D-I-TASSER P42229-D4

D-I-TASSER results for P42229-D4

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

Input Sequence in FASTA format

>P42229 (142 residues)
TFIIEKQPPQVLKTQTKFAATVRLLVGGKLNVHMNPPQVKATIISEQQAKSLLKNENTRN
ECSGEILNNCCVMEYHQATGTLSAHFRNMSLKRIKRADRRGAESVTEEKFTVLFESQFSV
GSNELVFQVKTLSLPVVVIVHG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| TFIIEKQPPQVLKTQTKFAATVRLLVGGKLNVHMNPPQVKATIISEQQAKSLLKNENTRNECSGEILNNCCVMEYHQATGTLSAHFRNMSLKRIKRADRRGAESVTEEKFTVLFESQFSVGSNELVFQVKTLSLPVVVIVHG
Prediction	CSSSSCCCCCSSSSCCSSSSSSSSSSCCCCCCCCCCCSSSSSSSCCHHHHHHHCCCCCCCCSSSSSCCCCCCCSSSCCCCCSSSSSCCCSSSSSSCCCCCCCCSSSSSSSSSSSSSSSSSCCCCSSSSSSSCCCCSSSSSCC
Confidence	9376338981576074889999763420007666785599999636777775126777873156771675202131689947999715524667417999862034124799999999973883699999812678999679
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| TFIIEKQPPQVLKTQTKFAATVRLLVGGKLNVHMNPPQVKATIISEQQAKSLLKNENTRNECSGEILNNCCVMEYHQATGTLSAHFRNMSLKRIKRADRRGAESVTEEKFTVLFESQFSVGSNELVFQVKTLSLPVVVIVHG
Prediction	7443553233123463411020120026405343543403030254652452456742444441413534440426666330303044141453444766423000432100103030324456040304230001002338
	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

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CSSSSCCCCCSSSSCCSSSSSSSSSSCCCCCCCCCCCSSSSSSSCCHHHHHHHCCCCCCCCSSSSSCCCCCCCSSSCCCCCSSSSSCCCSSSSSSCCCCCCCCSSSSSSSSSSSSSSSSSCCCCSSSSSSSCCCCSSSSSCC
TFIIEKQPPQVLKTQTKFAATVRLLVGGKLNVHMNPPQVKATIISEQQAKSLLKNENTRNECSGEILNNCCVMEYHQATGTLSAHFRNMSLKRIKRADRRGAESVTEEKFTVLFESQFSVGSNELVFQVKTLSLPVVVIVHG

1y1uA3

0.99

0.93

26.04

1.33

DEthreader

TFIIEKQPPQVLKTQTKFAATVRLLVGGKLNVHMNPPQVKATIISEQQAKSLLKNENTRNECSGEILNNCCVMEYHQATGTLSAHFRNMSLKR-----E----SVTEEKFTVLFESQFSVGSNELVFQVKTLSLPVVVIVHG

1y1uA

1.00

0.94

26.23

2.45

SPARKS-K

TFIIEKQPPQVLKTQTKFAATVRLLVGGKLNVHMNPPQVKATIISEQQAKSLLKNENTRNECSGEILNNCCVMEYHQATGTLSAHFRNMSLKR---------ESVTEEKFTVLFESQFSVGSNELVFQVKTLSLPVVVIVHG

1y1uA

0.88

0.81

22.78

1.08

MapAlign

TFIIEKQPPQVLKTQTKFAATVRLLVGGKLNVHMNPPQVKATIISEQQAKSLLNENTRNECSGEILN-NCCVMEYHQATGTLSAHFRNMSLK-R--------ESVTEEKFTVLFESQFSVGSNELVFQVKTLSLPVVVIV--

1y1uA3

1.00

0.94

26.23

1.03

CEthreader

TFIIEKQPPQVLKTQTKFAATVRLLVGGKLNVHMNPPQVKATIISEQQAKSLLKNENTRNECSGEILNNCCVMEYHQATGTLSAHFRNMSLKR---------ESVTEEKFTVLFESQFSVGSNELVFQVKTLSLPVVVIVHG

1y1uA3

1.00

0.94

26.23

1.96

MUSTER

TFIIEKQPPQVLKTQTKFAATVRLLVGGKLNVHMNPPQVKATIISEQQAKSLLKNENTRNECSGEILNNCCVMEYHQATGTLSAHFRNMSLKR---------ESVTEEKFTVLFESQFSVGSNELVFQVKTLSLPVVVIVHG

1y1uA

1.00

0.94

26.23

4.00

HHsearch

TFIIEKQPPQVLKTQTKFAATVRLLVGGKLNVHMNPPQVKATIISEQQAKSLLKNENTRNECSGEILNNCCVMEYHQATGTLSAHFRNMSLKR---------ESVTEEKFTVLFESQFSVGSNELVFQVKTLSLPVVVIVHG

1y1uA3

1.00

0.94

26.23

2.16

FFAS-3D

TFIIEKQPPQVLKTQTKFAATVRLLVGGKLNVHMNPPQVKATIISEQQAKSLLKNENTRNECSGEILNNCCVMEYHQATGTLSAHFRNMSLKR---------ESVTEEKFTVLFESQFSVGSNELVFQVKTLSLPVVVIVHG

1y1uA3

0.86

0.81

22.80

0.90

EigenThreader

TFIIEKQPPQVLKTQTKFAATVRLLVGGKLNVHMNPPQVKATIISEQQAKSLLKNENTRNECSGEILNNCCVMEYHQ-ATGTLSAHFRNMSLKR--------ESVTEEKFTVLFESQFSVGSNELVFQVKTLSLPVVVIVQD

1y1uA

1.00

0.94

26.23

3.46

CNFpred

TFIIEKQPPQVLKTQTKFAATVRLLVGGKLNVHMNPPQVKATIISEQQAKSLLKNENTRNECSGEILNNCCVMEYHQATGTLSAHFRNMSLKR---------ESVTEEKFTVLFESQFSVGSNELVFQVKTLSLPVVVIVHG

1y1uA

0.99

0.93

26.04

1.33

DEthreader

TFIIEKQPPQVLKTQTKFAATVRLLVGGKLNVHMNPPQVKATIISEQQAKSLLKNENTRNECSGEILNNCCVMEYHQATGTLSAHFRNMSLKR-----E----SVTEEKFTVLFESQFSVGSNELVFQVKTLSLPVVVIVHG

(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	0.803

(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	1y1uA	0.92	0.67	1.000	0.937	model1_1y1uA.pdb.gz
2	1bg1A	0.76	2.97	0.308	0.908	model1_1bg1A.pdb.gz
3	4y5uA	0.73	1.13	0.514	0.768	model1_4y5uA.pdb.gz
4	1yvlB4	0.73	2.71	0.323	0.852	model1_1yvlB4.pdb.gz
5	1uusA	0.65	2.79	0.219	0.803	model1_1uusA.pdb.gz
6	2blmA	0.31	5.31	0.046	0.578	model1_2blmA.pdb.gz
7	1g8pA1	0.29	5.87	0.043	0.641	model1_1g8pA1.pdb.gz
8	2jz4A1	0.27	4.97	0.059	0.479	model1_2jz4A1.pdb.gz
9	3gyxB	0.26	4.90	0.043	0.472	model1_3gyxB.pdb.gz
10	2ptkA1	0.26	4.55	0.063	0.430	model1_2ptkA1.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:1901363	0.74	heterocyclic compound binding
GO:0097159	0.74	organic cyclic compound binding
GO:0003676	0.69	nucleic acid binding
GO:0003677	0.68	DNA binding
GO:0003700	0.55	transcription factor activity, sequence-specific DNA 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:0065007	0.96	biological regulation
GO:0050789	0.96	regulation of biological process
GO:0050794	0.95	regulation of cellular process
GO:0009987	0.94	cellular process
GO:0048518	0.89	positive regulation of biological process
GO:0044699	0.89	single-organism process
GO:0007165	0.89	signal transduction
GO:0080090	0.86	regulation of primary metabolic process
GO:0060255	0.86	regulation of macromolecule metabolic process
GO:0031323	0.86	regulation of cellular metabolic process
GO:0006355	0.85	regulation of transcription, DNA-templated
GO:0048522	0.84	positive regulation of cellular process
GO:0035556	0.79	intracellular signal transduction
GO:0007259	0.78	JAK-STAT cascade
GO:0044763	0.77	single-organism cellular process
GO:0051239	0.75	regulation of multicellular organismal process
GO:0031325	0.75	positive regulation of cellular metabolic process
GO:0010604	0.75	positive regulation of macromolecule metabolic process
GO:0045935	0.74	positive regulation of nucleobase-containing compound metabolic process
GO:0031328	0.74	positive regulation of cellular biosynthetic process
GO:0010557	0.74	positive regulation of macromolecule biosynthetic process
GO:0045893	0.73	positive regulation of transcription, DNA-templated
GO:0050793	0.72	regulation of developmental process
GO:0019221	0.71	cytokine-mediated signaling pathway
GO:2000026	0.69	regulation of multicellular organismal development
GO:0045595	0.69	regulation of cell differentiation
GO:0048869	0.68	cellular developmental process
GO:0030154	0.65	cell differentiation
GO:0042127	0.62	regulation of cell proliferation
GO:0050896	0.60	response to stimulus
GO:0008284	0.60	positive regulation of cell proliferation
GO:0006357	0.60	regulation of transcription from RNA polymerase II promoter
GO:0048519	0.59	negative regulation of biological process
GO:0032502	0.58	developmental process
GO:0010033	0.57	response to organic substance
GO:0070887	0.56	cellular response to chemical stimulus
GO:0051240	0.55	positive regulation of multicellular organismal process
GO:0048583	0.55	regulation of response to stimulus
GO:0048523	0.55	negative regulation of cellular process
GO:0071310	0.54	cellular response to organic substance
GO:0045944	0.54	positive regulation of transcription from RNA polymerase II promoter
GO:0032501	0.54	multicellular organismal process
GO:0002682	0.53	regulation of immune system process
GO:0051246	0.50	regulation of protein metabolic process
GO:0045596	0.50	negative regulation of cell differentiation
GO:0042981	0.50	regulation of apoptotic process

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:0044424	1.00	intracellular part
GO:0005737	0.97	cytoplasm
GO:0043229	0.88	intracellular organelle
GO:0043227	0.87	membrane-bounded organelle
GO:0043231	0.86	intracellular membrane-bounded organelle
GO:0005634	0.85	nucleus
GO:0044446	0.59	intracellular organelle part
GO:0044428	0.55	nuclear part

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	0.066	1tnnA	0.455	2.76	0.036	0.585	2.7.11.1	NA
2	0.060	2b3rB	0.474	3.98	0.100	0.739	2.7.1.154	NA
3	0.060	1srdC	0.504	3.80	0.035	0.725	1.15.1.1	NA
4	0.060	3ce1A	0.502	3.82	0.035	0.732	1.15.1.1	NA
5	0.060	1srdA	0.501	3.81	0.035	0.725	1.15.1.1	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:

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
	1	0.15	1y1u0	0.918	0.67	1.000	0.937	0.62	III	complex1.pdb.gz	15,31,32,33,34,35,38,68,69,72,87,88,92,119,121,122,123,124

	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.