D-I-TASSER P55072-D2

D-I-TASSER results for P55072-D2

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

Input Sequence in FASTA format

>P55072 (89 residues)
VKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVE
TDPSPYCIVAPDTVIHCEGEPIKREDEEE

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| VKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKREDEEE
Prediction	CCCCCSSSSSSCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCSSSSCCCCCCSSSSSSSSCCCCCSSSCCCCSSSSCCCCCCCCCCCC
Confidence	99774899970445668866239999999998742666516939998479852799999844887279749948994996567220239
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| VKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKREDEEE
Prediction	46425401002143316524341043004410463333044423020424344031212624456202025603021445326366688
	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

CCCCCSSSSSSCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCSSSSCCCCCCSSSSSSSSCCCCCSSSCCCCSSSSCCCCCCCCCCCC
VKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKREDEEE

3cf1B

0.96

0.89

24.89

1.17

DEthreader

VKYGKRIHVLPIDDTVEGITGN-LFEYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIK------

3cf1B5

1.00

28.00

2.44

SPARKS-K

VKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKREDEEE

3cf1B5

1.00

0.94

26.43

1.37

MapAlign

VKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKR-----

3cf1B5

1.00

28.00

1.18

CEthreader

VKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKREDEEE

3cf1B5

1.00

28.00

2.16

MUSTER

VKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKREDEEE

3cf1B5

1.00

28.00

2.70

HHsearch

VKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKREDEEE

3cf1B5

1.00

28.00

1.67

FFAS-3D

VKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKREDEEE

3cf1B5

1.00

28.00

1.10

EigenThreader

VKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKREDEEE

3qwzA

0.99

27.70

1.96

CNFpred

VKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFMVVETDPSPYCIVAPDTVIHCEGEPIKREDEEE

3cf1B5

0.96

0.89

24.89

1.17

DEthreader

VKYGKRIHVLPIDDTVEGITGN-LFEYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIK------

(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	0.843

(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	3cf1B	0.98	0.43	1.000	1.000	model1_3cf1B.pdb.gz
2	5g4fA1	0.76	2.09	0.267	0.966	model1_5g4fA1.pdb.gz
3	6mdmB	0.70	2.65	0.034	0.921	model1_6mdmB.pdb.gz
4	1cz4A	0.70	3.02	0.259	0.955	model1_1cz4A.pdb.gz
5	1cr5A	0.69	2.28	0.105	0.854	model1_1cr5A.pdb.gz
6	2yujA	0.69	2.30	0.143	0.865	model1_2yujA.pdb.gz
7	1qcsA2	0.69	2.63	0.047	0.899	model1_1qcsA2.pdb.gz
8	1zc1A	0.67	2.41	0.169	0.865	model1_1zc1A.pdb.gz
9	1gvnB	0.36	3.73	0.087	0.573	model1_1gvnB.pdb.gz
10	1iqpA	0.35	4.72	0.051	0.640	model1_1iqpA.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	0.79	catalytic activity
GO:0016787	0.75	hydrolase activity
GO:0016887	0.72	ATPase 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	0.95	cellular process
GO:0044699	0.92	single-organism process
GO:0071704	0.89	organic substance metabolic process
GO:0044238	0.89	primary metabolic process
GO:0044260	0.88	cellular macromolecule metabolic process
GO:0019538	0.87	protein metabolic process
GO:0006511	0.85	ubiquitin-dependent protein catabolic process
GO:0044763	0.79	single-organism cellular process
GO:0050896	0.78	response to stimulus
GO:0016043	0.76	cellular component organization
GO:0030433	0.75	ER-associated ubiquitin-dependent protein catabolic process
GO:0006996	0.70	organelle organization
GO:1902589	0.69	single-organism organelle organization
GO:0042221	0.66	response to chemical
GO:0048284	0.64	organelle fusion
GO:0034641	0.64	cellular nitrogen compound metabolic process
GO:0006139	0.63	nucleobase-containing compound metabolic process
GO:0090304	0.62	nucleic acid metabolic process
GO:0044710	0.62	single-organism metabolic process
GO:0006914	0.59	autophagy
GO:1901576	0.58	organic substance biosynthetic process
GO:0065007	0.58	biological regulation
GO:0006464	0.58	cellular protein modification process
GO:0070647	0.57	protein modification by small protein conjugation or removal
GO:0050789	0.57	regulation of biological process
GO:0044271	0.57	cellular nitrogen compound biosynthetic process
GO:0034645	0.57	cellular macromolecule biosynthetic process
GO:0006950	0.57	response to stress
GO:0051716	0.56	cellular response to stimulus
GO:0034654	0.56	nucleobase-containing compound biosynthetic process
GO:0016567	0.56	protein ubiquitination
GO:0044723	0.55	single-organism carbohydrate metabolic process
GO:0034976	0.55	response to endoplasmic reticulum stress
GO:0018193	0.55	peptidyl-amino acid modification
GO:0010033	0.55	response to organic substance
GO:0006259	0.55	DNA metabolic process
GO:0097352	0.54	autophagosome maturation
GO:0036503	0.54	ERAD pathway
GO:0019985	0.54	translesion synthesis
GO:0018279	0.54	protein N-linked glycosylation via asparagine
GO:0006302	0.54	double-strand break repair
GO:0050794	0.51	regulation of cellular 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	1.00	cell part
GO:0044424	0.99	intracellular part
GO:0044446	0.84	intracellular organelle part
GO:0044444	0.72	cytoplasmic part
GO:0043226	0.72	organelle
GO:0043229	0.71	intracellular organelle
GO:0043227	0.70	membrane-bounded organelle
GO:0043231	0.69	intracellular membrane-bounded organelle
GO:0032991	0.59	macromolecular complex
GO:0005737	0.59	cytoplasm
GO:0044428	0.53	nuclear part
GO:0043234	0.50	protein complex
GO:0016020	0.50	membrane
GO:0005634	0.50	nucleus

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	1bxrA	0.469	4.23	0.047	0.910	6.3.5.5	NA
2	0.060	2rmcA	0.511	4.53	0.102	0.933	5.2.1.8	NA
3	0.060	2hqjA	0.471	4.13	0.085	0.820	5.2.1.8	NA
4	0.060	1m9cA	0.465	4.25	0.115	0.809	5.2.1.8	NA
5	0.060	1qngA	0.463	4.24	0.115	0.809	5.2.1.8	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	3cf1A	0.984	0.43	1.000	1.000	0.14	UUU	complex1.pdb.gz	40,41,42
2	0.15	1e32A	0.978	0.52	1.000	1.000	0.15	ADP	complex2.pdb.gz	78,80,81
3	0.14	3cf3A	0.983	0.45	1.000	1.000	0.14	ADP	complex3.pdb.gz	43,44,45
4	0.14	3tiwA	0.790	0.94	0.986	0.832	0.24	III	complex4.pdb.gz	41,42,43,57
5	0.01	3cf0A	0.336	4.60	0.084	0.652	0.24	ADP	complex5.pdb.gz	20,23,27
6	0.01	2jc6C	0.485	3.91	0.047	0.832	0.18	QPP	complex6.pdb.gz	79,80,81
7	0.01	1wuqA	0.470	3.52	0.073	0.730	0.26	8GT	complex7.pdb.gz	8,41,42
8	0.01	1yndB	0.469	4.22	0.115	0.809	0.13	SFA	complex8.pdb.gz	41,42,43,45,54,56
9	0.01	1awtC	0.464	4.02	0.114	0.798	0.15	III	complex9.pdb.gz	38,58,79,80
10	0.01	1nmkA	0.465	4.19	0.101	0.809	0.13	SFM	complex10.pdb.gz	77,78,79

	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.