D-I-TASSER P04156-D1

D-I-TASSER results for P04156-D1

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

Input Sequence in FASTA format

>P04156 (253 residues)
MANLGCWMLVLFVATWSDLGLCKKRPKPGGWNTGGSRYPGQGSPGGNRYPPQGGGGWGQP
HGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQGGGTHSQWNKPSKPKTNMKHMAGAAAAGA
VVGGLGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCV
NITIKQHTVTTTTKGENFTETDVKMMERVVEQMCITQYERESQAYYQRGSSMVLFSSPPV
ILLISFLIFLIVG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| MANLGCWMLVLFVATWSDLGLCKKRPKPGGWNTGGSRYPGQGSPGGNRYPPQGGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQGGGTHSQWNKPSKPKTNMKHMAGAAAAGAVVGGLGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCVNITIKQHTVTTTTKGENFTETDVKMMERVVEQMCITQYERESQAYYQRGSSMVLFSSPPVILLISFLIFLIVG
Prediction	CCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHCHHCCCCCCSCCCCCCCCCCCCHHHHHSSCSSSSSSSCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCSSSSSCCCCHHHHHHHHHHHHCC
Confidence	9740259999999998641211589999999999999999999999999999999999999999999999999999999999999999999999999999999998860011100235765677765224666787766789824554443122106886424788767763341232121023445642677897642245678999999999999999999987416516885497399999999996219
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| MANLGCWMLVLFVATWSDLGLCKKRPKPGGWNTGGSRYPGQGSPGGNRYPPQGGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQGGGTHSQWNKPSKPKTNMKHMAGAAAAGAVVGGLGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCVNITIKQHTVTTTTKGENFTETDVKMMERVVEQMCITQYERESQAYYQRGSSMVLFSSPPVILLISFLIFLIVG
Prediction	7431100000110101121110444375343451454424434443442323333332323323332144232342331222222321222232434443425433542432212332212112120100133243233315463353114513431454221432653454631022014131543424435645424432140143005410352045324422443210201133300021133333335
	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

CCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHCHHCCCCCCSCCCCCCCCCCCCHHHHHSSCSSSSSSSCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCSSSSSCCCCHHHHHHHHHHHHCC
MANLGCWMLVLFVATWSDLGLCKKRPKPGGWNTGGSRYPGQGSPGGNRYPPQGGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQGGGTHSQWNKPSKPKTNMKHMAGAAAAGAVVGGLGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCVNITIKQHTVTTTTKGENFTETDVKMMERVVEQMCITQYERESQAYYQRGSSMVLFSSPPVILLISFLIFLIVG

2kunA

0.99

0.56

15.61

1.53

FFAS-3D

-----------------------------------------------------------------------------------------GQGGGTHSQWNKPSKPKTNMKHMAGAAAAGAVVGGLGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCVNITIKQHTVTTTTKGENFTETDVKMMERVVEPMCITQYERESQAYYQRGSS----------------------

2kfoA

0.87

0.39

11.02

1.45

SPARKS-K

----------------------------------------------------------------------------------------------------------------------GSVVGGLGGYMLGSAMSRPMIHFGNDWEDRYYRENMYRYPNQVYYRPADQYSNQNNFVHDCVNITIKQHTVTTTTKGENFTETDVKMMERVVEQMCVTQYQKESQAYYDGRRSS---------------------

3exfC

0.08

3.24

0.38

CEthreader

TREDGLKYYRMMQTVRRMELKADQLYKQKIIRGFCHLCDGQTAYRAHGFTFTRGLSVREILAELTGRKGGCAKGKGGSMHMYAKNFYGGNGIVGAQVPLYNGKDEVCLTLYGDGAANQGQIFEAYNMAALWKLNNRYGMGTAVERAAASTDYYKRGDFIPGLRVDGMDILCVREATRFLMELQTYRYHGHSMSDPGVAYRTREEIQEVRSKSDPIMLLKDRMVNSNLASVEELKEIDVEVRKEIEDAAQFATA

4kmlA

1.00

0.43

12.06

1.15

CNFpred

--------------------------------------------------------------------------------------------------------------------AAGAVVGGLGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCVNITIKQHTVTTTTKGENFTETDVKMMERVVEQMCITQYERESQAY----------------------------

7btsA

0.06

2.60

0.53

EigenThreader

SLNAAKSELDKAIGKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYAASQQWTAGMGLLMALIVLLIVAGNVLVIVAIAKTASADLVMGLLVVPFGATIVVWGRWEYWTSVDVLCVTASIETLCVIALDRYLAITSLVCTVWAISALVSFLPILMGIIMGVFTLCWLPFFLANVVKAFHLFVFFNWLG

2kunA

0.95

0.56

15.63

1.20

MUSTER

-----------------------------------------------------------------------------------------GQGGGTHSQWNKPSKPKTNMKHMAGAAAAGAVVGGLGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCVNITIKQHTVTTTTKGENFTETDVKMMERVVEPMCITQYERESQAYYQRGSSHHHHHH----------------

2is6A

0.06

0.05

2.05

0.67

DEthreader

AGAGSGKTR-VTFTAMVGTFHGLAHRLLRA--H-HMDANLPQDFQ--L---DQLRLLKRL-----IKAMNLDEQWPPRQMW---------SLYC-----------NRIKTWQDLCLASMPYR-IYGGMRFFERIKLSYLRL-----DDAAFERVVNTPTR--LILAQETMVTDRVIKGLRTMYE-QEKG------------EK--GQ-TRIENLEELVTATRQFSYNDLMPASHAALEAGEMTLHSAKLEFQV

2kunA

0.91

0.53

14.99

4.92

HHsearch

---------------------------------------------------------------------------------------GQG--GGTHSQWNKPSKPKTNMKHMAGAAAAGAVVGGLGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCVNITIKQHTVTTTTKGENFTETDVKMMERVVEPMCITQYERESQAY----YQRG-SSHHHHHH-----------

3e6uA

0.06

2.60

0.66

MapAlign

PEFSQRLTNKIRELLQQMERGLKSADPRDGTGYTGWAGTFLCGDAGPLAVAAVLYHKMNNEKQAEDCITRLIHLNKIDPHAPNEMLYGRIGYIYALLFVNKNFVEKIPQSHIQQICETILTSGENLARKMYEWYQEYYVGAAHGLAGLLVHWCHGAPGVIYMLIQAYKVFREEKYLCDAYQCAIWQYGLLKKGYGLCHGSAGNAYAFLTLYNLTYLYRACKFAEWCHGCRTPDTPFSLFEGMAGTIYFLADL-

1b10A

0.87

0.35

9.90

1.29

FFAS-3D

----------------------------------------------------------------------------------------------------------------------------LGGYMLGSAMSRPMMHFGNDWEDRYYRENMNRYPNQVYYRPVDQYNNQNNFVHDCVNITIKQHTVTTTTKGENFTETDIKIMERVVEQMCTTQYQKESQAYY---------------------------

(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	0.517

(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	4lglA2	0.46	5.41	0.079	0.712	model1_4lglA2.pdb.gz
2	6i33A	0.45	5.58	0.073	0.715	model1_6i33A.pdb.gz
3	6z16A	0.44	6.35	0.041	0.790	model1_6z16A.pdb.gz
4	7d3uA	0.44	6.35	0.041	0.783	model1_7d3uA.pdb.gz
5	5dgqA2	0.44	5.96	0.034	0.743	model1_5dgqA2.pdb.gz
6	1w6jA	0.44	5.94	0.061	0.751	model1_1w6jA.pdb.gz
7	3h7lA	0.44	6.13	0.062	0.747	model1_3h7lA.pdb.gz
8	6lodC	0.44	6.04	0.053	0.739	model1_6lodC.pdb.gz
9	4m5dA	0.43	5.66	0.056	0.715	model1_4m5dA.pdb.gz
10	3sqcA	0.43	6.12	0.062	0.755	model1_3sqcA.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:0046872	0.77	metal ion binding
GO:0046914	0.76	transition metal ion binding
GO:0005507	0.75	copper ion 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	1.00	biological regulation
GO:0050794	0.97	regulation of cellular process
GO:0080090	0.83	regulation of primary metabolic process
GO:0031323	0.83	regulation of cellular metabolic process
GO:0032268	0.82	regulation of cellular protein metabolic process
GO:0001932	0.81	regulation of protein phosphorylation
GO:0009889	0.77	regulation of biosynthetic process
GO:0010556	0.76	regulation of macromolecule biosynthetic process
GO:0010468	0.76	regulation of gene expression
GO:0044699	0.71	single-organism process
GO:0009987	0.65	cellular process
GO:0050896	0.56	response to stimulus
GO:0048518	0.55	positive regulation of biological process
GO:0044763	0.54	single-organism cellular process
GO:0048522	0.53	positive regulation of cellular process
GO:0031325	0.52	positive regulation of cellular metabolic process
GO:0048519	0.51	negative regulation of biological process
GO:0010604	0.51	positive regulation of macromolecule metabolic process
GO:0048523	0.50	negative regulation of cellular process
GO:0001934	0.50	positive regulation of protein phosphorylation

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:0044425	0.95	membrane part
GO:0016020	0.95	membrane
GO:0045121	0.94	membrane raft
GO:0044464	0.70	cell part
GO:0044424	0.56	intracellular 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	0.060	2fhcA	0.396	5.90	0.031	0.660	3.2.1.41	120
2	0.060	2eabA	0.409	6.37	0.033	0.723	3.2.1.63	NA
3	0.060	3btaA	0.405	5.67	0.044	0.664	3.4.24.69	NA
4	0.060	3b8cB	0.403	5.52	0.053	0.640	3.6.3.6	114
5	0.060	1iv8A	0.365	6.34	0.034	0.656	5.4.99.15	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	3hs7A	0.416	5.92	0.058	0.692	0.16	COH	complex1.pdb.gz	51,52,56,57,78,90
2	0.01	1ddxB	0.417	6.06	0.058	0.704	0.28	PGX	complex2.pdb.gz	113,116,117,120,123,124
3	0.01	3krkA	0.416	5.93	0.058	0.692	0.11	ACD	complex3.pdb.gz	64,77,85,87
4	0.01	3mqeA	0.403	6.12	0.077	0.692	0.20	416	complex4.pdb.gz	26,27,30
5	0.01	3mdlB	0.417	5.94	0.053	0.696	0.13	COH	complex5.pdb.gz	49,51,52,61,67,79,85
6	0.01	3pghA	0.417	5.90	0.058	0.692	0.14	FLP	complex6.pdb.gz	241,242,245,246
7	0.01	1fceA	0.429	5.85	0.055	0.708	0.11	UUU	complex7.pdb.gz	57,133,217,220
8	0.01	1h3cC	0.435	6.14	0.066	0.759	0.10	R79	complex8.pdb.gz	24,81,235
9	0.01	4coxB	0.358	6.10	0.037	0.625	0.15	HEM	complex9.pdb.gz	52,58,59,60,61,67,85
10	0.01	3pghB	0.413	6.13	0.062	0.712	0.14	FLP	complex10.pdb.gz	88,91,94,97

	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.