D-I-TASSER Q9UBC3-D1

D-I-TASSER results for Q9UBC3-D1

[Click result.zip to download all results on this page]

Input Sequence in FASTA format

>Q9UBC3 (169 residues)
MKGDTRHLNGEEDAGGREDSILVNGACSDQSSDSPPILEAIRTPEIRGRRSSSRLSKREV
SSLLSYTQDLTGDGDGEDGDGSDTPVMPKLFRETRTRSESPAVRTRNNNSVSSRERHRPS
PRSTRGRQGRNHVDESPVEFPATRSLRRRATASAGTPWPSPPSSYLTID

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MKGDTRHLNGEEDAGGREDSILVNGACSDQSSDSPPILEAIRTPEIRGRRSSSRLSKREVSSLLSYTQDLTGDGDGEDGDGSDTPVMPKLFRETRTRSESPAVRTRNNNSVSSRERHRPSPRSTRGRQGRNHVDESPVEFPATRSLRRRATASAGTPWPSPPSSYLTID
Prediction	CCCCCCCCCCCCCCCCCCCSSSSCCCCCCCCCCCCHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCC
Confidence	9975433342246667642377537646666888167764155012575233303577766454203445566777778887764433566640587789752114688755432468997433454455555567644541023554224567998999998663579
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MKGDTRHLNGEEDAGGREDSILVNGACSDQSSDSPPILEAIRTPEIRGRRSSSRLSKREVSSLLSYTQDLTGDGDGEDGDGSDTPVMPKLFRETRTRSESPAVRTRNNNSVSSRERHRPSPRSTRGRQGRNHVDESPVEFPATRSLRRRATASAGTPWPSPPSSYLTID
Prediction	8646554146665364343110132414566453440053143462544445443344403411412451335354666635323202401453534474443444555444546444454444444534542453325244444144434544534244454434428
	Values range from 0 (buried residue) to 8 (highly exposed residue)

Predicted Contact, Hydrogen and Distance Map Used in D-I-TASSER simulation

Contact Map

Distance Map

Hydrogen bond networks

D-I-TASSER simulation is guided by the consensus contact map (left figure), distance map (middle figure) and Hydrogen bond network (right figure) derived based on confidence scores of DeepPotential. In the contact, distance map and hydrogen bond networks, the axes mark the residue index along the sequence. For the contact map, each dot represents a residue pair with predicted contact, while for the distance map and hydrogen bond network, a color scale represents a distance of 1-20+ angstroms or a angle of 0-180 degree.

Top 10 threading templates used by D-I-TASSER

Rank

PDB
hit

ID1

ID2

Cov

Norm.
Zscore

Download
alignment

                  20                  40                  60                  80                 100                 120                 140                 160

                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCCCSSSSCCCCCCCCCCCCHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCC
MKGDTRHLNGEEDAGGREDSILVNGACSDQSSDSPPILEAIRTPEIRGRRSSSRLSKREVSSLLSYTQDLTGDGDGEDGDGSDTPVMPKLFRETRTRSESPAVRTRNNNSVSSRERHRPSPRSTRGRQGRNHVDESPVEFPATRSLRRRATASAGTPWPSPPSSYLTID

1vt4I

0.09

0.08

3.20

0.51

CEthreader

GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG------GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG

6jcvA1

0.07

2.92

0.52

EigenThreader

LDANLDPLKGKFPPKSVDTIMVAPRMVGEGQGKGYPVLLGVKQDASGKAWDYAKAIAKGIGAIEEEALLDLMSEHTWVPILFGAIKACYDIAVKEYGVSPEAALLEFYASGELAEIARLIAEEGIFNQMVHHSKYYDVVRRIVENEAKYIWDGSFAKEWSLEQQAGYPV

6buzN

0.13

0.09

3.08

0.38

FFAS-3D

-----------------------------PMNELTTILKAWDFLSENQLQ---RQRKESVVQHLIHL---------CEEKRSDAALLDIIYMQFHQHQKMKQFKNSFKKVTVSFRETAVWIRIAWGTKPNQYKPTYVVYYSQRRNTPLLGQALTIAS------------

7abiA

0.13

0.12

4.32

0.90

SPARKS-K

NILDVEPLEAQLELDPEED-----APVLDWFYDHQPLRDS-RKYVNGSTYQRWQFTLPMMSTLYRLNQLLTDLVDDNYFYLFDLKAFFTSKALNMAIPGGPKFEPLVRDINLQDEDWNEFNDINKIIIRQPIRTEYKIAFPLPHHVHLTWYHTPNVVFIKTEDPDLPAF

7jh6A

0.25

0.08

2.38

0.50

CNFpred

----------------------------------EQVLEEIEELIQKHRQLASELPKLELQAIKQYREALE---------YVKLPVLAKILEDE---------------------------------------------------------------------------

3syjA

0.04

0.03

1.56

0.83

DEthreader

--YNLHYEDDYH---NPRL--F--------------PIDMPLINGIFQLVRKSYFDEIFERDLHTTLYFMGSLIVSPNSNQTWQGAGIH-------DRLSIIGLYFGLNAMIVVFGLLDENWTNLTTNLSATTNLLSGQGFYILFTLENDHVD-AGAL-----------

6nb2A

0.07

2.89

0.74

MapAlign

QPLYMTLNQGDMMTMPVPMMNILNGGAHADNNVDIQEFMIMPIGAPDFPVALQMG-TEIFHVLKSVLKKQGLNTAVGDEGGFAPDLLSEAIEKAGFRLGEDIVFALDVAASELFNEGFYHMYSENQKFDSHQLIEYYANLISSYPIVSIEDGLDEKDWSGWKQLTT---

6etxG

0.10

3.72

0.74

MUSTER

SWGAPEGESHQRYLRNKDFLLGVNFPLSFPNLCSCPLLKSLVFSSHCKAVSGYSDQVVHQRRSATSSLRRCLLTELPSFLCVASPRVTAVPLDSYCNDRSAEYERRVLKEGGSLAAKQCLLNGAPELAADWLNRRSQFFPEPAGGLWSIRPQNGWSFIRIPGKESLITD

2pffB

0.20

0.19

6.07

0.88

HHsearch

DKKSNSAL-FRAVGEGNAQLVAIFGGNTDPDKDSCPLIGVIQTAFTPGLRSYL-KGATGHSQGLAIAETDSWESFCYEAYPNTSLP-PSILEENKTNSHLPAGKQVEIVNGAKNLVVSGPPSLLRKAKAPSGLDQ-SRIPFSERKLK---FSNRFLPVASPFHSHLLVD

1vt4I3

0.09

0.08

3.20

0.49

CEthreader

GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG------GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG

(a)	ID1 is the number of template residues identical to query divided by number of aligned residues.
(b)	ID2 is the number of template residues identical to query divided by query sequence length.
(c)	Cov is equal the number of aligned template residues divided by query sequence length.
(d)	Norm. Zscore is the normalized Z-score of the threading alignments. A Normalized Z-score >1 means a good alignment and is highlighted in bold.
(e)	Download alignment lists the threading program used to identify the template, and provide the 3D structure of aligned regions of threading templates (threading[1-10].pdb.gz).
(f)	Template residues identical to query sequence are highlighted in color.

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.4908

(a)

D-I-TASSER simulations generate a large ensemble of structural conformations, i.e. decoys. These decoys are clustered by SPICKER based on pairwise structure similarity to report up to five final models from the five largest clusters. Models are ranked in descending order of cluster size. If the simulations converge well, it is possible to have less than 5 models generated, which is usually an indication of good model quality.

(b)

The model confidence is quantitatified by estimated TM-score (eTM-score), calculated based on significance of threading template alignments, contact map satisfaction rate, mean absolute error between distance of model and distance of DeepPotential, and convergence of D-I-TASSER simulations. eTM-score is typically in the range of [0, 1], with higher eTM-score signifies higher model confidence.

Proteins with similar structure

Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	6o9nA	0.46	5.31	0.060	0.793	model1_6o9nA.pdb.gz
2	6xutA	0.44	5.03	0.073	0.757	model1_6xutA.pdb.gz
3	2ckfA	0.44	5.52	0.097	0.799	model1_2ckfA.pdb.gz
4	1cf3A	0.44	4.91	0.034	0.734	model1_1cf3A.pdb.gz
5	5d06A	0.43	5.69	0.056	0.805	model1_5d06A.pdb.gz
6	6eu6A	0.43	4.97	0.054	0.728	model1_6eu6A.pdb.gz
7	6mltA	0.43	5.68	0.048	0.793	model1_6mltA.pdb.gz
8	2b2jA	0.43	4.86	0.061	0.698	model1_2b2jA.pdb.gz
9	5aexA	0.41	5.04	0.053	0.675	model1_5aexA.pdb.gz
10	1wqlA2	0.41	5.72	0.075	0.775	model1_1wqlA2.pdb.gz

(a)	Query structure is shown in cartoon, while the structural analog is displayed using backbone trace.
(b)	Ranking of proteins is based on TM-score of the structural alignment between the query structure and known structures in the PDB library.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of the alignment by TM-align and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Gene Ontology (GO) Terms

Molecular Function (MF)

GO term	Cscore^GO	Name
GO:0003886	1.00	DNA (cytosine-5-)-methyltransferase activity
GO:1901363	0.74	heterocyclic compound binding
GO:0097159	0.74	organic cyclic compound binding
GO:0003676	0.72	nucleic acid binding
GO:0003677	0.70	DNA binding
GO:0003712	0.56	transcription cofactor activity
GO:0003714	0.55	transcription corepressor activity
GO:0003682	0.50	chromatin binding

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Molecular Function. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Biological Process (BP)

GO term	Cscore^GO	Name
GO:0048522	1.00	positive regulation of cellular process
GO:0045892	1.00	negative regulation of transcription, DNA-templated
GO:0006306	1.00	DNA methylation
GO:0044699	0.74	single-organism process
GO:0044763	0.70	single-organism cellular process
GO:0050896	0.69	response to stimulus
GO:0044710	0.68	single-organism metabolic process
GO:0051716	0.67	cellular response to stimulus
GO:0010243	0.67	response to organonitrogen compound
GO:1901701	0.66	cellular response to oxygen-containing compound
GO:0071495	0.66	cellular response to endogenous stimulus
GO:0071310	0.66	cellular response to organic substance
GO:0032776	0.66	DNA methylation on cytosine
GO:0031325	0.59	positive regulation of cellular metabolic process
GO:0010604	0.59	positive regulation of macromolecule metabolic process
GO:0010628	0.58	positive regulation of gene expression
GO:0031399	0.57	regulation of protein modification process
GO:0006357	0.57	regulation of transcription from RNA polymerase II promoter
GO:0051130	0.56	positive regulation of cellular component organization
GO:0033043	0.56	regulation of organelle organization
GO:0031401	0.56	positive regulation of protein modification process
GO:0031400	0.56	negative regulation of protein modification process
GO:0051573	0.55	negative regulation of histone H3-K9 methylation
GO:0051571	0.55	positive regulation of histone H3-K4 methylation
GO:0045814	0.55	negative regulation of gene expression, epigenetic
GO:0000122	0.55	negative regulation of transcription from RNA polymerase II promoter

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Biological Process. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Cellular Component (CC)

GO term	Cscore^GO	Name
GO:0005634	1.00	nucleus
GO:0044446	0.69	intracellular organelle part
GO:0044428	0.65	nuclear part
GO:0005654	0.57	nucleoplasm

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Cellular Component. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Predicted Enzyme Commission (EC) Numbers

Top 5 enzyme homologs in PDB

Rank	Cscore^EC	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	EC Number	Predicted Active Site Residues
1	0.060	1qksB	0.313	6.12	0.015	0.633	1.7.2.1	NA
2	0.060	2ckjA	0.397	5.51	0.058	0.710	1.17.1.4 1.17.3.2	NA
3	0.060	2i7tA	0.393	5.66	0.032	0.740	3.1.27.-	15,163
4	0.060	1br2A	0.389	5.09	0.059	0.669	3.6.1.32	NA
5	0.060	1aomB	0.421	5.45	0.057	0.763	1.7.99.1 1.7.2.1	NA

	Click on the radio buttons to visualize predicted active site residues.
(a)	Cscore^EC is the confidence score for the Enzyme Commission (EC) number prediction. Cscore^EC values range in between [0-1]; where a higher score indicates a more reliable EC number prediction.
(b)	TM-score is a measure of global structural similarity between query and template protein.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Ligand Binding Sites

Template proteins with similar binding site:

Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
1	0.01	1qleA	0.361	5.47	0.039	0.663	0.51	CA	complex1.pdb.gz	11,14,15,16,18
2	0.01	1mneA	0.421	5.45	0.093	0.781	0.41	POP	complex2.pdb.gz	13,14,15,16,42,43
3	0.01	1g99A	0.416	5.47	0.071	0.751	0.43	ADP	complex3.pdb.gz	16,17,18,45,46,49
4	0.01	2nqaA	0.294	5.30	0.056	0.527	0.62	CA	complex4.pdb.gz	3,7,10,12
5	0.01	1mdwA	0.303	5.55	0.116	0.562	0.49	CA	complex5.pdb.gz	13,14,15
6	0.01	1mdwA	0.303	5.55	0.116	0.562	0.62	CA	complex6.pdb.gz	13,17,43
7	0.01	2gbwC	0.424	5.37	0.080	0.763	0.65	FES	complex7.pdb.gz	3,4,15,16,17
8	0.01	3dtuC	0.330	6.02	0.058	0.645	0.46	TRD	complex8.pdb.gz	66,69,70

	Click on the radio buttons to visualize predicted binding site and residues.
(a)	Cscore^LB is the confidence score of predicted binding site. Cscore^LB values range in between [0-1]; where a higher score indicates a more reliable ligand-binding site prediction.
(b)	BS-score is a measure of local similarity (sequence & structure) between template binding site and predicted binding site in the query structure. Based on large scale benchmarking analysis, we have observed that a BS-score >1 reflects a significant local match between the predicted and template binding site.
(c)	TM-score is a measure of global structural similarity between query and template protein.
(d)	RMSD^a the RMSD between residues that are structurally aligned by TM-align.
(e)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(f)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

[Click result.zip to download all results on this page]

References:
1.	Wei Zheng, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.