Citrus Sinensis ID: 038850

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------
Protein Sequence
MPQEAEEQNTETTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA
Secondary Structure (PSIPRED)
cccHHHHcccccccccccHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHc
Secondary Structure Prediction (SSPRO)
cccHHHHHccccccccccHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHcc
Coil and Loop (DISEMBL)
mpqeaeeqntettrpefpvgrvKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA
Flexible Loop (DISEMBL)
mpqeaeeqntettrpefpvgrvkkiikldedinkvtsealfivSRSTELFLRFLAEKSAEaaiekkrktiklgdmrva
Low Complexity Region (SEG)
MPQEAEEQNTETTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLaeksaeaaiekkrkTIKLGDMRVA
Disordered region (IsUnstruct)
******************VGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAE**********************
Disordered Region (DISOPRED)
*****************PVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEK**************LGDMRVA
Disordered Region (DISEMBL)
***************EFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA
Disordered Region (DISPRO)
*************RPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKR*T*********
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MPQEAEEQNTETTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA
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	78	2.2.26 [Sep-21-2011]
Q9FMV5	250	Nuclear transcription fac	no	no	0.961	0.3	0.355	2e-06
Q8L4B2	231	Nuclear transcription fac	no	no	0.923	0.311	0.333	6e-06
Q9ZVL3	217	Nuclear transcription fac	no	no	0.923	0.331	0.333	7e-06
Q9NR33	117	DNA polymerase epsilon su	yes	no	0.756	0.504	0.372	8e-06
A6QQ14	116	DNA polymerase epsilon su	yes	no	0.756	0.508	0.372	8e-06
Q9CQ36	118	DNA polymerase epsilon su	yes	no	0.756	0.5	0.372	8e-06
Q9SMP0	234	Nuclear transcription fac	no	no	0.923	0.307	0.347	9e-06
Q9FGP6	186	Nuclear transcription fac	no	no	0.769	0.322	0.366	1e-05
Q4PSE2	187	Nuclear transcription fac	no	no	0.923	0.385	0.333	2e-05
Q9FGP7	202	Nuclear transcription fac	no	no	0.807	0.311	0.365	2e-05

>sp|Q9FMV5|NFYC4_ARATH Nuclear transcription factor Y subunit C-4 OS=Arabidopsis thaliana GN=NFYC4 PE=2 SV=1

 Score = 51.2 bits (121), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 27/76 (35%), Positives = 47/76 (61%), Gaps = 1/76 (1%)

Query: 3   QEAEEQNTETTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAA 62
           QE E+ N +    + P+ R+KKI+K DED+  +++EA  + +++ ELF+  L  +S   A
Sbjct: 66  QEIEQVN-DFKNHQLPLARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHA 124

Query: 63  IEKKRKTIKLGDMRVA 78
            E KR+T++  D+  A
Sbjct: 125 EENKRRTLQKNDIAAA 140

Stimulates the transcription of various genes by recognizing and binding to a CCAAT motif in promoters (By similarity). Involved in the abscisic acid (ABA) signaling pathway.
Arabidopsis thaliana (taxid: 3702)

>sp|Q8L4B2|NFYC9_ARATH Nuclear transcription factor Y subunit C-9 OS=Arabidopsis thaliana GN=NFYC9 PE=2 SV=1

 Score = 49.7 bits (117), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 24/72 (33%), Positives = 43/72 (59%)

Query: 7   EQNTETTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKK 66
           E+ T+      P+ R+KKI+K DED+  +++EA  + +R+ E+F+  L  +S     E K
Sbjct: 71  EKTTDFKNHSLPLARIKKIMKADEDVRMISAEAPVVFARACEMFILELTLRSWNHTEENK 130

Query: 67  RKTIKLGDMRVA 78
           R+T++  D+  A
Sbjct: 131 RRTLQKNDIAAA 142

Stimulates the transcription of various genes by recognizing and binding to a CCAAT motif in promoters.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9ZVL3|NFYC3_ARATH Nuclear transcription factor Y subunit C-3 OS=Arabidopsis thaliana GN=NFYC3 PE=2 SV=1

 Score = 49.3 bits (116), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 24/72 (33%), Positives = 43/72 (59%)

Query: 7   EQNTETTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKK 66
           E+ T+      P+ R+KKI+K DED+  +++EA  + +R+ E+F+  L  +S     E K
Sbjct: 61  EKTTDFKNHSLPLARIKKIMKADEDVRMISAEAPVVFARACEMFILELTLRSWNHTEENK 120

Query: 67  RKTIKLGDMRVA 78
           R+T++  D+  A
Sbjct: 121 RRTLQKNDIAAA 132

Stimulates the transcription of various genes by recognizing and binding to a CCAAT motif in promoters.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9NR33|DPOE4_HUMAN DNA polymerase epsilon subunit 4 OS=Homo sapiens GN=POLE4 PE=1 SV=2

 Score = 49.3 bits (116), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 22/59 (37%), Positives = 38/59 (64%)

Query: 17 FPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDM 75
           P+ RVK ++K D D+     EA+FI++R+ ELF+  +A+ +   A + KRKT++  D+
Sbjct: 41 LPLARVKALVKADPDVTLAGQEAIFILARAAELFVETIAKDAYCCAQQGKRKTLQRRDL 99

May play a role in allowing polymerase epsilon to carry out its replication and/or repair function.

Homo sapiens (taxid: 9606)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 7

>sp|A6QQ14|DPOE4_BOVIN DNA polymerase epsilon subunit 4 OS=Bos taurus GN=POLE4 PE=3 SV=1

 Score = 48.9 bits (115), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 22/59 (37%), Positives = 38/59 (64%)

Query: 17 FPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDM 75
           P+ RVK ++K D D+     EA+FI++R+ ELF+  +A+ +   A + KRKT++  D+
Sbjct: 40 LPLARVKALVKADPDVTLAGQEAIFILARAAELFVETIAKDAYCCAQQGKRKTLQRRDL 98

May play a role in allowing polymerase epsilon to carry out its replication and/or repair function.

Bos taurus (taxid: 9913)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 7

>sp|Q9CQ36|DPOE4_MOUSE DNA polymerase epsilon subunit 4 OS=Mus musculus GN=Pole4 PE=3 SV=1

 Score = 48.9 bits (115), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 22/59 (37%), Positives = 38/59 (64%)

Query: 17  FPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDM 75
            P+ RVK ++K D D+     EA+FI++R+ ELF+  +A+ +   A + KRKT++  D+
Sbjct: 42  LPLARVKALVKADPDVTLAGQEAIFILARAAELFVETIAKDAYCCAQQGKRKTLQRRDL 100

May play a role in allowing polymerase epsilon to carry out its replication and/or repair function.

Mus musculus (taxid: 10090)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 7

>sp|Q9SMP0|NFYC1_ARATH Nuclear transcription factor Y subunit C-1 OS=Arabidopsis thaliana GN=NFYC1 PE=1 SV=1

 Score = 48.9 bits (115), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 25/72 (34%), Positives = 44/72 (61%)

Query: 7   EQNTETTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKK 66
           EQ  +    + P+ R+KKI+K DED+  +++EA  + +++ ELF+  L  +S   A E K
Sbjct: 56  EQVNDFKNHQLPLARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENK 115

Query: 67  RKTIKLGDMRVA 78
           R+T++  D+  A
Sbjct: 116 RRTLQKNDIAAA 127

Stimulates the transcription of various genes by recognizing and binding to a CCAAT motif in promoters.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FGP6|NFYC5_ARATH Nuclear transcription factor Y subunit C-5 OS=Arabidopsis thaliana GN=NFYC5 PE=2 SV=1

 Score = 48.5 bits (114), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 22/60 (36%), Positives = 39/60 (65%)

Query: 16 EFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDM 75
          EFP+ R+K+I+K D D++ + +EA  ++S++ E+F+  L  +S   A E  R TI+  D+
Sbjct: 36 EFPISRIKRIMKFDPDVSMIAAEAPNLLSKACEMFVMDLTMRSWLHAQESNRLTIRKSDV 95

Stimulates the transcription of various genes by recognizing and binding to a CCAAT motif in promoters.

Arabidopsis thaliana (taxid: 3702)

>sp|Q4PSE2|NFYC8_ARATH Nuclear transcription factor Y subunit C-8 OS=Arabidopsis thaliana GN=NFYC8 PE=2 SV=1

 Score = 47.8 bits (112), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 24/72 (33%), Positives = 42/72 (58%)

Query: 7  EQNTETTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKK 66
          E N +    + P+ R+KKI+K D D+  + SEA  ++S++ E+F+  L  +S   A E K
Sbjct: 27 EGNLDFKNHDLPITRIKKIMKYDPDVTMIASEAPILLSKACEMFIMDLTMRSWLHAQESK 86

Query: 67 RKTIKLGDMRVA 78
          R T++  ++  A
Sbjct: 87 RVTLQKSNVDAA 98

Stimulates the transcription of various genes by recognizing and binding to a CCAAT motif in promoters.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FGP7|NFYC6_ARATH Nuclear transcription factor Y subunit C-6 OS=Arabidopsis thaliana GN=NFYC6 PE=2 SV=1

 Score = 47.8 bits (112), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 23/63 (36%), Positives = 40/63 (63%)

Query: 16  EFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDM 75
           + P+ R+KKI+K D D++ V++EA  I +++ E+F+  L  +S   A E KR T++  D+
Sbjct: 54  QLPLARIKKIMKADPDVHMVSAEAPIIFAKACEMFIVDLTMRSWLKAEENKRHTLQKSDI 113

Query: 76  RVA 78
             A
Sbjct: 114 SNA 116

Stimulates the transcription of various genes by recognizing and binding to a CCAAT motif in promoters.

Arabidopsis thaliana (taxid: 3702)

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	78
255547732	141	DNA binding protein, putative [Ricinus c	0.948	0.524	0.786	4e-24
225425432	140	PREDICTED: nuclear transcription factor	0.948	0.528	0.675	5e-21
224053481	123	predicted protein [Populus trichocarpa]	0.884	0.560	0.724	8e-21
357463021	173	Nuclear transcription factor Y subunit C	0.935	0.421	0.698	1e-19
449452907	139	PREDICTED: nuclear transcription factor	0.935	0.525	0.698	1e-19
356538087	168	PREDICTED: nuclear transcription factor	0.935	0.434	0.671	5e-19
449489251	139	PREDICTED: LOW QUALITY PROTEIN: nuclear	0.935	0.525	0.684	6e-19
15239815	130	nuclear factor Y, subunit C13 [Arabidops	0.923	0.553	0.625	3e-18
297791585	131	hypothetical protein ARALYDRAFT_917343 [	0.923	0.549	0.635	1e-17
356569178	166	PREDICTED: dr1-associated corepressor ho	0.807	0.379	0.714	2e-17

>gi|255547732|ref|XP_002514923.1| DNA binding protein, putative [Ricinus communis] gi|223545974|gb|EEF47477.1| DNA binding protein, putative [Ricinus communis]

 Score =  115 bits (287), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 59/75 (78%), Positives = 67/75 (89%), Gaps = 1/75 (1%)

Query: 5  AEEQNT-ETTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAI 63
          AEE+NT ET RPEFP GRVKKI+KLD+DINKVTS+ALF+VSRSTELFLR LAEKSAE A 
Sbjct: 2  AEEENTVETIRPEFPTGRVKKIMKLDKDINKVTSDALFLVSRSTELFLRLLAEKSAEVAT 61

Query: 64 EKKRKTIKLGDMRVA 78
          E+KRKTIKL  +R+A
Sbjct: 62 EQKRKTIKLDHIRIA 76

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225425432|ref|XP_002271716.1| PREDICTED: nuclear transcription factor Y subunit gamma [Vitis vinifera]

 Score =  104 bits (260), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 50/74 (67%), Positives = 63/74 (85%)

Query: 5  AEEQNTETTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIE 64
          AEE+ +E   PE P+GRVKK++KLD DINKV SEALF++S STELFLRFLAE+SAE AI+
Sbjct: 2  AEEEKSEAIMPELPLGRVKKLVKLDRDINKVNSEALFLISCSTELFLRFLAEQSAEIAIQ 61

Query: 65 KKRKTIKLGDMRVA 78
          KKR+T+KL  +R+A
Sbjct: 62 KKRRTVKLEHLRIA 75

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224053481|ref|XP_002297836.1| predicted protein [Populus trichocarpa] gi|222845094|gb|EEE82641.1| predicted protein [Populus trichocarpa]

 Score =  104 bits (259), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 50/69 (72%), Positives = 59/69 (85%)

Query: 10 TETTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKT 69
          T TTRPEFP GR+K+I+KLD+D NKV ++ALF+VS STELFLRFLAEKSAE AIEKKRK 
Sbjct: 2  TTTTRPEFPTGRIKRIMKLDKDTNKVNADALFLVSSSTELFLRFLAEKSAEVAIEKKRKI 61

Query: 70 IKLGDMRVA 78
          +KL  +R A
Sbjct: 62 VKLDHIRAA 70

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357463021|ref|XP_003601792.1| Nuclear transcription factor Y subunit C-4 [Medicago truncatula] gi|355490840|gb|AES72043.1| Nuclear transcription factor Y subunit C-4 [Medicago truncatula] gi|388508356|gb|AFK42244.1| unknown [Medicago truncatula] gi|388523251|gb|AFK49678.1| nuclear transcription factor Y subunit C9 [Medicago truncatula]

 Score =  100 bits (249), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 51/73 (69%), Positives = 61/73 (83%)

Query: 6  EEQNTETTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEK 65
          EE+ T +  PEFP  RVKKII LD+D+ +V+SEALF+VSRSTELFL+ LAEKSAE AIEK
Sbjct: 21 EEEKTLSFEPEFPKSRVKKIITLDKDVKRVSSEALFLVSRSTELFLQLLAEKSAEVAIEK 80

Query: 66 KRKTIKLGDMRVA 78
          KRKT+KL  MR+A
Sbjct: 81 KRKTVKLEHMRIA 93

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449452907|ref|XP_004144200.1| PREDICTED: nuclear transcription factor Y subunit C-1-like [Cucumis sativus]

 Score =  100 bits (248), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 51/73 (69%), Positives = 61/73 (83%)

Query: 6  EEQNTETTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEK 65
          EE+  E  RPEFP GRVKKI+KLD+DI KV SEALF+VS +TELFL+ LAEKSAE+A EK
Sbjct: 3  EEEFGEAIRPEFPTGRVKKIMKLDKDIGKVNSEALFLVSCATELFLKLLAEKSAESAAEK 62

Query: 66 KRKTIKLGDMRVA 78
          KRKT+KL  +R+A
Sbjct: 63 KRKTVKLEHIRMA 75

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356538087|ref|XP_003537536.1| PREDICTED: nuclear transcription factor Y subunit C-4-like [Glycine max]

 Score = 98.2 bits (243), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 49/73 (67%), Positives = 62/73 (84%)

Query: 6  EEQNTETTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEK 65
          EE+N  + + EFP GRVKKI+ LD+D+ +V+SEALF+VSRSTELFL+FLAEKSA+ AIEK
Sbjct: 4  EEENGVSIQLEFPKGRVKKIMALDKDVKRVSSEALFLVSRSTELFLQFLAEKSAQVAIEK 63

Query: 66 KRKTIKLGDMRVA 78
          KRKT+ L  +RVA
Sbjct: 64 KRKTVNLEHIRVA 76

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449489251|ref|XP_004158259.1| PREDICTED: LOW QUALITY PROTEIN: nuclear transcription factor Y subunit C-1-like [Cucumis sativus]

 Score = 98.2 bits (243), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 50/73 (68%), Positives = 60/73 (82%)

Query: 6  EEQNTETTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEK 65
          EE+  E  RPEFP GRVKKI+KLD+DI KV SEALF+VS +TELFL+ LA KSAE+A EK
Sbjct: 3  EEEFGEAIRPEFPTGRVKKIMKLDKDIGKVNSEALFLVSCATELFLKLLAXKSAESAAEK 62

Query: 66 KRKTIKLGDMRVA 78
          KRKT+KL  +R+A
Sbjct: 63 KRKTVKLEHIRMA 75

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15239815|ref|NP_199139.1| nuclear factor Y, subunit C13 [Arabidopsis thaliana] gi|10177387|dbj|BAB10588.1| unnamed protein product [Arabidopsis thaliana] gi|225879084|dbj|BAH30612.1| hypothetical protein [Arabidopsis thaliana] gi|332007548|gb|AED94931.1| nuclear factor Y, subunit C13 [Arabidopsis thaliana]

 Score = 95.9 bits (237), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 45/72 (62%), Positives = 57/72 (79%)

Query: 7  EQNTETTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKK 66
          E+   + RPEFP+GRVKKI+KLD+DINK+ SEAL +++ STELFL FLAEKSA    EKK
Sbjct: 2  EEEEGSIRPEFPIGRVKKIMKLDKDINKINSEALHVITYSTELFLHFLAEKSAVVTAEKK 61

Query: 67 RKTIKLGDMRVA 78
          RKT+ L  +R+A
Sbjct: 62 RKTVNLDHLRIA 73

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297791585|ref|XP_002863677.1| hypothetical protein ARALYDRAFT_917343 [Arabidopsis lyrata subsp. lyrata] gi|297309512|gb|EFH39936.1| hypothetical protein ARALYDRAFT_917343 [Arabidopsis lyrata subsp. lyrata]

 Score = 94.0 bits (232), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 47/74 (63%), Positives = 59/74 (79%), Gaps = 2/74 (2%)

Query: 5  AEEQNTETTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIE 64
          AEE+ +  TRPEFP+GRVKKI+KLD++INK+ SEAL +++ STELFL FLAEKSA    E
Sbjct: 2  AEEETS--TRPEFPLGRVKKIMKLDKEINKINSEALHVITYSTELFLHFLAEKSAIVTAE 59

Query: 65 KKRKTIKLGDMRVA 78
          KKRKT+ L  +R A
Sbjct: 60 KKRKTVNLDHLRTA 73

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356569178|ref|XP_003552782.1| PREDICTED: dr1-associated corepressor homolog [Glycine max]

 Score = 93.2 bits (230), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 45/63 (71%), Positives = 55/63 (87%)

Query: 16 EFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDM 75
          EFP GRVKKI+ LD+D+ +V+SEALF+VSRSTELFL+FLAEKSA+ AIEKKRKT+ L  +
Sbjct: 14 EFPKGRVKKIMALDKDVKRVSSEALFLVSRSTELFLQFLAEKSAQVAIEKKRKTVNLEHI 73

Query: 76 RVA 78
          R A
Sbjct: 74 REA 76

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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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	78
TAIR|locus:2169238	130	NF-YC13 ""nuclear factor Y, su	0.923	0.553	0.486	4.9e-14
WB|WBGene00013150	179	Y53F4B.3 [Caenorhabditis elega	0.935	0.407	0.287	4.8e-07
FB|FBgn0034726	155	Mes4 "Mesoderm-expressed 4" [D	0.897	0.451	0.3	5.5e-06
DICTYBASE|DDB_G0272740	158	DDB_G0272740 "putative histone	0.5	0.246	0.410	1.1e-05
UNIPROTKB|E9PI99	141	NFYC "Nuclear transcription fa	0.807	0.446	0.285	5e-05
UNIPROTKB|Q5T6K7	129	NFYC "Nuclear transcription fa	0.807	0.488	0.285	5e-05
UNIPROTKB|E9PNC7	156	DRAP1 "Dr1-associated corepres	0.628	0.314	0.407	6.3e-05
FB|FBgn0034650	341	NC2alpha "Negative Cofactor 2a	0.910	0.208	0.328	6.9e-05
TAIR|locus:2114555	234	NF-YC1 ""nuclear factor Y, sub	0.961	0.320	0.289	7.1e-05
TAIR|locus:2010980	217	NF-YC3 ""nuclear factor Y, sub	0.923	0.331	0.277	7.7e-05

TAIR|locus:2169238 NF-YC13 ""nuclear factor Y, subunit C13"" [Arabidopsis thaliana (taxid:3702)]

 Score = 181 (68.8 bits), Expect = 4.9e-14, P = 4.9e-14
 Identities = 35/72 (48%), Positives = 47/72 (65%)

Query:     7 EQNTETTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLXXXXXXXXXXXX 66
             E+   + RPEFP+GRVKKI+KLD+DINK+ SEAL +++ STELFL FL            
Sbjct:     2 EEEEGSIRPEFPIGRVKKIMKLDKDINKINSEALHVITYSTELFLHFLAEKSAVVTAEKK 61

Query:    67 XXTIKLGDMRVA 78
               T+ L  +R+A
Sbjct:    62 RKTVNLDHLRIA 73

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

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;ISS

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

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

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

WB|WBGene00013150 Y53F4B.3 [Caenorhabditis elegans (taxid:6239)]

 Score = 115 (45.5 bits), Expect = 4.8e-07, P = 4.8e-07
 Identities = 21/73 (28%), Positives = 42/73 (57%)

Query:     3 QEAEEQNTETTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLXXXXXXXX 62
             +E EE   E  R + P+GRVKK+++++ D+  + +EAL +++++ ELF++ L        
Sbjct:    22 REIEEHVEELVRSQLPLGRVKKVVRMNPDVEMLNNEALQLMAKAAELFIKELSNAANQNA 81

Query:    63 XXXXXXTIKLGDM 75
                   T++  D+
Sbjct:    82 ALEKRKTVQTKDI 94

GO:0005622 "intracellular" evidence=IEA

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

GO:0003677 "DNA binding" evidence=IEA

GO:0040027 "negative regulation of vulval development" evidence=IMP

FB|FBgn0034726 Mes4 "Mesoderm-expressed 4" [Drosophila melanogaster (taxid:7227)]

 Score = 105 (42.0 bits), Expect = 5.5e-06, P = 5.5e-06
 Identities = 21/70 (30%), Positives = 38/70 (54%)

Query:     9 NTETTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLXXXXXXXXXXXXXX 68
             + E    + P+ R++ I+KLD D++   +EA+FIV+++ ELF+  L              
Sbjct:    70 DNEAKMTQLPLARIRNIMKLDPDLHMANNEAVFIVAKAVELFIASLSRESYTYTAQSKKK 129

Query:    69 TIKLGDMRVA 78
             TI+  D+ +A
Sbjct:   130 TIQKRDVDMA 139

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

GO:0006260 "DNA replication" evidence=IC

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

GO:0005622 "intracellular" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IEA

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

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

DICTYBASE|DDB_G0272740 DDB_G0272740 "putative histone-like transcription factor" [Dictyostelium discoideum (taxid:44689)]

 Score = 102 (41.0 bits), Expect = 1.1e-05, P = 1.1e-05
 Identities = 16/39 (41%), Positives = 32/39 (82%)

Query:    16 EFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFL 54
             + PV R+K+I++ D+D+  ++S+A+ +V++STE+FL +L
Sbjct:    78 QLPVARIKRIMRCDKDVKIISSDAVMLVAKSTEMFLDYL 116

GO:0046982 "protein heterodimerization activity" evidence=IEA

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

GO:0005622 "intracellular" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0005634 "nucleus" evidence=IEA

GO:0044351 "macropinocytosis" evidence=RCA

UNIPROTKB|E9PI99 NFYC "Nuclear transcription factor Y subunit gamma" [Homo sapiens (taxid:9606)]

 Score = 96 (38.9 bits), Expect = 5.0e-05, P = 5.0e-05
 Identities = 18/63 (28%), Positives = 36/63 (57%)

Query:    16 EFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLXXXXXXXXXXXXXXTIKLGDM 75
             E P+ R+KKI+KLDED+  +++EA  + +++ ++F+  L              T++  D+
Sbjct:    42 ELPLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDI 101

Query:    76 RVA 78
              +A
Sbjct:   102 AMA 104

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA

GO:0016602 "CCAAT-binding factor complex" evidence=IEA

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

GO:0046982 "protein heterodimerization activity" evidence=IEA

UNIPROTKB|Q5T6K7 NFYC "Nuclear transcription factor Y subunit gamma" [Homo sapiens (taxid:9606)]

 Score = 96 (38.9 bits), Expect = 5.0e-05, P = 5.0e-05
 Identities = 18/63 (28%), Positives = 36/63 (57%)

Query:    16 EFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLXXXXXXXXXXXXXXTIKLGDM 75
             E P+ R+KKI+KLDED+  +++EA  + +++ ++F+  L              T++  D+
Sbjct:    42 ELPLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDI 101

Query:    76 RVA 78
              +A
Sbjct:   102 AMA 104

GO:0016602 "CCAAT-binding factor complex" evidence=IEA

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

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=IEA

UNIPROTKB|E9PNC7 DRAP1 "Dr1-associated corepressor" [Homo sapiens (taxid:9606)]

 Score = 95 (38.5 bits), Expect = 6.3e-05, P = 6.3e-05
 Identities = 22/54 (40%), Positives = 32/54 (59%)

Query:     1 MPQEAEEQNTETTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFL 54
             MP + ++ N       FP  R+KKI++ DE+I KV +    I+SR+ ELFL  L
Sbjct:     1 MPSKKKKYNAR-----FPPARIKKIMQTDEEIGKVAAAVPVIISRALELFLESL 49

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

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

FB|FBgn0034650 NC2alpha "Negative Cofactor 2alpha" [Drosophila melanogaster (taxid:7227)]

 Score = 102 (41.0 bits), Expect = 6.9e-05, P = 6.9e-05
 Identities = 25/76 (32%), Positives = 36/76 (47%)

Query:     1 MPQEAEEQNTETTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLXXXXXX 60
             MP + ++ N       FP GR+KKI++ DE+I KV      I+SR+ ELF+  L      
Sbjct:     1 MPSKKKKYNAR-----FPAGRIKKIMQSDEEIGKVAQAVPVIISRTLELFVESLLTKTLR 55

Query:    61 XXXXXXXXTIKLGDMR 76
                     T+    MR
Sbjct:    56 ITNARNAKTLSPSHMR 71

GO:0017055 "negative regulation of RNA polymerase II transcriptional preinitiation complex assembly" evidence=NAS

GO:0017054 "negative cofactor 2 complex" evidence=NAS

GO:0001075 "RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity involved in preinitiation complex assembly" evidence=IPI

GO:0005634 "nucleus" evidence=IC

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

GO:0008134 "transcription factor binding" evidence=IPI

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

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

GO:0005622 "intracellular" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IEA

TAIR|locus:2114555 NF-YC1 ""nuclear factor Y, subunit C1"" [Arabidopsis thaliana (taxid:3702)]

 Score = 99 (39.9 bits), Expect = 7.1e-05, P = 7.1e-05
 Identities = 22/76 (28%), Positives = 40/76 (52%)

Query:     3 QEAEEQNTETTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLXXXXXXXX 62
             QE E+ N +    + P+ R+KKI+K DED+  +++EA  + +++ ELF+  L        
Sbjct:    53 QEIEQVN-DFKNHQLPLARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHA 111

Query:    63 XXXXXXTIKLGDMRVA 78
                   T++  D+  A
Sbjct:   112 EENKRRTLQKNDIAAA 127

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

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IC;ISS;IDA

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

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

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0005515 "protein binding" evidence=IPI

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=IDA

GO:0016602 "CCAAT-binding factor complex" evidence=ISS

TAIR|locus:2010980 NF-YC3 ""nuclear factor Y, subunit C3"" [Arabidopsis thaliana (taxid:3702)]

 Score = 98 (39.6 bits), Expect = 7.7e-05, P = 7.7e-05
 Identities = 20/72 (27%), Positives = 37/72 (51%)

Query:     7 EQNTETTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLXXXXXXXXXXXX 66
             E+ T+      P+ R+KKI+K DED+  +++EA  + +R+ E+F+  L            
Sbjct:    61 EKTTDFKNHSLPLARIKKIMKADEDVRMISAEAPVVFARACEMFILELTLRSWNHTEENK 120

Query:    67 XXTIKLGDMRVA 78
               T++  D+  A
Sbjct:   121 RRTLQKNDIAAA 132

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

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;ISS

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

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

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0005829 "cytosol" evidence=RCA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	78
pfam00808	65	pfam00808, CBFD_NFYB_HMF, Histone-like transcripti	7e-15
COG5247	113	COG5247, BUR6, Class 2 transcription repressor NC2	7e-07
COG5208	286	COG5208, HAP5, CCAAT-binding factor, subunit C [Tr	1e-06
pfam00125	75	pfam00125, Histone, Core histone H2A/H2B/H3/H4	9e-05
COG2036	91	COG2036, HHT1, Histones H3 and H4 [Chromatin struc	0.001

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

 Score = 61.9 bits (151), Expect = 7e-15
 Identities = 22/63 (34%), Positives = 41/63 (65%)

Query: 16 EFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDM 75
          E P+ RVK+I+K D D  +++ +A  +++   E F+ F+A ++AE   ++KRKTI    +
Sbjct: 2  ELPIARVKRIMKSDPDAGRISQDAKELIAECVEEFIEFIASEAAEICKKEKRKTINAEHI 61

Query: 76 RVA 78
          ++A
Sbjct: 62 KLA 64

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

>gnl|CDD|227572 COG5247, BUR6, Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]

 Score = 42.6 bits (100), Expect = 7e-07
 Identities = 23/70 (32%), Positives = 39/70 (55%)

Query: 1  MPQEAEEQNTETTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAE 60
          M    ++ + +  +  FP+ R+KKI++LDEDI KV      I S++ E+FL  +   S +
Sbjct: 8  MGTMPKQNSQKKKKTRFPIARLKKIMQLDEDIGKVGQSTPVIASKALEMFLTEIVGLSLK 67

Query: 61 AAIEKKRKTI 70
           A +K  K +
Sbjct: 68 EARKKSSKRM 77

Length = 113

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

 Score = 43.9 bits (103), Expect = 1e-06
 Identities = 21/61 (34%), Positives = 40/61 (65%)

Query: 18  PVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRV 77
           P+ R+KK++K DED+  +++EA  + ++ TE+F+  L  ++   A E KR+T++  D+  
Sbjct: 111 PLARIKKVMKTDEDVKMISAEAPVLFAKITEIFIEELTMRAWINAEENKRRTLQKSDIAA 170

Query: 78  A 78
           A
Sbjct: 171 A 171

Length = 286

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

 Score = 36.4 bits (85), Expect = 9e-05
 Identities = 17/65 (26%), Positives = 30/65 (46%), Gaps = 1/65 (1%)

Query: 15 PEFPVGRVKKIIKLDEDINK-VTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLG 73
           + P  RV + +K        ++S+A   +  + E  L  + E +   A   KRKTI   
Sbjct: 7  LKLPFSRVVRELKEGFYAELRISSKAPVALQEALEDLLEEILEDAGLLARHAKRKTITPR 66

Query: 74 DMRVA 78
          D+++A
Sbjct: 67 DIQLA 71

Length = 75

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

 Score = 33.8 bits (78), Expect = 0.001
 Identities = 20/66 (30%), Positives = 36/66 (54%), Gaps = 1/66 (1%)

Query: 13 TRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKL 72
          T    P   V++I++      +V+S A+  +  + E +L  +AE + E A   KRKT+K 
Sbjct: 16 TDLLLPKAPVRRILR-KAGAERVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKA 74

Query: 73 GDMRVA 78
           D+++A
Sbjct: 75 EDIKLA 80

Length = 91

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	78
PF00808	65	CBFD_NFYB_HMF: Histone-like transcription factor (	99.91
COG5208	286	HAP5 CCAAT-binding factor, subunit C [Transcriptio	99.78
KOG1657	236	consensus CCAAT-binding factor, subunit C (HAP5) [	99.78
KOG1659	224	consensus Class 2 transcription repressor NC2, alp	99.72
COG5247	113	BUR6 Class 2 transcription repressor NC2, alpha su	99.69
cd00074	115	H2A Histone 2A; H2A is a subunit of the nucleosome	99.34
KOG1658	162	consensus DNA polymerase epsilon, subunit C [Repli	99.31
COG2036	91	HHT1 Histones H3 and H4 [Chromatin structure and d	99.29
KOG0869	168	consensus CCAAT-binding factor, subunit A (HAP3) [	99.27
COG5262	132	HTA1 Histone H2A [Chromatin structure and dynamics	99.23
KOG0870	172	consensus DNA polymerase epsilon, subunit D [Trans	99.19
smart00803	65	TAF TATA box binding protein associated factor. TA	99.15
smart00414	106	H2A Histone 2A.	99.15
PF00125	75	Histone: Core histone H2A/H2B/H3/H4 histone h2a si	99.07
PTZ00017	134	histone H2A; Provisional	99.05
PLN00154	136	histone H2A; Provisional	99.04
smart00417	74	H4 Histone H4.	98.99
cd00076	85	H4 Histone H4, one of the four histones, along wit	98.96
PLN00153	129	histone H2A; Provisional	98.95
PLN00156	139	histone H2AX; Provisional	98.94
PLN00157	132	histone H2A; Provisional	98.94
PLN00035	103	histone H4; Provisional	98.92
KOG1756	131	consensus Histone 2A [Chromatin structure and dyna	98.89
PTZ00015	102	histone H4; Provisional	98.86
KOG0871	156	consensus Class 2 transcription repressor NC2, bet	98.84
PTZ00252	134	histone H2A; Provisional	98.81
cd07981	72	TAF12 TATA Binding Protein (TBP) Associated Factor	98.57
smart00428	105	H3 Histone H3.	98.49
cd08048	85	TAF11 TATA Binding Protein (TBP) Associated Factor	98.44
COG5150	148	Class 2 transcription repressor NC2, beta subunit	98.17
KOG1757	131	consensus Histone 2A [Chromatin structure and dyna	98.14
PF02969	66	TAF: TATA box binding protein associated factor (T	98.12
cd08050	343	TAF6 TATA Binding Protein (TBP) Associated Factor	97.99
PLN00121	136	histone H3; Provisional	97.98
PF04719	90	TAFII28: hTAFII28-like protein conserved region; I	97.97
smart00576	77	BTP Bromodomain transcription factors and PHD doma	97.96
PLN00160	97	histone H3; Provisional	97.95
PTZ00018	136	histone H3; Provisional	97.95
PLN00161	135	histone H3; Provisional	97.9
PF15510	102	CENP-W: Centromere kinetochore component W	97.89
cd07979	117	TAF9 TATA Binding Protein (TBP) Associated Factor	97.75
PF15511	414	CENP-T: Centromere kinetochore component CENP-T; P	97.72
PF09415	72	CENP-X: CENP-S associating Centromere protein X; I	97.57
smart00427	89	H2B Histone H2B.	97.53
KOG1658	162	consensus DNA polymerase epsilon, subunit C [Repli	97.34
PLN00158	116	histone H2B; Provisional	97.24
PTZ00463	117	histone H2B; Provisional	97.22
KOG1745	137	consensus Histones H3 and H4 [Chromatin structure	97.15
PF02269	93	TFIID-18kDa: Transcription initiation factor IID,	97.12
KOG3219	195	consensus Transcription initiation factor TFIID, s	97.11
PLN00155	58	histone H2A; Provisional	96.97
PF03847	68	TFIID_20kDa: Transcription initiation factor TFIID	96.96
KOG1744	127	consensus Histone H2B [Chromatin structure and dyn	96.53
PF15630	76	CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C	96.52
cd07978	92	TAF13 The TATA Binding Protein (TBP) Associated Fa	96.44
PF07524	77	Bromo_TP: Bromodomain associated; InterPro: IPR006	96.31
KOG3467	103	consensus Histone H4 [Chromatin structure and dyna	95.83
KOG2549	576	consensus Transcription initiation factor TFIID, s	95.04
KOG1142	258	consensus Transcription initiation factor TFIID, s	94.39
PF03540	51	TFIID_30kDa: Transcription initiation factor TFIID	93.91
PF05236	264	TAF4: Transcription initiation factor TFIID compon	93.47
COG5095	450	TAF6 Transcription initiation factor TFIID, subuni	93.35
KOG3423	176	consensus Transcription initiation factor TFIID, s	93.25
cd08045	212	TAF4 TATA Binding Protein (TBP) Associated Factor	91.27
PF02291	129	TFIID-31kDa: Transcription initiation factor IID,	90.58
PF10979	43	DUF2786: Protein of unknown function (DUF2786); In	85.03
PF12767	252	SAGA-Tad1: Transcriptional regulator of RNA polII,	80.21

>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=99.91  E-value=1.9e-24  Score=125.58  Aligned_cols=63  Identities=38%  Similarity=0.621  Sum_probs=58.4

Q ss_pred             CCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           16 EFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        16 ~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      .||+++|+||||.+|++.+||+||.+++++|+|+|+++|+.+|++.|.+++||||+|+||..|
T Consensus         2 ~lP~a~vkri~k~~~~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~~~rkti~~~Dv~~A   64 (65)
T PF00808_consen    2 SLPLARVKRIMKSDPDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQRDKRKTITYEDVAKA   64 (65)
T ss_dssp             SS-HHHHHHHHHHTSTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEE-HHHHHHH
T ss_pred             CCChHHHHHHhccCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHH
Confidence            699999999999999999999999999999999999999999999999999999999999865

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 ....

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

Probab=99.78  E-value=6e-20  Score=129.44  Aligned_cols=74  Identities=32%  Similarity=0.514  Sum_probs=67.9

Q ss_pred             Hhhhc-CCCCCCCCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850            5 AEEQN-TETTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus         5 ~e~e~-~~~~~~~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      +|+|+ ...+...||++||||+||.|.||+.||+||+++++++||.||.+|+-.||-.|.+++|+||+..||+.|
T Consensus        97 ~e~~~q~~~k~h~LPlARIkkvMKtdedVkMisaEaPvlFak~~EiFI~ELTmRAW~~ae~NkRRtLQksDia~A  171 (286)
T COG5208          97 AEEERQILLKDHNLPLARIKKVMKTDEDVKMISAEAPVLFAKITEIFIEELTMRAWINAEENKRRTLQKSDIAAA  171 (286)
T ss_pred             HHHhHHHHHHhccCcHHHHHHHHhcccchhheecccchHHHHHHHHHHHHHHHHHHHHHhHhhhhHHHHHHHHHH
Confidence            44443 556677899999999999999999999999999999999999999999999999999999999999875

>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]

Probab=99.78  E-value=1.2e-19  Score=128.52  Aligned_cols=72  Identities=33%  Similarity=0.496  Sum_probs=68.6

Q ss_pred             hhcCCCCCCCCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850            7 EQNTETTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus         7 ~e~~~~~~~~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      ++..+.+...||++|||+|||.|+++..|++||++++++|||+||..|+..+|..+..++|+|+++.||+.|
T Consensus        65 e~~~d~~~~~lPlaRiKkimK~dedv~mI~~Eapvl~aka~E~Fi~elt~~sw~~Tee~~rrtl~~sdia~a  136 (236)
T KOG1657|consen   65 EGQLDFKNHILPLARIKKIMKSDEDVSMITAEAPVLFAKACELFITELTLRSWVHTEENKRRTLQKSDIAAA  136 (236)
T ss_pred             ccccchhhccCcHhhccccccccccccccchhHHHHHHHHHHHHHHHHHHHhhhhhcccccccchHHHHHHH
Confidence            457788899999999999999999999999999999999999999999999999999999999999999864

>KOG1659 consensus Class 2 transcription repressor NC2, alpha subunit (DRAP1) [Transcription]

Probab=99.72  E-value=5.7e-18  Score=118.22  Aligned_cols=70  Identities=36%  Similarity=0.532  Sum_probs=66.2

Q ss_pred             cCCCCCCCCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850            9 NTETTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus         9 ~~~~~~~~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      ..+....+||.+||||||++|.||++|++.+++++++|+|+|++.|+..+++.++..+.|||+..||++|
T Consensus         6 ~~~~~~trfp~aRiKKIMQ~dEdIGKvaqavPViisralElFl~~l~~~t~~~t~~~~aKt~s~~hlkq~   75 (224)
T KOG1659|consen    6 SFKKYKTRFPPARIKKIMQSDEDIGKVAQAVPVIISRALELFLESLLQKTLEITRSRGAKTVSSSHLKQA   75 (224)
T ss_pred             hhhhhhccCCHHHHHHHHhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcCccccCHHHHHHH
Confidence            3456789999999999999999999999999999999999999999999999999999999999999864

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

Probab=99.69  E-value=1.8e-17  Score=104.67  Aligned_cols=70  Identities=33%  Similarity=0.491  Sum_probs=65.3

Q ss_pred             cCCCCCCCCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850            9 NTETTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus         9 ~~~~~~~~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      +.....++||++||||||+.|.|+++|++..+++.++|+|+|+..|...+...|+..+.+.++.++|..|
T Consensus        16 ~~~~~ktrFP~ar~KkIMQ~deDiGKV~q~tPVIaskalE~Fl~~iv~~s~k~aR~~~skR~t~e~lk~a   85 (113)
T COG5247          16 SQKKKKTRFPIARLKKIMQLDEDIGKVGQSTPVIASKALEMFLTEIVGLSLKEARKKSSKRMTSEFLKRA   85 (113)
T ss_pred             hhhhhhhcCCHHHHHHHHHhhhhhhhhhhcchHHHHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHH
Confidence            3345678999999999999999999999999999999999999999999999999999999999998764

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

Probab=99.34  E-value=4e-12  Score=81.84  Aligned_cols=68  Identities=24%  Similarity=0.341  Sum_probs=62.6

Q ss_pred             CCCCCCCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           11 ETTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        11 ~~~~~~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      ....+.||++||.|+||..-...+||.+|+++++..+|++..++.+.|.+.|...++++|+++||..|
T Consensus        15 ~ragL~fPV~ri~R~Lk~~~~a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lA   82 (115)
T cd00074          15 ARAGLQFPVGRIHRYLKKGRYAERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLA   82 (115)
T ss_pred             cccCccCcHHHHHHHHHcCccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHH
Confidence            34578999999999999866668999999999999999999999999999999999999999999764

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.

>KOG1658 consensus DNA polymerase epsilon, subunit C [Replication, recombination and repair]

Probab=99.31  E-value=1.3e-12  Score=87.77  Aligned_cols=67  Identities=30%  Similarity=0.495  Sum_probs=63.3

Q ss_pred             CCCCCCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           12 TTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        12 ~~~~~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      ....+||++|||.+||.+||+.....++.+++++|+|+|++.|...++.+++..+|+|++..|+..|
T Consensus        55 a~l~rLpL~rik~vvkl~pdl~l~~dea~~l~a~aaelfi~~Ln~~~~~~~q~~k~kt~qr~d~D~a  121 (162)
T KOG1658|consen   55 ASLSRLPLARIKQVVKLDPDLTLLNDEASQLIAKAAELFIQELNDVAYTTAQLRKRKTEQRRDYDTA  121 (162)
T ss_pred             hhhhhccHHHHHhhccCCcchhhhhhHHHHHHHHHHHHHHHHHHhccchhHHHHHhhhhhhhccccc
Confidence            5668999999999999999999999999999999999999999999999999999999999987643

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

Probab=99.29  E-value=5.6e-12  Score=78.33  Aligned_cols=65  Identities=31%  Similarity=0.422  Sum_probs=59.3

Q ss_pred             CCCCCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           13 TRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        13 ~~~~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      ....||.+.|+||||.-.. .+||.+|...+..++|.|+..+++.|..+|.+.|||||+.+||..|
T Consensus        16 ~~~~Lp~apv~Ri~r~~~~-~Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la   80 (91)
T COG2036          16 TDLLLPKAPVRRILRKAGA-ERVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLA   80 (91)
T ss_pred             hhhhcCchHHHHHHHHHhH-HHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHH
Confidence            4567999999999997543 3999999999999999999999999999999999999999999754

>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]

Probab=99.27  E-value=8.8e-12  Score=83.98  Aligned_cols=70  Identities=24%  Similarity=0.317  Sum_probs=63.4

Q ss_pred             cCCCCCCCCChHHHHHHhhc-CcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850            9 NTETTRPEFPVGRVKKIIKL-DEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus         9 ~~~~~~~~lP~arVkrImK~-d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      +......-||++.|-||||. -|...+||+||-..+..|+..||..+|.+|.+.|++.+||||+.+||.-|
T Consensus        25 ~~reqDr~LPIANV~RIMK~~lP~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwA   95 (168)
T KOG0869|consen   25 SLREQDRFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWA   95 (168)
T ss_pred             ccchhhhhccHHHHHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHH
Confidence            34556778999999999994 67778999999999999999999999999999999999999999998643

>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]

Probab=99.23  E-value=1.9e-11  Score=79.15  Aligned_cols=68  Identities=25%  Similarity=0.324  Sum_probs=63.2

Q ss_pred             CCCCCCCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           11 ETTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        11 ~~~~~~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      ....+.||++||+|+||.+-..++|+++|+++++.++|+.+.++++-|.+.|+..+.+.|.++||..|
T Consensus        21 a~agl~fpvgrvkr~lk~~~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlA   88 (132)
T COG5262          21 AKAGLIFPVGRVKRLLKKGNYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLA   88 (132)
T ss_pred             hhcCccccHHHHHHHHHcCccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHH
Confidence            34578999999999999887888999999999999999999999999999999999999999999754

>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]

Probab=99.19  E-value=3.4e-11  Score=81.62  Aligned_cols=66  Identities=27%  Similarity=0.402  Sum_probs=60.1

Q ss_pred             CCCCCChHHHHHHhhc-CcCc-cccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           13 TRPEFPVGRVKKIIKL-DEDI-NKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        13 ~~~~lP~arVkrImK~-d~dv-~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      ..+.||.+.|.|++|. -|+. ..||+||..+|++++-.|+.+|+..|.++|..++||||+.+||.+|
T Consensus         7 ~dl~lP~AiI~rlvke~l~E~~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~a   74 (172)
T KOG0870|consen    7 EDLNLPNAIITRLVKEVLPESNVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKA   74 (172)
T ss_pred             HHhhccHHHHHHHHHHhCccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHH
Confidence            4578999999999995 4555 5899999999999999999999999999999999999999999765

>smart00803 TAF TATA box binding protein associated factor

Probab=99.15  E-value=1.6e-10  Score=67.65  Aligned_cols=62  Identities=18%  Similarity=0.264  Sum_probs=58.6

Q ss_pred             CCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           16 EFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        16 ~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      .||.+-|++|.+.. ++.++|.++...++..+|.|+..++..|..+++..+||||+.+||..|
T Consensus         2 ~~p~~~i~ria~~~-Gi~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~A   63 (65)
T smart00803        2 WLPKETIKDVAESL-GIGNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSA   63 (65)
T ss_pred             CCCHHHHHHHHHHC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHH
Confidence            58999999999987 667999999999999999999999999999999999999999999764

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.

>smart00414 H2A Histone 2A

Probab=99.15  E-value=1.7e-10  Score=73.36  Aligned_cols=68  Identities=21%  Similarity=0.350  Sum_probs=62.6

Q ss_pred             CCCCCCCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           11 ETTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        11 ~~~~~~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      ....++||++||.|.||..-...+|+..|+++++.++|++..++.+.|.+.+...+++.|+++||..|
T Consensus         4 ~ragL~fPVgRi~r~Lk~~~~~~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~k~~rItp~hi~lA   71 (106)
T smart00414        4 ARAGLQFPVGRIHRLLRKGTYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRITPRHLQLA   71 (106)
T ss_pred             ccCCccCchHHHHHHHHcCccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHHHhhh
Confidence            34578999999999999876677999999999999999999999999999999999999999999765

>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=99.07  E-value=2.5e-10  Score=67.11  Aligned_cols=66  Identities=30%  Similarity=0.378  Sum_probs=57.9

Q ss_pred             CCCCCChHHHHHHhhcCcCc-cccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           13 TRPEFPVGRVKKIIKLDEDI-NKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        13 ~~~~lP~arVkrImK~d~dv-~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      ..+.+|+.||.|-+..+-.. .++|++|+.++..++|.|+..+...|+.+|...||+||+++||..|
T Consensus         5 ~~~~~~~~r~~r~i~~~~~~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~kR~tI~~~DI~~A   71 (75)
T PF00125_consen    5 LIPKFPFSRLLREIGEEILSKYRISSEALVALQSVLEYLLVEILEEAGNLARHAKRKTITPRDIQLA   71 (75)
T ss_dssp             SSSHHHHHHHHHHHHHTTSSSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBSEEGHHHHHHH
T ss_pred             ccCceEEeeeeehhhcccccccccccccchhhhhhhhhhhhhhhhHHHHHHhhcCCcEecHHHHHHH
Confidence            35667888888888776554 3899999999999999999999999999999999999999999754

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 ....

>PTZ00017 histone H2A; Provisional

Probab=99.05  E-value=5.4e-10  Score=73.65  Aligned_cols=67  Identities=25%  Similarity=0.348  Sum_probs=61.8

Q ss_pred             CCCCCCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           12 TTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        12 ~~~~~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      ...++||++||.|.||..--..+|+..|+++++..+|++..++.+.|.+.+...+++.|+++||..|
T Consensus        23 ragL~FPVgRi~R~Lk~g~~a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lA   89 (134)
T PTZ00017         23 KAGLQFPVGRVHRYLKKGRYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLA   89 (134)
T ss_pred             cCCcccchHHHHHHHhccchhccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhh
Confidence            4478999999999999866667999999999999999999999999999999999999999999764

>PLN00154 histone H2A; Provisional

Probab=99.04  E-value=7.5e-10  Score=73.10  Aligned_cols=67  Identities=22%  Similarity=0.285  Sum_probs=61.4

Q ss_pred             CCCCCCChHHHHHHhhcCc-CccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           12 TTRPEFPVGRVKKIIKLDE-DINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        12 ~~~~~lP~arVkrImK~d~-dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      ...++||++||.|+||..- ...+|++.|+++++..+|++..++.+.|.+.|+..+++.|+++||..|
T Consensus        34 rAgL~FPVgRi~r~Lk~g~~~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lA  101 (136)
T PLN00154         34 RAGLQFPVGRIHRQLKQRVSAHGRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLA  101 (136)
T ss_pred             ccCccCchHHHHHHHHhhhhhccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhh
Confidence            3478999999999999864 456999999999999999999999999999999999999999999765

>smart00417 H4 Histone H4

Probab=98.99  E-value=2.4e-09  Score=64.35  Aligned_cols=62  Identities=11%  Similarity=0.165  Sum_probs=58.5

Q ss_pred             CCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           16 EFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        16 ~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      .+|.+-|+||.+.. ++.+||.++...+...+|.|++.++..|..++...+||||+..||.-|
T Consensus        13 gI~k~~IrRLaRr~-GvkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~a   74 (74)
T smart00417       13 GITKPAIRRLARRG-GVKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVYA   74 (74)
T ss_pred             CCCHHHHHHHHHHc-CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHheeC
Confidence            59999999999977 778999999999999999999999999999999999999999999654

>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=98.96  E-value=2.6e-09  Score=65.67  Aligned_cols=62  Identities=13%  Similarity=0.179  Sum_probs=58.3

Q ss_pred             CCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           16 EFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        16 ~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      .+|.+-|+||.+.. ++.+||.++...+..+++.|++.++..|..++...+||||+..||..|
T Consensus        13 gi~k~~I~RLarr~-GvkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~a   74 (85)
T cd00076          13 GITKPAIRRLARRG-GVKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYA   74 (85)
T ss_pred             cCCHHHHHHHHHHc-CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHH
Confidence            49999999999987 588999999999999999999999999999999999999999999643

>PLN00153 histone H2A; Provisional

Probab=98.95  E-value=2.6e-09  Score=70.07  Aligned_cols=67  Identities=21%  Similarity=0.322  Sum_probs=61.6

Q ss_pred             CCCCCCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           12 TTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        12 ~~~~~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      ...++||++||.|.||..--..+|+..|+++++..+|++..++.+.|.+.+...+++.|+++||..|
T Consensus        20 ragL~FpVgRi~R~Lr~g~~a~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lA   86 (129)
T PLN00153         20 KAGLQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIVPRHIQLA   86 (129)
T ss_pred             ccCcccchHHHHHHHhcCchhhccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHhh
Confidence            3478999999999999765667999999999999999999999999999999999999999999764

>PLN00156 histone H2AX; Provisional

Probab=98.94  E-value=3e-09  Score=70.48  Aligned_cols=67  Identities=24%  Similarity=0.343  Sum_probs=61.4

Q ss_pred             CCCCCCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           12 TTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        12 ~~~~~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      ...++||++||.|.|+..--..+|+..|+++++..+|+...++.+.|.+.+...+++.|+++||..|
T Consensus        25 rAgL~FPVgRi~R~Lk~g~ya~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~RItPrHi~lA   91 (139)
T PLN00156         25 KAGLQFPVGRIARFLKAGKYAERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLA   91 (139)
T ss_pred             ccCcccchHHHHHHHhcCChhhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHhh
Confidence            3478899999999999865667999999999999999999999999999999999999999999764

>PLN00157 histone H2A; Provisional

Probab=98.94  E-value=3e-09  Score=69.96  Aligned_cols=67  Identities=22%  Similarity=0.323  Sum_probs=61.6

Q ss_pred             CCCCCCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           12 TTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        12 ~~~~~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      ...++||++||.|.||..--..+|+..|+++++..+|++..++.+.|.+.+...+++.|+++||..|
T Consensus        22 ragL~FPVgRi~R~Lk~g~~a~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lA   88 (132)
T PLN00157         22 KAGLQFPVGRIARYLKAGKYATRVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKSRIVPRHIQLA   88 (132)
T ss_pred             ccCcccchHHHHHHHhcCchhhhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHhhc
Confidence            3478999999999999865557999999999999999999999999999999999999999999765

>PLN00035 histone H4; Provisional

Probab=98.92  E-value=3.9e-09  Score=66.92  Aligned_cols=62  Identities=11%  Similarity=0.183  Sum_probs=58.2

Q ss_pred             CCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           16 EFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        16 ~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      .||.+-|+||.+.- ++.+||.++...+..++|.|++.++..|..++...+||||+.+||..|
T Consensus        29 ~ipk~~IrRLARr~-GvkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~A   90 (103)
T PLN00035         29 GITKPAIRRLARRG-GVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYA   90 (103)
T ss_pred             cCCHHHHHHHHHHc-CcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHH
Confidence            49999999999977 588999999999999999999999999999999999999999999643

>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]

Probab=98.89  E-value=3.4e-09  Score=69.28  Aligned_cols=68  Identities=21%  Similarity=0.345  Sum_probs=62.6

Q ss_pred             CCCCCCCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           11 ETTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        11 ~~~~~~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      ....++||++||.|+||..--..+|+..|+++++..+|+...++++.|.+.|+.+++..|+++||..|
T Consensus        22 ~~agl~fPvgri~r~Lr~~~~~~ri~~gapV~laavLeYL~Aeile~agnaardnkk~ri~PrH~~lA   89 (131)
T KOG1756|consen   22 SRAGLQFPVGRIHRLLRKGRYAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRITPRHLQLA   89 (131)
T ss_pred             hhcccccCHHHHHHHHHccchhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccccChHHHHHH
Confidence            34578999999999999966777999999999999999999999999999999999999999999754

>PTZ00015 histone H4; Provisional

Probab=98.86  E-value=9e-09  Score=65.15  Aligned_cols=63  Identities=16%  Similarity=0.242  Sum_probs=58.8

Q ss_pred             CCCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           15 PEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        15 ~~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      ..+|.+-|+||.+.. ++.+||.++...+...+|.|++.++.+|..+|...+||||+.+||..|
T Consensus        29 ~gI~k~~IrRLarr~-GvkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~A   91 (102)
T PTZ00015         29 RGITKGAIRRLARRG-GVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYA   91 (102)
T ss_pred             cCCCHHHHHHHHHHc-CCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHH
Confidence            459999999999987 778999999999999999999999999999999999999999999643

>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]

Probab=98.84  E-value=8.7e-09  Score=68.95  Aligned_cols=64  Identities=23%  Similarity=0.314  Sum_probs=59.3

Q ss_pred             CCCCChHHHHHHhhc-Cc-CccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           14 RPEFPVGRVKKIIKL-DE-DINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        14 ~~~lP~arVkrImK~-d~-dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      ...||-+-|.+|+|. -| |+ +|.+||..+|-.||-.||..|+.+|.+.|....+|||.++||.+|
T Consensus        10 e~sLPkAtv~KmIke~lP~d~-rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KA   75 (156)
T KOG0871|consen   10 ELSLPKATVNKMIKEMLPKDV-RVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKA   75 (156)
T ss_pred             cccCcHHHHHHHHHHhCCccc-ccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHH
Confidence            578999999999995 55 64 899999999999999999999999999999999999999999765

>PTZ00252 histone H2A; Provisional

Probab=98.81  E-value=2e-08  Score=66.23  Aligned_cols=67  Identities=24%  Similarity=0.312  Sum_probs=60.3

Q ss_pred             CCCCCCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHh--CCCCccCchhhhcC
Q 038850           12 TTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIE--KKRKTIKLGDMRVA   78 (78)
Q Consensus        12 ~~~~~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~--~~rkti~~~Di~~A   78 (78)
                      .-.++||++||.|.|+..--..+|+..|+++++..+|+...++.+.|.+.|++  .+++.|+++||..|
T Consensus        21 rAGL~FPVgRi~R~Lr~g~ya~RIga~ApVYLAAVLEYLtaEVLELAgnaa~d~~~kk~RItPrHi~lA   89 (134)
T PTZ00252         21 KAGLIFPVGRVGSLLRRGQYARRIGASGAVYMAAVLEYLTAELLELSVKAAAQQAKKPKRLTPRTVTLA   89 (134)
T ss_pred             ccCccCchHHHHHHHHcCCcccccCCccHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccccHHHHHhh
Confidence            44689999999999997666679999999999999999999999999999975  68899999999764

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

Probab=98.57  E-value=3.2e-07  Score=54.36  Aligned_cols=60  Identities=13%  Similarity=0.291  Sum_probs=53.8

Q ss_pred             CChHHHHHHhhc-CcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhc
Q 038850           17 FPVGRVKKIIKL-DEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRV   77 (78)
Q Consensus        17 lP~arVkrImK~-d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~   77 (78)
                      ++-..+..++|. ||. .+++.+|..++...+|.|+..+++.|...|+..||+||..+||.-
T Consensus         2 ~~k~~l~~lv~~id~~-~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l   62 (72)
T cd07981           2 LTKRKLQELLKEIDPR-EQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQL   62 (72)
T ss_pred             CcHHHHHHHHHhhCCC-CCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHH
Confidence            456677888884 776 689999999999999999999999999999999999999999964

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

>smart00428 H3 Histone H3

Probab=98.49  E-value=5.7e-07  Score=57.20  Aligned_cols=66  Identities=27%  Similarity=0.325  Sum_probs=55.0

Q ss_pred             CCCCCCChHHH-HHHhhc-Cc--CccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           12 TTRPEFPVGRV-KKIIKL-DE--DINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        12 ~~~~~lP~arV-krImK~-d~--dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      ..-..+|.+|+ +.|+.. .+  + -+++.+|..++..|+|.|+..|.+.|+.+|...||.||..+||..|
T Consensus        28 lLI~k~pF~RLVREI~~~~~~~~~-~R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~kDi~La   97 (105)
T smart00428       28 LLIRKAPFQRLVREIAQKFTTGVD-LRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQLA   97 (105)
T ss_pred             cccccccHHHHHHHHHHHcCCCCC-ceeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHhhHHHH
Confidence            34467888885 455554 22  3 3899999999999999999999999999999999999999999743

>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=98.44  E-value=7.9e-07  Score=54.53  Aligned_cols=64  Identities=19%  Similarity=0.337  Sum_probs=57.3

Q ss_pred             CCCCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC---CccCchhhhcC
Q 038850           14 RPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKR---KTIKLGDMRVA   78 (78)
Q Consensus        14 ~~~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~r---kti~~~Di~~A   78 (78)
                      ...||-+.|||||..--+ ..++.+.+.+++..+.+|+.+|+++|.+...+.+.   .-|+++||..|
T Consensus        14 ra~f~k~~iKr~~~~~~~-~~v~~~v~i~v~glaKvFVGeivE~A~~V~~~~~~~~~~Pl~P~HireA   80 (85)
T cd08048          14 RSSFPKAAIKRLIQSVTG-QSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGEANTGPLQPRHLREA   80 (85)
T ss_pred             HhhccHHHHHHHHHHHcC-CCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCCcHHHHHH
Confidence            456999999999998766 68999999999999999999999999999987654   89999999875

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

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

Probab=98.17  E-value=5.1e-06  Score=54.76  Aligned_cols=66  Identities=24%  Similarity=0.235  Sum_probs=58.5

Q ss_pred             CCCCCChHHHHHHhhc-CcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           13 TRPEFPVGRVKKIIKL-DEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        13 ~~~~lP~arVkrImK~-d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      ....||-+.|.+++-. -|--..+.+||..++-.||-.||.-|+.+|.+.|.....|||.|.||-+|
T Consensus         8 De~sLPKATVqKMvS~iLp~dl~ftKearei~in~cieFi~~lsseAne~ce~EaKKTIa~EHviKA   74 (148)
T COG5150           8 DENSLPKATVQKMVSSILPKDLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKA   74 (148)
T ss_pred             ccccCcHHHHHHHHHHhccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHH
Confidence            3568999999999984 33334799999999999999999999999999999999999999999765

>KOG1757 consensus Histone 2A [Chromatin structure and dynamics]

Probab=98.14  E-value=4.2e-06  Score=54.12  Aligned_cols=67  Identities=22%  Similarity=0.293  Sum_probs=59.1

Q ss_pred             CCCCCCChHHHHHHhhcC-cCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           12 TTRPEFPVGRVKKIIKLD-EDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        12 ~~~~~lP~arVkrImK~d-~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      ....+||++||+|.+|.. ...++|++.+.+..+..+|+...+..+-|.+.++.-+-|.|+++|+..|
T Consensus        26 raGlqFpVgRihr~LK~r~t~h~rVGataavy~aaileYLTaEVLeLAgNasKdLKvKRitprHlqLA   93 (131)
T KOG1757|consen   26 RAGLQFPVGRIHRHLKTRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLA   93 (131)
T ss_pred             hcccccchHHHHHHHHHhcccccccchHHHHHHHHHHHHHHHHHHHHcccccccceeeeccchhheee
Confidence            346899999999999974 4556999999999999999999999999999999999999999998754

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

Probab=98.12  E-value=1.4e-05  Score=47.01  Aligned_cols=62  Identities=23%  Similarity=0.257  Sum_probs=48.9

Q ss_pred             CCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           16 EFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        16 ~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      .||..-||-|-.+- ++..++.|+...++.-+|+-+.++...|..+++.++|++|+.+||..|
T Consensus         3 ~~~~esvk~iAes~-Gi~~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~A   64 (66)
T PF02969_consen    3 VFSQESVKDIAESL-GISNLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDDINSA   64 (66)
T ss_dssp             ---HHHHHHHHHHT-T---B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHH
T ss_pred             cCCHHHHHHHHHHc-CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHH
Confidence            47778888887776 667899999999999999999999999999999999999999999765

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.

>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=97.99  E-value=2e-05  Score=58.27  Aligned_cols=60  Identities=22%  Similarity=0.301  Sum_probs=53.9

Q ss_pred             ChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           18 PVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        18 P~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      |..-||-|.++- ++.+++.||...++..+|.++..++++|..+++..||+||+.+||..|
T Consensus         1 ~~~~i~~ia~~~-Gi~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~A   60 (343)
T cd08050           1 PQESIKLIAESL-GIDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHA   60 (343)
T ss_pred             ChhHHHHHHHHc-CCCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHH
Confidence            445678888876 567999999999999999999999999999999999999999999765

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

>PLN00121 histone H3; Provisional

Probab=97.98  E-value=2.2e-05  Score=51.94  Aligned_cols=65  Identities=26%  Similarity=0.353  Sum_probs=54.4

Q ss_pred             CCCCCCChHHHHH-Hhhc-CcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhc
Q 038850           12 TTRPEFPVGRVKK-IIKL-DEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRV   77 (78)
Q Consensus        12 ~~~~~lP~arVkr-ImK~-d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~   77 (78)
                      ..-..+|..|+-| |... .++. +...+|+.++..|+|.|+-.|-+.++.+|...+|-||..+||.-
T Consensus        61 lLI~k~pF~RLVREI~~~~~~~~-Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L  127 (136)
T PLN00121         61 LLIRKLPFQRLVREIAQDFKTDL-RFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQL  127 (136)
T ss_pred             cccccccHHHHHHHHHHHhCccc-eeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhHHH
Confidence            3456788888544 4443 3444 89999999999999999999999999999999999999999864

>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=97.97  E-value=1.8e-05  Score=49.09  Aligned_cols=65  Identities=18%  Similarity=0.264  Sum_probs=47.3

Q ss_pred             CCCCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCC-CCccCchhhhcC
Q 038850           14 RPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKK-RKTIKLGDMRVA   78 (78)
Q Consensus        14 ~~~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~-rkti~~~Di~~A   78 (78)
                      ...||-+.|||||+.--+...|+.....+++-.+.+|+.+|.+.|.+...+.+ ..-|++.||.+|
T Consensus        21 Rs~~~k~~ikkli~~~~~~qsv~~~v~i~v~g~aKvFVGEiVE~A~~Vq~~~~~~~pl~P~hlreA   86 (90)
T PF04719_consen   21 RSSFNKAAIKKLINQVLGNQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGETGPLQPDHLREA   86 (90)
T ss_dssp             H----HHHHHHHHHHHHS-S---HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SS--HHHHHHH
T ss_pred             HccCCHHHHHHHHHHHcCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcHHHHHH
Confidence            45699999999999855545799999999999999999999999999988654 448999999765

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.

>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins

Probab=97.96  E-value=3.6e-05  Score=45.83  Aligned_cols=56  Identities=20%  Similarity=0.249  Sum_probs=49.6

Q ss_pred             HHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           22 VKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        22 VkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      |-+|++.. +...++.+|...++..++.|+..|++.+.++|...||++.+..||..|
T Consensus        12 Vaqil~~~-Gf~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~A   67 (77)
T smart00576       12 VAQILESA-GFDSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLA   67 (77)
T ss_pred             HHHHHHHc-CccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHH
Confidence            55677755 445899999999999999999999999999999999999999999754

subdomain of archael histone-like transcription factors

>PLN00160 histone H3; Provisional

Probab=97.95  E-value=2.8e-05  Score=48.88  Aligned_cols=65  Identities=26%  Similarity=0.281  Sum_probs=54.0

Q ss_pred             CCCCCChHHHHH-Hhhc-CcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhc
Q 038850           13 TRPEFPVGRVKK-IIKL-DEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRV   77 (78)
Q Consensus        13 ~~~~lP~arVkr-ImK~-d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~   77 (78)
                      .-.++|..|+-| |... .++.-+...+|..++..|+|.|+-.|-+.++.+|...||-||.++|+.-
T Consensus        21 LI~k~pF~RLVREI~~~~~~~~~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl~~kD~~L   87 (97)
T PLN00160         21 LIRRLPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIMPKDMQL   87 (97)
T ss_pred             hhccccHHHHHHHHHHHcCCCCcEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcccccchhhHHH
Confidence            346788888644 4432 2343589999999999999999999999999999999999999999864

>PTZ00018 histone H3; Provisional

Probab=97.95  E-value=2.7e-05  Score=51.54  Aligned_cols=65  Identities=26%  Similarity=0.353  Sum_probs=54.4

Q ss_pred             CCCCCCChHHHHH-Hhhc-CcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhc
Q 038850           12 TTRPEFPVGRVKK-IIKL-DEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRV   77 (78)
Q Consensus        12 ~~~~~lP~arVkr-ImK~-d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~   77 (78)
                      ..-..+|..|+-| |... .++. +...+|+.++..|+|.|+-.|-+.++.+|...+|-||..+||.-
T Consensus        61 lLI~k~pF~RLVREI~~~~~~~~-rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L  127 (136)
T PTZ00018         61 LLIRKLPFQRLVREIAQDFKTDL-RFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQL  127 (136)
T ss_pred             hccccccHHHHHHHHHHHcCCcc-eeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchhhHHH
Confidence            3346788888554 4443 4454 89999999999999999999999999999999999999999864

>PLN00161 histone H3; Provisional

Probab=97.90  E-value=4.6e-05  Score=50.40  Aligned_cols=67  Identities=33%  Similarity=0.340  Sum_probs=55.3

Q ss_pred             CCCCCCCChHHHH-HHhhc-CcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhc
Q 038850           11 ETTRPEFPVGRVK-KIIKL-DEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRV   77 (78)
Q Consensus        11 ~~~~~~lP~arVk-rImK~-d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~   77 (78)
                      +..-..+|.+|+- .|+.. .++.-++..+|+.++..|+|.|+-.|-+.++.+|...+|-||..+||..
T Consensus        53 ~lLIpklPF~RLVREI~~~~~~~~~Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kDm~L  121 (135)
T PLN00161         53 ELLIRKLPFARLVREISNEMLREPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQL  121 (135)
T ss_pred             ccccccccHHHHHHHHHHhcCCCCcEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhhHHH
Confidence            3345788988864 45443 2333489999999999999999999999999999999999999999864

>PF15510 CENP-W: Centromere kinetochore component W

Probab=97.89  E-value=1.6e-05  Score=49.79  Aligned_cols=65  Identities=26%  Similarity=0.314  Sum_probs=56.6

Q ss_pred             CCCCChHHHHHHhhcCcCccccchHHHHH--------------HHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           14 RPEFPVGRVKKIIKLDEDINKVTSEALFI--------------VSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        14 ~~~lP~arVkrImK~d~dv~~vs~eA~~~--------------i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      ...-|.+.+||++|.....-++...+..+              +...|-+|+..|+++|-..|-+++-.+|+.+||.+|
T Consensus        14 krkaPrgfLkrv~Kr~KphlRl~~~~Dllv~~~~f~~~~~~~~vhLncLLFvhrLAEEaRtnA~EnK~~~Ik~~Hv~Aa   92 (102)
T PF15510_consen   14 KRKAPRGFLKRVFKRQKPHLRLETSGDLLVRFCPFSGWQWGGEVHLNCLLFVHRLAEEARTNACENKCGTIKKEHVLAA   92 (102)
T ss_pred             HHhCchHHHHHHHHhcCCceeecccccHHHhhcccccccccceeehhHHHHHHHHHHHHHHHHHHHhhccccHHHHHHH
Confidence            34679999999999655555788888777              888999999999999999999999999999999764

>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=97.75  E-value=0.00011  Score=47.24  Aligned_cols=58  Identities=10%  Similarity=0.098  Sum_probs=52.5

Q ss_pred             HHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           20 GRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        20 arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      .-|.+|+|.- ++..++.+++..+..-++-++..+...|..+|+..||+||+.+||.-|
T Consensus         5 ~~v~~iLk~~-Gv~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lA   62 (117)
T cd07979           5 RVIAAILKSM-GITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLA   62 (117)
T ss_pred             HHHHHHHHHC-CCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHH
Confidence            3578899876 567899999999999999999999999999999999999999999754

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=97.72  E-value=7.2e-05  Score=56.70  Aligned_cols=61  Identities=28%  Similarity=0.371  Sum_probs=45.8

Q ss_pred             CCCCChHHHHHHhhcC-----cCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchh
Q 038850           14 RPEFPVGRVKKIIKLD-----EDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGD   74 (78)
Q Consensus        14 ~~~lP~arVkrImK~d-----~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~D   74 (78)
                      -..||.+-||++...-     -.-.+|+++|+.+|.+|++-|-+.|+..=--+|.+.|||||...|
T Consensus       349 ~P~lP~~~vK~la~~~ak~s~~sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIdesD  414 (414)
T PF15511_consen  349 YPSLPPGVVKKLAQHFAKSSGGSKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDESD  414 (414)
T ss_dssp             ---S-HHHHHHHHHHHH-------S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHH
T ss_pred             CCCCCccHHHHHHHHHHHhhcccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCCCC
Confidence            4669999999987642     233589999999999999999999999999999999999998776

>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=97.57  E-value=0.00025  Score=42.26  Aligned_cols=60  Identities=17%  Similarity=0.332  Sum_probs=48.9

Q ss_pred             ChHHHHHHhhc--CcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCc-cCchhhhc
Q 038850           18 PVGRVKKIIKL--DEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKT-IKLGDMRV   77 (78)
Q Consensus        18 P~arVkrImK~--d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkt-i~~~Di~~   77 (78)
                      |..-|.||++.  ..+-.+|+++|..++++=.++|+.+-...|...++..|... |..+||.+
T Consensus         1 p~~li~rll~~~f~~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LEk   63 (72)
T PF09415_consen    1 PPELIARLLHEHFKDDKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLEK   63 (72)
T ss_dssp             -CHHHHHHHCTTSSSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHHH
T ss_pred             ChHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHH
Confidence            66778999996  23556899999999999999999999999999999999888 99999864

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.

>smart00427 H2B Histone H2B

Probab=97.53  E-value=0.00036  Score=43.24  Aligned_cols=57  Identities=19%  Similarity=0.302  Sum_probs=50.3

Q ss_pred             HHHHHhh-cCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           21 RVKKIIK-LDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        21 rVkrImK-~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      -|.|++| .+||. .+|..|...+.--.-.+.+.++.+|...+..++|+||+.++|..|
T Consensus         6 Yi~kvLKqVhpd~-giS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtA   63 (89)
T smart00427        6 YIYKVLKQVHPDT-GISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTA   63 (89)
T ss_pred             HHHHHHHHhCCCc-cccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHH
Confidence            4788888 58997 599999998988888888999999999999999999999999764

>KOG1658 consensus DNA polymerase epsilon, subunit C [Replication, recombination and repair]

Probab=97.34  E-value=0.00026  Score=47.91  Aligned_cols=49  Identities=27%  Similarity=0.429  Sum_probs=44.5

Q ss_pred             hcCCCCCCCCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHH
Q 038850            8 QNTETTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAE   56 (78)
Q Consensus         8 e~~~~~~~~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~   56 (78)
                      +........||++++++|-|.+|....-+.+|....+.++|.|++.|+.
T Consensus         3 ~~~~e~~p~~p~ekvkkiak~dPey~~te~~a~~etafatE~fvq~lv~   51 (162)
T KOG1658|consen    3 ASAPECSPKLPMEKVKKIAKNDPEYMDTEDDAFVETAFATEQFVQVLVH   51 (162)
T ss_pred             ccchhhCccccHHHHHHhhcCCchhhhcccchHHHHHHHHHHHHhhhhh
Confidence            3456678899999999999999999888889999999999999999998

>PLN00158 histone H2B; Provisional

Probab=97.24  E-value=0.0013  Score=42.56  Aligned_cols=59  Identities=19%  Similarity=0.255  Sum_probs=51.4

Q ss_pred             hHHHHHHhh-cCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           19 VGRVKKIIK-LDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        19 ~arVkrImK-~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      -.-|.|++| .+||.+ ||..|..++.--...+.+.++.+|...+..++|+||+.++|..|
T Consensus        30 ~~YI~kVLKQVhPd~g-IS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtA   89 (116)
T PLN00158         30 KIYIYKVLKQVHPDTG-ISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTA   89 (116)
T ss_pred             HHHHHHHHHHhCCCCC-ccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHH
Confidence            345888888 489975 89999988888888888899999999999999999999999865

>PTZ00463 histone H2B; Provisional

Probab=97.22  E-value=0.0016  Score=42.23  Aligned_cols=57  Identities=14%  Similarity=0.229  Sum_probs=50.0

Q ss_pred             HHHHHhh-cCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           21 RVKKIIK-LDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        21 rVkrImK-~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      -|.|++| .+||.+ ||..|..++.--.....+.++.+|...+...+|.||+.++|..|
T Consensus        33 YI~KVLKqVhPd~g-IS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~TltsrEIQtA   90 (117)
T PTZ00463         33 YIFKVLKQVHPDTG-ISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTA   90 (117)
T ss_pred             HHHHHHHhhCCCCC-ccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHH
Confidence            3888888 499975 89999988888778888899999999999999999999999865

>KOG1745 consensus Histones H3 and H4 [Chromatin structure and dynamics]

Probab=97.15  E-value=0.00069  Score=44.96  Aligned_cols=64  Identities=27%  Similarity=0.286  Sum_probs=56.2

Q ss_pred             CCCChHHHHH-HhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           15 PEFPVGRVKK-IIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        15 ~~lP~arVkr-ImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      ..+|..|+-| |++.-...-+..+.|..++..|.|.|+-.|-+.++-+|-..||-||-++||.-|
T Consensus        65 ~K~PFqRlvrei~q~f~~dLrfqs~Ai~ALQeA~EayLv~LfEdtnlcAihAkRVTimpkdiQlA  129 (137)
T KOG1745|consen   65 RKLPFQRLVREIAQDFKTDLRFQSSAIAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLA  129 (137)
T ss_pred             hcCcHHHHhHHHHhcccccceehHHHHHHHHHHHHHHHHHhccccchhhhccceeEecccceehh
Confidence            4788888877 888643345899999999999999999999999999999999999999999754

>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=97.12  E-value=0.00078  Score=41.67  Aligned_cols=55  Identities=18%  Similarity=0.264  Sum_probs=34.2

Q ss_pred             HHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhh
Q 038850           22 VKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMR   76 (78)
Q Consensus        22 VkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~   76 (78)
                      |+.+|-.-.|+..-..|.+.++-..+-.|+..|+..|...|...|+++|+.+|+.
T Consensus         7 I~~mMy~fGD~~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~   61 (93)
T PF02269_consen    7 IRQMMYGFGDVEEPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLL   61 (93)
T ss_dssp             CHHHHHCTTS-SS--HHHHHHHHHHHHHHHHHHHHHHHC----------------
T ss_pred             HHHHHHHcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHH
Confidence            6788999899999999999999999999999999999999999999999999984

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

>KOG3219 consensus Transcription initiation factor TFIID, subunit TAF11 [Transcription]

Probab=97.11  E-value=0.00038  Score=48.53  Aligned_cols=65  Identities=17%  Similarity=0.286  Sum_probs=55.9

Q ss_pred             CCCCCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhC-CCCccCchhhhcC
Q 038850           13 TRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEK-KRKTIKLGDMRVA   78 (78)
Q Consensus        13 ~~~~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~-~rkti~~~Di~~A   78 (78)
                      +...||-+.|||+|..=.+-. |+..+.++++--+.+|+.++.+.|...+... ...-|++.||..|
T Consensus       109 Rrs~f~Ka~iKkL~~~itg~~-v~~nv~Ia~~GiaKvFVGEvVEeAl~V~~~~~e~~PLqP~HIREA  174 (195)
T KOG3219|consen  109 RRSAFPKAQIKKLMSSITGQS-VSENVAIAMAGIAKVFVGEVVEEALDVREEWGESGPLQPKHIREA  174 (195)
T ss_pred             HHhcCCHHHHHHHHHHHhCCc-cCcceeeeecchhhHhHHHHHHHHHHHHHHhccCCCCCcHHHHHH
Confidence            467899999999999765544 9999999999999999999999999998754 4667999999765

>PLN00155 histone H2A; Provisional

Probab=96.97  E-value=0.001  Score=38.25  Aligned_cols=38  Identities=21%  Similarity=0.385  Sum_probs=33.2

Q ss_pred             CCCCCCChHHHHHHhhcCcCccccchHHHHHHHHHHHH
Q 038850           12 TTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTEL   49 (78)
Q Consensus        12 ~~~~~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~El   49 (78)
                      ...++||++||.|.++..--..+|+..|++.++..+|+
T Consensus        20 rAgL~FPVgri~r~Lr~g~~a~Rvga~apVYlAAVLEY   57 (58)
T PLN00155         20 KAGLQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEY   57 (58)
T ss_pred             ccccccchHHHHHHHhcCChhhcccCCcHHHHHHHHHh
Confidence            34789999999999998766679999999999998875

>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=96.96  E-value=0.0058  Score=35.94  Aligned_cols=56  Identities=14%  Similarity=0.285  Sum_probs=44.2

Q ss_pred             HHHHHHhhc-CcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhh
Q 038850           20 GRVKKIIKL-DEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMR   76 (78)
Q Consensus        20 arVkrImK~-d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~   76 (78)
                      .++..+++. ||. ..+..++-.++...++-||..++..|...|+..|..||..+||.
T Consensus         3 ~~l~~Lv~~iDp~-~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~tle~~Dv~   59 (68)
T PF03847_consen    3 RKLQELVKQIDPN-EKLDPDVEELLLELADDFVDDVVSFACRLAKHRKSSTLEVKDVQ   59 (68)
T ss_dssp             HHHHHHHHCC-SS-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHH
T ss_pred             HHHHHHHHHcCCC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHH
Confidence            356677774 777 47999999999999999999999999999999999999999985

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

>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]

Probab=96.53  E-value=0.0082  Score=39.40  Aligned_cols=56  Identities=23%  Similarity=0.342  Sum_probs=45.3

Q ss_pred             HHHHhh-cCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           22 VKKIIK-LDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        22 VkrImK-~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      |.|++| .+||.+ ++.++.-++.--.-.|.+.++.+|...|...||.||+.++|..|
T Consensus        43 v~kvlk~Vhpd~g-is~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta   99 (127)
T KOG1744|consen   43 VYKVLKQVHPDLG-ISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTA   99 (127)
T ss_pred             hhhhhhcccCCCC-cCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHH
Confidence            344777 588866 77777777766666678999999999999999999999998753

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

Probab=96.52  E-value=0.018  Score=34.60  Aligned_cols=55  Identities=24%  Similarity=0.239  Sum_probs=42.9

Q ss_pred             HHHHhhcC--cCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhh
Q 038850           22 VKKIIKLD--EDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMR   76 (78)
Q Consensus        22 VkrImK~d--~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~   76 (78)
                      |-+|.+.-  +.-..+|+....+++..+=.++..++..=..+|+..||+||+.+||.
T Consensus        11 v~ki~ee~~~~~~~~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~   67 (76)
T PF15630_consen   11 VGKIVEEEAKEKGVEVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVK   67 (76)
T ss_dssp             HHHHHHHCCCCTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHH
T ss_pred             HHHHHHHHHhccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHH
Confidence            44555542  23347999999999999999999999999999999999999999985

>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=96.44  E-value=0.019  Score=35.56  Aligned_cols=56  Identities=18%  Similarity=0.268  Sum_probs=49.5

Q ss_pred             HHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhh
Q 038850           20 GRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMR   76 (78)
Q Consensus        20 arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~   76 (78)
                      .-|+.+|-.-.|+..-..|.+.++-..+--|+..|+..|.+.|. .++..++.+|+.
T Consensus         6 ~ei~~mmy~~GD~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~-~r~~k~~~eD~~   61 (92)
T cd07978           6 KEIRQMMYGFGDVQNPLPETVDLLEDIVVEYIIELCHKAAEVAQ-RRRGKVKVEDLI   61 (92)
T ss_pred             HHHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCCCCHHHHH
Confidence            45889999999999999999999999999999999999999999 555556999874

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

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

Probab=96.31  E-value=0.022  Score=33.45  Aligned_cols=56  Identities=21%  Similarity=0.248  Sum_probs=47.0

Q ss_pred             HHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           22 VKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        22 VkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      |-+|++.. +-..+++.|+..++-.+..|++.|...+..+|...+|......||..|
T Consensus        12 va~il~~~-GF~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~a   67 (77)
T PF07524_consen   12 VAQILKHA-GFDSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQA   67 (77)
T ss_pred             HHHHHHHc-CccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHH
Confidence            34455443 344799999999999999999999999999999999999999998653

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 [, ].

>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]

Probab=95.83  E-value=0.036  Score=34.59  Aligned_cols=55  Identities=13%  Similarity=0.213  Sum_probs=48.3

Q ss_pred             HHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhh
Q 038850           21 RVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMR   76 (78)
Q Consensus        21 rVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~   76 (78)
                      -|+||-+.. .|.+|+.--..-+..+...|++....-|..++...+||||+..||.
T Consensus        34 aIRRlARr~-GVkRi~G~~yeE~~~~~k~fl~n~i~~A~~yt~HAKRKTvT~~dvv   88 (103)
T KOG3467|consen   34 AIRRLARRG-GVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVV   88 (103)
T ss_pred             HHHHHHHhc-CcchhchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhceeeHHHHH
Confidence            467776654 7788998888889999999999999999999999999999999874

>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]

Probab=95.04  E-value=0.073  Score=42.31  Aligned_cols=59  Identities=19%  Similarity=0.305  Sum_probs=51.6

Q ss_pred             hHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           19 VGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        19 ~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      .--+|-+.++- ++.+++.|+..+++.-.|+=+.+++..|.+++...+|.+++.+||..|
T Consensus        14 ~Es~k~vAEsl-Gi~nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~A   72 (576)
T KOG2549|consen   14 KESVKVVAESL-GITNLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYA   72 (576)
T ss_pred             HHHHHHHHHHh-CccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHH
Confidence            55556665554 677899999999999999999999999999999999999999999754

>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]

Probab=94.39  E-value=0.21  Score=36.33  Aligned_cols=62  Identities=15%  Similarity=0.318  Sum_probs=52.5

Q ss_pred             CCCCChHHHHHHhhc-CcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhh
Q 038850           14 RPEFPVGRVKKIIKL-DEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMR   76 (78)
Q Consensus        14 ~~~lP~arVkrImK~-d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~   76 (78)
                      ..-+-..++..+++. |++ ..+-.|+-.++...++-||..++..|-..|+..+..||-.+||.
T Consensus       152 ~~il~k~kl~dLvqqId~~-~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIq  214 (258)
T KOG1142|consen  152 NPILSKRKLDDLVQQIDGT-TKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQ  214 (258)
T ss_pred             CccccccchhHHHHhhcCc-ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhhee
Confidence            344445567777774 544 57999999999999999999999999999999999999999986

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

Probab=93.91  E-value=0.59  Score=26.14  Aligned_cols=48  Identities=10%  Similarity=0.100  Sum_probs=35.7

Q ss_pred             CCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 038850           16 EFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIE   64 (78)
Q Consensus        16 ~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~   64 (78)
                      .+|=+-+.-+|+.. +...--.-..-+++.|++-|+.+++..|+++++.
T Consensus         2 ~IPD~v~~~yL~~~-G~~~~D~rv~RLvSLaaQKFisdI~~dA~q~~k~   49 (51)
T PF03540_consen    2 TIPDEVTDYYLERS-GFQTSDPRVKRLVSLAAQKFISDIANDAMQYCKI   49 (51)
T ss_pred             CCCHHHHHHHHHHC-CCCCCCHhHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            35666677777754 2223344567799999999999999999999874

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

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

Probab=93.47  E-value=0.18  Score=35.96  Aligned_cols=45  Identities=31%  Similarity=0.341  Sum_probs=32.1

Q ss_pred             HHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Q 038850           20 GRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEK   65 (78)
Q Consensus        20 arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~   65 (78)
                      .+|.+|++... +..+..|.+.+|+.|||..+..|...+...++..
T Consensus        51 ~~i~~i~~~~g-~~~~~~d~l~llS~A~e~rLr~lie~~~~~s~hR   95 (264)
T PF05236_consen   51 KRIQKIAKKHG-LKSVDEDVLELLSLATEERLRNLIEKAIVLSRHR   95 (264)
T ss_dssp             HHHHHHHHCTT---EE-TCHHHHHHHHHHHHHHHHHHHHH------
T ss_pred             HHHHHHHHHcC-CcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            46777777665 5689999999999999999999999999998753

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

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

Probab=93.35  E-value=0.13  Score=38.95  Aligned_cols=58  Identities=16%  Similarity=0.289  Sum_probs=49.9

Q ss_pred             HHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           20 GRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        20 arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      ..||.+-.+- ++.++..|+.-+++.-.|+=|.+++++|..+....+|..++.+||..|
T Consensus         9 et~KdvAesl-Gi~Ni~Dd~l~alamDlEYRI~ev~qea~KFmvhSKRtvLt~dDis~A   66 (450)
T COG5095           9 ETLKDVAESL-GISNIDDDALRALAMDLEYRIKEVCQEASKFMVHSKRTVLTIDDISYA   66 (450)
T ss_pred             HHHHHHHHHc-CCcccccHHHHHHHHhHHHHHHHHHHHHHHHhhcccceeeeHHhHHHH
Confidence            3445444443 677899999999999999999999999999999999999999999865

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

Probab=93.25  E-value=0.47  Score=32.68  Aligned_cols=69  Identities=14%  Similarity=0.225  Sum_probs=52.2

Q ss_pred             cCCCCCCCCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCC--------------CCccCchh
Q 038850            9 NTETTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKK--------------RKTIKLGD   74 (78)
Q Consensus         9 ~~~~~~~~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~--------------rkti~~~D   74 (78)
                      .-......+|=+-+--.|+.. ++...-.-..-+|+.|+.-||.+++..|+++++-++              +-|++.+|
T Consensus        79 qLddYtP~IPDavt~~yL~~a-Gf~~~D~rv~RLvsLaAQKfvSDIa~DA~Q~~k~r~~~~~~~~k~~~kdkK~tLtmeD  157 (176)
T KOG3423|consen   79 QLDDYTPTIPDAVTDHYLKKA-GFQTSDPRVKRLVSLAAQKFVSDIANDALQHSKIRTKTAIGKDKKQAKDKKYTLTMED  157 (176)
T ss_pred             HHhcCCCCCcHHHHHHHHHhc-CCCcCcHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccccccccceeeeHHH
Confidence            445667788888888888876 333455567789999999999999999999998543              44677777


Q ss_pred             hhcC
Q 038850           75 MRVA   78 (78)
Q Consensus        75 i~~A   78 (78)
                      |..|
T Consensus       158 L~~A  161 (176)
T KOG3423|consen  158 LSPA  161 (176)
T ss_pred             HHHH
Confidence            6543

>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=91.27  E-value=0.94  Score=31.34  Aligned_cols=50  Identities=26%  Similarity=0.243  Sum_probs=38.5

Q ss_pred             CCCChHHHHH----HhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Q 038850           15 PEFPVGRVKK----IIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEK   65 (78)
Q Consensus        15 ~~lP~arVkr----ImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~   65 (78)
                      ..|....+.+    |++.. ++..++.+...+|+.|||.++..|.......+...
T Consensus        43 ~fl~~~~l~~~~~~i~~~~-g~~~~~~d~~~lis~a~e~rlr~li~k~~~~s~hR   96 (212)
T cd08045          43 SFLNPSPLAKKIRKIAKKH-GLKEVDEDVLDLISLALEERLRNLLEKLIEVSEHR   96 (212)
T ss_pred             hccCHHHHHHHHHHHHHHc-CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            4555555544    44443 34479999999999999999999999999998754

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

>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=90.58  E-value=1.2  Score=29.22  Aligned_cols=57  Identities=18%  Similarity=0.136  Sum_probs=38.0

Q ss_pred             HHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           21 RVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        21 rVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      -|..|+|.- +|......++.-+-.-+=-++..+...|..++...+|++|..+||..|
T Consensus        17 ~i~~iL~~~-Gv~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLA   73 (129)
T PF02291_consen   17 VIHLILKSM-GVTEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLA   73 (129)
T ss_dssp             HHHHHHHHT-T---B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHH
T ss_pred             HHHHHHHHc-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHH
Confidence            456666665 555555555555544445678889999999999999999999999754

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

>PF10979 DUF2786: Protein of unknown function (DUF2786); InterPro: IPR024498 This domain is found in proteins that have no known function

Probab=85.03  E-value=2.3  Score=22.70  Aligned_cols=35  Identities=17%  Similarity=0.406  Sum_probs=27.6

Q ss_pred             hHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHH
Q 038850           19 VGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRF   53 (78)
Q Consensus        19 ~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~   53 (78)
                      +.||++++..-.+.+.-..||-.++.+|-++..+|
T Consensus         4 l~kI~kLLalA~~~~~~~~EA~~A~~kAq~Lm~ky   38 (43)
T PF10979_consen    4 LEKIRKLLALAESTGSNEHEAEAALAKAQRLMAKY   38 (43)
T ss_pred             HHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHHHHh
Confidence            57999999987665444559999999999887665

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

Probab=80.21  E-value=5.4  Score=28.19  Aligned_cols=31  Identities=13%  Similarity=0.253  Sum_probs=27.3

Q ss_pred             CccccchHHHHHHHHHHHHHHHHHHHHHHHH
Q 038850           31 DINKVTSEALFIVSRSTELFLRFLAEKSAEA   61 (78)
Q Consensus        31 dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~   61 (78)
                      +...|+.+++.++..|+|.|+..|...+...
T Consensus       220 GL~gvs~~~a~ll~~ale~~LK~lI~s~l~~  250 (252)
T PF12767_consen  220 GLGGVSDDCANLLNLALEVHLKNLIKSCLDL  250 (252)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            4457999999999999999999999988764

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	78
1jfi_A	98	Crystal Structure Of The Nc2-Tbp-Dna Ternary Comple		7e-05
1n1j_B	97	Crystal Structure Of The Nf-YbNF-Yc Histone Pair Le		5e-04
4awl_C	94	The Nf-y Transcription Factor Is Structurally And F		5e-04

>pdb|1JFI|A Chain A, Crystal Structure Of The Nc2-Tbp-Dna Ternary Complex Length = 98

Iteration: 1
 Score = 42.4 bits (98), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 22/54 (40%), Positives = 32/54 (59%), Gaps = 5/54 (9%)
Query: 1  MPQEAEEQNTETTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFL 54
          MP + ++ N       FP  R+KKI++ DE+I KV +    I+SR+ ELFL  L
Sbjct: 1  MPSKKKKYNAR-----FPPARIKKIMQTDEEIGKVAAAVPVIISRALELFLESL 49

>pdb|1N1J|B Chain B, Crystal Structure Of The Nf-YbNF-Yc Histone Pair Length = 97

Iteration: 1
 Score = 39.3 bits (90), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 14/36 (38%), Positives = 28/36 (77%)
Query: 16 EFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFL 51
          E P+ R+KKI+KLDED+  +++EA  + +++ ++F+
Sbjct: 19 ELPLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFI 54

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

Iteration: 1
 Score = 39.3 bits (90), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 14/36 (38%), Positives = 28/36 (77%)
Query: 16 EFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFL 51
          E P+ R+KKI+KLDED+  +++EA  + +++ ++F+
Sbjct: 16 ELPLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFI 51

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	78
1jfi_A	98	Transcription regulator NC2 alpha chain; histone,	4e-16
1n1j_B	97	NF-YC; histone-like PAIR, DNA binding protein; 1.6	3e-15
2byk_A	140	Chrac-16; nucleosome sliding, histone fold, DNA-bi	5e-13
1n1j_A	93	NF-YB; histone-like PAIR, DNA binding protein; 1.6	1e-05
2byk_B	128	Chrac-14; nucleosome sliding, histone fold, DNA-bi	8e-05
1ku5_A	70	HPHA, archaeal histon; histone fold, DNA binding p	1e-04
1b67_A	68	Protein (histone HMFA); DNA binding protein; 1.48A	3e-04
1jfi_B	179	DR1 protein, transcription regulator NC2 beta chai	6e-04

>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 = 65.7 bits (160), Expect = 4e-16
 Identities = 25/78 (32%), Positives = 42/78 (53%), Gaps = 5/78 (6%)

Query: 1  MPQEAEEQNTETTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAE 60
          MP + ++ N       FP  R+KKI++ DE+I KV +    I+SR+ ELFL  L +K+ +
Sbjct: 1  MPSKKKKYNAR-----FPPARIKKIMQTDEEIGKVAAAVPVIISRALELFLESLLKKACQ 55

Query: 61 AAIEKKRKTIKLGDMRVA 78
              +  KT+    ++  
Sbjct: 56 VTQSRNAKTMTTSHLKQC 73

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

 Score = 63.4 bits (154), Expect = 3e-15
 Identities = 22/77 (28%), Positives = 46/77 (59%), Gaps = 1/77 (1%)

Query: 3  QEAEEQNTETTR-PEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEA 61
          +E      +  R  E P+ R+KKI+KLDED+  +++EA  + +++ ++F+  L  ++   
Sbjct: 5  EEIRNLTVKDFRVQELPLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIH 64

Query: 62 AIEKKRKTIKLGDMRVA 78
            + KR+T++  D+ +A
Sbjct: 65 TEDNKRRTLQRNDIAMA 81

>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 = 58.6 bits (141), Expect = 5e-13
 Identities = 20/76 (26%), Positives = 38/76 (50%), Gaps = 1/76 (1%)

Query: 4  EAEEQNTETTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSA-EAA 62
          +   +   T     P+ RV+ I+K   D   +T+E LF++++ TELF+R LA  +  E  
Sbjct: 7  QPPVERPPTAETFLPLSRVRTIMKSSMDTGLITNEVLFLMTKCTELFVRHLAGAAYTEEF 66

Query: 63 IEKKRKTIKLGDMRVA 78
           ++  + +K   +   
Sbjct: 67 GQRPGEALKYEHLSQV 82

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

 Score = 38.7 bits (90), Expect = 1e-05
 Identities = 17/63 (26%), Positives = 30/63 (47%), Gaps = 1/63 (1%)

Query: 17 FPVGRVKKIIKLD-EDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDM 75
           P+  V +I+K       K+  +A   V      F+ F+  +++E   ++KRKTI   D+
Sbjct: 9  LPIANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDI 68

Query: 76 RVA 78
            A
Sbjct: 69 LFA 71

>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 = 37.3 bits (86), Expect = 8e-05
 Identities = 17/65 (26%), Positives = 29/65 (44%), Gaps = 3/65 (4%)

Query: 16 EFPVGRVKKIIK--LDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLG 73
            P   + ++IK  L E    V+ EA   ++R+  +F  F+   S   A ++  KTI   
Sbjct: 9  NLPNAVIGRLIKEALPESA-SVSKEARAAIARAASVFAIFVTSSSTALAHKQNHKTITAK 67

Query: 74 DMRVA 78
          D+   
Sbjct: 68 DILQT 72

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

 Score = 35.4 bits (82), Expect = 1e-04
 Identities = 17/64 (26%), Positives = 36/64 (56%), Gaps = 1/64 (1%)

Query: 15 PEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGD 74
           E P+  V ++I+      +V+ +A  +++   E +   +A+K+ E A    RKT+K+ D
Sbjct: 5  GELPIAPVDRLIR-KAGAERVSEQAAKVLAEYLEEYAIEIAKKAVEFARHAGRKTVKVED 63

Query: 75 MRVA 78
          +++A
Sbjct: 64 IKLA 67

>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 = 34.6 bits (80), Expect = 3e-04
 Identities = 17/63 (26%), Positives = 32/63 (50%), Gaps = 1/63 (1%)

Query: 16 EFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDM 75
          E P+  + +IIK      +V+ +A   +++  E     +A ++ + A    RKTIK  D+
Sbjct: 2  ELPIAPIGRIIKNAGA-ERVSDDARIALAKVLEEMGEEIASEAVKLAKHAGRKTIKAEDI 60

Query: 76 RVA 78
           +A
Sbjct: 61 ELA 63

>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 = 35.2 bits (80), Expect = 6e-04
 Identities = 13/63 (20%), Positives = 28/63 (44%)

Query: 16 EFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDM 75
            P   + K+IK      +V ++A  +V      F+  ++ ++ E   + ++KTI    +
Sbjct: 15 TIPRAAINKMIKETLPNVRVANDARELVVNCCTEFIHLISSEANEICNKSEKKTISPEHV 74

Query: 76 RVA 78
            A
Sbjct: 75 IQA 77

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	78
4g92_C	119	HAPE; transcription factor, nucleosome, minor groo	99.93
1n1j_B	97	NF-YC; histone-like PAIR, DNA binding protein; 1.6	99.92
1jfi_A	98	Transcription regulator NC2 alpha chain; histone,	99.91
2byk_A	140	Chrac-16; nucleosome sliding, histone fold, DNA-bi	99.91
2byk_B	128	Chrac-14; nucleosome sliding, histone fold, DNA-bi	99.85
1n1j_A	93	NF-YB; histone-like PAIR, DNA binding protein; 1.6	99.84
3b0c_W	76	CENP-W, centromere protein W; histone fold, DNA bi	99.79
1b67_A	68	Protein (histone HMFA); DNA binding protein; 1.48A	99.76
1jfi_B	179	DR1 protein, transcription regulator NC2 beta chai	99.66
1ku5_A	70	HPHA, archaeal histon; histone fold, DNA binding p	99.51
1f1e_A	154	Histone fold protein; archaeal histone protein, DN	99.49
2nqb_C	123	Histone H2A; nucleosome, NCP, chromatin, structura	99.47
1id3_C	131	Histone H2A.1; nucleosome core particle, chromatin	99.47
1tzy_A	129	Histone H2A-IV; histone-fold, tetramer-dimer-dimer	99.46
2f8n_G	120	Core histone macro-H2A.1; nucleosome, NCP, macroh2	99.45
1f1e_A	154	Histone fold protein; archaeal histone protein, DN	99.43
1f66_C	128	Histone H2A.Z; nucleosome, chromatin, histone vari	99.42
2f8n_K	149	Histone H2A type 1; nucleosome, NCP, macroh2A, his	99.42
1tzy_D	103	Histone H4-VI; histone-fold, tetramer-dimer-dimer,	99.31
2yfw_B	103	Histone H4, H4; cell cycle, kinetochore, centromer	99.31
2hue_C	84	Histone H4; mini beta sheet, elongated beta sandwh	99.27
2jss_A	192	Chimera of histone H2B.1 and histone H2A.Z; histon	99.26
3b0c_T	111	CENP-T, centromere protein T; histone fold, DNA bi	99.25
1id3_B	102	Histone H4; nucleosome core particle, chromatin, p	99.24
1taf_B	70	TFIID TBP associated factor 62; transcription init	99.11
2hue_B	77	Histone H3; mini beta sheet, elongated beta sandwh	98.77
2yfv_A	100	Histone H3-like centromeric protein CSE4; cell cyc	98.52
3nqj_A	82	Histone H3-like centromeric protein A; alpha helix	98.52
1taf_A	68	TFIID TBP associated factor 42; transcription init	98.34
1tzy_C	136	Histone H3; histone-fold, tetramer-dimer-dimer, DN	98.31
3nqu_A	140	Histone H3-like centromeric protein A; alpha helix	98.24
3r45_A	156	Histone H3-like centromeric protein A; histone fol	98.23
2ly8_A	121	Budding yeast chaperone SCM3; centromere protein,	98.19
1bh9_B	89	TAFII28; histone fold, tata binding protein, trans	98.13
3b0b_B	107	CENP-S, centromere protein S; histone fold, DNA bi	98.09
3v9r_A	90	MHF1, uncharacterized protein YOL086W-A; histone f	98.09
4dra_A	113	Centromere protein S; DNA binding complex, DNA dam	98.07
3ksy_A	1049	SOS-1, SON of sevenless homolog 1; RAS, RAS activa	97.97
2l5a_A	235	Histone H3-like centromeric protein CSE4, protein	97.94
4dra_E	84	Centromere protein X; DNA binding complex, DNA dam	97.9
3b0b_C	81	CENP-X, centromere protein X; histone fold, DNA bi	97.89
2nqb_D	123	Histone H2B; nucleosome, NCP, chromatin, structura	97.86
3vh5_A	140	CENP-S; histone fold, chromosome segregation, DNA	97.85
1tzy_B	126	Histone H2B; histone-fold, tetramer-dimer-dimer, D	97.84
2l5a_A	235	Histone H3-like centromeric protein CSE4, protein	97.82
2jss_A	192	Chimera of histone H2B.1 and histone H2A.Z; histon	97.59
1h3o_B	76	Transcription initiation factor TFIID 20/15 kDa su	96.91
3v9r_B	88	MHF2, uncharacterized protein YDL160C-A; histone f	95.71
2ly8_A	121	Budding yeast chaperone SCM3; centromere protein,	95.16
1wwi_A	148	Hypothetical protein TTHA1479; structural genomics	89.42
1h3o_A	75	Transcription initiation factor TFIID 135 kDa subu	86.59
1r4v_A	171	Hypothetical protein AQ_328; structural genomics,	83.18
3kw6_A	78	26S protease regulatory subunit 8; structural geno	81.15

>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=99.93  E-value=4.4e-26  Score=146.01  Aligned_cols=74  Identities=24%  Similarity=0.468  Sum_probs=68.8

Q ss_pred             HhhhcCCCCCCCCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850            5 AEEQNTETTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus         5 ~e~e~~~~~~~~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      .|.++.+.+..+||++|||||||.||++++||++|++++++|+|+||++|+..|++.|..++||||+|+||..|
T Consensus        30 ~e~~~~d~k~~~lPvaRIkrImK~d~~~~~is~eA~v~la~a~E~Fi~~L~~~A~~~a~~~krktI~~~di~~A  103 (119)
T 4g92_C           30 LESDNHDYKIHQLPLARIKKVMKADPEVKMISAEAPILFAKGCDVFITELTMRAWIHAEDNKRRTLQRSDIAAA  103 (119)
T ss_dssp             HTCSCCCSSCCSSCHHHHHHHHHTSTTCCEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHH
T ss_pred             HHhcccccccCCCCHHHHHHHHhhCCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccCHHHHHHH
Confidence            34456677888999999999999999999999999999999999999999999999999999999999999864

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

Probab=99.92  E-value=1.9e-25  Score=138.55  Aligned_cols=70  Identities=29%  Similarity=0.520  Sum_probs=60.6

Q ss_pred             cCCCCCCCCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850            9 NTETTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus         9 ~~~~~~~~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      ..+.+.+.||++|||||||.||++++||++|++++++|+|+|+++|++.||+.|+.++||||+|+||..|
T Consensus        12 ~~~~~~~~lP~arIkrImK~~~~~~~is~eA~~~laka~E~Fi~~l~~~A~~~a~~~krktI~~~di~~A   81 (97)
T 1n1j_B           12 VKDFRVQELPLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDIAMA   81 (97)
T ss_dssp             --------CCHHHHHHHHTTSTTCCCBCTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHH
T ss_pred             cCCcCCCcCCHHHHHHHHccCccccccChHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCCHHHHHHH
Confidence            5677889999999999999999999999999999999999999999999999999999999999999864

>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=99.91  E-value=7.3e-25  Score=136.25  Aligned_cols=69  Identities=32%  Similarity=0.537  Sum_probs=59.8

Q ss_pred             CCCCCCCCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           10 TETTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        10 ~~~~~~~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      .....+.||++||+||||.|+++++||++|++++++|+|+|+++|++.||+.|+..+||||+|+||..|
T Consensus         5 ~kk~~~~fPvaRIkrimK~~~~~~~vs~~A~v~la~a~E~Fi~el~~~A~~~a~~~krktI~~~di~~a   73 (98)
T 1jfi_A            5 KKKYNARFPPARIKKIMQTDEEIGKVAAAVPVIISRALELFLESLLKKACQVTQSRNAKTMTTSHLKQC   73 (98)
T ss_dssp             -----CCCCHHHHHHHHTTSTTCCCBCTTHHHHHHHHHHHHHHHHHHHHHHHHHTC---CBCHHHHHTT
T ss_pred             ccccCCCCChHHHHHHHHcCccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHH
Confidence            455678999999999999999999999999999999999999999999999999999999999999875

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

Probab=99.91  E-value=2.5e-25  Score=146.11  Aligned_cols=69  Identities=28%  Similarity=0.459  Sum_probs=51.6

Q ss_pred             CCCCCCCCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHH-HhCCCCccCchhhhcC
Q 038850           10 TETTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAA-IEKKRKTIKLGDMRVA   78 (78)
Q Consensus        10 ~~~~~~~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a-~~~~rkti~~~Di~~A   78 (78)
                      .....+.||++|||||||.+|++++||++|++++++|+|+||++|+..||++| ++.+||||+|+||..|
T Consensus        13 ~~~~~~~LPlaRIKrIMK~dpdv~~Is~eA~vliakA~ElFI~~Lt~~A~~~a~~~~kRKtI~~~Dl~~A   82 (140)
T 2byk_A           13 PPTAETFLPLSRVRTIMKSSMDTGLITNEVLFLMTKCTELFVRHLAGAAYTEEFGQRPGEALKYEHLSQV   82 (140)
T ss_dssp             ----------------CCSSSSCSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSCEECHHHHHHH
T ss_pred             CcccCCCCCHHHHHHHHhcCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcccCHHHHHHH
Confidence            34578899999999999999999999999999999999999999999999999 9999999999999864

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

Probab=99.85  E-value=8.7e-22  Score=127.51  Aligned_cols=66  Identities=23%  Similarity=0.318  Sum_probs=59.2

Q ss_pred             CCCCCChHHHHHHhh-cCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           13 TRPEFPVGRVKKIIK-LDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        13 ~~~~lP~arVkrImK-~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      ....||++||+|||| .+|++.+||+||++++++|+|+||.+|+..|++.|...+||||+++||..|
T Consensus         6 ~d~~LP~A~I~rImK~~~pd~~~iS~dA~~~l~ka~e~FI~~lt~~A~~~a~~~kRKTI~~~Dv~~A   72 (128)
T 2byk_B            6 EDLNLPNAVIGRLIKEALPESASVSKEARAAIARAASVFAIFVTSSSTALAHKQNHKTITAKDILQT   72 (128)
T ss_dssp             -----CCSHHHHHHHHHSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHH
T ss_pred             ccccCCHHHHHHHHHHhCcccceECHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHH
Confidence            357899999999999 699999999999999999999999999999999999999999999999864

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

Probab=99.84  E-value=3.5e-21  Score=118.13  Aligned_cols=67  Identities=25%  Similarity=0.375  Sum_probs=61.8

Q ss_pred             CCCCCCChHHHHHHhhcC-cCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           12 TTRPEFPVGRVKKIIKLD-EDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        12 ~~~~~lP~arVkrImK~d-~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      .....||+++|+||||.+ |++.+||+||..++++|+|+||.+|+..|+.+|.+.|||||+++||..|
T Consensus         4 ~~d~~LP~a~i~ri~K~~~~~~~~is~dA~~~l~~a~e~Fi~~l~~~A~~~a~~~kRkTI~~~Dv~~A   71 (93)
T 1n1j_A            4 EQDIYLPIANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDILFA   71 (93)
T ss_dssp             ---CCCCHHHHHHHHHHTSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHH
T ss_pred             cccccCChhHHHHHHHHhCCccceeCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHH
Confidence            456799999999999998 9999999999999999999999999999999999999999999999764

>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=99.79  E-value=1.1e-19  Score=108.14  Aligned_cols=65  Identities=34%  Similarity=0.425  Sum_probs=59.1

Q ss_pred             CCCCCChHHHHHHhh-cCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           13 TRPEFPVGRVKKIIK-LDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        13 ~~~~lP~arVkrImK-~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      |...||.++|+|||| .+|++ +||+||..+++.++++|+++|+.+|++.|...+||||+++||..|
T Consensus         1 g~~~LP~A~V~rI~K~~~p~~-~is~~A~~~i~~~~~~Fi~~la~eA~~~a~~~~rKTI~~~dI~~A   66 (76)
T 3b0c_W            1 GRRTVPRGTLRKIIKKHKPHL-RLAANTDLLVHLSFLLFLHRLAEEARTNAFENKSKIIKPEHTIAA   66 (76)
T ss_dssp             ---CCCHHHHHHHHHHHCTTC-EECTTHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSBCHHHHHHH
T ss_pred             CCCcccccHHHHHHHHhCCCC-ccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHH
Confidence            457899999999999 78974 899999999999999999999999999999999999999999764

>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=99.76  E-value=1.4e-18  Score=100.90  Aligned_cols=62  Identities=27%  Similarity=0.389  Sum_probs=58.9

Q ss_pred             CCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           16 EFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        16 ~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      .||.++|+||||.. +..++|++|..+++.|+|.|+.+|++.|+.+|...||+||+++||..|
T Consensus         2 ~lP~a~v~Ri~k~~-~~~ris~~A~~~l~~a~e~fi~~l~~~A~~~a~~~kRkTI~~~Di~~A   63 (68)
T 1b67_A            2 ELPIAPIGRIIKNA-GAERVSDDARIALAKVLEEMGEEIASEAVKLAKHAGRKTIKAEDIELA   63 (68)
T ss_dssp             CSCHHHHHHHHHHT-TCSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHH
T ss_pred             CCCccHHHHHHhcC-CcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHH
Confidence            58999999999999 667999999999999999999999999999999999999999999754

>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=99.66  E-value=1.4e-16  Score=108.14  Aligned_cols=68  Identities=19%  Similarity=0.258  Sum_probs=60.7

Q ss_pred             CCCCCCCCChHHHHHHhhcC-cCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           10 TETTRPEFPVGRVKKIIKLD-EDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        10 ~~~~~~~lP~arVkrImK~d-~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      .......||++.|.||||.. | ..+||+||..+|.+|++.||.+|+..|++.|...+||||+++||..|
T Consensus         9 ~~~eD~~LP~A~V~RImK~alp-~~rISkDA~~al~ec~~eFI~~LtseA~e~a~~~~RKTI~~eDVl~A   77 (179)
T 1jfi_B            9 GNDDDLTIPRAAINKMIKETLP-NVRVANDARELVVNCCTEFIHLISSEANEICNKSEKKTISPEHVIQA   77 (179)
T ss_dssp             ---CCCCCCHHHHHHHHHHHST-TCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHH
T ss_pred             CchhhhhcCHHHHHHHHHHhCC-ccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHH
Confidence            34456789999999999976 6 56999999999999999999999999999999999999999999764

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

Probab=99.51  E-value=3.7e-14  Score=82.74  Aligned_cols=64  Identities=27%  Similarity=0.409  Sum_probs=59.3

Q ss_pred             CCCCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           14 RPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        14 ~~~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      ...||.+.|+||+|.. ++.++|+++...+..+++.|+..+++.|..+|...|||||+.+||..|
T Consensus         4 ~~~lp~a~v~Rl~r~~-g~~ris~~a~~~l~e~~~~~~~~v~~dA~~~a~hakRkTI~~~DV~lA   67 (70)
T 1ku5_A            4 MGELPIAPVDRLIRKA-GAERVSEQAAKVLAEYLEEYAIEIAKKAVEFARHAGRKTVKVEDIKLA   67 (70)
T ss_dssp             -CCSCHHHHHHHHHHT-TCSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHH
T ss_pred             cccCChHHHHHHHHHc-CcceeCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHH
Confidence            3579999999999976 678999999999999999999999999999999999999999999753

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

Probab=99.49  E-value=7.1e-14  Score=92.86  Aligned_cols=69  Identities=28%  Similarity=0.260  Sum_probs=63.6

Q ss_pred             cCCCCCCCCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850            9 NTETTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus         9 ~~~~~~~~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      ..+.....||++.|.||||.. ++.+||.+|...+..++|.|+.++++.|.++|...|||||+.+||..|
T Consensus        75 v~d~~~l~lP~a~V~Ri~k~~-g~~RVS~~A~~~l~~~le~f~~~I~~~A~~~a~ha~RKTIt~eDV~~A  143 (154)
T 1f1e_A           75 VEDYDGELFGRATVRRILKRA-GIERASSDAVDLYNKLICRATEELGEKAAEYADEDGRKTVQGEDVEKA  143 (154)
T ss_dssp             STTCCSCCCCHHHHHHHHHHT-TCCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHH
T ss_pred             CCccccccCCccHHHHHHHHc-CCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHH
Confidence            455667899999999999998 667999999999999999999999999999999999999999999754

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

Probab=99.47  E-value=1.1e-13  Score=88.92  Aligned_cols=66  Identities=21%  Similarity=0.347  Sum_probs=62.3

Q ss_pred             CCCCCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           13 TRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        13 ~~~~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      ..++||++||.|+||.+....+|+.+|+++++.++|+|..++.+.|++.|+..++++|+++||..|
T Consensus        20 agL~fPV~ri~R~Lk~~~~a~RV~~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~krItp~hi~lA   85 (123)
T 2nqb_C           20 AGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLA   85 (123)
T ss_dssp             HTCSSCHHHHHHHHHHTTSCSEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHH
T ss_pred             CCeeccHHHHHHHHHccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHHHH
Confidence            368999999999999988888999999999999999999999999999999999999999999754

>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=99.47  E-value=8.8e-14  Score=90.27  Aligned_cols=67  Identities=22%  Similarity=0.341  Sum_probs=63.0

Q ss_pred             CCCCCCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           12 TTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        12 ~~~~~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      ...++||++||.|+||.+....+|+.+|+++++.++|+|..++.+.|++.|+..++++|+++||..|
T Consensus        21 ragLqfPV~rI~R~Lk~~~~a~RVs~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~krItp~hI~lA   87 (131)
T 1id3_C           21 KAGLTFPVGRVHRLLRRGNYAQRIGSGAPVYLTAVLEYLAAEILELAGNAARDNKKTRIIPRHLQLA   87 (131)
T ss_dssp             GGTCSSCHHHHHHHHHTTCSCSEECSSHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHH
T ss_pred             cCCeecCHHHHHHHHHccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHhhcCCceEcHHHHHHH
Confidence            3468999999999999988888999999999999999999999999999999999999999999754

>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=99.46  E-value=1.4e-13  Score=89.15  Aligned_cols=66  Identities=23%  Similarity=0.349  Sum_probs=62.3

Q ss_pred             CCCCCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           13 TRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        13 ~~~~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      ..++||++||.|+||.+....+|+.+|+++++.++|+|..++.+.|++.|+..++++|+++||..|
T Consensus        22 agLqfPV~rI~R~Lk~~~~a~RVs~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~krItp~hi~lA   87 (129)
T 1tzy_A           22 AGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLA   87 (129)
T ss_dssp             HTCSSCHHHHHHHHHHTTSSSEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHH
T ss_pred             CceeccHHHHHHHHHccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeEcHHHHHHH
Confidence            368999999999999988888999999999999999999999999999999999999999999754

>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=99.45  E-value=1.2e-13  Score=88.52  Aligned_cols=66  Identities=21%  Similarity=0.253  Sum_probs=62.0

Q ss_pred             CCCCCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           13 TRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        13 ~~~~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      ..++||++||.|+||.+....+|+.+|+++++.++|+|..++.+.|.+.|+..++++|+++||..|
T Consensus        19 agLqfPV~ri~R~Lk~~~~a~RV~~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~~rItp~hi~lA   84 (120)
T 2f8n_G           19 AGVIFPVGRMLRYIKKGHPKYRIGVGAPVYMAAVLEYLTAEILELAVNAARDNKKGRVTPRHILLA   84 (120)
T ss_dssp             HTCSSCHHHHHHHHHHHSSSCEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHH
T ss_pred             cCccCChHHHHHHHHcCccccccccchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceEcHHHHHHH
Confidence            368999999999999987778999999999999999999999999999999999999999999754

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

Probab=99.43  E-value=2.1e-13  Score=90.55  Aligned_cols=63  Identities=11%  Similarity=0.224  Sum_probs=59.0

Q ss_pred             CCCChHHHHHHhhcC-cCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           15 PEFPVGRVKKIIKLD-EDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        15 ~~lP~arVkrImK~d-~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      ..||.+.|+||||.. |+ .+||.+|...+..+++.|+.+++++|.++|.+.|||||+.+||..|
T Consensus         3 ~~LP~a~V~Riik~~lg~-~rVS~dA~~~l~~~l~~f~~~i~~~A~~~a~ha~RKTv~a~DV~~a   66 (154)
T 1f1e_A            3 VELPKAAIERIFRQGIGE-RRLSQDAKDTIYDFVPTMAEYVANAAKSVLDASGKKTLMEEHLKAL   66 (154)
T ss_dssp             -CCCHHHHHHHHHTTSTT-CEECHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHH
T ss_pred             ccCCccHHHHHHHhcCCc-cchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHH
Confidence            479999999999998 87 7999999999999999999999999999999999999999999643

>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=99.42  E-value=3.2e-13  Score=87.32  Aligned_cols=66  Identities=23%  Similarity=0.294  Sum_probs=61.2

Q ss_pred             CCCCCChHHHHHHhhcCcCc-cccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           13 TRPEFPVGRVKKIIKLDEDI-NKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        13 ~~~~lP~arVkrImK~d~dv-~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      ..++||++||.|+||..... .+|+.+|+++++.++|+|..++.+.|++.|+..++++|+++||..|
T Consensus        24 agLqfPV~ri~R~Lk~~~~a~~RV~~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~krItprhi~lA   90 (128)
T 1f66_C           24 AGLQFPVGRIHRHLKSRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLA   90 (128)
T ss_dssp             HTCSSCHHHHHHHHHHTSCSSCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHH
T ss_pred             CCccCChHHHHHHHHHcccchhhccccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeEcHHHHHHH
Confidence            36899999999999998765 4999999999999999999999999999999999999999999754

>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=99.42  E-value=3.7e-13  Score=89.04  Aligned_cols=66  Identities=23%  Similarity=0.344  Sum_probs=62.3

Q ss_pred             CCCCCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           13 TRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        13 ~~~~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      ..++||++||.|+||.+....+|+.+|+++++.++|+|..++.+.|++.|+..++++|+++||..|
T Consensus        41 agLqFPVgrI~R~LK~~~~a~RVs~~A~VyLAAVLEYL~aEILelAgn~A~~~krkrItprhI~lA  106 (149)
T 2f8n_K           41 AGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLA  106 (149)
T ss_dssp             HTCSSCHHHHHHHHHHTTSCSEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHH
T ss_pred             CCeeccHHHHHHHHHccccccccCcCcHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHH
Confidence            368999999999999988888999999999999999999999999999999999999999999754

>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=99.31  E-value=3.8e-12  Score=79.25  Aligned_cols=63  Identities=13%  Similarity=0.177  Sum_probs=58.7

Q ss_pred             CCCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           15 PEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        15 ~~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      ..||.+.|+||++.. .+.+||.++...+..++|.|++.++..|..+|+..+|+||+.+||..|
T Consensus        28 ~gip~~~I~Rlar~~-G~~rIs~~a~~~l~~vle~~~~~V~~dA~~~a~hakRktIt~~DV~~A   90 (103)
T 1tzy_D           28 QGITKPAIRRLARRG-GVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYA   90 (103)
T ss_dssp             GGSCHHHHHHHHHHT-TCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHH
T ss_pred             ccCCHHHHHHHHHHc-CccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHH
Confidence            349999999999987 458999999999999999999999999999999999999999999754

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

Probab=99.31  E-value=3.9e-12  Score=79.25  Aligned_cols=63  Identities=14%  Similarity=0.177  Sum_probs=57.9

Q ss_pred             CCCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           15 PEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        15 ~~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      ..||.+.|+||++.. .+.+||.++...+..++|.|++.++..|..+|+..+|+||+.+||..|
T Consensus        28 ~gip~~~I~Rlar~~-G~~rIs~~a~~~l~~vle~~~~~V~~dA~~~a~hakRktvt~~DV~~A   90 (103)
T 2yfw_B           28 QGITKPAIRRLARRG-GVKRISGLIYEEVRNVLKTFLESVIRDAVTYTEHAKRKTVTSLDVVYA   90 (103)
T ss_dssp             --CCHHHHHHHHHHT-TCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHH
T ss_pred             ccCCHHHHHHHHHHc-CccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHHH
Confidence            349999999999987 458999999999999999999999999999999999999999999754

>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=99.27  E-value=8.5e-12  Score=75.15  Aligned_cols=63  Identities=13%  Similarity=0.177  Sum_probs=59.0

Q ss_pred             CCCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           15 PEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        15 ~~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      ..||.+.|+||++.. ++.+||.++...+..+++.|++.++..|..+|+..|||||+.+||..|
T Consensus         9 ~~ip~~~I~Riar~~-Gv~rIs~da~~~l~~~l~~~~~~I~~dA~~~a~ha~RKTvt~~DV~~A   71 (84)
T 2hue_C            9 QGITKPAIRRLARRG-GVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYA   71 (84)
T ss_dssp             CSSCHHHHHHHHHHT-TCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHH
T ss_pred             CCCCHHHHHHHHHHc-CchhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHHH
Confidence            459999999999987 568999999999999999999999999999999999999999999754

>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=99.26  E-value=7.8e-12  Score=85.10  Aligned_cols=66  Identities=27%  Similarity=0.348  Sum_probs=61.1

Q ss_pred             CCCCCChHHHHHHhhcCcCc-cccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           13 TRPEFPVGRVKKIIKLDEDI-NKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        13 ~~~~lP~arVkrImK~d~dv-~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      ..++||++||+|+||..... .+|+.+|+++++..+|+|..++.+.|++.|+..|+++|+++||..|
T Consensus       102 agl~fPv~ri~R~lk~~~~a~~Rv~~~A~vyLaavLEyl~~eIlelA~n~a~~~~~~~I~p~~i~lA  168 (192)
T 2jss_A          102 AGLQFPVGRIKRYLKRHATGRTRVGSKAAIYLTAVLEYLTAEVLELAGNAAKDLKVKRITPRHLQLA  168 (192)
T ss_dssp             SSCCSCHHHHHHHHHHTTCSSCCCCTTTHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSCCHHHHHHH
T ss_pred             CCCcCCHHHHHHHHHhcCccccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHH
Confidence            46899999999999998665 5899999999999999999999999999999999999999999754

>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=99.25  E-value=5.8e-12  Score=79.56  Aligned_cols=66  Identities=23%  Similarity=0.341  Sum_probs=55.7

Q ss_pred             CCCCCCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           12 TTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        12 ~~~~~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      .....||.+-|+||||.. ++.+||.++...+..+++.|++.++..|..+|+..|||||+.+||..|
T Consensus         3 ~~d~~lP~a~I~Ri~r~~-g~~rIS~~a~~~l~e~l~~f~~~v~~da~~~A~HA~RKTV~~eDV~la   68 (111)
T 3b0c_T            3 TREPEIASSLIKQIFSHY-VKTPVTRDAYKIVEKCSERYFKQISSDLEAYSQHAGRKTVEMADVELL   68 (111)
T ss_dssp             -------CHHHHHHHHHH-HCSCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHC-CCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHH
Confidence            345689999999999988 567999999999999999999999999999999999999999999743

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

Probab=99.24  E-value=1.5e-11  Score=76.63  Aligned_cols=63  Identities=16%  Similarity=0.174  Sum_probs=59.0

Q ss_pred             CCCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           15 PEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        15 ~~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      ..||.+-|+||++.. .+.+||.++...+..++|.|++.++.+|..+|+..+||||+.+||..|
T Consensus        27 ~~ip~~~I~Rlar~~-Gv~rIS~da~~~l~~~le~fi~~I~~dA~~~a~HakRKTVt~~DV~~A   89 (102)
T 1id3_B           27 QGITKPAIRRLARRG-GVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYA   89 (102)
T ss_dssp             GGSCHHHHHHHHHHT-TCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHH
T ss_pred             CCCCHHHHHHHHHHc-CchhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHHH
Confidence            459999999999987 578999999999999999999999999999999999999999999754

>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=3.7e-10  Score=66.34  Aligned_cols=65  Identities=12%  Similarity=0.202  Sum_probs=60.6

Q ss_pred             CCCCCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           13 TRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        13 ~~~~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      ....||.+-|++|.++- ++.++|.|+...++..+|+-+.+++++|.++++..||+||+.+||..|
T Consensus         3 ~~s~lp~~~v~~iaes~-Gi~~lsddaa~~LA~dvEyr~~eI~qeA~kfmrHakRk~Lt~~DI~~A   67 (70)
T 1taf_B            3 YGSSISAESMKVIAESI-GVGSLSDDAAKELAEDVSIKLKRIVQDAAKFMNHAKRQKLSVRDIDMS   67 (70)
T ss_dssp             CSCCCCHHHHHHHHHHT-TCCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHH
T ss_pred             ccccCCHHHHHHHHHHC-CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHH
Confidence            45689999999999998 557999999999999999999999999999999999999999999764

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

Probab=98.77  E-value=1.1e-08  Score=60.90  Aligned_cols=61  Identities=25%  Similarity=0.300  Sum_probs=50.4

Q ss_pred             CChHHHHHHhhc----C-cCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           17 FPVGRVKKIIKL----D-EDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        17 lP~arVkrImK~----d-~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      +|.....|+++.    - ++ -+++.+|..++..|+|.|+..|.+.++.+|...||+||.++||..|
T Consensus         4 i~k~PF~RLVRei~~~~~~~-~R~q~~Al~aLQea~Eaylv~lfeda~l~A~HAkRvTi~~kDiqLa   69 (77)
T 2hue_B            4 IRKLPFQRLVREIAQDFKTD-LRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLA   69 (77)
T ss_dssp             SCHHHHHHHHHHHHHTTCSS-CEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHH
T ss_pred             cccchHHHHHHHHHHHcCcc-ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCcHhhHHHH
Confidence            455544454443    2 34 5899999999999999999999999999999999999999999753

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

Probab=98.52  E-value=1.3e-07  Score=58.75  Aligned_cols=64  Identities=23%  Similarity=0.202  Sum_probs=50.4

Q ss_pred             CCCChHHHHHHhhc----C-c--CccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           15 PEFPVGRVKKIIKL----D-E--DINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        15 ~~lP~arVkrImK~----d-~--dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      +-+|.....|+++.    - +  ..-+++.+|..++..|+|.|+-.|.+.++.+|...||.||..+||..|
T Consensus        26 llIpk~PF~RLVREI~~~~~~~~~~~R~q~~Al~ALQeaaEayLv~Lfeda~l~A~HAkRvTi~~kDiqLa   96 (100)
T 2yfv_A           26 LLISRMPFARLVKEVTDQFTTESEPLRWQSMAIMALQEASEAYLVGLLEHTNLLALHAKRITIMRKDMQLA   96 (100)
T ss_dssp             --CCHHHHHHHHHHHHHTTC-----CEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHH
T ss_pred             hhhccccHHHHHHHHHHHhccccchhhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCCHHHHHHH
Confidence            34555555555553    1 1  135899999999999999999999999999999999999999999753

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

Probab=98.52  E-value=2.2e-07  Score=55.91  Aligned_cols=62  Identities=18%  Similarity=0.138  Sum_probs=50.4

Q ss_pred             CChHHHHHHhhcC-----c-CccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           17 FPVGRVKKIIKLD-----E-DINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        17 lP~arVkrImK~d-----~-dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      +|.....|+++.-     + .--+++.+|..++..|+|.|+-.|.+.|+.+|...||+||.++||.-|
T Consensus         4 I~klPF~RLVREI~~~~~~~~~~R~q~~Al~aLQea~E~ylv~Lfeda~lcAiHAkRvTi~~kDiqLa   71 (82)
T 3nqj_A            4 IRKLPFSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRVTLFPKDVQLA   71 (82)
T ss_dssp             SCHHHHHHHHHHHHHHHHSSCCCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHH
T ss_pred             cccccHHHHHHHHHHHhccCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCcHHHHHHH
Confidence            4555555555531     1 224899999999999999999999999999999999999999998743

>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=98.34  E-value=1.5e-06  Score=50.49  Aligned_cols=57  Identities=19%  Similarity=0.237  Sum_probs=52.5

Q ss_pred             HHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           21 RVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        21 rVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      .|.+|+|.- ++.+++..++..+...++.++..+++.|..+|...||+||+.+||..|
T Consensus         6 ~i~~iLk~~-G~~~~~~~v~~~L~e~~~ry~~~il~dA~~~a~HAgrktv~~eDVkLA   62 (68)
T 1taf_A            6 VIMSILKEL-NVQEYEPRVVNQLLEFTFRYVTSILDDAKVYANHARKKTIDLDDVRLA   62 (68)
T ss_dssp             HHHHHHHHT-TCCCBCTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHH
T ss_pred             HHHHHHHHC-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHH
Confidence            578899885 667999999999999999999999999999999999999999999754

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

Probab=98.31  E-value=1.6e-06  Score=56.47  Aligned_cols=63  Identities=24%  Similarity=0.275  Sum_probs=51.8

Q ss_pred             CCCChHHHHHHhhc-----CcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           15 PEFPVGRVKKIIKL-----DEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        15 ~~lP~arVkrImK~-----d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      +-+|...+.|+++.     .++ -+++.+|..++..|+|.|+..|.+.++.+|...||.||..+||..|
T Consensus        61 lLIpk~PF~RLVREI~~~~~~~-~R~q~~Al~aLQeaaEayLv~Lfeda~l~A~HAkRvTi~~kDiqLa  128 (136)
T 1tzy_C           61 LLIRKLPFQRLVREIAQDFKTD-LRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLA  128 (136)
T ss_dssp             CCSCHHHHHHHHHHHHHHHCTT-CEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHH
T ss_pred             hhhccchHHHHHHHHHHHhhhh-hcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCcHHhHHHH
Confidence            34555555555443     244 5899999999999999999999999999999999999999999753

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

Probab=98.24  E-value=1.9e-06  Score=56.33  Aligned_cols=46  Identities=24%  Similarity=0.273  Sum_probs=43.6

Q ss_pred             cccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           33 NKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        33 ~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      -+++.+|+.++..|+|.|+..|.+.|+.+|...||.||..+||..|
T Consensus        84 ~Rfq~~Al~ALQEAaEayLv~LFEdanlcAiHAkRVTIm~kDiqLA  129 (140)
T 3nqu_A           84 FNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRVTLFPKDVQLA  129 (140)
T ss_dssp             CEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHH
T ss_pred             ceecHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcccccHHHHHHH
Confidence            4899999999999999999999999999999999999999999753

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

Probab=98.23  E-value=1.7e-06  Score=57.42  Aligned_cols=65  Identities=17%  Similarity=0.128  Sum_probs=53.1

Q ss_pred             CCCCChHHHHHHhhc-----Cc-CccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           14 RPEFPVGRVKKIIKL-----DE-DINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        14 ~~~lP~arVkrImK~-----d~-dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      .+-+|...+.|+++.     .+ .--+++.+|+.++..|+|.|+..|.+.|+.+|...||.||..+||..|
T Consensus        75 eLLIpKlPF~RLVREIa~~~~~~~~lRfqs~Al~ALQEAaEayLV~LFEdanLcAiHAkRVTIm~kDIqLA  145 (156)
T 3r45_A           75 HLLIRKLPFSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRVTLFPKDVQLA  145 (156)
T ss_dssp             CCCSCHHHHHHHHHHHHHTTTTTCCCEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSEECHHHHHHH
T ss_pred             ccccccccHHHHHHHHHHHhccCccceecHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcccccHHHHHHH
Confidence            345666666666653     11 124899999999999999999999999999999999999999999753

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

Probab=98.19  E-value=1.9e-06  Score=55.06  Aligned_cols=48  Identities=19%  Similarity=0.129  Sum_probs=44.2

Q ss_pred             cCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhc
Q 038850           30 EDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRV   77 (78)
Q Consensus        30 ~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~   77 (78)
                      .++.+||.++...+..+++.|++.++..|..++...+||||+..||.-
T Consensus        60 gGvkRIS~~iy~e~r~vl~~~l~~i~rdav~yaehA~RKTVta~DV~~  107 (121)
T 2ly8_A           60 RGSKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVY  107 (121)
T ss_dssp             CCSSCCSSCHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCCBCHHHHHH
T ss_pred             cCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHH
Confidence            467799999999999999999999999999999999999999999864

>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=98.13  E-value=2.4e-06  Score=51.94  Aligned_cols=65  Identities=18%  Similarity=0.319  Sum_probs=56.2

Q ss_pred             CCCCCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhC-CCCccCchhhhcC
Q 038850           13 TRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEK-KRKTIKLGDMRVA   78 (78)
Q Consensus        13 ~~~~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~-~rkti~~~Di~~A   78 (78)
                      ....||-+.|||+|+.--+ ..++.+...+++-.+-+|+.+|++.|.+...+. .+.-|++.||..|
T Consensus        13 Rrs~f~k~~vKrl~~~~~~-~~v~~~v~i~v~glaKvfVgelVE~A~~V~~~~~~~~Pl~P~HireA   78 (89)
T 1bh9_B           13 RRSAFPKAAIKRLIQSITG-TSVSQNVVIAMSGISKVFVGEVVEEALDVCEKWGEMPPLQPKHMREA   78 (89)
T ss_dssp             HHCCCCHHHHHHHHHHHHS-SCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSSCCHHHHHHH
T ss_pred             HHhcCCHHHHHHHHHHHcC-CCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcHHHHHH
Confidence            3568999999999996544 369999999999999999999999999999865 4669999999765

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

Probab=98.09  E-value=3.4e-06  Score=52.90  Aligned_cols=56  Identities=16%  Similarity=0.026  Sum_probs=48.2

Q ss_pred             HHHHhhcCcC--ccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhc
Q 038850           22 VKKIIKLDED--INKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRV   77 (78)
Q Consensus        22 VkrImK~d~d--v~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~   77 (78)
                      |.||.+.-..  -.++|.+++..++..++-|+..++..+..+|+..|||||+.+||.-
T Consensus        25 V~rI~~~~g~~~~~~vs~~~i~aL~E~~~~~~~~ia~Da~~fA~HAgRkTI~~eDV~L   82 (107)
T 3b0b_B           25 TGCLCQDVAEDKGVLFSKQTVAAISEITFRQCENFARDLEMFARHAKRSTITSEDVKL   82 (107)
T ss_dssp             HHHHHHHHHHHHTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHH
T ss_pred             HHHHHHHHhhhcCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcCcCCHHHHHH
Confidence            6667664211  1379999999999999999999999999999999999999999974

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

Probab=98.09  E-value=9.6e-06  Score=49.41  Aligned_cols=45  Identities=16%  Similarity=0.049  Sum_probs=42.9

Q ss_pred             cccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhc
Q 038850           33 NKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRV   77 (78)
Q Consensus        33 ~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~   77 (78)
                      ..+|.++...++..++.++..++..+..+|+..|||||+.+||..
T Consensus        31 ~~vs~~~i~aL~e~~~~~~~~ia~Dl~~fA~HAgRkTI~~eDV~L   75 (90)
T 3v9r_A           31 IKYTPRFINSLLELAYLQLGEMGSDLQAFARHAGRGVVNKSDLML   75 (90)
T ss_dssp             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHH
T ss_pred             ceeCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHH
Confidence            469999999999999999999999999999999999999999964

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

Probab=98.07  E-value=4e-06  Score=53.08  Aligned_cols=55  Identities=18%  Similarity=0.155  Sum_probs=47.8

Q ss_pred             HHHHhhcC---cCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhc
Q 038850           22 VKKIIKLD---EDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRV   77 (78)
Q Consensus        22 VkrImK~d---~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~   77 (78)
                      |-||++.-   .++ .+|.++..+++..++-|+..+++.+..+|+..|||||+.+||..
T Consensus        33 V~rIvke~gaer~~-~vS~~ai~aL~El~~~~~~~ia~Dl~~fAkHAgRkTI~~eDV~L   90 (113)
T 4dra_A           33 VGCLCEEVALDKEM-QFSKQTIAAISELTFRQCENFAKDLEMFARHAKRTTINTEDVKL   90 (113)
T ss_dssp             HHHHHHHHHHHHTC-CBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHH
T ss_pred             HHHHHHHHHHHcCC-CcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHH
Confidence            55677642   233 59999999999999999999999999999999999999999964

>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=97.97  E-value=1.2e-05  Score=65.09  Aligned_cols=67  Identities=12%  Similarity=0.116  Sum_probs=59.3

Q ss_pred             CCCCCCCCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhc
Q 038850           10 TETTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRV   77 (78)
Q Consensus        10 ~~~~~~~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~   77 (78)
                      .....++||++||.|.+|..- ..+|+..|++.++..+|+...++.+-|++.++..+++.|+++||..
T Consensus        98 ~~~~~l~~pv~~~~~~l~~~~-~~r~~~~~~~y~~avleyl~~~~l~la~~~~~~~~~~~i~p~~~~~  164 (1049)
T 3ksy_A           98 KRRNPLSLPVEKIHPLLKEVL-GYKIDHQVSVYIVAVLEYISADILKLVGNYVRNIRHYEITKQDIKV  164 (1049)
T ss_dssp             CCSSSCSSCHHHHHHHHHHHH-CSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCBCCHHHHHH
T ss_pred             cccCCccccHHHHHHHhhccc-ccccCCCCcchhHHHHHHHHHHHHHHHHHHHHHcCCceecCccccc
Confidence            344578999999999996543 3599999999999999999999999999999999999999999864

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

Probab=97.94  E-value=4.9e-06  Score=58.30  Aligned_cols=48  Identities=19%  Similarity=0.155  Sum_probs=45.5

Q ss_pred             cCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhc
Q 038850           30 EDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRV   77 (78)
Q Consensus        30 ~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~   77 (78)
                      .++.+||.++...+..+++.|++.++..|..++...+||||+..||.-
T Consensus       174 gGVkRIS~~iyeelr~vLe~fle~IirdAv~yaeHA~RKTVta~DV~~  221 (235)
T 2l5a_A          174 GGVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVY  221 (235)
T ss_dssp             TTCCTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSCCHHHHHH
T ss_pred             CCchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHH
Confidence            377899999999999999999999999999999999999999999864

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

Probab=97.90  E-value=8.4e-05  Score=44.73  Aligned_cols=66  Identities=17%  Similarity=0.271  Sum_probs=56.9

Q ss_pred             CCCCCCChHHHHHHhhcC--cCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhc
Q 038850           12 TTRPEFPVGRVKKIIKLD--EDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRV   77 (78)
Q Consensus        12 ~~~~~lP~arVkrImK~d--~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~   77 (78)
                      .....||..-|.||++..  .+-.+|+.+|..++++=+++|+.+-...|...|...+...|..+||.+
T Consensus         8 ~~~~~i~~~li~ril~~~F~~~kTkIs~dAl~l~aeyl~iFV~EAv~RA~~~a~~e~~~~le~e~LEk   75 (84)
T 4dra_E            8 GAGSGFRKELVSRLLHLHFKDDKTKVSGDALQLMVELLKVFVVEAAVRGVRQAQAEDALRVDVDQLEK   75 (84)
T ss_dssp             ---CCCCHHHHHHHHHTTCSSTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHhcCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHH
Confidence            346789999999999963  345699999999999999999999999999999988999999999864

>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=97.89  E-value=7.4e-05  Score=44.64  Aligned_cols=65  Identities=17%  Similarity=0.359  Sum_probs=57.0

Q ss_pred             CCCCCChHHHHHHhhc--CcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhc
Q 038850           13 TRPEFPVGRVKKIIKL--DEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRV   77 (78)
Q Consensus        13 ~~~~lP~arVkrImK~--d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~   77 (78)
                      ....||..-|.||++.  ..+-.+|+++|..++++=+++|+.+-...|...|...+...|..+||.+
T Consensus         5 ~~~~~~~~lI~ril~~~f~~~ktrI~~dAl~l~aeyl~iFV~EAv~RA~~~a~~e~~~~le~~~LEk   71 (81)
T 3b0b_C            5 REGGFRKETVERLLRLHFRDGRTRVNGDALLLMAELLKVFVREAAARAARQAQAEDLEKVDIEHVEK   71 (81)
T ss_dssp             --CCCCHHHHHHHHHHHCCSTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHH
T ss_pred             cCCCCCHHHHHHHHHHHhccCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCeecHHHHHH
Confidence            3678999999999996  3345699999999999999999999999999999999999999999864

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

Probab=97.86  E-value=3.2e-05  Score=49.51  Aligned_cols=58  Identities=21%  Similarity=0.268  Sum_probs=52.4

Q ss_pred             HHHHHHhh-cCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           20 GRVKKIIK-LDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        20 arVkrImK-~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      .-|.|++| .+||. .||..|...+..-...+.+.++.+|...+..++|+||+.+||..|
T Consensus        37 ~YIyKVLKQVhpd~-gISskAm~ImnSfvnDiferIA~EAs~La~~nkr~TitsreIqtA   95 (123)
T 2nqb_D           37 IYIYTVLKQVHPDT-GISSKAMSIMNSFVNDIFERIAAEASRLAHYNKRSTITSREIQTA   95 (123)
T ss_dssp             HHHHHHHHHHCTTC-EECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCEECHHHHHHH
T ss_pred             HHHHHHHHHhCCCC-CcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHH
Confidence            45888888 58886 599999999999999999999999999999999999999999764

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

Probab=97.85  E-value=1.5e-05  Score=52.04  Aligned_cols=55  Identities=18%  Similarity=0.109  Sum_probs=47.2

Q ss_pred             HHHHhhc---CcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhc
Q 038850           22 VKKIIKL---DEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRV   77 (78)
Q Consensus        22 VkrImK~---d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~   77 (78)
                      |-+|.+.   +.+ ..+|.++...++..++-|+..++..+..+|+..||+||+.+||..
T Consensus        25 VgkIvee~~~~~~-~~vS~~ai~aL~El~~~~~e~ia~DLe~FAkHAGRKTI~~eDVkL   82 (140)
T 3vh5_A           25 TGALAQDVAEDKG-VLFSKQTVAAISEITFRQAENFARDLEMFARHAKRSTITSEDVKL   82 (140)
T ss_dssp             HHHHHHHHHHHHT-CEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHH
T ss_pred             HHHHHHHHHHhcC-CCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHH
Confidence            4455553   223 369999999999999999999999999999999999999999964

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

Probab=97.84  E-value=3.7e-05  Score=49.41  Aligned_cols=57  Identities=25%  Similarity=0.300  Sum_probs=52.1

Q ss_pred             HHHHHhh-cCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           21 RVKKIIK-LDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        21 rVkrImK-~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      -|.|++| .+||. .||..|...+..-...+.+.++.+|...+..++|+||+.+||..|
T Consensus        41 YIyKVLKQVhpd~-gISskAm~ImnSfvnDiferIA~EAs~La~~nkr~TitsreIqtA   98 (126)
T 1tzy_B           41 YVYKVLKQVHPDT-GISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTA   98 (126)
T ss_dssp             HHHHHHHHHCTTC-EECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHH
T ss_pred             HHHHHHHHhCCCC-CcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHH
Confidence            5888888 58996 599999999999999999999999999999999999999999764

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

Probab=97.82  E-value=4.1e-05  Score=53.61  Aligned_cols=65  Identities=28%  Similarity=0.299  Sum_probs=54.7

Q ss_pred             CCCCChHH-HHHHhhcCc---CccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           14 RPEFPVGR-VKKIIKLDE---DINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        14 ~~~lP~ar-VkrImK~d~---dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      -..+|..| ||.|.+.-.   +--+.+++|+.++..|+|.|+-.|-+.++.+|...+|-||.++||..|
T Consensus        12 I~KlPFqRLVREIaq~~~~~~~~lRfqs~Al~ALQEAaEayLV~LFEd~nLcaiHAkRVTim~kDiqLa   80 (235)
T 2l5a_A           12 ISKIPFARLVKEVTDEFTTKDQDLRWQSMAIMALQEASEAYLVGLLEHTNLLALHAKRITIMKKDMQLA   80 (235)
T ss_dssp             CSCCHHHHHHHHHHHTSCGGGTTCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHSTTTSGGGTTHHHHH
T ss_pred             ccCccHHHHHHHHHHHhccCCccceecHHHHHHHHHHHHHHHHHHHhhhHHHHhcccccccchhhHHHH
Confidence            35788888 566766422   235899999999999999999999999999999999999999998743

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

Probab=97.59  E-value=0.00016  Score=48.93  Aligned_cols=58  Identities=17%  Similarity=0.284  Sum_probs=52.4

Q ss_pred             HHHHHHhh-cCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           20 GRVKKIIK-LDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        20 arVkrImK-~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      ..|.|++| .+||. .+|.+|...+..-+..+.+.|+.+|...+...+|+||+.+||..|
T Consensus         7 ~yi~kvLkqv~p~~-~iS~~Am~~m~s~v~di~~rIa~eA~~L~~~~~r~Tit~~eIq~A   65 (192)
T 2jss_A            7 SYIYKVLKQTHPDT-GISQKSMSILNSFVNDIFERIATEASKLAAYNKKSTISAREIQTA   65 (192)
T ss_dssp             HHHHHHHHHHCSSC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCCSCCHHHHHHH
T ss_pred             HHHHHHHcccCCCC-CcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHH
Confidence            45888998 58886 599999999999999999999999999999999999999999754

>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=96.91  E-value=0.0043  Score=36.49  Aligned_cols=61  Identities=10%  Similarity=0.261  Sum_probs=55.2

Q ss_pred             CCCChHHHHHHhhc-CcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhh
Q 038850           15 PEFPVGRVKKIIKL-DEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMR   76 (78)
Q Consensus        15 ~~lP~arVkrImK~-d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~   76 (78)
                      --|+-.++..+++. ||. ..+..++-.++..-+..||...+..|...|+..|..||..+||.
T Consensus         4 ~vl~k~~L~~Lv~~idp~-~~ld~~vee~ll~lADdFV~~V~~~ac~lAKhR~s~~le~kDvq   65 (76)
T 1h3o_B            4 MVLTKKKLQDLVREVDPN-EQLDEDVEEMLLQIADDFIESVVTAACQLARHRKSSTLEVKDVQ   65 (76)
T ss_dssp             CSSCHHHHHHHHHHHCSS-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCEECHHHHH
T ss_pred             ccccHHHHHHHHHhcCCC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCccHHHHH
Confidence            35788899999985 776 47999999999999999999999999999999999999999985

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

Probab=95.71  E-value=0.037  Score=33.40  Aligned_cols=60  Identities=12%  Similarity=0.189  Sum_probs=46.2

Q ss_pred             CChHHHHHHhhc--CcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhC-------CCCccCchhhh
Q 038850           17 FPVGRVKKIIKL--DEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEK-------KRKTIKLGDMR   76 (78)
Q Consensus        17 lP~arVkrImK~--d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~-------~rkti~~~Di~   76 (78)
                      +|..-|-||++.  ..+-.+|+++|..++++=.+.|+.+-...|++.....       +...|+-.|+.
T Consensus         2 ip~~llaRIL~~~F~~~kTrIt~da~~lv~kY~diFVrEAv~Rs~e~ke~~~~~~~~~~d~~LeveDLE   70 (88)
T 3v9r_B            2 LSKEALIKILSQNEGGNDMKIADEVVPMIQKYLDIFIDEAVLRSLQSHKDINGERGDKSPLELSHQDLE   70 (88)
T ss_dssp             CCSHHHHHHHTTTSCSSCCEECTTTHHHHHHHHHHHHHHHHHHHHHHHHCC-----------CCHHHHH
T ss_pred             CCHHHHHHHHHHHhCCCCceecHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccCCCCCeeehHHHH
Confidence            688899999995  3344589999999999999999999999998876652       22567777664

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

Probab=95.16  E-value=0.054  Score=34.31  Aligned_cols=58  Identities=21%  Similarity=0.263  Sum_probs=44.6

Q ss_pred             CCCChHHH-HHHhhc-Cc--CccccchHHHHHHHHHHHHHHHHHHHHHHHHHHh---CCCCccCc
Q 038850           15 PEFPVGRV-KKIIKL-DE--DINKVTSEALFIVSRSTELFLRFLAEKSAEAAIE---KKRKTIKL   72 (78)
Q Consensus        15 ~~lP~arV-krImK~-d~--dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~---~~rkti~~   72 (78)
                      ..+|..|+ |.|.+. .+  ..-+.+++|..++..|+|.|+-.|-+.++.+|..   +|-+.|+.
T Consensus         3 ~klPF~RLVREI~~~~~~~~~~lRfq~~Al~ALQeAsEayLV~lFEd~nlcaiHA~~gGvkRIS~   67 (121)
T 2ly8_A            3 SKIPFARLVKEVTDEFTTKDQDLRWQSMAIMALQEASEAYLVGLLEHTNLLALHLVPRGSKRISG   67 (121)
T ss_dssp             SCCHHHHHHHHHHHHHTTCCSSCCBCHHHHHHHHHHHHHHHHHHHHHHHHHTTTCCCCCSSCCSS
T ss_pred             CccchHHHHHHHHHHhcCCCCCccccHHHHHHHHHHHHHHHHHHHHHHhHHHHcCCccCccchhH
Confidence            46888885 557653 22  2348999999999999999999999999998875   45566653

>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=89.42  E-value=1.2  Score=29.09  Aligned_cols=59  Identities=19%  Similarity=0.109  Sum_probs=45.8

Q ss_pred             CCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhh
Q 038850           16 EFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDM   75 (78)
Q Consensus        16 ~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di   75 (78)
                      -.|.+++.|+++.-.+.. |-++-..-++.-.+-=+.+|..-|...|+.+||..|.+.|+
T Consensus         2 vm~~~~~e~lFR~aa~Ld-vdK~d~~r~~d~V~~Kl~DLl~va~~~Ak~n~RdvI~~~DL   60 (148)
T 1wwi_A            2 LMKVAEFERLFRQAAGLD-VDKNDLKRVSDFLRNKLYDLLAVAERNAKYNGRDLIFEPDL   60 (148)
T ss_dssp             CSCHHHHHHHHHHHHCCC-CCGGGHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECGGGS
T ss_pred             cCCHHHHHHHHHHHhccC-CcHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeeccccC
Confidence            368899999999766654 33444444555566667889999999999999999999997

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

Probab=86.59  E-value=1.5  Score=25.52  Aligned_cols=43  Identities=30%  Similarity=0.309  Sum_probs=34.0

Q ss_pred             HHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 038850           20 GRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAI   63 (78)
Q Consensus        20 arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~   63 (78)
                      .||..||+. .++..+++|+..+++.|+|.=+..|.+.-...|+
T Consensus        10 kri~~I~~k-~gl~~~~~dv~~~iS~a~qeRLr~llekl~~~a~   52 (75)
T 1h3o_A           10 RRILEIGKK-HGITELHPDVVSYVSHATQQRLQNLVEKISETAQ   52 (75)
T ss_dssp             HHHHHHHHT-TTCCEECTTHHHHHHHHHHHHHHHHHHHHHC---
T ss_pred             HHHHHHHHh-cCCCcCChhHHHHhHHHHHHHHHHHHHHHHHHHH
Confidence            467778876 5888999999999999999998888887665554

>1r4v_A Hypothetical protein AQ_328; structural genomics, all-alpha, histon fold, PSI, protein ST initiative, midwest center for structural genomics; HET: MSE; 1.90A {Aquifex aeolicus} SCOP: a.22.1.4

Probab=83.18  E-value=1.7  Score=28.92  Aligned_cols=59  Identities=19%  Similarity=0.201  Sum_probs=48.3

Q ss_pred             CCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhh
Q 038850           16 EFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDM   75 (78)
Q Consensus        16 ~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di   75 (78)
                      -.|.+++.|+++.-.+.. |-++-..-+..-.+-=+-+|..-|...|+.+||..|.+.||
T Consensus        26 vmg~~kferlFR~aagLD-vdK~d~kr~~d~V~~Kl~DLl~va~~~Ak~NgRDvI~~~DL   84 (171)
T 1r4v_A           26 PKGFDKLDHYFRTELDID-LTDETIELLLNSVKAAFGKLFYGAEQRARWNGRDFIALADL   84 (171)
T ss_dssp             CTTHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHHHHHTTTTHHHHHHHTTCSEECGGGS
T ss_pred             cCChHHHHHHHHHHhccC-CcHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeeccccC
Confidence            679999999999866653 44555556666667778889999999999999999999997

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

Probab=81.15  E-value=0.96  Score=25.16  Aligned_cols=39  Identities=13%  Similarity=0.149  Sum_probs=31.3

Q ss_pred             HHHHHHHHHHH----HHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           40 LFIVSRSTELF----LRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        40 ~~~i~~A~ElF----i~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      ...++..++-|    |..|+.+|...|...++..|+.+|+..|
T Consensus        27 l~~la~~t~G~SGADi~~l~~eA~~~a~~~~~~~i~~~d~~~A   69 (78)
T 3kw6_A           27 LRKIAELMPGASGAEVKGVCTEAGMYALRERRVHVTQEDFEMA   69 (78)
T ss_dssp             HHHHHHTCTTCCHHHHHHHHHHHHHHHHHTTCSEECHHHHHHH
T ss_pred             HHHHHHHcCCCCHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHH
Confidence            44556666655    7789999999999999999999998764

---

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	78
d1jfia_	66	a.22.1.3 (A:) Negative cofactor 2, NC2, alpha chai	7e-15
d1n1jb_	78	a.22.1.3 (B:) Nuclear transcription factor Y subun	3e-12
d1ku5a_	66	a.22.1.2 (A:) Archaeal histone {Archaeon (Pyrococc	3e-10
d2byka1	72	a.22.1.3 (A:29-100) Chrac-16 {Fruit fly (Drosophil	1e-09
d1n1ja_	87	a.22.1.3 (A:) Nuclear transcription factor Y subun	2e-09
d2bykb1	89	a.22.1.3 (B:11-99) Chrac-14 {Fruit fly (Drosophila	2e-09
d1jfib_	135	a.22.1.3 (B:) Negative cofactor 2, NC2, beta chain	7e-09
d1htaa_	68	a.22.1.2 (A:) Archaeal histone {Archaeon Methanoth	5e-08
d1f1ea_	151	a.22.1.2 (A:) Archaeal histone {Archaeon Methanopy	2e-07
d1f1ea_	151	a.22.1.2 (A:) Archaeal histone {Archaeon Methanopy	0.001
d1q9ca_	172	a.22.1.3 (A:) Histone domain of Son of sevenless p	1e-04
d1tzyc_	95	a.22.1.1 (C:) Histone H3 {Chicken (Gallus gallus),	0.004

>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 = 60.5 bits (147), Expect = 7e-15
 Identities = 22/62 (35%), Positives = 36/62 (58%)

Query: 17 FPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMR 76
          FP  R+KKI++ DE+I KV +    I+SR+ ELFL  L +K+ +    +  KT+    ++
Sbjct: 3  FPPARIKKIMQTDEEIGKVAAAVPVIISRALELFLESLLKKACQVTQSRNAKTMTTSHLK 62

Query: 77 VA 78
            
Sbjct: 63 QC 64

>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 = 54.1 bits (130), Expect = 3e-12
 Identities = 19/61 (31%), Positives = 41/61 (67%)

Query: 18 PVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRV 77
          P+ R+KKI+KLDED+  +++EA  + +++ ++F+  L  ++     + KR+T++  D+ +
Sbjct: 2  PLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDIAM 61

Query: 78 A 78
          A
Sbjct: 62 A 62

>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 = 48.6 bits (116), Expect = 3e-10
 Identities = 17/63 (26%), Positives = 36/63 (57%), Gaps = 1/63 (1%)

Query: 16 EFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDM 75
          E P+  V ++I+      +V+ +A  +++   E +   +A+K+ E A    RKT+K+ D+
Sbjct: 2  ELPIAPVDRLIRKAGAE-RVSEQAAKVLAEYLEEYAIEIAKKAVEFARHAGRKTVKVEDI 60

Query: 76 RVA 78
          ++A
Sbjct: 61 KLA 63

>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 = 47.1 bits (112), Expect = 1e-09
 Identities = 14/54 (25%), Positives = 27/54 (50%), Gaps = 1/54 (1%)

Query: 26 IKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIE-KKRKTIKLGDMRVA 78
          +K   D   +T+E LF++++ TELF+R LA  +       +  + +K   +   
Sbjct: 1  MKSSMDTGLITNEVLFLMTKCTELFVRHLAGAAYTEEFGQRPGEALKYEHLSQV 54

>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 = 47.1 bits (112), Expect = 2e-09
 Identities = 17/63 (26%), Positives = 30/63 (47%), Gaps = 1/63 (1%)

Query: 17 FPVGRVKKIIK-LDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDM 75
           P+  V +I+K       K+  +A   V      F+ F+  +++E   ++KRKTI   D+
Sbjct: 3  LPIANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDI 62

Query: 76 RVA 78
            A
Sbjct: 63 LFA 65

>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 = 46.8 bits (111), Expect = 2e-09
 Identities = 15/62 (24%), Positives = 28/62 (45%), Gaps = 1/62 (1%)

Query: 18 PVGRVKKIIK-LDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMR 76
          P   + ++IK    +   V+ EA   ++R+  +F  F+   S   A ++  KTI   D+ 
Sbjct: 1  PNAVIGRLIKEALPESASVSKEARAAIARAASVFAIFVTSSSTALAHKQNHKTITAKDIL 60

Query: 77 VA 78
            
Sbjct: 61 QT 62

>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 = 46.8 bits (111), Expect = 7e-09
 Identities = 13/62 (20%), Positives = 28/62 (45%)

Query: 17 FPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMR 76
           P   + K+IK      +V ++A  +V      F+  ++ ++ E   + ++KTI    + 
Sbjct: 5  IPRAAINKMIKETLPNVRVANDARELVVNCCTEFIHLISSEANEICNKSEKKTISPEHVI 64

Query: 77 VA 78
           A
Sbjct: 65 QA 66

>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 = 43.2 bits (102), Expect = 5e-08
 Identities = 17/64 (26%), Positives = 32/64 (50%), Gaps = 1/64 (1%)

Query: 15 PEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGD 74
           E P+  + +IIK      +V+ +A   +++  E     +A ++ + A    RKTIK  D
Sbjct: 2  GELPIAPIGRIIKNA-GAERVSDDARIALAKVLEEMGEEIASEAVKLAKHAGRKTIKAED 60

Query: 75 MRVA 78
          + +A
Sbjct: 61 IELA 64

>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 = 43.2 bits (102), Expect = 2e-07
 Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 1/63 (1%)

Query: 16  EFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDM 75
            F    V++I+K    I + +S+A+ + ++        L EK+AE A E  RKT++  D+
Sbjct: 79  LFGRATVRRILK-RAGIERASSDAVDLYNKLICRATEELGEKAAEYADEDGRKTVQGEDV 137

Query: 76  RVA 78
             A
Sbjct: 138 EKA 140

>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 = 32.8 bits (75), Expect = 0.001
 Identities = 7/63 (11%), Positives = 23/63 (36%)

Query: 16 EFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDM 75
          E P   +++I +      +++ +A   +         ++A  +        +KT+    +
Sbjct: 1  ELPKAAIERIFRQGIGERRLSQDAKDTIYDFVPTMAEYVANAAKSVLDASGKKTLMEEHL 60

Query: 76 RVA 78
          +  
Sbjct: 61 KAL 63

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

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

 Score = 35.9 bits (83), Expect = 1e-04
 Identities = 9/62 (14%), Positives = 23/62 (37%), Gaps = 1/62 (1%)

Query: 17  FPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMR 76
            PV ++  ++K +    K+  +    +    E     + + +       +   I   D++
Sbjct: 100 LPVEKIHPLLK-EVLGYKIDHQVSVYIVAVLEYISADILKLAGNYVRNIRHYEITKQDIK 158

Query: 77  VA 78
           VA
Sbjct: 159 VA 160

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

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

 Score = 30.9 bits (70), Expect = 0.004
 Identities = 20/73 (27%), Positives = 38/73 (52%), Gaps = 1/73 (1%)

Query: 7  EQNTETTRPEFPVGR-VKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEK 65
          +++TE    + P  R V++I +  +   +  S A+  +  ++E +L  L E +   AI  
Sbjct: 15 QKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHA 74

Query: 66 KRKTIKLGDMRVA 78
          KR TI   D+++A
Sbjct: 75 KRVTIMPKDIQLA 87

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	78
d1jfia_	66	Negative cofactor 2, NC2, alpha chain {Human (Homo	99.94
d1n1jb_	78	Nuclear transcription factor Y subunit gamma (Nf-Y	99.92
d1n1ja_	87	Nuclear transcription factor Y subunit beta (Nf-Yb	99.88
d2bykb1	89	Chrac-14 {Fruit fly (Drosophila melanogaster) [Tax	99.85
d1ku5a_	66	Archaeal histone {Archaeon (Pyrococcus horikoshii)	99.85
d1jfib_	135	Negative cofactor 2, NC2, beta chain {Human (Homo	99.84
d1htaa_	68	Archaeal histone {Archaeon Methanothermus fervidus	99.8
d2byka1	72	Chrac-16 {Fruit fly (Drosophila melanogaster) [Tax	99.8
d1f1ea_	151	Archaeal histone {Archaeon Methanopyrus kandleri [	99.68
d1f1ea_	151	Archaeal histone {Archaeon Methanopyrus kandleri [	99.23
d1q9ca_	172	Histone domain of Son of sevenless protein {Human	99.18
d1u35c1	106	macro-H2A.1, histone domain {Human (Homo sapiens)	99.05
d1tzya_	106	Histone H2A {Chicken (Gallus gallus), erythrocytes	99.02
d1f66c_	103	Histone H2A {Human (Homo sapiens), variant H2A.Z [	98.99
d2huec1	82	Histone H4 {African clawed frog (Xenopus laevis) [	98.99
d1tzyc_	95	Histone H3 {Chicken (Gallus gallus), erythrocytes	98.24
d1tafb_	70	TAF(II)62 {Fruit fly (Drosophila melanogaster) [Ta	98.08
d1bh9b_	89	TAF(II)28 {Human (Homo sapiens) [TaxId: 9606]}	97.98
d1tzyb_	92	Histone H2B {Chicken (Gallus gallus), erythrocytes	97.68
d1h3ob_	74	TAF(II)-20, (TAF(II)-15, hTAF12), histone fold dom	96.25
d1tafa_	68	TAF(II)42 {Fruit fly (Drosophila melanogaster) [Ta	91.91
d1h3oa_	50	TAF(II)-135, (TAF(II)-130, hTAF4), histone fold do	91.31
d1wwia1	148	Hypothetical protein TTHA1479 {Thermus thermophilu	90.67
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	89.7
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	88.57

>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=99.94  E-value=2.3e-27  Score=136.76  Aligned_cols=63  Identities=35%  Similarity=0.587  Sum_probs=58.7

Q ss_pred             CCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           16 EFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        16 ~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      +||++|||||||.||++++||+||++++++|+|+|+++|++.|++.|+.++||||+|+||..|
T Consensus         2 ~fP~srVkkimk~~~~~~~is~~A~~~~~~a~E~Fi~~l~~~A~~~a~~~krktI~~~dl~~a   64 (66)
T d1jfia_           2 RFPPARIKKIMQTDEEIGKVAAAVPVIISRALELFLESLLKKACQVTQSRNAKTMTTSHLKQC   64 (66)
T ss_dssp             CCCHHHHHHHHTTSTTCCCBCTTHHHHHHHHHHHHHHHHHHHHHHHHHTC---CBCHHHHHTT
T ss_pred             CCChHHHHHHHhcCCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHH
Confidence            799999999999999999999999999999999999999999999999999999999999876

>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=99.92  E-value=5.1e-26  Score=134.32  Aligned_cols=62  Identities=31%  Similarity=0.589  Sum_probs=60.4

Q ss_pred             CChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           17 FPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        17 lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      ||++|||||||.||++.++|+||++++++|+|+|+++|++.|++.|++++||||+|+||..|
T Consensus         1 LP~srVkrImK~~~~~~~is~ea~~~i~~a~E~Fi~~l~~~A~~~a~~~~rkti~~~dl~~a   62 (78)
T d1n1jb_           1 LPLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDIAMA   62 (78)
T ss_dssp             CCHHHHHHHHTTSTTCCCBCTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHH
T ss_pred             CCHHHHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHH
Confidence            89999999999999999999999999999999999999999999999999999999999864

>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=99.88  E-value=2.6e-23  Score=124.99  Aligned_cols=63  Identities=27%  Similarity=0.405  Sum_probs=60.4

Q ss_pred             CCChHHHHHHhh-cCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           16 EFPVGRVKKIIK-LDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        16 ~lP~arVkrImK-~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      -||+|||+|||| .+|++.+||+||++++++|+|+||++|+.+|++.|..++||||+|+||..|
T Consensus         2 ~LP~a~v~ri~K~~~p~~~~is~ea~~~i~~a~e~Fi~~lt~~A~~~a~~~~rKTI~~~dv~~A   65 (87)
T d1n1ja_           2 YLPIANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDILFA   65 (87)
T ss_dssp             CCCHHHHHHHHHHTSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHH
T ss_pred             CCcHhHHHHHHHHhCCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHH
Confidence            599999999999 679999999999999999999999999999999999999999999999865

>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=99.85  E-value=3.4e-22  Score=120.54  Aligned_cols=61  Identities=25%  Similarity=0.343  Sum_probs=58.7

Q ss_pred             ChHHHHHHhh-cCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           18 PVGRVKKIIK-LDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        18 P~arVkrImK-~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      |++||+|||| .+|++.+||+||++++++|+|+||++|+..|+..|..++||||+|+||..|
T Consensus         1 P~a~i~ri~K~~~p~~~~iskeA~~~i~~aae~FI~~lt~~A~~~a~~~~rKtI~~~dv~~A   62 (89)
T d2bykb1           1 PNAVIGRLIKEALPESASVSKEARAAIARAASVFAIFVTSSSTALAHKQNHKTITAKDILQT   62 (89)
T ss_dssp             CCSHHHHHHHHHSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHH
T ss_pred             CccHHHHHHHHhCcccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCccCHHHHHHH
Confidence            8999999999 689999999999999999999999999999999999999999999999764

>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=6.5e-22  Score=113.44  Aligned_cols=62  Identities=27%  Similarity=0.438  Sum_probs=59.1

Q ss_pred             CCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           16 EFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        16 ~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      .||.++|+||||.+++ .+||+||+.++++|+|+|+++|+..|+.+|...|||||+++||..|
T Consensus         2 ~LP~a~I~rI~k~~~~-~ris~ea~~~l~~a~e~Fi~~l~~~a~~~a~~~~RKTI~~~Dv~~A   63 (66)
T d1ku5a_           2 ELPIAPVDRLIRKAGA-ERVSEQAAKVLAEYLEEYAIEIAKKAVEFARHAGRKTVKVEDIKLA   63 (66)
T ss_dssp             CSCHHHHHHHHHHTTC-SEECHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHH
T ss_pred             CCCHHHHHHHHHhCcc-cccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHH
Confidence            6999999999999977 4899999999999999999999999999999999999999999764

>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=99.84  E-value=9.2e-22  Score=126.51  Aligned_cols=65  Identities=20%  Similarity=0.256  Sum_probs=62.2

Q ss_pred             CCCCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           14 RPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        14 ~~~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      .+.||++||+||||.++++.+||+||+++|++|+++||.+|+..|+..|...+||||+|+||..|
T Consensus         2 dl~LP~a~I~kI~K~~~~~~~is~dA~~~i~~a~~~Fi~~lt~~A~~~a~~~~RkTi~~~Dv~~A   66 (135)
T d1jfib_           2 DLTIPRAAINKMIKETLPNVRVANDARELVVNCCTEFIHLISSEANEICNKSEKKTISPEHVIQA   66 (135)
T ss_dssp             CCCCCHHHHHHHHHHHSTTCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHH
T ss_pred             cccccHHHHHHHHhhCCccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcccHHHHHHH
Confidence            46899999999999999889999999999999999999999999999999999999999999865

>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=99.80  E-value=5.2e-20  Score=105.71  Aligned_cols=63  Identities=27%  Similarity=0.372  Sum_probs=58.9

Q ss_pred             CCCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           15 PEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        15 ~~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      ..||.++|+||||.++. .+||+||..++++++|+|+.+|+..|+.+|..+|||||+++||..|
T Consensus         2 aeLP~a~I~ri~k~~~~-~ris~ea~~~l~~~~e~fi~~l~~~a~~~a~~~kRkTi~~~DV~~A   64 (68)
T d1htaa_           2 GELPIAPIGRIIKNAGA-ERVSDDARIALAKVLEEMGEEIASEAVKLAKHAGRKTIKAEDIELA   64 (68)
T ss_dssp             CCSCHHHHHHHHHHTTC-SCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHH
T ss_pred             CcCcHHHHHHHHHHCCc-chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHH
Confidence            35999999999999854 6899999999999999999999999999999999999999999764

>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=99.80  E-value=2.4e-20  Score=108.91  Aligned_cols=53  Identities=26%  Similarity=0.453  Sum_probs=49.2

Q ss_pred             hhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHh-CCCCccCchhhhcC
Q 038850           26 IKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIE-KKRKTIKLGDMRVA   78 (78)
Q Consensus        26 mK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~-~~rkti~~~Di~~A   78 (78)
                      ||+||||++||+||++++++|||+||++|+.+||.++.+ +++|||+|+||++|
T Consensus         1 Mk~d~dv~~is~ea~~lvskAtElFi~~L~~~a~~~a~~~~~~ktl~~~dl~~a   54 (72)
T d2byka1           1 MKSSMDTGLITNEVLFLMTKCTELFVRHLAGAAYTEEFGQRPGEALKYEHLSQV   54 (72)
T ss_dssp             CCSSSSCSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSCEECHHHHHHH
T ss_pred             CCCCHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCccccHHHHHHH
Confidence            899999999999999999999999999999999999865 46699999999864

>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=99.68  E-value=3.6e-17  Score=106.33  Aligned_cols=69  Identities=28%  Similarity=0.260  Sum_probs=63.5

Q ss_pred             cCCCCCCCCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850            9 NTETTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus         9 ~~~~~~~~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      ..+.....||.++|+||||.. ++.++|+||+.+++.++|.|+.+|++.|+.+|.+.|||||+++||..|
T Consensus        72 ~~~~~~~~fp~a~IkRi~k~~-g~~ris~dA~~~l~~~~E~fi~~l~~~A~~~a~~~kRkTI~~~DI~~A  140 (151)
T d1f1ea_          72 VEDYDGELFGRATVRRILKRA-GIERASSDAVDLYNKLICRATEELGEKAAEYADEDGRKTVQGEDVEKA  140 (151)
T ss_dssp             STTCCSCCCCHHHHHHHHHHT-TCCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHH
T ss_pred             ccccccCccCHHHHHHHHHcC-CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHH
Confidence            445668899999999999954 678999999999999999999999999999999999999999999764

>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=99.23  E-value=1e-11  Score=80.14  Aligned_cols=62  Identities=11%  Similarity=0.202  Sum_probs=57.6

Q ss_pred             CCChHHHHHHhhc-CcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           16 EFPVGRVKKIIKL-DEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        16 ~lP~arVkrImK~-d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      .||++.|.||||. .|+. +||++|...+..+++.|+++++.+|...|...|||||+.+||..|
T Consensus         1 ~lP~a~I~rilk~~~~~~-ris~da~~~l~~~~~~~~~~Ia~eA~~l~~~~~rKTi~~edi~~a   63 (151)
T d1f1ea_           1 ELPKAAIERIFRQGIGER-RLSQDAKDTIYDFVPTMAEYVANAAKSVLDASGKKTLMEEHLKAL   63 (151)
T ss_dssp             CCCHHHHHHHHHTTSTTC-EECHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHH
T ss_pred             CCCccHHHHHHHHhCCcc-ccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHH
Confidence            4899999999995 5775 799999999999999999999999999999999999999998753

>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=99.18  E-value=1.1e-11  Score=82.03  Aligned_cols=66  Identities=14%  Similarity=0.131  Sum_probs=58.5

Q ss_pred             CCCCCCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           12 TTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        12 ~~~~~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      ...+.||++||.|+||.. ...+||.+|++.++.++|++..++.+.|.+.|...||++|+++||..|
T Consensus        95 ragL~fPV~rv~rlLk~~-~a~RVs~~A~vyLaavLEyl~aeILelAgn~a~~~krkrItp~dI~lA  160 (172)
T d1q9ca_          95 RNPLSLPVEKIHPLLKEV-LGYKIDHQVSVYIVAVLEYISADILKLAGNYVRNIRHYEITKQDIKVA  160 (172)
T ss_dssp             ----CCCHHHHHHHHHHH-HSSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSBCCHHHHHHH
T ss_pred             ccCceecHHHHHHHHHhc-cccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCceecHHHHHHH
Confidence            346899999999999975 566999999999999999999999999999999999999999999754

>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=99.05  E-value=1.6e-10  Score=71.18  Aligned_cols=66  Identities=21%  Similarity=0.253  Sum_probs=60.7

Q ss_pred             CCCCCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           13 TRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        13 ~~~~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      ..++||++||.|.||..--..+|++.|+++++..+|+...++.+.|.+.+...+++.|+++||..|
T Consensus         8 agL~FpV~ri~r~Lk~~~~~~rv~~~apVylaAVLEYL~aEILELAgn~a~~~k~~rItprhi~la   73 (106)
T d1u35c1           8 AGVIFPVGRMLRYIKKGHPKYRIGVGAPVYMAAVLEYLTAEILELAVNAARDNKKGRVTPRHILLA   73 (106)
T ss_dssp             HTCSSCHHHHHHHHHHHSTTSEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHH
T ss_pred             CCcccCHHHHHHHHhCCCCccccCCCCchhHHHHHHHHHHHHHHHHHHHHHHcCCCeeecchhhhc
Confidence            368999999999999765567999999999999999999999999999999999999999999643

>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=99.02  E-value=3.8e-10  Score=69.45  Aligned_cols=66  Identities=23%  Similarity=0.349  Sum_probs=61.1

Q ss_pred             CCCCCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           13 TRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        13 ~~~~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      ..++||++||.|.+|..--..+|+..|+++++..+|+...++.+.|++.|...+++.|+++||..|
T Consensus         9 AgL~FpV~rv~r~Lk~~~~~~rv~~~apVylaAVLEYLtaEiLELAgn~a~~~k~~rItPrhi~lA   74 (106)
T d1tzya_           9 AGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLA   74 (106)
T ss_dssp             HTCSSCHHHHHHHHHHTTSSSEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHH
T ss_pred             CCccCChHHHHHHHHcCccccccCCCchHHHHHHHHHHHHHHHHHhhHHHHhcCCceecchhhhhc
Confidence            368999999999999866667999999999999999999999999999999999999999999743

>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=98.99  E-value=5.2e-10  Score=68.42  Aligned_cols=66  Identities=23%  Similarity=0.298  Sum_probs=59.5

Q ss_pred             CCCCCChHHHHHHhhcCcCcc-ccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           13 TRPEFPVGRVKKIIKLDEDIN-KVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        13 ~~~~lP~arVkrImK~d~dv~-~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      ..++||++||.|.||..--.. +|+..|+++++..+|++..++.+.|.+.+..++++.|+++||..|
T Consensus         8 AgL~FpVgrv~r~L~~~~~~~~rv~~~A~VyLaAvLEYL~aEILelagn~a~~~~~~rItpr~l~la   74 (103)
T d1f66c_           8 AGLQFPVGRIHRHLKSRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLA   74 (103)
T ss_dssp             HTCSSCHHHHHHHHHHTSCSSCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHH
T ss_pred             CCcccChHHHHHHHhccCccceecCCCceeeHHHHHHHHHHHHHHHhhhhhccCCCCeeechhhhcc
Confidence            367999999999999765443 699999999999999999999999999999999999999999653

>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=98.99  E-value=4.9e-10  Score=65.88  Aligned_cols=62  Identities=13%  Similarity=0.180  Sum_probs=58.2

Q ss_pred             CCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           16 EFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        16 ~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      .+|.+-|+||++.. ++.+||.++...+...+|.|+..++.+|..+++..+||||+.+||..|
T Consensus         9 gI~k~~i~Riar~~-Gv~ris~d~~~~l~~~l~~~l~~i~~~a~~~~~hakRKTvt~~DV~~A   70 (82)
T d2huec1           9 GITKPAIRRLARRG-GVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYA   70 (82)
T ss_dssp             SSCHHHHHHHHHHT-TCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHH
T ss_pred             CcCHHHHHHHHHHc-CcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHH
Confidence            58999999999986 778999999999999999999999999999999999999999999753

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

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

Probab=98.24  E-value=8.5e-07  Score=53.10  Aligned_cols=63  Identities=29%  Similarity=0.374  Sum_probs=52.4

Q ss_pred             CCCCChHH-HHHHhhc-CcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhc
Q 038850           14 RPEFPVGR-VKKIIKL-DEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRV   77 (78)
Q Consensus        14 ~~~lP~ar-VkrImK~-d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~   77 (78)
                      -..+|..| ||.|+.. .++ .+++++|..++..|+|.|+-.|-+.|+.+|...||.||.++|+.-
T Consensus        22 Ipk~pF~RLVRei~~~~~~~-~r~~~~Al~aLQea~E~yLv~lfeda~~~a~HakRvTl~~kD~~L   86 (95)
T d1tzyc_          22 IRKLPFQRLVREIAQDFKTD-LRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQL   86 (95)
T ss_dssp             SCHHHHHHHHHHHHHHHCTT-CEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHH
T ss_pred             cccccHHHHHHHHHHhcCCC-CEeeHHHHHHHHHHHHHHHHHHHHHhHHHHHhcCCCcCCHHHHHH
Confidence            34455555 3555553 555 489999999999999999999999999999999999999999864

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

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

Probab=98.08  E-value=1.1e-05  Score=45.86  Aligned_cols=65  Identities=12%  Similarity=0.202  Sum_probs=59.6

Q ss_pred             CCCCCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           13 TRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        13 ~~~~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      .+..||..-||-|-.+- ++.+++.|+...++.-+|+=+.++.++|.++++..+|++|+.+||..|
T Consensus         3 ~~S~~~~esik~iAeS~-Gi~~l~de~a~~LA~DveYRl~eiiQeA~KFMrhskR~~Ltt~Did~A   67 (70)
T d1tafb_           3 YGSSISAESMKVIAESI-GVGSLSDDAAKELAEDVSIKLKRIVQDAAKFMNHAKRQKLSVRDIDMS   67 (70)
T ss_dssp             CSCCCCHHHHHHHHHHT-TCCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHH
T ss_pred             CcccCCHHHHHHHHHHc-CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCcCcHHHHHHH
Confidence            35679999999998877 677899999999999999999999999999999999999999999764

>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=97.98  E-value=8.4e-06  Score=48.17  Aligned_cols=64  Identities=19%  Similarity=0.325  Sum_probs=55.1

Q ss_pred             CCCCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhC-CCCccCchhhhcC
Q 038850           14 RPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEK-KRKTIKLGDMRVA   78 (78)
Q Consensus        14 ~~~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~-~rkti~~~Di~~A   78 (78)
                      ...||-+.|||||+.--+ ..||.....+++-.+.+|+.+|.+.|.+...+. ...-|+++||..|
T Consensus        14 Rs~~~K~~vkrl~~~~~g-~sv~~~v~i~v~giaKvFvGEiVE~A~~V~~~~~e~~PL~P~HireA   78 (89)
T d1bh9b_          14 RSAFPKAAIKRLIQSITG-TSVSQNVVIAMSGISKVFVGEVVEEALDVCEKWGEMPPLQPKHMREA   78 (89)
T ss_dssp             HCCCCHHHHHHHHHHHHS-SCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSSCCHHHHHHH
T ss_pred             HhhCCHHHHHHHHHHHcC-CCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCcHHHHHH
Confidence            356999999999997544 479999999999999999999999999998765 4458999999765

>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=97.68  E-value=4.8e-05  Score=45.02  Aligned_cols=57  Identities=25%  Similarity=0.300  Sum_probs=51.0

Q ss_pred             HHHHHhh-cCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           21 RVKKIIK-LDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        21 rVkrImK-~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      -|.|++| .+||. .+|+.|...+.--.....+.++.+|...+..++|+||+.++|..|
T Consensus         8 Yi~kVLKqVhp~~-giS~kam~imnsfvndiferIa~EA~~La~~~kr~TitsreIqtA   65 (92)
T d1tzyb_           8 YVYKVLKQVHPDT-GISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTA   65 (92)
T ss_dssp             HHHHHHHHHCTTC-EECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHH
T ss_pred             HHHHHHHhhCCCC-CccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCcHHHHHHH
Confidence            4778888 48997 599999999999888888999999999999999999999999764

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

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

Probab=96.25  E-value=0.011  Score=33.27  Aligned_cols=59  Identities=10%  Similarity=0.300  Sum_probs=51.5

Q ss_pred             CChHHHHHHhh-cCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhh
Q 038850           17 FPVGRVKKIIK-LDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMR   76 (78)
Q Consensus        17 lP~arVkrImK-~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~   76 (78)
                      |--.++..+++ .||+. .+..++-.++...+.-|+...+..|...|+..|..+|..+||.
T Consensus         4 l~K~~L~eLv~~idp~~-~ld~~vee~ll~iADdFV~~V~~~ac~lAKhR~s~~le~kDvq   63 (74)
T d1h3ob_           4 LTKKKLQDLVREVDPNE-QLDEDVEEMLLQIADDFIESVVTAACQLARHRKSSTLEVKDVQ   63 (74)
T ss_dssp             SCHHHHHHHHHHHCSSC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCEECHHHHH
T ss_pred             ccHHHHHHHHHHhCCCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCcHHHHH
Confidence            44556777776 47774 6999999999999999999999999999999999999999985

>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=91.91  E-value=0.38  Score=26.16  Aligned_cols=56  Identities=20%  Similarity=0.253  Sum_probs=38.9

Q ss_pred             HHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           22 VKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        22 VkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      |..|+|.- +|.....-.+.-+-.-+=-++..+...|.-++...|+++|..+||.-|
T Consensus         7 i~~iL~~~-GV~~yeprV~~qlLef~yRYtt~VL~DA~vys~HA~k~~id~dDVkLA   62 (68)
T d1tafa_           7 IMSILKEL-NVQEYEPRVVNQLLEFTFRYVTSILDDAKVYANHARKKTIDLDDVRLA   62 (68)
T ss_dssp             HHHHHHHT-TCCCBCTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHH
T ss_pred             HHHHHHHc-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHH
Confidence            45566654 454555555444433333467778899999999999999999999754

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

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

Probab=91.31  E-value=0.31  Score=25.13  Aligned_cols=37  Identities=30%  Similarity=0.323  Sum_probs=31.1

Q ss_pred             HHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHH
Q 038850           20 GRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEK   57 (78)
Q Consensus        20 arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~   57 (78)
                      +||+.|-|.. ++.-+++|++.+|+-||+.=+..|.++
T Consensus        10 ~ri~~I~~k~-Gl~e~~~dV~~lISHA~QeRLk~lvEK   46 (50)
T d1h3oa_          10 RRILEIGKKH-GITELHPDVVSYVSHATQQRLQNLVEK   46 (50)
T ss_dssp             HHHHHHHHTT-TCCEECTTHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHc-CCCccCHHHHHHHHHHHHHHHHHHHHH
Confidence            5788888876 667899999999999999888877765

>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=90.67  E-value=0.38  Score=29.86  Aligned_cols=59  Identities=19%  Similarity=0.109  Sum_probs=46.1

Q ss_pred             CCChHHHHHHhhcCcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCchhh
Q 038850           16 EFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFLAEKSAEAAIEKKRKTIKLGDM   75 (78)
Q Consensus        16 ~lP~arVkrImK~d~dv~~vs~eA~~~i~~A~ElFi~~L~~~A~~~a~~~~rkti~~~Di   75 (78)
                      -.|++++.++++.-.+.. |-++-..-+.--.+-=+.+|...|...|+.+||..|.+.|+
T Consensus         2 ~m~~~k~e~~FR~aa~Ld-vdK~d~~r~~d~V~~Kl~DLllva~~~A~~n~RdvI~~~DL   60 (148)
T d1wwia1           2 LMKVAEFERLFRQAAGLD-VDKNDLKRVSDFLRNKLYDLLAVAERNAKYNGRDLIFEPDL   60 (148)
T ss_dssp             CSCHHHHHHHHHHHHCCC-CCGGGHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECGGGS
T ss_pred             CCcHHHHHHHHHHHhccC-CcHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeeccccC
Confidence            368999999999866654 34444445555556667889999999999999999999997

>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=89.70  E-value=0.45  Score=29.11  Aligned_cols=45  Identities=24%  Similarity=0.211  Sum_probs=33.7

Q ss_pred             ccchHHHHHHHHHHH------------HHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           34 KVTSEALFIVSRSTE------------LFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        34 ~vs~eA~~~i~~A~E------------lFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      .++.++...++.-+.            --+..++..|...|..+++++|+.+||.+|
T Consensus       213 ~~~~~~l~~ia~~~~~~~~~~~~~G~~R~a~~ll~~a~~~A~~~~~~~I~~edv~~A  269 (276)
T d1fnna2         213 SYSEDILQMIADITGAQTPLDTNRGDARLAIDILYRSAYAAQQNGRKHIAPEDVRKS  269 (276)
T ss_dssp             SSCHHHHHHHHHHHSBSSTTCTTSCCHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHH
T ss_pred             cccHHHHHHHHHHhhhhhhhhhcCCCHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHH
Confidence            477888777765431            123456788899999999999999999875

>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=88.57  E-value=0.6  Score=28.67  Aligned_cols=45  Identities=16%  Similarity=0.002  Sum_probs=34.6

Q ss_pred             ccchHHHHHHHHHHH---------HHHHHHHHHHHHHHHhCCCCccCchhhhcC
Q 038850           34 KVTSEALFIVSRSTE---------LFLRFLAEKSAEAAIEKKRKTIKLGDMRVA   78 (78)
Q Consensus        34 ~vs~eA~~~i~~A~E---------lFi~~L~~~A~~~a~~~~rkti~~~Di~~A   78 (78)
                      .++.++..++++-+.         --...++..|...|...++..|+.+||.+|
T Consensus       230 ~~~~~al~~ia~~~~~~~~~~gd~R~ai~~l~~a~~~A~~~~~~~It~~~V~~A  283 (287)
T d1w5sa2         230 VWEPRHLELISDVYGEDKGGDGSARRAIVALKMACEMAEAMGRDSLSEDLVRKA  283 (287)
T ss_dssp             SCCHHHHHHHHHHHCGGGTSCCCHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHH
T ss_pred             CCCHHHHHHHHHHHhccccCCCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHH
Confidence            478888888776441         123457888999999999999999999875