D-I-TASSER P34949-D2

D-I-TASSER results for P34949-D2

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

Input Sequence in FASTA format

>P34949 (105 residues)
RPVEEIVTFLKKVPEFQFLIGDEAATHLKQTMSHDSQAVASSLQSCFSHLMKSEKKVVVE
QLNLLVKRISQQAAAGNNMEDIFGELLLQLHQQYPGDIGCFAIYF

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| RPVEEIVTFLKKVPEFQFLIGDEAATHLKQTMSHDSQAVASSLQSCFSHLMKSEKKVVVEQLNLLVKRISQQAAAGNNMEDIFGELLLQLHQQYPGDIGCFAIYF
Prediction	CCHHHHHHHHHHCCHHHHHHCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHCCCCSSSSSSCC
Confidence	969999999982936899839999999998324563789999999999998199999999999999999845422345306899999999947889826853049
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| RPVEEIVTFLKKVPEFQFLIGDEAATHLKQTMSHDSQAVASSLQSCFSHLMKSEKKVVVEQLNLLVKRISQQAAAGNNMEDIFGELLLQLHQQYPGDIGCFAIYF
Prediction	643630252066243036114672054037337544751361034004401615764036105501530574566474465412400230274234000011236
	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

                   |                   |                   |                   |                   |

SS
Seq

CCHHHHHHHHHHCCHHHHHHCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHCCCCSSSSSSCC
RPVEEIVTFLKKVPEFQFLIGDEAATHLKQTMSHDSQAVASSLQSCFSHLMKSEKKVVVEQLNLLVKRISQQAAAGNNMEDIFGELLLQLHQQYPGDIGCFAIYF

1pmiA3

0.26

7.93

1.33

DEthreader

KPLDQLAKTLATVPELNEIIGQELVDEFISGIKLDDVNNRKLLQKVFGKLMNTDDDVIKQQTAKLLERTDREP-QVFKDISRLPELIQRLNKQFPNDIGLFCGLL

1pmiA3

0.25

7.69

1.24

SPARKS-K

KPLDQLAKTLATVPELNEIIGQELVDEFISGIKLPAENNRKLLQKVFGKLMNTDDDVIKQQTAKLLERTDREPQVFKDIDSRLPELIQRLNKQFPNDIGLFCGCL

1pmiA

0.26

7.94

1.42

MapAlign

KPLDQLAKTLATVPELNEIIGQELVDEFISGIKLDDVNNRKLLQKVFGKLMNTDDDVIKQQTAKLLERTDREPQVFKDIDSRLPELIQRLNKQFPNDIGLFCCLL

1pmiA

0.25

7.69

1.21

CEthreader

KPLDQLAKTLATVPELNEIIGQELVDEFISGIKLPDVNNRKLLQKVFGKLMNTDDDVIKQQTAKLLERTDREPQVFKDIDSRLPELIQRLNKQFPNDIGLFCGCL

1pmiA3

0.25

7.69

1.07

MUSTER

KPLDQLAKTLATVPELNEIIGQELVDEFISGIKLPAVNNRKLLQKVFGKLMNTDDDVIKQQTAKLLERTDREPQVFKDIDSRLPELIQRLNKQFPNDIGLFCGCL

1pmiA3

0.26

7.94

2.15

HHsearch

KPLDQLAKTLATVPELNEIIGQELVDEFISGIKLDDVNNRKLLQKVFGKLMNTDDDVIKQQTAKLLERTDREPQVFKDIDSRLPELIQRLNKQFPNDIGLFCGLL

1pmiA3

0.25

7.69

1.32

FFAS-3D

KPLDQLAKTLATVPELNEIIGQELVDEFISGIKLPAVNNRKLLQKVFGKLMNTDDDVIKQQTAKLLERTDREPQVFKDIDSRLPELIQRLNKQFPNDIGLFCGCL

1pmiA

0.22

0.21

6.62

1.13

EigenThreader

P-LDQLAKTLATVPELNEIIGQELVDEFISGIKLPAVNNRKLLQKVFGKLMNTDDDVIKQQTAKLLERTDREFKDIDSRLPELIQRLNKQF---PNDIGLFCGCL

5nw7A

0.27

8.20

0.86

CNFpred

KPLDQLAKTLATVPELNEIIGQELVDEFISGISQDDVNNRKLLQKVFGKLMNTDDDVIKQQTAKLLERTDREPQVFKDIDSRLPELIQRLNKQFPNDIGLFCGCL

1pmiA

0.26

7.93

1.33

DEthreader

KPLDQLAKTLATVPELNEIIGQELVDEFISGIKLDDVNNRKLLQKVFGKLMNTDDDVIKQQTAKLLERTDREP-QVFKDISRLPELIQRLNKQFPNDIGLFCGLL

(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	0.8143

(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	1pmiA	0.91	1.67	0.260	0.991	model1_1pmiA.pdb.gz
2	3h1mA1	0.64	2.22	0.186	0.819	model1_3h1mA1.pdb.gz
3	5uj8A	0.61	3.46	0.110	0.895	model1_5uj8A.pdb.gz
4	6y79C	0.58	3.77	0.071	0.914	model1_6y79C.pdb.gz
5	5ezmA	0.58	3.79	0.069	0.924	model1_5ezmA.pdb.gz
6	1ygpA	0.58	3.34	0.088	0.867	model1_1ygpA.pdb.gz
7	3uqyL	0.57	4.22	0.019	0.924	model1_3uqyL.pdb.gz
8	4l22A2	0.57	3.28	0.112	0.848	model1_4l22A2.pdb.gz
9	5lr8A	0.57	3.18	0.067	0.848	model1_5lr8A.pdb.gz
10	2c4mC	0.57	3.35	0.133	0.857	model1_2c4mC.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:0004476	1.00	mannose-6-phosphate isomerase activity

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	0.90	cellular process
GO:0008152	0.90	metabolic process
GO:0044699	0.86	single-organism process
GO:0071704	0.85	organic substance metabolic process
GO:0044238	0.78	primary metabolic process
GO:0044237	0.71	cellular metabolic process
GO:0044710	0.69	single-organism metabolic process
GO:1901576	0.65	organic substance biosynthetic process
GO:0044763	0.63	single-organism cellular process
GO:0044281	0.61	small molecule metabolic process
GO:1901135	0.56	carbohydrate derivative metabolic process
GO:0044249	0.56	cellular biosynthetic process
GO:0006807	0.56	nitrogen compound metabolic process
GO:1901360	0.55	organic cyclic compound metabolic process
GO:0034641	0.55	cellular nitrogen compound metabolic process
GO:0006139	0.54	nucleobase-containing compound metabolic process
GO:1901362	0.50	organic cyclic compound biosynthetic process
GO:0044271	0.50	cellular nitrogen compound biosynthetic 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:0044464	0.95	cell part
GO:0044424	0.93	intracellular part
GO:0043227	0.90	membrane-bounded organelle
GO:0044444	0.81	cytoplasmic part
GO:0070062	0.75	extracellular exosome
GO:0005829	0.64	cytosol

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	1t3cA	0.505	4.64	0.050	0.924	3.4.24.69	NA
2	0.060	3h1mA	0.588	2.70	0.149	0.829	5.3.1.8	NA
3	0.060	1jqkF	0.534	4.30	0.038	0.895	1.2.99.2	NA
4	0.060	1u2zC	0.531	3.85	0.089	0.848	2.1.1.43	11,21
5	0.060	1l5jA	0.530	3.65	0.111	0.790	4.2.1.3	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	0.03	3dd1B	0.555	3.49	0.111	0.857	0.14	25D	complex1.pdb.gz	22,47,98
2	0.02	1e1yA	0.567	3.39	0.100	0.857	0.14	PLP	complex2.pdb.gz	16,21,66,101
3	0.02	1c8lA	0.567	3.39	0.100	0.857	0.20	BIN	complex3.pdb.gz	16,99,100
4	0.01	1z6pA	0.565	3.42	0.100	0.857	0.13	194	complex4.pdb.gz	13,16,17,20
5	0.01	3ms4A	0.564	3.43	0.100	0.857	0.31	21N	complex5.pdb.gz	62,65,66,100
6	0.01	2priA	0.566	3.42	0.100	0.857	0.19	D6G	complex6.pdb.gz	6,50,61,62
7	0.01	3mtdA	0.564	3.44	0.100	0.857	0.20	25E	complex7.pdb.gz	16,60,62,63,66,67
8	0.01	3np7A	0.443	4.39	0.038	0.790	0.15	Z15	complex8.pdb.gz	100,101,104

	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.