Psyllid ID: psy13691

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100---
Protein Sequence
MAESLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEVIIEILGKSYNAAVSIKVVT
Secondary Structure (PSIPRED)
ccccccccccHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
ccHHHHHcHHHHHHHHHHHHHHccccccccEcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHcccHHHHHHHHHHHHHHHccEEcc
Coil and Loop (DISEMBL)
maeslddlnlpSAIIQRLIKEalpkdaegkinvsKDVRLAAGKAASLFILHLTTEALSIAneknrktlsgvdviEGVKQIGFEVIIEILGKSYNAAVSIKVVT
Flexible Loop (DISEMBL)
maeslddlnlpSAIIQRLIKealpkdaegkinVSKDVRLAAGKAASLFILHLTTEALSianeknrktlsgvdvIEGVKQIGFEVIIEIlgksynaavsikvvt
Low Complexity Region (SEG)
MAESLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEVIIEILGKSYNAAVSIKVVT
Disordered region (IsUnstruct)
************AIIQRLIKEALPK*AEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEVIIEILGKSYNAAVSIKV**
Disordered Region (DISOPRED)
***SLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEVIIEILGKSYNAAVSI****
Disordered Region (DISEMBL)
MAESLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEVIIEILGKSYNAAVSIKVVT
Disordered Region (DISPRO)
****LDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEVIIEILGKSYNAAVSIKVVT
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAESLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEVIIEILGKSYNAAVSIKVVT
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	103	2.2.26 [Sep-21-2011]
Q9JKP7	145	DNA polymerase epsilon su	yes	N/A	0.883	0.627	0.431	1e-13
Q5R4W3	147	DNA polymerase epsilon su	yes	N/A	0.883	0.619	0.421	2e-13
Q9NRF9	147	DNA polymerase epsilon su	yes	N/A	0.883	0.619	0.421	2e-13
Q3SZN5	147	DNA polymerase epsilon su	yes	N/A	0.883	0.619	0.421	2e-13
Q642A5	145	DNA polymerase epsilon su	yes	N/A	0.883	0.627	0.421	2e-13
Q75JQ9	138	DNA polymerase epsilon su	yes	N/A	0.737	0.550	0.397	3e-08
Q750A4	204	DNA polymerase epsilon su	yes	N/A	0.805	0.406	0.340	5e-08
Q54WV0	490	Nuclear transcription fac	no	N/A	0.766	0.161	0.373	5e-07
P36611	116	Transcriptional activator	yes	N/A	0.815	0.724	0.359	2e-06
Q60EQ4	185	Nuclear transcription fac	yes	N/A	0.766	0.427	0.385	2e-06

>sp|Q9JKP7|DPOE3_MOUSE DNA polymerase epsilon subunit 3 OS=Mus musculus GN=Pole3 PE=2 SV=1

 Score = 75.1 bits (183), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 41/95 (43%), Positives = 65/95 (68%), Gaps = 4/95 (4%)

Query: 1  MAESLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIA 60
          MAE  +DLNLP+A+I R+IKEALP   +G +N+SK+ R A  +AAS+F+L+ T+ A + A
Sbjct: 1  MAERPEDLNLPNAVITRIIKEALP---DG-VNISKEARSAISRAASVFVLYATSCANNFA 56

Query: 61 NEKNRKTLSGVDVIEGVKQIGFEVIIEILGKSYNA 95
           +  RKTL+  DV+  ++++ F+  I  L ++  A
Sbjct: 57 MKGKRKTLNASDVLSAMEEMEFQRFITPLKEALEA 91

Forms a complex with DNA polymerase epsilon subunit CHRAC1 and binds naked DNA, which is then incorporated into chromatin, aided by the nucleosome-remodeling activity of ISWI/SNF2H and ACF1.
Mus musculus (taxid: 10090)
EC: 2EC: .EC: 7EC: .EC: 7EC: .EC: 7

>sp|Q5R4W3|DPOE3_PONAB DNA polymerase epsilon subunit 3 OS=Pongo abelii GN=POLE3 PE=2 SV=1

 Score = 74.7 bits (182), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 40/95 (42%), Positives = 65/95 (68%), Gaps = 4/95 (4%)

Query: 1  MAESLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIA 60
          MAE  +DLNLP+A+I R+IKEALP   +G +N+SK+ R A  +AAS+F+L+ T+ A + A
Sbjct: 1  MAERPEDLNLPNAVITRIIKEALP---DG-VNISKEARSAISRAASVFVLYATSCANNFA 56

Query: 61 NEKNRKTLSGVDVIEGVKQIGFEVIIEILGKSYNA 95
           +  RKTL+  DV+  ++++ F+  +  L ++  A
Sbjct: 57 MKGKRKTLNASDVLSAMEEMEFQRFVTPLKEALEA 91

Forms a complex with DNA polymerase epsilon subunit CHRAC1 and binds naked DNA, which is then incorporated into chromatin, aided by the nucleosome-remodeling activity of ISWI/SNF2H and ACF1.

Pongo abelii (taxid: 9601)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 7

>sp|Q9NRF9|DPOE3_HUMAN DNA polymerase epsilon subunit 3 OS=Homo sapiens GN=POLE3 PE=1 SV=1

 Score = 74.7 bits (182), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 40/95 (42%), Positives = 65/95 (68%), Gaps = 4/95 (4%)

Query: 1  MAESLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIA 60
          MAE  +DLNLP+A+I R+IKEALP   +G +N+SK+ R A  +AAS+F+L+ T+ A + A
Sbjct: 1  MAERPEDLNLPNAVITRIIKEALP---DG-VNISKEARSAISRAASVFVLYATSCANNFA 56

Query: 61 NEKNRKTLSGVDVIEGVKQIGFEVIIEILGKSYNA 95
           +  RKTL+  DV+  ++++ F+  +  L ++  A
Sbjct: 57 MKGKRKTLNASDVLSAMEEMEFQRFVTPLKEALEA 91

Forms a complex with DNA polymerase epsilon subunit CHRAC1 and binds naked DNA, which is then incorporated into chromatin, aided by the nucleosome-remodeling activity of ISWI/SNF2H and ACF1.

Homo sapiens (taxid: 9606)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 7

>sp|Q3SZN5|DPOE3_BOVIN DNA polymerase epsilon subunit 3 OS=Bos taurus GN=POLE3 PE=2 SV=1

 Score = 74.7 bits (182), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 40/95 (42%), Positives = 65/95 (68%), Gaps = 4/95 (4%)

Query: 1  MAESLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIA 60
          MAE  +DLNLP+A+I R+IKEALP   +G +N+SK+ R A  +AAS+F+L+ T+ A + A
Sbjct: 1  MAERPEDLNLPNAVITRIIKEALP---DG-VNISKEARSAISRAASVFVLYATSCANNFA 56

Query: 61 NEKNRKTLSGVDVIEGVKQIGFEVIIEILGKSYNA 95
           +  RKTL+  DV+  ++++ F+  +  L ++  A
Sbjct: 57 MKGKRKTLNASDVLSAMEEMEFQRFVTPLKEALEA 91

Forms a complex with DNA polymerase epsilon subunit CHRAC1 and binds naked DNA, which is then incorporated into chromatin, aided by the nucleosome-remodeling activity of ISWI/SNF2H and ACF1.

Bos taurus (taxid: 9913)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 7

>sp|Q642A5|DPOE3_RAT DNA polymerase epsilon subunit 3 OS=Rattus norvegicus GN=Pole3 PE=2 SV=1

 Score = 74.7 bits (182), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 40/95 (42%), Positives = 65/95 (68%), Gaps = 4/95 (4%)

Query: 1  MAESLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIA 60
          MAE  +DLNLP+A+I R+IKEALP   +G +N+SK+ R A  +AAS+F+L+ T+ A + A
Sbjct: 1  MAERPEDLNLPNAVITRIIKEALP---DG-VNISKEARSAISRAASVFVLYATSCANNFA 56

Query: 61 NEKNRKTLSGVDVIEGVKQIGFEVIIEILGKSYNA 95
           +  RKTL+  DV+  ++++ F+  +  L ++  A
Sbjct: 57 MKGKRKTLNASDVLSAMEEMEFQRFVTPLKEALEA 91

Forms a complex with DNA polymerase epsilon subunit CHRAC1 and binds naked DNA, which is then incorporated into chromatin, aided by the nucleosome-remodeling activity of ISWI/SNF2H and ACF1.

Rattus norvegicus (taxid: 10116)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 7

>sp|Q75JQ9|DPOE3_DICDI DNA polymerase epsilon subunit 3 OS=Dictyostelium discoideum GN=pole3 PE=3 SV=1

 Score = 57.4 bits (137), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 33/83 (39%), Positives = 52/83 (62%), Gaps = 7/83 (8%)

Query: 1  MAESLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIA 60
          M+ES D   LP AI+ R+IK +LP   EG +  +K+ RLA  KAA ++I +LT  ++  +
Sbjct: 1  MSESQD---LPGAIVNRIIKASLP---EG-VLCAKESRLAIAKAAKVWIHYLTAASIDFS 53

Query: 61 NEKNRKTLSGVDVIEGVKQIGFE 83
          +   R T+S  DV + +++I FE
Sbjct: 54 SHSGRSTISPKDVFQAIEEIDFE 76

Forms a complex with DNA polymerase epsilon subunit chrac1 and binds naked DNA, which is then incorporated into chromatin, aided by the nucleosome-remodeling activity of iswi/snf2h and acf1.

Dictyostelium discoideum (taxid: 44689)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 7

>sp|Q750A4|DPB4_ASHGO DNA polymerase epsilon subunit D OS=Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) GN=DPB4 PE=3 SV=1

 Score = 56.2 bits (134), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 31/91 (34%), Positives = 55/91 (60%), Gaps = 8/91 (8%)

Query: 4   SLDDLNLPSAIIQRLIKEALPK-----DAEGKINVSKDVRLAAGKAASLFILHLTTEALS 58
           ++DDL  P +II  L K+A+ +     + + ++ +SKD  LA  +++++F+ HL   A  
Sbjct: 66  TVDDLLFPRSIITSLAKDAVHQAVQTAEQDPRVMLSKDASLALQRSSTVFVNHLLMHARQ 125

Query: 59  IANEKNRKTLSGVDVIEGVKQI---GFEVII 86
           IA   +RK+ SG DV++ + QI   GFE ++
Sbjct: 126 IAQSNDRKSCSGEDVLKALDQIGLAGFESVV 156

DNA polymerase II participates in chromosomal DNA replication.

Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) (taxid: 284811)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 7

>sp|Q54WV0|NFYB_DICDI Nuclear transcription factor Y subunit beta OS=Dictyostelium discoideum GN=nfyB PE=3 SV=1

 Score = 53.1 bits (126), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 31/83 (37%), Positives = 48/83 (57%), Gaps = 4/83 (4%)

Query: 7   DLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRK 66
           D  LP A I R++K+ALP +A+    V+KD +       S FI  +T+EA     ++ RK
Sbjct: 50  DRYLPIANIIRIMKKALPNNAK----VAKDAKETVQDCVSEFISFITSEASDKCQQEKRK 105

Query: 67  TLSGVDVIEGVKQIGFEVIIEIL 89
           T++G D+I  +  +GFE  +E L
Sbjct: 106 TINGEDIIAAMVSLGFENYVEPL 128

Component of the NF-Y/HAP transcription factor complex. The NF-Y complex stimulates the transcription of various genes by recognizing and binding to a CCAAT motif in promoters.

Dictyostelium discoideum (taxid: 44689)

>sp|P36611|HAP3_SCHPO Transcriptional activator hap3 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=hap3 PE=3 SV=1

 Score = 51.2 bits (121), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 32/89 (35%), Positives = 51/89 (57%), Gaps = 5/89 (5%)

Query: 2  AESLDDLNL-PSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIA 60
          A+ LD  NL P A + R++K ALP++A+    +SK+ +       S FI  +T EA    
Sbjct: 3  ADGLDYTNLLPIANVARIMKSALPENAK----ISKEAKDCVQDCVSEFISFVTGEASEQC 58

Query: 61 NEKNRKTLSGVDVIEGVKQIGFEVIIEIL 89
           ++ RKT++G DV+  +  +GFE   E+L
Sbjct: 59 TQEKRKTITGEDVLLALNTLGFENYAEVL 87

Belongs to a complex that binds to the sequence CCAAT located upstream of genes involved in mitochondrial electron transport.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

>sp|Q60EQ4|NFYB3_ORYSJ Nuclear transcription factor Y subunit B-3 OS=Oryza sativa subsp. japonica GN=NFYB3 PE=1 SV=2

 Score = 51.2 bits (121), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 32/83 (38%), Positives = 48/83 (57%), Gaps = 4/83 (4%)

Query: 7   DLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRK 66
           D  LP A I R++K+A+P  A GKI  +KD +    +  S FI  +T+EA      + RK
Sbjct: 40  DRFLPIANISRIMKKAIP--ANGKI--AKDAKETVQECVSEFISFITSEASDKCQREKRK 95

Query: 67  TLSGVDVIEGVKQIGFEVIIEIL 89
           T++G D++  +  +GFE  IE L
Sbjct: 96  TINGDDLLWAMATLGFEDYIEPL 118

Component of the NF-Y/HAP transcription factor complex. The NF-Y complex stimulates the transcription of various genes by recognizing and binding to a CCAAT motif in promoters. May regulate the expression of photosynthetic genes, and may be involved in chloroplast and amyloplast development.

Oryza sativa subsp. japonica (taxid: 39947)

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	103
350426799	129	PREDICTED: DNA polymerase epsilon subuni	0.854	0.682	0.521	8e-17
340716954	129	PREDICTED: DNA polymerase epsilon subuni	0.854	0.682	0.521	8e-17
383858311	129	PREDICTED: DNA polymerase epsilon subuni	0.854	0.682	0.532	2e-16
110760577	129	PREDICTED: DNA polymerase epsilon subuni	0.854	0.682	0.510	3e-16
307201447	130	DNA polymerase epsilon subunit 3 [Harpeg	0.854	0.676	0.521	3e-16
380016781	129	PREDICTED: DNA polymerase epsilon subuni	0.854	0.682	0.510	3e-16
332031065	131	DNA polymerase epsilon subunit 3 [Acromy	0.854	0.671	0.5	6e-16
307174746	131	DNA polymerase epsilon subunit 3 [Campon	0.854	0.671	0.510	6e-16
322784123	130	hypothetical protein SINV_10840 [Solenop	0.854	0.676	0.489	2e-15
443697294	150	hypothetical protein CAPTEDRAFT_184024 [	0.883	0.606	0.473	2e-15

>gi|350426799|ref|XP_003494546.1| PREDICTED: DNA polymerase epsilon subunit 3-like [Bombus impatiens]

 Score = 90.9 bits (224), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 48/92 (52%), Positives = 67/92 (72%), Gaps = 4/92 (4%)

Query: 1  MAESLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIA 60
          MAE L+DLNLP+A++ R+IKEALP   EG + ++KD R A  KA+S+FIL+LT+ A  IA
Sbjct: 1  MAERLEDLNLPNAVVTRIIKEALP---EG-VTIAKDARTAVAKASSIFILYLTSSANIIA 56

Query: 61 NEKNRKTLSGVDVIEGVKQIGFEVIIEILGKS 92
           + NRKT+SG DVI+ +  I FE  ++ L +S
Sbjct: 57 KKGNRKTISGQDVIQAMNDIEFEQFVDPLQES 88

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340716954|ref|XP_003396955.1| PREDICTED: DNA polymerase epsilon subunit 3-like isoform 1 [Bombus terrestris] gi|340716956|ref|XP_003396956.1| PREDICTED: DNA polymerase epsilon subunit 3-like isoform 2 [Bombus terrestris]

 Score = 90.9 bits (224), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 48/92 (52%), Positives = 67/92 (72%), Gaps = 4/92 (4%)

Query: 1  MAESLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIA 60
          MAE L+DLNLP+A++ R+IKEALP   EG + ++KD R A  KA+S+FIL+LT+ A  IA
Sbjct: 1  MAERLEDLNLPNAVVTRIIKEALP---EG-VTIAKDARTAVAKASSIFILYLTSSANIIA 56

Query: 61 NEKNRKTLSGVDVIEGVKQIGFEVIIEILGKS 92
           + NRKT+SG DVI+ +  I FE  ++ L +S
Sbjct: 57 KKGNRKTISGQDVIQAMNDIEFEQFVDPLQES 88

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383858311|ref|XP_003704645.1| PREDICTED: DNA polymerase epsilon subunit 3-like [Megachile rotundata]

 Score = 90.1 bits (222), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 49/92 (53%), Positives = 66/92 (71%), Gaps = 4/92 (4%)

Query: 1  MAESLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIA 60
          MAE L+DLNLP+A++ R+IKEALP   EG + ++KD R A  KA+S+FIL+LT+ A  IA
Sbjct: 1  MAERLEDLNLPNAVVTRIIKEALP---EG-VTIAKDARTAIAKASSIFILYLTSSANIIA 56

Query: 61 NEKNRKTLSGVDVIEGVKQIGFEVIIEILGKS 92
           + NRKT+SG DVI  +  I FE  I+ L +S
Sbjct: 57 KKGNRKTISGSDVIHAMNDIEFEQFIDPLQES 88

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|110760577|ref|XP_001122640.1| PREDICTED: DNA polymerase epsilon subunit 3 [Apis mellifera]

 Score = 89.4 bits (220), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 47/92 (51%), Positives = 67/92 (72%), Gaps = 4/92 (4%)

Query: 1  MAESLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIA 60
          MAE L+DLNLP+A++ R+IKEALP   EG + ++KD R A  KA+S+FIL+LT+ A  IA
Sbjct: 1  MAERLEDLNLPNAVVTRIIKEALP---EG-VTIAKDARTAVAKASSIFILYLTSSANIIA 56

Query: 61 NEKNRKTLSGVDVIEGVKQIGFEVIIEILGKS 92
           + NRKT+SG DVI+ +  I F+  ++ L +S
Sbjct: 57 KKGNRKTISGQDVIQAMNDIEFDEFVDPLQES 88

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307201447|gb|EFN81238.1| DNA polymerase epsilon subunit 3 [Harpegnathos saltator]

 Score = 89.0 bits (219), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 48/92 (52%), Positives = 66/92 (71%), Gaps = 4/92 (4%)

Query: 1  MAESLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIA 60
          MAE L+DLNLP+A++ R+IKEALP   +G + V KD R A  KAAS+FIL+LT+ A  IA
Sbjct: 1  MAEKLEDLNLPNAVVTRIIKEALP---DG-VTVGKDARTAVAKAASIFILYLTSSANIIA 56

Query: 61 NEKNRKTLSGVDVIEGVKQIGFEVIIEILGKS 92
           + NRKT+SG DVI+ +  I F+  ++ L +S
Sbjct: 57 KKGNRKTISGQDVIQAMMDIEFDQFVDPLQES 88

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380016781|ref|XP_003692351.1| PREDICTED: DNA polymerase epsilon subunit 3-like [Apis florea]

 Score = 89.0 bits (219), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 47/92 (51%), Positives = 67/92 (72%), Gaps = 4/92 (4%)

Query: 1  MAESLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIA 60
          MAE L+DLNLP+A++ R+IKEALP   EG + ++KD R A  KA+S+FIL+LT+ A  IA
Sbjct: 1  MAERLEDLNLPNAVVTRIIKEALP---EG-VTIAKDARTAVAKASSIFILYLTSSANIIA 56

Query: 61 NEKNRKTLSGVDVIEGVKQIGFEVIIEILGKS 92
           + NRKT+SG DVI+ +  I F+  ++ L +S
Sbjct: 57 KKGNRKTISGQDVIQAMTDIEFDEFVDPLQES 88

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332031065|gb|EGI70651.1| DNA polymerase epsilon subunit 3 [Acromyrmex echinatior]

 Score = 88.2 bits (217), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 46/92 (50%), Positives = 64/92 (69%), Gaps = 4/92 (4%)

Query: 1  MAESLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIA 60
          MAE L+DLNLP+A++ R+IKEALP      + V KD R A  KAAS+FIL+LT+ A  +A
Sbjct: 1  MAERLEDLNLPNAVVTRIIKEALP----DGVTVGKDARTAVAKAASIFILYLTSAANIVA 56

Query: 61 NEKNRKTLSGVDVIEGVKQIGFEVIIEILGKS 92
           + NRKT+SG DVI+ +  + F+  +E L +S
Sbjct: 57 KKSNRKTVSGPDVIQAMIDVEFDQFVEPLQES 88

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307174746|gb|EFN65101.1| DNA polymerase epsilon subunit 3 [Camponotus floridanus]

 Score = 87.8 bits (216), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 47/92 (51%), Positives = 64/92 (69%), Gaps = 4/92 (4%)

Query: 1  MAESLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIA 60
          MAE L+DLNLP+A++ R+IKEALP      + V KD R A  KAAS+FIL+LT+ A  IA
Sbjct: 1  MAERLEDLNLPNAVVTRIIKEALP----DGVTVGKDARTAVAKAASIFILYLTSSANIIA 56

Query: 61 NEKNRKTLSGVDVIEGVKQIGFEVIIEILGKS 92
           + NRKT+SG DVI+ +  I F+  ++ L +S
Sbjct: 57 KKGNRKTISGQDVIQAMVDIEFDQFVDPLQES 88

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322784123|gb|EFZ11212.1| hypothetical protein SINV_10840 [Solenopsis invicta]

 Score = 86.7 bits (213), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 45/92 (48%), Positives = 64/92 (69%), Gaps = 4/92 (4%)

Query: 1  MAESLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIA 60
          MAE L+DLNLP+A++ R+IKEALP      + + KD R A  KAAS+FIL+LT+ A  +A
Sbjct: 1  MAERLEDLNLPNAVVTRIIKEALPD----GVTIGKDARTAVAKAASIFILYLTSSANIVA 56

Query: 61 NEKNRKTLSGVDVIEGVKQIGFEVIIEILGKS 92
           + NRKT+SG DV++ +  I F+  +E L +S
Sbjct: 57 KKGNRKTISGPDVLQAMIDIEFDQFVESLQES 88

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|443697294|gb|ELT97819.1| hypothetical protein CAPTEDRAFT_184024 [Capitella teleta]

 Score = 86.3 bits (212), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 45/95 (47%), Positives = 68/95 (71%), Gaps = 4/95 (4%)

Query: 1  MAESLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIA 60
          MAE  +DLNLP++II R+IK+A+P   +G +NVSKD RLA  KAAS+F+L+ T+ A + A
Sbjct: 1  MAERPEDLNLPNSIITRIIKDAIP---DG-VNVSKDARLAISKAASVFVLYATSCANNFA 56

Query: 61 NEKNRKTLSGVDVIEGVKQIGFEVIIEILGKSYNA 95
           +  RK +SG DV++ + ++ F+ ++E L KS  A
Sbjct: 57 QQNKRKMISGQDVLDSMTELEFDELVEPLKKSLEA 91

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

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	103
ZFIN|ZDB-GENE-040426-1773	148	pole3 "polymerase (DNA directe	0.883	0.614	0.463	6.9e-15
FB|FBgn0043002	128	Chrac-14 "Chromatin accessibil	0.825	0.664	0.404	3e-14
UNIPROTKB|F1SN88	147	POLE3 "Uncharacterized protein	0.883	0.619	0.431	3.8e-14
MGI|MGI:1933378	145	Pole3 "polymerase (DNA directe	0.883	0.627	0.431	6.2e-14
UNIPROTKB|F1P2L0	143	POLE3 "Uncharacterized protein	0.854	0.615	0.445	7.9e-14
UNIPROTKB|Q3SZN5	147	POLE3 "DNA polymerase epsilon	0.883	0.619	0.421	7.9e-14
UNIPROTKB|J9P0Z6	147	POLE3 "Uncharacterized protein	0.883	0.619	0.421	7.9e-14
UNIPROTKB|Q9NRF9	147	POLE3 "DNA polymerase epsilon	0.883	0.619	0.421	7.9e-14
UNIPROTKB|Q5R4W3	147	POLE3 "DNA polymerase epsilon	0.883	0.619	0.421	7.9e-14
RGD|1359475	145	Pole3 "polymerase (DNA directe	0.883	0.627	0.421	7.9e-14

ZFIN|ZDB-GENE-040426-1773 pole3 "polymerase (DNA directed), epsilon 3 (p17 subunit)" [Danio rerio (taxid:7955)]

 Score = 189 (71.6 bits), Expect = 6.9e-15, P = 6.9e-15
 Identities = 44/95 (46%), Positives = 66/95 (69%)

Query:     1 MAESLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIA 60
             MAE  +DLNLP+A+I R+IKEALP   EG +NVSK+ R A  +AAS+F+L+ T+ A S A
Sbjct:     1 MAERPEDLNLPNAVITRIIKEALP---EG-VNVSKEARRAISQAASVFVLYATSCANSFA 56

Query:    61 NEKNRKTLSGVDVIEGVKQIGFEVIIEILGKSYNA 95
              +  RKTL+  DV+  ++++ FE  ++ L ++  A
Sbjct:    57 MKAKRKTLNAGDVMSAMEEMEFERFLQPLREALEA 91

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

FB|FBgn0043002 Chrac-14 "Chromatin accessibility complex 14kD protein" [Drosophila melanogaster (taxid:7227)]

 Score = 183 (69.5 bits), Expect = 3.0e-14, P = 3.0e-14
 Identities = 36/89 (40%), Positives = 63/89 (70%)

Query:     1 MAESLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIA 60
             M E ++DLNLP+A+I RLIKEALP+ A    +VSK+ R A  +AAS+F + +T+ + ++A
Sbjct:     1 MVERIEDLNLPNAVIGRLIKEALPESA----SVSKEARAAIARAASVFAIFVTSSSTALA 56

Query:    61 NEKNRKTLSGVDVIEGVKQIGFEVIIEIL 89
             +++N KT++  D+++ + ++ FE  +  L
Sbjct:    57 HKQNHKTITAKDILQTLTELDFESFVPSL 85

GO:0008623 "CHRAC" evidence=IDA;NAS

GO:0046982 "protein heterodimerization activity" evidence=IPI

GO:0042766 "nucleosome mobilization" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0004402 "histone acetyltransferase activity" evidence=IDA

GO:0006338 "chromatin remodeling" evidence=IDA

GO:0016573 "histone acetylation" evidence=IDA

GO:0005671 "Ada2/Gcn5/Ada3 transcription activator complex" evidence=IPI

GO:0006974 "response to DNA damage stimulus" evidence=IMP

UNIPROTKB|F1SN88 POLE3 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 182 (69.1 bits), Expect = 3.8e-14, P = 3.8e-14
 Identities = 41/95 (43%), Positives = 65/95 (68%)

Query:     1 MAESLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIA 60
             MAE  +DLNLP+A+I R+IKEALP   EG +N+SK+ R A  +AAS+F+L+ T+ A + A
Sbjct:     1 MAERPEDLNLPNAVITRIIKEALP---EG-VNISKEARSAISRAASVFVLYATSCANNFA 56

Query:    61 NEKNRKTLSGVDVIEGVKQIGFEVIIEILGKSYNA 95
              +  RKTL+  DV+  ++++ F+  +  L ++  A
Sbjct:    57 MKGKRKTLNASDVLSAMEEMEFQRFVTPLKEALEA 91

GO:0043966 "histone H3 acetylation" evidence=IEA

GO:0008622 "epsilon DNA polymerase complex" evidence=IEA

GO:0005671 "Ada2/Gcn5/Ada3 transcription activator complex" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0043565 "sequence-specific DNA binding" evidence=IEA

MGI|MGI:1933378 Pole3 "polymerase (DNA directed), epsilon 3 (p17 subunit)" [Mus musculus (taxid:10090)]

 Score = 180 (68.4 bits), Expect = 6.2e-14, P = 6.2e-14
 Identities = 41/95 (43%), Positives = 65/95 (68%)

Query:     1 MAESLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIA 60
             MAE  +DLNLP+A+I R+IKEALP   +G +N+SK+ R A  +AAS+F+L+ T+ A + A
Sbjct:     1 MAERPEDLNLPNAVITRIIKEALP---DG-VNISKEARSAISRAASVFVLYATSCANNFA 56

Query:    61 NEKNRKTLSGVDVIEGVKQIGFEVIIEILGKSYNA 95
              +  RKTL+  DV+  ++++ F+  I  L ++  A
Sbjct:    57 MKGKRKTLNASDVLSAMEEMEFQRFITPLKEALEA 91

GO:0003677 "DNA binding" evidence=IEA

GO:0003887 "DNA-directed DNA polymerase activity" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005671 "Ada2/Gcn5/Ada3 transcription activator complex" evidence=ISO

GO:0008622 "epsilon DNA polymerase complex" evidence=ISO

GO:0016740 "transferase activity" evidence=IEA

GO:0016779 "nucleotidyltransferase activity" evidence=IEA

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0043966 "histone H3 acetylation" evidence=ISO

GO:0046982 "protein heterodimerization activity" evidence=IEA

UNIPROTKB|F1P2L0 POLE3 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 179 (68.1 bits), Expect = 7.9e-14, P = 7.9e-14
 Identities = 41/92 (44%), Positives = 64/92 (69%)

Query:     1 MAESLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIA 60
             MAE  +DLNLP+A+I R+IKEALP   +G +N+SK+ R A  +AAS+F+L+ T+ A + A
Sbjct:     1 MAERPEDLNLPNAVITRIIKEALP---DG-VNISKEARSAISRAASVFVLYATSCANNFA 56

Query:    61 NEKNRKTLSGVDVIEGVKQIGFEVIIEILGKS 92
              +  RKTL+  DV+  ++++ F+  I  L +S
Sbjct:    57 MKGKRKTLNAGDVLSAMEEMEFQRFIAPLKES 88

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0005671 "Ada2/Gcn5/Ada3 transcription activator complex" evidence=IEA

GO:0008622 "epsilon DNA polymerase complex" evidence=IEA

GO:0043966 "histone H3 acetylation" evidence=IEA

UNIPROTKB|Q3SZN5 POLE3 "DNA polymerase epsilon subunit 3" [Bos taurus (taxid:9913)]

 Score = 179 (68.1 bits), Expect = 7.9e-14, P = 7.9e-14
 Identities = 40/95 (42%), Positives = 65/95 (68%)

Query:     1 MAESLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIA 60
             MAE  +DLNLP+A+I R+IKEALP   +G +N+SK+ R A  +AAS+F+L+ T+ A + A
Sbjct:     1 MAERPEDLNLPNAVITRIIKEALP---DG-VNISKEARSAISRAASVFVLYATSCANNFA 56

Query:    61 NEKNRKTLSGVDVIEGVKQIGFEVIIEILGKSYNA 95
              +  RKTL+  DV+  ++++ F+  +  L ++  A
Sbjct:    57 MKGKRKTLNASDVLSAMEEMEFQRFVTPLKEALEA 91

GO:0008622 "epsilon DNA polymerase complex" evidence=ISS

GO:0043966 "histone H3 acetylation" evidence=IEA

GO:0005671 "Ada2/Gcn5/Ada3 transcription activator complex" evidence=IEA

GO:0003887 "DNA-directed DNA polymerase activity" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0043565 "sequence-specific DNA binding" evidence=IEA

UNIPROTKB|J9P0Z6 POLE3 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 179 (68.1 bits), Expect = 7.9e-14, P = 7.9e-14
 Identities = 40/95 (42%), Positives = 65/95 (68%)

Query:     1 MAESLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIA 60
             MAE  +DLNLP+A+I R+IKEALP   +G +N+SK+ R A  +AAS+F+L+ T+ A + A
Sbjct:     1 MAERPEDLNLPNAVITRIIKEALP---DG-VNISKEARSAISRAASVFVLYATSCANNFA 56

Query:    61 NEKNRKTLSGVDVIEGVKQIGFEVIIEILGKSYNA 95
              +  RKTL+  DV+  ++++ F+  +  L ++  A
Sbjct:    57 MKGKRKTLNASDVLSAMEEMEFQRFVTPLKEALEA 91

GO:0005634 "nucleus" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0043565 "sequence-specific DNA binding" evidence=IEA

UNIPROTKB|Q9NRF9 POLE3 "DNA polymerase epsilon subunit 3" [Homo sapiens (taxid:9606)]

 Score = 179 (68.1 bits), Expect = 7.9e-14, P = 7.9e-14
 Identities = 40/95 (42%), Positives = 65/95 (68%)

Query:     1 MAESLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIA 60
             MAE  +DLNLP+A+I R+IKEALP   +G +N+SK+ R A  +AAS+F+L+ T+ A + A
Sbjct:     1 MAERPEDLNLPNAVITRIIKEALP---DG-VNISKEARSAISRAASVFVLYATSCANNFA 56

Query:    61 NEKNRKTLSGVDVIEGVKQIGFEVIIEILGKSYNA 95
              +  RKTL+  DV+  ++++ F+  +  L ++  A
Sbjct:    57 MKGKRKTLNASDVLSAMEEMEFQRFVTPLKEALEA 91

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0003887 "DNA-directed DNA polymerase activity" evidence=IEA

GO:0008622 "epsilon DNA polymerase complex" evidence=IDA

GO:0005634 "nucleus" evidence=TAS

GO:0006260 "DNA replication" evidence=TAS

GO:0005515 "protein binding" evidence=IPI

GO:0043966 "histone H3 acetylation" evidence=IDA

GO:0005671 "Ada2/Gcn5/Ada3 transcription activator complex" evidence=IDA

UNIPROTKB|Q5R4W3 POLE3 "DNA polymerase epsilon subunit 3" [Pongo abelii (taxid:9601)]

 Score = 179 (68.1 bits), Expect = 7.9e-14, P = 7.9e-14
 Identities = 40/95 (42%), Positives = 65/95 (68%)

Query:     1 MAESLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIA 60
             MAE  +DLNLP+A+I R+IKEALP   +G +N+SK+ R A  +AAS+F+L+ T+ A + A
Sbjct:     1 MAERPEDLNLPNAVITRIIKEALP---DG-VNISKEARSAISRAASVFVLYATSCANNFA 56

Query:    61 NEKNRKTLSGVDVIEGVKQIGFEVIIEILGKSYNA 95
              +  RKTL+  DV+  ++++ F+  +  L ++  A
Sbjct:    57 MKGKRKTLNASDVLSAMEEMEFQRFVTPLKEALEA 91

GO:0008622 "epsilon DNA polymerase complex" evidence=ISS

RGD|1359475 Pole3 "polymerase (DNA directed), epsilon 3, accessory subunit" [Rattus norvegicus (taxid:10116)]

 Score = 179 (68.1 bits), Expect = 7.9e-14, P = 7.9e-14
 Identities = 40/95 (42%), Positives = 65/95 (68%)

Query:     1 MAESLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIA 60
             MAE  +DLNLP+A+I R+IKEALP   +G +N+SK+ R A  +AAS+F+L+ T+ A + A
Sbjct:     1 MAERPEDLNLPNAVITRIIKEALP---DG-VNISKEARSAISRAASVFVLYATSCANNFA 56

Query:    61 NEKNRKTLSGVDVIEGVKQIGFEVIIEILGKSYNA 95
              +  RKTL+  DV+  ++++ F+  +  L ++  A
Sbjct:    57 MKGKRKTLNASDVLSAMEEMEFQRFVTPLKEALEA 91

GO:0003887 "DNA-directed DNA polymerase activity" evidence=IEA

GO:0005671 "Ada2/Gcn5/Ada3 transcription activator complex" evidence=ISO

GO:0008622 "epsilon DNA polymerase complex" evidence=ISO;ISS

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0043966 "histone H3 acetylation" evidence=ISO

GO:0046982 "protein heterodimerization activity" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q3SZN5	DPOE3_BOVIN	2, ., 7, ., 7, ., 7	0.4210	0.8834	0.6190	yes	N/A
P36611	HAP3_SCHPO	No assigned EC number	0.3595	0.8155	0.7241	yes	N/A
Q642A5	DPOE3_RAT	2, ., 7, ., 7, ., 7	0.4210	0.8834	0.6275	yes	N/A
Q5R4W3	DPOE3_PONAB	2, ., 7, ., 7, ., 7	0.4210	0.8834	0.6190	yes	N/A
Q9NRF9	DPOE3_HUMAN	2, ., 7, ., 7, ., 7	0.4210	0.8834	0.6190	yes	N/A
Q9JKP7	DPOE3_MOUSE	2, ., 7, ., 7, ., 7	0.4315	0.8834	0.6275	yes	N/A

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	103
pfam00808	65	pfam00808, CBFD_NFYB_HMF, Histone-like transcripti	4e-08
COG5150	148	COG5150, COG5150, Class 2 transcription repressor	2e-07
COG2036	91	COG2036, HHT1, Histones H3 and H4 [Chromatin struc	6e-06
COG5208	286	COG5208, HAP5, CCAAT-binding factor, subunit C [Tr	5e-05

>gnl|CDD|201453 pfam00808, CBFD_NFYB_HMF, Histone-like transcription factor (CBF/NF-Y) and archaeal histone

 Score = 45.7 bits (109), Expect = 4e-08
 Identities = 15/65 (23%), Positives = 30/65 (46%), Gaps = 5/65 (7%)

Query: 10 LPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLS 69
          LP A ++R++K            +S+D +    +    FI  + +EA  I  ++ RKT++
Sbjct: 3  LPIARVKRIMKSD-----PDAGRISQDAKELIAECVEEFIEFIASEAAEICKKEKRKTIN 57

Query: 70 GVDVI 74
             + 
Sbjct: 58 AEHIK 62

This family includes archaebacterial histones and histone like transcription factors from eukaryotes. Length = 65

>gnl|CDD|227479 COG5150, COG5150, Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]

 Score = 45.7 bits (108), Expect = 2e-07
 Identities = 26/82 (31%), Positives = 45/82 (54%), Gaps = 4/82 (4%)

Query: 6  DDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNR 65
          D+ +LP A +Q+++   LPKD    +  +K+ R     A   FI  L++EA     E+ +
Sbjct: 8  DENSLPKATVQKMVSSILPKD----LVFTKEAREIFINACIEFINMLSSEANEACEEEAK 63

Query: 66 KTLSGVDVIEGVKQIGFEVIIE 87
          KT++   VI+ ++ + FE  IE
Sbjct: 64 KTIAYEHVIKALENLEFEEYIE 85

Length = 148

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

 Score = 40.8 bits (96), Expect = 6e-06
 Identities = 19/82 (23%), Positives = 39/82 (47%), Gaps = 6/82 (7%)

Query: 6  DDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNR 65
           DL LP A ++R++++A  +       VS        +A   ++  +  +A+ +A    R
Sbjct: 16 TDLLLPKAPVRRILRKAGAE------RVSSSAIEELQEALEEYLEEIAEDAVELAEHAKR 69

Query: 66 KTLSGVDVIEGVKQIGFEVIIE 87
          KT+   D+   +K++G  +  E
Sbjct: 70 KTVKAEDIKLALKRLGRRIYGE 91

Length = 91

>gnl|CDD|227533 COG5208, HAP5, CCAAT-binding factor, subunit C [Transcription]

 Score = 40.0 bits (93), Expect = 5e-05
 Identities = 27/88 (30%), Positives = 43/88 (48%), Gaps = 6/88 (6%)

Query: 5   LDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKN 64
           L D NLP A I++++K       E    +S +  +   K   +FI  LT  A   A E  
Sbjct: 105 LKDHNLPLARIKKVMKTD-----EDVKMISAEAPVLFAKITEIFIEELTMRAWINAEENK 159

Query: 65  RKTLSGVDVIEGVKQIG-FEVIIEILGK 91
           R+TL   D+   VK+   F+ +I+I+ +
Sbjct: 160 RRTLQKSDIAAAVKKSEMFDFLIDIVPR 187

Length = 286

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	103
KOG0869|consensus	168		100.0
KOG0871|consensus	156		99.97
KOG0870|consensus	172		99.95
COG5150	148	Class 2 transcription repressor NC2, beta subunit	99.93
PF00808	65	CBFD_NFYB_HMF: Histone-like transcription factor (	99.84
COG2036	91	HHT1 Histones H3 and H4 [Chromatin structure and d	99.76
cd00076	85	H4 Histone H4, one of the four histones, along wit	99.38
PLN00035	103	histone H4; Provisional	99.33
PTZ00015	102	histone H4; Provisional	99.28
smart00428	105	H3 Histone H3.	99.21
smart00803	65	TAF TATA box binding protein associated factor. TA	99.16
smart00417	74	H4 Histone H4.	99.15
PF00125	75	Histone: Core histone H2A/H2B/H3/H4 histone h2a si	99.12
cd07981	72	TAF12 TATA Binding Protein (TBP) Associated Factor	99.11
COG5208	286	HAP5 CCAAT-binding factor, subunit C [Transcriptio	99.08
PLN00160	97	histone H3; Provisional	99.02
PLN00161	135	histone H3; Provisional	98.98
PLN00121	136	histone H3; Provisional	98.91
PTZ00018	136	histone H3; Provisional	98.9
KOG1657|consensus	236		98.79
smart00576	77	BTP Bromodomain transcription factors and PHD doma	98.7
cd00074	115	H2A Histone 2A; H2A is a subunit of the nucleosome	98.65
KOG1659|consensus	224		98.3
KOG1745|consensus	137		98.22
cd07979	117	TAF9 TATA Binding Protein (TBP) Associated Factor	98.22
PF15511	414	CENP-T: Centromere kinetochore component CENP-T; P	98.22
cd08050	343	TAF6 TATA Binding Protein (TBP) Associated Factor	98.14
smart00427	89	H2B Histone H2B.	98.13
PF09415	72	CENP-X: CENP-S associating Centromere protein X; I	98.1
PF07524	77	Bromo_TP: Bromodomain associated; InterPro: IPR006	98.09
cd08048	85	TAF11 TATA Binding Protein (TBP) Associated Factor	98.05
PF03847	68	TFIID_20kDa: Transcription initiation factor TFIID	98.03
COG5247	113	BUR6 Class 2 transcription repressor NC2, alpha su	98.02
COG5262	132	HTA1 Histone H2A [Chromatin structure and dynamics	98.01
PF15630	76	CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C	97.99
PLN00158	116	histone H2B; Provisional	97.93
PTZ00463	117	histone H2B; Provisional	97.9
KOG3467|consensus	103		97.88
smart00414	106	H2A Histone 2A.	97.75
PF02969	66	TAF: TATA box binding protein associated factor (T	97.73
PF04719	90	TAFII28: hTAFII28-like protein conserved region; I	97.68
PLN00154	136	histone H2A; Provisional	97.61
PTZ00017	134	histone H2A; Provisional	97.49
KOG1756|consensus	131		97.45
PLN00153	129	histone H2A; Provisional	97.28
PLN00157	132	histone H2A; Provisional	97.26
PLN00156	139	histone H2AX; Provisional	97.25
KOG1142|consensus	258		97.2
KOG1658|consensus	162		97.18
KOG1744|consensus	127		97.03
PF15510	102	CENP-W: Centromere kinetochore component W	96.94
PF02269	93	TFIID-18kDa: Transcription initiation factor IID,	96.82
PTZ00252	134	histone H2A; Provisional	96.64
cd07978	92	TAF13 The TATA Binding Protein (TBP) Associated Fa	96.38
KOG3219|consensus	195		96.32
PF02291	129	TFIID-31kDa: Transcription initiation factor IID,	95.28
KOG4336|consensus	323		95.27
KOG3423|consensus	176		94.01
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	93.67
PRK00411	394	cdc6 cell division control protein 6; Reviewed	93.15
KOG2389|consensus	353		92.21
KOG2549|consensus	576		91.85
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	91.4
KOG1757|consensus	131		88.04
PF13654	509	AAA_32: AAA domain; PDB: 3K1J_B.	87.23
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	85.5
PF13335	96	Mg_chelatase_2: Magnesium chelatase, subunit ChlI	83.84
COG5095	450	TAF6 Transcription initiation factor TFIID, subuni	83.3
TIGR00764	608	lon_rel lon-related putative ATP-dependent proteas	83.14
COG1067	647	LonB Predicted ATP-dependent protease [Posttransla	82.78
PF08369	45	PCP_red: Proto-chlorophyllide reductase 57 kD subu	81.09
cd08045	212	TAF4 TATA Binding Protein (TBP) Associated Factor	80.25

>KOG0869|consensus

Probab=100.00  E-value=1.4e-35  Score=209.65  Aligned_cols=93  Identities=30%  Similarity=0.393  Sum_probs=90.8

Q ss_pred             CCccCCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCc
Q psy13691          3 ESLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGF   82 (103)
Q Consensus         3 ~~~~d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf   82 (103)
                      .+++|..||+|+|.||||..||.+    .+|||||++.+|+|+++||+|+|++|++.|..++||||+++||+|||..|||
T Consensus        26 ~reqDr~LPIANV~RIMK~~lP~n----aKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~tLGF  101 (168)
T KOG0869|consen   26 LREQDRFLPIANVSRIMKKALPAN----AKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMSTLGF  101 (168)
T ss_pred             cchhhhhccHHHHHHHHHhcCCcc----cccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHHHcCc
Confidence            478899999999999999999998    9999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHHHHHHHHHHHhc
Q psy13691         83 EVIIEILGKSYNAAVSI   99 (103)
Q Consensus        83 ~~~~~~l~~~l~~~k~~   99 (103)
                      ++|+++|+.||..||+.
T Consensus       102 e~Y~eplkiyL~kYRe~  118 (168)
T KOG0869|consen  102 ENYAEPLKIYLQKYREL  118 (168)
T ss_pred             HhHHHHHHHHHHHHHHH
Confidence            99999999999999985

>KOG0871|consensus

Probab=99.97  E-value=1.6e-30  Score=182.41  Aligned_cols=94  Identities=31%  Similarity=0.450  Sum_probs=90.7

Q ss_pred             CccCCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCch
Q psy13691          4 SLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFE   83 (103)
Q Consensus         4 ~~~d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~   83 (103)
                      ..+++.||+|+|++|||+.||.+    ++|.+||+++|..||.+||+.|+++||++|.++.||||++|||++||+.|||.
T Consensus         7 ~dde~sLPkAtv~KmIke~lP~d----~rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe~LgF~   82 (156)
T KOG0871|consen    7 EDDELSLPKATVNKMIKEMLPKD----VRVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALENLGFG   82 (156)
T ss_pred             ccccccCcHHHHHHHHHHhCCcc----cccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHHHcchH
Confidence            56799999999999999999988    99999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhccc
Q psy13691         84 VIIEILGKSYNAAVSIKV  101 (103)
Q Consensus        84 ~~~~~l~~~l~~~k~~~~  101 (103)
                      +|++.+.+.+++||...+
T Consensus        83 eYiee~~~vl~~~K~~~~  100 (156)
T KOG0871|consen   83 EYIEEAEEVLENCKEEAK  100 (156)
T ss_pred             HHHHHHHHHHHHHHHHHH
Confidence            999999999999997654

>KOG0870|consensus

Probab=99.95  E-value=1.6e-28  Score=174.93  Aligned_cols=97  Identities=38%  Similarity=0.631  Sum_probs=93.2

Q ss_pred             CCCCccCCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhc
Q psy13691          1 MAESLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQI   80 (103)
Q Consensus         1 m~~~~~d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~l   80 (103)
                      |+++++++.||+|+|.|++|+.||++   ++.|||||+.+|+++|++|++||++.|+++|..++||||+++||+.||+.+
T Consensus         2 e~eri~dl~lP~AiI~rlvke~l~E~---~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL~Ei   78 (172)
T KOG0870|consen    2 EDERIEDLNLPNAIITRLVKEVLPES---NVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALDEI   78 (172)
T ss_pred             cchhHHHhhccHHHHHHHHHHhCccc---cccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHHHh
Confidence            67899999999999999999999986   489999999999999999999999999999999999999999999999999


Q ss_pred             CchHHHHHHHHHHHHHHhcc
Q psy13691         81 GFEVIIEILGKSYNAAVSIK  100 (103)
Q Consensus        81 gf~~~~~~l~~~l~~~k~~~  100 (103)
                      ||.+|+.||+..|+.|+..+
T Consensus        79 efs~f~~plk~~Le~yk~~~   98 (172)
T KOG0870|consen   79 EFSSFVNPLKSALEAYKKAV   98 (172)
T ss_pred             chHHHhhHHHHHHHHHHHHH
Confidence            99999999999999999764

>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]

Probab=99.93  E-value=6.6e-26  Score=156.10  Aligned_cols=98  Identities=29%  Similarity=0.344  Sum_probs=93.7

Q ss_pred             CCC--CccCCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691          1 MAE--SLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK   78 (103)
Q Consensus         1 m~~--~~~d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~   78 (103)
                      |++  ..++..||+|+|++++.+.||.+    ..++|||+++++.||-+||+.|+++||++|.++.+|||.++||++||+
T Consensus         1 Mn~~~~dDe~sLPKATVqKMvS~iLp~d----l~ftKearei~in~cieFi~~lsseAne~ce~EaKKTIa~EHviKALe   76 (148)
T COG5150           1 MNMEKNDDENSLPKATVQKMVSSILPKD----LVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALE   76 (148)
T ss_pred             CCCccccccccCcHHHHHHHHHHhcccc----ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHH
Confidence            555  56789999999999999999999    999999999999999999999999999999999999999999999999


Q ss_pred             hcCchHHHHHHHHHHHHHHhcccc
Q psy13691         79 QIGFEVIIEILGKSYNAAVSIKVV  102 (103)
Q Consensus        79 ~lgf~~~~~~l~~~l~~~k~~~~~  102 (103)
                      .|||.+|++.+.+.+.+|++.+++
T Consensus        77 nLef~eyi~~~~e~~~n~k~~qK~  100 (148)
T COG5150          77 NLEFEEYIESCMEEHENYKSYQKQ  100 (148)
T ss_pred             hccHHHHHHHHHHHHHHHHHHHhh
Confidence            999999999999999999998775

>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=99.84  E-value=8.3e-21  Score=116.67  Aligned_cols=64  Identities=41%  Similarity=0.498  Sum_probs=58.7

Q ss_pred             CCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhh
Q psy13691          9 NLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGV   77 (103)
Q Consensus         9 ~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al   77 (103)
                      .||.++|.||||.. |+.    .+||+||..+|++|+++||.||+.+|++.|..++||||+++||..||
T Consensus         2 ~lP~a~vkri~k~~-~~~----~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~~~rkti~~~Dv~~Av   65 (65)
T PF00808_consen    2 SLPLARVKRIMKSD-PDV----MRVSKEAVEAIAKAAEEFIQYLAKEANEIAQRDKRKTITYEDVAKAV   65 (65)
T ss_dssp             SS-HHHHHHHHHHT-STT----SEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEE-HHHHHHHH
T ss_pred             CCChHHHHHHhccC-CCc----cchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHC
Confidence            69999999999999 777    79999999999999999999999999999999999999999999986

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 ....

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

Probab=99.76  E-value=1.6e-18  Score=113.76  Aligned_cols=76  Identities=24%  Similarity=0.373  Sum_probs=72.0

Q ss_pred             CccCCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCch
Q psy13691          4 SLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFE   83 (103)
Q Consensus         4 ~~~d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~   83 (103)
                      +..+..||+++|.||||+..++      +||.+|.+.+++|.++|+..|+..|++.|.++|||||+++||..|++.+||.
T Consensus        14 ~~~~~~Lp~apv~Ri~r~~~~~------Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~~~~~~   87 (91)
T COG2036          14 RSTDLLLPKAPVRRILRKAGAE------RVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKRLGRR   87 (91)
T ss_pred             hhhhhhcCchHHHHHHHHHhHH------HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHHHhccc
Confidence            5678899999999999999763      8999999999999999999999999999999999999999999999999997


Q ss_pred             HH
Q psy13691         84 VI   85 (103)
Q Consensus        84 ~~   85 (103)
                      .|
T Consensus        88 ~~   89 (91)
T COG2036          88 IY   89 (91)
T ss_pred             cc
Confidence            65

>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=99.38  E-value=2.9e-12  Score=83.22  Aligned_cols=71  Identities=18%  Similarity=0.287  Sum_probs=65.7

Q ss_pred             CCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCchHH
Q psy13691          9 NLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEVI   85 (103)
Q Consensus         9 ~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~   85 (103)
                      .||++.|.||++...-      .+||.|+.+.+.++.++|+..+..+|...|+++|||||+++||..||+..|-.-|
T Consensus        13 gi~k~~I~RLarr~Gv------kRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr~g~~~y   83 (85)
T cd00076          13 GITKPAIRRLARRGGV------KRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLY   83 (85)
T ss_pred             cCCHHHHHHHHHHcCc------chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHCCCCcc
Confidence            5999999999999742      5899999999999999999999999999999999999999999999999885533

>PLN00035 histone H4; Provisional

Probab=99.33  E-value=8e-12  Score=83.73  Aligned_cols=69  Identities=19%  Similarity=0.302  Sum_probs=64.5

Q ss_pred             CCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCch
Q psy13691          9 NLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFE   83 (103)
Q Consensus         9 ~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~   83 (103)
                      .||+++|.||++...-      .+||.|+.+.+.+..++|+..|..+|...|++.+||||+++||..||+..|-.
T Consensus        29 ~ipk~~IrRLARr~Gv------kRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~g~~   97 (103)
T PLN00035         29 GITKPAIRRLARRGGV------KRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRT   97 (103)
T ss_pred             cCCHHHHHHHHHHcCc------ccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHcCCc
Confidence            5999999999999842      58999999999999999999999999999999999999999999999987754

>PTZ00015 histone H4; Provisional

Probab=99.28  E-value=2.6e-11  Score=81.12  Aligned_cols=71  Identities=18%  Similarity=0.279  Sum_probs=65.6

Q ss_pred             CCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCchH
Q psy13691          8 LNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEV   84 (103)
Q Consensus         8 ~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~   84 (103)
                      ..||++.|.||++...-      .+||.|+.+.+.++.++|+..|..+|...|++++||||+++||..||+..|-.-
T Consensus        29 ~gI~k~~IrRLarr~Gv------kRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr~g~~~   99 (102)
T PTZ00015         29 RGITKGAIRRLARRGGV------KRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQGRTL   99 (102)
T ss_pred             cCCCHHHHHHHHHHcCC------ccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcCCCC
Confidence            46999999999999733      589999999999999999999999999999999999999999999999887643

>smart00428 H3 Histone H3

Probab=99.21  E-value=4.8e-11  Score=80.27  Aligned_cols=76  Identities=21%  Similarity=0.215  Sum_probs=68.1

Q ss_pred             CccCCCCcHHHHHHHHHhhCCCCCc-ccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhh
Q psy13691          4 SLDDLNLPSAIIQRLIKEALPKDAE-GKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQ   79 (103)
Q Consensus         4 ~~~d~~LP~a~V~ri~K~~l~~~~~-~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~   79 (103)
                      +..++.+|+.++.|++++..++... .+.+++.+|..+||++++.|+.-+...|+..|.+.||+||.++|+.-|..-
T Consensus        24 kst~lLI~k~pF~RLVREI~~~~~~~~~~R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~kDi~La~ri  100 (105)
T smart00428       24 KSTDLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQLARRI  100 (105)
T ss_pred             cCcccccccccHHHHHHHHHHHcCCCCCceeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHhhHHHHHHH
Confidence            5678999999999999999876422 258999999999999999999999999999999999999999999888643

>smart00803 TAF TATA box binding protein associated factor

Probab=99.16  E-value=2.3e-10  Score=70.80  Aligned_cols=64  Identities=20%  Similarity=0.230  Sum_probs=59.7

Q ss_pred             CCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691          9 NLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK   78 (103)
Q Consensus         9 ~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~   78 (103)
                      .||+++|.||.+...-      -+||.|+...+.+-.+.|+..|..+|...+++.||||++++||-.||+
T Consensus         2 ~~p~~~i~ria~~~Gi------~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Alk   65 (65)
T smart00803        2 WLPKETIKDVAESLGI------GNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR   65 (65)
T ss_pred             CCCHHHHHHHHHHCCC------ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHhC
Confidence            5899999999998732      479999999999999999999999999999999999999999999984

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.

>smart00417 H4 Histone H4

Probab=99.15  E-value=1.7e-10  Score=73.23  Aligned_cols=62  Identities=18%  Similarity=0.275  Sum_probs=57.7

Q ss_pred             CCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHh
Q psy13691          9 NLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEG   76 (103)
Q Consensus         9 ~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~A   76 (103)
                      .||++.|.||++...-      -+||.++.+.+.+..++|+..+..+|...|++.|||||+++||..|
T Consensus        13 gI~k~~IrRLaRr~Gv------kRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~a   74 (74)
T smart00417       13 GITKPAIRRLARRGGV------KRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVYA   74 (74)
T ss_pred             CCCHHHHHHHHHHcCc------chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHheeC
Confidence            6999999999999743      5899999999999999999999999999999999999999999653

>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=99.12  E-value=2.7e-10  Score=71.00  Aligned_cols=71  Identities=21%  Similarity=0.266  Sum_probs=63.4

Q ss_pred             CCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691          7 DLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK   78 (103)
Q Consensus         7 d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~   78 (103)
                      +..+|+..|.|+.|+..++. ....+||++|...|+.+++.|+.-|...|...|.+.||+||+++||..|++
T Consensus         3 ~~~~~~~~~~r~~r~i~~~~-~~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~kR~tI~~~DI~~A~r   73 (75)
T PF00125_consen    3 RRLIPKFPFSRLLREIGEEI-LSKYRISSEALVALQSVLEYLLVEILEEAGNLARHAKRKTITPRDIQLAVR   73 (75)
T ss_dssp             SHSSSHHHHHHHHHHHHHTT-SSSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBSEEGHHHHHHHHH
T ss_pred             ccccCceEEeeeeehhhccc-ccccccccccchhhhhhhhhhhhhhhhHHHHHHhhcCCcEecHHHHHHHHh
Confidence            45789999999999987763 111599999999999999999999999999999999999999999999975

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 ....

>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=99.11  E-value=8.2e-10  Score=69.36  Aligned_cols=65  Identities=25%  Similarity=0.281  Sum_probs=60.9

Q ss_pred             CcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhh
Q psy13691         10 LPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQ   79 (103)
Q Consensus        10 LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~   79 (103)
                      +|+..+..++|+.-|.     .+++.||.++|++.++.|+.-++..|...|++.||+||.++||..+++.
T Consensus         2 ~~k~~l~~lv~~id~~-----~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~r   66 (72)
T cd07981           2 LTKRKLQELLKEIDPR-----EQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLER   66 (72)
T ss_pred             CcHHHHHHHHHhhCCC-----CCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence            6888999999998653     7999999999999999999999999999999999999999999999975

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

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

Probab=99.08  E-value=1.3e-10  Score=86.99  Aligned_cols=77  Identities=30%  Similarity=0.382  Sum_probs=70.5

Q ss_pred             cCCCCcHHHHHHHHHhhCCCCCcccc-cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCchH
Q psy13691          6 DDLNLPSAIIQRLIKEALPKDAEGKI-NVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEV   84 (103)
Q Consensus         6 ~d~~LP~a~V~ri~K~~l~~~~~~~~-~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~   84 (103)
                      .+.+||.|+|.|+||..  ++    + .||.||..++.+.|+.||..||-.|+-.+++++|+|+-..||..|++..++.+
T Consensus       106 k~h~LPlARIkkvMKtd--ed----VkMisaEaPvlFak~~EiFI~ELTmRAW~~ae~NkRRtLQksDia~Av~kSeMfD  179 (286)
T COG5208         106 KDHNLPLARIKKVMKTD--ED----VKMISAEAPVLFAKITEIFIEELTMRAWINAEENKRRTLQKSDIAAAVKKSEMFD  179 (286)
T ss_pred             HhccCcHHHHHHHHhcc--cc----hhheecccchHHHHHHHHHHHHHHHHHHHHHhHhhhhHHHHHHHHHHHHHHHHHh
Confidence            36789999999999986  44    5 59999999999999999999999999999999999999999999999999888


Q ss_pred             HHHH
Q psy13691         85 IIEI   88 (103)
Q Consensus        85 ~~~~   88 (103)
                      |+-.
T Consensus       180 FLid  183 (286)
T COG5208         180 FLID  183 (286)
T ss_pred             HHhh
Confidence            8643

>PLN00160 histone H3; Provisional

Probab=99.02  E-value=7.4e-10  Score=73.55  Aligned_cols=75  Identities=19%  Similarity=0.119  Sum_probs=66.9

Q ss_pred             CccCCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691          4 SLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK   78 (103)
Q Consensus         4 ~~~d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~   78 (103)
                      +..++.+|+.+..|++++..++-..++.+++.+|..+||++++.|+.-+...|+-.|.+.||.||.+.|+.-|..
T Consensus        16 kst~lLI~k~pF~RLVREI~~~~~~~~~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl~~kD~~L~~r   90 (97)
T PLN00160         16 KSTDLLIRRLPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIMPKDMQLARR   90 (97)
T ss_pred             cchhhhhccccHHHHHHHHHHHcCCCCcEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcccccchhhHHHHHH
Confidence            567889999999999999976432234899999999999999999999999999999999999999999988764

>PLN00161 histone H3; Provisional

Probab=98.98  E-value=1.7e-09  Score=75.55  Aligned_cols=75  Identities=19%  Similarity=0.176  Sum_probs=67.1

Q ss_pred             CccCCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691          4 SLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK   78 (103)
Q Consensus         4 ~~~d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~   78 (103)
                      +..++.+|+.++.|++++...+....+.+++.+|..+||++++.|+.-+...|+-.|.+.||.||.+.|+.-|..
T Consensus        50 kst~lLIpklPF~RLVREI~~~~~~~~~Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kDm~La~r  124 (135)
T PLN00161         50 KSTELLIRKLPFARLVREISNEMLREPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLARR  124 (135)
T ss_pred             cccccccccccHHHHHHHHHHhcCCCCcEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhhHHHHHH
Confidence            567889999999999999976532234899999999999999999999999999999999999999999988864

>PLN00121 histone H3; Provisional

Probab=98.91  E-value=3.1e-09  Score=74.39  Aligned_cols=74  Identities=19%  Similarity=0.195  Sum_probs=67.2

Q ss_pred             CccCCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691          4 SLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK   78 (103)
Q Consensus         4 ~~~d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~   78 (103)
                      ...++.+|+..+.|++++...+. ..+.+++.+|..+||++++.|+.-+...++-.|.+.||.||.+.|+.-+..
T Consensus        57 kst~lLI~k~pF~RLVREI~~~~-~~~~Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~r  130 (136)
T PLN00121         57 KSTELLIRKLPFQRLVREIAQDF-KTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR  130 (136)
T ss_pred             cccccccccccHHHHHHHHHHHh-CccceeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhHHHHHH
Confidence            56789999999999999998763 234899999999999999999999999999999999999999999988764

>PTZ00018 histone H3; Provisional

Probab=98.90  E-value=3.2e-09  Score=74.29  Aligned_cols=74  Identities=19%  Similarity=0.195  Sum_probs=66.7

Q ss_pred             CccCCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691          4 SLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK   78 (103)
Q Consensus         4 ~~~d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~   78 (103)
                      +..++.+|+..+.|++++...+. ..+++++.+|..+||++++.|+.-|...++..|.+.||.||.+.|+.-|..
T Consensus        57 kst~lLI~k~pF~RLVREI~~~~-~~~~rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~r  130 (136)
T PTZ00018         57 KSTELLIRKLPFQRLVREIAQDF-KTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR  130 (136)
T ss_pred             ccchhccccccHHHHHHHHHHHc-CCcceeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchhhHHHHHH
Confidence            56789999999999999997653 234899999999999999999999999999999999999999999988764

>KOG1657|consensus

Probab=98.79  E-value=6.3e-09  Score=78.59  Aligned_cols=84  Identities=24%  Similarity=0.218  Sum_probs=69.7

Q ss_pred             CCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCchHH-
Q psy13691          7 DLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEVI-   85 (103)
Q Consensus         7 d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~-   85 (103)
                      ...||+++|.+|||..= +-    -.|+.||..++.+||+.||..|+..|+..+.+.+|+|+...|+..|+..-+-.+| 
T Consensus        72 ~~~lPlaRiKkimK~de-dv----~mI~~Eapvl~aka~E~Fi~elt~~sw~~Tee~~rrtl~~sdia~av~~s~~fdFL  146 (236)
T KOG1657|consen   72 NHILPLARIKKIMKSDE-DV----SMITAEAPVLFAKACELFITELTLRSWVHTEENKRRTLQKSDIAAAVTQSETFDFL  146 (236)
T ss_pred             hccCcHhhccccccccc-cc----cccchhHHHHHHHHHHHHHHHHHHHhhhhhcccccccchHHHHHHHhccCCCccce
Confidence            45899999999999972 22    2799999999999999999999999999999999999999999999996555444 


Q ss_pred             --HHHHHHHHHH
Q psy13691         86 --IEILGKSYNA   95 (103)
Q Consensus        86 --~~~l~~~l~~   95 (103)
                        +.|.+...+.
T Consensus       147 ~DivP~~~~~~~  158 (236)
T KOG1657|consen  147 RDIVPRKILAEK  158 (236)
T ss_pred             eccccchhcccc
Confidence              4444444433

>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins

Probab=98.70  E-value=1.9e-07  Score=59.06  Aligned_cols=66  Identities=15%  Similarity=0.127  Sum_probs=59.2

Q ss_pred             HHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCch
Q psy13691         12 SAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFE   83 (103)
Q Consensus        12 ~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~   83 (103)
                      +-.|.+|++.+.=      -+++.+|.+.|.+....|+..|+..+...|++.||++.++.||..||+++|+.
T Consensus         9 ~~~Vaqil~~~Gf------~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~~gi~   74 (77)
T smart00576        9 RIAVAQILESAGF------DSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALENLGIS   74 (77)
T ss_pred             HHHHHHHHHHcCc------cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCcc
Confidence            3457788887632      37999999999999999999999999999999999999999999999999974

subdomain of archael histone-like transcription factors

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

Probab=98.65  E-value=1.3e-07  Score=64.54  Aligned_cols=72  Identities=14%  Similarity=0.165  Sum_probs=63.7

Q ss_pred             CCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhh-cCch
Q psy13691          7 DLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQ-IGFE   83 (103)
Q Consensus         7 d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~-lgf~   83 (103)
                      .+.||.++|.|+||+.-. .    .|||.+|...|..+.+.+...|...|...|.+.+|++|+++||..|+.. -+|.
T Consensus        18 gL~fPV~ri~R~Lk~~~~-a----~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi~nD~EL~   90 (115)
T cd00074          18 GLQFPVGRIHRYLKKGRY-A----ERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVRNDEELN   90 (115)
T ss_pred             CccCcHHHHHHHHHcCcc-c----cccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHHhccHHHH
Confidence            678999999999998422 1    6999999999999999999999999999999999999999999999974 3443

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.

>KOG1659|consensus

Probab=98.30  E-value=3.4e-06  Score=62.89  Aligned_cols=79  Identities=19%  Similarity=0.263  Sum_probs=70.1

Q ss_pred             CCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCchHHHH
Q psy13691          8 LNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEVIIE   87 (103)
Q Consensus         8 ~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~~~   87 (103)
                      -.||.++|.|||...=+-+     +|+.-....+.++.+.|+.-|-..+.+++...+-|||+++|+..+++.-.-.+|+.
T Consensus        12 trfp~aRiKKIMQ~dEdIG-----KvaqavPViisralElFl~~l~~~t~~~t~~~~aKt~s~~hlkq~v~~~~~FdFLk   86 (224)
T KOG1659|consen   12 TRFPPARIKKIMQSDEDIG-----KVAQAVPVIISRALELFLESLLQKTLEITRSRGAKTVSSSHLKQAVESDPKFDFLK   86 (224)
T ss_pred             ccCCHHHHHHHHhhhhhhh-----hhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcCccccCHHHHHHHHhccchhHHHH
Confidence            3689999999998863222     89999999999999999999999999999999999999999999999888888887


Q ss_pred             HHHH
Q psy13691         88 ILGK   91 (103)
Q Consensus        88 ~l~~   91 (103)
                      .+-.
T Consensus        87 ~~v~   90 (224)
T KOG1659|consen   87 EVVE   90 (224)
T ss_pred             HHHH
Confidence            7544

>KOG1745|consensus

Probab=98.22  E-value=6.4e-07  Score=62.71  Aligned_cols=77  Identities=19%  Similarity=0.182  Sum_probs=66.4

Q ss_pred             CccCCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcC
Q psy13691          4 SLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIG   81 (103)
Q Consensus         4 ~~~d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lg   81 (103)
                      +..|+.+++.+..|++++..++. ..+.++...|..+||++++.|+.-|.-.+|-.|.+.||.||-+.|+.-|..--|
T Consensus        58 kstdLlI~K~PFqRlvrei~q~f-~~dLrfqs~Ai~ALQeA~EayLv~LfEdtnlcAihAkRVTimpkdiQlArrirg  134 (137)
T KOG1745|consen   58 KSTDLLIRKLPFQRLVREIAQDF-KTDLRFQSSAIAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG  134 (137)
T ss_pred             hhhHHHhhcCcHHHHhHHHHhcc-cccceehHHHHHHHHHHHHHHHHHhccccchhhhccceeEecccceehhhhccc
Confidence            45788899999999999665543 123899999999999999999999999999999999999999999998876443

>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=98.22  E-value=8.8e-06  Score=55.50  Aligned_cols=67  Identities=10%  Similarity=0.012  Sum_probs=58.3

Q ss_pred             HHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCchHHH
Q psy13691         14 IIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEVII   86 (103)
Q Consensus        14 ~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~~   86 (103)
                      .|.+|+|+..-      .+++.++...|.+.+..++.-+..+|...|+++||+||+.+||.-|++..+-..|.
T Consensus         6 ~v~~iLk~~Gv------~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~~~f~   72 (117)
T cd07979           6 VIAAILKSMGI------TEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVDYSFT   72 (117)
T ss_pred             HHHHHHHHCCC------CccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhccCCC
Confidence            57788887621      47999999999999999999999999999999999999999999999976654443

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

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

Probab=98.22  E-value=3.2e-06  Score=68.17  Aligned_cols=68  Identities=24%  Similarity=0.350  Sum_probs=47.7

Q ss_pred             ccCCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhh
Q psy13691          5 LDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVD   72 (103)
Q Consensus         5 ~~d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eD   72 (103)
                      +.--.||.+.|.|++.........++++|++||..+|.+|...|-..|+..=--.|.++|||||..+|
T Consensus       347 i~~P~lP~~~vK~la~~~ak~s~~sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIdesD  414 (414)
T PF15511_consen  347 IPYPSLPPGVVKKLAQHFAKSSGGSKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDESD  414 (414)
T ss_dssp             -----S-HHHHHHHHHHHH-------S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHH
T ss_pred             CCCCCCCccHHHHHHHHHHHhhcccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCCCC
Confidence            34457999999999877755322345899999999999999999999999888899999999999876

>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=98.14  E-value=1.4e-05  Score=63.01  Aligned_cols=67  Identities=16%  Similarity=0.190  Sum_probs=59.0

Q ss_pred             cHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCch
Q psy13691         11 PSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFE   83 (103)
Q Consensus        11 P~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~   83 (103)
                      |..+|.-|.++..-      .++++||...+.+..+.++..+..+|...+++.||||++++||-.||+.++.+
T Consensus         1 ~~~~i~~ia~~~Gi------~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~~~n~e   67 (343)
T cd08050           1 PQESIKLIAESLGI------DSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALRLRNVE   67 (343)
T ss_pred             ChhHHHHHHHHcCC------CcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHHhCCC
Confidence            45677777777622      38999999999999999999999999999999999999999999999976655

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

>smart00427 H2B Histone H2B

Probab=98.13  E-value=2.2e-05  Score=51.47  Aligned_cols=63  Identities=19%  Similarity=0.266  Sum_probs=57.8

Q ss_pred             HHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhc
Q psy13691         13 AIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQI   80 (103)
Q Consensus        13 a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~l   80 (103)
                      .-|+|+.|+.-|+     .-||..+...+.--...+..-|+.+|...|...+|+||+.++|..|++-+
T Consensus         5 ~Yi~kvLKqVhpd-----~giS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvrl~   67 (89)
T smart00427        5 IYIYKVLKQVHPD-----TGISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLI   67 (89)
T ss_pred             HHHHHHHHHhCCC-----ccccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHH
Confidence            3589999999987     58999999999999999999999999999999999999999999998754

>PF09415 CENP-X: CENP-S associating Centromere protein X; InterPro: IPR018552 Centromere protein X (CENP-X) is a component of the CENP-S complex

Probab=98.10  E-value=6.3e-06  Score=51.98  Aligned_cols=66  Identities=23%  Similarity=0.308  Sum_probs=54.8

Q ss_pred             cHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCC-cChhhHHHhhhh
Q psy13691         11 PSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKT-LSGVDVIEGVKQ   79 (103)
Q Consensus        11 P~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkT-I~~eDV~~Al~~   79 (103)
                      |+.+|.||++....++   +.+||+||..++.+....|+..-...|.+.+..+|... |..+|+-+.+-.
T Consensus         1 p~~li~rll~~~f~~~---~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LEki~pq   67 (72)
T PF09415_consen    1 PPELIARLLHEHFKDD---KTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLEKILPQ   67 (72)
T ss_dssp             -CHHHHHHHCTTSSST---T-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHHHHCHC
T ss_pred             ChHHHHHHHHHHhcCC---CCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHHH
Confidence            8899999999877543   38999999999999999999999999999999999999 999999887643

The CENP-S complex is composed of at least of CENP-S and CENP-X and is essential for the stable assembly of the outer kinetchore []. CENP-X is also a DNA-binding component of the Fanconi anemia (FA) core complex involved in DNA damage repair and genome maintenance. The FA complex is composed of CENPS, FANCA, FANCB, FANCC, FANCE, FANCF, FANCG, FANCL/PHF9, FANCM, FAAP24 and CENPX. Interacts with CENPS, FANCM and FAAP24 [, ].; PDB: 4DRB_L 4DRA_H 3V9R_D.

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

Probab=98.09  E-value=4.7e-05  Score=47.79  Aligned_cols=65  Identities=15%  Similarity=0.134  Sum_probs=56.9

Q ss_pred             HHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCch
Q psy13691         13 AIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFE   83 (103)
Q Consensus        13 a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~   83 (103)
                      -.|.+|.+...=      -.++..|.+.|...+..|+..|++.+...|...||...++.||..||+++|+.
T Consensus        10 ~~va~il~~~GF------~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~~gi~   74 (77)
T PF07524_consen   10 RSVAQILKHAGF------DSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALEEMGIS   74 (77)
T ss_pred             HHHHHHHHHcCc------cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCC
Confidence            346666666522      26999999999999999999999999999999999999999999999999984

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 [, ].

>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=98.05  E-value=4.6e-05  Score=49.43  Aligned_cols=66  Identities=26%  Similarity=0.377  Sum_probs=60.4

Q ss_pred             CCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC---CCcChhhHHHhhhhc
Q psy13691          9 NLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNR---KTLSGVDVIEGVKQI   80 (103)
Q Consensus         9 ~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~R---kTI~~eDV~~Al~~l   80 (103)
                      .||++.|.|||...++      -.++.+...+|.-.+-+||.-|.-+|.++..+.+.   ..|.|+||-+|...|
T Consensus        16 ~f~k~~iKr~~~~~~~------~~v~~~v~i~v~glaKvFVGeivE~A~~V~~~~~~~~~~Pl~P~HireA~rrl   84 (85)
T cd08048          16 SFPKAAIKRLIQSVTG------QSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGEANTGPLQPRHLREAYRRL   84 (85)
T ss_pred             hccHHHHHHHHHHHcC------CCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCCcHHHHHHHHHh
Confidence            5999999999999976      36999999999999999999999999999877665   889999999999876

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

>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=98.03  E-value=4.1e-05  Score=47.75  Aligned_cols=63  Identities=22%  Similarity=0.219  Sum_probs=51.2

Q ss_pred             HHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhh
Q psy13691         12 SAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQ   79 (103)
Q Consensus        12 ~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~   79 (103)
                      +..+..++++.-|.     ..+.+|+.++|.+.|..||.-++..|...|++.|-.|+...||.-.|++
T Consensus         2 K~~l~~Lv~~iDp~-----~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~tle~~Dv~~~Ler   64 (68)
T PF03847_consen    2 KRKLQELVKQIDPN-----EKLDPDVEELLLELADDFVDDVVSFACRLAKHRKSSTLEVKDVQLHLER   64 (68)
T ss_dssp             HHHHHHHHHCC-SS---------HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHHH
T ss_pred             hHHHHHHHHHcCCC-----CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHHHh
Confidence            45678899998554     6999999999999999999999999999999999999999999998874

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

>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]

Probab=98.02  E-value=2.7e-05  Score=52.23  Aligned_cols=80  Identities=14%  Similarity=0.143  Sum_probs=69.5

Q ss_pred             CCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCchHHHH
Q psy13691          8 LNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEVIIE   87 (103)
Q Consensus         8 ~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~~~   87 (103)
                      ..+|.|.|.|||.-.-+-     -+|+.-......++.+.|+..|-.++.+.++..+-|.++.+++..|.+.-+=.+|+.
T Consensus        22 trFP~ar~KkIMQ~deDi-----GKV~q~tPVIaskalE~Fl~~iv~~s~k~aR~~~skR~t~e~lk~a~~sdekFdFL~   96 (113)
T COG5247          22 TRFPIARLKKIMQLDEDI-----GKVGQSTPVIASKALEMFLTEIVGLSLKEARKKSSKRMTSEFLKRATESDEKFDFLK   96 (113)
T ss_pred             hcCCHHHHHHHHHhhhhh-----hhhhhcchHHHHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHhhhHHHHHHH
Confidence            369999999999876332     289999999999999999999999999999999999999999999999877777776


Q ss_pred             HHHHH
Q psy13691         88 ILGKS   92 (103)
Q Consensus        88 ~l~~~   92 (103)
                      ...++
T Consensus        97 ~~~~~  101 (113)
T COG5247          97 NMEQF  101 (113)
T ss_pred             HHHHh
Confidence            65543

>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]

Probab=98.01  E-value=1.8e-05  Score=54.34  Aligned_cols=67  Identities=12%  Similarity=0.198  Sum_probs=60.4

Q ss_pred             CCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691          7 DLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK   78 (103)
Q Consensus         7 d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~   78 (103)
                      -+.+|.+.|.|+||.. ...    +||+++|...+.-|.+-.+..++..|-..|...|+|.|.|.|+..|+.
T Consensus        24 gl~fpvgrvkr~lk~~-~~~----~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlAIr   90 (132)
T COG5262          24 GLIFPVGRVKRLLKKG-NYR----MRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAIR   90 (132)
T ss_pred             CccccHHHHHHHHHcC-ccc----eeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHHhc
Confidence            5689999999999943 223    899999999999999999999999999999999999999999999986

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

Probab=97.99  E-value=4.5e-05  Score=48.56  Aligned_cols=62  Identities=18%  Similarity=0.187  Sum_probs=51.2

Q ss_pred             HHHHHHHhhC-CCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhh
Q psy13691         14 IIQRLIKEAL-PKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQ   79 (103)
Q Consensus        14 ~V~ri~K~~l-~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~   79 (103)
                      .|.||+.+.. +.+    +.+|+.+..+|.+-+-.++..++..-..-|+++||+||+++||+-...+
T Consensus        10 ~v~ki~ee~~~~~~----~~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~Rr   72 (76)
T PF15630_consen   10 TVGKIVEEEAKEKG----VEVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLARR   72 (76)
T ss_dssp             HHHHHHHHCCCCTT----SEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTTT
T ss_pred             HHHHHHHHHHhccC----CccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhhc
Confidence            5788888874 334    8999999999999999999999998888999999999999999876653

>PLN00158 histone H2B; Provisional

Probab=97.93  E-value=7.6e-05  Score=51.01  Aligned_cols=65  Identities=17%  Similarity=0.217  Sum_probs=58.9

Q ss_pred             cHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhc
Q psy13691         11 PSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQI   80 (103)
Q Consensus        11 P~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~l   80 (103)
                      ...-|+|+.|++-|+     ..||..+...|.-....+..-|+.+|...|...+|+||+..+|..|++-+
T Consensus        29 y~~YI~kVLKQVhPd-----~gIS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvrLv   93 (116)
T PLN00158         29 YKIYIYKVLKQVHPD-----TGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRLI   93 (116)
T ss_pred             HHHHHHHHHHHhCCC-----CCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHh
Confidence            345699999999987     58999999999999999999999999999999999999999999998644

>PTZ00463 histone H2B; Provisional

Probab=97.90  E-value=9.2e-05  Score=50.63  Aligned_cols=62  Identities=18%  Similarity=0.239  Sum_probs=56.9

Q ss_pred             HHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhc
Q psy13691         14 IIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQI   80 (103)
Q Consensus        14 ~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~l   80 (103)
                      -|+|+.|+.-|+     .-||..+...|+-.......-|+.+|...|...+|+||++.+|..|++-+
T Consensus        33 YI~KVLKqVhPd-----~gIS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvrLl   94 (117)
T PTZ00463         33 YIFKVLKQVHPD-----TGISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIRLV   94 (117)
T ss_pred             HHHHHHHhhCCC-----CCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHhhc
Confidence            499999999987     57999999999998888889999999999999999999999999998644

>KOG3467|consensus

Probab=97.88  E-value=9.4e-05  Score=48.53  Aligned_cols=68  Identities=19%  Similarity=0.302  Sum_probs=59.3

Q ss_pred             CcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCch
Q psy13691         10 LPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFE   83 (103)
Q Consensus        10 LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~   83 (103)
                      +.+-.|.||.+...-      -+|+.-.-+.+..++.+|+..+-+.|...+.+.+||||++-||+-+|++.|.-
T Consensus        30 itKpaIRRlARr~GV------kRi~G~~yeE~~~~~k~fl~n~i~~A~~yt~HAKRKTvT~~dvv~~LKR~G~~   97 (103)
T KOG3467|consen   30 ITKPAIRRLARRGGV------KRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRT   97 (103)
T ss_pred             cchHHHHHHHHhcCc------chhchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhceeeHHHHHHHHHHcCce
Confidence            456678888887622      37888888999999999999999999999999999999999999999998753

>smart00414 H2A Histone 2A

Probab=97.75  E-value=0.00013  Score=49.09  Aligned_cols=68  Identities=12%  Similarity=0.198  Sum_probs=60.7

Q ss_pred             CCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhh
Q psy13691          7 DLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQ   79 (103)
Q Consensus         7 d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~   79 (103)
                      .+.||.+.|.|++|+.-- .    .+|+..|...|.-+.+-+...+-..|-..|...+++.|+++|+..|+..
T Consensus         7 gL~fPVgRi~r~Lk~~~~-~----~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~k~~rItp~hi~lAi~n   74 (106)
T smart00414        7 GLQFPVGRIHRLLRKGTY-A----KRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRITPRHLQLAIRN   74 (106)
T ss_pred             CccCchHHHHHHHHcCcc-c----cccccccHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHHHhhhccC
Confidence            678999999999998632 2    5999999999999999999998888999999999999999999999874

>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=97.73  E-value=0.00041  Score=43.09  Aligned_cols=64  Identities=14%  Similarity=0.208  Sum_probs=49.6

Q ss_pred             CCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691          9 NLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK   78 (103)
Q Consensus         9 ~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~   78 (103)
                      .+|..+|.-+.... +-     ..++.|+...|.+=++.-|..|..+|.....+.+|++++++||-.||+
T Consensus         3 ~~~~esvk~iAes~-Gi-----~~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~ALr   66 (66)
T PF02969_consen    3 VFSQESVKDIAESL-GI-----SNLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDDINSALR   66 (66)
T ss_dssp             ---HHHHHHHHHHT-T--------B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred             cCCHHHHHHHHHHc-CC-----CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence            57888887766554 32     279999999999999999999999999999999999999999999985

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.

>PF04719 TAFII28: hTAFII28-like protein conserved region; InterPro: IPR006809 The general transcription factor, TFIID, consists of the TATA-binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex

Probab=97.68  E-value=0.00034  Score=45.88  Aligned_cols=67  Identities=24%  Similarity=0.355  Sum_probs=51.4

Q ss_pred             CCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCC-CcChhhHHHhhhhc
Q psy13691          9 NLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRK-TLSGVDVIEGVKQI   80 (103)
Q Consensus         9 ~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~Rk-TI~~eDV~~Al~~l   80 (103)
                      .||++.|.|||...+++     -.++.....++.-.+..|+-.|-.+|.+++.+.+.. .|.|.|+-+|...|
T Consensus        23 ~~~k~~ikkli~~~~~~-----qsv~~~v~i~v~g~aKvFVGEiVE~A~~Vq~~~~~~~pl~P~hlreA~rrL   90 (90)
T PF04719_consen   23 SFNKAAIKKLINQVLGN-----QSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGETGPLQPDHLREAYRRL   90 (90)
T ss_dssp             ---HHHHHHHHHHHHS------S---HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SS--HHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHcCC-----CCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcHHHHHHHHhC
Confidence            69999999999999873     479999999999999999999999999998765543 79999999998765

The conserved region is found at the C terminus of most member proteins. The crystal structure of hTAFII28 with hTAFII18 shows that this region is involved in the binding of these two subunits. The conserved region contains four alpha helices and three loops arranged as in histone H3 [, ].; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005634 nucleus; PDB: 1BH9_B 1BH8_B.

>PLN00154 histone H2A; Provisional

Probab=97.61  E-value=0.00025  Score=49.75  Aligned_cols=69  Identities=12%  Similarity=0.149  Sum_probs=60.1

Q ss_pred             CCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhh
Q psy13691          7 DLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQ   79 (103)
Q Consensus         7 d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~   79 (103)
                      .+.||.++|.|++|+...-.    .||+..|...+.-..+-+...+-..|-..|...+++-|+|.||..|+..
T Consensus        36 gL~FPVgRi~r~Lk~g~~~~----~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lAIrn  104 (136)
T PLN00154         36 GLQFPVGRIHRQLKQRVSAH----GRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRG  104 (136)
T ss_pred             CccCchHHHHHHHHhhhhhc----cccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhhccC
Confidence            67899999999999975323    5999999999999888888888888888899999999999999999863

>PTZ00017 histone H2A; Provisional

Probab=97.49  E-value=0.00033  Score=49.01  Aligned_cols=67  Identities=12%  Similarity=0.183  Sum_probs=60.3

Q ss_pred             CCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691          7 DLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK   78 (103)
Q Consensus         7 d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~   78 (103)
                      .+.||.+.|.|++|+.--.     .||+..|...|.-+.+.+...|-..|-..|...+++-|+|+||..|+.
T Consensus        25 gL~FPVgRi~R~Lk~g~~a-----~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lAI~   91 (134)
T PTZ00017         25 GLQFPVGRVHRYLKKGRYA-----KRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIR   91 (134)
T ss_pred             CcccchHHHHHHHhccchh-----ccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhhcc
Confidence            5789999999999986322     599999999999999999999998999999999999999999999986

>KOG1756|consensus

Probab=97.45  E-value=0.00047  Score=47.87  Aligned_cols=68  Identities=12%  Similarity=0.207  Sum_probs=57.0

Q ss_pred             cCCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691          6 DDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK   78 (103)
Q Consensus         6 ~d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~   78 (103)
                      ..+.+|.+.|.|++|+.  ..   ..+|+.+|...+.-+.+.....++..|-..+..+++.-|+|+|+..|+.
T Consensus        24 agl~fPvgri~r~Lr~~--~~---~~ri~~gapV~laavLeYL~Aeile~agnaardnkk~ri~PrH~~lAI~   91 (131)
T KOG1756|consen   24 AGLQFPVGRIHRLLRKG--RY---AQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRITPRHLQLAIR   91 (131)
T ss_pred             cccccCHHHHHHHHHcc--ch---hhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccccChHHHHHHHh
Confidence            36789999999999993  22   2699999999999777766777777777778888999999999999997

>PLN00153 histone H2A; Provisional

Probab=97.28  E-value=0.00081  Score=46.80  Aligned_cols=67  Identities=10%  Similarity=0.149  Sum_probs=59.7

Q ss_pred             CCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691          7 DLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK   78 (103)
Q Consensus         7 d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~   78 (103)
                      .+.||.+.|.|.+|+.--.     .||+..|...+.-+.+.....+-..|-..|...+++-|+|+|+..|+.
T Consensus        22 gL~FpVgRi~R~Lr~g~~a-----~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~   88 (129)
T PLN00153         22 GLQFPVGRIARYLKKGKYA-----ERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIVPRHIQLAIR   88 (129)
T ss_pred             CcccchHHHHHHHhcCchh-----hccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHhhcc
Confidence            5789999999999985322     599999999999999988888888888889999999999999999986

>PLN00157 histone H2A; Provisional

Probab=97.26  E-value=0.00081  Score=46.98  Aligned_cols=67  Identities=13%  Similarity=0.153  Sum_probs=59.4

Q ss_pred             CCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691          7 DLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK   78 (103)
Q Consensus         7 d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~   78 (103)
                      .+.||.+.|.|.+|+.-- .    .||+..|...|.-+.+.....|-..|-..|...+++-|+++||..|+.
T Consensus        24 gL~FPVgRi~R~Lk~g~~-a----~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~   90 (132)
T PLN00157         24 GLQFPVGRIARYLKAGKY-A----TRVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKSRIVPRHIQLAVR   90 (132)
T ss_pred             CcccchHHHHHHHhcCch-h----hhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHhhccc
Confidence            578999999999998522 2    599999999999998888888888888889999999999999999986

>PLN00156 histone H2AX; Provisional

Probab=97.25  E-value=0.0011  Score=46.63  Aligned_cols=67  Identities=13%  Similarity=0.155  Sum_probs=58.8

Q ss_pred             CCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691          7 DLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK   78 (103)
Q Consensus         7 d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~   78 (103)
                      .+.||.++|.|.+|+.-- .    .||+..|...|.-+.+-....+-..|-..|...+++-|+|+|+..|+.
T Consensus        27 gL~FPVgRi~R~Lk~g~y-a----~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~RItPrHi~lAIr   93 (139)
T PLN00156         27 GLQFPVGRIARFLKAGKY-A----ERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR   93 (139)
T ss_pred             CcccchHHHHHHHhcCCh-h----hccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHhhcc
Confidence            578999999999998622 2    599999999999998888888888888889999999999999999986

>KOG1142|consensus

Probab=97.20  E-value=0.001  Score=50.94  Aligned_cols=69  Identities=13%  Similarity=0.137  Sum_probs=61.4

Q ss_pred             ccCCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691          5 LDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK   78 (103)
Q Consensus         5 ~~d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~   78 (103)
                      ..+..|-+-.+..+++..-++     .++-+|+.++|.+.|..||..|+..|...|++.|..||-..||...||
T Consensus       150 ~~~~il~k~kl~dLvqqId~~-----~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIqLhLE  218 (258)
T KOG1142|consen  150 GNNPILSKRKLDDLVQQIDGT-----TKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQLHLE  218 (258)
T ss_pred             CCCccccccchhHHHHhhcCc-----ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhheeeeee
Confidence            345566677888889988443     699999999999999999999999999999999999999999999998

>KOG1658|consensus

Probab=97.18  E-value=0.0003  Score=50.31  Aligned_cols=67  Identities=28%  Similarity=0.368  Sum_probs=57.4

Q ss_pred             CCCcHHHHHHHHHhhCCCCCccccc-ccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhc
Q psy13691          8 LNLPSAIIQRLIKEALPKDAEGKIN-VSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQI   80 (103)
Q Consensus         8 ~~LP~a~V~ri~K~~l~~~~~~~~~-iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~l   80 (103)
                      ..||.++|..+||-.  ++    .+ ..+|+..++.++++.||..|...++..+...+|||+.-.|+=.|.+.-
T Consensus        58 ~rLpL~rik~vvkl~--pd----l~l~~dea~~l~a~aaelfi~~Ln~~~~~~~q~~k~kt~qr~d~D~ai~~~  125 (162)
T KOG1658|consen   58 SRLPLARIKQVVKLD--PD----LTLLNDEASQLIAKAAELFIQELNDVAYTTAQLRKRKTEQRRDYDTAIEAV  125 (162)
T ss_pred             hhccHHHHHhhccCC--cc----hhhhhhHHHHHHHHHHHHHHHHHHhccchhHHHHHhhhhhhhcccccccch
Confidence            479999999999875  44    54 567889999999999999999999999999999999988887776543

>KOG1744|consensus

Probab=97.03  E-value=0.0036  Score=43.45  Aligned_cols=62  Identities=16%  Similarity=0.274  Sum_probs=56.3

Q ss_pred             HHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhc
Q psy13691         14 IIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQI   80 (103)
Q Consensus        14 ~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~l   80 (103)
                      .|+|+.|++-|+     .-|+.++...+.-....+...|+.+|+..+...||.||+..+|..|..-+
T Consensus        42 yv~kvlk~Vhpd-----~gis~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~rLl  103 (127)
T KOG1744|consen   42 YVYKVLKQVHPD-----LGISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVRLL  103 (127)
T ss_pred             ehhhhhhcccCC-----CCcCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHHHh
Confidence            478899999886     46999999999999999999999999999999999999999999998643

>PF15510 CENP-W: Centromere kinetochore component W

Probab=96.94  E-value=0.0024  Score=42.22  Aligned_cols=66  Identities=23%  Similarity=0.320  Sum_probs=54.0

Q ss_pred             CCcHHHHHHHHHhhCCCCCcccccccHHHHHH--------------HHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHH
Q psy13691          9 NLPSAIIQRLIKEALPKDAEGKINVSKDVRLA--------------AGKAASLFILHLTTEALSIANEKNRKTLSGVDVI   74 (103)
Q Consensus         9 ~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~--------------l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~   74 (103)
                      .-|++.+.|++|..=|.     .++....-.+              +.-.|-.|++-|+-||...|=+++-.||.++||+
T Consensus        16 kaPrgfLkrv~Kr~Kph-----lRl~~~~Dllv~~~~f~~~~~~~~vhLncLLFvhrLAEEaRtnA~EnK~~~Ik~~Hv~   90 (102)
T PF15510_consen   16 KAPRGFLKRVFKRQKPH-----LRLETSGDLLVRFCPFSGWQWGGEVHLNCLLFVHRLAEEARTNACENKCGTIKKEHVL   90 (102)
T ss_pred             hCchHHHHHHHHhcCCc-----eeecccccHHHhhcccccccccceeehhHHHHHHHHHHHHHHHHHHHhhccccHHHHH
Confidence            46999999999987664     5665554444              5667889999999999998888899999999999


Q ss_pred             Hhhhh
Q psy13691         75 EGVKQ   79 (103)
Q Consensus        75 ~Al~~   79 (103)
                      .|-+.
T Consensus        91 AaaKv   95 (102)
T PF15510_consen   91 AAAKV   95 (102)
T ss_pred             HHHHH
Confidence            98653

>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=96.82  E-value=0.0019  Score=42.35  Aligned_cols=48  Identities=15%  Similarity=0.183  Sum_probs=24.9

Q ss_pred             ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691         31 INVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK   78 (103)
Q Consensus        31 ~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~   78 (103)
                      -.-..|...+|-+....||..+...|..+|...|++.|+.+|++-+|+
T Consensus        18 ~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR   65 (93)
T PF02269_consen   18 EEPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLR   65 (93)
T ss_dssp             SS--HHHHHHHHHHHHHHHHHHHHHHHC--------------------
T ss_pred             CCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHh
Confidence            478899999999999999999999999999999999999999999997

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

>PTZ00252 histone H2A; Provisional

Probab=96.64  E-value=0.0088  Score=41.88  Aligned_cols=67  Identities=15%  Similarity=0.161  Sum_probs=52.5

Q ss_pred             CCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHh--CCCCCcChhhHHHhhh
Q psy13691          7 DLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANE--KNRKTLSGVDVIEGVK   78 (103)
Q Consensus         7 d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~--~~RkTI~~eDV~~Al~   78 (103)
                      .+.||.+.|.|.+++.--.     .||+.-|...|.-+.+-....+-..|-..|..  .+++-|+++||..|+.
T Consensus        23 GL~FPVgRi~R~Lr~g~ya-----~RIga~ApVYLAAVLEYLtaEVLELAgnaa~d~~~kk~RItPrHi~lAIr   91 (134)
T PTZ00252         23 GLIFPVGRVGSLLRRGQYA-----RRIGASGAVYMAAVLEYLTAELLELSVKAAAQQAKKPKRLTPRTVTLAVR   91 (134)
T ss_pred             CccCchHHHHHHHHcCCcc-----cccCCccHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccccHHHHHhhcc
Confidence            5799999999999986332     59999999988887666555555556565643  5778899999999986

>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=96.38  E-value=0.083  Score=34.60  Aligned_cols=78  Identities=13%  Similarity=0.071  Sum_probs=56.3

Q ss_pred             HHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh----hcCchHHHHH
Q psy13691         13 AIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK----QIGFEVIIEI   88 (103)
Q Consensus        13 a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~----~lgf~~~~~~   88 (103)
                      .-|..+|-...+.     -.-..|...++-+....||..++.+|.+.|. .+|.-++.+|++-++.    .++--.++-.
T Consensus         6 ~ei~~mmy~~GD~-----~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~-~r~~k~~~eD~~FliR~D~~Kl~Rl~~lL~   79 (92)
T cd07978           6 KEIRQMMYGFGDV-----QNPLPETVDLLEDIVVEYIIELCHKAAEVAQ-RRRGKVKVEDLIFLLRKDPKKLARLRELLS   79 (92)
T ss_pred             HHHHHHHHHcCCC-----CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCCCCHHHHHHHHhcCHHHHHHHHHHHH
Confidence            3466777766443     3678899999999999999999999999998 4455569999999997    3333333333


Q ss_pred             HHHHHHHH
Q psy13691         89 LGKSYNAA   96 (103)
Q Consensus        89 l~~~l~~~   96 (103)
                      .+..+++.
T Consensus        80 ~k~~~k~a   87 (92)
T cd07978          80 MKDELKKA   87 (92)
T ss_pred             HHHHHHHH
Confidence            44444433

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

>KOG3219|consensus

Probab=96.32  E-value=0.0065  Score=44.92  Aligned_cols=71  Identities=23%  Similarity=0.347  Sum_probs=61.9

Q ss_pred             CCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC-CCcChhhHHHhhhhcCchH
Q psy13691          8 LNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNR-KTLSGVDVIEGVKQIGFEV   84 (103)
Q Consensus         8 ~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~R-kTI~~eDV~~Al~~lgf~~   84 (103)
                      ..||++.|.|+|.+....      .|+.-+..++.-.+.+||-.|--+|.++|..-+. -.|.|.||-.|...|+...
T Consensus       111 s~f~Ka~iKkL~~~itg~------~v~~nv~Ia~~GiaKvFVGEvVEeAl~V~~~~~e~~PLqP~HIREA~rrL~~qg  182 (195)
T KOG3219|consen  111 SAFPKAQIKKLMSSITGQ------SVSENVAIAMAGIAKVFVGEVVEEALDVREEWGESGPLQPKHIREAYRRLKLQG  182 (195)
T ss_pred             hcCCHHHHHHHHHHHhCC------ccCcceeeeecchhhHhHHHHHHHHHHHHHHhccCCCCCcHHHHHHHHHHHhcC
Confidence            479999999999999653      3999999999999999999999999999977654 4599999999999887643

>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=95.28  E-value=0.15  Score=35.42  Aligned_cols=63  Identities=13%  Similarity=0.035  Sum_probs=41.7

Q ss_pred             cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh-hcCchHHHHHHHHHHH
Q psy13691         32 NVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK-QIGFEVIIEILGKSYN   94 (103)
Q Consensus        32 ~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~-~lgf~~~~~~l~~~l~   94 (103)
                      .....+...|.+.+-.|+.-|-..|...|.+.||++|+.+||..|++ .+++.-.-++-++++-
T Consensus        29 ~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~~r~~~~f~~pppre~ll   92 (129)
T PF02291_consen   29 EYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQSRLDHSFTQPPPREFLL   92 (129)
T ss_dssp             -B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHHHT---------------
T ss_pred             ccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHhhhccCCCChHHHH
Confidence            57788889999999999999999999999999999999999999999 5666655555555543

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

>KOG4336|consensus

Probab=95.27  E-value=0.17  Score=39.95  Aligned_cols=65  Identities=9%  Similarity=0.045  Sum_probs=58.2

Q ss_pred             cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCchHHHHHHHHHHHHHHh
Q psy13691         32 NVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEVIIEILGKSYNAAVS   98 (103)
Q Consensus        32 ~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~~~~l~~~l~~~k~   98 (103)
                      .|++-|++.|.+....+|.-++.++...|...||...+.-||...|-++|+.  +..|..+++.+-.
T Consensus        22 ~is~~aletlvell~~yi~eigrq~~n~celagRT~pT~~Dv~l~Li~mnI~--v~sL~~~~q~~~~   86 (323)
T KOG4336|consen   22 SISNAALETLVELLQSYIREIGRQLHNYCELAGRTIPTQGDVKLTLIEMNIK--VSSLYAYFQKQEF   86 (323)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHhCCC--hhhhHHHHHhccc
Confidence            5999999999999999999999999999999999999999999999999997  4666666665543

>KOG3423|consensus

Probab=94.01  E-value=0.52  Score=34.33  Aligned_cols=70  Identities=20%  Similarity=0.297  Sum_probs=55.5

Q ss_pred             CCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC--------------CCCcChhhH
Q psy13691          8 LNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKN--------------RKTLSGVDV   73 (103)
Q Consensus         8 ~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~--------------RkTI~~eDV   73 (103)
                      ..+|-+.+.-.++.+.=.      ..-.-.+-++.=++..||.-|+..|.+.|+-.+              |-|++-+|+
T Consensus        85 P~IPDavt~~yL~~aGf~------~~D~rv~RLvsLaAQKfvSDIa~DA~Q~~k~r~~~~~~~~k~~~kdkK~tLtmeDL  158 (176)
T KOG3423|consen   85 PTIPDAVTDHYLKKAGFQ------TSDPRVKRLVSLAAQKFVSDIANDALQHSKIRTKTAIGKDKKQAKDKKYTLTMEDL  158 (176)
T ss_pred             CCCcHHHHHHHHHhcCCC------cCcHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccccccccceeeeHHHH
Confidence            468888888888876321      234456788999999999999999999986433              458999999


Q ss_pred             HHhhhhcCch
Q psy13691         74 IEGVKQIGFE   83 (103)
Q Consensus        74 ~~Al~~lgf~   83 (103)
                      ..||.+.|..
T Consensus       159 ~~AL~EyGin  168 (176)
T KOG3423|consen  159 SPALAEYGIN  168 (176)
T ss_pred             HHHHHHhCcc
Confidence            9999999874

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

Probab=93.67  E-value=0.36  Score=35.46  Aligned_cols=52  Identities=21%  Similarity=0.154  Sum_probs=46.9

Q ss_pred             ccccHHHHHHHHHHHHH---HHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCc
Q psy13691         31 INVSKDVRLAAGKAASL---FILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGF   82 (103)
Q Consensus        31 ~~iskda~~~l~~~~~~---Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf   82 (103)
                      ..++.++...|.+.+.-   .|+.++..|...+-..+.++|+.++|..++.++.|
T Consensus       214 ~~~~~~~~~~i~~~s~G~p~~i~~l~~~~~~~a~~~~~~~i~~~~v~~~~~~~~~  268 (269)
T TIGR03015       214 PVFSEGAFDAIHRFSRGIPRLINILCDRLLLSAFLEEKREIGGEEVREVIAEIDF  268 (269)
T ss_pred             CCcCHHHHHHHHHHcCCcccHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhhc
Confidence            46999999999999886   89999999999988889999999999999998764

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.

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=93.15  E-value=0.99  Score=35.16  Aligned_cols=73  Identities=14%  Similarity=0.090  Sum_probs=50.3

Q ss_pred             HHHHHHHHHhhCCCCCcccccccHHHHHHHHHHH------HHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCchHH
Q psy13691         12 SAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAA------SLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEVI   85 (103)
Q Consensus        12 ~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~------~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~   85 (103)
                      ..-+..|++..+... -....++.++.+.+.+.+      -..+..+...|...|...++.+|+.+||..|++.+....+
T Consensus       209 ~~e~~~il~~r~~~~-~~~~~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~~~~~~~~  287 (394)
T PRK00411        209 ADEIFDILKDRVEEG-FYPGVVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYEKSEIVHL  287 (394)
T ss_pred             HHHHHHHHHHHHHhh-cccCCCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHHHHHH
Confidence            445555655543211 001358899988887766      3345566678888899999999999999999998854433

>KOG2389|consensus

Probab=92.21  E-value=0.45  Score=38.13  Aligned_cols=69  Identities=10%  Similarity=0.128  Sum_probs=58.5

Q ss_pred             CCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCch
Q psy13691          9 NLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFE   83 (103)
Q Consensus         9 ~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~   83 (103)
                      .|-+..|..|+....-+      ....-|.+.|+.-+..||+-|+..|...+...||.-.+..||..||++|+..
T Consensus        29 sla~~avaQIcqslg~~------~~~~sale~Ltd~~~qyvQ~lgk~a~~~~n~anR~epnl~Div~Al~dls~s   97 (353)
T KOG2389|consen   29 SLARVAVAQICQSLGYS------STQNSALETLTDVLQQYVQNLGKTAHRYSNLANRTEPNLFDIVLALQDLSAS   97 (353)
T ss_pred             HHHHHHHHHHHHhcCCc------ccccHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCccHHHHHHHHHHhhhh
Confidence            45667788888776332      3445599999999999999999999999999999999999999999988765

>KOG2549|consensus

Probab=91.85  E-value=1.1  Score=37.91  Aligned_cols=65  Identities=17%  Similarity=0.237  Sum_probs=54.2

Q ss_pred             cHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcC
Q psy13691         11 PSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIG   81 (103)
Q Consensus        11 P~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lg   81 (103)
                      |...+.-++ +++.-     ..++.|+..+|..=.+.=|..++.+|.+.-.+.+|.+++.+||..||+.+.
T Consensus        13 ~~Es~k~vA-EslGi-----~nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr~~n   77 (576)
T KOG2549|consen   13 PKESVKVVA-ESLGI-----TNLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALRSLN   77 (576)
T ss_pred             cHHHHHHHH-HHhCc-----cccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHhhcc
Confidence            345554444 44443     369999999999999999999999999999999999999999999999553

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=91.40  E-value=2.2  Score=32.74  Aligned_cols=78  Identities=13%  Similarity=0.102  Sum_probs=50.2

Q ss_pred             HHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHH------HHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCchHH
Q psy13691         12 SAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAAS------LFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEVI   85 (103)
Q Consensus        12 ~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~------~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~   85 (103)
                      ..-+..|++..+... ..+..++.|+...+.+.+.      -.+..+...|.+.|..+++.+|+.+||..|++.+..+.+
T Consensus       201 ~~e~~~il~~r~~~~-~~~~~~~~~~l~~i~~~~~~~~Gd~R~al~~l~~a~~~a~~~~~~~it~~~v~~a~~~~~~~~~  279 (365)
T TIGR02928       201 AEELRDILENRAEKA-FYDGVLDDGVIPLCAALAAQEHGDARKAIDLLRVAGEIAEREGAERVTEDHVEKAQEKIEKDRL  279 (365)
T ss_pred             HHHHHHHHHHHHHhh-ccCCCCChhHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHH
Confidence            344556665544210 0003588888777665442      244456667888888889999999999999998865555


Q ss_pred             HHHHH
Q psy13691         86 IEILG   90 (103)
Q Consensus        86 ~~~l~   90 (103)
                      ...+.
T Consensus       280 ~~~i~  284 (365)
T TIGR02928       280 LELIR  284 (365)
T ss_pred             HHHHH
Confidence            44333

Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.

>KOG1757|consensus

Probab=88.04  E-value=1.1  Score=30.76  Aligned_cols=64  Identities=19%  Similarity=0.260  Sum_probs=48.4

Q ss_pred             CCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhC----CCCCcChhhHHHhhh
Q psy13691          7 DLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEK----NRKTLSGVDVIEGVK   78 (103)
Q Consensus         7 d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~----~RkTI~~eDV~~Al~   78 (103)
                      -+.||..+|.|..|.-....    .++..-+..-    ..-.+.|||.|-.+.|.+.    +-|.|+|.|+..|+.
T Consensus        28 GlqFpVgRihr~LK~r~t~h----~rVGataavy----~aaileYLTaEVLeLAgNasKdLKvKRitprHlqLAiR   95 (131)
T KOG1757|consen   28 GLQFPVGRIHRHLKTRTTSH----GRVGATAAVY----SAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR   95 (131)
T ss_pred             ccccchHHHHHHHHHhcccc----cccchHHHHH----HHHHHHHHHHHHHHHcccccccceeeeccchhheeeec
Confidence            46899999999999987765    6776544433    2345789999888877654    457899999998876

>PF13654 AAA_32: AAA domain; PDB: 3K1J_B

Probab=87.23  E-value=4.3  Score=33.93  Aligned_cols=49  Identities=12%  Similarity=0.123  Sum_probs=38.5

Q ss_pred             cccHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhc
Q psy13691         32 NVSKDVRLAAGKAASL-----------FILHLTTEALSIANEKNRKTLSGVDVIEGVKQI   80 (103)
Q Consensus        32 ~iskda~~~l~~~~~~-----------Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~l   80 (103)
                      .++.+|...|.+.+..           -|.-|-.+|+..|...+++.|+++||..|++.-
T Consensus       447 ~~~~~Av~~li~~~~R~~q~kLsl~~~~l~~ll~EA~~~A~~~~~~~I~~~~V~~Ai~~r  506 (509)
T PF13654_consen  447 PFDRSAVARLIEYSARLDQDKLSLRFSWLADLLREANYWARKEGAKVITAEHVEQAIEER  506 (509)
T ss_dssp             -BBHHHHHHHHHHHHHCC-SEEE--HHHHHHHHHHHHHHHHHCT-SSB-HHHHHHHHHH-
T ss_pred             CCCHHHHHHHHHHHHHHhCCEeCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHcc
Confidence            4788888887776653           567788999999999999999999999999753

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=85.50  E-value=3.4  Score=34.47  Aligned_cols=68  Identities=24%  Similarity=0.131  Sum_probs=45.9

Q ss_pred             HHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHH--HHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCc
Q psy13691         12 SAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASL--FILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGF   82 (103)
Q Consensus        12 ~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~--Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf   82 (103)
                      ..-+.+|++..+...   ...+++++...|.+.+..  .+..+...|..+|..++|++|+.+||.+++..-.|
T Consensus       265 ~eei~~Il~~~a~k~---~i~is~~al~~I~~y~~n~Rel~nll~~Aa~~A~~~~~~~It~~dI~~vl~~~~~  334 (531)
T TIGR02902       265 DEEIKEIAKNAAEKI---GINLEKHALELIVKYASNGREAVNIVQLAAGIALGEGRKRILAEDIEWVAENGNY  334 (531)
T ss_pred             HHHHHHHHHHHHHHc---CCCcCHHHHHHHHHhhhhHHHHHHHHHHHHHHHhhCCCcEEcHHHHHHHhCCccc
Confidence            344555666655432   267999999988777652  22233345666788889999999999999765444

Members of this protein are LonB, a paralog of the ATP-dependent protease La (LonA, TIGR00763). LonB proteins are found strictly, and almost universally, in endospore-forming bacteria. This protease was shown, in Bacillus subtilis, to be expressed specifically in the forespore, during sporulation, under control of sigma(F). The lonB gene, despite location immediately upstream of lonA, was shown to be monocistronic. LonB appears able to act on sigma(H) for post-translation control, but lonB mutation did not produce an obvious sporulation defect under the conditions tested. Note that additional paralogs of LonA and LonB occur in the Clostridium lineage and this model selects only one per species as the protein that corresponds to LonB in B. subtilis.

>PF13335 Mg_chelatase_2: Magnesium chelatase, subunit ChlI

Probab=83.84  E-value=5.8  Score=25.76  Aligned_cols=48  Identities=15%  Similarity=0.183  Sum_probs=41.5

Q ss_pred             ccccHHHHHHHHHHHHHH------HHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691         31 INVSKDVRLAAGKAASLF------ILHLTTEALSIANEKNRKTLSGVDVIEGVK   78 (103)
Q Consensus        31 ~~iskda~~~l~~~~~~F------i~~lt~~A~~~a~~~~RkTI~~eDV~~Al~   78 (103)
                      ..+++++..+|..++..|      .+-|..-|..+|--++...|..+||..||.
T Consensus        41 ~~l~~~~~~~l~~~~~~~~lS~R~~~rilrvARTIADL~~~~~I~~~hi~EAl~   94 (96)
T PF13335_consen   41 CPLSSEAKKLLEQAAEKLNLSARGYHRILRVARTIADLEGSERITREHIAEALS   94 (96)
T ss_pred             cCCCHHHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHhHcCCCCCCHHHHHHHHh
Confidence            468889999999888876      566778899999999999999999999984

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

Probab=83.30  E-value=4.9  Score=32.47  Aligned_cols=52  Identities=19%  Similarity=0.190  Sum_probs=48.7

Q ss_pred             cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCch
Q psy13691         32 NVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFE   83 (103)
Q Consensus        32 ~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~   83 (103)
                      .|.+|+..++..-.+-=|+.+..+|..--.+.||..++-+||..||..+..+
T Consensus        22 Ni~Dd~l~alamDlEYRI~ev~qea~KFmvhSKRtvLt~dDis~ALr~lNVe   73 (450)
T COG5095          22 NIDDDALRALAMDLEYRIKEVCQEASKFMVHSKRTVLTIDDISYALRSLNVE   73 (450)
T ss_pred             ccccHHHHHHHHhHHHHHHHHHHHHHHHhhcccceeeeHHhHHHHHHhcCCC
Confidence            7999999999999999999999999999999999999999999999987654

>TIGR00764 lon_rel lon-related putative ATP-dependent protease

Probab=83.14  E-value=7.5  Score=33.08  Aligned_cols=50  Identities=16%  Similarity=0.103  Sum_probs=40.6

Q ss_pred             cccHHHHHHHHHHHH-------------HHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcC
Q psy13691         32 NVSKDVRLAAGKAAS-------------LFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIG   81 (103)
Q Consensus        32 ~iskda~~~l~~~~~-------------~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lg   81 (103)
                      .++++|...|.+.++             .=+.-|-.+|..+|..+++.+|+.+||.+|++.-.
T Consensus       330 ~~s~~Av~~Li~~~~R~ag~r~~lsl~~R~L~~llR~A~~iA~~~~~~~I~~ehV~~Ai~~~~  392 (608)
T TIGR00764       330 HFTRDAVEEIVREAQRRAGRKDHLTLRLRELGGLVRAAGDIAKSSGKVYVTAEHVLKAKKLAK  392 (608)
T ss_pred             cCCHHHHHHHHHHHHHHHhcccccCCCHHHHHHHHHHHHHHHHhcCCceecHHHHHHHHHHHH
Confidence            589999988876554             34556778898899999999999999999987553

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

>COG1067 LonB Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]

Probab=82.78  E-value=1.7  Score=37.38  Aligned_cols=49  Identities=27%  Similarity=0.238  Sum_probs=35.6

Q ss_pred             cccHHHHHHHHHHHHHH-------------HHHHHHHHHHHHHhCCCCCcChhhHHHhhhhc
Q psy13691         32 NVSKDVRLAAGKAASLF-------------ILHLTTEALSIANEKNRKTLSGVDVIEGVKQI   80 (103)
Q Consensus        32 ~iskda~~~l~~~~~~F-------------i~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~l   80 (103)
                      -++++|..-|.+-+..-             +.-|-.+|..+|..+|++-|+++||.+|++.-
T Consensus       338 ~~~~~Av~~li~~a~R~Ag~~~~Ltl~~rdl~~lv~~A~~ia~~~~~~~I~ae~Ve~a~~~~  399 (647)
T COG1067         338 HLDKDAVEELIREAARRAGDQNKLTLRLRDLGNLVREAGDIAVSEGRKLITAEDVEEALQKR  399 (647)
T ss_pred             CCCHHHHHHHHHHHHHhccccceeccCHHHHHHHHHHhhHHHhcCCcccCcHHHHHHHHHhh
Confidence            36666665555444322             23334489999999999999999999999873

>PF08369 PCP_red: Proto-chlorophyllide reductase 57 kD subunit; InterPro: IPR013580 This domain is found in bacteria and plant chloroplast proteins

Probab=81.09  E-value=3  Score=23.68  Aligned_cols=42  Identities=12%  Similarity=0.120  Sum_probs=26.9

Q ss_pred             cHHHHHHHHHHHHHHHHHHHH-HHHHHHHhCCCCCcChhhHHHh
Q psy13691         34 SKDVRLAAGKAASLFILHLTT-EALSIANEKNRKTLSGVDVIEG   76 (103)
Q Consensus        34 skda~~~l~~~~~~Fi~~lt~-~A~~~a~~~~RkTI~~eDV~~A   76 (103)
                      +.||...|.+. =.|+.--.. .+-..|.+.|...|+.++|..|
T Consensus         2 ~~eA~~~L~~i-P~fvR~~~r~~~E~~Ar~~G~~~IT~e~v~~A   44 (45)
T PF08369_consen    2 TDEAEARLDRI-PFFVRKKLRDAAEKYARERGYDEITVEVVDAA   44 (45)
T ss_dssp             -HHHHHHHCTS--HHHHHHHHHHHHHHHHHCT-SEE-HHHHHHH
T ss_pred             CHHHHHHHHHC-CHHHHHHHHHHHHHHHHHcCCCeECHHHHHhh
Confidence            46677776665 446654444 4446789999999999998876

It often appears at the C-terminal of nitrogenase component 1 type oxidoreductases (IPR000510 from INTERPRO) and sometimes independently in bacterial proteins such as the proto-chlorophyllide reductase subunit B of the cyanobacterium Synechocystis. This domain is also associated with chlorophyllide reductase subunit Z, converts chlorophylls (Chl) into bacteriochlorophylls (BChl) by reducing ring B of the tetrapyrrole.; GO: 0016491 oxidoreductase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process, 0055114 oxidation-reduction process; PDB: 2KRU_A 2L09_A.

>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=80.25  E-value=21  Score=26.21  Aligned_cols=77  Identities=14%  Similarity=0.104  Sum_probs=56.5

Q ss_pred             cCCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhC------CCCCcChhhHHHhhhh
Q psy13691          6 DDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEK------NRKTLSGVDVIEGVKQ   79 (103)
Q Consensus         6 ~d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~------~RkTI~~eDV~~Al~~   79 (103)
                      +...|....+.+.|...+...+  -..++.|...+|..||+.++..|-......|++-      ...+.-..||-.-|..
T Consensus        41 ~~~fl~~~~l~~~~~~i~~~~g--~~~~~~d~~~lis~a~e~rlr~li~k~~~~s~hR~~~~~~~~r~~~~sdvr~qL~~  118 (212)
T cd08045          41 DPSFLNPSPLAKKIRKIAKKHG--LKEVDEDVLDLISLALEERLRNLLEKLIEVSEHRVDSEKEDERYEITSDVRKQLRF  118 (212)
T ss_pred             hhhccCHHHHHHHHHHHHHHcC--CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCceeecchHHHHHHH
Confidence            3456777777777777766541  1169999999999999999999999998888763      3355667788777765


Q ss_pred             cCchH
Q psy13691         80 IGFEV   84 (103)
Q Consensus        80 lgf~~   84 (103)
                      |+--+
T Consensus       119 l~~~e  123 (212)
T cd08045         119 LEQLE  123 (212)
T ss_pred             HHHHH
Confidence            55443

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	103
2byk_B	128	Histone Fold Heterodimer Of The Chromatin Accessibi		6e-12
1n1j_A	93	Crystal Structure Of The Nf-YbNF-Yc Histone Pair Le		2e-07
4awl_B	94	The Nf-y Transcription Factor Is Structurally And F		2e-07
1jfi_B	179	Crystal Structure Of The Nc2-Tbp-Dna Ternary Comple		2e-07
4g91_B	92	Ccaat-Binding Complex From Aspergillus Nidulans Len		1e-06

>pdb|2BYK|B Chain B, Histone Fold Heterodimer Of The Chromatin Accessibility Complex Length = 128

Iteration: 1
 Score = 65.9 bits (159), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 36/91 (39%), Positives = 64/91 (70%), Gaps = 4/91 (4%)
Query: 1  MAESLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIA 60
          M E ++DLNLP+A+I RLIKEALP+ A    +VSK+ R A  +AAS+F + +T+ + ++A
Sbjct: 1  MVERIEDLNLPNAVIGRLIKEALPESA----SVSKEARAAIARAASVFAIFVTSSSTALA 56
Query: 61 NEKNRKTLSGVDVIEGVKQIGFEVIIEILGK 91
          +++N KT++  D+++ + ++ FE  +  L +
Sbjct: 57 HKQNHKTITAKDILQTLTELDFESFVPSLTQ 87

>pdb|1N1J|A Chain A, Crystal Structure Of The Nf-YbNF-Yc Histone Pair Length = 93

Iteration: 1
 Score = 50.8 bits (120), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 28/83 (33%), Positives = 50/83 (60%), Gaps = 4/83 (4%)
Query: 7  DLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRK 66
          D+ LP A + R++K A+P+   GKI  +KD +    +  S FI  +T+EA    +++ RK
Sbjct: 6  DIYLPIANVARIMKNAIPQT--GKI--AKDAKECVQECVSEFISFITSEASERCHQEKRK 61
Query: 67 TLSGVDVIEGVKQIGFEVIIEIL 89
          T++G D++  +  +GF+  +E L
Sbjct: 62 TINGEDILFAMSTLGFDSYVEPL 84

>pdb|4AWL|B Chain B, The Nf-y Transcription Factor Is Structurally And Functionally A Sequence Specific Histone Length = 94

Iteration: 1
 Score = 50.4 bits (119), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 28/83 (33%), Positives = 50/83 (60%), Gaps = 4/83 (4%)
Query: 7  DLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRK 66
          D+ LP A + R++K A+P+   GKI  +KD +    +  S FI  +T+EA    +++ RK
Sbjct: 7  DIYLPIANVARIMKNAIPQT--GKI--AKDAKECVQECVSEFISFITSEASERCHQEKRK 62
Query: 67 TLSGVDVIEGVKQIGFEVIIEIL 89
          T++G D++  +  +GF+  +E L
Sbjct: 63 TINGEDILFAMSTLGFDSYVEPL 85

>pdb|1JFI|B Chain B, Crystal Structure Of The Nc2-Tbp-Dna Ternary Complex Length = 179

Iteration: 1
 Score = 50.4 bits (119), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 27/77 (35%), Positives = 43/77 (55%), Gaps = 5/77 (6%)
Query: 6  DDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNR 65
          DDL +P A I ++IKE LP      + V+ D R       + FI  +++EA  I N+  +
Sbjct: 12 DDLTIPRAAINKMIKETLPN-----VRVANDARELVVNCCTEFIHLISSEANEICNKSEK 66
Query: 66 KTLSGVDVIEGVKQIGF 82
          KT+S   VI+ ++ +GF
Sbjct: 67 KTISPEHVIQALESLGF 83

>pdb|4G91|B Chain B, Ccaat-Binding Complex From Aspergillus Nidulans Length = 92

Iteration: 1
 Score = 47.8 bits (112), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 27/84 (32%), Positives = 47/84 (55%), Gaps = 4/84 (4%)
Query: 6  DDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNR 65
           D  LP A + R++K ALP++A     ++K+ +    +  S FI  +T+EA     ++ R
Sbjct: 4  QDRWLPIANVARIMKLALPENA----KIAKEAKECMQECVSEFISFITSEASEKCQQEKR 59
Query: 66 KTLSGVDVIEGVKQIGFEVIIEIL 89
          KT++G D++  +  +GFE   E L
Sbjct: 60 KTVNGEDILFAMTSLGFENYAEAL 83

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	103
2byk_B	128	Chrac-14; nucleosome sliding, histone fold, DNA-bi	2e-22
1n1j_A	93	NF-YB; histone-like PAIR, DNA binding protein; 1.6	4e-21
1jfi_B	179	DR1 protein, transcription regulator NC2 beta chai	9e-20
1n1j_B	97	NF-YC; histone-like PAIR, DNA binding protein; 1.6	2e-08
2byk_A	140	Chrac-16; nucleosome sliding, histone fold, DNA-bi	3e-06
1jfi_A	98	Transcription regulator NC2 alpha chain; histone,	5e-06
1b67_A	68	Protein (histone HMFA); DNA binding protein; 1.48A	2e-05
1ku5_A	70	HPHA, archaeal histon; histone fold, DNA binding p	3e-05
3b0c_T	111	CENP-T, centromere protein T; histone fold, DNA bi	9e-04

>2byk_B Chrac-14; nucleosome sliding, histone fold, DNA-binding protein; 2.4A {Drosophila melanogaster} SCOP: a.22.1.3 PDB: 2bym_B Length = 128

 Score = 83.9 bits (207), Expect = 2e-22
 Identities = 35/89 (39%), Positives = 62/89 (69%), Gaps = 4/89 (4%)

Query: 1  MAESLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIA 60
          M E ++DLNLP+A+I RLIKEALP+      +VSK+ R A  +AAS+F + +T+ + ++A
Sbjct: 1  MVERIEDLNLPNAVIGRLIKEALPES----ASVSKEARAAIARAASVFAIFVTSSSTALA 56

Query: 61 NEKNRKTLSGVDVIEGVKQIGFEVIIEIL 89
          +++N KT++  D+++ + ++ FE  +  L
Sbjct: 57 HKQNHKTITAKDILQTLTELDFESFVPSL 85

>1n1j_A NF-YB; histone-like PAIR, DNA binding protein; 1.67A {Homo sapiens} SCOP: a.22.1.3 Length = 93

 Score = 79.1 bits (195), Expect = 4e-21
 Identities = 25/84 (29%), Positives = 48/84 (57%), Gaps = 4/84 (4%)

Query: 6  DDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNR 65
           D+ LP A + R++K A+P+       ++KD +    +  S FI  +T+EA    +++ R
Sbjct: 5  QDIYLPIANVARIMKNAIPQTG----KIAKDAKECVQECVSEFISFITSEASERCHQEKR 60

Query: 66 KTLSGVDVIEGVKQIGFEVIIEIL 89
          KT++G D++  +  +GF+  +E L
Sbjct: 61 KTINGEDILFAMSTLGFDSYVEPL 84

>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 Length = 179

 Score = 77.9 bits (191), Expect = 9e-20
 Identities = 28/84 (33%), Positives = 45/84 (53%), Gaps = 5/84 (5%)

Query: 6  DDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNR 65
          DDL +P A I ++IKE LP      + V+ D R       + FI  +++EA  I N+  +
Sbjct: 12 DDLTIPRAAINKMIKETLPN-----VRVANDARELVVNCCTEFIHLISSEANEICNKSEK 66

Query: 66 KTLSGVDVIEGVKQIGFEVIIEIL 89
          KT+S   VI+ ++ +GF   I  +
Sbjct: 67 KTISPEHVIQALESLGFGSYISEV 90

>1n1j_B NF-YC; histone-like PAIR, DNA binding protein; 1.67A {Homo sapiens} SCOP: a.22.1.3 Length = 97

 Score = 46.9 bits (111), Expect = 2e-08
 Identities = 19/79 (24%), Positives = 33/79 (41%), Gaps = 5/79 (6%)

Query: 1  MAESLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIA 60
            +      LP A I++++K       E    +S +  +   KAA +FI  LT  A    
Sbjct: 11 TVKDFRVQELPLARIKKIMKLD-----EDVKMISAEAPVLFAKAAQIFITELTLRAWIHT 65

Query: 61 NEKNRKTLSGVDVIEGVKQ 79
           +  R+TL   D+   + +
Sbjct: 66 EDNKRRTLQRNDIAMAITK 84

>2byk_A Chrac-16; nucleosome sliding, histone fold, DNA-binding protein; 2.4A {Drosophila melanogaster} SCOP: a.22.1.3 PDB: 2bym_A Length = 140

 Score = 42.0 bits (98), Expect = 3e-06
 Identities = 12/74 (16%), Positives = 29/74 (39%), Gaps = 6/74 (8%)

Query: 7  DLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKN-R 65
          +  LP + ++ ++K +          ++ +V     K   LF+ HL   A +    +   
Sbjct: 17 ETFLPLSRVRTIMKSS-----MDTGLITNEVLFLMTKCTELFVRHLAGAAYTEEFGQRPG 71

Query: 66 KTLSGVDVIEGVKQ 79
          + L    + + V +
Sbjct: 72 EALKYEHLSQVVNK 85

>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 Length = 98

 Score = 40.7 bits (95), Expect = 5e-06
 Identities = 14/73 (19%), Positives = 33/73 (45%), Gaps = 5/73 (6%)

Query: 7  DLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRK 66
          +   P A I+++++       E    V+  V +   +A  LF+  L  +A  +   +N K
Sbjct: 9  NARFPPARIKKIMQTD-----EEIGKVAAAVPVIISRALELFLESLLKKACQVTQSRNAK 63

Query: 67 TLSGVDVIEGVKQ 79
          T++   + + ++ 
Sbjct: 64 TMTTSHLKQCIEL 76

>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 = 38.4 bits (90), Expect = 2e-05
 Identities = 22/71 (30%), Positives = 31/71 (43%), Gaps = 6/71 (8%)

Query: 10 LPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLS 69
          LP A I R+IK A  +       VS D R+A  K        + +EA+ +A    RKT+ 
Sbjct: 3  LPIAPIGRIIKNAGAE------RVSDDARIALAKVLEEMGEEIASEAVKLAKHAGRKTIK 56

Query: 70 GVDVIEGVKQI 80
            D+    K  
Sbjct: 57 AEDIELARKMF 67

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

 Score = 38.1 bits (89), Expect = 3e-05
 Identities = 16/69 (23%), Positives = 30/69 (43%), Gaps = 6/69 (8%)

Query: 10 LPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLS 69
          LP A + RLI++A  +       VS+       +    + + +  +A+  A    RKT+ 
Sbjct: 7  LPIAPVDRLIRKAGAE------RVSEQAAKVLAEYLEEYAIEIAKKAVEFARHAGRKTVK 60

Query: 70 GVDVIEGVK 78
            D+   +K
Sbjct: 61 VEDIKLAIK 69

>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 = 35.0 bits (80), Expect = 9e-04
 Identities = 12/74 (16%), Positives = 32/74 (43%), Gaps = 6/74 (8%)

Query: 9  NLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTL 68
           + S++I+++           K  V++D      K +  +   ++++  + +    RKT+
Sbjct: 7  EIASSLIKQIFSHY------VKTPVTRDAYKIVEKCSERYFKQISSDLEAYSQHAGRKTV 60

Query: 69 SGVDVIEGVKQIGF 82
             DV   +++ G 
Sbjct: 61 EMADVELLMRRQGL 74

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	103
2byk_B	128	Chrac-14; nucleosome sliding, histone fold, DNA-bi	100.0
1jfi_B	179	DR1 protein, transcription regulator NC2 beta chai	99.98
1n1j_A	93	NF-YB; histone-like PAIR, DNA binding protein; 1.6	99.98
3b0c_W	76	CENP-W, centromere protein W; histone fold, DNA bi	99.91
1f1e_A	154	Histone fold protein; archaeal histone protein, DN	99.87
1b67_A	68	Protein (histone HMFA); DNA binding protein; 1.48A	99.85
3b0c_T	111	CENP-T, centromere protein T; histone fold, DNA bi	99.8
2byk_A	140	Chrac-16; nucleosome sliding, histone fold, DNA-bi	99.78
4g92_C	119	HAPE; transcription factor, nucleosome, minor groo	99.77
1n1j_B	97	NF-YC; histone-like PAIR, DNA binding protein; 1.6	99.76
1f1e_A	154	Histone fold protein; archaeal histone protein, DN	99.75
2hue_C	84	Histone H4; mini beta sheet, elongated beta sandwh	99.68
1ku5_A	70	HPHA, archaeal histon; histone fold, DNA binding p	99.68
1id3_B	102	Histone H4; nucleosome core particle, chromatin, p	99.67
1tzy_D	103	Histone H4-VI; histone-fold, tetramer-dimer-dimer,	99.62
2yfw_B	103	Histone H4, H4; cell cycle, kinetochore, centromer	99.61
1jfi_A	98	Transcription regulator NC2 alpha chain; histone,	99.6
2hue_B	77	Histone H3; mini beta sheet, elongated beta sandwh	99.43
2yfv_A	100	Histone H3-like centromeric protein CSE4; cell cyc	99.3
3nqj_A	82	Histone H3-like centromeric protein A; alpha helix	99.28
1tzy_C	136	Histone H3; histone-fold, tetramer-dimer-dimer, DN	99.2
3nqu_A	140	Histone H3-like centromeric protein A; alpha helix	99.2
3r45_A	156	Histone H3-like centromeric protein A; histone fol	99.19
1taf_B	70	TFIID TBP associated factor 62; transcription init	99.11
4dra_A	113	Centromere protein S; DNA binding complex, DNA dam	98.97
3b0b_B	107	CENP-S, centromere protein S; histone fold, DNA bi	98.86
3v9r_A	90	MHF1, uncharacterized protein YOL086W-A; histone f	98.85
2nqb_C	123	Histone H2A; nucleosome, NCP, chromatin, structura	98.83
2f8n_G	120	Core histone macro-H2A.1; nucleosome, NCP, macroh2	98.82
1tzy_A	129	Histone H2A-IV; histone-fold, tetramer-dimer-dimer	98.8
3vh5_A	140	CENP-S; histone fold, chromosome segregation, DNA	98.8
1f66_C	128	Histone H2A.Z; nucleosome, chromatin, histone vari	98.8
1id3_C	131	Histone H2A.1; nucleosome core particle, chromatin	98.78
2ly8_A	121	Budding yeast chaperone SCM3; centromere protein,	98.75
2f8n_K	149	Histone H2A type 1; nucleosome, NCP, macroh2A, his	98.74
1taf_A	68	TFIID TBP associated factor 42; transcription init	98.74
2jss_A	192	Chimera of histone H2B.1 and histone H2A.Z; histon	98.59
4dra_E	84	Centromere protein X; DNA binding complex, DNA dam	98.56
2nqb_D	123	Histone H2B; nucleosome, NCP, chromatin, structura	98.53
2l5a_A	235	Histone H3-like centromeric protein CSE4, protein	98.53
1tzy_B	126	Histone H2B; histone-fold, tetramer-dimer-dimer, D	98.5
2l5a_A	235	Histone H3-like centromeric protein CSE4, protein	98.36
3b0b_C	81	CENP-X, centromere protein X; histone fold, DNA bi	98.36
2jss_A	192	Chimera of histone H2B.1 and histone H2A.Z; histon	98.24
1h3o_B	76	Transcription initiation factor TFIID 20/15 kDa su	98.19
1bh9_B	89	TAFII28; histone fold, tata binding protein, trans	97.91
3v9r_B	88	MHF2, uncharacterized protein YDL160C-A; histone f	97.3
2ly8_A	121	Budding yeast chaperone SCM3; centromere protein,	97.13
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	93.77
3ksy_A	1049	SOS-1, SON of sevenless homolog 1; RAS, RAS activa	93.7
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	89.61
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	89.32
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	87.25
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	87.1
3kw6_A	78	26S protease regulatory subunit 8; structural geno	86.87
1khy_A	148	CLPB protein; alpha helix, chaperone; 1.95A {Esche	84.8
3fh2_A	146	Probable ATP-dependent protease (heat shock prote;	84.1
3aji_B	83	S6C, proteasome (prosome, macropain) 26S subunit,	81.52
2dzn_B	82	26S protease regulatory subunit 6B homolog; ankyri	81.39
1wwi_A	148	Hypothetical protein TTHA1479; structural genomics	81.2
2y1q_A	150	CLPC N-domain, negative regulator of genetic compe	81.0
2y1q_A	150	CLPC N-domain, negative regulator of genetic compe	80.97
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	80.93
3fh2_A	146	Probable ATP-dependent protease (heat shock prote;	80.31
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	80.09

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

Probab=100.00  E-value=6e-34  Score=195.94  Aligned_cols=97  Identities=36%  Similarity=0.617  Sum_probs=85.0

Q ss_pred             CCCCccCCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhc
Q psy13691          1 MAESLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQI   80 (103)
Q Consensus         1 m~~~~~d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~l   80 (103)
                      ||++++|+.||+|+|.||||+++|+.    .+||+||+.+|++||++||+|||++|+++|.+++||||+++||++||+.+
T Consensus         1 m~e~~~d~~LP~A~I~rImK~~~pd~----~~iS~dA~~~l~ka~e~FI~~lt~~A~~~a~~~kRKTI~~~Dv~~Al~~l   76 (128)
T 2byk_B            1 MVERIEDLNLPNAVIGRLIKEALPES----ASVSKEARAAIARAASVFAIFVTSSSTALAHKQNHKTITAKDILQTLTEL   76 (128)
T ss_dssp             ----------CCSHHHHHHHHHSCTT----CEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHT
T ss_pred             CCCccccccCCHHHHHHHHHHhCccc----ceECHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHHc
Confidence            99999999999999999999999988    99999999999999999999999999999999999999999999999999


Q ss_pred             CchHHHHHHHHHHHHHHhccc
Q psy13691         81 GFEVIIEILGKSYNAAVSIKV  101 (103)
Q Consensus        81 gf~~~~~~l~~~l~~~k~~~~  101 (103)
                      ||.+|+++|+.+|+.||+.+.
T Consensus        77 ~f~~fl~~lk~~l~~yr~~~~   97 (128)
T 2byk_B           77 DFESFVPSLTQDLEVYRKVVK   97 (128)
T ss_dssp             TCTTTHHHHHHHHHHHHHHHT
T ss_pred             CcHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999998764

>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=99.98  E-value=2.1e-32  Score=197.21  Aligned_cols=92  Identities=30%  Similarity=0.506  Sum_probs=88.2

Q ss_pred             CccCCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCch
Q psy13691          4 SLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFE   83 (103)
Q Consensus         4 ~~~d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~   83 (103)
                      ..+|+.||+|+|.||||++|| +    ++||+||+++|++||++||+|||++|+++|.++|||||+++||++||+.|||+
T Consensus        10 ~~eD~~LP~A~V~RImK~alp-~----~rISkDA~~al~ec~~eFI~~LtseA~e~a~~~~RKTI~~eDVl~Al~~LgF~   84 (179)
T 1jfi_B           10 NDDDLTIPRAAINKMIKETLP-N----VRVANDARELVVNCCTEFIHLISSEANEICNKSEKKTISPEHVIQALESLGFG   84 (179)
T ss_dssp             --CCCCCCHHHHHHHHHHHST-T----CCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHHTTG
T ss_pred             chhhhhcCHHHHHHHHHHhCC-c----cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHhcChH
Confidence            568999999999999999999 7    89999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhcc
Q psy13691         84 VIIEILGKSYNAAVSIK  100 (103)
Q Consensus        84 ~~~~~l~~~l~~~k~~~  100 (103)
                      +|+++|+.+|+.||+.+
T Consensus        85 ~fv~~lk~~L~~yre~~  101 (179)
T 1jfi_B           85 SYISEVKEVLQECKTVA  101 (179)
T ss_dssp             GGHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            99999999999999865

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

Probab=99.98  E-value=6.6e-32  Score=176.19  Aligned_cols=91  Identities=27%  Similarity=0.444  Sum_probs=85.7

Q ss_pred             CccCCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCch
Q psy13691          4 SLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFE   83 (103)
Q Consensus         4 ~~~d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~   83 (103)
                      +++|+.||+++|.||||+.+|++    .+||+||+.++++||++||.||+++|++.|.++|||||+++||..|++.+||+
T Consensus         3 ~~~d~~LP~a~i~ri~K~~~~~~----~~is~dA~~~l~~a~e~Fi~~l~~~A~~~a~~~kRkTI~~~Dv~~Al~~l~F~   78 (93)
T 1n1j_A            3 REQDIYLPIANVARIMKNAIPQT----GKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDILFAMSTLGFD   78 (93)
T ss_dssp             ----CCCCHHHHHHHHHHTSCTT----CEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHTTCG
T ss_pred             CcccccCChhHHHHHHHHhCCcc----ceeCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHHcCcH
Confidence            57899999999999999999988    89999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHh
Q psy13691         84 VIIEILGKSYNAAVS   98 (103)
Q Consensus        84 ~~~~~l~~~l~~~k~   98 (103)
                      +|+++++.++++||+
T Consensus        79 ~~i~~~~~~l~~~r~   93 (93)
T 1n1j_A           79 SYVEPLKLYLQKFRE   93 (93)
T ss_dssp             GGHHHHHHHHHHHHC
T ss_pred             hhHHHHHHHHHHHhC
Confidence            999999999999985

>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=99.91  E-value=2.9e-24  Score=135.55  Aligned_cols=69  Identities=23%  Similarity=0.342  Sum_probs=64.3

Q ss_pred             CCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhc
Q psy13691          7 DLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQI   80 (103)
Q Consensus         7 d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~l   80 (103)
                      ...||+|+|.||||+++| +    ++||+||+++|++|+++||++|+++|++.|.++|||||+++||..|++.+
T Consensus         2 ~~~LP~A~V~rI~K~~~p-~----~~is~~A~~~i~~~~~~Fi~~la~eA~~~a~~~~rKTI~~~dI~~A~~~l   70 (76)
T 3b0c_W            2 RRTVPRGTLRKIIKKHKP-H----LRLAANTDLLVHLSFLLFLHRLAEEARTNAFENKSKIIKPEHTIAAAKVI   70 (76)
T ss_dssp             --CCCHHHHHHHHHHHCT-T----CEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSBCHHHHHHHHHHH
T ss_pred             CCcccccHHHHHHHHhCC-C----CccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHH
Confidence            358999999999999999 4    79999999999999999999999999999999999999999999999754

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

Probab=99.87  E-value=1.3e-22  Score=143.24  Aligned_cols=74  Identities=18%  Similarity=0.216  Sum_probs=71.2

Q ss_pred             CCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCchHHHH
Q psy13691          9 NLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEVIIE   87 (103)
Q Consensus         9 ~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~~~   87 (103)
                      +||+++|.||||++||.     .+||+||++.+++|+++|+.+++++|++.|.++|||||+++||++||..|||++|.+
T Consensus         4 ~LP~a~V~Riik~~lg~-----~rVS~dA~~~l~~~l~~f~~~i~~~A~~~a~ha~RKTv~a~DV~~a~~~lg~~~v~d   77 (154)
T 1f1e_A            4 ELPKAAIERIFRQGIGE-----RRLSQDAKDTIYDFVPTMAEYVANAAKSVLDASGKKTLMEEHLKALADVLMVEGVED   77 (154)
T ss_dssp             CCCHHHHHHHHHTTSTT-----CEECHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHHHHTCTTSTT
T ss_pred             cCCccHHHHHHHhcCCc-----cchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHhcccccCCc
Confidence            89999999999999986     699999999999999999999999999999999999999999999999999998753

>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=99.85  E-value=3e-21  Score=118.88  Aligned_cols=66  Identities=33%  Similarity=0.391  Sum_probs=63.2

Q ss_pred             CCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhc
Q psy13691          9 NLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQI   80 (103)
Q Consensus         9 ~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~l   80 (103)
                      .||+++|.||||+.  ++    .+||+||..++++|+++|+.+|+.+|+..|.++|||||+++||..|++.|
T Consensus         2 ~lP~a~v~Ri~k~~--~~----~ris~~A~~~l~~a~e~fi~~l~~~A~~~a~~~kRkTI~~~Di~~A~~~l   67 (68)
T 1b67_A            2 ELPIAPIGRIIKNA--GA----ERVSDDARIALAKVLEEMGEEIASEAVKLAKHAGRKTIKAEDIELARKMF   67 (68)
T ss_dssp             CSCHHHHHHHHHHT--TC----SEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHGGGG
T ss_pred             CCCccHHHHHHhcC--Cc----ccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHhc
Confidence            69999999999998  34    79999999999999999999999999999999999999999999999876

>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=99.80  E-value=8.1e-20  Score=122.73  Aligned_cols=88  Identities=15%  Similarity=0.176  Sum_probs=76.9

Q ss_pred             CccCCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCch
Q psy13691          4 SLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFE   83 (103)
Q Consensus         4 ~~~d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~   83 (103)
                      ..+|..||++.|.||+|..  ..    .+||+|+.+++.+|+.+|+..++.+|...|+++|||||+++||..|++..|+.
T Consensus         2 ~~~d~~lP~a~I~Ri~r~~--g~----~rIS~~a~~~l~e~l~~f~~~v~~da~~~A~HA~RKTV~~eDV~lalrr~g~~   75 (111)
T 3b0c_T            2 STREPEIASSLIKQIFSHY--VK----TPVTRDAYKIVEKCSERYFKQISSDLEAYSQHAGRKTVEMADVELLMRRQGLV   75 (111)
T ss_dssp             --------CHHHHHHHHHH--HC----SCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHTTSS
T ss_pred             CCCCCCCCHHHHHHHHHHC--CC----CccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHHCCCc
Confidence            4578899999999999998  23    79999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHH
Q psy13691         84 VIIEILGKSYNAAV   97 (103)
Q Consensus        84 ~~~~~l~~~l~~~k   97 (103)
                      .|..++..++++|.
T Consensus        76 ~~~~~l~~l~~~~l   89 (111)
T 3b0c_T           76 TDKMPLHVLVERHL   89 (111)
T ss_dssp             BTTBCHHHHHHHHS
T ss_pred             cccccHHHHHHHhC
Confidence            99999999999993

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

Probab=99.78  E-value=3.2e-20  Score=129.17  Aligned_cols=91  Identities=15%  Similarity=0.184  Sum_probs=61.6

Q ss_pred             ccCCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHH-HhCCCCCcChhhHHHhhhh---c
Q psy13691          5 LDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIA-NEKNRKTLSGVDVIEGVKQ---I   80 (103)
Q Consensus         5 ~~d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a-~~~~RkTI~~eDV~~Al~~---l   80 (103)
                      ..+..||.++|.||||.. |+.    .+||++|..++++|++.||.+|+.+|+..| ...+||||+++||..|+..   +
T Consensus        15 ~~~~~LPlaRIKrIMK~d-pdv----~~Is~eA~vliakA~ElFI~~Lt~~A~~~a~~~~kRKtI~~~Dl~~AV~~~e~~   89 (140)
T 2byk_A           15 TAETFLPLSRVRTIMKSS-MDT----GLITNEVLFLMTKCTELFVRHLAGAAYTEEFGQRPGEALKYEHLSQVVNKNKNL   89 (140)
T ss_dssp             --------------CCSS-SSC----SCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSCEECHHHHHHHHHTCSTT
T ss_pred             ccCCCCCHHHHHHHHhcC-ccc----ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcccCHHHHHHHHhcCchh
Confidence            356789999999999998 666    699999999999999999999999999999 9999999999999999985   5


Q ss_pred             CchHHHHHHHHHHHHHHhcc
Q psy13691         81 GFEVIIEILGKSYNAAVSIK  100 (103)
Q Consensus        81 gf~~~~~~l~~~l~~~k~~~  100 (103)
                      +|..++.|.+..+++|++..
T Consensus        90 dFL~divP~ki~l~~~~~~~  109 (140)
T 2byk_A           90 EFLLQIVPQKIRVHQFQEML  109 (140)
T ss_dssp             GGGTTTSCSCC---------
T ss_pred             hhHhccccchhhHHHHHHHH
Confidence            55555568899999998765

>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=99.77  E-value=5.3e-19  Score=119.88  Aligned_cols=75  Identities=24%  Similarity=0.340  Sum_probs=68.8

Q ss_pred             CCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCchHHH
Q psy13691          7 DLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEVII   86 (103)
Q Consensus         7 d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~~   86 (103)
                      ...||.|+|.||||.. |+.    .+||+||..++++|++.||.+|+.+|+..|..++||||+++||..|++..+..+|+
T Consensus        39 ~~~lPvaRIkrImK~d-~~~----~~is~eA~v~la~a~E~Fi~~L~~~A~~~a~~~krktI~~~di~~Av~~~e~~dFL  113 (119)
T 4g92_C           39 IHQLPLARIKKVMKAD-PEV----KMISAEAPILFAKGCDVFITELTMRAWIHAEDNKRRTLQRSDIAAALSKSDMFDFL  113 (119)
T ss_dssp             CCSSCHHHHHHHHHTS-TTC----CEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHTTCGGGGGG
T ss_pred             cCCCCHHHHHHHHhhC-Ccc----ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccCHHHHHHHHhcCchhhHH
Confidence            5679999999999976 666    79999999999999999999999999999999999999999999999877665564

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

Probab=99.76  E-value=1.2e-18  Score=114.21  Aligned_cols=78  Identities=23%  Similarity=0.274  Sum_probs=68.7

Q ss_pred             ccCCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCchH
Q psy13691          5 LDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEV   84 (103)
Q Consensus         5 ~~d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~   84 (103)
                      ..+..||.|+|.||||.. |+.    .+||+||..++++|++.|+.+|+.+|++.|.++|||||+++||..|++..++.+
T Consensus        15 ~~~~~lP~arIkrImK~~-~~~----~~is~eA~~~laka~E~Fi~~l~~~A~~~a~~~krktI~~~di~~Av~~~e~~~   89 (97)
T 1n1j_B           15 FRVQELPLARIKKIMKLD-EDV----KMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDIAMAITKFDQFD   89 (97)
T ss_dssp             -----CCHHHHHHHHTTS-TTC----CCBCTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHTTCGGGG
T ss_pred             cCCCcCCHHHHHHHHccC-ccc----cccChHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCCHHHHHHHHhcCcHHH
Confidence            346789999999999998 554    589999999999999999999999999999999999999999999999988888


Q ss_pred             HHH
Q psy13691         85 IIE   87 (103)
Q Consensus        85 ~~~   87 (103)
                      |+.
T Consensus        90 FL~   92 (97)
T 1n1j_B           90 FLI   92 (97)
T ss_dssp             GGT
T ss_pred             HHH
Confidence            764

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

Probab=99.75  E-value=4.4e-18  Score=120.03  Aligned_cols=70  Identities=26%  Similarity=0.224  Sum_probs=66.0

Q ss_pred             CccCCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhh
Q psy13691          4 SLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQ   79 (103)
Q Consensus         4 ~~~d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~   79 (103)
                      ..+++.||+++|.||||+.  ..    .|||+||++.+++|+++|+.+++++|.+.|.++|||||+++||.+|++.
T Consensus        77 d~~~l~lP~a~V~Ri~k~~--g~----~RVS~~A~~~l~~~le~f~~~I~~~A~~~a~ha~RKTIt~eDV~~Al~~  146 (154)
T 1f1e_A           77 DYDGELFGRATVRRILKRA--GI----ERASSDAVDLYNKLICRATEELGEKAAEYADEDGRKTVQGEDVEKAITY  146 (154)
T ss_dssp             TCCSCCCCHHHHHHHHHHT--TC----CEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHH
T ss_pred             ccccccCCccHHHHHHHHc--CC----ccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHh
Confidence            4678899999999999998  33    7999999999999999999999999999999999999999999999985

>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=99.68  E-value=6.1e-17  Score=103.68  Aligned_cols=76  Identities=17%  Similarity=0.245  Sum_probs=69.5

Q ss_pred             CccCCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCch
Q psy13691          4 SLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFE   83 (103)
Q Consensus         4 ~~~d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~   83 (103)
                      +.....||+++|.||++....      .+||+|+.+.++++.++|+..++.+|...|+++|||||+++||..||+.+|++
T Consensus         5 r~~~~~ip~~~I~Riar~~Gv------~rIs~da~~~l~~~l~~~~~~I~~dA~~~a~ha~RKTvt~~DV~~Alk~~g~~   78 (84)
T 2hue_C            5 RDNIQGITKPAIRRLARRGGV------KRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRT   78 (84)
T ss_dssp             GGGCCSSCHHHHHHHHHHTTC------CEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTTTCEE
T ss_pred             cccCCCCCHHHHHHHHHHcCc------hhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHHHHHHcCCC
Confidence            344567999999999999743      58999999999999999999999999999999999999999999999999987


Q ss_pred             HH
Q psy13691         84 VI   85 (103)
Q Consensus        84 ~~   85 (103)
                      -|
T Consensus        79 lY   80 (84)
T 2hue_C           79 LY   80 (84)
T ss_dssp             EE
T ss_pred             CC
Confidence            55

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

Probab=99.68  E-value=1.8e-16  Score=98.04  Aligned_cols=64  Identities=25%  Similarity=0.350  Sum_probs=60.8

Q ss_pred             CCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691          9 NLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK   78 (103)
Q Consensus         9 ~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~   78 (103)
                      .||+++|.||+|+.  ..    .++|+++..+++++++.|+..|+..|+..|.++|||||+++||..|++
T Consensus         6 ~lp~a~v~Rl~r~~--g~----~ris~~a~~~l~e~~~~~~~~v~~dA~~~a~hakRkTI~~~DV~lA~~   69 (70)
T 1ku5_A            6 ELPIAPVDRLIRKA--GA----ERVSEQAAKVLAEYLEEYAIEIAKKAVEFARHAGRKTVKVEDIKLAIK   69 (70)
T ss_dssp             CSCHHHHHHHHHHT--TC----SEECHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHT
T ss_pred             cCChHHHHHHHHHc--Cc----ceeCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHH
Confidence            79999999999996  23    699999999999999999999999999999999999999999999986

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

Probab=99.67  E-value=1.3e-16  Score=105.58  Aligned_cols=75  Identities=16%  Similarity=0.221  Sum_probs=69.0

Q ss_pred             ccCCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCchH
Q psy13691          5 LDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEV   84 (103)
Q Consensus         5 ~~d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~   84 (103)
                      .....||+++|.||++....      .+||+|+.+.++++.++|+..++.+|...|++++||||+++||..||+.+|++-
T Consensus        24 ~~i~~ip~~~I~Rlar~~Gv------~rIS~da~~~l~~~le~fi~~I~~dA~~~a~HakRKTVt~~DV~~ALkr~g~~l   97 (102)
T 1id3_B           24 DNIQGITKPAIRRLARRGGV------KRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQGRTL   97 (102)
T ss_dssp             CCGGGSCHHHHHHHHHHTTC------CEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHTTCCE
T ss_pred             hccCCCCHHHHHHHHHHcCc------hhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHHHHHHcCCCC
Confidence            34557999999999999743      589999999999999999999999999999999999999999999999999875


Q ss_pred             H
Q psy13691         85 I   85 (103)
Q Consensus        85 ~   85 (103)
                      |
T Consensus        98 Y   98 (102)
T 1id3_B           98 Y   98 (102)
T ss_dssp             E
T ss_pred             C
Confidence            5

>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=99.62  E-value=1.1e-15  Score=101.13  Aligned_cols=75  Identities=17%  Similarity=0.249  Sum_probs=68.8

Q ss_pred             ccCCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCchH
Q psy13691          5 LDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEV   84 (103)
Q Consensus         5 ~~d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~   84 (103)
                      ...-.||+++|.||++....      .+||.|+.+.+.++.+.|+..|+.+|...|++++||||+++||..||+.+|++.
T Consensus        25 ~~~~gip~~~I~Rlar~~G~------~rIs~~a~~~l~~vle~~~~~V~~dA~~~a~hakRktIt~~DV~~Alr~~g~~l   98 (103)
T 1tzy_D           25 DNIQGITKPAIRRLARRGGV------KRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTL   98 (103)
T ss_dssp             CGGGGSCHHHHHHHHHHTTC------CEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHTTCEE
T ss_pred             hhcccCCHHHHHHHHHHcCc------cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHHcCCCC
Confidence            34556999999999999844      489999999999999999999999999999999999999999999999999865


Q ss_pred             H
Q psy13691         85 I   85 (103)
Q Consensus        85 ~   85 (103)
                      |
T Consensus        99 Y   99 (103)
T 1tzy_D           99 Y   99 (103)
T ss_dssp             E
T ss_pred             c
Confidence            4

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

Probab=99.61  E-value=1.5e-15  Score=100.56  Aligned_cols=75  Identities=17%  Similarity=0.236  Sum_probs=63.6

Q ss_pred             ccCCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCchH
Q psy13691          5 LDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEV   84 (103)
Q Consensus         5 ~~d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~   84 (103)
                      ...-.||+++|.||++....      .+||.|+.+.+.++.+.|+..|+.+|...|++++||||+++||..||+.+|++.
T Consensus        25 ~~~~gip~~~I~Rlar~~G~------~rIs~~a~~~l~~vle~~~~~V~~dA~~~a~hakRktvt~~DV~~Alr~~g~~l   98 (103)
T 2yfw_B           25 DNIQGITKPAIRRLARRGGV------KRISGLIYEEVRNVLKTFLESVIRDAVTYTEHAKRKTVTSLDVVYALKRQGRTL   98 (103)
T ss_dssp             -----CCHHHHHHHHHHTTC------CEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHHC---
T ss_pred             hhhccCCHHHHHHHHHHcCc------cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHHHHHHcCCCC
Confidence            33456999999999999744      489999999999999999999999999999999999999999999999999875


Q ss_pred             H
Q psy13691         85 I   85 (103)
Q Consensus        85 ~   85 (103)
                      |
T Consensus        99 Y   99 (103)
T 2yfw_B           99 Y   99 (103)
T ss_dssp             -
T ss_pred             c
Confidence            5

>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=99.60  E-value=1.2e-15  Score=100.19  Aligned_cols=77  Identities=18%  Similarity=0.273  Sum_probs=59.4

Q ss_pred             CCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCchHHH
Q psy13691          7 DLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEVII   86 (103)
Q Consensus         7 d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~~   86 (103)
                      ...||.++|.||||.. |+.    .+||.||..++.++++.|+.+|+..|+..|.+.|||||+++||..|++.-+..+|+
T Consensus         9 ~~~fPvaRIkrimK~~-~~~----~~vs~~A~v~la~a~E~Fi~el~~~A~~~a~~~krktI~~~di~~av~~~e~l~FL   83 (98)
T 1jfi_A            9 NARFPPARIKKIMQTD-EEI----GKVAAAVPVIISRALELFLESLLKKACQVTQSRNAKTMTTSHLKQCIELEGDPAAN   83 (98)
T ss_dssp             -CCCCHHHHHHHHTTS-TTC----CCBCTTHHHHHHHHHHHHHHHHHHHHHHHHHTC---CBCHHHHHTTCC--------
T ss_pred             CCCCChHHHHHHHHcC-ccc----cccchHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHhcCchhhHH
Confidence            5789999999999985 444    59999999999999999999999999999999999999999999999876666665


Q ss_pred             HH
Q psy13691         87 EI   88 (103)
Q Consensus        87 ~~   88 (103)
                      ..
T Consensus        84 ~d   85 (98)
T 1jfi_A           84 KA   85 (98)
T ss_dssp             --
T ss_pred             Hh
Confidence            43

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

Probab=99.43  E-value=4.9e-13  Score=84.53  Aligned_cols=74  Identities=16%  Similarity=0.157  Sum_probs=66.0

Q ss_pred             CCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcC
Q psy13691          7 DLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIG   81 (103)
Q Consensus         7 d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lg   81 (103)
                      ++.+|++++.|++|+...+. .++.+++.+|..+||++++.|+.-|...||..|.+.||+||.++||.-|..--|
T Consensus         1 ~lli~k~PF~RLVRei~~~~-~~~~R~q~~Al~aLQea~Eaylv~lfeda~l~A~HAkRvTi~~kDiqLa~rirg   74 (77)
T 2hue_B            1 MALIRKLPFQRLVREIAQDF-KTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRG   74 (77)
T ss_dssp             -CCSCHHHHHHHHHHHHHTT-CSSCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHTT
T ss_pred             CCccccchHHHHHHHHHHHc-CccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCcHhhHHHHHHHhC
Confidence            46899999999999996543 234899999999999999999999999999999999999999999999987554

>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=99.30  E-value=6.1e-12  Score=83.00  Aligned_cols=75  Identities=17%  Similarity=0.159  Sum_probs=61.4

Q ss_pred             CccCCCCcHHHHHHHHHhhCCCCCc--ccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691          4 SLDDLNLPSAIIQRLIKEALPKDAE--GKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK   78 (103)
Q Consensus         4 ~~~d~~LP~a~V~ri~K~~l~~~~~--~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~   78 (103)
                      +..++.+|++++.|++++...+...  .+.+++.+|..+||++++.|+.-|...||..|.+.||+||.++||.-|..
T Consensus        22 kst~llIpk~PF~RLVREI~~~~~~~~~~~R~q~~Al~ALQeaaEayLv~Lfeda~l~A~HAkRvTi~~kDiqLa~r   98 (100)
T 2yfv_A           22 RSTDLLISRMPFARLVKEVTDQFTTESEPLRWQSMAIMALQEASEAYLVGLLEHTNLLALHAKRITIMRKDMQLARR   98 (100)
T ss_dssp             ------CCHHHHHHHHHHHHHTTC-----CEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHH
T ss_pred             ccchhhhccccHHHHHHHHHHHhccccchhhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCCHHHHHHHHH
Confidence            4678899999999999999754311  24899999999999999999999999999999999999999999998863

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

Probab=99.28  E-value=1.6e-11  Score=78.42  Aligned_cols=74  Identities=27%  Similarity=0.225  Sum_probs=64.5

Q ss_pred             CCCcHHHHHHHHHhhCCCCC-cccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcC
Q psy13691          8 LNLPSAIIQRLIKEALPKDA-EGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIG   81 (103)
Q Consensus         8 ~~LP~a~V~ri~K~~l~~~~-~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lg   81 (103)
                      +.+|++++.|++|+...+-. +.+.+++.+|..+||++++.|+.-|...||..|.+.||+||.++|+.-|..--|
T Consensus         2 lLI~klPF~RLVREI~~~~~~~~~~R~q~~Al~aLQea~E~ylv~Lfeda~lcAiHAkRvTi~~kDiqLa~rirg   76 (82)
T 3nqj_A            2 LLIRKLPFSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRVTLFPKDVQLARRIRG   76 (82)
T ss_dssp             CSSCHHHHHHHHHHHHHHHHSSCCCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHHC
T ss_pred             CCcccccHHHHHHHHHHHhccCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCcHHHHHHHHHHcc
Confidence            46899999999999874210 123799999999999999999999999999999999999999999999976544

>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=99.20  E-value=3.6e-11  Score=83.09  Aligned_cols=77  Identities=17%  Similarity=0.186  Sum_probs=67.9

Q ss_pred             CccCCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcC
Q psy13691          4 SLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIG   81 (103)
Q Consensus         4 ~~~d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lg   81 (103)
                      ...++.||++++.|++++...+. .++.+++.+|..+||++++.|+.-|...||..|.+.||+||.++||..|..--|
T Consensus        57 kst~lLIpk~PF~RLVREI~~~~-~~~~R~q~~Al~aLQeaaEayLv~Lfeda~l~A~HAkRvTi~~kDiqLa~rirg  133 (136)
T 1tzy_C           57 KSTELLIRKLPFQRLVREIAQDF-KTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG  133 (136)
T ss_dssp             HCCSCCSCHHHHHHHHHHHHHHH-CTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHHT
T ss_pred             cchhhhhccchHHHHHHHHHHHh-hhhhcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCcHHhHHHHHHHhC
Confidence            45789999999999999995421 123899999999999999999999999999999999999999999999986544

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

Probab=99.20  E-value=2.9e-11  Score=83.87  Aligned_cols=79  Identities=25%  Similarity=0.213  Sum_probs=66.6

Q ss_pred             CccCCCCcHHHHHHHHHhhCCCCC-cccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCc
Q psy13691          4 SLDDLNLPSAIIQRLIKEALPKDA-EGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGF   82 (103)
Q Consensus         4 ~~~d~~LP~a~V~ri~K~~l~~~~-~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf   82 (103)
                      ...++.||++.+.|++++...+-. +.+.+++.+|..+||++++.|+.-|...||..|.+.||+||.++||..|..--|.
T Consensus        56 kst~LLIpKlPF~RLVREI~~~~~~~~~~Rfq~~Al~ALQEAaEayLv~LFEdanlcAiHAkRVTIm~kDiqLArrirg~  135 (140)
T 3nqu_A           56 KSTHLLIRKLPFSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRVTLFPKDVQLARRIRGL  135 (140)
T ss_dssp             ---CCCSCTTHHHHHHHHHHHHHHTTCCCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHHC-
T ss_pred             cccccccccccHHHHHHHHHHHhcccccceecHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcccccHHHHHHHHHhccc
Confidence            467899999999999999874210 1137999999999999999999999999999999999999999999999876554

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

Probab=99.19  E-value=3e-11  Score=84.99  Aligned_cols=78  Identities=26%  Similarity=0.207  Sum_probs=66.7

Q ss_pred             CccCCCCcHHHHHHHHHhhCCCCC-cccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcC
Q psy13691          4 SLDDLNLPSAIIQRLIKEALPKDA-EGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIG   81 (103)
Q Consensus         4 ~~~d~~LP~a~V~ri~K~~l~~~~-~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lg   81 (103)
                      ...++.||++.+.||+++...+-. +.+.+++.+|..+||++++.|+.-|...||..|.+.||+||.++||..|..--|
T Consensus        72 kSteLLIpKlPF~RLVREIa~~~~~~~~lRfqs~Al~ALQEAaEayLV~LFEdanLcAiHAkRVTIm~kDIqLArrIrg  150 (156)
T 3r45_A           72 KSTHLLIRKLPFSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRVTLFPKDVQLARRIRG  150 (156)
T ss_dssp             ---CCCSCHHHHHHHHHHHHHTTTTTCCCEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSEECHHHHHHHHHHHH
T ss_pred             cccccccccccHHHHHHHHHHHhccCccceecHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcccccHHHHHHHHHHcc
Confidence            467899999999999999975421 124799999999999999999999999999999999999999999999976443

>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=99.11  E-value=6.7e-10  Score=68.92  Aligned_cols=65  Identities=15%  Similarity=0.168  Sum_probs=60.8

Q ss_pred             CCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691          8 LNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK   78 (103)
Q Consensus         8 ~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~   78 (103)
                      ..||.++|.+|.++..-      .++|.|+...|.+-.+..+..|+.+|...+.+.||||++.+||-.||+
T Consensus         5 s~lp~~~v~~iaes~Gi------~~lsddaa~~LA~dvEyr~~eI~qeA~kfmrHakRk~Lt~~DI~~Alk   69 (70)
T 1taf_B            5 SSISAESMKVIAESIGV------GSLSDDAAKELAEDVSIKLKRIVQDAAKFMNHAKRQKLSVRDIDMSLK   69 (70)
T ss_dssp             CCCCHHHHHHHHHHTTC------CCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHC
T ss_pred             ccCCHHHHHHHHHHCCC------CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHc
Confidence            38999999999999843      379999999999999999999999999999999999999999999985

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

Probab=98.97  E-value=2.3e-09  Score=71.97  Aligned_cols=64  Identities=16%  Similarity=0.087  Sum_probs=58.1

Q ss_pred             HHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhc
Q psy13691         14 IIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQI   80 (103)
Q Consensus        14 ~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~l   80 (103)
                      +|.||+++...+   .++.+|+++..+|.+.+..|+.-++..+...|+++|||||+++||..+++..
T Consensus        32 ~V~rIvke~gae---r~~~vS~~ai~aL~El~~~~~~~ia~Dl~~fAkHAgRkTI~~eDV~La~Rr~   95 (113)
T 4dra_A           32 TVGCLCEEVALD---KEMQFSKQTIAAISELTFRQCENFAKDLEMFARHAKRTTINTEDVKLLARRS   95 (113)
T ss_dssp             HHHHHHHHHHHH---HTCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTTC
T ss_pred             HHHHHHHHHHHH---cCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHhC
Confidence            588999988543   1277999999999999999999999999999999999999999999999875

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

Probab=98.86  E-value=1.3e-08  Score=67.75  Aligned_cols=79  Identities=11%  Similarity=0.085  Sum_probs=63.9

Q ss_pred             HHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCchHHHHHHHHHH
Q psy13691         14 IIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEVIIEILGKSY   93 (103)
Q Consensus        14 ~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~~~~l~~~l   93 (103)
                      +|.||+++...+   ...++|+++..+|.+.+..|+.-++..|...|++.|||||+.+||.-|++..  +.....++.+.
T Consensus        24 ~V~rI~~~~g~~---~~~~vs~~~i~aL~E~~~~~~~~ia~Da~~fA~HAgRkTI~~eDV~La~Rrn--~~l~~~l~~~~   98 (107)
T 3b0b_B           24 TTGCLCQDVAED---KGVLFSKQTVAAISEITFRQCENFARDLEMFARHAKRSTITSEDVKLLARRS--NSLLKYITQKS   98 (107)
T ss_dssp             HHHHHHHHHHHH---HTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTTC--HHHHHHHHHHH
T ss_pred             HHHHHHHHHhhh---cCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcCcCCHHHHHHHHHhC--HHHHHHHHHHH
Confidence            488999887542   1168999999999999999999999999999999999999999999999875  23344444444


Q ss_pred             HHHH
Q psy13691         94 NAAV   97 (103)
Q Consensus        94 ~~~k   97 (103)
                      ++-+
T Consensus        99 ~el~  102 (107)
T 3b0b_B           99 DELA  102 (107)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            4433

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

Probab=98.85  E-value=1.4e-08  Score=65.73  Aligned_cols=64  Identities=11%  Similarity=0.150  Sum_probs=58.4

Q ss_pred             HHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhc
Q psy13691         14 IIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQI   80 (103)
Q Consensus        14 ~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~l   80 (103)
                      .|.||+.+.++.+   ++.+|+++..+|.+.+..++..++..+...|+++|||||+++||.-+++..
T Consensus        17 ~V~ki~~e~~~~~---g~~vs~~~i~aL~e~~~~~~~~ia~Dl~~fA~HAgRkTI~~eDV~L~~Rrn   80 (90)
T 3v9r_A           17 RVEERLQQVLSSE---DIKYTPRFINSLLELAYLQLGEMGSDLQAFARHAGRGVVNKSDLMLYLRKQ   80 (90)
T ss_dssp             HHHHHHHHHSCSS---CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTTC
T ss_pred             HHHHHHHHHHHhc---CceeCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHhC
Confidence            5789999997643   278999999999999999999999999999999999999999999998864

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

Probab=98.83  E-value=1.7e-08  Score=68.52  Aligned_cols=67  Identities=12%  Similarity=0.158  Sum_probs=62.3

Q ss_pred             CCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691          7 DLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK   78 (103)
Q Consensus         7 d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~   78 (103)
                      .+.||.+.|.|+||+.-..     .+|+.+|...|..+.+.|...|...|...|.+.+|++|+++||..|++
T Consensus        21 gL~fPV~ri~R~Lk~~~~a-----~RV~~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~krItp~hi~lAI~   87 (123)
T 2nqb_C           21 GLQFPVGRIHRLLRKGNYA-----ERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR   87 (123)
T ss_dssp             TCSSCHHHHHHHHHHTTSC-----SEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHH
T ss_pred             CeeccHHHHHHHHHccccc-----cccchhhHHHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHHHHHh
Confidence            5789999999999997322     599999999999999999999999999999999999999999999987

>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=98.82  E-value=1.9e-08  Score=68.00  Aligned_cols=67  Identities=12%  Similarity=0.220  Sum_probs=62.4

Q ss_pred             CCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691          7 DLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK   78 (103)
Q Consensus         7 d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~   78 (103)
                      .+.||.+.|.|+||+.-. .    .+|+.+|...|..+.+.|...|...|...|.+.||++|+++||..|++
T Consensus        20 gLqfPV~ri~R~Lk~~~~-a----~RV~~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~~rItp~hi~lAI~   86 (120)
T 2f8n_G           20 GVIFPVGRMLRYIKKGHP-K----YRIGVGAPVYMAAVLEYLTAEILELAVNAARDNKKGRVTPRHILLAVA   86 (120)
T ss_dssp             TCSSCHHHHHHHHHHHSS-S----CEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHH
T ss_pred             CccCChHHHHHHHHcCcc-c----cccccchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceEcHHHHHHHHh
Confidence            578999999999999843 2    599999999999999999999999999999999999999999999987

>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=98.80  E-value=2.2e-08  Score=68.51  Aligned_cols=67  Identities=10%  Similarity=0.157  Sum_probs=62.3

Q ss_pred             CCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691          7 DLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK   78 (103)
Q Consensus         7 d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~   78 (103)
                      .+.||.+.|.|+||+.-..     .+|+.+|...|..+.+.|...|...|...|.+.+|++|+++||..|++
T Consensus        23 gLqfPV~rI~R~Lk~~~~a-----~RVs~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~krItp~hi~lAI~   89 (129)
T 1tzy_A           23 GLQFPVGRVHRLLRKGNYA-----ERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIR   89 (129)
T ss_dssp             TCSSCHHHHHHHHHHTTSS-----SEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHH
T ss_pred             ceeccHHHHHHHHHccccc-----cccchhhHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeEcHHHHHHHHh
Confidence            5789999999999997322     599999999999999999999999999999999999999999999987

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

Probab=98.80  E-value=1.9e-08  Score=69.67  Aligned_cols=64  Identities=14%  Similarity=0.079  Sum_probs=57.4

Q ss_pred             HHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhc
Q psy13691         14 IIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQI   80 (103)
Q Consensus        14 ~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~l   80 (103)
                      +|.||+++...+.   ++.+|+++..+|.+.+..|+..|+..+...|++.|||||+++||..+++..
T Consensus        24 ~VgkIvee~~~~~---~~~vS~~ai~aL~El~~~~~e~ia~DLe~FAkHAGRKTI~~eDVkLa~Rrn   87 (140)
T 3vh5_A           24 TTGALAQDVAEDK---GVLFSKQTVAAISEITFRQAENFARDLEMFARHAKRSTITSEDVKLLARRS   87 (140)
T ss_dssp             HHHHHHHHHHHHH---TCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHTTS
T ss_pred             HHHHHHHHHHHhc---CCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHhC
Confidence            5788888874431   278999999999999999999999999999999999999999999999875

>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=98.80  E-value=2.3e-08  Score=68.31  Aligned_cols=69  Identities=12%  Similarity=0.129  Sum_probs=63.1

Q ss_pred             CCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhh
Q psy13691          7 DLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQ   79 (103)
Q Consensus         7 d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~   79 (103)
                      .+.||.+.|.|+||+.-.-.    .+|+.+|...|..+.+.|...|...|...|.+.||++|+++||..|+..
T Consensus        25 gLqfPV~ri~R~Lk~~~~a~----~RV~~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~krItprhi~lAI~n   93 (128)
T 1f66_C           25 GLQFPVGRIHRHLKSRTTSH----GRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRG   93 (128)
T ss_dssp             TCSSCHHHHHHHHHHTSCSS----CEECTTHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHHH
T ss_pred             CccCChHHHHHHHHHcccch----hhccccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeEcHHHHHHHHhc
Confidence            57899999999999975322    4999999999999999999999999999999999999999999999873

>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=98.78  E-value=2.1e-08  Score=68.81  Aligned_cols=67  Identities=9%  Similarity=0.148  Sum_probs=62.3

Q ss_pred             CCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691          7 DLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK   78 (103)
Q Consensus         7 d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~   78 (103)
                      .+.||.+.|.|+||+.-..     .+|+.+|...|..+.+.|...|...|...|.+.+|++|+++||..|++
T Consensus        23 gLqfPV~rI~R~Lk~~~~a-----~RVs~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~krItp~hI~lAI~   89 (131)
T 1id3_C           23 GLTFPVGRVHRLLRRGNYA-----QRIGSGAPVYLTAVLEYLAAEILELAGNAARDNKKTRIIPRHLQLAIR   89 (131)
T ss_dssp             TCSSCHHHHHHHHHTTCSC-----SEECSSHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHH
T ss_pred             CeecCHHHHHHHHHccccc-----cccchhhHHHHHHHHHHHHHHHHHHHHHHHhhcCCceEcHHHHHHHHh
Confidence            6799999999999997322     599999999999999999999999999999999999999999999987

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

Probab=98.75  E-value=2.3e-08  Score=67.79  Aligned_cols=57  Identities=18%  Similarity=0.292  Sum_probs=47.7

Q ss_pred             ccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCchHH
Q psy13691         29 GKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEVI   85 (103)
Q Consensus        29 ~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~   85 (103)
                      |..|||.|+-+.+.+..+.|+..+...|...+++.|||||+++||.-||+..|-.-|
T Consensus        61 GvkRIS~~iy~e~r~vl~~~l~~i~rdav~yaehA~RKTVta~DV~~Alkr~G~~ly  117 (121)
T 2ly8_A           61 GSKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQGRTLY  117 (121)
T ss_dssp             CSSCCSSCHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCCBCHHHHHHHHHHTTCGGG
T ss_pred             CccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHhCCCcCC
Confidence            455777777777777777777888889999999999999999999999999886543

>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=98.74  E-value=3.9e-08  Score=68.81  Aligned_cols=67  Identities=10%  Similarity=0.160  Sum_probs=62.2

Q ss_pred             CCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691          7 DLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK   78 (103)
Q Consensus         7 d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~   78 (103)
                      .+.||.+.|.|+||+.-.-     .||+.+|...|..+.+.|...|...|...|.+.+|++|+++||..|++
T Consensus        42 gLqFPVgrI~R~LK~~~~a-----~RVs~~A~VyLAAVLEYL~aEILelAgn~A~~~krkrItprhI~lAI~  108 (149)
T 2f8n_K           42 GLQFPVGRVHRLLRKGNYS-----ERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIR  108 (149)
T ss_dssp             TCSSCHHHHHHHHHHTTSC-----SEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHH
T ss_pred             CeeccHHHHHHHHHccccc-----cccCcCcHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHh
Confidence            5789999999999997322     599999999999999999999999999999999999999999999987

>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=98.74  E-value=7.6e-08  Score=59.26  Aligned_cols=61  Identities=18%  Similarity=0.111  Sum_probs=55.8

Q ss_pred             HHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhh
Q psy13691         13 AIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQ   79 (103)
Q Consensus        13 a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~   79 (103)
                      ..|.||+|+..-      .+++.++...|.+.+..++.-+..+|...|.+.|||||+.+||..|++.
T Consensus         5 ~~i~~iLk~~G~------~~~~~~v~~~L~e~~~ry~~~il~dA~~~a~HAgrktv~~eDVkLAi~~   65 (68)
T 1taf_A            5 QVIMSILKELNV------QEYEPRVVNQLLEFTFRYVTSILDDAKVYANHARKKTIDLDDVRLATEV   65 (68)
T ss_dssp             HHHHHHHHHTTC------CCBCTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHH
T ss_pred             HHHHHHHHHCCC------cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHh
Confidence            368899999743      3799999999999999999999999999999999999999999999874

>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=98.59  E-value=1.5e-07  Score=67.89  Aligned_cols=68  Identities=13%  Similarity=0.158  Sum_probs=62.4

Q ss_pred             CCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691          7 DLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK   78 (103)
Q Consensus         7 d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~   78 (103)
                      .+.||.+.|.|+||+.-...    .+|+.+|...|..+.+.+...|...|...|.+.||++|+|+||..|+.
T Consensus       103 gl~fPv~ri~R~lk~~~~a~----~Rv~~~A~vyLaavLEyl~~eIlelA~n~a~~~~~~~I~p~~i~lAi~  170 (192)
T 2jss_A          103 GLQFPVGRIKRYLKRHATGR----TRVGSKAAIYLTAVLEYLTAEVLELAGNAAKDLKVKRITPRHLQLAIR  170 (192)
T ss_dssp             SCCSCHHHHHHHHHHTTCSS----CCCCTTTHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSCCHHHHHHHHH
T ss_pred             CCcCCHHHHHHHHHhcCccc----cccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHh
Confidence            67999999999999973222    489999999999999999999999999999999999999999999987

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

Probab=98.56  E-value=5.9e-07  Score=57.36  Aligned_cols=77  Identities=14%  Similarity=0.182  Sum_probs=63.5

Q ss_pred             CCCCccCCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhc
Q psy13691          1 MAESLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQI   80 (103)
Q Consensus         1 m~~~~~d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~l   80 (103)
                      |.+...+..+|..+|.||++....++   +.+||+||..++.+....|+..-...|...+..++..+|..+|+-+.+-.|
T Consensus         4 ~~~~~~~~~i~~~li~ril~~~F~~~---kTkIs~dAl~l~aeyl~iFV~EAv~RA~~~a~~e~~~~le~e~LEki~pQL   80 (84)
T 4dra_E            4 MEGAGAGSGFRKELVSRLLHLHFKDD---KTKVSGDALQLMVELLKVFVVEAAVRGVRQAQAEDALRVDVDQLEKVLPQL   80 (84)
T ss_dssp             -------CCCCHHHHHHHHHTTCSST---TCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHH
T ss_pred             cccCCCCCCCCHHHHHHHHHHHhcCC---CccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHHH
Confidence            44455678999999999999988743   389999999999999999999999999999999999999999998877544

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

Probab=98.53  E-value=3.6e-07  Score=62.03  Aligned_cols=67  Identities=15%  Similarity=0.179  Sum_probs=60.7

Q ss_pred             HHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCchH
Q psy13691         13 AIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEV   84 (103)
Q Consensus        13 a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~   84 (103)
                      ..|+|++|++-|+     ..||.+|...|+.....+..-|+.+|...+...+|+||+.+||..|++.+==++
T Consensus        37 ~YIyKVLKQVhpd-----~gISskAm~ImnSfvnDiferIA~EAs~La~~nkr~TitsreIqtAvrLlLpGE  103 (123)
T 2nqb_D           37 IYIYTVLKQVHPD-----TGISSKAMSIMNSFVNDIFERIAAEASRLAHYNKRSTITSREIQTAVRLLLPGE  103 (123)
T ss_dssp             HHHHHHHHHHCTT-----CEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCEECHHHHHHHHHHHSCHH
T ss_pred             HHHHHHHHHhCCC-----CCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHHHhCcHH
Confidence            5689999999886     589999999999999999999999999999999999999999999997554343

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

Probab=98.53  E-value=1.6e-07  Score=69.80  Aligned_cols=76  Identities=17%  Similarity=0.164  Sum_probs=65.4

Q ss_pred             cCCCCcHHHHHHHHHhhCCCCCc--ccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcC
Q psy13691          6 DDLNLPSAIIQRLIKEALPKDAE--GKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIG   81 (103)
Q Consensus         6 ~d~~LP~a~V~ri~K~~l~~~~~--~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lg   81 (103)
                      ..+.+|+.+++|++++..++...  .+.+++.+|..+||++++.|+.-|...+|-.|.+.||.||.+.|+.-|..--|
T Consensus         8 ~~~lI~KlPFqRLVREIaq~~~~~~~~lRfqs~Al~ALQEAaEayLV~LFEd~nLcaiHAkRVTim~kDiqLarrirg   85 (235)
T 2l5a_A            8 KKLLISKIPFARLVKEVTDEFTTKDQDLRWQSMAIMALQEASEAYLVGLLEHTNLLALHAKRITIMKKDMQLARRIRG   85 (235)
T ss_dssp             ---CCSCCHHHHHHHHHHHTSCGGGTTCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHSTTTSGGGTTHHHHHHTSSC
T ss_pred             ccccccCccHHHHHHHHHHHhccCCccceecHHHHHHHHHHHHHHHHHHHhhhHHHHhcccccccchhhHHHHHHHhh
Confidence            46789999999999999776322  25899999999999999999999999999999999999999999999976544

>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=98.50  E-value=4.7e-07  Score=61.64  Aligned_cols=67  Identities=13%  Similarity=0.169  Sum_probs=60.7

Q ss_pred             HHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCchH
Q psy13691         13 AIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEV   84 (103)
Q Consensus        13 a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~   84 (103)
                      ..|+|++|++-|+     ..||.+|...|+.....+..-|+.+|...+...+|+||+.+||..|++.+==++
T Consensus        40 ~YIyKVLKQVhpd-----~gISskAm~ImnSfvnDiferIA~EAs~La~~nkr~TitsreIqtAvrLlLpGE  106 (126)
T 1tzy_B           40 IYVYKVLKQVHPD-----TGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGE  106 (126)
T ss_dssp             HHHHHHHHHHCTT-----CEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHHSCHH
T ss_pred             HHHHHHHHHhCCC-----CCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCcHH
Confidence            4699999999886     589999999999999999999999999999999999999999999997554443

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

Probab=98.36  E-value=5.9e-07  Score=66.77  Aligned_cols=53  Identities=19%  Similarity=0.316  Sum_probs=50.5

Q ss_pred             ccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcC
Q psy13691         29 GKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIG   81 (103)
Q Consensus        29 ~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lg   81 (103)
                      |.-|||.++.+.+....+.|+.-+...|...|++.+||||+++||..||+..|
T Consensus       175 GVkRIS~~iyeelr~vLe~fle~IirdAv~yaeHA~RKTVta~DV~~ALKr~g  227 (235)
T 2l5a_A          175 GVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQG  227 (235)
T ss_dssp             TCCTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHH
T ss_pred             CchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHhcC
Confidence            44699999999999999999999999999999999999999999999999776

>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=98.36  E-value=3.6e-06  Score=53.34  Aligned_cols=73  Identities=14%  Similarity=0.184  Sum_probs=63.6

Q ss_pred             ccCCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhc
Q psy13691          5 LDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQI   80 (103)
Q Consensus         5 ~~d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~l   80 (103)
                      ..+..+|...|.||++....+.   +.||++||..++.+....||..-...|...++.++-..|..+|+-+.+-.|
T Consensus         4 ~~~~~~~~~lI~ril~~~f~~~---ktrI~~dAl~l~aeyl~iFV~EAv~RA~~~a~~e~~~~le~~~LEki~pqL   76 (81)
T 3b0b_C            4 EREGGFRKETVERLLRLHFRDG---RTRVNGDALLLMAELLKVFVREAAARAARQAQAEDLEKVDIEHVEKVLPQL   76 (81)
T ss_dssp             ---CCCCHHHHHHHHHHHCCST---TCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHH
T ss_pred             ccCCCCCHHHHHHHHHHHhccC---cccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCeecHHHHHHHHHHH
Confidence            3467899999999999998854   379999999999999999999999999999999999999999998876543

>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=98.24  E-value=4.9e-06  Score=59.89  Aligned_cols=63  Identities=19%  Similarity=0.269  Sum_probs=58.6

Q ss_pred             HHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhh
Q psy13691         12 SAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQ   79 (103)
Q Consensus        12 ~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~   79 (103)
                      ..-|+|+.|+.-|+     ..||.+|...|......+...|+.+|...+...+|+||+.+||..|++.
T Consensus         6 ~~yi~kvLkqv~p~-----~~iS~~Am~~m~s~v~di~~rIa~eA~~L~~~~~r~Tit~~eIq~Avrl   68 (192)
T 2jss_A            6 SSYIYKVLKQTHPD-----TGISQKSMSILNSFVNDIFERIATEASKLAAYNKKSTISAREIQTAVRL   68 (192)
T ss_dssp             HHHHHHHHHHHCSS-----CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCCSCCHHHHHHHHHH
T ss_pred             HHHHHHHHcccCCC-----CCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHH
Confidence            35689999999885     5899999999999999999999999999999999999999999999973

>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=98.19  E-value=1.6e-05  Score=49.83  Aligned_cols=66  Identities=26%  Similarity=0.274  Sum_probs=61.5

Q ss_pred             CCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhh
Q psy13691          9 NLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQ   79 (103)
Q Consensus         9 ~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~   79 (103)
                      -|++..+..++++.-|.     ..+..|+.++|.+.|..||.-++..|...|++-|-.|+...||.-.|++
T Consensus         5 vl~k~~L~~Lv~~idp~-----~~ld~~vee~ll~lADdFV~~V~~~ac~lAKhR~s~~le~kDvql~Ler   70 (76)
T 1h3o_B            5 VLTKKKLQDLVREVDPN-----EQLDEDVEEMLLQIADDFIESVVTAACQLARHRKSSTLEVKDVQLHLER   70 (76)
T ss_dssp             SSCHHHHHHHHHHHCSS-----CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCEECHHHHHHHHHH
T ss_pred             cccHHHHHHHHHhcCCC-----CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCccHHHHHHHHHh
Confidence            47999999999999664     6999999999999999999999999999999999999999999998874

>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=97.91  E-value=9.2e-05  Score=47.49  Aligned_cols=67  Identities=25%  Similarity=0.383  Sum_probs=60.3

Q ss_pred             CCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC-CCCcChhhHHHhhhhcC
Q psy13691          9 NLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKN-RKTLSGVDVIEGVKQIG   81 (103)
Q Consensus         9 ~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~-RkTI~~eDV~~Al~~lg   81 (103)
                      .||++.|.|+|...++      ..++.+...++.-.+-+||..|..+|.++..+.+ +..|.|.||-.|...|.
T Consensus        16 ~f~k~~vKrl~~~~~~------~~v~~~v~i~v~glaKvfVgelVE~A~~V~~~~~~~~Pl~P~HireA~rrl~   83 (89)
T 1bh9_B           16 AFPKAAIKRLIQSITG------TSVSQNVVIAMSGISKVFVGEVVEEALDVCEKWGEMPPLQPKHMREAVRRLK   83 (89)
T ss_dssp             CCCHHHHHHHHHHHHS------SCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSSCCHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHcC------CCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHH
Confidence            7999999999999974      4799999999999999999999999999997765 55899999999988764

>3v9r_B MHF2, uncharacterized protein YDL160C-A; histone fold, fanconi anemia, DNA repair, DNA BI protein; 2.40A {Saccharomyces cerevisiae}

Probab=97.30  E-value=0.00065  Score=43.45  Aligned_cols=50  Identities=12%  Similarity=0.225  Sum_probs=43.0

Q ss_pred             CcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy13691         10 LPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANE   62 (103)
Q Consensus        10 LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~   62 (103)
                      +|+.+|.||++....+.   +.||++||..++++....||..-...|++....
T Consensus         2 ip~~llaRIL~~~F~~~---kTrIt~da~~lv~kY~diFVrEAv~Rs~e~ke~   51 (88)
T 3v9r_B            2 LSKEALIKILSQNEGGN---DMKIADEVVPMIQKYLDIFIDEAVLRSLQSHKD   51 (88)
T ss_dssp             CCSHHHHHHHTTTSCSS---CCEECTTTHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCHHHHHHHHHHHhCCC---CceecHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            79999999999877654   489999999999999999999888888765544

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

Probab=97.13  E-value=0.00043  Score=46.69  Aligned_cols=61  Identities=18%  Similarity=0.227  Sum_probs=48.7

Q ss_pred             CcHHHHHHHHHhhCCCCC--cccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhC---CCCCcCh
Q psy13691         10 LPSAIIQRLIKEALPKDA--EGKINVSKDVRLAAGKAASLFILHLTTEALSIANEK---NRKTLSG   70 (103)
Q Consensus        10 LP~a~V~ri~K~~l~~~~--~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~---~RkTI~~   70 (103)
                      +|+.+..|++++...+-.  +.+.+++.+|..+||++++.|+.-|...+|-.|.+.   |=|-|+.
T Consensus         2 I~klPF~RLVREI~~~~~~~~~~lRfq~~Al~ALQeAsEayLV~lFEd~nlcaiHA~~gGvkRIS~   67 (121)
T 2ly8_A            2 ISKIPFARLVKEVTDEFTTKDQDLRWQSMAIMALQEASEAYLVGLLEHTNLLALHLVPRGSKRISG   67 (121)
T ss_dssp             CSCCHHHHHHHHHHHHHTTCCSSCCBCHHHHHHHHHHHHHHHHHHHHHHHHHTTTCCCCCSSCCSS
T ss_pred             CCccchHHHHHHHHHHhcCCCCCccccHHHHHHHHHHHHHHHHHHHHHHhHHHHcCCccCccchhH
Confidence            788999999988654311  124899999999999999999999999999888776   4455665

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

Probab=93.77  E-value=0.3  Score=35.99  Aligned_cols=81  Identities=7%  Similarity=0.101  Sum_probs=54.5

Q ss_pred             CcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHH----HHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhh-cCchH
Q psy13691         10 LPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAAS----LFILHLTTEALSIANEKNRKTLSGVDVIEGVKQ-IGFEV   84 (103)
Q Consensus        10 LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~----~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~-lgf~~   84 (103)
                      ++...+..|++..+...   ...++.++...+.+.+.    -.+..+...|...|...++++|+.+||..|++. ++...
T Consensus       259 ~~~~e~~~il~~~~~~~---~~~~~~~~l~~l~~~~~~G~~r~~~~ll~~a~~~A~~~~~~~It~~~v~~a~~~~~~~~~  335 (368)
T 3uk6_A          259 YSEKDTKQILRIRCEEE---DVEMSEDAYTVLTRIGLETSLRYAIQLITAASLVCRKRKGTEVQVDDIKRVYSLFLDESR  335 (368)
T ss_dssp             CCHHHHHHHHHHHHHHT---TCCBCHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHSBCHHH
T ss_pred             CCHHHHHHHHHHHHHHc---CCCCCHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHhcCHHH
Confidence            34556666666544321   16799999999988876    245556666777788889999999999999986 55444


Q ss_pred             HHHHHHHHH
Q psy13691         85 IIEILGKSY   93 (103)
Q Consensus        85 ~~~~l~~~l   93 (103)
                      -...++++-
T Consensus       336 ~~~~~~~~~  344 (368)
T 3uk6_A          336 STQYMKEYQ  344 (368)
T ss_dssp             HHHHHC---
T ss_pred             HHHHHHHhh
Confidence            444444433

>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=93.70  E-value=0.29  Score=42.41  Aligned_cols=67  Identities=15%  Similarity=0.158  Sum_probs=56.0

Q ss_pred             CCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhh
Q psy13691          7 DLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQ   79 (103)
Q Consensus         7 d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~   79 (103)
                      .+.+|.++|.|++|....      -||+..|..-+.-..+-....+...|-..|...+++.|+++|+..|+..
T Consensus       102 ~l~~pv~~~~~~l~~~~~------~r~~~~~~~y~~avleyl~~~~l~la~~~~~~~~~~~i~p~~~~~ai~~  168 (1049)
T 3ksy_A          102 PLSLPVEKIHPLLKEVLG------YKIDHQVSVYIVAVLEYISADILKLVGNYVRNIRHYEITKQDIKVAMCA  168 (1049)
T ss_dssp             SCSSCHHHHHHHHHHHHC------SCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCBCCHHHHHHHHHH
T ss_pred             CccccHHHHHHHhhcccc------cccCCCCcchhHHHHHHHHHHHHHHHHHHHHHcCCceecCccccccccC
Confidence            578999999999976643      4899999988888777777777777778888899999999999999863

>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=89.61  E-value=1.3  Score=34.39  Aligned_cols=80  Identities=18%  Similarity=0.197  Sum_probs=52.3

Q ss_pred             cHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHH-H---HHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhc-CchHH
Q psy13691         11 PSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAA-S---LFILHLTTEALSIANEKNRKTLSGVDVIEGVKQI-GFEVI   85 (103)
Q Consensus        11 P~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~-~---~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~l-gf~~~   85 (103)
                      +...+..+++..+...   ...++.++...+.+.+ .   .....+...|...|..+++..|+.+||..|+.-+ +...-
T Consensus       367 ~~~e~~~iL~~~~~~~---~~~~~~~~~~~i~~~a~~g~~r~a~~ll~~a~~~A~~~~~~~v~~~~v~~~~~~~~d~~~~  443 (456)
T 2c9o_A          367 TPQEMKQIIKIRAQTE---GINISEEALNHLGEIGTKTTLRYSVQLLTPANLLAKINGKDSIEKEHVEEISELFYDAKSS  443 (456)
T ss_dssp             CHHHHHHHHHHHHHHH---TCCBCHHHHHHHHHHHHHSCHHHHHHTHHHHHHHHHHTTCSSBCHHHHHHHHHHSCCHHHH
T ss_pred             CHHHHHHHHHHHHHHh---CCCCCHHHHHHHHHHccCCCHHHHHHHHHHHHHHHhhcCCCccCHHHHHHHHHHhcChHHH
Confidence            3445555555443210   1568999988888876 2   3455666778888999999999999999998653 44444


Q ss_pred             HHHHHHHH
Q psy13691         86 IEILGKSY   93 (103)
Q Consensus        86 ~~~l~~~l   93 (103)
                      +.-|+++.
T Consensus       444 ~~~~~~~~  451 (456)
T 2c9o_A          444 AKILADQQ  451 (456)
T ss_dssp             HHHHHC--
T ss_pred             HHHHHHHH
Confidence            44444433

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

Probab=89.32  E-value=2.3  Score=30.90  Aligned_cols=71  Identities=14%  Similarity=0.091  Sum_probs=50.7

Q ss_pred             HHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHH------HHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCch
Q psy13691         12 SAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAAS------LFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFE   83 (103)
Q Consensus        12 ~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~------~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~   83 (103)
                      ..-+..|++..+... ..+..++.++...+.+.+.      -.+..+...|...|...++.+|+.+||..|++....+
T Consensus       203 ~~~~~~il~~~~~~~-~~~~~~~~~~~~~l~~~~~~~~G~~r~~~~~l~~a~~~a~~~~~~~i~~~~v~~a~~~~~~~  279 (387)
T 2v1u_A          203 APQLRDILETRAEEA-FNPGVLDPDVVPLCAALAAREHGDARRALDLLRVAGEIAERRREERVRREHVYSARAEIERD  279 (387)
T ss_dssp             HHHHHHHHHHHHHHH-BCTTTBCSSHHHHHHHHHHSSSCCHHHHHHHHHHHHHHHHHTTCSCBCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhh-ccCCCCCHHHHHHHHHHHHHhccCHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHhhc
Confidence            556666666543210 0015789999998888876      4556667778888888899999999999999877433

>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA replication initation factor, cell cycle control factor; HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11 c.37.1.20

Probab=87.25  E-value=3.2  Score=30.21  Aligned_cols=74  Identities=14%  Similarity=0.170  Sum_probs=51.1

Q ss_pred             CcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHH------------HHHHHHHHHHHHHHHHhCCCCCcChhhHHHhh
Q psy13691         10 LPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAA------------SLFILHLTTEALSIANEKNRKTLSGVDVIEGV   77 (103)
Q Consensus        10 LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~------------~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al   77 (103)
                      ++...+..+++..+... .....++.++...+.+.+            --++..+...|...|..+++.+|+.+||..++
T Consensus       193 l~~~~~~~~l~~~~~~~-~~~~~~~~~~~~~l~~~~~~~~~~~~~~G~~r~~~~~l~~a~~~a~~~~~~~i~~~~v~~~~  271 (389)
T 1fnn_A          193 YTKDQIFDILLDRAKAG-LAEGSYSEDILQMIADITGAQTPLDTNRGDARLAIDILYRSAYAAQQNGRKHIAPEDVRKSS  271 (389)
T ss_dssp             CBHHHHHHHHHHHHHHH-BCTTSSCHHHHHHHHHHHSBSSTTCTTSCCHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHhh-cCCCCCCHHHHHHHHHHHhhcccCCCCCCcHHHHHHHHHHHHHHHHHhCCCCcCHHHHHHHH
Confidence            34455666665544320 001368999999888887            23455666778888888899999999999998


Q ss_pred             hhcCchH
Q psy13691         78 KQIGFEV   84 (103)
Q Consensus        78 ~~lgf~~   84 (103)
                      +......
T Consensus       272 ~~~~~~~  278 (389)
T 1fnn_A          272 KEVLFGI  278 (389)
T ss_dssp             HHHSCCC
T ss_pred             HHHhhhh
Confidence            8765443

>2qby_A CDC6 homolog 1, cell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=87.10  E-value=5.6  Score=28.68  Aligned_cols=76  Identities=11%  Similarity=0.007  Sum_probs=51.3

Q ss_pred             CcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHH------HHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCch
Q psy13691         10 LPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAAS------LFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFE   83 (103)
Q Consensus        10 LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~------~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~   83 (103)
                      |+..-+..+++..+... .....++.++...+.+.+.      ..+..+...|...+..+++.+|+.+||..|++.+..+
T Consensus       197 l~~~~~~~il~~~~~~~-~~~~~~~~~~~~~l~~~~~~~~G~~r~~~~ll~~a~~~a~~~~~~~i~~~~v~~a~~~~~~~  275 (386)
T 2qby_A          197 YNAEELEDILTKRAQMA-FKPGVLPDNVIKLCAALAAREHGDARRALDLLRVSGEIAERMKDTKVKEEYVYMAKEEIERD  275 (386)
T ss_dssp             CCHHHHHHHHHHHHHHH-BCSSCSCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHhh-ccCCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHHhhc
Confidence            34555666666533210 0014689999888887775      2344566778888888899999999999999877544


Q ss_pred             HHH
Q psy13691         84 VII   86 (103)
Q Consensus        84 ~~~   86 (103)
                      .+.
T Consensus       276 ~~~  278 (386)
T 2qby_A          276 RVR  278 (386)
T ss_dssp             HHH
T ss_pred             hHH
Confidence            433

>3kw6_A 26S protease regulatory subunit 8; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; 2.10A {Homo sapiens}

Probab=86.87  E-value=0.76  Score=27.18  Aligned_cols=43  Identities=16%  Similarity=0.029  Sum_probs=33.7

Q ss_pred             HHHHHHHHHHH----HHHHHHHHHHHHHhCCCCCcChhhHHHhhhhc
Q psy13691         38 RLAAGKAASLF----ILHLTTEALSIANEKNRKTLSGVDVIEGVKQI   80 (103)
Q Consensus        38 ~~~l~~~~~~F----i~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~l   80 (103)
                      ...|.+.+.-|    |..|..+|...|...++..|+.+|+..|++..
T Consensus        27 l~~la~~t~G~SGADi~~l~~eA~~~a~~~~~~~i~~~d~~~Al~~v   73 (78)
T 3kw6_A           27 LRKIAELMPGASGAEVKGVCTEAGMYALRERRVHVTQEDFEMAVAKV   73 (78)
T ss_dssp             HHHHHHTCTTCCHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHH
T ss_pred             HHHHHHHcCCCCHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHH
Confidence            44455555545    77788889888999999999999999999753

>1khy_A CLPB protein; alpha helix, chaperone; 1.95A {Escherichia coli} SCOP: a.174.1.1

Probab=84.80  E-value=1.5  Score=28.39  Aligned_cols=35  Identities=14%  Similarity=0.266  Sum_probs=30.4

Q ss_pred             cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691         32 NVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK   78 (103)
Q Consensus        32 ~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~   78 (103)
                      +++..++.+|..            |...|...+...|.++|++.||=
T Consensus         5 ~~t~~~~~~l~~------------A~~~A~~~~~~~i~~eHlLlaLl   39 (148)
T 1khy_A            5 RLTNKFQLALAD------------AQSLALGHDNQFIEPLHLMSALL   39 (148)
T ss_dssp             CBCHHHHHHHHH------------HHHHHHHTTCSSBCHHHHHHHHH
T ss_pred             hhhHHHHHHHHH------------HHHHHHHcCCCccCHHHHHHHHH
Confidence            678888888776            77889999999999999999984

>3fh2_A Probable ATP-dependent protease (heat shock prote; struct genomics, PSI2, MCSG, protein structure initiative; 1.60A {Corynebacterium glutamicum}

Probab=84.10  E-value=1.7  Score=28.50  Aligned_cols=36  Identities=14%  Similarity=0.095  Sum_probs=31.0

Q ss_pred             cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhh
Q psy13691         32 NVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQ   79 (103)
Q Consensus        32 ~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~   79 (103)
                      ++|..+..+|+.            |.+.|...+...|.++|++.||=.
T Consensus         6 ~~t~~~~~~l~~------------A~~~A~~~~~~~i~~eHLLlaLl~   41 (146)
T 3fh2_A            6 RFTDRARRVIVL------------AQEEARMLNHNYIGTEHILLGLIH   41 (146)
T ss_dssp             GBCHHHHHHHHH------------HHHHHHHTTCSSBCHHHHHHHHHH
T ss_pred             hcCHHHHHHHHH------------HHHHHHHcCCCCchHHHHHHHHHh
Confidence            678888888876            778899999999999999999854

>3aji_B S6C, proteasome (prosome, macropain) 26S subunit, ATPA; gankyrin, S6 ATPase, P-benzoyl-L-phenylalanine, PBPA, amber suppression; HET: PBF; 2.05A {Mus musculus} PDB: 2dwz_B* 2dvw_B*

Probab=81.52  E-value=1.7  Score=25.89  Aligned_cols=33  Identities=21%  Similarity=0.158  Sum_probs=27.4

Q ss_pred             HHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcC
Q psy13691         49 ILHLTTEALSIANEKNRKTLSGVDVIEGVKQIG   81 (103)
Q Consensus        49 i~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lg   81 (103)
                      |..|..+|...|...++..|+.+|+..|++..-
T Consensus        40 i~~l~~eA~~~a~~~~~~~i~~~df~~Al~~~~   72 (83)
T 3aji_B           40 INSICQESGMLAVRENRYIVLAKDFEKAYKTVI   72 (83)
T ss_dssp             HHHHHHHHHHGGGTSCCSSBCHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHhccCCcCHHHHHHHHHHHc
Confidence            445667788888899999999999999998754

>2dzn_B 26S protease regulatory subunit 6B homolog; ankyrin repeats, A-helical domain, structural genomics, NPPSFA; 2.20A {Saccharomyces cerevisiae} PDB: 2dzo_B

Probab=81.39  E-value=1.8  Score=25.84  Aligned_cols=30  Identities=27%  Similarity=0.107  Sum_probs=24.6

Q ss_pred             HHHHHHHHHHhCCCCCcChhhHHHhhhhcC
Q psy13691         52 LTTEALSIANEKNRKTLSGVDVIEGVKQIG   81 (103)
Q Consensus        52 lt~~A~~~a~~~~RkTI~~eDV~~Al~~lg   81 (103)
                      |..+|...|...++..|+.+|+..|++..-
T Consensus        40 l~~eAa~~ai~~~~~~i~~~df~~Al~~v~   69 (82)
T 2dzn_B           40 IMQEAGLRAVRKNRYVILQSDLEEAYATQV   69 (82)
T ss_dssp             HHHHHHHHHHHTTCSEECHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHhccCCcCHHHHHHHHHHHH
Confidence            445677778888899999999999998763

>1wwi_A Hypothetical protein TTHA1479; structural genomics, unknown function, riken structural genomics/proteomics initiative, RSGI; 1.58A {Thermus thermophilus HB8} SCOP: a.22.1.4 PDB: 1wws_A

Probab=81.20  E-value=5.3  Score=27.46  Aligned_cols=58  Identities=19%  Similarity=0.121  Sum_probs=50.8

Q ss_pred             CcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhH
Q psy13691         10 LPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDV   73 (103)
Q Consensus        10 LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV   73 (103)
                      +|-+.+.|+.+.+.+-      -|-|+-..-+....+.=+.-|.--|...|+.+||.+|.+.|+
T Consensus         3 m~~~~~e~lFR~aa~L------dvdK~d~~r~~d~V~~Kl~DLl~va~~~Ak~n~RdvI~~~DL   60 (148)
T 1wwi_A            3 MKVAEFERLFRQAAGL------DVDKNDLKRVSDFLRNKLYDLLAVAERNAKYNGRDLIFEPDL   60 (148)
T ss_dssp             SCHHHHHHHHHHHHCC------CCCGGGHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECGGGS
T ss_pred             CCHHHHHHHHHHHhcc------CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeeccccC
Confidence            5778899999999764      477888888888888888889999999999999999999886

>2y1q_A CLPC N-domain, negative regulator of genetic competence CLPC/MEC; transcription, proteolysis; 1.50A {Bacillus subtilis} PDB: 2y1r_A* 2k77_A

Probab=81.00  E-value=3.7  Score=26.57  Aligned_cols=35  Identities=9%  Similarity=0.081  Sum_probs=30.4

Q ss_pred             cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691         32 NVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK   78 (103)
Q Consensus        32 ~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~   78 (103)
                      +++..+..+|+.            |.+.|...+...|.++|++.||=
T Consensus         5 ~~t~~~~~al~~------------A~~~A~~~~h~~i~~eHlLlaLl   39 (150)
T 2y1q_A            5 RFTERAQKVLAL------------AQEEALRLGHNNIGTEHILLGLV   39 (150)
T ss_dssp             CBCHHHHHHHHH------------HHHHHHHTTCSEECHHHHHHHHH
T ss_pred             hhCHHHHHHHHH------------HHHHHHHcCCCCccHHHHHHHHH
Confidence            688888888876            77789999999999999999984

>2y1q_A CLPC N-domain, negative regulator of genetic competence CLPC/MEC; transcription, proteolysis; 1.50A {Bacillus subtilis} PDB: 2y1r_A* 2k77_A

Probab=80.97  E-value=6.3  Score=25.41  Aligned_cols=56  Identities=11%  Similarity=0.148  Sum_probs=36.7

Q ss_pred             cHHHHHHHHHhhCCCCC--cccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691         11 PSAIIQRLIKEALPKDA--EGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK   78 (103)
Q Consensus        11 P~a~V~ri~K~~l~~~~--~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~   78 (103)
                      ....+.+-+...+...+  .+...+|..+..+|..            |...|..-|...|+.+|++.||=
T Consensus        56 ~~~~l~~~l~~~l~~~~~~~~~~~~s~~~~~vL~~------------A~~~A~~~~~~~i~~ehlLlall  113 (150)
T 2y1q_A           56 GSEKIQKEVESLIGRAQEMSQTIHYTPRAKKVIEL------------SMDEARKLGHSYVGTEHILLGLI  113 (150)
T ss_dssp             CHHHHHHHHHHHHCCC-----CCEECHHHHHHHHH------------HHHHHHHTTCSSBCHHHHHHHHH
T ss_pred             CHHHHHHHHHHHhccCCcccccCCCCHHHHHHHHH------------HHHHHHHcCCCeecHHHHHHHHH
Confidence            34445555554443322  1235677777777665            67778888999999999999984

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

Probab=80.93  E-value=11  Score=30.18  Aligned_cols=64  Identities=20%  Similarity=0.090  Sum_probs=45.8

Q ss_pred             ccccHHHHHHHHHHHH-------------HHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCchHHHHHHHHHHHH
Q psy13691         31 INVSKDVRLAAGKAAS-------------LFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEVIIEILGKSYNA   95 (103)
Q Consensus        31 ~~iskda~~~l~~~~~-------------~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~~~~l~~~l~~   95 (103)
                      ..++.++...|.+.+.             .-+.-+...|..+|..+++..|+.+||..|++.-.. -.-..++.++..
T Consensus       313 ~~ls~eAl~~Li~~~~r~~g~r~~l~~~~R~l~~llr~A~~~A~~~~~~~I~~edv~~A~~~~~~-i~~~~~e~~l~~  389 (604)
T 3k1j_A          313 PHFTKEAVEEIVREAQKRAGRKGHLTLRLRDLGGIVRAAGDIAVKKGKKYVEREDVIEAVKMAKP-LEKQLADWYIER  389 (604)
T ss_dssp             CCBBHHHHHHHHHHHHHTTCSTTEEECCHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHTCC-HHHHHHHHHHHH
T ss_pred             ccCCHHHHHHHHHHHhhhhccccccccCHHHHHHHHHHHHHHHHhcCcccccHHHHHHHHHhhhh-hHHHHHHHHhcc
Confidence            4699999999888663             345556677888999999999999999999964322 222334444444

>3fh2_A Probable ATP-dependent protease (heat shock prote; struct genomics, PSI2, MCSG, protein structure initiative; 1.60A {Corynebacterium glutamicum}

Probab=80.31  E-value=9.6  Score=24.70  Aligned_cols=60  Identities=10%  Similarity=0.153  Sum_probs=42.4

Q ss_pred             CCcHHHHHHHHHhhCCCCC---cccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhc
Q psy13691          9 NLPSAIIQRLIKEALPKDA---EGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQI   80 (103)
Q Consensus         9 ~LP~a~V~ri~K~~l~~~~---~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~l   80 (103)
                      .+....+.+.+.+.++..+   ++...+|..+..+|.+            |...|...|...|+.+|++.||=.-
T Consensus        55 gv~~~~l~~~l~~~l~~~~~~~~~~~~~s~~~~~vL~~------------A~~~a~~~~~~~i~~eHlLlall~~  117 (146)
T 3fh2_A           55 GISLDAVRQEVEEIIGQGSQPTTGHIPFTPRAKKVLEL------------SLREGLQMGHKYIGTEFLLLGLIRE  117 (146)
T ss_dssp             TCCHHHHHHHHHHHHCCCSCCCCSCCCBCHHHHHHHHH------------HHHHHHHTTCSSBCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHhccCCCCCcCCCcCCHHHHHHHHH------------HHHHHHHcCCCcCcHHHHHHHHHhC
Confidence            3444555555555544322   2346789999988887            6777888899999999999998543

>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=80.09  E-value=6.4  Score=28.34  Aligned_cols=50  Identities=8%  Similarity=-0.015  Sum_probs=39.8

Q ss_pred             ccccHHHHHHHHHHHHH-------HHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhc
Q psy13691         31 INVSKDVRLAAGKAASL-------FILHLTTEALSIANEKNRKTLSGVDVIEGVKQI   80 (103)
Q Consensus        31 ~~iskda~~~l~~~~~~-------Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~l   80 (103)
                      +.++.++...|.+.+..       -+..+...|...|...++.+|+.+||..|+...
T Consensus       266 ~~ls~~~~~~l~~~~~~~~~~~~R~~~~ll~~a~~~A~~~~~~~v~~~~v~~a~~~~  322 (350)
T 1g8p_A          266 VEAPNTALYDCAALCIALGSDGLRGELTLLRSARALAALEGATAVGRDHLKRVATMA  322 (350)
T ss_dssp             CBCCHHHHHHHHHHHHHSSSCSHHHHHHHHHHHHHHHHHTTCSBCCHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHHH
Confidence            58999999998877653       345566667778888899999999999998753

---

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	103
d2bykb1	89	a.22.1.3 (B:11-99) Chrac-14 {Fruit fly (Drosophila	2e-16
d1jfib_	135	a.22.1.3 (B:) Negative cofactor 2, NC2, beta chain	4e-16
d1n1ja_	87	a.22.1.3 (A:) Nuclear transcription factor Y subun	2e-14
d1ku5a_	66	a.22.1.2 (A:) Archaeal histone {Archaeon (Pyrococc	2e-09
d1htaa_	68	a.22.1.2 (A:) Archaeal histone {Archaeon Methanoth	6e-09
d1n1jb_	78	a.22.1.3 (B:) Nuclear transcription factor Y subun	1e-07
d1jfia_	66	a.22.1.3 (A:) Negative cofactor 2, NC2, alpha chai	2e-07
d1f1ea_	151	a.22.1.2 (A:) Archaeal histone {Archaeon Methanopy	6e-06
d1f1ea_	151	a.22.1.2 (A:) Archaeal histone {Archaeon Methanopy	4e-05
d2byka1	72	a.22.1.3 (A:29-100) Chrac-16 {Fruit fly (Drosophil	0.001

>d2bykb1 a.22.1.3 (B:11-99) Chrac-14 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 89

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]

 Score = 65.6 bits (160), Expect = 2e-16
 Identities = 29/79 (36%), Positives = 54/79 (68%), Gaps = 4/79 (5%)

Query: 11 PSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSG 70
          P+A+I RLIKEALP+      +VSK+ R A  +AAS+F + +T+ + ++A+++N KT++ 
Sbjct: 1  PNAVIGRLIKEALPES----ASVSKEARAAIARAASVFAIFVTSSSTALAHKQNHKTITA 56

Query: 71 VDVIEGVKQIGFEVIIEIL 89
           D+++ + ++ FE  +  L
Sbjct: 57 KDILQTLTELDFESFVPSL 75

>d1jfib_ a.22.1.3 (B:) Negative cofactor 2, NC2, beta chain {Human (Homo sapiens) [TaxId: 9606]} Length = 135

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]

 Score = 66.5 bits (162), Expect = 4e-16
 Identities = 28/84 (33%), Positives = 45/84 (53%), Gaps = 5/84 (5%)

Query: 6  DDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNR 65
          DDL +P A I ++IKE LP      + V+ D R       + FI  +++EA  I N+  +
Sbjct: 1  DDLTIPRAAINKMIKETLPN-----VRVANDARELVVNCCTEFIHLISSEANEICNKSEK 55

Query: 66 KTLSGVDVIEGVKQIGFEVIIEIL 89
          KT+S   VI+ ++ +GF   I  +
Sbjct: 56 KTISPEHVIQALESLGFGSYISEV 79

>d1n1ja_ a.22.1.3 (A:) Nuclear transcription factor Y subunit beta (Nf-Yb3) {Human (Homo sapiens) [TaxId: 9606]} Length = 87

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]

 Score = 60.6 bits (147), Expect = 2e-14
 Identities = 24/82 (29%), Positives = 47/82 (57%), Gaps = 4/82 (4%)

Query: 8  LNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKT 67
          + LP A + R++K A+P+       ++KD +    +  S FI  +T+EA    +++ RKT
Sbjct: 1  IYLPIANVARIMKNAIPQT----GKIAKDAKECVQECVSEFISFITSEASERCHQEKRKT 56

Query: 68 LSGVDVIEGVKQIGFEVIIEIL 89
          ++G D++  +  +GF+  +E L
Sbjct: 57 INGEDILFAMSTLGFDSYVEPL 78

>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 = 47.4 bits (113), Expect = 2e-09
 Identities = 16/69 (23%), Positives = 30/69 (43%), Gaps = 6/69 (8%)

Query: 10 LPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLS 69
          LP A + RLI++A  +       VS+       +    + + +  +A+  A    RKT+ 
Sbjct: 3  LPIAPVDRLIRKAGAE------RVSEQAAKVLAEYLEEYAIEIAKKAVEFARHAGRKTVK 56

Query: 70 GVDVIEGVK 78
            D+   +K
Sbjct: 57 VEDIKLAIK 65

>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 = 46.3 bits (110), Expect = 6e-09
 Identities = 22/70 (31%), Positives = 31/70 (44%), Gaps = 6/70 (8%)

Query: 10 LPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLS 69
          LP A I R+IK A  +       VS D R+A  K        + +EA+ +A    RKT+ 
Sbjct: 4  LPIAPIGRIIKNAGAE------RVSDDARIALAKVLEEMGEEIASEAVKLAKHAGRKTIK 57

Query: 70 GVDVIEGVKQ 79
            D+    K 
Sbjct: 58 AEDIELARKM 67

>d1n1jb_ a.22.1.3 (B:) Nuclear transcription factor Y subunit gamma (Nf-Yc2) {Human (Homo sapiens) [TaxId: 9606]} Length = 78

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]

 Score = 43.3 bits (102), Expect = 1e-07
 Identities = 22/83 (26%), Positives = 40/83 (48%), Gaps = 6/83 (7%)

Query: 10 LPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLS 69
          LP A I++++K       E    +S +  +   KAA +FI  LT  A     +  R+TL 
Sbjct: 1  LPLARIKKIMKLD-----EDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQ 55

Query: 70 GVDVIEGVKQIG-FEVIIEILGK 91
            D+   + +   F+ +I+I+ +
Sbjct: 56 RNDIAMAITKFDQFDFLIDIVPR 78

>d1jfia_ a.22.1.3 (A:) Negative cofactor 2, NC2, alpha chain {Human (Homo sapiens) [TaxId: 9606]} Length = 66

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]

 Score = 42.4 bits (100), Expect = 2e-07
 Identities = 14/69 (20%), Positives = 32/69 (46%), Gaps = 5/69 (7%)

Query: 10 LPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLS 69
           P A I+++++       E    V+  V +   +A  LF+  L  +A  +   +N KT++
Sbjct: 3  FPPARIKKIMQTD-----EEIGKVAAAVPVIISRALELFLESLLKKACQVTQSRNAKTMT 57

Query: 70 GVDVIEGVK 78
             + + ++
Sbjct: 58 TSHLKQCIE 66

>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 = 40.2 bits (94), Expect = 6e-06
 Identities = 19/77 (24%), Positives = 29/77 (37%), Gaps = 6/77 (7%)

Query: 3   ESLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANE 62
           E  D      A ++R++K A  +        S D      K        L  +A   A+E
Sbjct: 73  EDYDGELFGRATVRRILKRAGIE------RASSDAVDLYNKLICRATEELGEKAAEYADE 126

Query: 63  KNRKTLSGVDVIEGVKQ 79
             RKT+ G DV + +  
Sbjct: 127 DGRKTVQGEDVEKAITY 143

>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 = 37.8 bits (88), Expect = 4e-05
 Identities = 13/74 (17%), Positives = 29/74 (39%), Gaps = 5/74 (6%)

Query: 10 LPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLS 69
          LP A I+R+ ++ + +       +S+D +            ++   A S+ +   +KTL 
Sbjct: 2  LPKAAIERIFRQGIGER-----RLSQDAKDTIYDFVPTMAEYVANAAKSVLDASGKKTLM 56

Query: 70 GVDVIEGVKQIGFE 83
             +      +  E
Sbjct: 57 EEHLKALADVLMVE 70

>d2byka1 a.22.1.3 (A:29-100) Chrac-16 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 72

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]

 Score = 32.4 bits (74), Expect = 0.001
 Identities = 11/62 (17%), Positives = 26/62 (41%), Gaps = 2/62 (3%)

Query: 32 NVSKDVRLAAGKAASLFILHLTTEALSIANEKN-RKTLSGVDVIEGVKQIG-FEVIIEIL 89
           ++ +V     K   LF+ HL   A +    +   + L    + + V +    E +++I+
Sbjct: 9  LITNEVLFLMTKCTELFVRHLAGAAYTEEFGQRPGEALKYEHLSQVVNKNKNLEFLLQIV 68

Query: 90 GK 91
           +
Sbjct: 69 PQ 70

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	103
d1n1ja_	87	Nuclear transcription factor Y subunit beta (Nf-Yb	99.97
d2bykb1	89	Chrac-14 {Fruit fly (Drosophila melanogaster) [Tax	99.97
d1jfib_	135	Negative cofactor 2, NC2, beta chain {Human (Homo	99.97
d1htaa_	68	Archaeal histone {Archaeon Methanothermus fervidus	99.86
d1ku5a_	66	Archaeal histone {Archaeon (Pyrococcus horikoshii)	99.85
d1n1jb_	78	Nuclear transcription factor Y subunit gamma (Nf-Y	99.84
d1jfia_	66	Negative cofactor 2, NC2, alpha chain {Human (Homo	99.76
d1f1ea_	151	Archaeal histone {Archaeon Methanopyrus kandleri [	99.71
d1f1ea_	151	Archaeal histone {Archaeon Methanopyrus kandleri [	99.58
d2huec1	82	Histone H4 {African clawed frog (Xenopus laevis) [	99.36
d1tzyc_	95	Histone H3 {Chicken (Gallus gallus), erythrocytes	99.17
d2byka1	72	Chrac-16 {Fruit fly (Drosophila melanogaster) [Tax	99.04
d1q9ca_	172	Histone domain of Son of sevenless protein {Human	98.69
d1tzyb_	92	Histone H2B {Chicken (Gallus gallus), erythrocytes	98.21
d1h3ob_	74	TAF(II)-20, (TAF(II)-15, hTAF12), histone fold dom	97.94
d1bh9b_	89	TAF(II)28 {Human (Homo sapiens) [TaxId: 9606]}	97.85
d1f66c_	103	Histone H2A {Human (Homo sapiens), variant H2A.Z [	97.85
d1u35c1	106	macro-H2A.1, histone domain {Human (Homo sapiens)	97.71
d1tafb_	70	TAF(II)62 {Fruit fly (Drosophila melanogaster) [Ta	97.55
d1tzya_	106	Histone H2A {Chicken (Gallus gallus), erythrocytes	97.52
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	96.2
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	95.92
d1tafa_	68	TAF(II)42 {Fruit fly (Drosophila melanogaster) [Ta	95.56
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	89.61
d1khya_	139	N-terminal domain of ClpB (heat shock protein F84.	89.08
d1qvra1	145	N-terminal domain of ClpB (heat shock protein F84.	86.58
d1wwia1	148	Hypothetical protein TTHA1479 {Thermus thermophilu	85.43
d1k6ka_	142	N-terminal, ClpS-binding domain of ClpA, an Hsp100	84.03
d1qvra1	145	N-terminal domain of ClpB (heat shock protein F84.	83.35
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	80.14

>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=99.97  E-value=6.9e-31  Score=168.08  Aligned_cols=87  Identities=28%  Similarity=0.454  Sum_probs=84.8

Q ss_pred             CCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCchHHHH
Q psy13691          8 LNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEVIIE   87 (103)
Q Consensus         8 ~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~~~   87 (103)
                      +.||+|+|.||||+.+|++    .+||+||+.++++||++||+||+++|++.|..+|||||+++||..|++.+||.+|++
T Consensus         1 l~LP~a~v~ri~K~~~p~~----~~is~ea~~~i~~a~e~Fi~~lt~~A~~~a~~~~rKTI~~~dv~~Al~~~~~~~fl~   76 (87)
T d1n1ja_           1 IYLPIANVARIMKNAIPQT----GKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDILFAMSTLGFDSYVE   76 (87)
T ss_dssp             CCCCHHHHHHHHHHTSCTT----CEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHTTCGGGHH
T ss_pred             CCCcHhHHHHHHHHhCCcc----ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHcCcHhHHH
Confidence            4699999999999999988    899999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHh
Q psy13691         88 ILGKSYNAAVS   98 (103)
Q Consensus        88 ~l~~~l~~~k~   98 (103)
                      +++.++++||+
T Consensus        77 ~l~~~~~~~ke   87 (87)
T d1n1ja_          77 PLKLYLQKFRE   87 (87)
T ss_dssp             HHHHHHHHHHC
T ss_pred             HHHHHHHHhcC
Confidence            99999999986

>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=99.97  E-value=4.1e-31  Score=169.83  Aligned_cols=87  Identities=33%  Similarity=0.574  Sum_probs=85.1

Q ss_pred             cHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCchHHHHHHH
Q psy13691         11 PSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEVIIEILG   90 (103)
Q Consensus        11 P~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~~~~l~   90 (103)
                      |+|+|.||||+++|++    .+||+||+.++++||++||+||+++|++.|..++||||+++||++||+.+||++|+++|+
T Consensus         1 P~a~i~ri~K~~~p~~----~~iskeA~~~i~~aae~FI~~lt~~A~~~a~~~~rKtI~~~dv~~Al~~~~f~~~~~~l~   76 (89)
T d2bykb1           1 PNAVIGRLIKEALPES----ASVSKEARAAIARAASVFAIFVTSSSTALAHKQNHKTITAKDILQTLTELDFESFVPSLT   76 (89)
T ss_dssp             CCSHHHHHHHHHSCTT----CEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCTTTHHHHH
T ss_pred             CccHHHHHHHHhCccc----chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHHCCcHHHHHHHH
Confidence            8999999999999998    999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhccc
Q psy13691         91 KSYNAAVSIKV  101 (103)
Q Consensus        91 ~~l~~~k~~~~  101 (103)
                      .+++.||+.++
T Consensus        77 ~~l~~~~e~~~   87 (89)
T d2bykb1          77 QDLEVYRKVVK   87 (89)
T ss_dssp             HHHHHHHHHHT
T ss_pred             HHHHHHHHHHc
Confidence            99999999865

>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=99.97  E-value=2.8e-30  Score=177.14  Aligned_cols=91  Identities=31%  Similarity=0.529  Sum_probs=87.6

Q ss_pred             cCCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCchHH
Q psy13691          6 DDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEVI   85 (103)
Q Consensus         6 ~d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~   85 (103)
                      +|+.||+|+|.||||..+| +    ++||+||+.+|++||++||+||+++|+++|..++||||+++||++||+.+||++|
T Consensus         1 ddl~LP~a~I~kI~K~~~~-~----~~is~dA~~~i~~a~~~Fi~~lt~~A~~~a~~~~RkTi~~~Dv~~Al~~~~f~~f   75 (135)
T d1jfib_           1 DDLTIPRAAINKMIKETLP-N----VRVANDARELVVNCCTEFIHLISSEANEICNKSEKKTISPEHVIQALESLGFGSY   75 (135)
T ss_dssp             CCCCCCHHHHHHHHHHHST-T----CCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHHTTGGG
T ss_pred             CcccccHHHHHHHHhhCCc-c----chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHHHcCcHHH
Confidence            6899999999999999998 5    7999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhccc
Q psy13691         86 IEILGKSYNAAVSIKV  101 (103)
Q Consensus        86 ~~~l~~~l~~~k~~~~  101 (103)
                      +++|..++..|++..+
T Consensus        76 ~~~l~~~l~~~ke~~~   91 (135)
T d1jfib_          76 ISEVKEVLQECKTVAL   91 (135)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            9999999999998753

>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=99.86  E-value=1.3e-21  Score=119.11  Aligned_cols=66  Identities=33%  Similarity=0.377  Sum_probs=62.4

Q ss_pred             CCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhc
Q psy13691          9 NLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQI   80 (103)
Q Consensus         9 ~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~l   80 (103)
                      +||+++|.||||+.++      .+||+|+.+++++|+++||.+|+.+|++.|.++|||||+++||..||+.+
T Consensus         3 eLP~a~I~ri~k~~~~------~ris~ea~~~l~~~~e~fi~~l~~~a~~~a~~~kRkTi~~~DV~~Alk~~   68 (68)
T d1htaa_           3 ELPIAPIGRIIKNAGA------ERVSDDARIALAKVLEEMGEEIASEAVKLAKHAGRKTIKAEDIELARKMF   68 (68)
T ss_dssp             CSCHHHHHHHHHHTTC------SCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHTC
T ss_pred             cCcHHHHHHHHHHCCc------chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHhC
Confidence            5999999999999754      58999999999999999999999999999999999999999999999864

>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=99.85  E-value=1.9e-21  Score=117.94  Aligned_cols=64  Identities=25%  Similarity=0.336  Sum_probs=61.3

Q ss_pred             CCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691          9 NLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK   78 (103)
Q Consensus         9 ~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~   78 (103)
                      +||+++|.||||+.++      .+||+||.+++++|+++||.+|+.+|++.|.++|||||+++||..||+
T Consensus         2 ~LP~a~I~rI~k~~~~------~ris~ea~~~l~~a~e~Fi~~l~~~a~~~a~~~~RKTI~~~Dv~~Al~   65 (66)
T d1ku5a_           2 ELPIAPVDRLIRKAGA------ERVSEQAAKVLAEYLEEYAIEIAKKAVEFARHAGRKTVKVEDIKLAIK   65 (66)
T ss_dssp             CSCHHHHHHHHHHTTC------SEECHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHT
T ss_pred             CCCHHHHHHHHHhCcc------cccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHh
Confidence            6999999999999854      589999999999999999999999999999999999999999999986

>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=99.84  E-value=1.4e-21  Score=121.88  Aligned_cols=73  Identities=25%  Similarity=0.284  Sum_probs=68.5

Q ss_pred             CcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCchHHHH
Q psy13691         10 LPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEVIIE   87 (103)
Q Consensus        10 LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~~~   87 (103)
                      ||.|+|.||||. .|+.    .+||+||..++++|+++||.||+.+|++.|..+|||||+++||..|++..+..+|+.
T Consensus         1 LP~srVkrImK~-~~~~----~~is~ea~~~i~~a~E~Fi~~l~~~A~~~a~~~~rkti~~~dl~~av~~~~~~~FL~   73 (78)
T d1n1jb_           1 LPLARIKKIMKL-DEDV----KMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDIAMAITKFDQFDFLI   73 (78)
T ss_dssp             CCHHHHHHHHTT-STTC----CCBCTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHTTCGGGGGGT
T ss_pred             CCHHHHHHHHhc-CCcc----cccchHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHhcCChhHHHH
Confidence            899999999996 4766    899999999999999999999999999999999999999999999999998878754

>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=99.76  E-value=4.1e-19  Score=107.59  Aligned_cols=65  Identities=20%  Similarity=0.348  Sum_probs=58.3

Q ss_pred             CCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691          9 NLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK   78 (103)
Q Consensus         9 ~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~   78 (103)
                      .||.|+|.||||.. |+.    .+||+||..++.+|++.|+.+|+.+|++.|..+|||||+++||..|++
T Consensus         2 ~fP~srVkkimk~~-~~~----~~is~~A~~~~~~a~E~Fi~~l~~~A~~~a~~~krktI~~~dl~~ai~   66 (66)
T d1jfia_           2 RFPPARIKKIMQTD-EEI----GKVAAAVPVIISRALELFLESLLKKACQVTQSRNAKTMTTSHLKQCIE   66 (66)
T ss_dssp             CCCHHHHHHHHTTS-TTC----CCBCTTHHHHHHHHHHHHHHHHHHHHHHHHHTC---CBCHHHHHTTCC
T ss_pred             CCChHHHHHHHhcC-Ccc----ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHhC
Confidence            58999999999997 665    799999999999999999999999999999999999999999998864

>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=99.71  E-value=1.1e-17  Score=115.56  Aligned_cols=68  Identities=18%  Similarity=0.218  Sum_probs=65.5

Q ss_pred             CCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcC
Q psy13691          9 NLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIG   81 (103)
Q Consensus         9 ~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lg   81 (103)
                      +||+|+|.||||+.+|+     .+||+||++.|+.|+++|+.+|+++|+.+|.++|||||+++||..|++.+|
T Consensus         1 ~lP~a~I~rilk~~~~~-----~ris~da~~~l~~~~~~~~~~Ia~eA~~l~~~~~rKTi~~edi~~a~~~~~   68 (151)
T d1f1ea_           1 ELPKAAIERIFRQGIGE-----RRLSQDAKDTIYDFVPTMAEYVANAAKSVLDASGKKTLMEEHLKALADVLM   68 (151)
T ss_dssp             CCCHHHHHHHHHTTSTT-----CEECHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHHHHT
T ss_pred             CCCccHHHHHHHHhCCc-----cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHhcc
Confidence            59999999999999885     699999999999999999999999999999999999999999999999888

>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=99.58  E-value=3.1e-15  Score=103.06  Aligned_cols=69  Identities=26%  Similarity=0.209  Sum_probs=64.0

Q ss_pred             ccCCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhh
Q psy13691          5 LDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQ   79 (103)
Q Consensus         5 ~~d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~   79 (103)
                      -++..||+++|.||+|+..  .    .+||+||..+|+++++.|+..|+.+|+..|.+.|||||+++||..||..
T Consensus        75 ~~~~~fp~a~IkRi~k~~g--~----~ris~dA~~~l~~~~E~fi~~l~~~A~~~a~~~kRkTI~~~DI~~Av~~  143 (151)
T d1f1ea_          75 YDGELFGRATVRRILKRAG--I----ERASSDAVDLYNKLICRATEELGEKAAEYADEDGRKTVQGEDVEKAITY  143 (151)
T ss_dssp             CCSCCCCHHHHHHHHHHTT--C----CEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHH
T ss_pred             cccCccCHHHHHHHHHcCC--c----chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHH
Confidence            4577999999999999852  3    6999999999999999999999999999999999999999999999974

>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=99.36  E-value=9.5e-13  Score=82.39  Aligned_cols=68  Identities=19%  Similarity=0.305  Sum_probs=63.6

Q ss_pred             CCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCc
Q psy13691          9 NLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGF   82 (103)
Q Consensus         9 ~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf   82 (103)
                      .+|++.|.||++.+.-      .+||+|+.+.+.++.+.|+..+..+|...|.+++||||+++||..||+.+|-
T Consensus         9 gI~k~~i~Riar~~Gv------~ris~d~~~~l~~~l~~~l~~i~~~a~~~~~hakRKTvt~~DV~~Alkr~g~   76 (82)
T d2huec1           9 GITKPAIRRLARRGGV------KRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGR   76 (82)
T ss_dssp             SSCHHHHHHHHHHTTC------CEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTTTCE
T ss_pred             CcCHHHHHHHHHHcCc------ccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHhcCC
Confidence            6999999999999732      5899999999999999999999999999999999999999999999998763

>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=99.17  E-value=1.7e-11  Score=78.63  Aligned_cols=77  Identities=17%  Similarity=0.186  Sum_probs=68.1

Q ss_pred             CccCCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcC
Q psy13691          4 SLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIG   81 (103)
Q Consensus         4 ~~~d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lg   81 (103)
                      +..++.+|++++.|++++...+. ..+.+++.+|..+||++++.|+.-+...||..|.+.||.||.+.|+.-|..--|
T Consensus        16 kst~lLIpk~pF~RLVRei~~~~-~~~~r~~~~Al~aLQea~E~yLv~lfeda~~~a~HakRvTl~~kD~~LarrirG   92 (95)
T d1tzyc_          16 KSTELLIRKLPFQRLVREIAQDF-KTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG   92 (95)
T ss_dssp             HCCSCCSCHHHHHHHHHHHHHHH-CTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHHT
T ss_pred             CCcccccccccHHHHHHHHHHhc-CCCCEeeHHHHHHHHHHHHHHHHHHHHHhHHHHHhcCCCcCCHHHHHHHHHHhc
Confidence            45688999999999999987653 234899999999999999999999999999999999999999999998875433

>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=99.04  E-value=1.8e-10  Score=70.07  Aligned_cols=57  Identities=16%  Similarity=0.111  Sum_probs=50.2

Q ss_pred             ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHh-CCCCCcChhhHHHhhhhcCchHHHH
Q psy13691         31 INVSKDVRLAAGKAASLFILHLTTEALSIANE-KNRKTLSGVDVIEGVKQIGFEVIIE   87 (103)
Q Consensus        31 ~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~-~~RkTI~~eDV~~Al~~lgf~~~~~   87 (103)
                      ..||.||..++.+|++.||.+|+.+|+..+.. .+||||+++||..|++.-+-.+|+.
T Consensus         8 ~~is~ea~~lvskAtElFi~~L~~~a~~~a~~~~~~ktl~~~dl~~aV~~~~~f~FL~   65 (72)
T d2byka1           8 GLITNEVLFLMTKCTELFVRHLAGAAYTEEFGQRPGEALKYEHLSQVVNKNKNLEFLL   65 (72)
T ss_dssp             SCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSCEECHHHHHHHHHTCSTTGGGT
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCccccHHHHHHHHccCchhhHHH
Confidence            48999999999999999999999999988855 5569999999999999777666654

>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=98.69  E-value=2.6e-08  Score=69.38  Aligned_cols=67  Identities=16%  Similarity=0.169  Sum_probs=61.5

Q ss_pred             CCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhh
Q psy13691          7 DLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQ   79 (103)
Q Consensus         7 d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~   79 (103)
                      .+.||.+.|.|++|+.+.      .|||.+|...|..+.+.+...|...|...|++.||++|+++||..|+..
T Consensus        97 gL~fPV~rv~rlLk~~~a------~RVs~~A~vyLaavLEyl~aeILelAgn~a~~~krkrItp~dI~lAi~n  163 (172)
T d1q9ca_          97 PLSLPVEKIHPLLKEVLG------YKIDHQVSVYIVAVLEYISADILKLAGNYVRNIRHYEITKQDIKVAMCA  163 (172)
T ss_dssp             --CCCHHHHHHHHHHHHS------SCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSBCCHHHHHHHHHT
T ss_pred             CceecHHHHHHHHHhccc------cccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCceecHHHHHHHHhC
Confidence            578999999999999843      6999999999999999999999999999999999999999999999873

>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=98.21  E-value=3.2e-06  Score=53.22  Aligned_cols=63  Identities=14%  Similarity=0.237  Sum_probs=58.6

Q ss_pred             HHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhc
Q psy13691         13 AIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQI   80 (103)
Q Consensus        13 a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~l   80 (103)
                      .-|+|+.|+.-|+     ..||..|...|+--......-|+.+|...|.-.+|+||+..+|..|+.-+
T Consensus         7 ~Yi~kVLKqVhp~-----~giS~kam~imnsfvndiferIa~EA~~La~~~kr~TitsreIqtAvrL~   69 (92)
T d1tzyb_           7 IYVYKVLKQVHPD-----TGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLL   69 (92)
T ss_dssp             HHHHHHHHHHCTT-----CEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHH
T ss_pred             HHHHHHHHhhCCC-----CCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCcHHHHHHHHHHH
Confidence            3589999999986     68999999999999999999999999999999999999999999999744

>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=97.94  E-value=4.4e-05  Score=46.04  Aligned_cols=65  Identities=26%  Similarity=0.290  Sum_probs=60.0

Q ss_pred             CcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhh
Q psy13691         10 LPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQ   79 (103)
Q Consensus        10 LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~   79 (103)
                      |-+..+..++++.-|.     ..+.+|+-+++.+.|..||.-++..|...|++.|-.||...||.-.|++
T Consensus         4 l~K~~L~eLv~~idp~-----~~ld~~vee~ll~iADdFV~~V~~~ac~lAKhR~s~~le~kDvql~LeR   68 (74)
T d1h3ob_           4 LTKKKLQDLVREVDPN-----EQLDEDVEEMLLQIADDFIESVVTAACQLARHRKSSTLEVKDVQLHLER   68 (74)
T ss_dssp             SCHHHHHHHHHHHCSS-----CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCEECHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHhCCC-----CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCcHHHHHHHHHh
Confidence            5678899999999664     6899999999999999999999999999999999999999999998874

>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=97.85  E-value=6.5e-05  Score=46.74  Aligned_cols=68  Identities=25%  Similarity=0.374  Sum_probs=60.3

Q ss_pred             CCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC-CCcChhhHHHhhhhcCc
Q psy13691          9 NLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNR-KTLSGVDVIEGVKQIGF   82 (103)
Q Consensus         9 ~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~R-kTI~~eDV~~Al~~lgf   82 (103)
                      .||++.|.|||...++      ..||.....++.-.|..||-.|-.+|.+++.+.+- ..|.|+||-.|...|.-
T Consensus        16 ~~~K~~vkrl~~~~~g------~sv~~~v~i~v~giaKvFvGEiVE~A~~V~~~~~e~~PL~P~HireA~rrl~~   84 (89)
T d1bh9b_          16 AFPKAAIKRLIQSITG------TSVSQNVVIAMSGISKVFVGEVVEEALDVCEKWGEMPPLQPKHMREAVRRLKS   84 (89)
T ss_dssp             CCCHHHHHHHHHHHHS------SCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSSCCHHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHHHHHcC------CCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCcHHHHHHHHHHHH
Confidence            5999999999999975      46999999999999999999999999999876544 47999999999987643

>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=97.85  E-value=4.8e-05  Score=48.47  Aligned_cols=69  Identities=12%  Similarity=0.129  Sum_probs=59.7

Q ss_pred             CCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhh
Q psy13691          7 DLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQ   79 (103)
Q Consensus         7 d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~   79 (103)
                      .+.||.+.|.|.+|+.--..    .+|+..|...+.-+.+-....+-..|...|...+++.|+++||..|+..
T Consensus         9 gL~FpVgrv~r~L~~~~~~~----~rv~~~A~VyLaAvLEYL~aEILelagn~a~~~~~~rItpr~l~lai~n   77 (103)
T d1f66c_           9 GLQFPVGRIHRHLKSRTTSH----GRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRG   77 (103)
T ss_dssp             TCSSCHHHHHHHHHHTSCSS----CEECTTHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHHH
T ss_pred             CcccChHHHHHHHhccCccc----eecCCCceeeHHHHHHHHHHHHHHHhhhhhccCCCCeeechhhhccccC
Confidence            57899999999999864332    4699999999999888888888888888899999999999999999874

>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=97.71  E-value=0.00011  Score=47.06  Aligned_cols=67  Identities=12%  Similarity=0.220  Sum_probs=58.9

Q ss_pred             CCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691          7 DLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK   78 (103)
Q Consensus         7 d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~   78 (103)
                      .+.||.+.|.|++|+.-. .    .+|+..|...+.-+.+-....+-..|-..|...+++-|+++||..|+.
T Consensus         9 gL~FpV~ri~r~Lk~~~~-~----~rv~~~apVylaAVLEYL~aEILELAgn~a~~~k~~rItprhi~lair   75 (106)
T d1u35c1           9 GVIFPVGRMLRYIKKGHP-K----YRIGVGAPVYMAAVLEYLTAEILELAVNAARDNKKGRVTPRHILLAVA   75 (106)
T ss_dssp             TCSSCHHHHHHHHHHHST-T----SEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHH
T ss_pred             CcccCHHHHHHHHhCCCC-c----cccCCCCchhHHHHHHHHHHHHHHHHHHHHHHcCCCeeecchhhhccc
Confidence            578999999999999633 2    699999999999988888888888888889999999999999999985

>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=97.55  E-value=0.00045  Score=41.03  Aligned_cols=65  Identities=15%  Similarity=0.182  Sum_probs=57.3

Q ss_pred             CCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691          8 LNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK   78 (103)
Q Consensus         8 ~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~   78 (103)
                      -.+|..+|.-|.-.. +-     ..+++|+...|..=++-=|..+..+|.....+.+|++++.+||-.||+
T Consensus         5 S~~~~esik~iAeS~-Gi-----~~l~de~a~~LA~DveYRl~eiiQeA~KFMrhskR~~Ltt~Did~ALk   69 (70)
T d1tafb_           5 SSISAESMKVIAESI-GV-----GSLSDDAAKELAEDVSIKLKRIVQDAAKFMNHAKRQKLSVRDIDMSLK   69 (70)
T ss_dssp             CCCCHHHHHHHHHHT-TC-----CCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHC
T ss_pred             ccCCHHHHHHHHHHc-CC-----CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCcCcHHHHHHHHc
Confidence            368899987776654 32     269999999999999999999999999999999999999999999985

>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=97.52  E-value=0.0003  Score=44.89  Aligned_cols=68  Identities=10%  Similarity=0.159  Sum_probs=56.3

Q ss_pred             CCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhh
Q psy13691          7 DLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQ   79 (103)
Q Consensus         7 d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~   79 (103)
                      .+.||-+.|.|++|+.-- .    .+|+..|...+.-..+-....+--.|-..|...+++-|+++|+..|+..
T Consensus        10 gL~FpV~rv~r~Lk~~~~-~----~rv~~~apVylaAVLEYLtaEiLELAgn~a~~~k~~rItPrhi~lAirn   77 (106)
T d1tzya_          10 GLQFPVGRVHRLLRKGNY-A----ERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRN   77 (106)
T ss_dssp             TCSSCHHHHHHHHHHTTS-S----SEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHT
T ss_pred             CccCChHHHHHHHHcCcc-c----cccCCCchHHHHHHHHHHHHHHHHHhhHHHHhcCCceecchhhhhcccC
Confidence            578999999999999522 2    5899999998887766666666666777889999999999999999863

>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=96.20  E-value=0.019  Score=38.19  Aligned_cols=53  Identities=17%  Similarity=0.202  Sum_probs=40.1

Q ss_pred             ccccHHHHHHHHHHHH------------HHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCch
Q psy13691         31 INVSKDVRLAAGKAAS------------LFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFE   83 (103)
Q Consensus        31 ~~iskda~~~l~~~~~------------~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~   83 (103)
                      ..++.++.+.+.+-+.            --+.-+...|...|..+++++|+.+||..|++++.|+
T Consensus       212 ~~~~~~~l~~ia~~~~~~~~~~~~~G~~R~a~~ll~~a~~~A~~~~~~~I~~edv~~A~~~~~~g  276 (276)
T d1fnna2         212 GSYSEDILQMIADITGAQTPLDTNRGDARLAIDILYRSAYAAQQNGRKHIAPEDVRKSSKEVLFG  276 (276)
T ss_dssp             TSSCHHHHHHHHHHHSBSSTTCTTSCCHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHHSCC
T ss_pred             ccccHHHHHHHHHHhhhhhhhhhcCCCHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHhCC
Confidence            4688888887766431            1223344668888999999999999999999998774

>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=95.92  E-value=0.031  Score=37.35  Aligned_cols=49  Identities=14%  Similarity=-0.047  Sum_probs=38.3

Q ss_pred             ccccHHHHHHHHHHHHH---------HHHHHHHHHHHHHHhCCCCCcChhhHHHhhhh
Q psy13691         31 INVSKDVRLAAGKAASL---------FILHLTTEALSIANEKNRKTLSGVDVIEGVKQ   79 (103)
Q Consensus        31 ~~iskda~~~l~~~~~~---------Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~   79 (103)
                      ..+++++.+.+.+-+..         -+..+..+|...|..+++.+|+.+||.+|+++
T Consensus       229 ~~~~~~al~~ia~~~~~~~~~~gd~R~ai~~l~~a~~~A~~~~~~~It~~~V~~A~~e  286 (287)
T d1w5sa2         229 TVWEPRHLELISDVYGEDKGGDGSARRAIVALKMACEMAEAMGRDSLSEDLVRKAVSE  286 (287)
T ss_dssp             TSCCHHHHHHHHHHHCGGGTSCCCHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHhccccCCCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHhc
Confidence            36889888887764421         23456677889999999999999999999875

>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=95.56  E-value=0.07  Score=30.98  Aligned_cols=47  Identities=17%  Similarity=0.082  Sum_probs=43.0

Q ss_pred             cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691         32 NVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK   78 (103)
Q Consensus        32 ~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~   78 (103)
                      ....-....+.+.+-.++.-+-..|.-.+.+.||++|+.+||.-|++
T Consensus        18 ~yeprV~~qlLef~yRYtt~VL~DA~vys~HA~k~~id~dDVkLAi~   64 (68)
T d1tafa_          18 EYEPRVVNQLLEFTFRYVTSILDDAKVYANHARKKTIDLDDVRLATE   64 (68)
T ss_dssp             CBCTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHH
Confidence            47777888899999999999999999999999999999999999986

>d1ixsb2 c.37.1.20 (B:4-242) Holliday junction helicase RuvB {Thermus thermophilus [TaxId: 274]}

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: Holliday junction helicase RuvB
species: Thermus thermophilus [TaxId: 274]

Probab=89.61  E-value=0.61  Score=30.73  Aligned_cols=70  Identities=9%  Similarity=0.196  Sum_probs=50.3

Q ss_pred             cHHHHHHHHHhhCC-CCCcccccccHHHHHHHHHHHH---HHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCchH
Q psy13691         11 PSAIIQRLIKEALP-KDAEGKINVSKDVRLAAGKAAS---LFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEV   84 (103)
Q Consensus        11 P~a~V~ri~K~~l~-~~~~~~~~iskda~~~l~~~~~---~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~   84 (103)
                      +...+.++++..+. .+    +.++.|+...+.+.+.   -....+...+...+...+...|+.+++.++|..|+.++
T Consensus       166 ~~~~~~~i~~~~~~~~~----i~~~~~~l~~ia~~s~gd~R~a~~~l~~~~~~a~~~~~~~It~~~~~~~l~~l~~De  239 (239)
T d1ixsb2         166 TPEELAQGVMRDARLLG----VRITEEAALEIGRRSRGTMRVAKRLFRRVRDFAQVAGEEVITRERALEALAALGLDE  239 (239)
T ss_dssp             CHHHHHHHHHHHHGGGC----CCBCHHHHHHHHHHTTSSHHHHHHHHHHHHHHHTTSCCSCBCHHHHHHHHHHHTCCT
T ss_pred             ChhhhhHHHHHHHHHhC----CccchHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhCCCCcCHHHHHHHHhhhCcCC
Confidence            34555555554443 23    7899999999988775   34444445566678888899999999999999998764

>d1khya_ a.174.1.1 (A:) N-terminal domain of ClpB (heat shock protein F84.1) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: Double Clp-N motif
superfamily: Double Clp-N motif
family: Double Clp-N motif
domain: N-terminal domain of ClpB (heat shock protein F84.1)
species: Escherichia coli [TaxId: 562]

Probab=89.08  E-value=0.3  Score=30.00  Aligned_cols=35  Identities=14%  Similarity=0.266  Sum_probs=29.9

Q ss_pred             cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691         32 NVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK   78 (103)
Q Consensus        32 ~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~   78 (103)
                      +++..+..+|+.            |...|...+...|+++|++.||=
T Consensus         2 kfT~~~~~~l~~------------A~~~A~~~~h~~v~~eHlL~all   36 (139)
T d1khya_           2 RLTNKFQLALAD------------AQSLALGHDNQFIEPLHLMSALL   36 (139)
T ss_dssp             CBCHHHHHHHHH------------HHHHHHHTTCSSBCHHHHHHHHH
T ss_pred             ccCHHHHHHHHH------------HHHHHHHcCCCcccHHHHHHHHH
Confidence            567777777766            88899999999999999999983

>d1qvra1 a.174.1.1 (A:4-148) N-terminal domain of ClpB (heat shock protein F84.1) {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: Double Clp-N motif
superfamily: Double Clp-N motif
family: Double Clp-N motif
domain: N-terminal domain of ClpB (heat shock protein F84.1)
species: Thermus thermophilus [TaxId: 274]

Probab=86.58  E-value=0.39  Score=30.33  Aligned_cols=34  Identities=12%  Similarity=0.098  Sum_probs=29.0

Q ss_pred             cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhh
Q psy13691         32 NVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGV   77 (103)
Q Consensus        32 ~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al   77 (103)
                      +++..++.+|..            |.+.|...+...|.++|++.||
T Consensus         2 kfT~~a~~~l~~------------A~~~A~~~~~~~i~~~HlL~al   35 (145)
T d1qvra1           2 RWTQAAREALAQ------------AQVLAQRMKHQAIDLPHLWAVL   35 (145)
T ss_dssp             CSCHHHHHHHHH------------HHHHHHHTTCSEECHHHHHHHH
T ss_pred             ccCHHHHHHHHH------------HHHHHHHcCCCcccHHHHHHHH
Confidence            466777777765            8889999999999999999998

>d1wwia1 a.22.1.4 (A:1-148) Hypothetical protein TTHA1479 {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Bacterial histone-fold protein
domain: Hypothetical protein TTHA1479
species: Thermus thermophilus [TaxId: 274]

Probab=85.43  E-value=1.3  Score=28.84  Aligned_cols=58  Identities=19%  Similarity=0.121  Sum_probs=51.7

Q ss_pred             CcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhH
Q psy13691         10 LPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDV   73 (103)
Q Consensus        10 LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV   73 (103)
                      +|.+-+.|+.+.+.+-      -+.|+-..-+....+.=+.-|.--|...|+.+||.+|.+.|+
T Consensus         3 m~~~k~e~~FR~aa~L------dvdK~d~~r~~d~V~~Kl~DLllva~~~A~~n~RdvI~~~DL   60 (148)
T d1wwia1           3 MKVAEFERLFRQAAGL------DVDKNDLKRVSDFLRNKLYDLLAVAERNAKYNGRDLIFEPDL   60 (148)
T ss_dssp             SCHHHHHHHHHHHHCC------CCCGGGHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECGGGS
T ss_pred             CcHHHHHHHHHHHhcc------CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeeccccC
Confidence            6889999999999764      478888888899999888899999999999999999999886

>d1k6ka_ a.174.1.1 (A:) N-terminal, ClpS-binding domain of ClpA, an Hsp100 chaperone {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: Double Clp-N motif
superfamily: Double Clp-N motif
family: Double Clp-N motif
domain: N-terminal, ClpS-binding domain of ClpA, an Hsp100 chaperone
species: Escherichia coli [TaxId: 562]

Probab=84.03  E-value=0.43  Score=29.32  Aligned_cols=33  Identities=12%  Similarity=0.259  Sum_probs=27.2

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhh
Q psy13691         33 VSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGV   77 (103)
Q Consensus        33 iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al   77 (103)
                      +|++...+|+.            |...|...|..-|+++|++.||
T Consensus         2 ~s~~l~~~l~~------------A~~~A~~~~h~~i~~EHLL~aL   34 (142)
T d1k6ka_           2 LNQELELSLNM------------AFARAREHRHEFMTVEHLLLAL   34 (142)
T ss_dssp             BCHHHHHHHHH------------HHHHHHHHTBSEECHHHHHHHH
T ss_pred             CCHHHHHHHHH------------HHHHHHHcCCCcccHHHHHHHH
Confidence            45666555554            8889999999999999999998

>d1qvra1 a.174.1.1 (A:4-148) N-terminal domain of ClpB (heat shock protein F84.1) {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: Double Clp-N motif
superfamily: Double Clp-N motif
family: Double Clp-N motif
domain: N-terminal domain of ClpB (heat shock protein F84.1)
species: Thermus thermophilus [TaxId: 274]

Probab=83.35  E-value=0.82  Score=28.69  Aligned_cols=62  Identities=10%  Similarity=0.002  Sum_probs=45.8

Q ss_pred             cccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhc-CchHHHHHHHHHHHHHHhccccC
Q psy13691         30 KINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQI-GFEVIIEILGKSYNAAVSIKVVT  103 (103)
Q Consensus        30 ~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~l-gf~~~~~~l~~~l~~~k~~~~~~  103 (103)
                      ...+|.+...+|.+            |...+..-|...|+.+|++-||=.- +...=+..++..+.+.|...+|+
T Consensus        77 ~~~~s~~l~~il~~------------A~~~a~~~gd~~Is~ehLllal~~~~~~~~~l~~l~~~i~~~R~g~~v~  139 (145)
T d1qvra1          77 GQYLTSRLSGALNR------------AEGLMEELKDRYVAVDTLVLALAEATPGLPGLEALKGALKELRGGRTVQ  139 (145)
T ss_dssp             TCEECHHHHHHHHH------------HHHHHHTTTCSSCCHHHHHHHHHHHSTTSCCHHHHHHHHTSSCSCCSSC
T ss_pred             cCCCCHHHHHHHHH------------HHHHHHHcCCccccHHHHHHHHHhcccchhhHHHHHHHHHHHHCCCCCC
Confidence            46789999888877            8889999999999999999998532 22212356777777766666654

>d1in4a2 c.37.1.20 (A:17-254) Holliday junction helicase RuvB {Thermotoga maritima [TaxId: 2336]}

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: Holliday junction helicase RuvB
species: Thermotoga maritima [TaxId: 2336]

Probab=80.14  E-value=1.7  Score=28.32  Aligned_cols=54  Identities=7%  Similarity=0.124  Sum_probs=37.8

Q ss_pred             ccccHHHHHHHHHHHH---HHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCchH
Q psy13691         31 INVSKDVRLAAGKAAS---LFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEV   84 (103)
Q Consensus        31 ~~iskda~~~l~~~~~---~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~   84 (103)
                      ..++.++...+.+.+.   ..+..+...+.+.+...+...|+.+++..||+.|+.+|
T Consensus       182 ~~~~~~~l~~i~~~s~gd~R~ai~~l~~~~~~~~~~~~~~it~~~~~~al~~l~iDd  238 (238)
T d1in4a2         182 VEIEDAAAEMIAKRSRGTPRIAIRLTKRVRDMLTVVKADRINTDIVLKTMEVLNIDD  238 (238)
T ss_dssp             CCBCHHHHHHHHHTSTTCHHHHHHHHHHHHHHHHHHTCSSBCHHHHHHHHHHHTCCT
T ss_pred             chhhHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhcCCccCHHHHHHHHHhhCCCC
Confidence            5788888888876643   23333344455556555666799999999999988764