D-I-TASSER P18074-D2

D-I-TASSER results for P18074-D2

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

Input Sequence in FASTA format

>P18074 (92 residues)
SSRKNLCIHPEVTPLRFGKDVDGKCHSLTASYVRAQYQHDTSLPHCRFYEEFDAHGREVP
LPAGIYNLDDLKALGRRQGWCPYFLARYSILH

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| SSRKNLCIHPEVTPLRFGKDVDGKCHSLTASYVRAQYQHDTSLPHCRFYEEFDAHGREVPLPAGIYNLDDLKALGRRQGWCPYFLARYSILH
Prediction	CCCCCCCCCHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCCCHHHHHHHCC
Confidence	94210588977743466117899999975177887752268889883344377724111245579889999999553297955999998629
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| SSRKNLCIHPEVTPLRFGKDVDGKCHSLTASYVRAQYQHDTSLPHCRFYEEFDAHGREVPLPAGIYNLDDLKALGRRQGWCPYFLARYSILH
Prediction	73464151265046465464125203611565346436656746405225515744564414640330430252067352001110343278
	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

                   |                   |                   |                   |

SS
Seq

CCCCCCCCCHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCCCHHHHHHHCC
SSRKNLCIHPEVTPLRFGKDVDGKCHSLTASYVRAQYQHDTSLPHCRFYEEFDAHGREVPLPAGIYNLDDLKALGRRQGWCPYFLARYSILH

6gym01

0.28

0.25

7.64

1.00

DEthreader

TSRKNLCLH--PEERKG-TVVDEKCRRMTNGQAKRKLEE-----LCEYHENLYNIEVEDYLGV-FS-FEKLLKYCEEKTLCPYFIVRRMISC

6gym0

0.34

0.33

9.77

1.91

SPARKS-K

TSRKNLCLHPEVSKERKGTVVDEKCRRMTNGQAKRKLEEV---ELCEYHENLYNIEVEDYLPKGVFSFEKLLKYCEEKTLCPYFIVRRMISL

2vsfA1

0.14

0.13

4.43

1.08

MapAlign

QGRVNMCIL--YLHEINAESLAKFCNMKKREVMAGNE------AACPYFNKIRSDETKRFLFDELPTAEEFYDYGERNNVCPYESMKAALPD

2vsfA

0.12

4.21

1.08

CEthreader

QGRVNMCIL--YRMVDDLHEINAESLAKFCNMKKREVMAGNEAACPYFNFKIRSDETKRFLFDELPTAEEFYDYGERNNVCPYESMKAALPD

5ivwW

1.00

28.00

1.58

MUSTER

SSRKNLCIHPEVTPLRFGKDVDGKCHSLTASYVRAQYQHDTSLPHCRFYEEFDAHGREVPLPAGIYNLDDLKALGRRQGWCPYFLARYSILH

6gym0

0.34

0.33

9.77

2.47

HHsearch

TSRKNLCLHPEVSKERKGTVVDEKCRRMTNGQAKRK---LEEVELCEYHENLYNIEVEDYLPKGVFSFEKLLKYCEEKTLCPYFIVRRMISL

5ivwW1

1.00

28.00

0.68

FFAS-3D

SSRKNLCIHPEVTPLRFGKDVDGKCHSLTASYVRAQYQHDTSLPHCRFYEEFDAHGREVPLPAGIYNLDDLKALGRRQGWCPYFLARYSILH

5ivwW

1.00

28.00

0.98

EigenThreader

SSRKNLCIHPEVTPLRFGKDVDGKCHSLTASYVRAQYQHDTSLPHCRFYEEFDAHGREVPLPAGIYNLDDLKALGRRQGWCPYFLARYSILH

5ivwW

1.00

28.00

1.72

CNFpred

SSRKNLCIHPEVTPLRFGKDVDGKCHSLTASYVRAQYQHDTSLPHCRFYEEFDAHGREVPLPAGIYNLDDLKALGRRQGWCPYFLARYSILH

6gym0

0.28

0.25

7.64

1.00

DEthreader

TSRKNLCLH--PEERKG-TVVDEKCRRMTNGQAKRKLEE-----LCEYHENLYNIEVEDYLGV-FS-FEKLLKYCEEKTLCPYFIVRRMISC

(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	0.6504

(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	5ivwW1	0.90	1.49	0.978	0.978	model1_5ivwW1.pdb.gz
2	6gym0	0.81	1.72	0.284	0.957	model1_6gym0.pdb.gz
3	2vsfA	0.73	2.38	0.122	0.978	model1_2vsfA.pdb.gz
4	5fmfY	0.66	2.32	0.247	0.880	model1_5fmfY.pdb.gz
5	6bldA	0.54	3.33	0.067	0.848	model1_6bldA.pdb.gz
6	1sdiA	0.54	4.09	0.034	0.902	model1_1sdiA.pdb.gz
7	1h7wD1	0.41	4.50	0.077	0.783	model1_1h7wD1.pdb.gz
8	2a5uA2	0.41	4.48	0.060	0.793	model1_2a5uA2.pdb.gz
9	3ziuB2	0.40	4.42	0.011	0.772	model1_3ziuB2.pdb.gz
10	1ulqC	0.39	4.82	0.069	0.696	model1_1ulqC.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:0003824	0.96	catalytic activity
GO:0003678	0.95	DNA helicase activity
GO:0043139	0.76	5'-3' DNA helicase activity
GO:0008094	0.72	DNA-dependent ATPase activity
GO:1901363	0.50	heterocyclic compound binding
GO:0097159	0.50	organic cyclic compound 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:0009987	0.97	cellular process
GO:0008152	0.95	metabolic process
GO:0090304	0.94	nucleic acid metabolic process
GO:0044260	0.89	cellular macromolecule metabolic process
GO:0006950	0.87	response to stress
GO:0065007	0.79	biological regulation
GO:0006259	0.79	DNA metabolic process
GO:0050794	0.78	regulation of cellular process
GO:0051716	0.69	cellular response to stimulus
GO:0006974	0.68	cellular response to DNA damage stimulus
GO:0044699	0.66	single-organism process
GO:0006281	0.64	DNA repair
GO:0016070	0.62	RNA metabolic process
GO:0044249	0.61	cellular biosynthetic process
GO:0009059	0.61	macromolecule biosynthetic process
GO:0034654	0.60	nucleobase-containing compound biosynthetic process
GO:0032774	0.59	RNA biosynthetic process
GO:0016043	0.57	cellular component organization
GO:0006289	0.57	nucleotide-excision repair
GO:0051726	0.56	regulation of cell cycle
GO:1901990	0.55	regulation of mitotic cell cycle phase transition
GO:0060255	0.55	regulation of macromolecule metabolic process
GO:0080090	0.54	regulation of primary metabolic process
GO:0031323	0.54	regulation of cellular metabolic process
GO:0051171	0.53	regulation of nitrogen compound metabolic process
GO:0044763	0.52	single-organism cellular process
GO:0019219	0.52	regulation of nucleobase-containing compound metabolic 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:0044446	0.92	intracellular organelle part
GO:0044428	0.89	nuclear part
GO:0032991	0.87	macromolecular complex
GO:0043226	0.86	organelle
GO:0043229	0.85	intracellular organelle
GO:0043234	0.84	protein complex
GO:0043231	0.78	intracellular membrane-bounded organelle
GO:0005634	0.74	nucleus
GO:1990234	0.73	transferase complex
GO:0061695	0.72	transferase complex, transferring phosphorus-containing groups
GO:0032806	0.71	carboxy-terminal domain protein kinase complex
GO:0044451	0.67	nucleoplasm part
GO:0090575	0.65	RNA polymerase II transcription factor complex
GO:0005675	0.63	holo TFIIH complex
GO:0043232	0.60	intracellular non-membrane-bounded organelle
GO:0005737	0.57	cytoplasm

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	1w0dA	0.463	3.71	0.014	0.772	1.1.1.85	NA
2	0.060	2jbwD	0.463	4.37	0.022	0.826	3.7.1.-	NA
3	0.060	2vsfA	0.727	2.38	0.122	0.978	3.6.4.12	NA
4	0.060	2z8yP	0.492	3.70	0.033	0.761	2.3.1.169	NA
5	0.060	2fp0B	0.457	4.52	0.077	0.902	3.2.1.143	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	0.15	2zujA	0.522	3.51	0.078	0.815	0.12	HEM	complex1.pdb.gz	60,61,73,74,75,81
2	0.01	2z36A	0.341	4.39	0.034	0.576	0.13	HEM	complex2.pdb.gz	69,70,71,75
3	0.01	2qblA	0.383	3.91	0.041	0.620	0.16	HEM	complex3.pdb.gz	6,71,75,79,83
4	0.01	3ol5A	0.517	3.80	0.044	0.826	0.18	HEM	complex4.pdb.gz	56,57,60,71,72,73,77,86
5	0.01	3abbA	0.524	3.72	0.044	0.859	0.11	HEM	complex5.pdb.gz	21,24,25,28,29,32
6	0.01	3p6vA	0.367	3.80	0.053	0.652	0.12	HEM	complex6.pdb.gz	84,85,86,89,90
7	0.01	2iagA	0.526	3.88	0.077	0.880	0.13	HEM	complex7.pdb.gz	50,74,75,81,82,84,87
8	0.01	1iwjA	0.526	3.50	0.078	0.815	0.12	HEM	complex8.pdb.gz	52,53,56,74,75
9	0.01	2zawA	0.521	3.65	0.078	0.826	0.13	6HE	complex9.pdb.gz	3,24,25,28,29,32,33

	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.