D-I-TASSER P62502-D1

D-I-TASSER results for P62502-D1

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

Input Sequence in FASTA format

>P62502 (163 residues)
MGGLLLAAFLALVSVPRAQAVWLGRLDPEQLLGPWYVLAVASREKGFAMEKDMKNVVGVV
VTLTPENNLRTLSSQHGLGGCDQSVMDLIKRNSGWVFENPSIGVLELWVLATNFRDYAII
FTQLEFGDEPFNTVELYSLTETASQEAMGLFTKWSRSLGFLSQ

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MGGLLLAAFLALVSVPRAQAVWLGRLDPEQLLGPWYVLAVASREKGFAMEKDMKNVVGVVVTLTPENNLRTLSSQHGLGGCDQSVMDLIKRNSGWVFENPSIGVLELWVLATNFRDYAIIFTQLEFGDEPFNTVELYSLTETASQEAMGLFTKWSRSLGFLSQ
Prediction	CCHHHHHHHHHHHHHHCCCCCCCCCCCHHHCCSSSSSSSSSSCCHHHHHCCCCCSSSSSSSSSCCCCCSSSSSSSSCCCCSSSSSSSSSSCCCCCSSSSCCCCSSSSSSSSCCCCCSSSSSSSSCCCCSSSSSSSSSSCCCCCCHHHHHHHHHHHHHHCCCCC
Confidence	9038999999998521245655679973456547599999858713410157714788999995999689999995299479999999985898199855677189999943899689999997029945899999977999999999999999999199999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MGGLLLAAFLALVSVPRAQAVWLGRLDPEQLLGPWYVLAVASREKGFAMEKDMKNVVGVVVTLTPENNLRTLSSQHGLGGCDQSVMDLIKRNSGWVFENPSIGVLELWVLATNFRDYAIIFTQLEFGDEPFNTVELYSLTETASQEAMGLFTKWSRSLGFLSQ
Prediction	4331222111000011305232375153631343411000014354236665514021230313673302010123477304424230452755140314444433010110425300000022346643122010102446246602630351067362488
	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

                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCHHHHHHHHHHHHHHCCCCCCCCCCCHHHCCSSSSSSSSSSCCHHHHHCCCCCSSSSSSSSSCCCCCSSSSSSSSCCCCSSSSSSSSSSCCCCCSSSSCCCCSSSSSSSSCCCCCSSSSSSSSCCCCSSSSSSSSSSCCCCCCHHHHHHHHHHHHHHCCCCC
MGGLLLAAFLALVSVPRAQAVWLGRLDPEQLLGPWYVLAVASREKGFAMEKDMKNVVGVVVTLTPENNLRTLSSQHGLGGCDQSVMDLIKRNSGWVFENPSIGVLELWVLATNFRDYAIIFTQLEFGDEPFNTVELYSLTETASQEAMGLFTKWSRSLGFLSQ

3qkgA

0.20

0.18

5.70

1.33

DEthreader

---------------DN--IQVQENFNISRIYGKWYNLAIGSTSPWLKKIMDRMTVSTLVLGEGAEAEISMTSTRWRKGVCEETSGAYEKTDTDGKFLYHKWITMESYVVHTNYDEYAIFLTKKFSRHHPTITAKLYGRAPQLRETLLQDFRVVAQGVGIPED

5x7yA

0.18

0.16

5.19

2.37

SPARKS-K

-------------------DVVKGNFDISKISGDWYSILLASDIKEKIEENGSMRVFVKDIEVLSNSSLIFTMHTKVNGKCTKISLICNKTEKDGEYDVVHDGYNLFRIIETAYEDYIIFHLNNVNQEQEFQLMELYGRKPDVSPKVKEKFVRYCQGMEIPKE

2l5pA

0.13

0.12

4.02

1.08

MapAlign

-------------------FSQMTSFQSNKFQGEWFVLGLADNT--YKREHRPLLSFITLFKLRDNSEFQVTNSMTRGKHCSTWSYTLIPTNKPGQFTRDGADKENIQVIETDYVKFALVLSLRQASNQNITRVSLLGRDWKITHKTIDRFIALTKTQNLNLL

2l5pA

0.12

0.11

3.91

0.79

CEthreader

----------GQSPTMPQGFSQMTSFQSNKFQGEWFVLGLADNT-YKREHRPLLHSFITLFKLRDNSEFQVTNSMTRGKHCSTWSYTLIPTNKPGQFTRDNADKENIQVIETDYVKFALVLSLRQASNQNITRVSLLGRDWKITHKTIDRFIALTKTQNLTKN

5x7yA

0.18

0.16

5.19

1.89

MUSTER

-------------------DVVKGNFDISKISGDWYSILLASDIKEKIEENGSMRVFVKDIEVLSNSSLIFTMHTKVNGKCTKISLICNKTEKDGEYDVVHDGYNLFRIIETAYEDYIIFHLNNVNQEQEFQLMELYGRKPDVSPKVKEKFVRYCQGMEIPKE

1jzuA

0.21

0.18

5.83

1.89

HHsearch

----------------------MTVPDRSEIAGKWYVVALASNTEFFLREKDKMKMAMARISFLGEDELKVSYAVPKPNGCRKWETTFKKTSDDGEVYYSEEAKKKVEVLDTDYKSYAVIYATRVKDGRTLHMMRLYSRSPEVSPAATAIFRKLAGERNYTDE

5x7yA

0.18

0.16

5.18

2.07

FFAS-3D

--------------------VVKGNFDISKISGDWYSILLASDIKEKIEENGSMRVFVKDIEVLSNSSLIFTMHTKVNGKCTKISLICNKTEKDGEYDVVHDGYNLFRIIETAYEDYIIFHLNNVNQEQEFQLMELYGRKPDVSPKVKEKFVRYCQGMEIPKE

2e4jA

0.22

0.20

6.38

1.22

EigenThreader

--------------GSQGHDTVQPNFQQDKFLGRWYSAGLASNSSWFREKKAVLYMCKTVVAPSTEGGLNLTSTFLRKNQAETKIMVLQPAGAPGHYTYSSGSIHSVSVVEANYDEYALLFSRGTKGPGQFRMATLYSRTQTLKDELKEKFTTFSKAQGLTEE

5x7yA

0.18

0.16

5.19

2.31

CNFpred

-------------------DVVKGNFDISKISGDWYSILLASDIKEKIEENGSMRVFVKDIEVLSNSSLIFTMHTKVNGKCTKISLICNKTEKDGEYDVVHDGYNLFRIIETAYEDYIIFHLNNVNQEQEFQLMELYGRKPDVSPKVKEKFVRYCQGMEIPKE

3zq3A

0.22

0.19

6.01

1.33

DEthreader

-------------------SFERGNLDVDKLNGDWFSIVVASDKREKIEENGSMRVFVQHIDVL-ENSLGFTFRIKENGVCTEFSLVADKTAKDGEYFVEYDGENTFTILKTDYDNYVMFHLVNVNNGETFQLMELYGRTKDLSSDIKEKFAKLCVAHGITRD

(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	0.78

(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	3qkgA	0.82	1.66	0.199	0.896	model1_3qkgA.pdb.gz
2	2l5pA	0.82	1.99	0.132	0.914	model1_2l5pA.pdb.gz
3	2qosC	0.79	2.00	0.152	0.883	model1_2qosC.pdb.gz
4	5nghA	0.79	2.29	0.164	0.871	model1_5nghA.pdb.gz
5	2xstA	0.78	1.73	0.241	0.865	model1_2xstA.pdb.gz
6	1gm6A	0.78	2.40	0.197	0.871	model1_1gm6A.pdb.gz
7	3zq3A	0.78	2.50	0.212	0.883	model1_3zq3A.pdb.gz
8	1epbB	0.78	2.00	0.232	0.871	model1_1epbB.pdb.gz
9	1bsqA	0.77	2.78	0.211	0.902	model1_1bsqA.pdb.gz
10	1df3A	0.76	2.63	0.144	0.883	model1_1df3A.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:0005215	0.76	transporter activity
GO:0003824	0.76	catalytic activity
GO:0008289	0.72	lipid binding
GO:0005549	0.61	odorant binding
GO:0005550	0.58	pheromone binding
GO:0005501	0.56	retinoid binding
GO:0004872	0.53	receptor activity
GO:0099600	0.52	transmembrane receptor activity
GO:0004871	0.52	signal transducer activity
GO:0016740	0.51	transferase activity
GO:0004888	0.51	transmembrane signaling receptor activity
GO:0016772	0.50	transferase activity, transferring phosphorus-containing groups

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:0044699	0.95	single-organism process
GO:0009987	0.93	cellular process
GO:0044763	0.89	single-organism cellular process
GO:0008152	0.87	metabolic process
GO:0065007	0.86	biological regulation
GO:0044710	0.84	single-organism metabolic process
GO:0050789	0.82	regulation of biological process
GO:0044237	0.78	cellular metabolic process
GO:0050896	0.75	response to stimulus
GO:0050794	0.73	regulation of cellular process
GO:0071704	0.71	organic substance metabolic process
GO:0044238	0.70	primary metabolic process
GO:0032502	0.68	developmental process
GO:0044767	0.67	single-organism developmental process
GO:0042221	0.67	response to chemical
GO:0048519	0.66	negative regulation of biological process
GO:0048523	0.65	negative regulation of cellular process
GO:0051716	0.64	cellular response to stimulus
GO:0016043	0.62	cellular component organization
GO:0006629	0.62	lipid metabolic process
GO:1901700	0.61	response to oxygen-containing compound
GO:0019222	0.61	regulation of metabolic process
GO:0060255	0.60	regulation of macromolecule metabolic process
GO:0048583	0.60	regulation of response to stimulus
GO:0032501	0.60	multicellular organismal process
GO:0031323	0.60	regulation of cellular metabolic process
GO:0023051	0.60	regulation of signaling
GO:0010646	0.60	regulation of cell communication
GO:0080090	0.59	regulation of primary metabolic process
GO:0065008	0.59	regulation of biological quality
GO:0044281	0.59	small molecule metabolic process
GO:0009966	0.59	regulation of signal transduction
GO:0051223	0.58	regulation of protein transport
GO:0048585	0.58	negative regulation of response to stimulus
GO:0048518	0.58	positive regulation of biological process
GO:0031324	0.58	negative regulation of cellular metabolic process
GO:0023057	0.58	negative regulation of signaling
GO:0010648	0.58	negative regulation of cell communication
GO:0010033	0.58	response to organic substance
GO:0060341	0.57	regulation of cellular localization
GO:0051224	0.57	negative regulation of protein transport
GO:0048522	0.57	positive regulation of cellular process
GO:0045833	0.57	negative regulation of lipid metabolic process
GO:0042592	0.57	homeostatic process
GO:0010605	0.57	negative regulation of macromolecule metabolic process
GO:0044707	0.56	single-multicellular organism process
GO:0070887	0.55	cellular response to chemical stimulus
GO:0033993	0.55	response to lipid
GO:0071310	0.54	cellular response to organic substance
GO:0009893	0.52	positive regulation of metabolic process
GO:0009653	0.52	anatomical structure morphogenesis
GO:1902531	0.51	regulation of intracellular signal transduction
GO:0050708	0.51	regulation of protein secretion
GO:0048584	0.51	positive regulation of response to stimulus
GO:0031325	0.51	positive regulation of cellular metabolic process
GO:0023056	0.51	positive regulation of signaling
GO:0010817	0.51	regulation of hormone levels
GO:0010647	0.51	positive regulation of cell communication
GO:0010604	0.51	positive regulation of macromolecule metabolic process
GO:0010468	0.51	regulation of gene expression
GO:0007165	0.51	signal transduction
GO:0006996	0.51	organelle organization
GO:1902533	0.50	positive regulation of intracellular signal transduction
GO:1901701	0.50	cellular response to oxygen-containing compound
GO:0051171	0.50	regulation of nitrogen compound metabolic process
GO:0050796	0.50	regulation of insulin secretion
GO:0048869	0.50	cellular developmental process
GO:0031326	0.50	regulation of cellular biosynthetic process
GO:0014070	0.50	response to organic cyclic compound
GO:0009725	0.50	response to hormone

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:0005576	0.97	extracellular region
GO:0044464	0.95	cell part
GO:0044421	0.93	extracellular region part
GO:0005615	0.92	extracellular space
GO:0044424	0.87	intracellular part
GO:0043226	0.86	organelle
GO:0043227	0.85	membrane-bounded organelle
GO:0044444	0.79	cytoplasmic part
GO:0043229	0.75	intracellular organelle
GO:0043231	0.74	intracellular membrane-bounded organelle
GO:0005783	0.54	endoplasmic reticulum

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	2x4mA	0.457	4.79	0.015	0.712	3.4.23.48	68
2	0.060	1ksiA	0.470	3.79	0.046	0.663	1.4.3.21	NA
3	0.060	2oqeB	0.445	3.94	0.075	0.656	1.4.3.21 1.4.3.6	NA
4	0.060	1tu5A	0.470	3.82	0.074	0.663	1.4.3.21	NA
5	0.060	1aorB	0.463	4.98	0.069	0.767	1.2.7.5	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	0.25	3uexA	0.758	2.50	0.215	0.877	0.75	STE	complex1.pdb.gz	28,61,69,99,107,109
2	0.24	3qzkA	0.767	2.62	0.211	0.902	0.64	EIC	complex2.pdb.gz	61,69,71,75,77,85,107,109,119,121
3	0.21	2gj5A	0.762	2.62	0.212	0.896	0.88	VD3	complex3.pdb.gz	71,75,85,99,101,120,122
4	0.21	1epbA	0.757	1.97	0.239	0.847	0.63	REA	complex4.pdb.gz	28,31,35,59,61,105,107,109,118,120
5	0.09	1fenA	0.729	2.88	0.102	0.883	0.76	AZE	complex5.pdb.gz	61,71,77,84,99,107
6	0.05	1epa0	0.755	2.01	0.246	0.847	0.68	III	complex6.pdb.gz	141,144,146,148,149,152

	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.