Citrus Sinensis ID: 032408

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-------140-
MEEETNGIDEERKQQHEEDASVTEILRDRFRLSTISIAEAEANQIGMEISKPIIACISDLAFKYTEQLAKDLELFAQHAGRKSVRMEDVILSAHRNERLAATLRSFRNDLKAKEPRSERKRKKSSTREDITTTNVVQVPDL
cccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHccHHHHHHHHHHHHHHHHccccHHHHccccccccccccccccccccc
cccccccccHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccEcHHHHHHHHHccHHHHHHHHHHHHHHHHcccccHccccccccccccccccEEEcccc
meeetngiDEERKQQHEEDASVTEILRDRFRLSTISIAEAEANQIGMEISKPIIACISDLAFKYTEQLAKDLELFAQHAGRKSVRMEDVILSAHRNERLAATLRSFRNDlkakeprserkrkksstreditttnvvqvpdl
meeetngideerkqqheedasvteilrdrfRLSTISIAEaeanqigmeISKPIIACISDLAFKYTEQLAKDLELFAQHAGRKSVRMEDVILSAHRNERLAATLrsfrndlkakeprserkrkksstreditttnvvqvpdl
MEEETNGIDEERKQQHEEDASVTEILRDRFRLSTISIAEAEANQIGMEISKPIIACISDLAFKYTEQLAKDLELFAQHAGRKSVRMEDVILSAHRNERLAATLRSFRNDLKAkeprserkrkksstreDITTTNVVQVPDL
***********************EILRDRFRLSTISIAEAEANQIGMEISKPIIACISDLAFKYTEQLAKDLELFAQHAGRKSVRMEDVILSA************************************************
***************************DRFRLSTISIAEAE*******IS*PIIACISDLAFKYTEQLAKDLELFAQHAGRKSVRMEDVILSAHRNERLAA****************************************
********************SVTEILRDRFRLSTISIAEAEANQIGMEISKPIIACISDLAFKYTEQLAKDLELFAQHAGRKSVRMEDVILSAHRNERLAATLRSFRNDL*******************ITTTNVVQVPDL
************KQQHEEDASVTEILRDRFRLSTISIAEAEANQIGMEISKPIIACISDLAFKYTEQLAKDLELFAQHAGRKSVRMEDVILSAHRNERLAATLRSFRNDLKAK****************************
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MEEETNGIDEERKQQHEEDASVTEILRDRFRLSTISIAEAEANQIGMEISKPIIACISDLAFKYTEQLAKDLELFAQHAGRKSVRMEDVILSAHRNERLAATLRSFRNDLKAKEPRSERKRKKSSTREDITTTNVVQVPDL
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 ?
Query141 2.2.26 [Sep-21-2011]
Q6NRI8135 Centromere protein S OS=X N/A no 0.680 0.711 0.354 1e-07
Q8N2Z9138 Centromere protein S OS=H yes no 0.375 0.384 0.509 1e-07
Q9D084142 Centromere protein S OS=M yes no 0.375 0.373 0.509 4e-07
Q2TBR7138 Centromere protein S OS=B yes no 0.453 0.463 0.437 6e-07
E1BSW7139 Centromere protein S OS=G yes no 0.524 0.532 0.378 8e-07
O74807110 Uncharacterized protein C yes no 0.354 0.454 0.42 3e-06
>sp|Q6NRI8|CENPS_XENLA Centromere protein S OS=Xenopus laevis GN=apitd1 PE=2 SV=1 Back     alignment and function desciption
 Score = 55.5 bits (132), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 34/96 (35%), Positives = 54/96 (56%)

Query: 17  EEDASVTEILRDRFRLSTISIAEAEANQIGMEISKPIIACISDLAFKYTEQLAKDLELFA 76
           EE  S T+ L+        S+ +  A+   ++ SK  IA IS++ F+  E  AKDLE+FA
Sbjct: 6   EEHFSRTQRLKAAVHYVVGSLCQEVADDKEIDFSKQAIAAISEITFRQCESFAKDLEIFA 65

Query: 77  QHAGRKSVRMEDVILSAHRNERLAATLRSFRNDLKA 112
           +HA R ++ M+DV L A R+  L A +    +++ A
Sbjct: 66  RHAKRTTINMDDVKLLARRSRSLYAHISKCSDEIAA 101
Probable DNA-binding component of the FA core complex involved in DNA damage repair and genome maintenance. Probable component of a centromeric complex involved in assembly of kinetochore proteins, mitotic progression and chromosome segregation.
Xenopus laevis (taxid: 8355)
>sp|Q8N2Z9|CENPS_HUMAN Centromere protein S OS=Homo sapiens GN=APITD1 PE=1 SV=1 Back     alignment and function description
>sp|Q9D084|CENPS_MOUSE Centromere protein S OS=Mus musculus GN=Apitd1 PE=2 SV=1 Back     alignment and function description
>sp|Q2TBR7|CENPS_BOVIN Centromere protein S OS=Bos taurus GN=APITD1 PE=2 SV=1 Back     alignment and function description
>sp|E1BSW7|CENPS_CHICK Centromere protein S OS=Gallus gallus GN=APITD1 PE=1 SV=2 Back     alignment and function description
>sp|O74807|YGNG_SCHPO Uncharacterized protein C2D10.16 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPBC2D10.16 PE=4 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 ?
Query141
224134152136 predicted protein [Populus trichocarpa] 0.957 0.992 0.676 2e-44
225456487135 PREDICTED: centromere protein S [Vitis v 0.829 0.866 0.760 2e-44
255540055135 conserved hypothetical protein [Ricinus 0.950 0.992 0.669 3e-44
297734508136 unnamed protein product [Vitis vinifera] 0.829 0.860 0.754 4e-43
449454798129 PREDICTED: centromere protein S-like iso 0.801 0.875 0.743 5e-42
15241317 242 Histone 2A domain-containing protein [Ar 0.929 0.541 0.593 1e-38
297792397184 hypothetical protein ARALYDRAFT_331481 [ 0.858 0.657 0.629 4e-38
242072834169 hypothetical protein SORBIDRAFT_06g01465 0.751 0.627 0.660 6e-35
357464945128 Centromere protein S [Medicago truncatul 0.780 0.859 0.681 9e-34
357163179142 PREDICTED: uncharacterized protein C2D10 0.765 0.760 0.620 4e-33
>gi|224134152|ref|XP_002321749.1| predicted protein [Populus trichocarpa] gi|222868745|gb|EEF05876.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
 Score =  183 bits (465), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 94/139 (67%), Positives = 111/139 (79%), Gaps = 4/139 (2%)

Query: 3   EETNGIDEERKQQHEEDASVTEILRDRFRLSTISIAEAEANQIGMEISKPIIACISDLAF 62
           E  NG + ER    EED SV++IL+DRFRLS ISIAE EA + G+EIS+PI +CI+DLA 
Sbjct: 2   EGGNGNEVER----EEDDSVSDILQDRFRLSAISIAENEAKKNGVEISEPITSCIADLAL 57

Query: 63  KYTEQLAKDLELFAQHAGRKSVRMEDVILSAHRNERLAATLRSFRNDLKAKEPRSERKRK 122
            YTEQLAK+LE FAQHAGRKSV MEDVILSAHRNE L A LRSF NDLK KEP+SERKR+
Sbjct: 58  NYTEQLAKELEAFAQHAGRKSVNMEDVILSAHRNEHLTALLRSFCNDLKEKEPQSERKRR 117

Query: 123 KSSTREDITTTNVVQVPDL 141
           K+S +ED  TT+ V +PD+
Sbjct: 118 KTSKKEDKATTSAVNIPDI 136

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|225456487|ref|XP_002284609.1| PREDICTED: centromere protein S [Vitis vinifera] gi|147791927|emb|CAN67893.1| hypothetical protein VITISV_040390 [Vitis vinifera] Back     alignment and taxonomy information
>gi|255540055|ref|XP_002511092.1| conserved hypothetical protein [Ricinus communis] gi|223550207|gb|EEF51694.1| conserved hypothetical protein [Ricinus communis] Back     alignment and taxonomy information
>gi|297734508|emb|CBI15755.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|449454798|ref|XP_004145141.1| PREDICTED: centromere protein S-like isoform 1 [Cucumis sativus] gi|449454800|ref|XP_004145142.1| PREDICTED: centromere protein S-like isoform 2 [Cucumis sativus] gi|449473866|ref|XP_004154006.1| PREDICTED: centromere protein S-like isoform 1 [Cucumis sativus] gi|449473870|ref|XP_004154007.1| PREDICTED: centromere protein S-like isoform 2 [Cucumis sativus] gi|449523429|ref|XP_004168726.1| PREDICTED: centromere protein S-like isoform 1 [Cucumis sativus] gi|449523431|ref|XP_004168727.1| PREDICTED: centromere protein S-like isoform 2 [Cucumis sativus] Back     alignment and taxonomy information
>gi|15241317|ref|NP_199906.1| Histone 2A domain-containing protein [Arabidopsis thaliana] gi|9758240|dbj|BAB08739.1| unnamed protein product [Arabidopsis thaliana] gi|332008629|gb|AED96012.1| Histone 2A domain-containing protein [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|297792397|ref|XP_002864083.1| hypothetical protein ARALYDRAFT_331481 [Arabidopsis lyrata subsp. lyrata] gi|297309918|gb|EFH40342.1| hypothetical protein ARALYDRAFT_331481 [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|242072834|ref|XP_002446353.1| hypothetical protein SORBIDRAFT_06g014650 [Sorghum bicolor] gi|241937536|gb|EES10681.1| hypothetical protein SORBIDRAFT_06g014650 [Sorghum bicolor] Back     alignment and taxonomy information
>gi|357464945|ref|XP_003602754.1| Centromere protein S [Medicago truncatula] gi|355491802|gb|AES73005.1| Centromere protein S [Medicago truncatula] gi|388505116|gb|AFK40624.1| unknown [Medicago truncatula] Back     alignment and taxonomy information
>gi|357163179|ref|XP_003579649.1| PREDICTED: uncharacterized protein C2D10.16-like [Brachypodium distachyon] 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 ?
Query141
TAIR|locus:2157393242 AT5G50930 [Arabidopsis thalian 0.744 0.433 0.628 2.3e-30
UNIPROTKB|Q6NRI8135 apitd1 "Centromere protein S" 0.680 0.711 0.354 5.2e-10
ASPGD|ASPL0000059159104 AN0598 [Emericella nidulans (t 0.631 0.855 0.325 1.1e-09
UNIPROTKB|Q8N2Z9138 APITD1 "Centromere protein S" 0.652 0.666 0.358 1.1e-09
UNIPROTKB|F1RIF6139 APITD1 "Uncharacterized protei 0.730 0.741 0.320 1.1e-09
UNIPROTKB|Q2TBR7138 APITD1 "Centromere protein S" 0.730 0.746 0.320 1.4e-09
UNIPROTKB|E2QRZ7159 APITD1 "Uncharacterized protei 0.652 0.578 0.347 2.9e-09
UNIPROTKB|F6V9H4143 APITD1-CORT "Uncharacterized p 0.652 0.643 0.347 2.9e-09
UNIPROTKB|K7ESB076 APITD1 "Centromere protein S" 0.375 0.697 0.509 2e-08
UNIPROTKB|E1BSW7139 APITD1 "Centromere protein S" 0.588 0.597 0.349 3.3e-08
TAIR|locus:2157393 AT5G50930 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 335 (123.0 bits), Expect = 2.3e-30, P = 2.3e-30
 Identities = 66/105 (62%), Positives = 84/105 (80%)

Query:     8 IDEERKQQHEEDASVTEILRDRFRLSTISIAEAEANQIGMEISKPIIACISDLAFKYTEQ 67
             I + +  Q  E+ S+ +++RDRFRLS ISIAEAEA + GMEI  P++AC++DLAFKY E 
Sbjct:   106 ISDLQVDQIVEEYSMDDLIRDRFRLSAISIAEAEAKKNGMEIGGPVVACVADLAFKYAEN 165

Query:    68 LAKDLELFAQHAGRKSVRMEDVILSAHRNERLAATLRSFRNDLKA 112
             +AKDLELFA HAGRK V M+DV+LSAHRN+ LAA+LRS  N+LKA
Sbjct:   166 VAKDLELFAHHAGRKVVNMDDVVLSAHRNDNLAASLRSLCNELKA 210
GO:0003677 "DNA binding" evidence=IEA
GO:0005634 "nucleus" evidence=ISM
GO:0008150 "biological_process" evidence=ND
UNIPROTKB|Q6NRI8 apitd1 "Centromere protein S" [Xenopus laevis (taxid:8355)] Back     alignment and assigned GO terms
ASPGD|ASPL0000059159 AN0598 [Emericella nidulans (taxid:162425)] Back     alignment and assigned GO terms
UNIPROTKB|Q8N2Z9 APITD1 "Centromere protein S" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|F1RIF6 APITD1 "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
UNIPROTKB|Q2TBR7 APITD1 "Centromere protein S" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|E2QRZ7 APITD1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|F6V9H4 APITD1-CORT "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|K7ESB0 APITD1 "Centromere protein S" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|E1BSW7 APITD1 "Centromere protein S" [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

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

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Your Input:
GSVIVG00018039001
SubName- Full=Putative uncharacterized protein (Chromosome chr17 scaffold_16, whole genome shotgun sequence); (135 aa)
(Vitis vinifera)
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 ?
Query141
COG203691 COG2036, HHT1, Histones H3 and H4 [Chromatin struc 3e-04
>gnl|CDD|224947 COG2036, HHT1, Histones H3 and H4 [Chromatin structure and dynamics] Back     alignment and domain information 
 Score = 37.3 bits (87), Expect = 3e-04
 Identities = 16/47 (34%), Positives = 28/47 (59%)

Query: 49 ISKPIIACISDLAFKYTEQLAKDLELFAQHAGRKSVRMEDVILSAHR 95
          +S   I  + +   +Y E++A+D    A+HA RK+V+ ED+ L+  R
Sbjct: 37 VSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKR 83

Length = 91

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 141
PF1563076 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 100.0
cd07979117 TAF9 TATA Binding Protein (TBP) Associated Factor 99.54
cd0007685 H4 Histone H4, one of the four histones, along wit 99.43
COG203691 HHT1 Histones H3 and H4 [Chromatin structure and d 99.42
PLN00035103 histone H4; Provisional 99.42
PTZ00015102 histone H4; Provisional 99.36
PF15511414 CENP-T: Centromere kinetochore component CENP-T; P 99.33
smart0080365 TAF TATA box binding protein associated factor. TA 99.29
smart0057677 BTP Bromodomain transcription factors and PHD doma 99.23
PF02291129 TFIID-31kDa: Transcription initiation factor IID, 99.21
smart0041774 H4 Histone H4. 99.19
cd0798172 TAF12 TATA Binding Protein (TBP) Associated Factor 99.09
KOG3334148 consensus Transcription initiation factor TFIID, s 99.08
PF0012575 Histone: Core histone H2A/H2B/H3/H4 histone h2a si 98.92
smart00428105 H3 Histone H3. 98.85
PF0752477 Bromo_TP: Bromodomain associated; InterPro: IPR006 98.8
PF0080865 CBFD_NFYB_HMF: Histone-like transcription factor ( 98.53
cd08050 343 TAF6 TATA Binding Protein (TBP) Associated Factor 98.49
COG5094145 TAF9 Transcription initiation factor TFIID, subuni 98.41
PF0296966 TAF: TATA box binding protein associated factor (T 98.41
cd00074115 H2A Histone 2A; H2A is a subunit of the nucleosome 98.37
PLN00161135 histone H3; Provisional 98.2
PLN0016097 histone H3; Provisional 98.16
KOG0870172 consensus DNA polymerase epsilon, subunit D [Trans 98.14
PTZ00018136 histone H3; Provisional 98.04
PLN00121136 histone H3; Provisional 98.04
KOG3467103 consensus Histone H4 [Chromatin structure and dyna 97.93
PF0226993 TFIID-18kDa: Transcription initiation factor IID, 97.92
cd0797892 TAF13 The TATA Binding Protein (TBP) Associated Fa 97.48
KOG0869168 consensus CCAAT-binding factor, subunit A (HAP3) [ 97.44
PF0384768 TFIID_20kDa: Transcription initiation factor TFIID 97.39
KOG4336 323 consensus TBP-associated transcription factor Prod 97.19
KOG2389 353 consensus Predicted bromodomain transcription fact 97.18
KOG1745137 consensus Histones H3 and H4 [Chromatin structure 96.76
KOG2549 576 consensus Transcription initiation factor TFIID, s 96.69
smart00414106 H2A Histone 2A. 96.6
smart0042789 H2B Histone H2B. 96.41
KOG0871156 consensus Class 2 transcription repressor NC2, bet 96.4
PLN00154136 histone H2A; Provisional 96.09
PTZ00463117 histone H2B; Provisional 96.01
PTZ00017134 histone H2A; Provisional 95.97
PLN00158116 histone H2B; Provisional 95.88
PLN00157132 histone H2A; Provisional 95.68
KOG1142258 consensus Transcription initiation factor TFIID, s 95.46
KOG3901109 consensus Transcription initiation factor IID subu 95.25
PLN00156139 histone H2AX; Provisional 95.03
COG5248126 TAF19 Transcription initiation factor TFIID, subun 94.99
PLN00153129 histone H2A; Provisional 94.89
KOG1744127 consensus Histone H2B [Chromatin structure and dyn 94.69
PTZ00252134 histone H2A; Provisional 94.1
KOG1756131 consensus Histone 2A [Chromatin structure and dyna 94.05
PRK07452326 DNA polymerase III subunit delta; Validated 93.57
PRK07914320 hypothetical protein; Reviewed 92.02
PRK05907311 hypothetical protein; Provisional 91.84
PRK06585343 holA DNA polymerase III subunit delta; Reviewed 91.73
PRK05629318 hypothetical protein; Validated 91.58
PRK08487328 DNA polymerase III subunit delta; Validated 90.91
TIGR01128302 holA DNA polymerase III, delta subunit. subunit ar 90.68
COG5095 450 TAF6 Transcription initiation factor TFIID, subuni 90.38
COG5262132 HTA1 Histone H2A [Chromatin structure and dynamics 89.22
TIGR02902 531 spore_lonB ATP-dependent protease LonB. Members of 88.62
PRK05574340 holA DNA polymerase III subunit delta; Reviewed 88.39
cd08045212 TAF4 TATA Binding Protein (TBP) Associated Factor 87.6
PRK14962 472 DNA polymerase III subunits gamma and tau; Provisi 86.92
COG1466334 HolA DNA polymerase III, delta subunit [DNA replic 85.88
PF13654509 AAA_32: AAA domain; PDB: 3K1J_B. 85.35
PRK12402337 replication factor C small subunit 2; Reviewed 85.13
COG5150148 Class 2 transcription repressor NC2, beta subunit 85.05
PRK04195 482 replication factor C large subunit; Provisional 82.52
PRK00440319 rfc replication factor C small subunit; Reviewed 81.83
PRK13765 637 ATP-dependent protease Lon; Provisional 81.82
TIGR00764 608 lon_rel lon-related putative ATP-dependent proteas 81.76
PF05236 264 TAF4: Transcription initiation factor TFIID compon 81.75
PRK14970367 DNA polymerase III subunits gamma and tau; Provisi 81.35
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C Back     alignment and domain information 
Probab=100.00  E-value=3.2e-33  Score=195.86  Aligned_cols=76  Identities=43%  Similarity=0.648  Sum_probs=70.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhcCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHHHhhcHHH
Q 032408           24 EILRDRFRLSTISIAEAEANQIGMEISKPIIACISDLAFKYTEQLAKDLELFAQHAGRKSVRMEDVILSAHRNERL   99 (141)
Q Consensus        24 ~~LKaaL~y~V~rI~ee~~~~~~~~vs~~~v~aL~Elv~~~~~~ia~DLe~FAkHAgRkTI~~eDV~Ll~Rrn~~L   99 (141)
                      ++||++|||+|++||++++.+.|+.+||+||++|+||+|.|+.++|.||++||+||||+||++|||+|++||||+|
T Consensus         1 ~~LKaal~~~v~ki~ee~~~~~~~~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~Rrn~~L   76 (76)
T PF15630_consen    1 QRLKAALWYTVGKIVEEEAKEKGVEVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLARRNPSL   76 (76)
T ss_dssp             HHHHHHHHHHHHHHHHHCCCCTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTTT-HHH
T ss_pred             ChHHHHHHHHHHHHHHHHHhccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhhcCCCC
Confidence            5899999999999999999999999999999999999999999999999999999999999999999999999987

>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
>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
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics] Back     alignment and domain information
>PLN00035 histone H4; Provisional Back     alignment and domain information
>PTZ00015 histone H4; Provisional 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
>smart00803 TAF TATA box binding protein associated factor Back     alignment and domain information
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins 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
>smart00417 H4 Histone H4 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
>KOG3334 consensus Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription] 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
>smart00428 H3 Histone H3 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
>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
>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
>COG5094 TAF9 Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription] 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
>cd00074 H2A Histone 2A; H2A is a subunit of the nucleosome 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
>PTZ00018 histone H3; Provisional Back     alignment and domain information
>PLN00121 histone H3; Provisional Back     alignment and domain information
>KOG3467 consensus Histone H4 [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
>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
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [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
>KOG4336 consensus TBP-associated transcription factor Prodos [Transcription] Back     alignment and domain information
>KOG2389 consensus Predicted bromodomain transcription factor [Transcription] Back     alignment and domain information
>KOG1745 consensus Histones H3 and H4 [Chromatin structure and dynamics] 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
>smart00414 H2A Histone 2A Back     alignment and domain information
>smart00427 H2B Histone H2B Back     alignment and domain information
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription] Back     alignment and domain information
>PLN00154 histone H2A; Provisional Back     alignment and domain information
>PTZ00463 histone H2B; Provisional Back     alignment and domain information
>PTZ00017 histone H2A; Provisional Back     alignment and domain information
>PLN00158 histone H2B; Provisional Back     alignment and domain information
>PLN00157 histone H2A; 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
>KOG3901 consensus Transcription initiation factor IID subunit [Transcription] Back     alignment and domain information
>PLN00156 histone H2AX; Provisional Back     alignment and domain information
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription] Back     alignment and domain information
>PLN00153 histone H2A; Provisional Back     alignment and domain information
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics] Back     alignment and domain information
>PTZ00252 histone H2A; Provisional Back     alignment and domain information
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics] Back     alignment and domain information
>PRK07452 DNA polymerase III subunit delta; Validated Back     alignment and domain information
>PRK07914 hypothetical protein; Reviewed Back     alignment and domain information
>PRK05907 hypothetical protein; Provisional Back     alignment and domain information
>PRK06585 holA DNA polymerase III subunit delta; Reviewed Back     alignment and domain information
>PRK05629 hypothetical protein; Validated Back     alignment and domain information
>PRK08487 DNA polymerase III subunit delta; Validated Back     alignment and domain information
>TIGR01128 holA DNA polymerase III, delta subunit 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
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics] Back     alignment and domain information
>TIGR02902 spore_lonB ATP-dependent protease LonB Back     alignment and domain information
>PRK05574 holA DNA polymerase III subunit delta; Reviewed 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
>PRK14962 DNA polymerase III subunits gamma and tau; Provisional Back     alignment and domain information
>COG1466 HolA DNA polymerase III, delta subunit [DNA replication, recombination, and repair] Back     alignment and domain information
>PF13654 AAA_32: AAA domain; PDB: 3K1J_B Back     alignment and domain information
>PRK12402 replication factor C small subunit 2; Reviewed Back     alignment and domain information
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription] Back     alignment and domain information
>PRK04195 replication factor C large subunit; Provisional Back     alignment and domain information
>PRK00440 rfc replication factor C small subunit; Reviewed Back     alignment and domain information
>PRK13765 ATP-dependent protease Lon; Provisional Back     alignment and domain information
>TIGR00764 lon_rel lon-related putative ATP-dependent protease 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
>PRK14970 DNA polymerase III subunits gamma and tau; Provisional 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 ?
Query141
4dra_A113 Crystal Structure Of Mhf Complex Length = 113 2e-08
3vh5_A140 Crystal Structure Of The Chicken Cenp-T Histone Fol 2e-08
4drb_A120 The Crystal Structure Of Fancm Bound Mhf Complex Le 2e-07
3b0b_B107 Crystal Structure Of The Chicken Cenp-SCENP-X Compl 4e-07
3b0c_T111 Crystal Structure Of The Chicken Cenp-T Histone Fol 8e-04
3vh5_T111 Crystal Structure Of The Chicken Cenp-T Histone Fol 9e-04
>pdb|4DRA|A Chain A, Crystal Structure Of Mhf Complex Length = 113 Back     alignment and structure 
Iteration: 1

 Score = 54.7 bits (130), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 27/53 (50%), Positives = 35/53 (66%)
Query: 47 MEISKPIIACISDLAFKYTEQLAKDLELFAQHAGRKSVRMEDVILSAHRNERL 99
          M+ SK  IA IS+L F+  E  AKDLE+FA+HA R ++  EDV L A R+  L
Sbjct: 46 MQFSKQTIAAISELTFRQCENFAKDLEMFARHAKRTTINTEDVKLLARRSNSL 98
>pdb|3VH5|A Chain A, Crystal Structure Of The Chicken Cenp-T Histone FoldCENP-WCENP- SCENP-X Heterotetrameric Complex, Crystal Form I Length = 140 Back     alignment and structure
>pdb|4DRB|A Chain A, The Crystal Structure Of Fancm Bound Mhf Complex Length = 120 Back     alignment and structure
>pdb|3B0B|B Chain B, Crystal Structure Of The Chicken Cenp-SCENP-X Complex Length = 107 Back     alignment and structure
>pdb|3B0C|T Chain T, Crystal Structure Of The Chicken Cenp-T Histone FoldCENP-W Complex, Crystal Form I Length = 111 Back     alignment and structure
>pdb|3VH5|T Chain T, Crystal Structure Of The Chicken Cenp-T Histone FoldCENP-WCENP- SCENP-X Heterotetrameric Complex, Crystal Form I Length = 111 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 ?
Query141
3vh5_A140 CENP-S; histone fold, chromosome segregation, DNA 8e-21
4dra_A113 Centromere protein S; DNA binding complex, DNA dam 8e-20
3b0b_B107 CENP-S, centromere protein S; histone fold, DNA bi 3e-19
3v9r_A90 MHF1, uncharacterized protein YOL086W-A; histone f 7e-18
3b0c_T111 CENP-T, centromere protein T; histone fold, DNA bi 7e-11
>3vh5_A CENP-S; histone fold, chromosome segregation, DNA binding, nucleus, binding protein; 2.40A {Gallus gallus} PDB: 3vh6_A Length = 140 Back     alignment and structure
 Score = 81.4 bits (200), Expect = 8e-21
 Identities = 35/112 (31%), Positives = 59/112 (52%)

Query: 14  QQHEEDASVTEILRDRFRLSTISIAEAEANQIGMEISKPIIACISDLAFKYTEQLAKDLE 73
              E+   + + LR     +T ++A+  A   G+  SK  +A IS++ F+  E  A+DLE
Sbjct: 5   AGGEQRELLIQRLRAAVHYTTGALAQDVAEDKGVLFSKQTVAAISEITFRQAENFARDLE 64

Query: 74  LFAQHAGRKSVRMEDVILSAHRNERLAATLRSFRNDLKAKEPRSERKRKKSS 125
           +FA+HA R ++  EDV L A R+  L   +    ++L +     + K+KK S
Sbjct: 65  MFARHAKRSTITSEDVKLLARRSNSLLKYITQKSDELASSNMEQKEKKKKKS 116
>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
>3b0b_B CENP-S, centromere protein S; histone fold, DNA binding, DNA, nucleus, DNA binding protein; 2.15A {Gallus gallus} Length = 107 Back     alignment and structure
>3v9r_A MHF1, uncharacterized protein YOL086W-A; histone fold, fanconi anemia, DNA repair, DNA BI protein; 2.40A {Saccharomyces cerevisiae} Length = 90 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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query141
3vh5_A140 CENP-S; histone fold, chromosome segregation, DNA 100.0
4dra_A113 Centromere protein S; DNA binding complex, DNA dam 100.0
3b0b_B107 CENP-S, centromere protein S; histone fold, DNA bi 100.0
3v9r_A90 MHF1, uncharacterized protein YOL086W-A; histone f 100.0
1taf_A68 TFIID TBP associated factor 42; transcription init 99.68
3b0c_T111 CENP-T, centromere protein T; histone fold, DNA bi 99.67
1ku5_A70 HPHA, archaeal histon; histone fold, DNA binding p 99.6
2hue_C84 Histone H4; mini beta sheet, elongated beta sandwh 99.48
1id3_B102 Histone H4; nucleosome core particle, chromatin, p 99.45
2yfw_B103 Histone H4, H4; cell cycle, kinetochore, centromer 99.39
1tzy_D103 Histone H4-VI; histone-fold, tetramer-dimer-dimer, 99.38
1taf_B70 TFIID TBP associated factor 62; transcription init 99.29
1b67_A68 Protein (histone HMFA); DNA binding protein; 1.48A 99.26
1f1e_A154 Histone fold protein; archaeal histone protein, DN 99.11
2l5a_A235 Histone H3-like centromeric protein CSE4, protein 99.04
1jfi_B179 DR1 protein, transcription regulator NC2 beta chai 99.03
2ly8_A121 Budding yeast chaperone SCM3; centromere protein, 99.03
2hue_B77 Histone H3; mini beta sheet, elongated beta sandwh 99.01
3nqj_A82 Histone H3-like centromeric protein A; alpha helix 98.99
1n1j_A93 NF-YB; histone-like PAIR, DNA binding protein; 1.6 98.99
1f1e_A154 Histone fold protein; archaeal histone protein, DN 98.95
2yfv_A100 Histone H3-like centromeric protein CSE4; cell cyc 98.89
2byk_B128 Chrac-14; nucleosome sliding, histone fold, DNA-bi 98.88
3b0c_W76 CENP-W, centromere protein W; histone fold, DNA bi 98.84
3nqu_A140 Histone H3-like centromeric protein A; alpha helix 98.78
3r45_A156 Histone H3-like centromeric protein A; histone fol 98.73
1tzy_C136 Histone H3; histone-fold, tetramer-dimer-dimer, DN 98.68
2f8n_G120 Core histone macro-H2A.1; nucleosome, NCP, macroh2 98.29
1n1j_B97 NF-YC; histone-like PAIR, DNA binding protein; 1.6 98.27
2nqb_C123 Histone H2A; nucleosome, NCP, chromatin, structura 98.26
1tzy_A129 Histone H2A-IV; histone-fold, tetramer-dimer-dimer 98.23
1f66_C128 Histone H2A.Z; nucleosome, chromatin, histone vari 98.18
2f8n_K149 Histone H2A type 1; nucleosome, NCP, macroh2A, his 98.15
1id3_C131 Histone H2A.1; nucleosome core particle, chromatin 98.1
2jss_A192 Chimera of histone H2B.1 and histone H2A.Z; histon 98.06
2nqb_D123 Histone H2B; nucleosome, NCP, chromatin, structura 98.0
1jfi_A98 Transcription regulator NC2 alpha chain; histone, 97.96
1tzy_B126 Histone H2B; histone-fold, tetramer-dimer-dimer, D 97.96
4g92_C119 HAPE; transcription factor, nucleosome, minor groo 97.85
2l5a_A 235 Histone H3-like centromeric protein CSE4, protein 97.74
2jss_A192 Chimera of histone H2B.1 and histone H2A.Z; histon 97.56
1h3o_B76 Transcription initiation factor TFIID 20/15 kDa su 97.13
2byk_A140 Chrac-16; nucleosome sliding, histone fold, DNA-bi 97.05
3uk6_A368 RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding 94.25
1g8p_A350 Magnesium-chelatase 38 kDa subunit; parallel beta 90.87
3bos_A242 Putative DNA replication factor; P-loop containing 90.18
3k1j_A 604 LON protease, ATP-dependent protease LON; ATP-bind 89.69
2ly8_A121 Budding yeast chaperone SCM3; centromere protein, 89.59
1jr3_D343 DNA polymerase III, delta subunit; processivity, p 88.54
2chg_A226 Replication factor C small subunit; DNA-binding pr 87.64
2c9o_A456 RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP- 87.21
4dra_E84 Centromere protein X; DNA binding complex, DNA dam 85.9
2r44_A331 Uncharacterized protein; putative ATPase, structur 84.99
1sxj_D353 Activator 1 41 kDa subunit; clamp loader, processi 84.17
3ksy_A 1049 SOS-1, SON of sevenless homolog 1; RAS, RAS activa 83.9
3b0b_C81 CENP-X, centromere protein X; histone fold, DNA bi 83.28
2v1u_A387 Cell division control protein 6 homolog; DNA repli 83.2
>3vh5_A CENP-S; histone fold, chromosome segregation, DNA binding, nucleus, binding protein; 2.40A {Gallus gallus} PDB: 3vh6_A Back     alignment and structure
Probab=100.00  E-value=3.1e-35  Score=225.35  Aligned_cols=109  Identities=31%  Similarity=0.465  Sum_probs=93.9

Q ss_pred             hhhhhhHHHHHHHHHHHHHHHHHHHHHhhcCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHHHhh
Q 032408           16 HEEDASVTEILRDRFRLSTISIAEAEANQIGMEISKPIIACISDLAFKYTEQLAKDLELFAQHAGRKSVRMEDVILSAHR   95 (141)
Q Consensus        16 ~~~~~~~~~~LKaaL~y~V~rI~ee~~~~~~~~vs~~~v~aL~Elv~~~~~~ia~DLe~FAkHAgRkTI~~eDV~Ll~Rr   95 (141)
                      .|+.+.+.++||++|||+|++||++++...|+.|||+|+++|+|++|+|+.+||.||+.||+||||+||+++||+|++||
T Consensus         7 ~~~~~~~~~rLKaAl~y~VgkIvee~~~~~~~~vS~~ai~aL~El~~~~~e~ia~DLe~FAkHAGRKTI~~eDVkLa~Rr   86 (140)
T 3vh5_A            7 GEQRELLIQRLRAAVHYTTGALAQDVAEDKGVLFSKQTVAAISEITFRQAENFARDLEMFARHAKRSTITSEDVKLLARR   86 (140)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHTT
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHh
Confidence            45566678999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cHHHHHHHHHHHHHhhccCCchhhhhhcc
Q 032408           96 NERLAATLRSFRNDLKAKEPRSERKRKKS  124 (141)
Q Consensus        96 n~~L~~~l~~~~~el~~~~~~~~~krKk~  124 (141)
                      ||+|.++|++|.++|...+..++.||||.
T Consensus        87 n~~L~~~L~~~~~el~~~~~~~~~~~k~k  115 (140)
T 3vh5_A           87 SNSLLKYITQKSDELASSNMEQKEKKKKK  115 (140)
T ss_dssp             SHHHHHHHHHHHHHHHHC-----------
T ss_pred             CHHHHHHHHHHHHHHHhhhHHHhhhhhcc
Confidence            99999999999999987665544444443
>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
>3b0b_B CENP-S, centromere protein S; histone fold, DNA binding, DNA, nucleus, DNA binding protein; 2.15A {Gallus gallus} 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
>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
>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
>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
>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
>2yfw_B Histone H4, H4; cell cycle, kinetochore, centromere, histone chaperone, BUDD; 2.60A {Kluyveromyces lactis nrrl y-1140} 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
>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
>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
>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
>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
>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
>2ly8_A Budding yeast chaperone SCM3; centromere protein, CENH3 variants, partially unfolded; NMR {Saccharomyces cerevisiae} 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
>1n1j_A NF-YB; histone-like PAIR, DNA binding protein; 1.67A {Homo sapiens} 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
>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
>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
>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
>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
>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
>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
>1n1j_B NF-YC; histone-like PAIR, DNA binding protein; 1.67A {Homo sapiens} SCOP: a.22.1.3 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
>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
>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_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
>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
>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
>2nqb_D Histone H2B; nucleosome, NCP, chromatin, structural protein/DNA complex; 2.30A {Drosophila melanogaster} PDB: 2pyo_D* 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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>2ly8_A Budding yeast chaperone SCM3; centromere protein, CENH3 variants, partially unfolded; NMR {Saccharomyces cerevisiae} Back     alignment and structure
>1jr3_D DNA polymerase III, delta subunit; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1jqj_C* 1xxh_A* 1xxi_A* 3glf_A* 3glg_A* 3glh_A* 3gli_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
>2c9o_A RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-binding, chromatin regulator, growth regulation, hydrolase, nuclear protein, DNA recombination; HET: ADP; 2.2A {Homo sapiens} PDB: 2xsz_A* 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
>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
>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20 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
>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
>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix} 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 141
d2huec182 a.22.1.1 (C:20-101) Histone H4 {African clawed fro 1e-05
>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 = 39.0 bits (91), Expect = 1e-05
 Identities = 20/75 (26%), Positives = 34/75 (45%), Gaps = 1/75 (1%)

Query: 25 ILRDRFRLSTISIAEAEANQIGME-ISKPIIACISDLAFKYTEQLAKDLELFAQHAGRKS 83
          +LRD  +  T       A + G++ IS  I      +   + E + +D   + +HA RK+
Sbjct: 2  VLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKT 61

Query: 84 VRMEDVILSAHRNER 98
          V   DV+ +  R  R
Sbjct: 62 VTAMDVVYALKRQGR 76

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query141
d2huec182 Histone H4 {African clawed frog (Xenopus laevis) [ 99.43
d1tafa_68 TAF(II)42 {Fruit fly (Drosophila melanogaster) [Ta 99.41
d1htaa_68 Archaeal histone {Archaeon Methanothermus fervidus 99.23
d1ku5a_66 Archaeal histone {Archaeon (Pyrococcus horikoshii) 99.09
d1f1ea_151 Archaeal histone {Archaeon Methanopyrus kandleri [ 98.9
d1tzyc_95 Histone H3 {Chicken (Gallus gallus), erythrocytes 98.57
d1f1ea_151 Archaeal histone {Archaeon Methanopyrus kandleri [ 98.56
d1n1ja_87 Nuclear transcription factor Y subunit beta (Nf-Yb 98.51
d1q9ca_172 Histone domain of Son of sevenless protein {Human 98.48
d1jfib_135 Negative cofactor 2, NC2, beta chain {Human (Homo 98.45
d2bykb189 Chrac-14 {Fruit fly (Drosophila melanogaster) [Tax 98.28
d1tafb_70 TAF(II)62 {Fruit fly (Drosophila melanogaster) [Ta 98.19
d1n1jb_78 Nuclear transcription factor Y subunit gamma (Nf-Y 98.02
d1jfia_66 Negative cofactor 2, NC2, alpha chain {Human (Homo 97.7
d1h3ob_74 TAF(II)-20, (TAF(II)-15, hTAF12), histone fold dom 97.13
d1u35c1106 macro-H2A.1, histone domain {Human (Homo sapiens) 97.11
d1tzyb_92 Histone H2B {Chicken (Gallus gallus), erythrocytes 97.08
d1tzya_106 Histone H2A {Chicken (Gallus gallus), erythrocytes 96.89
d1f66c_103 Histone H2A {Human (Homo sapiens), variant H2A.Z [ 96.82
d2byka172 Chrac-16 {Fruit fly (Drosophila melanogaster) [Tax 96.21
d1fnna2276 CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T 91.28
d1w5sa2287 CDC6-like protein APE0152, N-terminal domain {Aero 91.14
d1sxjc2227 Replication factor C3 {Baker's yeast (Saccharomyce 81.51
>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=99.43  E-value=6.3e-14  Score=96.34  Aligned_cols=62  Identities=23%  Similarity=0.288  Sum_probs=58.8

Q ss_pred             HHHHHHHHHHhhcCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHHHhhcH
Q 032408           33 STISIAEAEANQIGMEISKPIIACISDLAFKYTEQLAKDLELFAQHAGRKSVRMEDVILSAHRNE   97 (141)
Q Consensus        33 ~V~rI~ee~~~~~~~~vs~~~v~aL~Elv~~~~~~ia~DLe~FAkHAgRkTI~~eDV~Ll~Rrn~   97 (141)
                      +|.||+++.|..   ++|+++..+|.+.+..++.++++|+..||+||||+||+.+||.+++|||.
T Consensus        14 ~i~Riar~~Gv~---ris~d~~~~l~~~l~~~l~~i~~~a~~~~~hakRKTvt~~DV~~Alkr~g   75 (82)
T d2huec1          14 AIRRLARRGGVK---RISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQG   75 (82)
T ss_dssp             HHHHHHHHTTCC---EECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTTTC
T ss_pred             HHHHHHHHcCcc---cchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHhcC
Confidence            688999988877   89999999999999999999999999999999999999999999999873
>d1tafa_ a.22.1.3 (A:) TAF(II)42 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} 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
>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
>d1tzyc_ a.22.1.1 (C:) Histone H3 {Chicken (Gallus gallus), erythrocytes [TaxId: 9031]} 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
>d1q9ca_ a.22.1.3 (A:) Histone domain of Son of sevenless protein {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
>d2bykb1 a.22.1.3 (B:11-99) Chrac-14 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} 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
>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
>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
>d1u35c1 a.22.1.1 (C:814-919) macro-H2A.1, histone domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1tzyb_ a.22.1.1 (B:) Histone H2B {Chicken (Gallus gallus), erythrocytes [TaxId: 9031]} Back     information, alignment and structure
>d1tzya_ a.22.1.1 (A:) Histone H2A {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
>d2byka1 a.22.1.3 (A:29-100) Chrac-16 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} 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
>d1sxjc2 c.37.1.20 (C:12-238) Replication factor C3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure