Citrus Sinensis ID: 047769

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-
THEVRNKKVKLSRITLIYSSDTQYQRKIMSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYGFGG
ccccccEEEEEccEEEccccccHHHHHHHccccccccccccccccccccccccccccccHHHHHHHHHHccccEEccHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHcccccccccc
cccEEccEEEEEccEEEEcccccEEEEEEccccccccccccccccccccccccHHHHccHHHHHHHHHHccccEEcccHHHHHHHHHHHHHHHHHHHHHHHHHHccccEEcHHHHHHHHHHcccEEEcccc
thevrnkkvkLSRITLIYSSDTQYQRKImsgrgkggkglgkggakRHRKVLRDNIQGITKPAIRRLARrggvkrisgliyeETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQgrtlygfgg
thevrnkkvklsritliyssdtqyqrkimsgrgkggkglgkggakrhrkvlrdniqgitkpairrlarrggvkrisgliyeetrgvLKIFLENVIRDAVTyteharrktvtamDVVYALKrqgrtlygfgg
THEVRNKKVKLSRITLIYSSDTQYQRKIMSgrgkggkglgkggakrhrkVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYGFGG
************RITLIY************************************IQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYG***
*************ITLIYS***********************************IQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYGFG*
*********KLSRITLIYSSDTQYQRKIMSG****************RKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYGFGG
**EVRNKKVKLSRITLIYSSDTQYQRKIMS******************KVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYGFGG
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
ooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
THEVRNKKVKLSRITLIYSSDTQYQRKIMSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYGFGG
no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST ?

Original result of BLAST against SWISS-PROT Database

ID ?Alignment graph ?Length ? Definition ? RBH(Q2H) ? RBH(H2Q) ? Q cover ? H cover ? Identity ? E-value ?
Query131 2.2.26 [Sep-21-2011]
P0CG89103 Histone H4 OS=Glycine max no no 0.786 1.0 1.0 9e-52
Q76H85103 Histone H4 OS=Silene lati N/A no 0.786 1.0 1.0 9e-52
P62788103 Histone H4 OS=Pisum sativ N/A no 0.786 1.0 1.0 9e-52
P62787103 Histone H4 OS=Zea mays GN N/A no 0.786 1.0 1.0 9e-52
P62887103 Histone H4 OS=Lolium temu N/A no 0.786 1.0 1.0 9e-52
Q6LAF3103 Histone H4 OS=Flaveria tr N/A no 0.786 1.0 1.0 9e-52
Q6WZ83103 Histone H4 OS=Eucalyptus N/A no 0.786 1.0 1.0 9e-52
Q6PMI5103 Histone H4 OS=Chelidonium N/A no 0.786 1.0 1.0 9e-52
P59259103 Histone H4 OS=Arabidopsis yes no 0.786 1.0 1.0 9e-52
P62785103 Histone H4 variant TH011 N/A no 0.786 1.0 1.0 9e-52
>sp|P0CG89|H4_SOYBN Histone H4 OS=Glycine max PE=3 SV=1 Back     alignment and function desciption
 Score =  201 bits (512), Expect = 9e-52,   Method: Compositional matrix adjust.
 Identities = 103/103 (100%), Positives = 103/103 (100%)

Query: 29  MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK 88
           MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
Sbjct: 1   MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK 60

Query: 89  IFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYGFGG 131
           IFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYGFGG
Sbjct: 61  IFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYGFGG 103
Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling.
Glycine max (taxid: 3847)
>sp|Q76H85|H4_SILLA Histone H4 OS=Silene latifolia GN=SlH4 PE=3 SV=3 Back     alignment and function description
>sp|P62788|H4_PEA Histone H4 OS=Pisum sativum PE=1 SV=2 Back     alignment and function description
>sp|P62787|H4_MAIZE Histone H4 OS=Zea mays GN=H4C7 PE=1 SV=2 Back     alignment and function description
>sp|P62887|H4_LOLTE Histone H4 OS=Lolium temulentum PE=3 SV=2 Back     alignment and function description
>sp|Q6LAF3|H4_FLATR Histone H4 OS=Flaveria trinervia GN=hh4 PE=3 SV=3 Back     alignment and function description
>sp|Q6WZ83|H4_EUCGL Histone H4 OS=Eucalyptus globulus PE=3 SV=3 Back     alignment and function description
>sp|Q6PMI5|H4_CHEMJ Histone H4 OS=Chelidonium majus PE=3 SV=3 Back     alignment and function description
>sp|P59259|H4_ARATH Histone H4 OS=Arabidopsis thaliana GN=At1g07660 PE=1 SV=2 Back     alignment and function description
>sp|P62785|H41_WHEAT Histone H4 variant TH011 OS=Triticum aestivum PE=3 SV=2 Back     alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query131
414589551 248 TPA: histone H4.3 [Zea mays] 0.786 0.415 1.0 1e-52
413947466221 hypothetical protein ZEAMMB73_313798 [Ze 0.786 0.466 1.0 2e-52
326512852 456 predicted protein [Hordeum vulgare subsp 0.786 0.225 1.0 3e-52
391344310228 PREDICTED: histone H2B.3-like [Metaseiul 0.801 0.460 0.980 4e-52
410932519 318 PREDICTED: uncharacterized protein LOC10 0.923 0.380 0.859 9e-52
443708142186 hypothetical protein CAPTEDRAFT_219998 [ 0.877 0.618 0.913 2e-51
390461177 498 PREDICTED: uncharacterized protein LOC10 0.786 0.206 0.980 2e-51
195617694149 histone H4 [Zea mays] 0.786 0.691 1.0 3e-51
357479669 381 Histone H4 [Medicago truncatula] gi|3555 0.778 0.267 1.0 3e-51
403271042 251 PREDICTED: uncharacterized protein LOC10 0.786 0.410 0.980 3e-51
>gi|414589551|tpg|DAA40122.1| TPA: histone H4.3 [Zea mays] Back     alignment and taxonomy information
 Score =  210 bits (534), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 103/103 (100%), Positives = 103/103 (100%)

Query: 29  MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK 88
           MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
Sbjct: 146 MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK 205

Query: 89  IFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYGFGG 131
           IFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYGFGG
Sbjct: 206 IFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYGFGG 248

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|413947466|gb|AFW80115.1| hypothetical protein ZEAMMB73_313798 [Zea mays] Back     alignment and taxonomy information
>gi|326512852|dbj|BAK03333.1| predicted protein [Hordeum vulgare subsp. vulgare] Back     alignment and taxonomy information
>gi|391344310|ref|XP_003746444.1| PREDICTED: histone H2B.3-like [Metaseiulus occidentalis] gi|391344318|ref|XP_003746448.1| PREDICTED: histone H2B.3-like [Metaseiulus occidentalis] gi|391344320|ref|XP_003746449.1| PREDICTED: histone H2B.3-like [Metaseiulus occidentalis] Back     alignment and taxonomy information
>gi|410932519|ref|XP_003979641.1| PREDICTED: uncharacterized protein LOC101077311 [Takifugu rubripes] Back     alignment and taxonomy information
>gi|443708142|gb|ELU03397.1| hypothetical protein CAPTEDRAFT_219998 [Capitella teleta] Back     alignment and taxonomy information
>gi|390461177|ref|XP_003732622.1| PREDICTED: uncharacterized protein LOC100397108 [Callithrix jacchus] Back     alignment and taxonomy information
>gi|195617694|gb|ACG30677.1| histone H4 [Zea mays] Back     alignment and taxonomy information
>gi|357479669|ref|XP_003610120.1| Histone H4 [Medicago truncatula] gi|355511175|gb|AES92317.1| Histone H4 [Medicago truncatula] Back     alignment and taxonomy information
>gi|403271042|ref|XP_003927456.1| PREDICTED: uncharacterized protein LOC101029452 [Saimiri boliviensis boliviensis] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query131
TAIR|locus:2026570103 AT1G07660 [Arabidopsis thalian 0.625 0.796 1.0 2.6e-38
TAIR|locus:2026565103 AT1G07820 [Arabidopsis thalian 0.625 0.796 1.0 2.6e-38
TAIR|locus:2053195103 HIS4 "histone H4" [Arabidopsis 0.625 0.796 1.0 2.6e-38
TAIR|locus:2077127103 AT3G45930 [Arabidopsis thalian 0.625 0.796 1.0 2.6e-38
TAIR|locus:2078166103 AT3G46320 [Arabidopsis thalian 0.625 0.796 1.0 2.6e-38
TAIR|locus:2084380103 AT3G53730 [Arabidopsis thalian 0.625 0.796 1.0 2.6e-38
TAIR|locus:2174314103 AT5G59690 [Arabidopsis thalian 0.625 0.796 1.0 2.6e-38
TAIR|locus:2168037103 AT5G59970 [Arabidopsis thalian 0.625 0.796 1.0 2.6e-38
FB|FBgn0051611103 His4:CG31611 "His4:CG31611" [D 0.625 0.796 0.975 7e-38
FB|FBgn0053869103 His4:CG33869 "His4:CG33869" [D 0.625 0.796 0.975 7e-38
TAIR|locus:2026570 AT1G07660 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 410 (149.4 bits), Expect = 2.6e-38, P = 2.6e-38
 Identities = 82/82 (100%), Positives = 82/82 (100%)

Query:    50 VLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKT 109
             VLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKT
Sbjct:    22 VLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKT 81

Query:   110 VTAMDVVYALKRQGRTLYGFGG 131
             VTAMDVVYALKRQGRTLYGFGG
Sbjct:    82 VTAMDVVYALKRQGRTLYGFGG 103
GO:0000786 "nucleosome" evidence=IEA
GO:0003677 "DNA binding" evidence=ISS
GO:0005634 "nucleus" evidence=ISM;IEA
GO:0006334 "nucleosome assembly" evidence=IEA
GO:0009507 "chloroplast" evidence=IDA
GO:0005774 "vacuolar membrane" evidence=IDA
GO:0005515 "protein binding" evidence=IPI
GO:0005886 "plasma membrane" evidence=IDA
GO:0005829 "cytosol" evidence=IDA
GO:0009506 "plasmodesma" evidence=IDA
GO:0005794 "Golgi apparatus" evidence=RCA
TAIR|locus:2026565 AT1G07820 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2053195 HIS4 "histone H4" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2077127 AT3G45930 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2078166 AT3G46320 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2084380 AT3G53730 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2174314 AT5G59690 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2168037 AT5G59970 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
FB|FBgn0051611 His4:CG31611 "His4:CG31611" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
FB|FBgn0053869 His4:CG33869 "His4:CG33869" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries ?

Original result of BLAST against SWISS-PROT

ID ?Name ?Annotated EC number ?Identity ?Query coverage ?Hit coverage ?RBH(Q2H) ?RBH(H2Q) ?
P62796H4_ORENINo assigned EC number0.98050.78621.0yesno
P62797H4_ONCMYNo assigned EC number0.98050.78621.0N/Ano
P62794H4_URECANo assigned EC number0.98050.78621.0N/Ano
P62795H4_PLADUNo assigned EC number0.98050.78621.0N/Ano
P0CG89H4_SOYBNNo assigned EC number1.00.78621.0nono
P62798H4_XENBONo assigned EC number0.98050.78621.0N/Ano
P62799H4_XENLANo assigned EC number0.98050.78621.0N/Ano
P84042H4_DROHYNo assigned EC number0.97670.65640.8349N/Ano
P84043H4_DROSINo assigned EC number0.97670.65640.8349N/Ano
P84040H4_DROMENo assigned EC number0.97670.65640.8349yesno
Q43083H4_PYRSANo assigned EC number0.98050.78621.0N/Ano
P84041H4_DROERNo assigned EC number0.97670.65640.8349N/Ano
P62806H4_MOUSENo assigned EC number0.98050.78621.0yesno
Q28DR4H4_XENTRNo assigned EC number0.98050.78621.0yesno
Q7KQD1H4_CHAVRNo assigned EC number0.98050.78621.0N/Ano
P62804H4_RATNo assigned EC number0.98050.78621.0nono
Q6WZ83H4_EUCGLNo assigned EC number1.00.78621.0N/Ano
Q9U7D0H4_MASBANo assigned EC number0.88880.78620.9537N/Ano
P62787H4_MAIZENo assigned EC number1.00.78621.0N/Ano
P84049H4_MYRRUNo assigned EC number0.97670.65640.8349N/Ano
Q76H85H4_SILLANo assigned EC number1.00.78621.0N/Ano
Q6LAF3H4_FLATRNo assigned EC number1.00.78621.0N/Ano
Q6WV73H4_MYTCANo assigned EC number0.98050.78621.0N/Ano
Q6WV72H4_MYTTRNo assigned EC number0.98050.78621.0N/Ano
Q76FF5H4_DROTENo assigned EC number0.97670.65640.8349N/Ano
Q4R362H4_MACFANo assigned EC number0.98050.78621.0N/Ano
Q7K8C0H4_MYTEDNo assigned EC number0.98050.78621.0N/Ano
P62801H4_CHICKNo assigned EC number0.98050.78621.0yesno
P84044H4_DROYANo assigned EC number0.97670.65640.8349N/Ano
P82888H4_OLILUNo assigned EC number0.98050.78621.0N/Ano
P84045H4_TIGCANo assigned EC number0.97670.65640.8349N/Ano
P62785H41_WHEATNo assigned EC number1.00.78621.0N/Ano
Q71V09H4_CAPANNo assigned EC number0.99020.78621.0N/Ano
P62786H42_WHEATNo assigned EC number0.99020.78621.0N/Ano
P62788H4_PEANo assigned EC number1.00.78621.0N/Ano
Q76FD9H4_DROSENo assigned EC number0.97670.65640.8349N/Ano
P84050H4_RHYAMNo assigned EC number0.97670.65640.8349N/Ano
Q76FF1H4_DROORNo assigned EC number0.97670.65640.8349N/Ano
Q6PMI5H4_CHEMJNo assigned EC number1.00.78621.0N/Ano
P35057H4_SOLLCNo assigned EC number0.99020.78621.0N/Ano
P62805H4_HUMANNo assigned EC number0.98050.78621.0yesno
P62802H4_PIGNo assigned EC number0.98050.78621.0yesno
P62803H4_BOVINNo assigned EC number0.98050.78621.0yesno
P62800H4_CAIMONo assigned EC number0.98050.78621.0N/Ano
Q6WV90H4_MYTGANo assigned EC number0.98050.78621.0N/Ano
P62887H4_LOLTENo assigned EC number1.00.78621.0N/Ano
Q76FE7H4_DROMANo assigned EC number0.97670.65640.8349N/Ano
Q6V9I2H4_SOLCHNo assigned EC number0.99020.78621.0N/Ano
P59259H4_ARATHNo assigned EC number1.00.78621.0yesno
Q5RCS7H4_PONABNo assigned EC number0.98050.78621.0yesno

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Your Input:
JGI116843
hypothetical protein; Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling (By similarity) (216 aa)
(Branchiostoma floridae)
Predicted Functional Partners:
 
Sorry, there are no predicted associations at the current settings.
 

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query131
PLN00035103 PLN00035, PLN00035, histone H4; Provisional 4e-54
PTZ00015102 PTZ00015, PTZ00015, histone H4; Provisional 1e-50
cd0007685 cd00076, H4, Histone H4, one of the four histones, 2e-41
smart0041774 smart00417, H4, Histone H4 2e-38
COG203691 COG2036, HHT1, Histones H3 and H4 [Chromatin struc 4e-26
PLN0016359 PLN00163, PLN00163, histone H4; Provisional 3e-19
pfam0012575 pfam00125, Histone, Core histone H2A/H2B/H3/H4 1e-11
smart0080365 smart00803, TAF, TATA box binding protein associat 7e-05
cd08050 343 cd08050, TAF6, TATA Binding Protein (TBP) Associat 4e-04
cd0798172 cd07981, TAF12, TATA Binding Protein (TBP) Associa 0.003
>gnl|CDD|177669 PLN00035, PLN00035, histone H4; Provisional Back     alignment and domain information 
 Score =  164 bits (417), Expect = 4e-54
 Identities = 103/103 (100%), Positives = 103/103 (100%)

Query: 29  MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK 88
           MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
Sbjct: 1   MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK 60

Query: 89  IFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYGFGG 131
           IFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYGFGG
Sbjct: 61  IFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYGFGG 103

Length = 103
>gnl|CDD|185397 PTZ00015, PTZ00015, histone H4; Provisional Back     alignment and domain information
>gnl|CDD|238031 cd00076, H4, Histone H4, one of the four histones, along with H2A, H2B and H3, which forms the eukaryotic nucleosome core; along with H3, it plays a central role in nucleosome formation; histones bind to DNA and wrap the genetic material into "beads on a string" in which DNA (the string) is wrapped around small blobs of histones (the beads) at regular intervals; play a role in the inheritance of specialized chromosome structures and the control of gene activity; defects in the establishment of proper chromosome structure by histones may activate or silence genes aberrantly and thus lead to disease; the sequence of histone H4 has remained almost invariant in more than 2 billion years of evolution Back     alignment and domain information
>gnl|CDD|128694 smart00417, H4, Histone H4 Back     alignment and domain information
>gnl|CDD|224947 COG2036, HHT1, Histones H3 and H4 [Chromatin structure and dynamics] Back     alignment and domain information
>gnl|CDD|165730 PLN00163, PLN00163, histone H4; Provisional Back     alignment and domain information
>gnl|CDD|201020 pfam00125, Histone, Core histone H2A/H2B/H3/H4 Back     alignment and domain information
>gnl|CDD|129039 smart00803, TAF, TATA box binding protein associated factor Back     alignment and domain information
>gnl|CDD|173968 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 Back     alignment and domain information
>gnl|CDD|173964 cd07981, TAF12, TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 131
PLN00035103 histone H4; Provisional 100.0
PTZ00015102 histone H4; Provisional 100.0
KOG3467103 consensus Histone H4 [Chromatin structure and dyna 100.0
cd0007685 H4 Histone H4, one of the four histones, along wit 100.0
smart0041774 H4 Histone H4. 99.97
PLN0016359 histone H4; Provisional 99.91
COG203691 HHT1 Histones H3 and H4 [Chromatin structure and d 99.9
smart0080365 TAF TATA box binding protein associated factor. TA 99.87
cd08050 343 TAF6 TATA Binding Protein (TBP) Associated Factor 99.58
PF0296966 TAF: TATA box binding protein associated factor (T 99.55
cd07979117 TAF9 TATA Binding Protein (TBP) Associated Factor 99.54
smart0057677 BTP Bromodomain transcription factors and PHD doma 99.5
PF15511414 CENP-T: Centromere kinetochore component CENP-T; P 99.38
PF0012575 Histone: Core histone H2A/H2B/H3/H4 histone h2a si 99.36
KOG0869168 consensus CCAAT-binding factor, subunit A (HAP3) [ 99.34
cd0798172 TAF12 TATA Binding Protein (TBP) Associated Factor 99.33
PF0080865 CBFD_NFYB_HMF: Histone-like transcription factor ( 99.3
KOG2549 576 consensus Transcription initiation factor TFIID, s 99.29
COG5095 450 TAF6 Transcription initiation factor TFIID, subuni 99.25
PF0752477 Bromo_TP: Bromodomain associated; InterPro: IPR006 99.11
PF1563076 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 99.09
cd00074115 H2A Histone 2A; H2A is a subunit of the nucleosome 99.03
smart00428105 H3 Histone H3. 98.94
PF02291129 TFIID-31kDa: Transcription initiation factor IID, 98.91
KOG3334148 consensus Transcription initiation factor TFIID, s 98.71
PLN00161135 histone H3; Provisional 98.28
PLN0016097 histone H3; Provisional 98.25
KOG0870172 consensus DNA polymerase epsilon, subunit D [Trans 98.25
PLN00121136 histone H3; Provisional 98.25
PTZ00018136 histone H3; Provisional 98.2
PF0384768 TFIID_20kDa: Transcription initiation factor TFIID 98.19
KOG2389 353 consensus Predicted bromodomain transcription fact 98.18
COG5094145 TAF9 Transcription initiation factor TFIID, subuni 98.08
PLN00153129 histone H2A; Provisional 98.05
PLN00154136 histone H2A; Provisional 98.02
KOG4336 323 consensus TBP-associated transcription factor Prod 98.0
PLN00157132 histone H2A; Provisional 97.94
PLN00156139 histone H2AX; Provisional 97.91
KOG1142258 consensus Transcription initiation factor TFIID, s 97.88
PTZ00017134 histone H2A; Provisional 97.88
KOG0871156 consensus Class 2 transcription repressor NC2, bet 97.76
KOG1756131 consensus Histone 2A [Chromatin structure and dyna 97.7
PF0226993 TFIID-18kDa: Transcription initiation factor IID, 97.37
smart00414106 H2A Histone 2A. 97.36
COG5262132 HTA1 Histone H2A [Chromatin structure and dynamics 97.32
PLN00158116 histone H2B; Provisional 97.27
PTZ00463117 histone H2B; Provisional 97.1
smart0042789 H2B Histone H2B. 96.95
cd0797892 TAF13 The TATA Binding Protein (TBP) Associated Fa 96.89
cd0804885 TAF11 TATA Binding Protein (TBP) Associated Factor 96.82
KOG1745137 consensus Histones H3 and H4 [Chromatin structure 96.77
KOG3423176 consensus Transcription initiation factor TFIID, s 96.61
PTZ00252134 histone H2A; Provisional 96.21
PF0941572 CENP-X: CENP-S associating Centromere protein X; I 96.12
COG5150148 Class 2 transcription repressor NC2, beta subunit 96.11
COG5208 286 HAP5 CCAAT-binding factor, subunit C [Transcriptio 95.9
PF0354051 TFIID_30kDa: Transcription initiation factor TFIID 95.88
PF0471990 TAFII28: hTAFII28-like protein conserved region; I 95.85
KOG1744127 consensus Histone H2B [Chromatin structure and dyn 95.21
KOG1657236 consensus CCAAT-binding factor, subunit C (HAP5) [ 94.76
PF13654509 AAA_32: AAA domain; PDB: 3K1J_B. 94.7
cd08045212 TAF4 TATA Binding Protein (TBP) Associated Factor 94.3
KOG1659 224 consensus Class 2 transcription repressor NC2, alp 94.13
PLN0015558 histone H2A; Provisional 93.53
PF05236 264 TAF4: Transcription initiation factor TFIID compon 93.17
TIGR00764 608 lon_rel lon-related putative ATP-dependent proteas 91.54
KOG3901109 consensus Transcription initiation factor IID subu 91.06
TIGR02902 531 spore_lonB ATP-dependent protease LonB. Members of 90.92
COG5248126 TAF19 Transcription initiation factor TFIID, subun 89.68
KOG3219195 consensus Transcription initiation factor TFIID, s 89.34
COG5247113 BUR6 Class 2 transcription repressor NC2, alpha su 88.6
COG5162197 Transcription initiation factor TFIID, subunit TAF 88.03
COG1067 647 LonB Predicted ATP-dependent protease [Posttransla 87.03
PRK07452 326 DNA polymerase III subunit delta; Validated 86.33
TIGR03015269 pepcterm_ATPase putative secretion ATPase, PEP-CTE 85.54
cd0831380 Death_TNFR1 Death domain of Tumor Necrosis Factor 85.07
PRK00411 394 cdc6 cell division control protein 6; Reviewed 84.01
PRK06585 343 holA DNA polymerase III subunit delta; Reviewed 83.51
PRK05574 340 holA DNA polymerase III subunit delta; Reviewed 82.72
TIGR01128 302 holA DNA polymerase III, delta subunit. subunit ar 81.69
PRK07914 320 hypothetical protein; Reviewed 80.64
PF12767252 SAGA-Tad1: Transcriptional regulator of RNA polII, 80.15
KOG1757131 consensus Histone 2A [Chromatin structure and dyna 80.04
>PLN00035 histone H4; Provisional Back     alignment and domain information 
Probab=100.00  E-value=1.1e-45  Score=266.78  Aligned_cols=103  Identities=100%  Similarity=1.472  Sum_probs=102.0

Q ss_pred             ccCCCCCCccCCCCCCccccccccccccccchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCc
Q 047769           29 MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRK  108 (131)
Q Consensus        29 m~g~gkggkg~gk~g~kR~rKvlrd~i~gIpk~aIrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RK  108 (131)
                      |+|+||||+|+|++|+|||+|+++|+|++||+++|+||||++|++|||++||+++++++++|+++|++||++||+||+||
T Consensus         1 m~~~~k~~~g~g~~g~kr~~k~~~d~i~~ipk~~IrRLARr~GvkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RK   80 (103)
T PLN00035          1 MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRK   80 (103)
T ss_pred             CCCCCCCCCCCCCCcchHHHHHHHhhhccCCHHHHHHHHHHcCcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecHHHHHHHHHHcCCcccccCC
Q 047769          109 TVTAMDVVYALKRQGRTLYGFGG  131 (131)
Q Consensus       109 TVt~~DV~~ALkr~G~~lYGF~~  131 (131)
                      ||+++||++||+++|+|||||++
T Consensus        81 TV~~~DV~~Alkr~g~~lyGf~~  103 (103)
T PLN00035         81 TVTAMDVVYALKRQGRTLYGFGG  103 (103)
T ss_pred             cCcHHHHHHHHHHcCCcCCCCCC
Confidence            99999999999999999999985

>PTZ00015 histone H4; Provisional Back     alignment and domain information
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics] Back     alignment and domain information
>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 Back     alignment and domain information
>smart00417 H4 Histone H4 Back     alignment and domain information
>PLN00163 histone H4; Provisional Back     alignment and domain information
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics] Back     alignment and domain information
>smart00803 TAF TATA box binding protein associated factor Back     alignment and domain information
>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 Back     alignment and domain information
>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 Back     alignment and domain information
>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 Back     alignment and domain information
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins Back     alignment and domain information
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T Back     alignment and domain information
>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 [, ] Back     alignment and domain information
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription] Back     alignment and domain information
>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 Back     alignment and domain information
>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 Back     alignment and domain information
>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription] Back     alignment and domain information
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription] Back     alignment and domain information
>PF07524 Bromo_TP: Bromodomain associated; InterPro: IPR006565 This bromodomain is found in eukaryotic transcription factors and PHD domain containing proteins (IPR001965 from INTERPRO) Back     alignment and domain information
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C Back     alignment and domain information
>cd00074 H2A Histone 2A; H2A is a subunit of the nucleosome Back     alignment and domain information
>smart00428 H3 Histone H3 Back     alignment and domain information
>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 [] Back     alignment and domain information
>KOG3334 consensus Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription] Back     alignment and domain information
>PLN00161 histone H3; Provisional Back     alignment and domain information
>PLN00160 histone H3; Provisional Back     alignment and domain information
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription] Back     alignment and domain information
>PLN00121 histone H3; Provisional Back     alignment and domain information
>PTZ00018 histone H3; Provisional Back     alignment and domain information
>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 [] Back     alignment and domain information
>KOG2389 consensus Predicted bromodomain transcription factor [Transcription] Back     alignment and domain information
>COG5094 TAF9 Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription] Back     alignment and domain information
>PLN00153 histone H2A; Provisional Back     alignment and domain information
>PLN00154 histone H2A; Provisional Back     alignment and domain information
>KOG4336 consensus TBP-associated transcription factor Prodos [Transcription] Back     alignment and domain information
>PLN00157 histone H2A; Provisional Back     alignment and domain information
>PLN00156 histone H2AX; Provisional Back     alignment and domain information
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription] Back     alignment and domain information
>PTZ00017 histone H2A; Provisional Back     alignment and domain information
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription] Back     alignment and domain information
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics] Back     alignment and domain information
>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) Back     alignment and domain information
>smart00414 H2A Histone 2A Back     alignment and domain information
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics] Back     alignment and domain information
>PLN00158 histone H2B; Provisional Back     alignment and domain information
>PTZ00463 histone H2B; Provisional Back     alignment and domain information
>smart00427 H2B Histone H2B Back     alignment and domain information
>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 Back     alignment and domain information
>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 Back     alignment and domain information
>KOG1745 consensus Histones H3 and H4 [Chromatin structure and dynamics] Back     alignment and domain information
>KOG3423 consensus Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription] Back     alignment and domain information
>PTZ00252 histone H2A; Provisional Back     alignment and domain information
>PF09415 CENP-X: CENP-S associating Centromere protein X; InterPro: IPR018552 Centromere protein X (CENP-X) is a component of the CENP-S complex Back     alignment and domain information
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription] Back     alignment and domain information
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription] Back     alignment and domain information
>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 Back     alignment and domain information
>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 Back     alignment and domain information
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics] Back     alignment and domain information
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription] Back     alignment and domain information
>PF13654 AAA_32: AAA domain; PDB: 3K1J_B Back     alignment and domain information
>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 Back     alignment and domain information
>KOG1659 consensus Class 2 transcription repressor NC2, alpha subunit (DRAP1) [Transcription] Back     alignment and domain information
>PLN00155 histone H2A; Provisional Back     alignment and domain information
>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 Back     alignment and domain information
>TIGR00764 lon_rel lon-related putative ATP-dependent protease Back     alignment and domain information
>KOG3901 consensus Transcription initiation factor IID subunit [Transcription] Back     alignment and domain information
>TIGR02902 spore_lonB ATP-dependent protease LonB Back     alignment and domain information
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription] Back     alignment and domain information
>KOG3219 consensus Transcription initiation factor TFIID, subunit TAF11 [Transcription] Back     alignment and domain information
>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription] Back     alignment and domain information
>COG5162 Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription] Back     alignment and domain information
>COG1067 LonB Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information
>PRK07452 DNA polymerase III subunit delta; Validated Back     alignment and domain information
>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily Back     alignment and domain information
>cd08313 Death_TNFR1 Death domain of Tumor Necrosis Factor Receptor 1 Back     alignment and domain information
>PRK00411 cdc6 cell division control protein 6; Reviewed Back     alignment and domain information
>PRK06585 holA DNA polymerase III subunit delta; Reviewed Back     alignment and domain information
>PRK05574 holA DNA polymerase III subunit delta; Reviewed Back     alignment and domain information
>TIGR01128 holA DNA polymerase III, delta subunit Back     alignment and domain information
>PRK07914 hypothetical protein; Reviewed Back     alignment and domain information
>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 [, ] Back     alignment and domain information
>KOG1757 consensus Histone 2A [Chromatin structure and dynamics] Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query131
2hue_C84 Structure Of The H3-h4 Chaperone Asf1 Bound To Hist 3e-41
1eqz_D103 X-Ray Structure Of The Nucleosome Core Particle At 3e-41
1kx3_B102 X-Ray Structure Of The Nucleosome Core Particle, Nc 4e-41
3a6n_B106 The Nucleosome Containing A Testis-Specific Histone 4e-41
3kwq_B83 Structural Characterization Of H3k56q Nucleosomes A 4e-41
1aoi_B87 Complex Between Nucleosome Core Particle (H3,H4,H2a 4e-41
2pyo_B102 Drosophila Nucleosome Core Length = 102 4e-41
2nqb_B103 Drosophila Nucleosome Structure Length = 103 4e-41
3azl_B106 Crystal Structure Of Human Nucleosome Core Particle 4e-41
3c1b_B102 The Effect Of H3 K79 Dimethylation And H4 K20 Trime 4e-41
1p3p_B102 Crystallographic Studies Of Nucleosome Core Particl 6e-41
3azn_B106 Crystal Structure Of Human Nucleosome Core Particle 8e-41
3azm_B106 Crystal Structure Of Human Nucleosome Core Particle 8e-41
3azk_B106 Crystal Structure Of Human Nucleosome Core Particle 8e-41
3azj_B106 Crystal Structure Of Human Nucleosome Core Particle 8e-41
3azi_B106 Crystal Structure Of Human Nucleosome Core Particle 8e-41
1p3o_B102 Crystallographic Studies Of Nucleosome Core Particl 1e-40
1p3i_B102 Crystallographic Studies Of Nucleosome Core Particl 1e-40
1p3g_B102 Crystallographic Studies Of Nucleosome Core Particl 1e-40
1p3b_B102 Crystallographic Studies Of Nucleosome Core Particl 2e-40
1p3f_B102 Crystallographic Studies Of Nucleosome Core Particl 2e-40
4eo5_C83 Yeast Asf1 Bound To H3H4G94P MUTANT Length = 83 2e-40
2hio_D103 Histone Octamer (Chicken), Chromosomal Protein Leng 3e-40
2yfw_B103 Heterotetramer Structure Of Kluyveromyces Lactis Cs 5e-38
1id3_B102 Crystal Structure Of The Yeast Nucleosome Core Part 1e-37
1hio_D76 Histone Octamer (Chicken), Chromosomal Protein, Alp 1e-37
2yfv_B74 The Heterotrimeric Complex Of Kluyveromyces Lactis 3e-33
2l5a_A235 Structural Basis For Recognition Of Centromere Spec 5e-27
2ly8_A121 The Budding Yeast Chaperone Scm3 Recognizes The Par 2e-25
3c9c_B27 Structural Basis Of Histone H4 Recognition By P55 L 1e-05
2xyi_B20 Crystal Structure Of Nurf55 In Complex With A H4 Pe 2e-04
3cfv_E18 Structural Basis Of The Interaction Of Rbap46RBAP48 5e-04
>pdb|2HUE|C Chain C, Structure Of The H3-h4 Chaperone Asf1 Bound To Histones H3 And H4 Length = 84 Back     alignment and structure 
Iteration: 1

 Score =  163 bits (412), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 80/82 (97%), Positives = 82/82 (100%)
Query: 50  VLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKT 109
           VLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK+FLENVIRDAVTYTEHA+RKT
Sbjct: 3   VLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKT 62
Query: 110 VTAMDVVYALKRQGRTLYGFGG 131
           VTAMDVVYALKRQGRTLYGFGG
Sbjct: 63  VTAMDVVYALKRQGRTLYGFGG 84
>pdb|1EQZ|D Chain D, X-Ray Structure Of The Nucleosome Core Particle At 2.5 A Resolution Length = 103 Back     alignment and structure
>pdb|1KX3|B Chain B, X-Ray Structure Of The Nucleosome Core Particle, Ncp146, At 2.0 A Resolution Length = 102 Back     alignment and structure
>pdb|3A6N|B Chain B, The Nucleosome Containing A Testis-Specific Histone Variant, Human H3t Length = 106 Back     alignment and structure
>pdb|3KWQ|B Chain B, Structural Characterization Of H3k56q Nucleosomes And Nucleo Arrays Length = 83 Back     alignment and structure
>pdb|1AOI|B Chain B, Complex Between Nucleosome Core Particle (H3,H4,H2a,H2b) And 146 Bp Long Dna Fragment Length = 87 Back     alignment and structure
>pdb|2PYO|B Chain B, Drosophila Nucleosome Core Length = 102 Back     alignment and structure
>pdb|2NQB|B Chain B, Drosophila Nucleosome Structure Length = 103 Back     alignment and structure
>pdb|3AZL|B Chain B, Crystal Structure Of Human Nucleosome Core Particle Containing H4k77q Mutation Length = 106 Back     alignment and structure
>pdb|3C1B|B Chain B, The Effect Of H3 K79 Dimethylation And H4 K20 Trimethylation On Nucleosome And Chromatin Structure Length = 102 Back     alignment and structure
>pdb|1P3P|B Chain B, Crystallographic Studies Of Nucleosome Core Particles Containing Histone 'sin' Mutants Length = 102 Back     alignment and structure
>pdb|3AZN|B Chain B, Crystal Structure Of Human Nucleosome Core Particle Containing H4k91q Mutation Length = 106 Back     alignment and structure
>pdb|3AZM|B Chain B, Crystal Structure Of Human Nucleosome Core Particle Containing H4k79q Mutation Length = 106 Back     alignment and structure
>pdb|3AZK|B Chain B, Crystal Structure Of Human Nucleosome Core Particle Containing H4k59q Mutation Length = 106 Back     alignment and structure
>pdb|3AZJ|B Chain B, Crystal Structure Of Human Nucleosome Core Particle Containing H4k44q Mutation Length = 106 Back     alignment and structure
>pdb|3AZI|B Chain B, Crystal Structure Of Human Nucleosome Core Particle Containing H4k31q Mutation Length = 106 Back     alignment and structure
>pdb|1P3O|B Chain B, Crystallographic Studies Of Nucleosome Core Particles Containing Histone 'sin' Mutants Length = 102 Back     alignment and structure
>pdb|1P3I|B Chain B, Crystallographic Studies Of Nucleosome Core Particles Containing Histone 'sin' Mutants Length = 102 Back     alignment and structure
>pdb|1P3G|B Chain B, Crystallographic Studies Of Nucleosome Core Particles Containing Histone 'sin' Mutants Length = 102 Back     alignment and structure
>pdb|1P3B|B Chain B, Crystallographic Studies Of Nucleosome Core Particles Containing Histone 'sin' Mutants Length = 102 Back     alignment and structure
>pdb|1P3F|B Chain B, Crystallographic Studies Of Nucleosome Core Particles Containing Histone 'sin' Mutants Length = 102 Back     alignment and structure
>pdb|4EO5|C Chain C, Yeast Asf1 Bound To H3H4G94P MUTANT Length = 83 Back     alignment and structure
>pdb|2HIO|D Chain D, Histone Octamer (Chicken), Chromosomal Protein Length = 103 Back     alignment and structure
>pdb|2YFW|B Chain B, Heterotetramer Structure Of Kluyveromyces Lactis Cse4,H4 Length = 103 Back     alignment and structure
>pdb|1ID3|B Chain B, Crystal Structure Of The Yeast Nucleosome Core Particle Reveals Fundamental Differences In Inter-Nucleosome Interactions Length = 102 Back     alignment and structure
>pdb|1HIO|D Chain D, Histone Octamer (Chicken), Chromosomal Protein, Alpha Carbons Only Length = 76 Back     alignment and structure
>pdb|2YFV|B Chain B, The Heterotrimeric Complex Of Kluyveromyces Lactis Scm3, Cse4 And H4 Length = 74 Back     alignment and structure
>pdb|2L5A|A Chain A, Structural Basis For Recognition Of Centromere Specific Histone H3 Variant By Nonhistone Scm3 Length = 235 Back     alignment and structure
>pdb|2LY8|A Chain A, The Budding Yeast Chaperone Scm3 Recognizes The Partially Unfolded Dimer Of The Centromere-specific Cse4/h4 Histone Variant Length = 121 Back     alignment and structure
>pdb|3C9C|B Chain B, Structural Basis Of Histone H4 Recognition By P55 Length = 27 Back     alignment and structure
>pdb|2XYI|B Chain B, Crystal Structure Of Nurf55 In Complex With A H4 Peptide Length = 20 Back     alignment and structure
>pdb|3CFV|E Chain E, Structural Basis Of The Interaction Of Rbap46RBAP48 WITH Histone H4 Length = 18 Back     alignment and structure

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query131
1tzy_D103 Histone H4-VI; histone-fold, tetramer-dimer-dimer, 6e-50
2yfw_B103 Histone H4, H4; cell cycle, kinetochore, centromer 6e-47
2hue_C84 Histone H4; mini beta sheet, elongated beta sandwh 7e-46
1id3_B102 Histone H4; nucleosome core particle, chromatin, p 3e-45
2l5a_A235 Histone H3-like centromeric protein CSE4, protein 7e-41
3b0c_T111 CENP-T, centromere protein T; histone fold, DNA bi 1e-26
1ku5_A70 HPHA, archaeal histon; histone fold, DNA binding p 4e-20
1b67_A68 Protein (histone HMFA); DNA binding protein; 1.48A 2e-18
1f1e_A154 Histone fold protein; archaeal histone protein, DN 9e-06
4dra_A113 Centromere protein S; DNA binding complex, DNA dam 6e-04
>1tzy_D Histone H4-VI; histone-fold, tetramer-dimer-dimer, DNA binding protein; 1.90A {Gallus gallus} SCOP: a.22.1.1 PDB: 1f66_B 1eqz_D 1hq3_D 1u35_B 2aro_D 2cv5_B* 2f8n_B 3nqu_B 3r45_B 3azg_B 3a6n_B 3an2_B 3av1_B 3av2_B 3ayw_B 3aze_B 3azf_B 3afa_B 3azh_B 3azk_B ... Length = 103 Back     alignment and structure
 Score =  153 bits (388), Expect = 6e-50
 Identities = 101/103 (98%), Positives = 103/103 (100%)

Query: 29  MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK 88
           MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
Sbjct: 1   MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK 60

Query: 89  IFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYGFGG 131
           +FLENVIRDAVTYTEHA+RKTVTAMDVVYALKRQGRTLYGFGG
Sbjct: 61  VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG 103
>2yfw_B Histone H4, H4; cell cycle, kinetochore, centromere, histone chaperone, BUDD; 2.60A {Kluyveromyces lactis nrrl y-1140} Length = 103 Back     alignment and structure
>2hue_C Histone H4; mini beta sheet, elongated beta sandwhich, DNA binding prote; 1.70A {Xenopus laevis} SCOP: a.22.1.1 PDB: 3nqj_B 1aoi_B 3kwq_B* 1hio_D 2yfv_B Length = 84 Back     alignment and structure
>1id3_B Histone H4; nucleosome core particle, chromatin, protein/DNA interaction, nucleoprotein, supercoiled DNA; 3.10A {Saccharomyces cerevisiae} SCOP: a.22.1.1 Length = 102 Back     alignment and structure
>2l5a_A Histone H3-like centromeric protein CSE4, protein histone H4; A single chain of CSE4+SCM3+H4, fusion protein; NMR {Saccharomyces cerevisiae} Length = 235 Back     alignment and structure
>3b0c_T CENP-T, centromere protein T; histone fold, DNA binding, DNA binding protein; HET: CIT; 2.20A {Gallus gallus} PDB: 3b0d_T* 3vh5_T 3vh6_T Length = 111 Back     alignment and structure
>1ku5_A HPHA, archaeal histon; histone fold, DNA binding protein; 2.30A {Pyrococcus horikoshii} SCOP: a.22.1.2 Length = 70 Back     alignment and structure
>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 Back     alignment and structure
>1f1e_A Histone fold protein; archaeal histone protein, DNA binding protein; HET: MSE; 1.37A {Methanopyrus kandleri} SCOP: a.22.1.2 Length = 154 Back     alignment and structure
>4dra_A Centromere protein S; DNA binding complex, DNA damage repair, histone-fold, DNA BI protein; 2.41A {Homo sapiens} PDB: 4drb_A Length = 113 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query131
1id3_B102 Histone H4; nucleosome core particle, chromatin, p 100.0
1tzy_D103 Histone H4-VI; histone-fold, tetramer-dimer-dimer, 100.0
2yfw_B103 Histone H4, H4; cell cycle, kinetochore, centromer 100.0
2hue_C84 Histone H4; mini beta sheet, elongated beta sandwh 100.0
2l5a_A235 Histone H3-like centromeric protein CSE4, protein 99.95
2ly8_A121 Budding yeast chaperone SCM3; centromere protein, 99.93
3b0c_T111 CENP-T, centromere protein T; histone fold, DNA bi 99.88
1ku5_A70 HPHA, archaeal histon; histone fold, DNA binding p 99.85
1f1e_A154 Histone fold protein; archaeal histone protein, DN 99.78
1taf_B70 TFIID TBP associated factor 62; transcription init 99.77
1f1e_A154 Histone fold protein; archaeal histone protein, DN 99.77
1b67_A68 Protein (histone HMFA); DNA binding protein; 1.48A 99.71
1taf_A68 TFIID TBP associated factor 42; transcription init 99.65
1n1j_A93 NF-YB; histone-like PAIR, DNA binding protein; 1.6 99.63
3b0b_B107 CENP-S, centromere protein S; histone fold, DNA bi 99.54
4dra_A113 Centromere protein S; DNA binding complex, DNA dam 99.54
3v9r_A90 MHF1, uncharacterized protein YOL086W-A; histone f 99.44
3b0c_W76 CENP-W, centromere protein W; histone fold, DNA bi 99.42
3vh5_A140 CENP-S; histone fold, chromosome segregation, DNA 99.4
1jfi_B179 DR1 protein, transcription regulator NC2 beta chai 99.37
2hue_B77 Histone H3; mini beta sheet, elongated beta sandwh 99.32
2f8n_K149 Histone H2A type 1; nucleosome, NCP, macroh2A, his 99.3
2byk_B128 Chrac-14; nucleosome sliding, histone fold, DNA-bi 99.3
1tzy_A129 Histone H2A-IV; histone-fold, tetramer-dimer-dimer 99.28
1id3_C131 Histone H2A.1; nucleosome core particle, chromatin 99.27
2f8n_G120 Core histone macro-H2A.1; nucleosome, NCP, macroh2 99.22
2nqb_C123 Histone H2A; nucleosome, NCP, chromatin, structura 99.21
1f66_C128 Histone H2A.Z; nucleosome, chromatin, histone vari 99.21
3nqj_A82 Histone H3-like centromeric protein A; alpha helix 99.2
2yfv_A100 Histone H3-like centromeric protein CSE4; cell cyc 99.09
1tzy_C136 Histone H3; histone-fold, tetramer-dimer-dimer, DN 99.07
1n1j_B97 NF-YC; histone-like PAIR, DNA binding protein; 1.6 99.07
3nqu_A140 Histone H3-like centromeric protein A; alpha helix 99.02
3r45_A156 Histone H3-like centromeric protein A; histone fol 98.99
4gqb_C26 Histone H4 peptide; TIM barrel, beta-propeller, me 98.83
4g92_C119 HAPE; transcription factor, nucleosome, minor groo 98.81
1jfi_A98 Transcription regulator NC2 alpha chain; histone, 98.8
2jss_A192 Chimera of histone H2B.1 and histone H2A.Z; histon 98.56
1tzy_B126 Histone H2B; histone-fold, tetramer-dimer-dimer, D 98.51
2nqb_D123 Histone H2B; nucleosome, NCP, chromatin, structura 98.49
2byk_A140 Chrac-16; nucleosome sliding, histone fold, DNA-bi 98.47
1h3o_B76 Transcription initiation factor TFIID 20/15 kDa su 98.21
2jss_A 192 Chimera of histone H2B.1 and histone H2A.Z; histon 97.98
2l5a_A 235 Histone H3-like centromeric protein CSE4, protein 97.75
4dra_E84 Centromere protein X; DNA binding complex, DNA dam 97.2
3b0b_C81 CENP-X, centromere protein X; histone fold, DNA bi 96.77
1bh9_B89 TAFII28; histone fold, tata binding protein, trans 96.56
1h3o_A75 Transcription initiation factor TFIID 135 kDa subu 94.99
2ly8_A121 Budding yeast chaperone SCM3; centromere protein, 94.5
3v9r_B88 MHF2, uncharacterized protein YDL160C-A; histone f 93.55
3uk6_A368 RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding 92.9
3ksy_A 1049 SOS-1, SON of sevenless homolog 1; RAS, RAS activa 91.51
3k1j_A 604 LON protease, ATP-dependent protease LON; ATP-bind 90.93
3kw6_A78 26S protease regulatory subunit 8; structural geno 90.23
2v1u_A 387 Cell division control protein 6 homolog; DNA repli 89.63
3bos_A242 Putative DNA replication factor; P-loop containing 89.59
2dzn_B82 26S protease regulatory subunit 6B homolog; ankyri 87.93
1g8p_A350 Magnesium-chelatase 38 kDa subunit; parallel beta 87.54
2krk_A86 26S protease regulatory subunit 8; structural geno 86.48
1in4_A334 RUVB, holliday junction DNA helicase RUVB; AAA+-cl 86.17
2chg_A226 Replication factor C small subunit; DNA-binding pr 84.92
3vlf_B88 26S protease regulatory subunit 7 homolog; heat re 84.48
2qby_A 386 CDC6 homolog 1, cell division control protein 6 ho 84.33
2qby_B 384 CDC6 homolog 3, cell division control protein 6 ho 83.7
3aji_B83 S6C, proteasome (prosome, macropain) 26S subunit, 83.66
1fnn_A 389 CDC6P, cell division control protein 6; ORC1, AAA 83.54
2r44_A331 Uncharacterized protein; putative ATPase, structur 82.74
>1id3_B Histone H4; nucleosome core particle, chromatin, protein/DNA interaction, nucleoprotein, supercoiled DNA; 3.10A {Saccharomyces cerevisiae} SCOP: a.22.1.1 Back     alignment and structure
Probab=100.00  E-value=1.2e-44  Score=258.99  Aligned_cols=102  Identities=91%  Similarity=1.395  Sum_probs=78.3

Q ss_pred             cCCCCCCccCCCCCCccccccccccccccchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCce
Q 047769           30 SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKT  109 (131)
Q Consensus        30 ~g~gkggkg~gk~g~kR~rKvlrd~i~gIpk~aIrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKT  109 (131)
                      +|+||||||+|++|+|||||+++|+|++||+++|+|||+++|++|||++||+++++++++|+++|++||++||+||+|||
T Consensus         1 ~~~~~~~~g~~~~g~kr~~k~~r~~i~~ip~~~I~Rlar~~Gv~rIS~da~~~l~~~le~fi~~I~~dA~~~a~HakRKT   80 (102)
T 1id3_B            1 SGRGKGGKGLGKGGAKRHRKILRDNIQGITKPAIRRLARRGGVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKT   80 (102)
T ss_dssp             -----------------------CCGGGSCHHHHHHHHHHTTCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSE
T ss_pred             CCCCCCCCCCCCCccchHHHHHHhccCCCCHHHHHHHHHHcCchhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCc
Confidence            58899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecHHHHHHHHHHcCCcccccCC
Q 047769          110 VTAMDVVYALKRQGRTLYGFGG  131 (131)
Q Consensus       110 Vt~~DV~~ALkr~G~~lYGF~~  131 (131)
                      ||++||++||+++|+|||||++
T Consensus        81 Vt~~DV~~ALkr~g~~lYGf~~  102 (102)
T 1id3_B           81 VTSLDVVYALKRQGRTLYGFGG  102 (102)
T ss_dssp             ECHHHHHHHHHHTTCCEESSCC
T ss_pred             CcHHHHHHHHHHcCCCCCCCCC
Confidence            9999999999999999999985
>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 ... Back     alignment and structure
>2yfw_B Histone H4, H4; cell cycle, kinetochore, centromere, histone chaperone, BUDD; 2.60A {Kluyveromyces lactis nrrl y-1140} Back     alignment and structure
>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 Back     alignment and structure
>2l5a_A Histone H3-like centromeric protein CSE4, protein histone H4; A single chain of CSE4+SCM3+H4, fusion protein; NMR {Saccharomyces cerevisiae} Back     alignment and structure
>2ly8_A Budding yeast chaperone SCM3; centromere protein, CENH3 variants, partially unfolded; NMR {Saccharomyces cerevisiae} Back     alignment and structure
>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 Back     alignment and structure
>1ku5_A HPHA, archaeal histon; histone fold, DNA binding protein; 2.30A {Pyrococcus horikoshii} SCOP: a.22.1.2 Back     alignment and structure
>1f1e_A Histone fold protein; archaeal histone protein, DNA binding protein; HET: MSE; 1.37A {Methanopyrus kandleri} SCOP: a.22.1.2 Back     alignment and structure
>1taf_B TFIID TBP associated factor 62; transcription initiation, histone fold, complex (TWO transcr factors); 2.00A {Drosophila melanogaster} SCOP: a.22.1.3 Back     alignment and structure
>1f1e_A Histone fold protein; archaeal histone protein, DNA binding protein; HET: MSE; 1.37A {Methanopyrus kandleri} SCOP: a.22.1.2 Back     alignment and structure
>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 Back     alignment and structure
>1taf_A TFIID TBP associated factor 42; transcription initiation, histone fold, complex (TWO transcr factors); 2.00A {Drosophila melanogaster} SCOP: a.22.1.3 Back     alignment and structure
>1n1j_A NF-YB; histone-like PAIR, DNA binding protein; 1.67A {Homo sapiens} SCOP: a.22.1.3 Back     alignment and structure
>3b0b_B CENP-S, centromere protein S; histone fold, DNA binding, DNA, nucleus, DNA binding protein; 2.15A {Gallus gallus} Back     alignment and structure
>4dra_A Centromere protein S; DNA binding complex, DNA damage repair, histone-fold, DNA BI protein; 2.41A {Homo sapiens} PDB: 4drb_A Back     alignment and structure
>3v9r_A MHF1, uncharacterized protein YOL086W-A; histone fold, fanconi anemia, DNA repair, DNA BI protein; 2.40A {Saccharomyces cerevisiae} Back     alignment and structure
>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 Back     alignment and structure
>3vh5_A CENP-S; histone fold, chromosome segregation, DNA binding, nucleus, binding protein; 2.40A {Gallus gallus} PDB: 3vh6_A Back     alignment and structure
>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 Back     alignment and structure
>2hue_B Histone H3; mini beta sheet, elongated beta sandwhich, DNA binding prote; 1.70A {Xenopus laevis} Back     alignment and structure
>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 Back     alignment and structure
>2byk_B Chrac-14; nucleosome sliding, histone fold, DNA-binding protein; 2.4A {Drosophila melanogaster} SCOP: a.22.1.3 PDB: 2bym_B Back     alignment and structure
>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 ... Back     alignment and structure
>1id3_C Histone H2A.1; nucleosome core particle, chromatin, protein/DNA interaction, nucleoprotein, supercoiled DNA; 3.10A {Saccharomyces cerevisiae} SCOP: a.22.1.1 Back     alignment and structure
>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 Back     alignment and structure
>2nqb_C Histone H2A; nucleosome, NCP, chromatin, structural protein/DNA complex; 2.30A {Drosophila melanogaster} PDB: 2pyo_C* Back     alignment and structure
>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 Back     alignment and structure
>3nqj_A Histone H3-like centromeric protein A; alpha helix, histone fold, centromere, DNA binding protein; 2.10A {Homo sapiens} Back     alignment and structure
>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 Back     alignment and structure
>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 ... Back     alignment and structure
>1n1j_B NF-YC; histone-like PAIR, DNA binding protein; 1.67A {Homo sapiens} SCOP: a.22.1.3 Back     alignment and structure
>3nqu_A Histone H3-like centromeric protein A; alpha helix, histone fold, centromere, DNA binding protein; 2.50A {Homo sapiens} PDB: 3an2_A Back     alignment and structure
>3r45_A Histone H3-like centromeric protein A; histone fold, centromere, CENP-A, histone chaperone, hjurp; 2.60A {Homo sapiens} Back     alignment and structure
>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* Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>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 ... Back     alignment and structure
>2nqb_D Histone H2B; nucleosome, NCP, chromatin, structural protein/DNA complex; 2.30A {Drosophila melanogaster} PDB: 2pyo_D* Back     alignment and structure
>2byk_A Chrac-16; nucleosome sliding, histone fold, DNA-binding protein; 2.4A {Drosophila melanogaster} SCOP: a.22.1.3 PDB: 2bym_A Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>2l5a_A Histone H3-like centromeric protein CSE4, protein histone H4; A single chain of CSE4+SCM3+H4, fusion protein; NMR {Saccharomyces cerevisiae} Back     alignment and structure
>4dra_E Centromere protein X; DNA binding complex, DNA damage repair, histone-fold, DNA BI protein; 2.41A {Homo sapiens} PDB: 4drb_J Back     alignment and structure
>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 Back     alignment and structure
>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* Back     alignment and structure
>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 Back     alignment and structure
>2ly8_A Budding yeast chaperone SCM3; centromere protein, CENH3 variants, partially unfolded; NMR {Saccharomyces cerevisiae} Back     alignment and structure
>3v9r_B MHF2, uncharacterized protein YDL160C-A; histone fold, fanconi anemia, DNA repair, DNA BI protein; 2.40A {Saccharomyces cerevisiae} Back     alignment and structure
>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D* Back     alignment and structure
>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 Back     alignment and structure
>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus} Back     alignment and structure
>3kw6_A 26S protease regulatory subunit 8; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; 2.10A {Homo sapiens} Back     alignment and structure
>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix} Back     alignment and structure
>3bos_A Putative DNA replication factor; P-loop containing nucleoside triphosphate hydrolases, struct genomics; HET: MSE CDP; 1.75A {Shewanella amazonensis} PDB: 3sc3_A Back     alignment and structure
>2dzn_B 26S protease regulatory subunit 6B homolog; ankyrin repeats, A-helical domain, structural genomics, NPPSFA; 2.20A {Saccharomyces cerevisiae} PDB: 2dzo_B Back     alignment and structure
>1g8p_A Magnesium-chelatase 38 kDa subunit; parallel beta sheet, P-loop, rossman fold, AAA+, photosynthesis, metal transport; 2.10A {Rhodobacter capsulatus} SCOP: c.37.1.20 PDB: 2x31_G Back     alignment and structure
>2krk_A 26S protease regulatory subunit 8; structural genomics, northeast structural genomics consortium (NESG), target HR3102A, PSI-2; NMR {Homo sapiens} Back     alignment and structure
>1in4_A RUVB, holliday junction DNA helicase RUVB; AAA+-class ATPase, winged-helix domain, ATP hydrolysis, walker A, walker B, sensor 1, sensor 2; HET: ADP; 1.60A {Thermotoga maritima} SCOP: a.4.5.11 c.37.1.20 PDB: 1in5_A* 1in6_A* 1in8_A* 1in7_A* 1j7k_A* Back     alignment and structure
>2chg_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATPase, ATP-binding, nucleotide-binding; HET: ANP; 2.1A {Archaeoglobus fulgidus} Back     alignment and structure
>3vlf_B 26S protease regulatory subunit 7 homolog; heat repeat, chaperone, chaperone-protein binding complex; HET: DNA; 3.80A {Saccharomyces cerevisiae} PDB: 4a3v_B* Back     alignment and structure
>2qby_A CDC6 homolog 1, cell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus} Back     alignment and structure
>2qby_B CDC6 homolog 3, cell division control protein 6 homolog 3; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus} Back     alignment and structure
>3aji_B S6C, proteasome (prosome, macropain) 26S subunit, ATPA; gankyrin, S6 ATPase, P-benzoyl-L-phenylalanine, PBPA, amber suppression; HET: PBF; 2.05A {Mus musculus} PDB: 2dwz_B* 2dvw_B* Back     alignment and structure
>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA replication initation factor, cell cycle control factor; HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11 c.37.1.20 Back     alignment and structure
>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406} Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

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

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 131
d2huec182 a.22.1.1 (C:20-101) Histone H4 {African clawed fro 4e-40
d1f1ea_151 a.22.1.2 (A:) Archaeal histone {Archaeon Methanopy 7e-19
d1f1ea_151 a.22.1.2 (A:) Archaeal histone {Archaeon Methanopy 1e-09
d1htaa_68 a.22.1.2 (A:) Archaeal histone {Archaeon Methanoth 9e-19
d1ku5a_66 a.22.1.2 (A:) Archaeal histone {Archaeon (Pyrococc 5e-16
d1q9ca_172 a.22.1.3 (A:) Histone domain of Son of sevenless p 7e-11
d1tafa_68 a.22.1.3 (A:) TAF(II)42 {Fruit fly (Drosophila mel 0.002
d1tafb_70 a.22.1.3 (B:) TAF(II)62 {Fruit fly (Drosophila mel 0.004
>d2huec1 a.22.1.1 (C:20-101) Histone H4 {African clawed frog (Xenopus laevis) [TaxId: 8355]} Length = 82 Back     information, alignment and structure

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

 Score =  126 bits (319), Expect = 4e-40
 Identities = 80/82 (97%), Positives = 82/82 (100%)

Query: 49  KVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRK 108
           KVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK+FLENVIRDAVTYTEHA+RK
Sbjct: 1   KVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRK 60

Query: 109 TVTAMDVVYALKRQGRTLYGFG 130
           TVTAMDVVYALKRQGRTLYGFG
Sbjct: 61  TVTAMDVVYALKRQGRTLYGFG 82
>d1f1ea_ a.22.1.2 (A:) Archaeal histone {Archaeon Methanopyrus kandleri [TaxId: 2320]} Length = 151 Back     information, alignment and structure
>d1f1ea_ a.22.1.2 (A:) Archaeal histone {Archaeon Methanopyrus kandleri [TaxId: 2320]} Length = 151 Back     information, alignment and structure
>d1htaa_ a.22.1.2 (A:) Archaeal histone {Archaeon Methanothermus fervidus, histone A [TaxId: 2180]} Length = 68 Back     information, alignment and structure
>d1ku5a_ a.22.1.2 (A:) Archaeal histone {Archaeon (Pyrococcus horikoshii) [TaxId: 53953]} Length = 66 Back     information, alignment and structure
>d1q9ca_ a.22.1.3 (A:) Histone domain of Son of sevenless protein {Human (Homo sapiens) [TaxId: 9606]} Length = 172 Back     information, alignment and structure
>d1tafa_ a.22.1.3 (A:) TAF(II)42 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 68 Back     information, alignment and structure
>d1tafb_ a.22.1.3 (B:) TAF(II)62 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 70 Back     information, alignment and structure

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query131
d2huec182 Histone H4 {African clawed frog (Xenopus laevis) [ 100.0
d1htaa_68 Archaeal histone {Archaeon Methanothermus fervidus 99.79
d1ku5a_66 Archaeal histone {Archaeon (Pyrococcus horikoshii) 99.73
d1f1ea_151 Archaeal histone {Archaeon Methanopyrus kandleri [ 99.58
d1tafb_70 TAF(II)62 {Fruit fly (Drosophila melanogaster) [Ta 99.58
d1f1ea_151 Archaeal histone {Archaeon Methanopyrus kandleri [ 99.44
d1n1ja_87 Nuclear transcription factor Y subunit beta (Nf-Yb 99.2
d1tafa_68 TAF(II)42 {Fruit fly (Drosophila melanogaster) [Ta 99.18
d1jfib_135 Negative cofactor 2, NC2, beta chain {Human (Homo 99.02
d2bykb189 Chrac-14 {Fruit fly (Drosophila melanogaster) [Tax 99.0
d1q9ca_172 Histone domain of Son of sevenless protein {Human 98.98
d1n1jb_78 Nuclear transcription factor Y subunit gamma (Nf-Y 98.96
d1jfia_66 Negative cofactor 2, NC2, alpha chain {Human (Homo 98.9
d1tzyc_95 Histone H3 {Chicken (Gallus gallus), erythrocytes 98.7
d1h3ob_74 TAF(II)-20, (TAF(II)-15, hTAF12), histone fold dom 98.08
d2byka172 Chrac-16 {Fruit fly (Drosophila melanogaster) [Tax 97.67
d1tzyb_92 Histone H2B {Chicken (Gallus gallus), erythrocytes 97.48
d1f66c_103 Histone H2A {Human (Homo sapiens), variant H2A.Z [ 97.47
d1u35c1106 macro-H2A.1, histone domain {Human (Homo sapiens) 97.35
d1tzya_106 Histone H2A {Chicken (Gallus gallus), erythrocytes 97.22
d1bh9b_89 TAF(II)28 {Human (Homo sapiens) [TaxId: 9606]} 96.44
d1fnna2276 CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T 94.13
d1w5sa2287 CDC6-like protein APE0152, N-terminal domain {Aero 93.42
d1h3oa_50 TAF(II)-135, (TAF(II)-130, hTAF4), histone fold do 90.98
d1ixsb2239 Holliday junction helicase RuvB {Thermus thermophi 88.51
d1wwia1148 Hypothetical protein TTHA1479 {Thermus thermophilu 81.15
>d2huec1 a.22.1.1 (C:20-101) Histone H4 {African clawed frog (Xenopus laevis) [TaxId: 8355]} Back     information, alignment and structure
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=100.00  E-value=2.6e-34  Score=196.79  Aligned_cols=82  Identities=98%  Similarity=1.410  Sum_probs=80.7

Q ss_pred             ccccccccccchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHcCCcccc
Q 047769           49 KVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYG  128 (131)
Q Consensus        49 Kvlrd~i~gIpk~aIrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~G~~lYG  128 (131)
                      |+++|+|++||+++|+|||+++|++|||+++|+++++++++|+++|++||+.||+|++|||||++||.+||+++|+||||
T Consensus         1 ~~~~d~i~gI~k~~i~Riar~~Gv~ris~d~~~~l~~~l~~~l~~i~~~a~~~~~hakRKTvt~~DV~~Alkr~g~plyG   80 (82)
T d2huec1           1 KVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYG   80 (82)
T ss_dssp             CCGGGGCCSSCHHHHHHHHHHTTCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTTTCEEEES
T ss_pred             CchhhhhcCcCHHHHHHHHHHcCcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHhcCCCCCC
Confidence            67899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cC
Q 047769          129 FG  130 (131)
Q Consensus       129 F~  130 (131)
                      |+
T Consensus        81 fg   82 (82)
T d2huec1          81 FG   82 (82)
T ss_dssp             CC
T ss_pred             CC
Confidence            96
>d1htaa_ a.22.1.2 (A:) Archaeal histone {Archaeon Methanothermus fervidus, histone A [TaxId: 2180]} Back     information, alignment and structure
>d1ku5a_ a.22.1.2 (A:) Archaeal histone {Archaeon (Pyrococcus horikoshii) [TaxId: 53953]} Back     information, alignment and structure
>d1f1ea_ a.22.1.2 (A:) Archaeal histone {Archaeon Methanopyrus kandleri [TaxId: 2320]} Back     information, alignment and structure
>d1tafb_ a.22.1.3 (B:) TAF(II)62 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
>d1f1ea_ a.22.1.2 (A:) Archaeal histone {Archaeon Methanopyrus kandleri [TaxId: 2320]} Back     information, alignment and structure
>d1n1ja_ a.22.1.3 (A:) Nuclear transcription factor Y subunit beta (Nf-Yb3) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1tafa_ a.22.1.3 (A:) TAF(II)42 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
>d1jfib_ a.22.1.3 (B:) Negative cofactor 2, NC2, beta chain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2bykb1 a.22.1.3 (B:11-99) Chrac-14 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
>d1q9ca_ a.22.1.3 (A:) Histone domain of Son of sevenless protein {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1n1jb_ a.22.1.3 (B:) Nuclear transcription factor Y subunit gamma (Nf-Yc2) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1jfia_ a.22.1.3 (A:) Negative cofactor 2, NC2, alpha chain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1tzyc_ a.22.1.1 (C:) Histone H3 {Chicken (Gallus gallus), erythrocytes [TaxId: 9031]} Back     information, alignment and structure
>d1h3ob_ a.22.1.3 (B:) TAF(II)-20, (TAF(II)-15, hTAF12), histone fold domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2byka1 a.22.1.3 (A:29-100) Chrac-16 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
>d1tzyb_ a.22.1.1 (B:) Histone H2B {Chicken (Gallus gallus), erythrocytes [TaxId: 9031]} Back     information, alignment and structure
>d1f66c_ a.22.1.1 (C:) Histone H2A {Human (Homo sapiens), variant H2A.Z [TaxId: 9606]} Back     information, alignment and structure
>d1u35c1 a.22.1.1 (C:814-919) macro-H2A.1, histone domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1tzya_ a.22.1.1 (A:) Histone H2A {Chicken (Gallus gallus), erythrocytes [TaxId: 9031]} Back     information, alignment and structure
>d1bh9b_ a.22.1.3 (B:) TAF(II)28 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} Back     information, alignment and structure
>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]} Back     information, alignment and structure
>d1h3oa_ a.22.1.3 (A:) TAF(II)-135, (TAF(II)-130, hTAF4), histone fold domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1ixsb2 c.37.1.20 (B:4-242) Holliday junction helicase RuvB {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1wwia1 a.22.1.4 (A:1-148) Hypothetical protein TTHA1479 {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure