D-I-TASSER Q9UBD5-D1

D-I-TASSER results for Q9UBD5-D1

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

Input Sequence in FASTA format

>Q9UBD5 (257 residues)
MATSSMSKGCFVFKPNSKKRKISLPIEDYFNKGKNEPEDSKLRFETYQLIWQQMKSENER
LQEELLSCKEHLTTVLDKLLLTTQFPFKINEKVLQVLTNIFLYHDFSVQNFIKGLQLSLL
EHFYSQPLSVLCCNLPEAKRRINFLSNNQCENIRRLPSFRRYVEKQASEKQVALLTNERY
LKEETQLLLENLHVYHMNYFLVLRCLHKFTSSLPKYPLGRQIRELYCTCLEKPPETQPLH
EVVYFSAAHALREHLNA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| MATSSMSKGCFVFKPNSKKRKISLPIEDYFNKGKNEPEDSKLRFETYQLIWQQMKSENERLQEELLSCKEHLTTVLDKLLLTTQFPFKINEKVLQVLTNIFLYHDFSVQNFIKGLQLSLLEHFYSQPLSVLCCNLPEAKRRINFLSNNQCENIRRLPSFRRYVEKQASEKQVALLTNERYLKEETQLLLENLHVYHMNYFLVLRCLHKFTSSLPKYPLGRQIRELYCTCLEKPPETQPLHEVVYFSAAHALREHLNA
Prediction	CCCCCCCCCSSSSCCCCCCCCCCCCHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHSSSSCCHHHHHHHHHHHHHCCCCCCSSSCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCHHHHHCCCHHHHHHHHHCCHHHHHHHHCCHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHCCCCCCHHHHHHHHCCHHHHHHHHCC
Confidence	98544456415645775545446884777522567872034679999999999998765321454486899999999997179984566779999999999983448999999999999999845974655179456676775399999999965815899998245067888602559999999999999999999999999999999985678976332999999998177651169999844118999998659
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| MATSSMSKGCFVFKPNSKKRKISLPIEDYFNKGKNEPEDSKLRFETYQLIWQQMKSENERLQEELLSCKEHLTTVLDKLLLTTQFPFKINEKVLQVLTNIFLYHDFSVQNFIKGLQLSLLEHFYSQPLSVLCCNLPEAKRRINFLSNNQCENIRRLPSFRRYVEKQASEKQVALLTNERYLKEETQLLLENLHVYHMNYFLVLRCLHKFTSSLPKYPLGRQIRELYCTCLEKPPETQPLHEVVYFSAAHALREHLNA
Prediction	75443223000002253554637152542044447636414121400431154143415434041340552034005401033612030133003101420342222041004102100000024320100014366255405504562053036142024205534676335105436302510350054035114201200200120153035333133013000300266154540350042232530364278
	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 AttentionPotential. 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                 180                 200                 220                 240

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCSSSSCCCCCCCCCCCCHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHSSSSCCHHHHHHHHHHHHHCCCCCCSSSCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCHHHHHCCCHHHHHHHHHCCHHHHHHHHCCHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHCCCCCCHHHHHHHHCCHHHHHHHHCC
MATSSMSKGCFVFKPNSKKRKISLPIEDYFNKGKNEPEDSKLRFETYQLIWQQMKSENERLQEELLSCKEHLTTVLDKLLLTTQFPFKINEKVLQVLTNIFLYHDFSVQNFIKGLQLSLLEHFYSQPLSVLCCNLPEAKRRINFLSNNQCENIRRLPSFRRYVEKQASEKQVALLTNERYLKEETQLLLENLHVYHMNYFLVLRCLHKFTSSLPKYPLGRQIRELYCTCLEKPPETQPLHEVVYFSAAHALREHLNA

5uj8A

0.75

0.65

18.52

1.17

DEthreader

LRFE----Q---------------------------L--WQQMKSENERLQENHLTFKFGIAQSLSCK-EHLTTVLDKLLLTTQFPFKINEKVLQVLTNIFLYHDFSVQNFIKGLQLSLLEHFYSQPLSVLCCNLPEAKRRINFLSNNQCENIRRLPSFRRYVEKQASEKQVALLTNERYLKEETQLLLENLHVYHMNYFLVLRCLHKFTSSLPKYPLGRQIRELYCTCLEKNIWDEEYASVLQLRALFLQFQSLDA

5uj8A

0.68

19.39

1.69

SPARKS-K

LISQLMDCCVDIKSYMTVTQKTDPKMLSKKRTTSSQWQSSQHLHEFPLILIFGIATSPIIIHRLLLSCKEHLTTVLDKLLLTTQFPFKINEKVLQVLTNIFLYHDFSVQNFIKGLQLSLLEHFYSQPLSVLCCNLPEAKRRINFLSNNQCENIRRLPSFRRYVEKQASEKQVALLTNERYLKEETQLLLENLHVYHMNYFLVLRCLHKFTSSLPKYPLGRQIRELYCTCLEKNIDSEEYASVLQLLRMLELMTILEK

4xgcC

0.27

8.25

1.21

MapAlign

KSWYTNNFDSEQKRRQLVVILPDFECFNASVLQDLILILSAHCGSLPFVLVLGVATAMTAVHGTTQAAPTGLNEVLDKVLLSPKYAFHLSGKTFKFLTHIFLYYDFSIHGFIQGFKYCLMEHFFGGNAFALCTDYSKALGRIKQLTHEDMETIRRLPSFRPYVEQIDCKRIIAVLTDDDYLKKKLPQLLRDCLLHFLLFRCSLEFLTELVGDLPRCPLGKLRRELYVNCLNRIISTPEYKECLKVNRALERTEQFL-

4xgcC

0.27

8.35

1.11

CEthreader

RSQCTMKQLKSWYTNNFDSEQKRRQLVVILPDFECFNASSAHCGSLPFVLVLGVATAMTAVHGTLPYAPTGLNEVLDKVLLSPKYAFHLSGKTFKFLTHIFLYYDFSIHGFIQGFKYCLMEHFFGGNAFALCTDYSKALGRIKQLTHEDMETIRRLPSFRPYVEQINCKRIIAVLTDDDYLKKKLPQLLRDCLLHFLLFRCSLEFLTELVGDLPRCPLGKLRRELYVNCLNRAIISTPEYKECLQMLSFLSKDEFVA

4xgcC3

0.35

0.26

7.79

1.05

MUSTER

----------------------------------------------------------------TQAAPTGLNEVLDKVLLSPKYAFHLSGKTFKFLTHIFLYYDFSIHGFIQGFKYCLMEHFFGGNAFALCTDYSKALGRIKQLTHEDMETIRRLPSFRPYVEQIDCKRIIAVLTDDDYLKKKLPQLLRDCLLHFLLFRCSLEFLTELVGDLPRCPLGKLRRELYVNCLNRAISTPEYKECLQMLSKDEFVAKVNR

5uj8A

0.69

0.68

19.38

5.09

HHsearch

MDCCDVQKPTTS-SQW-QSPPVVVILKDMFATKVLQDISSQHLHEFPLILIFGIATSPIIIHRLLPSCKEHLTTVLDKLLLTTQFPFKINEKVLQVLTNIFLYHDFSVQNFIKGLQLSLLEHFYSQPLSVLCCNLPEAKRRINFLSNNQCENIRRLPSFRRYVEKQASEKQVALLTNERYLKEETQLLLENLHVYHMNYFLVLRCLHKFTSSLPKYPLGRQIRELYCTCLEKNIDSEEYASVLAKDELMTILEKCFK

4xgcC3

0.35

0.26

7.68

1.91

FFAS-3D

-----------------------------------------------------------------QAAPTGLNEVLDKVLLSPKYAFHLSGKTFKFLTHIFLYYDFSIHGFIQGFKYCLMEHFFGGNAFALCTDYSKALGRIKQLTHEDMETIRRLPSFRPYVEQIDCKRIIAVLTDDDYLKKKLPQLLRDCLLHFLLFRCSLEFLTELVGDLPRCPLGKLRRELYVNCLNRAIISKECLQMLSFLSKDEFVAKVN-

5uj8A

0.68

0.67

19.16

1.63

EigenThreader

VTQKTDPKMLSKKRTTSSQDMESFATKVLQDFIIISSQHLHEFPLILIFG---IATSPIIIHRLLLSCKEHLTTVLDKLLLTTQFPFKINEKVLQVLTNIFLYHDFSVQNFIKGLQLSLLEHFYSQPLSVLCCNLPEAKRRINFLSNNQCENIRRLPSFRRYVEKQASEKQVALLTNERYLKEETQLLLENLHVYHMNYFLVLRCLHKFTSSLPKYPLGRQIRELYCTCLEKNIWDSEEYASVLQLLRMLAKDELMT

5uj8A

0.77

0.68

19.26

1.67

CNFpred

-------------------------LQDFIII------SSQHLHEFPLILIFGIATSPIIIHRLLLSCKEHLTTVLDKLLLTTQFPFKINEKVLQVLTNIFLYHDFSVQNFIKGLQLSLLEHFYSQPLSVLCCNLPEAKRRINFLSNNQCENIRRLPSFRRYVEKQASEKQVALLTNERYLKEETQLLLENLHVYHMNYFLVLRCLHKFTSSLPKYPLGRQIRELYCTCLEKNIDSEEYASVLQLLAKDELMTILEK

4xgcC

0.30

0.26

7.91

1.17

DEthreader

EERK----N-----------------------------QINDHIADLQHRSYARTLLALLTGQTQAAP-TGLNEVLDKVLLSPKYAFHLSGKTFKFLTHIFLYYDFSIHGFIQGFKYCLMEHFFGGNAFALCTDYSKALGRIKQLTHEDMETIRRLPSFRPYVEQINCKRIIAVLTDDDYLKKKLPQLLRDCLLHFLLFRCSLEFLTELVGDLPRCPLGKLRRELYVNCLNRAISTPEYKECLQMLSFVKVNRAVDE

(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	0.6307

(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 AttentionPotential, 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	5uj8A	0.83	3.61	0.692	0.961	model1_5uj8A.pdb.gz
2	4xgcC	0.81	2.71	0.297	0.903	model1_4xgcC.pdb.gz
3	5udbC1	0.59	4.73	0.126	0.833	model1_5udbC1.pdb.gz
4	7astN	0.46	5.49	0.028	0.693	model1_7astN.pdb.gz
5	6rflA	0.45	5.53	0.050	0.689	model1_6rflA.pdb.gz
6	7a6hA	0.44	5.37	0.058	0.681	model1_7a6hA.pdb.gz
7	6vr4A	0.43	5.98	0.029	0.728	model1_6vr4A.pdb.gz
8	5flmA	0.43	6.01	0.039	0.700	model1_5flmA.pdb.gz
9	5teeA	0.43	6.13	0.065	0.751	model1_5teeA.pdb.gz
10	6xasJ	0.43	5.65	0.027	0.650	model1_6xasJ.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:0003677	1.00	DNA binding
GO:0003688	0.96	DNA replication origin 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:0022402	1.00	cell cycle process
GO:0016043	1.00	cellular component organization
GO:0006270	1.00	DNA replication initiation
GO:0006267	0.96	pre-replicative complex assembly involved in nuclear cell cycle DNA replication

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:0005664	1.00	nuclear origin of replication recognition complex
GO:0044451	0.94	nucleoplasm part
GO:0031261	0.92	DNA replication preinitiation complex
GO:0005656	0.92	nuclear pre-replicative complex
GO:0000784	0.92	nuclear chromosome, telomeric region
GO:0000428	0.52	DNA-directed RNA polymerase complex

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	2vdcA	0.391	6.78	0.033	0.735	1.4.1.13	NA
2	0.060	2w90B	0.375	6.07	0.041	0.642	1.1.1.44	NA
3	0.060	2vkzG	0.377	6.18	0.094	0.661	2.3.1.38 3.1.2.14	NA
4	0.060	1ea0A	0.391	6.78	0.033	0.735	1.4.1.13	NA
5	0.060	3gtgB	0.375	6.30	0.044	0.661	2.7.7.6	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:

No Binding sites was predicted

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues

	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, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. In preparation, 2020.