67_A            7 PIGRIIKNAGAERVSDDARIALAKVLEEMGEEIASEAVKLAKHAGRKTIKAEDIELARKM   66 (68)
T ss_dssp             HHHHHHHHTTCSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHGGG
T ss_pred             HHHHHHhcCCcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHh
Confidence            578889888999999999999999999999999999999999999999999999999853

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

Probab=98.70  E-value=2.6e-08  Score=72.71  Aligned_cols=75  Identities=17%  Similarity=0.189  Sum_probs=62.9

Q ss_pred             HHHHHHHHhcCC--cccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhcCCCCCCCCChhhh
Q psy8542          66 QVIVNMFQEAGI--KNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQLSGSFAKPPPRESK  141 (182)
Q Consensus        66 qlI~rIlk~~Gv--~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~~~~F~~pppke~L  141 (182)
                      ..|.+|+|+.|-  .+++.++...|.+.++.|+..+..+|..+|.|+||+||+.+||..|++ +.++.-.-+|-+++|
T Consensus        12 a~i~ri~K~~~~~~~~is~dA~~~l~~a~e~Fi~~l~~~A~~~a~~~kRkTI~~~Dv~~Al~-~l~F~~~i~~~~~~l   88 (93)
T 1n1j_A           12 ANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDILFAMS-TLGFDSYVEPLKLYL   88 (93)
T ss_dssp             HHHHHHHHHTSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHH-HTTCGGGHHHHHHHH
T ss_pred             hHHHHHHHHhCCccceeCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHH-HcCcHhhHHHHHHHH
Confidence            358899998865  799999999999999999999999999999999999999999999997 444333334444444

>2hue_B Histone H3; mini beta sheet, elongated beta sandwhich, DNA binding prote; 1.70A {Xenopus laevis}

Probab=98.65  E-value=1e-07  Score=68.28  Aligned_cols=64  Identities=23%  Similarity=0.318  Sum_probs=57.6

Q ss_pred             HHHHHHHHh-cCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhcC
Q psy8542          66 QVIVNMFQE-AGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQLS  129 (182)
Q Consensus        66 qlI~rIlk~-~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~~  129 (182)
                      ++++.|..+ .|..|++..++..|-|.+|.|..++.+||...|.||||+||...||+||.+.|+.
T Consensus        11 RLVRei~~~~~~~~R~q~~Al~aLQea~Eaylv~lfeda~l~A~HAkRvTi~~kDiqLa~rirg~   75 (77)
T 2hue_B           11 RLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGE   75 (77)
T ss_dssp             HHHHHHHHTTCSSCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHcCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCcHhhHHHHHHHhCc
Confidence            566666654 3778999999999999999999999999999999999999999999999988764

>3nqj_A Histone H3-like centromeric protein A; alpha helix, histone fold, centromere, DNA binding protein; 2.10A {Homo sapiens}

Probab=98.64  E-value=1.2e-07  Score=68.73  Aligned_cols=66  Identities=15%  Similarity=0.168  Sum_probs=57.5

Q ss_pred             HHHHHHHHHhc---CCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhcCC
Q psy8542          65 AQVIVNMFQEA---GIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQLSG  130 (182)
Q Consensus        65 aqlI~rIlk~~---Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~~~  130 (182)
                      .++++.|..+.   +..|+++.++..|-|.+|.|..++.+||...|.||||+||...||+||..-|+.+
T Consensus        10 ~RLVREI~~~~~~~~~~R~q~~Al~aLQea~E~ylv~Lfeda~lcAiHAkRvTi~~kDiqLa~rirg~~   78 (82)
T 3nqj_A           10 SRLAREICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRVTLFPKDVQLARRIRGLE   78 (82)
T ss_dssp             HHHHHHHHHHHHSSCCCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHHC--
T ss_pred             HHHHHHHHHHhccCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCcHHHHHHHHHHcccc
Confidence            46777777553   2579999999999999999999999999999999999999999999999888753

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

Probab=98.54  E-value=2.7e-07  Score=65.09  Aligned_cols=62  Identities=11%  Similarity=0.017  Sum_probs=56.9

Q ss_pred             HHHHHHHHhc-CCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHh
Q psy8542          66 QVIVNMFQEA-GIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQ  127 (182)
Q Consensus        66 qlI~rIlk~~-Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r  127 (182)
                      ..|.+|+++. +-.++|.++...+.++++.|...+..+|...|.|+||+||+.+||..|++..
T Consensus         8 A~V~rI~K~~~p~~~is~~A~~~i~~~~~~Fi~~la~eA~~~a~~~~rKTI~~~dI~~A~~~l   70 (76)
T 3b0c_W            8 GTLRKIIKKHKPHLRLAANTDLLVHLSFLLFLHRLAEEARTNAFENKSKIIKPEHTIAAAKVI   70 (76)
T ss_dssp             HHHHHHHHHHCTTCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSBCHHHHHHHHHHH
T ss_pred             cHHHHHHHHhCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHH
Confidence            3578999954 7778999999999999999999999999999999999999999999999864

>3nqu_A Histone H3-like centromeric protein A; alpha helix, histone fold, centromere, DNA binding protein; 2.50A {Homo sapiens} PDB: 3an2_A

Probab=98.40  E-value=6.6e-07  Score=70.54  Aligned_cols=85  Identities=14%  Similarity=0.144  Sum_probs=58.5

Q ss_pred             HhhhcccccccHhhhhhhh-------hHHHHHHHHHhc---CCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCC
Q psy8542          45 NNYTTTILEDSRVYANHAR-------DAQVIVNMFQEA---GIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKT  114 (182)
Q Consensus        45 yryt~~vL~DA~vys~har-------daqlI~rIlk~~---Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRkt  114 (182)
                      +||-..+|..-..|-....       =.++|+.|..+.   ...+++..++..|-|.+|.|..++.+||...|-||+|.|
T Consensus        41 ~r~rpg~LrEIR~yQkst~LLIpKlPF~RLVREI~~~~~~~~~~Rfq~~Al~ALQEAaEayLv~LFEdanlcAiHAkRVT  120 (140)
T 3nqu_A           41 SRRRQGWLKEIRKLQKSTHLLIRKLPFSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRVT  120 (140)
T ss_dssp             ------------------CCCSCTTHHHHHHHHHHHHHHTTCCCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSE
T ss_pred             CCCCCccHHHHHHhccccccccccccHHHHHHHHHHHhcccccceecHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCccc
Confidence            3444444666666644432       346788887653   257999999999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHhcC
Q psy8542         115 VDVEDIKLAITNQLS  129 (182)
Q Consensus       115 I~~eDVrLAI~~r~~  129 (182)
                      |...||+||...|+.
T Consensus       121 Im~kDiqLArrirg~  135 (140)
T 3nqu_A          121 LFPKDVQLARRIRGL  135 (140)
T ss_dssp             ECHHHHHHHHHHHC-
T ss_pred             ccHHHHHHHHHhccc
Confidence            999999999988765

>1tzy_C Histone H3; histone-fold, tetramer-dimer-dimer, DNA binding protein; 1.90A {Gallus gallus} SCOP: a.22.1.1 PDB: 1eqz_C 1hq3_C 2aro_C 2f8n_A 2hio_C 3av1_A 3lel_A 3afa_A 3azi_A 3azj_A 3azk_A 3azl_A 3azm_A 3azn_A 2cv5_A* 1u35_A* 2nqb_A 2io5_B 2pyo_A* 3c9k_C ...

Probab=98.37  E-value=1.3e-06  Score=68.64  Aligned_cols=65  Identities=23%  Similarity=0.294  Sum_probs=58.8

Q ss_pred             HHHHHHHHHhc-CCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhcC
Q psy8542          65 AQVIVNMFQEA-GIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQLS  129 (182)
Q Consensus        65 aqlI~rIlk~~-Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~~  129 (182)
                      .++|+.|..+. |.-+++..++..|-|.+|.|..++.+|+...|-||||.||...||+||...|+.
T Consensus        69 ~RLVREI~~~~~~~~R~q~~Al~aLQeaaEayLv~Lfeda~l~A~HAkRvTi~~kDiqLa~rirg~  134 (136)
T 1tzy_C           69 QRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE  134 (136)
T ss_dssp             HHHHHHHHHHHCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHhhhhhcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCcHHhHHHHHHHhCc
Confidence            46777776643 778999999999999999999999999999999999999999999999988764

>3r45_A Histone H3-like centromeric protein A; histone fold, centromere, CENP-A, histone chaperone, hjurp; 2.60A {Homo sapiens}

Probab=98.37  E-value=8.1e-07  Score=71.12  Aligned_cols=85  Identities=14%  Similarity=0.152  Sum_probs=58.8

Q ss_pred             HhhhcccccccHhhhhhhh-------hHHHHHHHHHhcC---CcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCC
Q psy8542          45 NNYTTTILEDSRVYANHAR-------DAQVIVNMFQEAG---IKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKT  114 (182)
Q Consensus        45 yryt~~vL~DA~vys~har-------daqlI~rIlk~~G---v~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRkt  114 (182)
                      +||-..+|..-..|-....       =.++|+.|..+..   ..+++..++..|-|.+|.|..++.+||...|-||+|.|
T Consensus        57 ~r~rpg~LrEIR~yQkSteLLIpKlPF~RLVREIa~~~~~~~~lRfqs~Al~ALQEAaEayLV~LFEdanLcAiHAkRVT  136 (156)
T 3r45_A           57 SRRRQGWLKEIRKLQKSTHLLIRKLPFSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRVT  136 (156)
T ss_dssp             ------------------CCCSCHHHHHHHHHHHHHTTTTTCCCEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSE
T ss_pred             CCCCCchHHHHHHhccccccccccccHHHHHHHHHHHhccCccceecHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCccc
Confidence            4554445666666654432       2467888876543   56999999999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHhcC
Q psy8542         115 VDVEDIKLAITNQLS  129 (182)
Q Consensus       115 I~~eDVrLAI~~r~~  129 (182)
                      |...||+||...|+.
T Consensus       137 Im~kDIqLArrIrg~  151 (156)
T 3r45_A          137 LFPKDVQLARRIRGL  151 (156)
T ss_dssp             ECHHHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHccc
Confidence            999999999987753

>2yfv_A Histone H3-like centromeric protein CSE4; cell cycle, kinetochore, centromere, histone chaperone, BUDD; 2.32A {Kluyveromyces lactis nrrl y-1140} PDB: 2yfw_A

Probab=98.35  E-value=1.2e-06  Score=65.50  Aligned_cols=62  Identities=21%  Similarity=0.288  Sum_probs=54.5

Q ss_pred             HHHHHHHHHhcC----CcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHH
Q psy8542          65 AQVIVNMFQEAG----IKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITN  126 (182)
Q Consensus        65 aqlI~rIlk~~G----v~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~  126 (182)
                      .++|+.|..+..    .-+++..++..|-|.+|.|..++.+||...|-||||.||...||+||..-
T Consensus        34 ~RLVREI~~~~~~~~~~~R~q~~Al~ALQeaaEayLv~Lfeda~l~A~HAkRvTi~~kDiqLa~ri   99 (100)
T 2yfv_A           34 ARLVKEVTDQFTTESEPLRWQSMAIMALQEASEAYLVGLLEHTNLLALHAKRITIMRKDMQLARRI   99 (100)
T ss_dssp             HHHHHHHHHTTC-----CEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHC
T ss_pred             HHHHHHHHHHhccccchhhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCCHHHHHHHHHh
Confidence            367777776532    67999999999999999999999999999999999999999999999753

>2nqb_C Histone H2A; nucleosome, NCP, chromatin, structural protein/DNA complex; 2.30A {Drosophila melanogaster} PDB: 2pyo_C*

Probab=98.33  E-value=1.2e-06  Score=67.44  Aligned_cols=61  Identities=16%  Similarity=0.165  Sum_probs=57.9

Q ss_pred             HHHHHHHHhc-CCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHH
Q psy8542          66 QVIVNMFQEA-GIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITN  126 (182)
Q Consensus        66 qlI~rIlk~~-Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~  126 (182)
                      .-|+|+|++. ++.|++..++..|...+|.++.+|++.|..+|.|+++++|+.+||++||+.
T Consensus        27 ~ri~R~Lk~~~~a~RV~~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~krItp~hi~lAI~n   88 (123)
T 2nqb_C           27 GRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRN   88 (123)
T ss_dssp             HHHHHHHHHTTSCSEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHT
T ss_pred             HHHHHHHHccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHHHHHhc
Confidence            3688999986 999999999999999999999999999999999999999999999999984

>2f8n_G Core histone macro-H2A.1; nucleosome, NCP, macroh2A, histone variant, chromatin, X- RAY structure, crystallography, structural protein/DNA complex; 2.90A {Homo sapiens} SCOP: a.22.1.1 PDB: 1u35_C

Probab=98.32  E-value=1.3e-06  Score=67.09  Aligned_cols=61  Identities=21%  Similarity=0.157  Sum_probs=58.1

Q ss_pred             HHHHHHHHhcC-CcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHH
Q psy8542          66 QVIVNMFQEAG-IKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITN  126 (182)
Q Consensus        66 qlI~rIlk~~G-v~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~  126 (182)
                      .-|+|+|++.+ +.|++..+...|...+|.++.+|++.|..+|.|+|+++|+.+||++||+.
T Consensus        26 ~ri~R~Lk~~~~a~RV~~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~~rItp~hi~lAI~n   87 (120)
T 2f8n_G           26 GRMLRYIKKGHPKYRIGVGAPVYMAAVLEYLTAEILELAVNAARDNKKGRVTPRHILLAVAN   87 (120)
T ss_dssp             HHHHHHHHHHSSSCEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHT
T ss_pred             HHHHHHHHcCccccccccchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceEcHHHHHHHHhc
Confidence            36899999998 89999999999999999999999999999999999999999999999974

>2byk_B Chrac-14; nucleosome sliding, histone fold, DNA-binding protein; 2.4A {Drosophila melanogaster} SCOP: a.22.1.3 PDB: 2bym_B

Probab=98.30  E-value=3.1e-06  Score=65.45  Aligned_cols=77  Identities=17%  Similarity=0.141  Sum_probs=67.6

Q ss_pred             HHHHHHHhcC--CcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhcCCCCCCCCChhhhhcc
Q psy8542          67 VIVNMFQEAG--IKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQLSGSFAKPPPRESKGSG  144 (182)
Q Consensus        67 lI~rIlk~~G--v~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~~~~F~~pppke~Ll~l  144 (182)
                      .|.+|+++.+  ..+++.++...|.+.++-|+..+...|...|.|.+|+||+.+||..|++....+.|-. |-+++|-+.
T Consensus        14 ~I~rImK~~~pd~~~iS~dA~~~l~ka~e~FI~~lt~~A~~~a~~~kRKTI~~~Dv~~Al~~l~f~~fl~-~lk~~l~~y   92 (128)
T 2byk_B           14 VIGRLIKEALPESASVSKEARAAIARAASVFAIFVTSSSTALAHKQNHKTITAKDILQTLTELDFESFVP-SLTQDLEVY   92 (128)
T ss_dssp             HHHHHHHHHSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCTTTHH-HHHHHHHHH
T ss_pred             HHHHHHHHhCcccceECHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHHcCcHHHHH-HHHHHHHHH
Confidence            5899999765  8899999999999999999999999999999999999999999999999887777764 455555544

>1tzy_A Histone H2A-IV; histone-fold, tetramer-dimer-dimer, DNA binding protein; 1.90A {Gallus gallus} SCOP: a.22.1.1 PDB: 1eqz_A 1hq3_A 2aro_A 2hio_A 3c9k_A 3azg_C 3a6n_C 3an2_C 3av1_C 3av2_C 3ayw_C 3aze_C 3azf_C 3afa_C 3azh_C 3azi_C 3azj_C 3azk_C 3azl_C 3azm_C ...

Probab=98.29  E-value=1.8e-06  Score=67.06  Aligned_cols=61  Identities=18%  Similarity=0.176  Sum_probs=57.8

Q ss_pred             HHHHHHHHhc-CCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHH
Q psy8542          66 QVIVNMFQEA-GIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITN  126 (182)
Q Consensus        66 qlI~rIlk~~-Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~  126 (182)
                      .-|+|+|++. ++.|++..++..|...+|.++.+|++.|..+|.|+++++|+.+||++||+.
T Consensus        29 ~rI~R~Lk~~~~a~RVs~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~krItp~hi~lAI~n   90 (129)
T 1tzy_A           29 GRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRN   90 (129)
T ss_dssp             HHHHHHHHHTTSSSEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHT
T ss_pred             HHHHHHHHccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeEcHHHHHHHHhc
Confidence            3688999985 999999999999999999999999999999999999999999999999984

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

Probab=98.27  E-value=1.4e-06  Score=64.05  Aligned_cols=67  Identities=16%  Similarity=0.151  Sum_probs=59.9

Q ss_pred             HHHHHHHHhcCC-cccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhcCCCC
Q psy8542          66 QVIVNMFQEAGI-KNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQLSGSF  132 (182)
Q Consensus        66 qlI~rIlk~~Gv-~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~~~~F  132 (182)
                      .-|++|++..+- .+++.+++..+-..++.|+.++++.|...|.+.+|+||+.+||.+|++.--.+.|
T Consensus        23 arIkrImK~~~~~~~is~eA~~~laka~E~Fi~~l~~~A~~~a~~~krktI~~~di~~Av~~~e~~~F   90 (97)
T 1n1j_B           23 ARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDIAMAITKFDQFDF   90 (97)
T ss_dssp             HHHHHHHTTSTTCCCBCTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHTTCGGGGG
T ss_pred             HHHHHHHccCccccccChHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCCHHHHHHHHhcCcHHHH
Confidence            368999997654 7899999999999999999999999999999999999999999999986555544

>2f8n_K Histone H2A type 1; nucleosome, NCP, macroh2A, histone variant, chromatin, X- RAY structure, crystallography, structural protein/DNA complex; 2.90A {Mus musculus} SCOP: a.22.1.1

Probab=98.24  E-value=2.2e-06  Score=68.14  Aligned_cols=60  Identities=18%  Similarity=0.179  Sum_probs=57.6

Q ss_pred             HHHHHHHhc-CCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHH
Q psy8542          67 VIVNMFQEA-GIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITN  126 (182)
Q Consensus        67 lI~rIlk~~-Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~  126 (182)
                      -|.|+|++. ++.|++..++..|...+|.++.+|++-|..+|.++++++|+.+||++||+.
T Consensus        49 rI~R~LK~~~~a~RVs~~A~VyLAAVLEYL~aEILelAgn~A~~~krkrItprhI~lAI~n  109 (149)
T 2f8n_K           49 RVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRN  109 (149)
T ss_dssp             HHHHHHHHTTSCSEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHH
T ss_pred             HHHHHHHccccccccCcCcHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHhc
Confidence            689999986 999999999999999999999999999999999999999999999999984

>1jfi_B DR1 protein, transcription regulator NC2 beta chain; histone, H2A/H2B, tata-DNA, transcription initiation, NC2, negative cofactor, structural genomics, PSI; 2.62A {Homo sapiens} SCOP: a.22.1.3

Probab=98.22  E-value=4.2e-06  Score=68.34  Aligned_cols=76  Identities=17%  Similarity=0.195  Sum_probs=65.3

Q ss_pred             HHHHHHHHhcCC-cccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhcCCCCCCCCChhhhh
Q psy8542          66 QVIVNMFQEAGI-KNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQLSGSFAKPPPRESKG  142 (182)
Q Consensus        66 qlI~rIlk~~Gv-~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~~~~F~~pppke~Ll  142 (182)
                      ..|.||+|+.+- .+++.++...|.+.+..|+..|...|...|.|.|||||+.+||..|++......|.. |-+++|-
T Consensus        19 A~V~RImK~alp~~rISkDA~~al~ec~~eFI~~LtseA~e~a~~~~RKTI~~eDVl~Al~~LgF~~fv~-~lk~~L~   95 (179)
T 1jfi_B           19 AAINKMIKETLPNVRVANDARELVVNCCTEFIHLISSEANEICNKSEKKTISPEHVIQALESLGFGSYIS-EVKEVLQ   95 (179)
T ss_dssp             HHHHHHHHHHSTTCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHHTTGGGHH-HHHHHHH
T ss_pred             HHHHHHHHHhCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHhcChHHHHH-HHHHHHH
Confidence            468999999874 799999999999999999999999999999999999999999999998665555543 4444443

>1id3_C Histone H2A.1; nucleosome core particle, chromatin, protein/DNA interaction, nucleoprotein, supercoiled DNA; 3.10A {Saccharomyces cerevisiae} SCOP: a.22.1.1

Probab=98.21  E-value=2.3e-06  Score=66.57  Aligned_cols=61  Identities=16%  Similarity=0.165  Sum_probs=57.7

Q ss_pred             HHHHHHHHhc-CCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHH
Q psy8542          66 QVIVNMFQEA-GIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITN  126 (182)
Q Consensus        66 qlI~rIlk~~-Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~  126 (182)
                      .-|+|+|++. ++.|++..++..|...++.++.+|++-|..+|.|+++++|+.+||++||+.
T Consensus        29 ~rI~R~Lk~~~~a~RVs~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~krItp~hI~lAI~n   90 (131)
T 1id3_C           29 GRVHRLLRRGNYAQRIGSGAPVYLTAVLEYLAAEILELAGNAARDNKKTRIIPRHLQLAIRN   90 (131)
T ss_dssp             HHHHHHHHTTCSCSEECSSHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHT
T ss_pred             HHHHHHHHccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHhhcCCceEcHHHHHHHHhc
Confidence            4688999985 999999999999999999999999999999999999999999999999984

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

Probab=98.21  E-value=3e-06  Score=64.69  Aligned_cols=95  Identities=14%  Similarity=0.180  Sum_probs=79.5

Q ss_pred             HHHHHHHHhhhcccccccHhhhhhhhhHHHHHHHHH-hcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCC
Q psy8542          38 QQMLEFVNNYTTTILEDSRVYANHARDAQVIVNMFQ-EAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVD  116 (182)
Q Consensus        38 ~qll~f~yryt~~vL~DA~vys~hardaqlI~rIlk-~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~  116 (182)
                      .+|-+||-+...++-.+..-+..|-=-..-|++|+| +..+.+++.+++..+-..++-++.++++.|...|...+|+||+
T Consensus        17 ~~l~~fw~~~~~~~e~~~~d~k~~~lPvaRIkrImK~d~~~~~is~eA~v~la~a~E~Fi~~L~~~A~~~a~~~krktI~   96 (119)
T 4g92_C           17 DILTTYWQHVINHLESDNHDYKIHQLPLARIKKVMKADPEVKMISAEAPILFAKGCDVFITELTMRAWIHAEDNKRRTLQ   96 (119)
T ss_dssp             HHHHHHHHHHHHHHTCSCCCSSCCSSCHHHHHHHHHTSTTCCEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEEC
T ss_pred             HHHHHHHHHHHHHHHhcccccccCCCCHHHHHHHHhhCCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccC
Confidence            688999999888776665555555333456888998 4688899999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhcCCCC
Q psy8542         117 VEDIKLAITNQLSGSF  132 (182)
Q Consensus       117 ~eDVrLAI~~r~~~~F  132 (182)
                      .+||..||+.--.+.|
T Consensus        97 ~~di~~Av~~~e~~dF  112 (119)
T 4g92_C           97 RSDIAAALSKSDMFDF  112 (119)
T ss_dssp             HHHHHHHHTTCGGGGG
T ss_pred             HHHHHHHHhcCchhhH
Confidence            9999999976555444

>1f66_C Histone H2A.Z; nucleosome, chromatin, histone variant, protein DNA interaction, nucleoprotein, supercoiled DNA, complex (nucleosome core/DNA); 2.60A {Homo sapiens} SCOP: a.22.1.1

Probab=98.16  E-value=4.3e-06  Score=64.82  Aligned_cols=61  Identities=15%  Similarity=0.120  Sum_probs=57.3

Q ss_pred             HHHHHHHHhcC-C-cccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHH
Q psy8542          66 QVIVNMFQEAG-I-KNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITN  126 (182)
Q Consensus        66 qlI~rIlk~~G-v-~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~  126 (182)
                      .-|+|+|++.+ + .|++..+...|...+|.++.+|++-|..+|.|.|+++|+.+||++||+.
T Consensus        31 ~ri~R~Lk~~~~a~~RV~~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~krItprhi~lAI~n   93 (128)
T 1f66_C           31 GRIHRHLKSRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRG   93 (128)
T ss_dssp             HHHHHHHHHTSCSSCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHHH
T ss_pred             HHHHHHHHHcccchhhccccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeEcHHHHHHHHhc
Confidence            36899999998 4 4999999999999999999999999999999999999999999999984

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

Probab=98.15  E-value=1.4e-06  Score=60.26  Aligned_cols=51  Identities=20%  Similarity=0.421  Sum_probs=47.4

Q ss_pred             CCCchHHHHHHHHHHcCCCccChHHHHHHHHHHHhhhcccccccHhhhhhhhh
Q psy8542          12 KLPRDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHARD   64 (182)
Q Consensus        12 ~~prda~~i~~il~~~gi~~yep~v~~qll~f~yryt~~vL~DA~vys~hard   64 (182)
                      .+|+.  .|.-|+++.|+..+++.++.+|.|+.++|+..+++||..|+.|++.
T Consensus         6 ~lp~a--~v~Rl~r~~g~~ris~~a~~~l~e~~~~~~~~v~~dA~~~a~hakR   56 (70)
T 1ku5_A            6 ELPIA--PVDRLIRKAGAERVSEQAAKVLAEYLEEYAIEIAKKAVEFARHAGR   56 (70)
T ss_dssp             CSCHH--HHHHHHHHTTCSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTC
T ss_pred             cCChH--HHHHHHHHcCcceeCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCC
Confidence            46765  7899999999999999999999999999999999999999999974

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

Probab=98.05  E-value=3.7e-06  Score=62.05  Aligned_cols=67  Identities=12%  Similarity=0.107  Sum_probs=52.9

Q ss_pred             HHHHHHHHhcC-CcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhcCCCC
Q psy8542          66 QVIVNMFQEAG-IKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQLSGSF  132 (182)
Q Consensus        66 qlI~rIlk~~G-v~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~~~~F  132 (182)
                      .-|++|++..+ +.+++.+++..+-..++-|+.++++.|...|.+.||+||+.+||.+||+.--.+.|
T Consensus        15 aRIkrimK~~~~~~~vs~~A~v~la~a~E~Fi~el~~~A~~~a~~~krktI~~~di~~av~~~e~l~F   82 (98)
T 1jfi_A           15 ARIKKIMQTDEEIGKVAAAVPVIISRALELFLESLLKKACQVTQSRNAKTMTTSHLKQCIELEGDPAA   82 (98)
T ss_dssp             HHHHHHHTTSTTCCCBCTTHHHHHHHHHHHHHHHHHHHHHHHHHTC---CBCHHHHHTTCC-------
T ss_pred             HHHHHHHHcCccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHhcCchhhH
Confidence            35889999754 48999999999999999999999999999999999999999999999987555544

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

Probab=97.99  E-value=1.1e-05  Score=60.82  Aligned_cols=56  Identities=13%  Similarity=0.256  Sum_probs=45.0

Q ss_pred             HHHHHHHHHcCCCccChHHHHHHHHHHHhhhcccccccHhhhhhhh----hHHHHHHHHHh
Q psy8542          18 QVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAR----DAQVIVNMFQE   74 (182)
Q Consensus        18 ~~i~~il~~~gi~~yep~v~~qll~f~yryt~~vL~DA~vys~har----daqlI~rIlk~   74 (182)
                      |++....+++|+ .|+|+++.+|.||.|+|+.++..|+..|+.||+    +..-|...+++
T Consensus        27 rI~~~~g~~~~~-~vs~~~i~aL~E~~~~~~~~ia~Da~~fA~HAgRkTI~~eDV~La~Rr   86 (107)
T 3b0b_B           27 CLCQDVAEDKGV-LFSKQTVAAISEITFRQCENFARDLEMFARHAKRSTITSEDVKLLARR   86 (107)
T ss_dssp             HHHHHHHHHHTC-EECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTT
T ss_pred             HHHHHHhhhcCC-ccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcCcCCHHHHHHHHHh
Confidence            555566666666 799999999999999999999999999999998    33445555554

>2jss_A Chimera of histone H2B.1 and histone H2A.Z; histone/chaperone complex, intrinsically unfolded protein, chaperone/structural protein complex; NMR {Saccharomyces cerevisiae} SCOP: a.22.1.1 a.22.1.1

Probab=97.98  E-value=1.7e-05  Score=64.93  Aligned_cols=60  Identities=17%  Similarity=0.166  Sum_probs=56.2

Q ss_pred             HHHHHHHhc-CC-cccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHH
Q psy8542          67 VIVNMFQEA-GI-KNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITN  126 (182)
Q Consensus        67 lI~rIlk~~-Gv-~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~  126 (182)
                      -|+|++++. ++ .|++..++..|...++.++.+|++-|..+|.|+|+++|+.+||++||+.
T Consensus       110 ri~R~lk~~~~a~~Rv~~~A~vyLaavLEyl~~eIlelA~n~a~~~~~~~I~p~~i~lAi~n  171 (192)
T 2jss_A          110 RIKRYLKRHATGRTRVGSKAAIYLTAVLEYLTAEVLELAGNAAKDLKVKRITPRHLQLAIRG  171 (192)
T ss_dssp             HHHHHHHHTTCSSCCCCTTTHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSCCHHHHHHHHHT
T ss_pred             HHHHHHHhcCccccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHhc
Confidence            588999986 66 5999999999999999999999999999999999999999999999973

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

Probab=97.57  E-value=0.00018  Score=54.84  Aligned_cols=56  Identities=9%  Similarity=0.225  Sum_probs=44.3

Q ss_pred             HHHHHHHHHcCCCccChHHHHHHHHHHHhhhcccccccHhhhhhhh----hHHHHHHHHHh
Q psy8542          18 QVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAR----DAQVIVNMFQE   74 (182)
Q Consensus        18 ~~i~~il~~~gi~~yep~v~~qll~f~yryt~~vL~DA~vys~har----daqlI~rIlk~   74 (182)
                      |++....++.|++ +.|+++.+|.|+.|+|..++.+|+..|+.||+    ++.-|...+++
T Consensus        35 rIvke~gaer~~~-vS~~ai~aL~El~~~~~~~ia~Dl~~fAkHAgRkTI~~eDV~La~Rr   94 (113)
T 4dra_A           35 CLCEEVALDKEMQ-FSKQTIAAISELTFRQCENFAKDLEMFARHAKRTTINTEDVKLLARR   94 (113)
T ss_dssp             HHHHHHHHHHTCC-BCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTT
T ss_pred             HHHHHHHHHcCCC-cCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHh
Confidence            4555555666665 99999999999999999999999999999998    33445555554

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

Probab=97.49  E-value=4.1e-05  Score=56.13  Aligned_cols=45  Identities=22%  Similarity=0.412  Sum_probs=40.1

Q ss_pred             HHHHHHHHHcCCCccChHHHHHHHHHHHhhhcccccccHhhhhhhh
Q psy8542          18 QVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAR   63 (182)
Q Consensus        18 ~~i~~il~~~gi~~yep~v~~qll~f~yryt~~vL~DA~vys~har   63 (182)
                      ++....++++|+ ++.|+++.+|.|+.|+|..++.+|+..|+.||+
T Consensus        20 ki~~e~~~~~g~-~vs~~~i~aL~e~~~~~~~~ia~Dl~~fA~HAg   64 (90)
T 3v9r_A           20 ERLQQVLSSEDI-KYTPRFINSLLELAYLQLGEMGSDLQAFARHAG   64 (90)
T ss_dssp             HHHHHHSCSSCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHhcCc-eeCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence            455566677787 599999999999999999999999999999997

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

Probab=97.44  E-value=0.00038  Score=53.68  Aligned_cols=63  Identities=19%  Similarity=0.268  Sum_probs=58.0

Q ss_pred             HHHHHHHHhcCCc-ccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhc
Q psy8542          66 QVIVNMFQEAGIK-NYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQL  128 (182)
Q Consensus        66 qlI~rIlk~~Gv~-r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~  128 (182)
                      .-|.++|++.+-. .+|.++...|.-|++.....|+.+|..++.|++|+||+..||+.|+.-.+
T Consensus        37 ~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkr~TitsreIqtAvrLlL  100 (123)
T 2nqb_D           37 IYIYTVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEASRLAHYNKRSTITSREIQTAVRLLL  100 (123)
T ss_dssp             HHHHHHHHHHCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCEECHHHHHHHHHHHS
T ss_pred             HHHHHHHHHhCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHHHhC
Confidence            3589999998866 79999999999999999999999999999999999999999999997554

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

Probab=97.34  E-value=0.00059  Score=52.84  Aligned_cols=62  Identities=18%  Similarity=0.268  Sum_probs=57.7

Q ss_pred             HHHHHHHhcCCc-ccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhc
Q psy8542          67 VIVNMFQEAGIK-NYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQL  128 (182)
Q Consensus        67 lI~rIlk~~Gv~-r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~  128 (182)
                      -|.++|++.+-. .+|.++...|.-|+......|+.+|..++.|++|+||+..||+.|+.-.+
T Consensus        41 YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkr~TitsreIqtAvrLlL  103 (126)
T 1tzy_B           41 YVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLL  103 (126)
T ss_dssp             HHHHHHHHHCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHHS
T ss_pred             HHHHHHHHhCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhC
Confidence            599999998876 79999999999999999999999999999999999999999999997554

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

Probab=97.33  E-value=0.00053  Score=53.93  Aligned_cols=72  Identities=11%  Similarity=0.314  Sum_probs=55.3

Q ss_pred             HHHHHHHHHcCCCccChHHHHHHHHHHHhhhcccccccHhhhhhhh----hHHHHHHHHHhcCCcccChHHHHHHHHHHH
Q psy8542          18 QVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAR----DAQVIVNMFQEAGIKNYDPRCVQQMLEFVN   93 (182)
Q Consensus        18 ~~i~~il~~~gi~~yep~v~~qll~f~yryt~~vL~DA~vys~har----daqlI~rIlk~~Gv~r~sp~v~~qLle~~~   93 (182)
                      +++.....+.|++ +.|.++.+|.|+.|+|..++..|+..|+.||+    ++.-|...+++.          ..|++++.
T Consensus        27 kIvee~~~~~~~~-vS~~ai~aL~El~~~~~e~ia~DLe~FAkHAGRKTI~~eDVkLa~Rrn----------~~L~~~L~   95 (140)
T 3vh5_A           27 ALAQDVAEDKGVL-FSKQTVAAISEITFRQAENFARDLEMFARHAKRSTITSEDVKLLARRS----------NSLLKYIT   95 (140)
T ss_dssp             HHHHHHHHHHTCE-ECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHTTS----------HHHHHHHH
T ss_pred             HHHHHHHHhcCCC-cCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHhC----------HHHHHHHH
Confidence            4555556666755 99999999999999999999999999999998    334555555553          35667777


Q ss_pred             HHHHHHH
Q psy8542          94 NYTTTIL  100 (182)
Q Consensus        94 ry~~~Vl  100 (182)
                      .|..++.
T Consensus        96 ~~~~el~  102 (140)
T 3vh5_A           96 QKSDELA  102 (140)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            7777765

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

Probab=97.16  E-value=0.00079  Score=50.69  Aligned_cols=80  Identities=13%  Similarity=0.164  Sum_probs=63.0

Q ss_pred             CCCCchHHHHHHHHHHcCCCccChHHHHHHHHHHHhhhcccccccHhhhhhhh----hHHHHHHHHHhcCCcccChHHHH
Q psy8542          11 SKLPRDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAR----DAQVIVNMFQEAGIKNYDPRCVQ   86 (182)
Q Consensus        11 ~~~prda~~i~~il~~~gi~~yep~v~~qll~f~yryt~~vL~DA~vys~har----daqlI~rIlk~~Gv~r~sp~v~~   86 (182)
                      ..+|+-  .|.-|++..|+....+.+...|.|+.++|...|..|+..|++|++    ++.-|...+++.|...+..... 
T Consensus         6 ~~lP~a--~I~Ri~r~~g~~rIS~~a~~~l~e~l~~f~~~v~~da~~~A~HA~RKTV~~eDV~lalrr~g~~~~~~~l~-   82 (111)
T 3b0c_T            6 PEIASS--LIKQIFSHYVKTPVTRDAYKIVEKCSERYFKQISSDLEAYSQHAGRKTVEMADVELLMRRQGLVTDKMPLH-   82 (111)
T ss_dssp             ----CH--HHHHHHHHHHCSCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHTTSSBTTBCHH-
T ss_pred             CCCCHH--HHHHHHHHCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHHCCCccccccHH-
Confidence            456664  678899999999999999999999999999999999999999998    4567888888888776544443 


Q ss_pred             HHHHHHHHHH
Q psy8542          87 QMLEFVNNYT   96 (182)
Q Consensus        87 qLle~~~ry~   96 (182)
                         .++++|.
T Consensus        83 ---~l~~~~l   89 (111)
T 3b0c_T           83 ---VLVERHL   89 (111)
T ss_dssp             ---HHHHHHS
T ss_pred             ---HHHHHhC
Confidence               4555553

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

Probab=97.13  E-value=0.0028  Score=45.00  Aligned_cols=54  Identities=19%  Similarity=0.386  Sum_probs=49.8

Q ss_pred             cCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhc
Q psy8542          75 AGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQL  128 (182)
Q Consensus        75 ~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~  128 (182)
                      -|-...+|+|-+.|++++..|+.+|+..|..+|.|.|.+|+++-||++.++..-
T Consensus        19 dp~~~ld~~vee~ll~lADdFV~~V~~~ac~lAKhR~s~~le~kDvql~Ler~w   72 (76)
T 1h3o_B           19 DPNEQLDEDVEEMLLQIADDFIESVVTAACQLARHRKSSTLEVKDVQLHLERQW   72 (76)
T ss_dssp             CSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCEECHHHHHHHHHHHT
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCccHHHHHHHHHhhc
Confidence            355779999999999999999999999999999999999999999999997643

>2jss_A Chimera of histone H2B.1 and histone H2A.Z; histone/chaperone complex, intrinsically unfolded protein, chaperone/structural protein complex; NMR {Saccharomyces cerevisiae} SCOP: a.22.1.1 a.22.1.1

Probab=97.01  E-value=0.0028  Score=51.66  Aligned_cols=62  Identities=19%  Similarity=0.274  Sum_probs=56.7

Q ss_pred             HHHHHHHhcCC-cccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhc
Q psy8542          67 VIVNMFQEAGI-KNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQL  128 (182)
Q Consensus        67 lI~rIlk~~Gv-~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~  128 (182)
                      -|.++|++.+- ..+|.++...|-.|+.+....|..+|..++.|.+|+|++..||+.|++.-.
T Consensus         8 yi~kvLkqv~p~~~iS~~Am~~m~s~v~di~~rIa~eA~~L~~~~~r~Tit~~eIq~Avrl~l   70 (192)
T 2jss_A            8 YIYKVLKQTHPDTGISQKSMSILNSFVNDIFERIATEASKLAAYNKKSTISAREIQTAVRLIL   70 (192)
T ss_dssp             HHHHHHHHHCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCCSCCHHHHHHHHHHHS
T ss_pred             HHHHHHcccCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhc
Confidence            48889998765 679999999999999999999999999999999999999999999997544

>2byk_A Chrac-16; nucleosome sliding, histone fold, DNA-binding protein; 2.4A {Drosophila melanogaster} SCOP: a.22.1.3 PDB: 2bym_A

Probab=97.00  E-value=0.00089  Score=52.41  Aligned_cols=68  Identities=4%  Similarity=0.054  Sum_probs=56.5

Q ss_pred             HHHHHHHh-cCCcccChHHHHHHHHHHHHHHHHHHHHHHHHh-hhcCCCCCCHHHHHHHHHHhcCCCCCC
Q psy8542          67 VIVNMFQE-AGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYA-NHAKKKTVDVEDIKLAITNQLSGSFAK  134 (182)
Q Consensus        67 lI~rIlk~-~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA-~HAgRktI~~eDVrLAI~~r~~~~F~~  134 (182)
                      -|++|++. ..+..++..++..+-..++-|+..++..|...| ...+|+||+..||..||+..-.+.|-.
T Consensus        24 RIKrIMK~dpdv~~Is~eA~vliakA~ElFI~~Lt~~A~~~a~~~~kRKtI~~~Dl~~AV~~~e~~dFL~   93 (140)
T 2byk_A           24 RVRTIMKSSMDTGLITNEVLFLMTKCTELFVRHLAGAAYTEEFGQRPGEALKYEHLSQVVNKNKNLEFLL   93 (140)
T ss_dssp             -----CCSSSSCSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSCEECHHHHHHHHHTCSTTGGGT
T ss_pred             HHHHHHhcCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcccCHHHHHHHHhcCchhhhHh
Confidence            47888874 566789999999999999999999999999999 989999999999999999876677743

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

Probab=96.71  E-value=0.0027  Score=53.73  Aligned_cols=65  Identities=22%  Similarity=0.266  Sum_probs=58.6

Q ss_pred             HHHHHHHHHhcC----CcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhcC
Q psy8542          65 AQVIVNMFQEAG----IKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQLS  129 (182)
Q Consensus        65 aqlI~rIlk~~G----v~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~~  129 (182)
                      +++++.|..+..    --+++..++..|-|.++.|...+.+|+...|-||+|-||..-|++||-.-|+.
T Consensus        18 qRLVREIaq~~~~~~~~lRfqs~Al~ALQEAaEayLV~LFEd~nLcaiHAkRVTim~kDiqLarrirg~   86 (235)
T 2l5a_A           18 ARLVKEVTDEFTTKDQDLRWQSMAIMALQEASEAYLVGLLEHTNLLALHAKRITIMKKDMQLARRIRGQ   86 (235)
T ss_dssp             HHHHHHHHHTSCGGGTTCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHSTTTSGGGTTHHHHHHTSSCS
T ss_pred             HHHHHHHHHHhccCCccceecHHHHHHHHHHHHHHHHHHHhhhHHHHhcccccccchhhHHHHHHHhhc
Confidence            478899988753    35899999999999999999999999999999999999999999999876665

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

Probab=96.15  E-value=0.0038  Score=44.49  Aligned_cols=66  Identities=17%  Similarity=0.311  Sum_probs=56.8

Q ss_pred             CCCchHHHHHHHHHHcCCCccChHHHHHHHHHHHhhhcccccccHhhhhhhh----hHHHHHHHHHhcCCcc
Q psy8542          12 KLPRDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAR----DAQVIVNMFQEAGIKN   79 (182)
Q Consensus        12 ~~prda~~i~~il~~~gi~~yep~v~~qll~f~yryt~~vL~DA~vys~har----daqlI~rIlk~~Gv~r   79 (182)
                      .+|+++  |.-|+++.|+....+.+...|.+....|..+|++||..|++|++    ++.-|...|+..|..-
T Consensus        10 ~ip~~~--I~Riar~~Gv~rIs~da~~~l~~~l~~~~~~I~~dA~~~a~ha~RKTvt~~DV~~Alk~~g~~l   79 (84)
T 2hue_C           10 GITKPA--IRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTL   79 (84)
T ss_dssp             SSCHHH--HHHHHHHTTCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTTTCEEE
T ss_pred             CCCHHH--HHHHHHHcCchhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHHHHHHcCCCC
Confidence            377775  89999999999999999999999999999999999999999998    4456677777766543

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

Probab=95.85  E-value=0.01  Score=43.87  Aligned_cols=67  Identities=16%  Similarity=0.365  Sum_probs=57.3

Q ss_pred             CCCchHHHHHHHHHHcCCCccChHHHHHHHHHHHhhhcccccccHhhhhhhh----hHHHHHHHHHhcCCccc
Q psy8542          12 KLPRDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAR----DAQVIVNMFQEAGIKNY   80 (182)
Q Consensus        12 ~~prda~~i~~il~~~gi~~yep~v~~qll~f~yryt~~vL~DA~vys~har----daqlI~rIlk~~Gv~r~   80 (182)
                      .+|++  .|.-|+++.|+....+.+...|.++...|..+|++||..|++|++    ++.-|...|+..|..-|
T Consensus        28 ~ip~~--~I~Rlar~~Gv~rIS~da~~~l~~~le~fi~~I~~dA~~~a~HakRKTVt~~DV~~ALkr~g~~lY   98 (102)
T 1id3_B           28 GITKP--AIRRLARRGGVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQGRTLY   98 (102)
T ss_dssp             GSCHH--HHHHHHHHTTCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHTTCCEE
T ss_pred             CCCHH--HHHHHHHHcCchhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHHHHHHcCCCCC
Confidence            36766  489999999999999999999999999999999999999999998    45667777777775433

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

Probab=95.81  E-value=0.0099  Score=43.88  Aligned_cols=65  Identities=14%  Similarity=0.347  Sum_probs=53.9

Q ss_pred             CCCchHHHHHHHHHHcCCCccChHHHHHHHHHHHhhhcccccccHhhhhhhhh----HHHHHHHHHhcCCc
Q psy8542          12 KLPRDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHARD----AQVIVNMFQEAGIK   78 (182)
Q Consensus        12 ~~prda~~i~~il~~~gi~~yep~v~~qll~f~yryt~~vL~DA~vys~hard----aqlI~rIlk~~Gv~   78 (182)
                      .+|+.  .|+-|+++.|+....+.+...|-++.-.|..+|++||..|++|++.    +.-|...++..|..
T Consensus        29 gip~~--~I~Rlar~~G~~rIs~~a~~~l~~vle~~~~~V~~dA~~~a~hakRktvt~~DV~~Alr~~g~~   97 (103)
T 2yfw_B           29 GITKP--AIRRLARRGGVKRISGLIYEEVRNVLKTFLESVIRDAVTYTEHAKRKTVTSLDVVYALKRQGRT   97 (103)
T ss_dssp             -CCHH--HHHHHHHHTTCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHHC--
T ss_pred             cCCHH--HHHHHHHHcCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHHHHHHcCCC
Confidence            36766  4899999999999999999999999999999999999999999983    35566666666643

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

Probab=95.69  E-value=0.012  Score=43.45  Aligned_cols=67  Identities=16%  Similarity=0.332  Sum_probs=56.4

Q ss_pred             CCCchHHHHHHHHHHcCCCccChHHHHHHHHHHHhhhcccccccHhhhhhhhh----HHHHHHHHHhcCCccc
Q psy8542          12 KLPRDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHARD----AQVIVNMFQEAGIKNY   80 (182)
Q Consensus        12 ~~prda~~i~~il~~~gi~~yep~v~~qll~f~yryt~~vL~DA~vys~hard----aqlI~rIlk~~Gv~r~   80 (182)
                      .+|+.  .|+-|+++.|+....+.+...|-+..-.|..+|++||..|++|++.    +.-|...++..|..-|
T Consensus        29 gip~~--~I~Rlar~~G~~rIs~~a~~~l~~vle~~~~~V~~dA~~~a~hakRktIt~~DV~~Alr~~g~~lY   99 (103)
T 1tzy_D           29 GITKP--AIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLY   99 (103)
T ss_dssp             GSCHH--HHHHHHHHTTCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHTTCEEE
T ss_pred             cCCHH--HHHHHHHHcCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHHcCCCCc
Confidence            36666  5899999999999999999999999999999999999999999983    4566667777775433

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=92.20  E-value=0.79  Score=38.18  Aligned_cols=60  Identities=13%  Similarity=0.197  Sum_probs=50.1

Q ss_pred             HHHHHHHhcCCcccChHHHHHHHHHHH----HHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHh
Q psy8542          67 VIVNMFQEAGIKNYDPRCVQQMLEFVN----NYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQ  127 (182)
Q Consensus        67 lI~rIlk~~Gv~r~sp~v~~qLle~~~----ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r  127 (182)
                      ++...++..|+ .+++++...+.+.+.    |++..+++.|..+|...|+..|+.+||+.|++..
T Consensus       267 il~~~~~~~~~-~~~~~~l~~l~~~~~~G~~r~~~~ll~~a~~~A~~~~~~~It~~~v~~a~~~~  330 (368)
T 3uk6_A          267 ILRIRCEEEDV-EMSEDAYTVLTRIGLETSLRYAIQLITAASLVCRKRKGTEVQVDDIKRVYSLF  330 (368)
T ss_dssp             HHHHHHHHTTC-CBCHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHS
T ss_pred             HHHHHHHHcCC-CCCHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHh
Confidence            44445555665 489999999999885    7899999999999999999999999999999853

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

Probab=90.08  E-value=2.2  Score=32.39  Aligned_cols=61  Identities=15%  Similarity=0.284  Sum_probs=48.7

Q ss_pred             HHHHHHHHHhcC----CcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCC---CCC---HHHHHHHHH
Q psy8542          65 AQVIVNMFQEAG----IKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKK---TVD---VEDIKLAIT  125 (182)
Q Consensus        65 aqlI~rIlk~~G----v~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRk---tI~---~eDVrLAI~  125 (182)
                      +++++.|..+..    --|+++.++..|-|.+|.|..++.+|+...|-||-|.   .|+   .+.++-+++
T Consensus         8 ~RLVREI~~~~~~~~~~lRfq~~Al~ALQeAsEayLV~lFEd~nlcaiHA~~gGvkRIS~~iy~e~r~vl~   78 (121)
T 2ly8_A            8 ARLVKEVTDEFTTKDQDLRWQSMAIMALQEASEAYLVGLLEHTNLLALHLVPRGSKRISGLIYEEVRAVLK   78 (121)
T ss_dssp             HHHHHHHHHHHTTCCSSCCBCHHHHHHHHHHHHHHHHHHHHHHHHHTTTCCCCCSSCCSSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCCCCccccHHHHHHHHHHHHHHHHHHHHHHhHHHHcCCccCccchhHHHHHHHHHHHH
Confidence            478888887642    3589999999999999999999999999999999664   454   445555554

>4dra_E Centromere protein X; DNA binding complex, DNA damage repair, histone-fold, DNA BI protein; 2.41A {Homo sapiens} PDB: 4drb_J

Probab=89.02  E-value=2.1  Score=30.61  Aligned_cols=60  Identities=12%  Similarity=0.218  Sum_probs=52.1

Q ss_pred             hHHHHHHHHHhcCC----cccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHH
Q psy8542          64 DAQVIVNMFQEAGI----KNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAI  124 (182)
Q Consensus        64 daqlI~rIlk~~Gv----~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI  124 (182)
                      ...+|.+|++ ..+    +++++++...+.+++.-|+.|...-|...|+--|...|+.+|++--+
T Consensus        14 ~~~li~ril~-~~F~~~kTkIs~dAl~l~aeyl~iFV~EAv~RA~~~a~~e~~~~le~e~LEki~   77 (84)
T 4dra_E           14 RKELVSRLLH-LHFKDDKTKVSGDALQLMVELLKVFVVEAAVRGVRQAQAEDALRVDVDQLEKVL   77 (84)
T ss_dssp             CHHHHHHHHH-TTCSSTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHH
T ss_pred             CHHHHHHHHH-HHhcCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHH
Confidence            4578999998 555    47999999999999999999999999999887788899999997643

>3bos_A Putative DNA replication factor; P-loop containing nucleoside triphosphate hydrolases, struct genomics; HET: MSE CDP; 1.75A {Shewanella amazonensis} PDB: 3sc3_A

Probab=88.68  E-value=1.5  Score=33.37  Aligned_cols=59  Identities=7%  Similarity=0.044  Sum_probs=45.3

Q ss_pred             HHHHHHHHHhcCCcccChHHHHHHHHHHH---HHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHH
Q psy8542          65 AQVIVNMFQEAGIKNYDPRCVQQMLEFVN---NYTTTILEDSRVYANHAKKKTVDVEDIKLAIT  125 (182)
Q Consensus        65 aqlI~rIlk~~Gv~r~sp~v~~qLle~~~---ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~  125 (182)
                      .+++..+++..|+ .+++++...+.+.+.   |.+..+++.+..+|...+ ++|+.+||+.+++
T Consensus       180 ~~~l~~~~~~~~~-~~~~~~~~~l~~~~~g~~r~l~~~l~~~~~~a~~~~-~~It~~~v~~~l~  241 (242)
T 3bos_A          180 LAALQRRAAMRGL-QLPEDVGRFLLNRMARDLRTLFDVLDRLDKASMVHQ-RKLTIPFVKEMLR  241 (242)
T ss_dssp             HHHHHHHHHHTTC-CCCHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHT-CCCCHHHHHHHHT
T ss_pred             HHHHHHHHHHcCC-CCCHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHhC-CCCcHHHHHHHhh
Confidence            3466666677776 589999998888776   566778888888886655 5699999998874

>1g8p_A Magnesium-chelatase 38 kDa subunit; parallel beta sheet, P-loop, rossman fold, AAA+, photosynthesis, metal transport; 2.10A {Rhodobacter capsulatus} SCOP: c.37.1.20 PDB: 2x31_G

Probab=88.04  E-value=2.7  Score=34.45  Aligned_cols=54  Identities=17%  Similarity=0.127  Sum_probs=46.0

Q ss_pred             ccChHHHHHHHHHHH-------HHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhcCCCC
Q psy8542          79 NYDPRCVQQMLEFVN-------NYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQLSGSF  132 (182)
Q Consensus        79 r~sp~v~~qLle~~~-------ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~~~~F  132 (182)
                      .+++++...+.+++.       |....+++-|..+|.-.|+.+|+.+||+.|+.....+.+
T Consensus       267 ~ls~~~~~~l~~~~~~~~~~~~R~~~~ll~~a~~~A~~~~~~~v~~~~v~~a~~~~l~~r~  327 (350)
T 1g8p_A          267 EAPNTALYDCAALCIALGSDGLRGELTLLRSARALAALEGATAVGRDHLKRVATMALSHRL  327 (350)
T ss_dssp             BCCHHHHHHHHHHHHHSSSCSHHHHHHHHHHHHHHHHHTTCSBCCHHHHHHHHHHHHGGGC
T ss_pred             CCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHHHHhhcc
Confidence            799999999998876       677889999999999899999999999999986544444

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

Probab=86.67  E-value=0.61  Score=32.27  Aligned_cols=53  Identities=17%  Similarity=0.302  Sum_probs=44.6

Q ss_pred             CCCCchHHHHHHHHHHcCCCccChHHHHHHHHHHHhhhcccccccHhhhhhhhhH
Q psy8542          11 SKLPRDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHARDA   65 (182)
Q Consensus        11 ~~~prda~~i~~il~~~gi~~yep~v~~qll~f~yryt~~vL~DA~vys~harda   65 (182)
                      ..+|.+  .|..|.+|.||+.-.+.+...|-+-.=-+-.+|.++|..|+.|+++.
T Consensus         5 s~lp~~--~v~~iaes~Gi~~lsddaa~~LA~dvEyr~~eI~qeA~kfmrHakRk   57 (70)
T 1taf_B            5 SSISAE--SMKVIAESIGVGSLSDDAAKELAEDVSIKLKRIVQDAAKFMNHAKRQ   57 (70)
T ss_dssp             CCCCHH--HHHHHHHHTTCCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCS
T ss_pred             ccCCHH--HHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCC
Confidence            346654  68999999999999999999998766666699999999999999743

>2c9o_A RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-binding, chromatin regulator, growth regulation, hydrolase, nuclear protein, DNA recombination; HET: ADP; 2.2A {Homo sapiens} PDB: 2xsz_A*

Probab=85.84  E-value=3  Score=36.68  Aligned_cols=65  Identities=15%  Similarity=0.258  Sum_probs=50.4

Q ss_pred             hHHHHHHHH----HhcCCcccChHHHHHHHHHH-H---HHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhcC
Q psy8542          64 DAQVIVNMF----QEAGIKNYDPRCVQQMLEFV-N---NYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQLS  129 (182)
Q Consensus        64 daqlI~rIl----k~~Gv~r~sp~v~~qLle~~-~---ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~~  129 (182)
                      +..-+..++    +..|+. +++++...+..++ .   |++..+++.|..+|.-.|+..|+.+||+.|+..-.+
T Consensus       367 ~~~e~~~iL~~~~~~~~~~-~~~~~~~~i~~~a~~g~~r~a~~ll~~a~~~A~~~~~~~v~~~~v~~~~~~~~d  439 (456)
T 2c9o_A          367 TPQEMKQIIKIRAQTEGIN-ISEEALNHLGEIGTKTTLRYSVQLLTPANLLAKINGKDSIEKEHVEEISELFYD  439 (456)
T ss_dssp             CHHHHHHHHHHHHHHHTCC-BCHHHHHHHHHHHHHSCHHHHHHTHHHHHHHHHHTTCSSBCHHHHHHHHHHSCC
T ss_pred             CHHHHHHHHHHHHHHhCCC-CCHHHHHHHHHHccCCCHHHHHHHHHHHHHHHhhcCCCccCHHHHHHHHHHhcC
Confidence            444444444    344653 8999999888887 3   789999999999999999999999999999875443

>3b0b_C CENP-X, centromere protein X; histone fold, DNA binding, DNA, nucleus, DNA binding protein; 2.15A {Gallus gallus} PDB: 3vh5_D 3vh6_D

Probab=85.21  E-value=2.8  Score=29.66  Aligned_cols=60  Identities=12%  Similarity=0.202  Sum_probs=49.8

Q ss_pred             hHHHHHHHHHhc---CCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHH
Q psy8542          64 DAQVIVNMFQEA---GIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLA  123 (182)
Q Consensus        64 daqlI~rIlk~~---Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLA  123 (182)
                      +..+|.+|++..   --+++++++...+.+++.-|+.|...-|..-|+--|...|+.+|++--
T Consensus        10 ~~~lI~ril~~~f~~~ktrI~~dAl~l~aeyl~iFV~EAv~RA~~~a~~e~~~~le~~~LEki   72 (81)
T 3b0b_C           10 RKETVERLLRLHFRDGRTRVNGDALLLMAELLKVFVREAAARAARQAQAEDLEKVDIEHVEKV   72 (81)
T ss_dssp             CHHHHHHHHHHHCCSTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHH
T ss_pred             CHHHHHHHHHHHhccCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCeecHHHHHHH
Confidence            445677777751   245799999999999999999999999999888778889999999763

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=84.13  E-value=4.2  Score=37.20  Aligned_cols=51  Identities=20%  Similarity=0.208  Sum_probs=45.2

Q ss_pred             CCcccChHHHHHHHHHHH-------------HHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHH
Q psy8542          76 GIKNYDPRCVQQMLEFVN-------------NYTTTILEDSRVYANHAKKKTVDVEDIKLAITN  126 (182)
Q Consensus        76 Gv~r~sp~v~~qLle~~~-------------ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~  126 (182)
                      ....+++++...|++...             |....+++.|..+|...++..|+.+||+.|++.
T Consensus       311 ~~~~ls~eAl~~Li~~~~r~~g~r~~l~~~~R~l~~llr~A~~~A~~~~~~~I~~edv~~A~~~  374 (604)
T 3k1j_A          311 KIPHFTKEAVEEIVREAQKRAGRKGHLTLRLRDLGGIVRAAGDIAVKKGKKYVEREDVIEAVKM  374 (604)
T ss_dssp             SSCCBBHHHHHHHHHHHHHTTCSTTEEECCHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHH
T ss_pred             CcccCCHHHHHHHHHHHhhhhccccccccCHHHHHHHHHHHHHHHHhcCcccccHHHHHHHHHh
Confidence            456899999999999874             667789999999999999999999999999964

>1bh9_B TAFII28; histone fold, tata binding protein, transcription regulation complex; HET: PMB; 2.60A {Homo sapiens} SCOP: a.22.1.3 PDB: 1bh8_B*

Probab=83.19  E-value=9.1  Score=27.33  Aligned_cols=62  Identities=10%  Similarity=0.104  Sum_probs=51.7

Q ss_pred             HHHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcC-CCCCCHHHHHHHHHHh
Q psy8542          66 QVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAK-KKTVDVEDIKLAITNQ  127 (182)
Q Consensus        66 qlI~rIlk~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAg-RktI~~eDVrLAI~~r  127 (182)
                      ..|++++....-..++++++.-+--+++-|+.++.+.|....+.-| ...|.-.-|+.|....
T Consensus        20 ~~vKrl~~~~~~~~v~~~v~i~v~glaKvfVgelVE~A~~V~~~~~~~~Pl~P~HireA~rrl   82 (89)
T 1bh9_B           20 AAIKRLIQSITGTSVSQNVVIAMSGISKVFVGEVVEEALDVCEKWGEMPPLQPKHMREAVRRL   82 (89)
T ss_dssp             HHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSSCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcHHHHHHHHHH
Confidence            3566666655556799999999999999999999999999998765 4589999999998754

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=82.08  E-value=6.5  Score=32.19  Aligned_cols=50  Identities=16%  Similarity=0.145  Sum_probs=44.4

Q ss_pred             cccChHHHHHHHHHHH------HHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHh
Q psy8542          78 KNYDPRCVQQMLEFVN------NYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQ  127 (182)
Q Consensus        78 ~r~sp~v~~qLle~~~------ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r  127 (182)
                      ..+++++...+.+.+.      |++..+++.|..+|...|+.+|+.+||+.|++..
T Consensus       221 ~~~~~~~~~~l~~~~~~~~G~~r~~~~~l~~a~~~a~~~~~~~i~~~~v~~a~~~~  276 (387)
T 2v1u_A          221 GVLDPDVVPLCAALAAREHGDARRALDLLRVAGEIAERRREERVRREHVYSARAEI  276 (387)
T ss_dssp             TTBCSSHHHHHHHHHHSSSCCHHHHHHHHHHHHHHHHHTTCSCBCHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHhccCHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHH
Confidence            4688999999999988      7888999999999988899999999999998754

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

Probab=81.27  E-value=2  Score=30.21  Aligned_cols=45  Identities=16%  Similarity=0.217  Sum_probs=36.5

Q ss_pred             HHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcC
Q psy8542          67 VIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAK  111 (182)
Q Consensus        67 lI~rIlk~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAg  111 (182)
                      =|..|.++.|++.++++|+..+-=.++.....+++.-...|.|.-
T Consensus        11 ri~~I~~k~gl~~~~~dv~~~iS~a~qeRLr~llekl~~~a~~R~   55 (75)
T 1h3o_A           11 RILEIGKKHGITELHPDVVSYVSHATQQRLQNLVEKISETAQQKN   55 (75)
T ss_dssp             HHHHHHHTTTCCEECTTHHHHHHHHHHHHHHHHHHHHHC------
T ss_pred             HHHHHHHhcCCCcCChhHHHHhHHHHHHHHHHHHHHHHHHHHhhh
Confidence            366788999999999999999999999999999999999999853

>3ksy_A SOS-1, SON of sevenless homolog 1; RAS, RAS activator, disease mutation, guanine-nucleotide releasing factor, signaling protein; 3.18A {Homo sapiens} PDB: 1xd4_A 1xdv_A 1q9c_A

Probab=80.67  E-value=4.3  Score=40.08  Aligned_cols=60  Identities=17%  Similarity=0.213  Sum_probs=54.6

Q ss_pred             HHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHH
Q psy8542          67 VIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITN  126 (182)
Q Consensus        67 lI~rIlk~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~  126 (182)
                      -|+++|+..-+.|++..+..-|..+++--+.+||+=|..+|...+++.|+-.+|.+|+..
T Consensus       109 ~~~~~l~~~~~~r~~~~~~~y~~avleyl~~~~l~la~~~~~~~~~~~i~p~~~~~ai~~  168 (1049)
T 3ksy_A          109 KIHPLLKEVLGYKIDHQVSVYIVAVLEYISADILKLVGNYVRNIRHYEITKQDIKVAMCA  168 (1049)
T ss_dssp             HHHHHHHHHHCSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCBCCHHHHHHHHHH
T ss_pred             HHHHHhhcccccccCCCCcchhHHHHHHHHHHHHHHHHHHHHHcCCceecCccccccccC
Confidence            477878655567999999999999999999999999999999999999999999999964

---

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	182
d1tafa_	68	a.22.1.3 (A:) TAF(II)42 {Fruit fly (Drosophila mel	5e-26
d1tafa_	68	a.22.1.3 (A:) TAF(II)42 {Fruit fly (Drosophila mel	5e-19
d1f1ea_	151	a.22.1.2 (A:) Archaeal histone {Archaeon Methanopy	9e-07
d1f1ea_	151	a.22.1.2 (A:) Archaeal histone {Archaeon Methanopy	0.002
d2huec1	82	a.22.1.1 (C:20-101) Histone H4 {African clawed fro	2e-06
d1htaa_	68	a.22.1.2 (A:) Archaeal histone {Archaeon Methanoth	4e-05
d1tzyc_	95	a.22.1.1 (C:) Histone H3 {Chicken (Gallus gallus),	4e-04
d1ku5a_	66	a.22.1.2 (A:) Archaeal histone {Archaeon (Pyrococc	5e-04
d1q9ca_	172	a.22.1.3 (A:) Histone domain of Son of sevenless p	0.004

>d1tafa_ a.22.1.3 (A:) TAF(II)42 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 68

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: TAF(II)42
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 92.4 bits (230), Expect = 5e-26
 Identities = 33/66 (50%), Positives = 52/66 (78%)

Query: 63  RDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKL 122
           +DAQVI+++ +E  ++ Y+PR V Q+LEF   Y T+IL+D++VYANHA+KKT+D++D++L
Sbjct: 2   KDAQVIMSILKELNVQEYEPRVVNQLLEFTFRYVTSILDDAKVYANHARKKTIDLDDVRL 61

Query: 123 AITNQL 128
           A    L
Sbjct: 62  ATEVTL 67

>d1tafa_ a.22.1.3 (A:) TAF(II)42 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 68

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: TAF(II)42
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 74.7 bits (184), Expect = 5e-19
 Identities = 27/57 (47%), Positives = 43/57 (75%)

Query: 14 PRDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHARDAQVIVN 70
          P+DAQVI+++ +E  ++ Y+PR V Q+LEF   Y T+IL+D++VYANHAR   + ++
Sbjct: 1  PKDAQVIMSILKELNVQEYEPRVVNQLLEFTFRYVTSILDDAKVYANHARKKTIDLD 57

>d1f1ea_ a.22.1.2 (A:) Archaeal histone {Archaeon Methanopyrus kandleri [TaxId: 2320]} Length = 151

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

 Score = 44.4 bits (105), Expect = 9e-07
 Identities = 17/72 (23%), Positives = 30/72 (41%)

Query: 58  YANHARDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDV 117
           Y         +  + + AGI+      V    + +   T  + E +  YA+   +KTV  
Sbjct: 75  YDGELFGRATVRRILKRAGIERASSDAVDLYNKLICRATEELGEKAAEYADEDGRKTVQG 134

Query: 118 EDIKLAITNQLS 129
           ED++ AIT  + 
Sbjct: 135 EDVEKAITYSMP 146

>d1f1ea_ a.22.1.2 (A:) Archaeal histone {Archaeon Methanopyrus kandleri [TaxId: 2320]} Length = 151

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

 Score = 35.1 bits (81), Expect = 0.002
 Identities = 7/45 (15%), Positives = 17/45 (37%)

Query: 86  QQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQLSG 130
             + +FV      +   ++   + + KKT+  E +K      +  
Sbjct: 26  DTIYDFVPTMAEYVANAAKSVLDASGKKTLMEEHLKALADVLMVE 70

>d2huec1 a.22.1.1 (C:20-101) Histone H4 {African clawed frog (Xenopus laevis) [TaxId: 8355]} Length = 82

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

 Score = 42.1 bits (99), Expect = 2e-06
 Identities = 13/56 (23%), Positives = 25/56 (44%)

Query: 68  IVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLA 123
           I  + +  G+K       ++    +  +   ++ D+  Y  HAK+KTV   D+  A
Sbjct: 15  IRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYA 70

>d1htaa_ a.22.1.2 (A:) Archaeal histone {Archaeon Methanothermus fervidus, histone A [TaxId: 2180]} Length = 68

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

 Score = 37.8 bits (88), Expect = 4e-05
 Identities = 14/57 (24%), Positives = 25/57 (43%)

Query: 68  IVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAI 124
           I  + + AG +         + + +      I  ++   A HA +KT+  EDI+LA 
Sbjct: 9   IGRIIKNAGAERVSDDARIALAKVLEEMGEEIASEAVKLAKHAGRKTIKAEDIELAR 65

>d1tzyc_ a.22.1.1 (C:) Histone H3 {Chicken (Gallus gallus), erythrocytes [TaxId: 9031]} Length = 95

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Nucleosome core histones
domain: Histone H3
species: Chicken (Gallus gallus), erythrocytes [TaxId: 9031]

 Score = 35.9 bits (83), Expect = 4e-04
 Identities = 14/39 (35%), Positives = 23/39 (58%), Gaps = 3/39 (7%)

Query: 85  VQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLA 123
           +Q+  E    Y   + ED+ + A HAK+ T+  +DI+LA
Sbjct: 52  LQEASE---AYLVGLFEDTNLCAIHAKRVTIMPKDIQLA 87

>d1ku5a_ a.22.1.2 (A:) Archaeal histone {Archaeon (Pyrococcus horikoshii) [TaxId: 53953]} Length = 66

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

 Score = 34.7 bits (80), Expect = 5e-04
 Identities = 19/60 (31%), Positives = 34/60 (56%)

Query: 67  VIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITN 126
            +  + ++AG +    +  + + E++  Y   I + +  +A HA +KTV VEDIKLAI +
Sbjct: 7   PVDRLIRKAGAERVSEQAAKVLAEYLEEYAIEIAKKAVEFARHAGRKTVKVEDIKLAIKS 66

>d1q9ca_ a.22.1.3 (A:) Histone domain of Son of sevenless protein {Human (Homo sapiens) [TaxId: 9606]} Length = 172

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: Histone domain of Son of sevenless protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.4 bits (79), Expect = 0.004
 Identities = 7/33 (21%), Positives = 16/33 (48%)

Query: 94  NYTTTILEDSRVYANHAKKKTVDVEDIKLAITN 126
             +  IL+ +  Y  + +   +  +DIK+A+  
Sbjct: 131 YISADILKLAGNYVRNIRHYEITKQDIKVAMCA 163

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	182
d1tafa_	68	TAF(II)42 {Fruit fly (Drosophila melanogaster) [Ta	100.0
d1tafa_	68	TAF(II)42 {Fruit fly (Drosophila melanogaster) [Ta	99.51
d2huec1	82	Histone H4 {African clawed frog (Xenopus laevis) [	99.39
d1htaa_	68	Archaeal histone {Archaeon Methanothermus fervidus	99.12
d1f1ea_	151	Archaeal histone {Archaeon Methanopyrus kandleri [	99.03
d1ku5a_	66	Archaeal histone {Archaeon (Pyrococcus horikoshii)	99.03
d1q9ca_	172	Histone domain of Son of sevenless protein {Human	98.54
d1f1ea_	151	Archaeal histone {Archaeon Methanopyrus kandleri [	98.5
d1tafb_	70	TAF(II)62 {Fruit fly (Drosophila melanogaster) [Ta	98.18
d1tzyc_	95	Histone H3 {Chicken (Gallus gallus), erythrocytes	98.16
d1n1ja_	87	Nuclear transcription factor Y subunit beta (Nf-Yb	98.13
d1jfia_	66	Negative cofactor 2, NC2, alpha chain {Human (Homo	97.88
d1n1jb_	78	Nuclear transcription factor Y subunit gamma (Nf-Y	97.76
d2bykb1	89	Chrac-14 {Fruit fly (Drosophila melanogaster) [Tax	97.62
d1jfib_	135	Negative cofactor 2, NC2, beta chain {Human (Homo	97.55
d1h3ob_	74	TAF(II)-20, (TAF(II)-15, hTAF12), histone fold dom	96.81
d1f66c_	103	Histone H2A {Human (Homo sapiens), variant H2A.Z [	96.45
d1tzya_	106	Histone H2A {Chicken (Gallus gallus), erythrocytes	96.33
d1u35c1	106	macro-H2A.1, histone domain {Human (Homo sapiens)	96.31
d2byka1	72	Chrac-16 {Fruit fly (Drosophila melanogaster) [Tax	95.77
d1tzyb_	92	Histone H2B {Chicken (Gallus gallus), erythrocytes	94.9
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	93.89
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	93.41
d2huec1	82	Histone H4 {African clawed frog (Xenopus laevis) [	89.48
d1tafb_	70	TAF(II)62 {Fruit fly (Drosophila melanogaster) [Ta	83.35
d1bh9b_	89	TAF(II)28 {Human (Homo sapiens) [TaxId: 9606]}	82.51

>d1tafa_ a.22.1.3 (A:) TAF(II)42 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: TAF(II)42
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=100.00  E-value=2.6e-34  Score=200.79  Aligned_cols=68  Identities=50%  Similarity=0.919  Sum_probs=63.1

Q ss_pred             CchHHHHHHHHHHcCCCccChHHHHHHHHHHHhhhcccccccHhhhhhhhhHHHHHHHHHhcCCcccChHHHHHHHHHHH
Q psy8542          14 PRDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHARDAQVIVNMFQEAGIKNYDPRCVQQMLEFVN   93 (182)
Q Consensus        14 prda~~i~~il~~~gi~~yep~v~~qll~f~yryt~~vL~DA~vys~hardaqlI~rIlk~~Gv~r~sp~v~~qLle~~~   93 (182)
                      |||+|+|++||+||||++||||||+|||||+||||++||+||.+|                                   
T Consensus         1 PrDa~~i~~iL~~~GV~~yeprV~~qlLef~yRYtt~VL~DA~vy-----------------------------------   45 (68)
T d1tafa_           1 PKDAQVIMSILKELNVQEYEPRVVNQLLEFTFRYVTSILDDAKVY-----------------------------------   45 (68)
T ss_dssp             CHHHHHHHHHHHHTTCCCBCTHHHHHHHHHHHHHHHHHHHHHHHH-----------------------------------
T ss_pred             CcHHHHHHHHHHHcCCccccHHHHHHHHHHHHHHHHHHHHHHHHH-----------------------------------
Confidence            999999999999999999999999999999999998888888777                                   


Q ss_pred             HHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhcC
Q psy8542          94 NYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQLS  129 (182)
Q Consensus        94 ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~~  129 (182)
                                   |+||||++|+++||||||++|++
T Consensus        46 -------------s~HA~k~~id~dDVkLAi~~r~d   68 (68)
T d1tafa_          46 -------------ANHARKKTIDLDDVRLATEVTLD   68 (68)
T ss_dssp             -------------HHHTTCSSBCHHHHHHHHHHTC-
T ss_pred             -------------HhhcCCCCCCHHHHHHHHHhccC
Confidence                         66789999999999999999874

>d1tafa_ a.22.1.3 (A:) TAF(II)42 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: TAF(II)42
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.51  E-value=8.5e-15  Score=101.26  Aligned_cols=42  Identities=45%  Similarity=0.869  Sum_probs=41.4

Q ss_pred             hhhHHHHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHH
Q psy8542          62 ARDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDS  103 (182)
Q Consensus        62 ardaqlI~rIlk~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA  103 (182)
                      |+|+++|+.||+++||++|+|+|++|||||+|||+++||+||
T Consensus         1 PrDa~~i~~iL~~~GV~~yeprV~~qlLef~yRYtt~VL~DA   42 (68)
T d1tafa_           1 PKDAQVIMSILKELNVQEYEPRVVNQLLEFTFRYVTSILDDA   42 (68)
T ss_dssp             CHHHHHHHHHHHHTTCCCBCTHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHcCCccccHHHHHHHHHHHHHHHHHHHHHH
Confidence            899999999999999999999999999999999999999998

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

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

Probab=99.39  E-value=1.9e-13  Score=97.08  Aligned_cols=60  Identities=22%  Similarity=0.387  Sum_probs=58.5

Q ss_pred             HHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHH
Q psy8542          67 VIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITN  126 (182)
Q Consensus        67 lI~rIlk~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~  126 (182)
                      .|++|++++|++++|++++..|.+.++.|..+|++||..|++|++||||+.+||.+|++.
T Consensus        14 ~i~Riar~~Gv~ris~d~~~~l~~~l~~~l~~i~~~a~~~~~hakRKTvt~~DV~~Alkr   73 (82)
T d2huec1          14 AIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKR   73 (82)
T ss_dssp             HHHHHHHHTTCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTT
T ss_pred             HHHHHHHHcCcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHh
Confidence            699999999999999999999999999999999999999999999999999999999973

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

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

Probab=99.12  E-value=1.4e-10  Score=78.53  Aligned_cols=61  Identities=23%  Similarity=0.305  Sum_probs=58.3

Q ss_pred             HHHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHH
Q psy8542          66 QVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITN  126 (182)
Q Consensus        66 qlI~rIlk~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~  126 (182)
                      ..|++|+++.|+.+++.+++..+.+.++.|..+++++|..++.|+|||||+.+||..|++.
T Consensus         7 a~I~ri~k~~~~~ris~ea~~~l~~~~e~fi~~l~~~a~~~a~~~kRkTi~~~DV~~Alk~   67 (68)
T d1htaa_           7 APIGRIIKNAGAERVSDDARIALAKVLEEMGEEIASEAVKLAKHAGRKTIKAEDIELARKM   67 (68)
T ss_dssp             HHHHHHHHHTTCSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHT
T ss_pred             HHHHHHHHHCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHh
Confidence            3588999999999999999999999999999999999999999999999999999999973

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

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

Probab=99.03  E-value=7.8e-10  Score=85.64  Aligned_cols=107  Identities=20%  Similarity=0.326  Sum_probs=95.4

Q ss_pred             HHHHHHH-cCCCccChHHHHHHHHHHHhhhcccccccHhhhhhhhh-----------------------------HHHHH
Q psy8542          20 IVNMFQE-AGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHARD-----------------------------AQVIV   69 (182)
Q Consensus        20 i~~il~~-~gi~~yep~v~~qll~f~yryt~~vL~DA~vys~hard-----------------------------aqlI~   69 (182)
                      |.-||+. .|-.--.......|.+|.--+...|-.+|..++.|.++                             ...|+
T Consensus         7 I~rilk~~~~~~ris~da~~~l~~~~~~~~~~Ia~eA~~l~~~~~rKTi~~edi~~a~~~~~~~~~~~~~~~~fp~a~Ik   86 (151)
T d1f1ea_           7 IERIFRQGIGERRLSQDAKDTIYDFVPTMAEYVANAAKSVLDASGKKTLMEEHLKALADVLMVEGVEDYDGELFGRATVR   86 (151)
T ss_dssp             HHHHHHTTSTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHHHHTCTTSTTCCSCCCCHHHHH
T ss_pred             HHHHHHHhCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHhcccccccccccCccCHHHHH
Confidence            5667765 47777788888889998888888899999999999752                             12799


Q ss_pred             HHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHH
Q psy8542          70 NMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITN  126 (182)
Q Consensus        70 rIlk~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~  126 (182)
                      +|+++.|+.+++.+++..|.+.++.|+.+++++|..+|.|+||+||+.+||.+|+..
T Consensus        87 Ri~k~~g~~ris~dA~~~l~~~~E~fi~~l~~~A~~~a~~~kRkTI~~~DI~~Av~~  143 (151)
T d1f1ea_          87 RILKRAGIERASSDAVDLYNKLICRATEELGEKAAEYADEDGRKTVQGEDVEKAITY  143 (151)
T ss_dssp             HHHHHTTCCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHH
T ss_pred             HHHHcCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999974

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

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

Probab=99.03  E-value=2.4e-10  Score=77.07  Aligned_cols=60  Identities=32%  Similarity=0.539  Sum_probs=57.8

Q ss_pred             HHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHH
Q psy8542          67 VIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITN  126 (182)
Q Consensus        67 lI~rIlk~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~  126 (182)
                      .|++|+++.|..+++.+++..+.+.++.|...++++|..++.|+|||||+.+||..|+++
T Consensus         7 ~I~rI~k~~~~~ris~ea~~~l~~a~e~Fi~~l~~~a~~~a~~~~RKTI~~~Dv~~Al~s   66 (66)
T d1ku5a_           7 PVDRLIRKAGAERVSEQAAKVLAEYLEEYAIEIAKKAVEFARHAGRKTVKVEDIKLAIKS   66 (66)
T ss_dssp             HHHHHHHHTTCSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHTC
T ss_pred             HHHHHHHhCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHhC
Confidence            589999999999999999999999999999999999999999999999999999999863

>d1q9ca_ a.22.1.3 (A:) Histone domain of Son of sevenless protein {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: Histone domain of Son of sevenless protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.54  E-value=8.2e-08  Score=76.07  Aligned_cols=60  Identities=17%  Similarity=0.225  Sum_probs=58.1

Q ss_pred             HHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHH
Q psy8542          67 VIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITN  126 (182)
Q Consensus        67 lI~rIlk~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~  126 (182)
                      -|+++||+.|..|++..+...|..+++.++.+|++.|..+|.|+||++|+.+||++||..
T Consensus       104 rv~rlLk~~~a~RVs~~A~vyLaavLEyl~aeILelAgn~a~~~krkrItp~dI~lAi~n  163 (172)
T d1q9ca_         104 KIHPLLKEVLGYKIDHQVSVYIVAVLEYISADILKLAGNYVRNIRHYEITKQDIKVAMCA  163 (172)
T ss_dssp             HHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSBCCHHHHHHHHHT
T ss_pred             HHHHHHHhccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCceecHHHHHHHHhC
Confidence            589999999999999999999999999999999999999999999999999999999974

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

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

Probab=98.50  E-value=1.2e-07  Score=73.10  Aligned_cols=63  Identities=16%  Similarity=0.268  Sum_probs=58.4

Q ss_pred             HHHHHHHHh-cCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhc
Q psy8542          66 QVIVNMFQE-AGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQL  128 (182)
Q Consensus        66 qlI~rIlk~-~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~  128 (182)
                      ..|.+|+++ .|..++|.++...|.+++..+...|+.+|..+++|+|||||+.+||+.|+...+
T Consensus         5 a~I~rilk~~~~~~ris~da~~~l~~~~~~~~~~Ia~eA~~l~~~~~rKTi~~edi~~a~~~~~   68 (151)
T d1f1ea_           5 AAIERIFRQGIGERRLSQDAKDTIYDFVPTMAEYVANAAKSVLDASGKKTLMEEHLKALADVLM   68 (151)
T ss_dssp             HHHHHHHHTTSTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHHHHT
T ss_pred             cHHHHHHHHhCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHhcc
Confidence            358899986 699999999999999999999999999999999999999999999999997544

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

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

Probab=98.18  E-value=3.9e-06  Score=57.37  Aligned_cols=60  Identities=20%  Similarity=0.386  Sum_probs=57.1

Q ss_pred             HHHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHH
Q psy8542          66 QVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAIT  125 (182)
Q Consensus        66 qlI~rIlk~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~  125 (182)
                      ..|+-|..+.|+...++++...|.+-.+--..+|+++|..+-.|++|++++.+||-.|++
T Consensus        10 esik~iAeS~Gi~~l~de~a~~LA~DveYRl~eiiQeA~KFMrhskR~~Ltt~Did~ALk   69 (70)
T d1tafb_          10 ESMKVIAESIGVGSLSDDAAKELAEDVSIKLKRIVQDAAKFMNHAKRQKLSVRDIDMSLK   69 (70)
T ss_dssp             HHHHHHHHHTTCCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHC
T ss_pred             HHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCcCcHHHHHHHHc
Confidence            458889999999999999999999999999999999999999999999999999999974

>d1tzyc_ a.22.1.1 (C:) Histone H3 {Chicken (Gallus gallus), erythrocytes [TaxId: 9031]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Nucleosome core histones
domain: Histone H3
species: Chicken (Gallus gallus), erythrocytes [TaxId: 9031]

Probab=98.16  E-value=4.1e-06  Score=60.25  Aligned_cols=65  Identities=23%  Similarity=0.294  Sum_probs=58.1

Q ss_pred             HHHHHHHHHhcC-CcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhcC
Q psy8542          65 AQVIVNMFQEAG-IKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQLS  129 (182)
Q Consensus        65 aqlI~rIlk~~G-v~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~~  129 (182)
                      .++|+.|..+.+ --++++.+...|-+.+|.|..++++||...|-|++|.||...|++||...|+.
T Consensus        28 ~RLVRei~~~~~~~~r~~~~Al~aLQea~E~yLv~lfeda~~~a~HakRvTl~~kD~~LarrirG~   93 (95)
T d1tzyc_          28 QRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE   93 (95)
T ss_dssp             HHHHHHHHHHHCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHhcCCCCEeeHHHHHHHHHHHHHHHHHHHHHhHHHHHhcCCCcCCHHHHHHHHHHhcc
Confidence            468888887642 23799999999999999999999999999999999999999999999988875

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

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

Probab=98.13  E-value=4.8e-06  Score=58.16  Aligned_cols=67  Identities=18%  Similarity=0.267  Sum_probs=61.5

Q ss_pred             HHHHHHHhc--CCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhcCCCCC
Q psy8542          67 VIVNMFQEA--GIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQLSGSFA  133 (182)
Q Consensus        67 lI~rIlk~~--Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~~~~F~  133 (182)
                      .|.+|+|+.  +...++.+++..+...++-|+..+..+|...|...|||||+.+||..|++....+.|-
T Consensus         7 ~v~ri~K~~~p~~~~is~ea~~~i~~a~e~Fi~~lt~~A~~~a~~~~rKTI~~~dv~~Al~~~~~~~fl   75 (87)
T d1n1ja_           7 NVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDILFAMSTLGFDSYV   75 (87)
T ss_dssp             HHHHHHHHTSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHTTCGGGH
T ss_pred             HHHHHHHHhCCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHcCcHhHH
Confidence            578999864  8899999999999999999999999999999999999999999999999987766554

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

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

Probab=97.88  E-value=5.8e-06  Score=55.01  Aligned_cols=59  Identities=14%  Similarity=0.185  Sum_probs=52.0

Q ss_pred             HHHHHHH-hcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHH
Q psy8542          67 VIVNMFQ-EAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAIT  125 (182)
Q Consensus        67 lI~rIlk-~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~  125 (182)
                      -|++|++ +-.+..++.+++..+...++-++.++++.|...+...+|+||+.+||..||+
T Consensus         7 rVkkimk~~~~~~~is~~A~~~~~~a~E~Fi~~l~~~A~~~a~~~krktI~~~dl~~ai~   66 (66)
T d1jfia_           7 RIKKIMQTDEEIGKVAAAVPVIISRALELFLESLLKKACQVTQSRNAKTMTTSHLKQCIE   66 (66)
T ss_dssp             HHHHHHTTSTTCCCBCTTHHHHHHHHHHHHHHHHHHHHHHHHHTC---CBCHHHHHTTCC
T ss_pred             HHHHHHhcCCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHhC
Confidence            4788898 6788899999999999999999999999999999999999999999998874

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

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

Probab=97.76  E-value=2.4e-05  Score=53.18  Aligned_cols=66  Identities=17%  Similarity=0.223  Sum_probs=59.4

Q ss_pred             HHHHHHH-hcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhcCCCC
Q psy8542          67 VIVNMFQ-EAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQLSGSF  132 (182)
Q Consensus        67 lI~rIlk-~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~~~~F  132 (182)
                      -|++|++ +-.+..++.+++..+-..++-++..+.+.|...|...+|+||+.+||..|++....|.|
T Consensus         5 rVkrImK~~~~~~~is~ea~~~i~~a~E~Fi~~l~~~A~~~a~~~~rkti~~~dl~~av~~~~~~~F   71 (78)
T d1n1jb_           5 RIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDIAMAITKFDQFDF   71 (78)
T ss_dssp             HHHHHHTTSTTCCCBCTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHTTCGGGGG
T ss_pred             HHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHhcCChhHH
Confidence            4688887 56778999999999999999999999999999999999999999999999986665555

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

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

Probab=97.62  E-value=0.00018  Score=50.09  Aligned_cols=74  Identities=16%  Similarity=0.147  Sum_probs=61.9

Q ss_pred             HHHHHHHhc--CCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhcCCCCCCCCChhhh
Q psy8542          67 VIVNMFQEA--GIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQLSGSFAKPPPRESK  141 (182)
Q Consensus        67 lI~rIlk~~--Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~~~~F~~pppke~L  141 (182)
                      .|.+|+|+.  +...++.+++..+...++-|+..+...|...|...+|+||+.+||..|++... +.+.-+|-+++|
T Consensus         4 ~i~ri~K~~~p~~~~iskeA~~~i~~aae~FI~~lt~~A~~~a~~~~rKtI~~~dv~~Al~~~~-f~~~~~~l~~~l   79 (89)
T d2bykb1           4 VIGRLIKEALPESASVSKEARAAIARAASVFAIFVTSSSTALAHKQNHKTITAKDILQTLTELD-FESFVPSLTQDL   79 (89)
T ss_dssp             HHHHHHHHHSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHTT-CTTTHHHHHHHH
T ss_pred             HHHHHHHHhCcccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHHCC-cHHHHHHHHHHH
Confidence            478899853  77889999999999999999999999999999999999999999999998654 433334444444

>d1jfib_ a.22.1.3 (B:) Negative cofactor 2, NC2, beta chain {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=97.55  E-value=0.00016  Score=54.22  Aligned_cols=68  Identities=18%  Similarity=0.232  Sum_probs=60.3

Q ss_pred             HHHHHHHhc-CCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhcCCCCCC
Q psy8542          67 VIVNMFQEA-GIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQLSGSFAK  134 (182)
Q Consensus        67 lI~rIlk~~-Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~~~~F~~  134 (182)
                      .|.+|++.. -...++.+++..+.+.++-|+..+...|...|...+|+||+.+||..||.....+.|-.
T Consensus         9 ~I~kI~K~~~~~~~is~dA~~~i~~a~~~Fi~~lt~~A~~~a~~~~RkTi~~~Dv~~Al~~~~f~~f~~   77 (135)
T d1jfib_           9 AINKMIKETLPNVRVANDARELVVNCCTEFIHLISSEANEICNKSEKKTISPEHVIQALESLGFGSYIS   77 (135)
T ss_dssp             HHHHHHHHHSTTCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHHTTGGGHH
T ss_pred             HHHHHHhhCCccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHHHcCcHHHHH
Confidence            467777753 46789999999999999999999999999999999999999999999999877767743

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

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

Probab=96.81  E-value=0.0038  Score=42.48  Aligned_cols=53  Identities=19%  Similarity=0.397  Sum_probs=48.9

Q ss_pred             cCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHh
Q psy8542          75 AGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQ  127 (182)
Q Consensus        75 ~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r  127 (182)
                      -+-...+|+|-..|+++|..|+.+|...|..+|.|.|-++|+.-||.+-++..
T Consensus        17 dp~~~ld~~vee~ll~iADdFV~~V~~~ac~lAKhR~s~~le~kDvql~LeR~   69 (74)
T d1h3ob_          17 DPNEQLDEDVEEMLLQIADDFIESVVTAACQLARHRKSSTLEVKDVQLHLERQ   69 (74)
T ss_dssp             CSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCEECHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCcHHHHHHHHHhh
Confidence            35567999999999999999999999999999999999999999999998754

>d1f66c_ a.22.1.1 (C:) Histone H2A {Human (Homo sapiens), variant H2A.Z [TaxId: 9606]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Nucleosome core histones
domain: Histone H2A
species: Human (Homo sapiens), variant H2A.Z [TaxId: 9606]

Probab=96.45  E-value=0.0045  Score=44.36  Aligned_cols=61  Identities=15%  Similarity=0.136  Sum_probs=55.4

Q ss_pred             HHHHHHHHhcCC-c-ccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHH
Q psy8542          66 QVIVNMFQEAGI-K-NYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITN  126 (182)
Q Consensus        66 qlI~rIlk~~Gv-~-r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~  126 (182)
                      --++++|++... + ++++.++..|...+|.-+.||++-|...+...+++.|+..||.+||..
T Consensus        15 grv~r~L~~~~~~~~rv~~~A~VyLaAvLEYL~aEILelagn~a~~~~~~rItpr~l~lai~n   77 (103)
T d1f66c_          15 GRIHRHLKSRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRG   77 (103)
T ss_dssp             HHHHHHHHHTSCSSCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHHH
T ss_pred             HHHHHHHhccCccceecCCCceeeHHHHHHHHHHHHHHHhhhhhccCCCCeeechhhhccccC
Confidence            357889998775 3 499999999999999999999999999999999999999999999984

>d1tzya_ a.22.1.1 (A:) Histone H2A {Chicken (Gallus gallus), erythrocytes [TaxId: 9031]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Nucleosome core histones
domain: Histone H2A
species: Chicken (Gallus gallus), erythrocytes [TaxId: 9031]

Probab=96.33  E-value=0.0061  Score=43.98  Aligned_cols=61  Identities=18%  Similarity=0.172  Sum_probs=55.5

Q ss_pred             HHHHHHHHh-cCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHH
Q psy8542          66 QVIVNMFQE-AGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITN  126 (182)
Q Consensus        66 qlI~rIlk~-~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~  126 (182)
                      --|+++|++ .-..|++..++.-|..++|--+.|||+-|-.+|...+++.|+-.||.+||+.
T Consensus        16 ~rv~r~Lk~~~~~~rv~~~apVylaAVLEYLtaEiLELAgn~a~~~k~~rItPrhi~lAirn   77 (106)
T d1tzya_          16 GRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRN   77 (106)
T ss_dssp             HHHHHHHHHTTSSSEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHT
T ss_pred             HHHHHHHHcCccccccCCCchHHHHHHHHHHHHHHHHHhhHHHHhcCCceecchhhhhcccC
Confidence            358888987 4557899999999999999999999999999999999999999999999974

>d1u35c1 a.22.1.1 (C:814-919) macro-H2A.1, histone domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Nucleosome core histones
domain: macro-H2A.1, histone domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.31  E-value=0.0058  Score=44.09  Aligned_cols=61  Identities=21%  Similarity=0.156  Sum_probs=55.8

Q ss_pred             HHHHHHHHhc-CCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHH
Q psy8542          66 QVIVNMFQEA-GIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITN  126 (182)
Q Consensus        66 qlI~rIlk~~-Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~  126 (182)
                      .-|+++|++. -..|++..++..|..++|.-+.|||+-|..+|...+++.|+-.||.+||..
T Consensus        15 ~ri~r~Lk~~~~~~rv~~~apVylaAVLEYL~aEILELAgn~a~~~k~~rItprhi~lairn   76 (106)
T d1u35c1          15 GRMLRYIKKGHPKYRIGVGAPVYMAAVLEYLTAEILELAVNAARDNKKGRVTPRHILLAVAN   76 (106)
T ss_dssp             HHHHHHHHHHSTTSEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHH
T ss_pred             HHHHHHHhCCCCccccCCCCchhHHHHHHHHHHHHHHHHHHHHHHcCCCeeecchhhhcccC
Confidence            3578888874 577999999999999999999999999999999999999999999999974

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

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

Probab=95.77  E-value=0.013  Score=39.05  Aligned_cols=59  Identities=5%  Similarity=0.052  Sum_probs=51.4

Q ss_pred             hcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHh-hhcCCCCCCHHHHHHHHHHhcCCCC
Q psy8542          74 EAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYA-NHAKKKTVDVEDIKLAITNQLSGSF  132 (182)
Q Consensus        74 ~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA-~HAgRktI~~eDVrLAI~~r~~~~F  132 (182)
                      +..+.-++.+++..+-..+|-|+.++.++|...+ .+.+++||+-+||..||+....|.|
T Consensus         4 d~dv~~is~ea~~lvskAtElFi~~L~~~a~~~a~~~~~~ktl~~~dl~~aV~~~~~f~F   63 (72)
T d2byka1           4 SMDTGLITNEVLFLMTKCTELFVRHLAGAAYTEEFGQRPGEALKYEHLSQVVNKNKNLEF   63 (72)
T ss_dssp             SSSCSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSCEECHHHHHHHHHTCSTTGG
T ss_pred             CHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCccccHHHHHHHHccCchhhH
Confidence            3456778999999999999999999999998887 5677799999999999987777766

>d1tzyb_ a.22.1.1 (B:) Histone H2B {Chicken (Gallus gallus), erythrocytes [TaxId: 9031]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Nucleosome core histones
domain: Histone H2B
species: Chicken (Gallus gallus), erythrocytes [TaxId: 9031]

Probab=94.90  E-value=0.048  Score=38.16  Aligned_cols=61  Identities=18%  Similarity=0.270  Sum_probs=50.7

Q ss_pred             HHHHHHhcC-CcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHhc
Q psy8542          68 IVNMFQEAG-IKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQL  128 (182)
Q Consensus        68 I~rIlk~~G-v~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r~  128 (182)
                      |.++||+.- -...+..+...+-.|+......|+.+|..++.+.+|+||+..||+.|+.-.+
T Consensus         9 i~kVLKqVhp~~giS~kam~imnsfvndiferIa~EA~~La~~~kr~TitsreIqtAvrL~L   70 (92)
T d1tzyb_           9 VYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLL   70 (92)
T ss_dssp             HHHHHHHHCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHHS
T ss_pred             HHHHHHhhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCcHHHHHHHHHHHC
Confidence            556666532 1236788999999999999999999999999999999999999999997544

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

Probab=93.89  E-value=0.15  Score=38.08  Aligned_cols=55  Identities=9%  Similarity=0.133  Sum_probs=43.0

Q ss_pred             HHHhcCCc-ccChHHHHHHHHHHHH---------HHHHHHHHHHHHhhhcCCCCCCHHHHHHHHH
Q psy8542          71 MFQEAGIK-NYDPRCVQQMLEFVNN---------YTTTILEDSRVYANHAKKKTVDVEDIKLAIT  125 (182)
Q Consensus        71 Ilk~~Gv~-r~sp~v~~qLle~~~r---------y~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~  125 (182)
                      .++..+.. .++++++..+.+.+.+         -+-++++.|...|+..|+..|+.+||+.|++
T Consensus       221 r~~~~~~~~~~~~~al~~ia~~~~~~~~~~gd~R~ai~~l~~a~~~A~~~~~~~It~~~V~~A~~  285 (287)
T d1w5sa2         221 RAELGLRDTVWEPRHLELISDVYGEDKGGDGSARRAIVALKMACEMAEAMGRDSLSEDLVRKAVS  285 (287)
T ss_dssp             HHHHHBCTTSCCHHHHHHHHHHHCGGGTSCCCHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHH
T ss_pred             hHHHhhccCCCCHHHHHHHHHHHhccccCCCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHh
Confidence            33333433 4788988888777643         4567899999999999999999999999986

>d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6, N-domain
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=93.41  E-value=0.24  Score=36.72  Aligned_cols=59  Identities=15%  Similarity=0.200  Sum_probs=44.6

Q ss_pred             HHHHHhcCC-cccChHHHHHHHHHH------------HHHHHHHHHHHHHHhhhcCCCCCCHHHHHHHHHHh
Q psy8542          69 VNMFQEAGI-KNYDPRCVQQMLEFV------------NNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQ  127 (182)
Q Consensus        69 ~rIlk~~Gv-~r~sp~v~~qLle~~------------~ry~~~Vl~dA~~yA~HAgRktI~~eDVrLAI~~r  127 (182)
                      ...++..+. ..++++++..+.+..            -|.+-++++.|...|...|+.+|+.+||+.|++..
T Consensus       202 ~~r~~~~~~~~~~~~~~l~~ia~~~~~~~~~~~~~G~~R~a~~ll~~a~~~A~~~~~~~I~~edv~~A~~~~  273 (276)
T d1fnna2         202 LDRAKAGLAEGSYSEDILQMIADITGAQTPLDTNRGDARLAIDILYRSAYAAQQNGRKHIAPEDVRKSSKEV  273 (276)
T ss_dssp             HHHHHHHBCTTSSCHHHHHHHHHHHSBSSTTCTTSCCHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHH
T ss_pred             HHHHHHhcccccccHHHHHHHHHHhhhhhhhhhcCCCHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHH
Confidence            333444333 347888888777665            25677889999999999999999999999999754

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

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

Probab=89.48  E-value=0.16  Score=34.24  Aligned_cols=62  Identities=16%  Similarity=0.353  Sum_probs=53.4

Q ss_pred             CCchHHHHHHHHHHcCCCccChHHHHHHHHHHHhhhcccccccHhhhhhhh----hHHHHHHHHHhcC
Q psy8542          13 LPRDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAR----DAQVIVNMFQEAG   76 (182)
Q Consensus        13 ~prda~~i~~il~~~gi~~yep~v~~qll~f~yryt~~vL~DA~vys~har----daqlI~rIlk~~G   76 (182)
                      +|+.  .|.-|.++.||..-...+...|-+..--|-.+|.+|+..|+.|++    .+.-|...|+++|
T Consensus        10 I~k~--~i~Riar~~Gv~ris~d~~~~l~~~l~~~l~~i~~~a~~~~~hakRKTvt~~DV~~Alkr~g   75 (82)
T d2huec1          10 ITKP--AIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQG   75 (82)
T ss_dssp             SCHH--HHHHHHHHTTCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTTTC
T ss_pred             cCHH--HHHHHHHHcCcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHhcC
Confidence            5665  688999999999999999999999999999999999999999998    4456667777766

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

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

Probab=83.35  E-value=0.58  Score=30.91  Aligned_cols=51  Identities=12%  Similarity=0.306  Sum_probs=44.1

Q ss_pred             CCCchHHHHHHHHHHcCCCccChHHHHHH-HHHHHhhhcccccccHhhhhhhhhH
Q psy8542          12 KLPRDAQVIVNMFQEAGIKNYDPRCVQQM-LEFVNNYTTTILEDSRVYANHARDA   65 (182)
Q Consensus        12 ~~prda~~i~~il~~~gi~~yep~v~~ql-l~f~yryt~~vL~DA~vys~harda   65 (182)
                      .+|+|  .|+.|-.|.||..-.+.|...| .|..||- .+|+|||..|-.|.++.
T Consensus         6 ~~~~e--sik~iAeS~Gi~~l~de~a~~LA~DveYRl-~eiiQeA~KFMrhskR~   57 (70)
T d1tafb_           6 SISAE--SMKVIAESIGVGSLSDDAAKELAEDVSIKL-KRIVQDAAKFMNHAKRQ   57 (70)
T ss_dssp             CCCHH--HHHHHHHHTTCCCBCHHHHHHHHHHHHHHH-HHHHHHHHHHHHHTTCS
T ss_pred             cCCHH--HHHHHHHHcCCCCCCHHHHHHHHHHHHHHH-HHHHHHHHHHHHHhccC
Confidence            45654  6899999999999999998887 5799998 89999999999999854

>d1bh9b_ a.22.1.3 (B:) TAF(II)28 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: TAF(II)28
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.51  E-value=4.5  Score=27.44  Aligned_cols=62  Identities=10%  Similarity=0.118  Sum_probs=50.7

Q ss_pred             HHHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHhhhcCC-CCCCHHHHHHHHHHh
Q psy8542          66 QVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKK-KTVDVEDIKLAITNQ  127 (182)
Q Consensus        66 qlI~rIlk~~Gv~r~sp~v~~qLle~~~ry~~~Vl~dA~~yA~HAgR-ktI~~eDVrLAI~~r  127 (182)
                      ..|++|+.+.--..+++.++..+.-+++-|+.||.+.|...-+.-|. ..+.-+.|+.|....
T Consensus        20 ~~vkrl~~~~~g~sv~~~v~i~v~giaKvFvGEiVE~A~~V~~~~~e~~PL~P~HireA~rrl   82 (89)
T d1bh9b_          20 AAIKRLIQSITGTSVSQNVVIAMSGISKVFVGEVVEEALDVCEKWGEMPPLQPKHMREAVRRL   82 (89)
T ss_dssp             HHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSSCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCcHHHHHHHHHH
Confidence            35666666543367999999999999999999999999999875554 488999999998753