Citrus Sinensis ID: 032777

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----
MARSLRMLRILYRNVSLSSSASLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMRYREMEGDTKGSARGGDGSAKRDTIGALPGQNAQYALQGPLNYANPHAQGQHMIVPSMQGNE
cccHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHccccccHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccc
ccHHHHHHHHccccccEcccccccHHEHHHHHHHHHHHHHcccccEcHHHHHHHHHHcccHHHHHHHHHHHHHHHcHHcccccccccccccccccccccccccccccccccccccccccccccccEEEEEcccc
MARSLRMLRILYRNvslsssaslpasfsflscrasdkcqkekrktingDDLLWAMATLGFEDYIDPLKAYLMRYREmegdtkgsarggdgsakrdtigalpgqnaqyalqgplnyanphaqgqhmivpsmqgne
MARSLRMLRILYRNvslsssaslpASFSFLScrasdkcqkekrktingddLLWAMATLGFEDYIDPLKAYLMRYREMEGdtkgsarggdgsAKRDTIGALPGQNAQYALQGPLNYANPHAQGQHMIVPSMQGNE
MARSLRMLRILYRNVslsssaslpasfsflsCRASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMRYREMEGDTKGSARGGDGSAKRDTIGALPGQNAQYALQGPLNYANPHAQGQHMIVPSMQGNE
******MLRILYRNVSL********SFSFLSCRA*********KTINGDDLLWAMATLGFEDYIDPLKAYLMRYR***********************************************************
********RILYRNVSLSSSASLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLM**************************************************************
MARSLRMLRILYRNVSLSSSASLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMRYREMEG*************KRDTIGALPGQNAQYALQGPLNYANPHAQGQHMIVPSMQGNE
MARSLRMLRILYRNVSLSSSASLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMRYREMEG*****************************LQGPLNYANPHAQGQHMIVPSMQ***
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MARSLRMLRILYRNVSLSSSASLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMRYREMEGDTKGSARGGDGSAKRDTIGALPGQNAQYALQGPLNYANPHAQGQHMIVPSMQGNE
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 ?
Query134 2.2.26 [Sep-21-2011]
Q8VYK4173 Nuclear transcription fac yes no 0.738 0.572 0.705 2e-35
Q67XJ2176 Nuclear transcription fac no no 0.977 0.744 0.540 2e-32
Q60EQ4185 Nuclear transcription fac yes no 0.529 0.383 0.732 2e-27
P25209179 Nuclear transcription fac N/A no 0.694 0.519 0.58 2e-27
Q9SLG0141 Nuclear transcription fac no no 0.567 0.539 0.701 2e-26
Q5QMG3178 Nuclear transcription fac yes no 0.537 0.404 0.694 5e-25
Q9FGJ3190 Nuclear transcription fac no no 0.529 0.373 0.64 9e-22
Q65XK1143 Nuclear transcription fac no no 0.522 0.489 0.647 3e-21
O23310161 Nuclear transcription fac no no 0.619 0.515 0.544 6e-21
Q9SIT9215 Nuclear transcription fac no no 0.447 0.279 0.616 1e-18
>sp|Q8VYK4|NFYB8_ARATH Nuclear transcription factor Y subunit B-8 OS=Arabidopsis thaliana GN=NFYB8 PE=2 SV=1 Back     alignment and function desciption
 Score =  147 bits (370), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 72/102 (70%), Positives = 83/102 (81%), Gaps = 3/102 (2%)

Query: 27  FSFLSCRASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMRYREMEGDTKGSAR 86
            SF++  ASDKCQ+EKRKTINGDDLLWAMATLGFEDY++PLK YLMRYREMEGDTKGSA+
Sbjct: 70  ISFVTSEASDKCQREKRKTINGDDLLWAMATLGFEDYMEPLKVYLMRYREMEGDTKGSAK 129

Query: 87  GGDGSAKRDTIGALPGQNAQYALQGPLNYANPHAQGQHMIVP 128
           GGD +AK+D   +  GQ +Q A QGP  Y N  AQ QHM+VP
Sbjct: 130 GGDPNAKKDGQSSQNGQFSQLAHQGP--YGNSQAQ-QHMMVP 168
Component of the NF-Y/HAP transcription factor complex. The NF-Y complex stimulates the transcription of various genes by recognizing and binding to a CCAAT motif in promoters.
Arabidopsis thaliana (taxid: 3702)
>sp|Q67XJ2|NFYBA_ARATH Nuclear transcription factor Y subunit B-10 OS=Arabidopsis thaliana GN=NFYB10 PE=2 SV=1 Back     alignment and function description
>sp|Q60EQ4|NFYB3_ORYSJ Nuclear transcription factor Y subunit B-3 OS=Oryza sativa subsp. japonica GN=NFYB3 PE=1 SV=2 Back     alignment and function description
>sp|P25209|NFYB_MAIZE Nuclear transcription factor Y subunit B OS=Zea mays GN=NFY2 PE=2 SV=1 Back     alignment and function description
>sp|Q9SLG0|NFYB1_ARATH Nuclear transcription factor Y subunit B-1 OS=Arabidopsis thaliana GN=NFYB1 PE=1 SV=2 Back     alignment and function description
>sp|Q5QMG3|NFYB2_ORYSJ Nuclear transcription factor Y subunit B-2 OS=Oryza sativa subsp. japonica GN=NFYB2 PE=2 SV=1 Back     alignment and function description
>sp|Q9FGJ3|NFYB2_ARATH Nuclear transcription factor Y subunit B-2 OS=Arabidopsis thaliana GN=NFYB2 PE=2 SV=1 Back     alignment and function description
>sp|Q65XK1|NFYB4_ORYSJ Nuclear transcription factor Y subunit B-4 OS=Oryza sativa subsp. japonica GN=NFYB4 PE=2 SV=2 Back     alignment and function description
>sp|O23310|NFYB3_ARATH Nuclear transcription factor Y subunit B-3 OS=Arabidopsis thaliana GN=NFYB3 PE=2 SV=1 Back     alignment and function description
>sp|Q9SIT9|NFYB7_ARATH Nuclear transcription factor Y subunit B-7 OS=Arabidopsis thaliana GN=NFYB7 PE=2 SV=1 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 ?
Query134
255565846174 ccaat-binding transcription factor subun 0.805 0.620 0.824 6e-48
224109668176 predicted protein [Populus trichocarpa] 0.805 0.613 0.763 2e-44
224100855176 predicted protein [Populus trichocarpa] 0.805 0.613 0.754 6e-44
225449176178 PREDICTED: nuclear transcription factor 0.805 0.606 0.714 1e-40
449451715175 PREDICTED: nuclear transcription factor 0.791 0.605 0.724 3e-39
296086079176 unnamed protein product [Vitis vinifera] 0.791 0.602 0.705 3e-38
358248768174 nuclear transcription factor Y subunit B 0.798 0.614 0.712 3e-38
217071240176 unknown [Medicago truncatula] gi|3885000 0.805 0.613 0.657 3e-38
356576428173 PREDICTED: nuclear transcription factor 0.798 0.618 0.694 8e-37
356505184171 PREDICTED: nuclear transcription factor 0.776 0.608 0.709 8e-36
>gi|255565846|ref|XP_002523912.1| ccaat-binding transcription factor subunit A, putative [Ricinus communis] gi|223536842|gb|EEF38481.1| ccaat-binding transcription factor subunit A, putative [Ricinus communis] Back     alignment and taxonomy information
 Score =  195 bits (495), Expect = 6e-48,   Method: Compositional matrix adjust.
 Identities = 89/108 (82%), Positives = 95/108 (87%)

Query: 27  FSFLSCRASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMRYREMEGDTKGSAR 86
            SF++  ASDKCQKEKRKTINGDDLLWAMATLGFEDYI+PLK YL RYREMEGDTKGSAR
Sbjct: 67  ISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYIEPLKVYLARYREMEGDTKGSAR 126

Query: 87  GGDGSAKRDTIGALPGQNAQYALQGPLNYANPHAQGQHMIVPSMQGNE 134
           GGDGS KRD +G LPGQN Q+ALQG +NY N  AQGQHMIVPSMQGNE
Sbjct: 127 GGDGSGKRDAMGGLPGQNPQFALQGSMNYINSQAQGQHMIVPSMQGNE 174

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|224109668|ref|XP_002315272.1| predicted protein [Populus trichocarpa] gi|222864312|gb|EEF01443.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|224100855|ref|XP_002312041.1| predicted protein [Populus trichocarpa] gi|222851861|gb|EEE89408.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|225449176|ref|XP_002278716.1| PREDICTED: nuclear transcription factor Y subunit B-8-like isoform 1 [Vitis vinifera] gi|359486707|ref|XP_003633465.1| PREDICTED: nuclear transcription factor Y subunit B-8-like [Vitis vinifera] Back     alignment and taxonomy information
>gi|449451715|ref|XP_004143607.1| PREDICTED: nuclear transcription factor Y subunit B-8-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|296086079|emb|CBI31520.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|358248768|ref|NP_001239681.1| nuclear transcription factor Y subunit B-8-like [Glycine max] gi|257136303|gb|ACV44453.1| CCAAT-binding transcription factor family protein [Glycine max] gi|257136305|gb|ACV44454.1| CCAAT-binding transcription factor family protein [Glycine max] Back     alignment and taxonomy information
>gi|217071240|gb|ACJ83980.1| unknown [Medicago truncatula] gi|388500098|gb|AFK38115.1| unknown [Medicago truncatula] Back     alignment and taxonomy information
>gi|356576428|ref|XP_003556333.1| PREDICTED: nuclear transcription factor Y subunit B-8-like isoform 1 [Glycine max] Back     alignment and taxonomy information
>gi|356505184|ref|XP_003521372.1| PREDICTED: nuclear transcription factor Y subunit B-8-like [Glycine max] 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 ?
Query134
TAIR|locus:2061789173 NF-YB8 ""nuclear factor Y, sub 0.723 0.560 0.712 1.4e-32
TAIR|locus:2083941176 NF-YB10 ""nuclear factor Y, su 0.731 0.556 0.663 1.3e-29
TAIR|locus:2168983190 NF-YB2 ""nuclear factor Y, sub 0.664 0.468 0.555 3.9e-21
TAIR|locus:2129885161 NF-YB3 ""nuclear factor Y, sub 0.417 0.347 0.736 4e-19
TAIR|locus:2054095215 NF-YB7 ""nuclear factor Y, sub 0.604 0.376 0.493 1.1e-16
TAIR|locus:2169028234 NF-YB6 ""nuclear factor Y, sub 0.738 0.423 0.428 3.7e-16
TAIR|locus:2043293160 NF-YB5 ""nuclear factor Y, sub 0.440 0.368 0.6 8.8e-15
TAIR|locus:2201163238 LEC1 "LEAFY COTYLEDON 1" [Arab 0.477 0.268 0.507 1.4e-14
DICTYBASE|DDB_G0279419 490 nfyB "putative histone-like tr 0.440 0.120 0.557 1.6e-14
UNIPROTKB|P25207205 NFYB "Nuclear transcription fa 0.522 0.341 0.493 4.9e-14
TAIR|locus:2061789 NF-YB8 ""nuclear factor Y, subunit B8"" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 356 (130.4 bits), Expect = 1.4e-32, P = 1.4e-32
 Identities = 72/101 (71%), Positives = 82/101 (81%)

Query:    34 ASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMRYREMEGDTKGSARGGDGSAK 93
             ASDKCQ+EKRKTINGDDLLWAMATLGFEDY++PLK YLMRYREMEGDTKGSA+GGD +AK
Sbjct:    77 ASDKCQREKRKTINGDDLLWAMATLGFEDYMEPLKVYLMRYREMEGDTKGSAKGGDPNAK 136

Query:    94 RDTIGALPGQNAQYALQGPLNYANPHAQGQHMIVPSMQGNE 134
             +D   +  GQ +Q A QGP  Y N  AQ QHM+VP M G +
Sbjct:   137 KDGQSSQNGQFSQLAHQGP--YGNSQAQ-QHMMVP-MPGTD 173
GO:0003677 "DNA binding" evidence=IEA
GO:0005622 "intracellular" evidence=IEA
GO:0005634 "nucleus" evidence=ISM;IEA
GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA
GO:0043565 "sequence-specific DNA binding" evidence=IEA
GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS
TAIR|locus:2083941 NF-YB10 ""nuclear factor Y, subunit B10"" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2168983 NF-YB2 ""nuclear factor Y, subunit B2"" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2129885 NF-YB3 ""nuclear factor Y, subunit B3"" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2054095 NF-YB7 ""nuclear factor Y, subunit B7"" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2169028 NF-YB6 ""nuclear factor Y, subunit B6"" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2043293 NF-YB5 ""nuclear factor Y, subunit B5"" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2201163 LEC1 "LEAFY COTYLEDON 1" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
DICTYBASE|DDB_G0279419 nfyB "putative histone-like transcription factor" [Dictyostelium discoideum (taxid:44689)] Back     alignment and assigned GO terms
UNIPROTKB|P25207 NFYB "Nuclear transcription factor Y subunit beta" [Gallus gallus (taxid:9031)] 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) ?
Q8VYK4NFYB8_ARATHNo assigned EC number0.70580.73880.5722yesno
Q60EQ4NFYB3_ORYSJNo assigned EC number0.73230.52980.3837yesno

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:
grail3.0022035801
hypothetical protein (176 aa)
(Populus trichocarpa)
Predicted Functional Partners:
 
Sorry, there are no predicted associations at the current settings.
 

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query134
pfam0080865 pfam00808, CBFD_NFYB_HMF, Histone-like transcripti 2e-07
COG203691 COG2036, HHT1, Histones H3 and H4 [Chromatin struc 4e-04
COG5150148 COG5150, COG5150, Class 2 transcription repressor 4e-04
>gnl|CDD|201453 pfam00808, CBFD_NFYB_HMF, Histone-like transcription factor (CBF/NF-Y) and archaeal histone Back     alignment and domain information 
 Score = 44.9 bits (107), Expect = 2e-07
 Identities = 12/28 (42%), Positives = 20/28 (71%)

Query: 28 SFLSCRASDKCQKEKRKTINGDDLLWAM 55
           F++  A++ C+KEKRKTIN + +  A+
Sbjct: 38 EFIASEAAEICKKEKRKTINAEHIKLAV 65

This family includes archaebacterial histones and histone like transcription factors from eukaryotes. Length = 65
>gnl|CDD|224947 COG2036, HHT1, Histones H3 and H4 [Chromatin structure and dynamics] Back     alignment and domain information
>gnl|CDD|227479 COG5150, COG5150, Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription] Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 134
KOG0869168 consensus CCAAT-binding factor, subunit A (HAP3) [ 100.0
KOG0871156 consensus Class 2 transcription repressor NC2, bet 99.9
KOG0870172 consensus DNA polymerase epsilon, subunit D [Trans 99.85
COG5150148 Class 2 transcription repressor NC2, beta subunit 99.77
PF0080865 CBFD_NFYB_HMF: Histone-like transcription factor ( 99.47
COG203691 HHT1 Histones H3 and H4 [Chromatin structure and d 99.1
cd0007685 H4 Histone H4, one of the four histones, along wit 97.78
PTZ00015102 histone H4; Provisional 97.6
PLN00035103 histone H4; Provisional 97.6
PF0012575 Histone: Core histone H2A/H2B/H3/H4 histone h2a si 97.49
smart0080365 TAF TATA box binding protein associated factor. TA 97.43
cd0798172 TAF12 TATA Binding Protein (TBP) Associated Factor 97.26
smart0041774 H4 Histone H4. 96.35
smart0042789 H2B Histone H2B. 96.09
smart0057677 BTP Bromodomain transcription factors and PHD doma 95.84
KOG3467103 consensus Histone H4 [Chromatin structure and dyna 95.62
cd00074115 H2A Histone 2A; H2A is a subunit of the nucleosome 95.6
PF0752477 Bromo_TP: Bromodomain associated; InterPro: IPR006 95.2
PF1563076 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 95.12
PLN00158116 histone H2B; Provisional 95.05
PTZ00463117 histone H2B; Provisional 94.81
KOG1657236 consensus CCAAT-binding factor, subunit C (HAP5) [ 94.39
PF0384768 TFIID_20kDa: Transcription initiation factor TFIID 94.35
cd08050 343 TAF6 TATA Binding Protein (TBP) Associated Factor 93.91
cd07979117 TAF9 TATA Binding Protein (TBP) Associated Factor 92.99
PF0226993 TFIID-18kDa: Transcription initiation factor IID, 92.56
smart00414106 H2A Histone 2A. 90.48
smart00428105 H3 Histone H3. 90.36
COG5262132 HTA1 Histone H2A [Chromatin structure and dynamics 90.16
COG5208286 HAP5 CCAAT-binding factor, subunit C [Transcriptio 89.27
PLN00154136 histone H2A; Provisional 87.79
PF0296966 TAF: TATA box binding protein associated factor (T 87.77
PHA03328316 nuclear egress lamina protein UL31; Provisional 87.65
KOG1744127 consensus Histone H2B [Chromatin structure and dyn 86.99
PLN00157132 histone H2A; Provisional 85.67
PLN00156139 histone H2AX; Provisional 85.07
KOG1756131 consensus Histone 2A [Chromatin structure and dyna 84.57
cd0797892 TAF13 The TATA Binding Protein (TBP) Associated Fa 84.52
PF15510102 CENP-W: Centromere kinetochore component W 82.86
PF0286153 Clp_N: Clp amino terminal domain; InterPro: IPR004 82.35
KOG1658162 consensus DNA polymerase epsilon, subunit C [Repli 82.16
cd0804885 TAF11 TATA Binding Protein (TBP) Associated Factor 81.88
PF15511414 CENP-T: Centromere kinetochore component CENP-T; P 80.13
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription] Back     alignment and domain information 
Probab=100.00  E-value=2.4e-38  Score=244.99  Aligned_cols=109  Identities=46%  Similarity=0.758  Sum_probs=92.3

Q ss_pred             ChhHHHHH-HhcCCCceeccch------hHHHHHHHHHhHhhhHhhhcCCCccChhHHHHHhhhcCCccchhHHHHHHHH
Q 032777            1 MARSLRML-RILYRNVSLSSSA------SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMR   73 (134)
Q Consensus         1 ~anv~Rik-~~LP~n~kISKDA------caseFI~ylTSeAnd~c~~~kRKTI~~dDVL~AL~~LgF~dyv~~Lk~~L~~   73 (134)
                      ||||.||| +.||+|.||||||      |++|||+|||+||+|+|+++||||||+|||||||.+|||++|++||+.||.+
T Consensus        35 IANV~RIMK~~lP~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~tLGFe~Y~eplkiyL~k  114 (168)
T KOG0869|consen   35 IANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMSTLGFENYAEPLKIYLQK  114 (168)
T ss_pred             HHHHHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHHHcCcHhHHHHHHHHHHH
Confidence            69999996 5999999999999      9999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhcccCCCCCCCCCCCcccccCCCCCchhhhhhcC
Q 032777           74 YREMEGDTKGSARGGDGSAKRDTIGALPGQNAQYALQG  111 (134)
Q Consensus        74 yre~~~~kk~s~k~~~~~~~~~~~~~~~~~~~~~~~~~  111 (134)
                      ||+.++++..+.+++...  .+.....-++..++..||
T Consensus       115 YRe~e~e~~~~~~~~~~~--~~~~~~~~~~~~~~~~~g  150 (168)
T KOG0869|consen  115 YRELEGERGRSGKGGQMT--GGNGIDEHGPSGEVPEQG  150 (168)
T ss_pred             HHHHhhhcccccccCccc--ccccccccCCCcCCCCCC
Confidence            999999988877766522  322222333344445555

>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription] Back     alignment and domain information
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription] Back     alignment and domain information
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription] 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
>COG2036 HHT1 Histones H3 and 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
>PTZ00015 histone H4; Provisional Back     alignment and domain information
>PLN00035 histone H4; Provisional 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
>smart00803 TAF TATA box binding protein associated factor 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
>smart00417 H4 Histone H4 Back     alignment and domain information
>smart00427 H2B Histone H2B Back     alignment and domain information
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins Back     alignment and domain information
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics] Back     alignment and domain information
>cd00074 H2A Histone 2A; H2A is a subunit of the nucleosome 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
>PLN00158 histone H2B; Provisional Back     alignment and domain information
>PTZ00463 histone H2B; Provisional Back     alignment and domain information
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription] 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
>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
>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
>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
>smart00428 H3 Histone H3 Back     alignment and domain information
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics] Back     alignment and domain information
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription] Back     alignment and domain information
>PLN00154 histone H2A; Provisional 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
>PHA03328 nuclear egress lamina protein UL31; Provisional Back     alignment and domain information
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics] Back     alignment and domain information
>PLN00157 histone H2A; Provisional Back     alignment and domain information
>PLN00156 histone H2AX; Provisional Back     alignment and domain information
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics] 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
>PF15510 CENP-W: Centromere kinetochore component W Back     alignment and domain information
>PF02861 Clp_N: Clp amino terminal domain; InterPro: IPR004176 This short domain is found in one or two copies at the amino terminus of ClpA and ClpB proteins from bacteria and eukaryotes Back     alignment and domain information
>KOG1658 consensus DNA polymerase epsilon, subunit C [Replication, recombination and repair] 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
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T 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 ?
Query134
1n1j_A93 Crystal Structure Of The Nf-YbNF-Yc Histone Pair Le 3e-13
4awl_B94 The Nf-y Transcription Factor Is Structurally And F 3e-13
4g91_B92 Ccaat-Binding Complex From Aspergillus Nidulans Len 1e-12
>pdb|1N1J|A Chain A, Crystal Structure Of The Nf-YbNF-Yc Histone Pair Length = 93 Back     alignment and structure 
Iteration: 1

 Score = 70.1 bits (170), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 27/43 (62%), Positives = 39/43 (90%)
Query: 34 ASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMRYRE 76
          AS++C +EKRKTING+D+L+AM+TLGF+ Y++PLK YL ++RE
Sbjct: 51 ASERCHQEKRKTINGEDILFAMSTLGFDSYVEPLKLYLQKFRE 93
>pdb|4AWL|B Chain B, The Nf-y Transcription Factor Is Structurally And Functionally A Sequence Specific Histone Length = 94 Back     alignment and structure
>pdb|4G91|B Chain B, Ccaat-Binding Complex From Aspergillus Nidulans Length = 92 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 ?
Query134
1jfi_B179 DR1 protein, transcription regulator NC2 beta chai 4e-25
2byk_B128 Chrac-14; nucleosome sliding, histone fold, DNA-bi 8e-25
1n1j_A93 NF-YB; histone-like PAIR, DNA binding protein; 1.6 5e-22
1b67_A68 Protein (histone HMFA); DNA binding protein; 1.48A 3e-06
1ku5_A70 HPHA, archaeal histon; histone fold, DNA binding p 4e-05
2byk_A140 Chrac-16; nucleosome sliding, histone fold, DNA-bi 3e-04
>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 Back     alignment and structure
 Score = 92.9 bits (230), Expect = 4e-25
 Identities = 20/106 (18%), Positives = 42/106 (39%), Gaps = 1/106 (0%)

Query: 28  SFLSCRASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMRYREMEGDTKGSARG 87
             +S  A++ C K ++KTI+ + ++ A+ +LGF  YI  +K  L   + +    + ++  
Sbjct: 51  HLISSEANEICNKSEKKTISPEHVIQALESLGFGSYISEVKEVLQECKTVALKRRKASSR 110

Query: 88  GDGSAKRDTIGALPGQNAQYALQGPLNYANPHAQGQHMIVPSMQGN 133
            +     +    L  Q   +A            +   M   + Q  
Sbjct: 111 LENLGIPEE-ELLRQQQELFAKARQQQAELAQQEWLQMQQAAQQAQ 155
>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 Back     alignment and structure
>1n1j_A NF-YB; histone-like PAIR, DNA binding protein; 1.67A {Homo sapiens} SCOP: a.22.1.3 Length = 93 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
>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
>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 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query134
1jfi_B179 DR1 protein, transcription regulator NC2 beta chai 99.93
2byk_B128 Chrac-14; nucleosome sliding, histone fold, DNA-bi 99.93
1n1j_A93 NF-YB; histone-like PAIR, DNA binding protein; 1.6 99.9
3b0c_W76 CENP-W, centromere protein W; histone fold, DNA bi 99.72
1f1e_A154 Histone fold protein; archaeal histone protein, DN 99.7
3b0c_T111 CENP-T, centromere protein T; histone fold, DNA bi 99.49
1b67_A68 Protein (histone HMFA); DNA binding protein; 1.48A 99.46
2byk_A140 Chrac-16; nucleosome sliding, histone fold, DNA-bi 99.45
4g92_C119 HAPE; transcription factor, nucleosome, minor groo 99.34
1id3_B102 Histone H4; nucleosome core particle, chromatin, p 99.21
2hue_C84 Histone H4; mini beta sheet, elongated beta sandwh 99.21
1f1e_A154 Histone fold protein; archaeal histone protein, DN 99.2
1n1j_B97 NF-YC; histone-like PAIR, DNA binding protein; 1.6 99.19
1tzy_D103 Histone H4-VI; histone-fold, tetramer-dimer-dimer, 99.13
2yfw_B103 Histone H4, H4; cell cycle, kinetochore, centromer 99.1
1ku5_A70 HPHA, archaeal histon; histone fold, DNA binding p 98.9
1jfi_A98 Transcription regulator NC2 alpha chain; histone, 98.55
3vh5_A140 CENP-S; histone fold, chromosome segregation, DNA 97.52
4dra_A113 Centromere protein S; DNA binding complex, DNA dam 97.44
2ly8_A121 Budding yeast chaperone SCM3; centromere protein, 97.35
3v9r_A90 MHF1, uncharacterized protein YOL086W-A; histone f 97.22
3b0b_B107 CENP-S, centromere protein S; histone fold, DNA bi 97.17
2nqb_D123 Histone H2B; nucleosome, NCP, chromatin, structura 97.09
1tzy_B126 Histone H2B; histone-fold, tetramer-dimer-dimer, D 97.06
1taf_B70 TFIID TBP associated factor 62; transcription init 96.58
2jss_A192 Chimera of histone H2B.1 and histone H2A.Z; histon 96.46
2l5a_A235 Histone H3-like centromeric protein CSE4, protein 96.33
1f66_C128 Histone H2A.Z; nucleosome, chromatin, histone vari 95.64
2f8n_G120 Core histone macro-H2A.1; nucleosome, NCP, macroh2 95.56
2nqb_C123 Histone H2A; nucleosome, NCP, chromatin, structura 95.52
1id3_C131 Histone H2A.1; nucleosome core particle, chromatin 95.52
1tzy_A129 Histone H2A-IV; histone-fold, tetramer-dimer-dimer 95.44
2f8n_K149 Histone H2A type 1; nucleosome, NCP, macroh2A, his 95.19
1taf_A68 TFIID TBP associated factor 42; transcription init 94.5
2jss_A192 Chimera of histone H2B.1 and histone H2A.Z; histon 93.79
1h3o_B76 Transcription initiation factor TFIID 20/15 kDa su 93.08
2hue_B77 Histone H3; mini beta sheet, elongated beta sandwh 91.89
3nqj_A82 Histone H3-like centromeric protein A; alpha helix 89.71
1bh9_B89 TAFII28; histone fold, tata binding protein, trans 84.37
3r45_A156 Histone H3-like centromeric protein A; histone fol 83.87
1tzy_C136 Histone H3; histone-fold, tetramer-dimer-dimer, DN 83.38
2yfv_A100 Histone H3-like centromeric protein CSE4; cell cyc 83.23
3nqu_A140 Histone H3-like centromeric protein A; alpha helix 82.85
>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
Probab=99.93  E-value=7.1e-27  Score=182.97  Aligned_cols=82  Identities=26%  Similarity=0.429  Sum_probs=77.3

Q ss_pred             ChhHHHHH-HhcCCCceeccch------hHHHHHHHHHhHhhhHhhhcCCCccChhHHHHHhhhcCCccchhHHHHHHHH
Q 032777            1 MARSLRML-RILYRNVSLSSSA------SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMR   73 (134)
Q Consensus         1 ~anv~Rik-~~LP~n~kISKDA------caseFI~ylTSeAnd~c~~~kRKTI~~dDVL~AL~~LgF~dyv~~Lk~~L~~   73 (134)
                      +|||.||+ ++|| +++||+||      ||++||+|||++|+++|..++||||+++||++||++|||++|+++|+.+|+.
T Consensus        18 ~A~V~RImK~alp-~~rISkDA~~al~ec~~eFI~~LtseA~e~a~~~~RKTI~~eDVl~Al~~LgF~~fv~~lk~~L~~   96 (179)
T 1jfi_B           18 RAAINKMIKETLP-NVRVANDARELVVNCCTEFIHLISSEANEICNKSEKKTISPEHVIQALESLGFGSYISEVKEVLQE   96 (179)
T ss_dssp             HHHHHHHHHHHST-TCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHHTTGGGHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCC-ccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHhcChHHHHHHHHHHHHH
Confidence            48999995 5899 99999999      9999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhcccCC
Q 032777           74 YREMEGDTKG   83 (134)
Q Consensus        74 yre~~~~kk~   83 (134)
                      ||+..+.|+.
T Consensus        97 yre~~~~kkr  106 (179)
T 1jfi_B           97 CKTVALKRRK  106 (179)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHhCcc
Confidence            9998877643
>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
>1n1j_A NF-YB; histone-like PAIR, DNA binding protein; 1.67A {Homo sapiens} SCOP: a.22.1.3 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
>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
>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
>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
>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
>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
>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
>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
>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
>1n1j_B NF-YC; histone-like PAIR, DNA binding protein; 1.67A {Homo sapiens} SCOP: a.22.1.3 Back     alignment and structure
>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
>1ku5_A HPHA, archaeal histon; histone fold, DNA binding protein; 2.30A {Pyrococcus horikoshii} SCOP: a.22.1.2 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
>3vh5_A CENP-S; histone fold, chromosome segregation, DNA binding, nucleus, binding protein; 2.40A {Gallus gallus} PDB: 3vh6_A 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
>2ly8_A Budding yeast chaperone SCM3; centromere protein, CENH3 variants, partially unfolded; NMR {Saccharomyces cerevisiae} 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
>3b0b_B CENP-S, centromere protein S; histone fold, DNA binding, DNA, nucleus, DNA binding protein; 2.15A {Gallus gallus} 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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>2hue_B Histone H3; mini beta sheet, elongated beta sandwhich, DNA binding prote; 1.70A {Xenopus laevis} 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
>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
>3r45_A Histone H3-like centromeric protein A; histone fold, centromere, CENP-A, histone chaperone, hjurp; 2.60A {Homo sapiens} 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
>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
>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

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 134
d2bykb189 a.22.1.3 (B:11-99) Chrac-14 {Fruit fly (Drosophila 4e-20
d1jfib_135 a.22.1.3 (B:) Negative cofactor 2, NC2, beta chain 1e-18
d1n1ja_87 a.22.1.3 (A:) Nuclear transcription factor Y subun 5e-17
d1ku5a_66 a.22.1.2 (A:) Archaeal histone {Archaeon (Pyrococc 2e-06
d1n1jb_78 a.22.1.3 (B:) Nuclear transcription factor Y subun 7e-05
d1htaa_68 a.22.1.2 (A:) Archaeal histone {Archaeon Methanoth 1e-04
d1f1ea_151 a.22.1.2 (A:) Archaeal histone {Archaeon Methanopy 2e-04
d1f1ea_151 a.22.1.2 (A:) Archaeal histone {Archaeon Methanopy 7e-04
d1jfia_66 a.22.1.3 (A:) Negative cofactor 2, NC2, alpha chai 0.001
>d2bykb1 a.22.1.3 (B:11-99) Chrac-14 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 89 Back     information, alignment and structure

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 = 76.4 bits (188), Expect = 4e-20
 Identities = 14/55 (25%), Positives = 26/55 (47%)

Query: 26 SFSFLSCRASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMRYREMEGD 80
             F++  ++    K+  KTI   D+L  +  L FE ++  L   L  YR++  +
Sbjct: 34 FAIFVTSSSTALAHKQNHKTITAKDILQTLTELDFESFVPSLTQDLEVYRKVVKE 88
>d1jfib_ a.22.1.3 (B:) Negative cofactor 2, NC2, beta chain {Human (Homo sapiens) [TaxId: 9606]} Length = 135 Back     information, alignment and structure
>d1n1ja_ a.22.1.3 (A:) Nuclear transcription factor Y subunit beta (Nf-Yb3) {Human (Homo sapiens) [TaxId: 9606]} Length = 87 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
>d1n1jb_ a.22.1.3 (B:) Nuclear transcription factor Y subunit gamma (Nf-Yc2) {Human (Homo sapiens) [TaxId: 9606]} Length = 78 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
>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
>d1jfia_ a.22.1.3 (A:) Negative cofactor 2, NC2, alpha chain {Human (Homo sapiens) [TaxId: 9606]} Length = 66 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 ?
Query134
d2bykb189 Chrac-14 {Fruit fly (Drosophila melanogaster) [Tax 99.93
d1n1ja_87 Nuclear transcription factor Y subunit beta (Nf-Yb 99.89
d1jfib_135 Negative cofactor 2, NC2, beta chain {Human (Homo 99.89
d1n1jb_78 Nuclear transcription factor Y subunit gamma (Nf-Y 99.55
d1ku5a_66 Archaeal histone {Archaeon (Pyrococcus horikoshii) 99.42
d1htaa_68 Archaeal histone {Archaeon Methanothermus fervidus 99.41
d1jfia_66 Negative cofactor 2, NC2, alpha chain {Human (Homo 99.22
d1f1ea_151 Archaeal histone {Archaeon Methanopyrus kandleri [ 99.17
d1f1ea_151 Archaeal histone {Archaeon Methanopyrus kandleri [ 98.54
d2huec182 Histone H4 {African clawed frog (Xenopus laevis) [ 98.33
d2byka172 Chrac-16 {Fruit fly (Drosophila melanogaster) [Tax 96.97
d1tzyb_92 Histone H2B {Chicken (Gallus gallus), erythrocytes 96.05
d1f66c_103 Histone H2A {Human (Homo sapiens), variant H2A.Z [ 93.12
d1q9ca_172 Histone domain of Son of sevenless protein {Human 92.99
d1tzya_106 Histone H2A {Chicken (Gallus gallus), erythrocytes 90.12
d1u35c1106 macro-H2A.1, histone domain {Human (Homo sapiens) 90.06
d1h3ob_74 TAF(II)-20, (TAF(II)-15, hTAF12), histone fold dom 89.9
d1tzyc_95 Histone H3 {Chicken (Gallus gallus), erythrocytes 89.52
d1fnna2276 CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T 87.26
d1bh9b_89 TAF(II)28 {Human (Homo sapiens) [TaxId: 9606]} 82.69
>d2bykb1 a.22.1.3 (B:11-99) Chrac-14 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
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=99.93  E-value=2.6e-26  Score=158.73  Aligned_cols=81  Identities=25%  Similarity=0.374  Sum_probs=77.3

Q ss_pred             ChhHHHHHH-hcCCCceeccch------hHHHHHHHHHhHhhhHhhhcCCCccChhHHHHHhhhcCCccchhHHHHHHHH
Q 032777            1 MARSLRMLR-ILYRNVSLSSSA------SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMR   73 (134)
Q Consensus         1 ~anv~Rik~-~LP~n~kISKDA------caseFI~ylTSeAnd~c~~~kRKTI~~dDVL~AL~~LgF~dyv~~Lk~~L~~   73 (134)
                      +|+|.||++ .||++++||+||      |+.+||+|||++|++.|..++||||+++||++||+++||++|+++|+.+|+.
T Consensus         2 ~a~i~ri~K~~~p~~~~iskeA~~~i~~aae~FI~~lt~~A~~~a~~~~rKtI~~~dv~~Al~~~~f~~~~~~l~~~l~~   81 (89)
T d2bykb1           2 NAVIGRLIKEALPESASVSKEARAAIARAASVFAIFVTSSSTALAHKQNHKTITAKDILQTLTELDFESFVPSLTQDLEV   81 (89)
T ss_dssp             CSHHHHHHHHHSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCTTTHHHHHHHHHH
T ss_pred             ccHHHHHHHHhCcccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHHCCcHHHHHHHHHHHHH
Confidence            589999975 899999999999      8999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhccc
Q 032777           74 YREMEGDT   81 (134)
Q Consensus        74 yre~~~~k   81 (134)
                      ||+..+.|
T Consensus        82 ~~e~~~~k   89 (89)
T d2bykb1          82 YRKVVKEK   89 (89)
T ss_dssp             HHHHHTTC
T ss_pred             HHHHHccC
Confidence            99987764
>d1n1ja_ a.22.1.3 (A:) Nuclear transcription factor Y subunit beta (Nf-Yb3) {Human (Homo sapiens) [TaxId: 9606]} 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
>d1n1jb_ a.22.1.3 (B:) Nuclear transcription factor Y subunit gamma (Nf-Yc2) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1ku5a_ a.22.1.2 (A:) Archaeal histone {Archaeon (Pyrococcus horikoshii) [TaxId: 53953]} Back     information, alignment and structure
>d1htaa_ a.22.1.2 (A:) Archaeal histone {Archaeon Methanothermus fervidus, histone A [TaxId: 2180]} 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
>d1f1ea_ a.22.1.2 (A:) Archaeal histone {Archaeon Methanopyrus kandleri [TaxId: 2320]} Back     information, alignment and structure
>d1f1ea_ a.22.1.2 (A:) Archaeal histone {Archaeon Methanopyrus kandleri [TaxId: 2320]} Back     information, alignment and structure
>d2huec1 a.22.1.1 (C:20-101) Histone H4 {African clawed frog (Xenopus laevis) [TaxId: 8355]} 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
>d1q9ca_ a.22.1.3 (A:) Histone domain of Son of sevenless protein {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
>d1u35c1 a.22.1.1 (C:814-919) macro-H2A.1, histone domain {Human (Homo sapiens) [TaxId: 9606]} 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
>d1tzyc_ a.22.1.1 (C:) Histone H3 {Chicken (Gallus gallus), erythrocytes [TaxId: 9031]} 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
>d1bh9b_ a.22.1.3 (B:) TAF(II)28 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure