D-I-TASSER Q6R2W3-D2

D-I-TASSER results for Q6R2W3-D2

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

Input Sequence in FASTA format

>Q6R2W3 (60 residues)
NPDGEYRFILHYQDLCTKLTFLRSLKSKRPTEVAHALLDIFTIIGAPSVLQSDNGREFSS

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| NPDGEYRFILHYQDLCTKLTFLRSLKSKRPTEVAHALLDIFTIIGAPSVLQSDNGREFSS
Prediction	CCCCCCSSSSSSSSCCCCCSSSSSCCCCCHHHHHHHHHHHHHHHCCCCSSSCCCCCCCCC
Confidence	999982599999976788489998699989999999999998609998898189988679
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| NPDGEYRFILHYQDLCTKLTFLRSLKSKRPTEVAHALLDIFTIIGAPSVLQSDNGREFSS
Prediction	857562300000003313211031156450540041024103433324303026256268
	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 DeepPotential. 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

                   |                   |                   |

SS
Seq

CCCCCCSSSSSSSSCCCCCSSSSSCCCCCHHHHHHHHHHHHHHHCCCCSSSCCCCCCCCC
NPDGEYRFILHYQDLCTKLTFLRSLKSKRPTEVAHALLDIFTIIGAPSVLQSDNGREFSS

1c0mC

0.11

0.10

3.62

1.17

DEthreader

-RMAPRSWLAVTVDTASSAIVVTQHGRVTSVAVQHHWATAIAVLGRPKAIKT-D-N--GS

6qbtA

0.20

6.40

1.38

SPARKS-K

KYKKYKYCLHVWVDTFSGAVSVSCKKKETSCETISAFLQAISLLGKPLHINTDNGPAFLS

6qbtA

0.20

6.40

0.97

MapAlign

KYKKYKYCLHVWVDTFSGAVSVSCKKKETSCETISAFLQAISLLGKPLHINTDNGPAFLS

6qbtA

0.20

6.40

0.74

CEthreader

KYKKYKYCLHVWVDTFSGAVSVSCKKKETSCETISAFLQAISLLGKPLHINTDNGPAFLS

4mq3A

0.18

0.17

5.45

1.04

MUSTER

--HFDGKIILVGIHVESGYIWAQIISQETADCTVKAVLQLLSAHNVT-ELQTDNGPNFKN

3l2rA

0.31

0.30

9.08

1.53

HHsearch

PPSQGYLYVLVVVDGMTGFTWLYPTKAPSTSATVKSL-NVLTSIAIPKVIHSDQGAAFTS

3hpgB2

0.26

0.25

7.70

0.92

FFAS-3D

--HYEDKIILVWVETNSGLIYAERVKGETGQEFRVQTMKWY-AMFAPKSLQSDNGPAFVA

1c0mC

0.17

5.50

0.62

EigenThreader

PRMAPRSWLAVTVDTASSAIVVTQHGRVTSVAVQHHWATAIAVLGRPKAIKTDNGSCFTS

1c0mA

0.17

5.50

1.04

CNFpred

PRMAPRSWLAVTVDTASSAIVVTQHGRVTSVAVQHHWATAIAVLGRPKAIKTDNGSCFTS

1c0mC1

0.11

0.10

3.62

1.17

DEthreader

-RMAPRSWLAVTVDTASSAIVVTQHGRVTSVAVQHHWATAIAVLGRPKAIKT-D-N--GS

(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	0.644

(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 DeepPotential, 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	6qbtA	0.90	1.00	0.200	1.000	model1_6qbtA.pdb.gz
2	1c0mC	0.87	1.36	0.167	1.000	model1_1c0mC.pdb.gz
3	3jcaA2	0.87	1.28	0.200	1.000	model1_3jcaA2.pdb.gz
4	3l2rA	0.81	1.72	0.288	0.983	model1_3l2rA.pdb.gz
5	3kkrA	0.79	1.63	0.196	0.933	model1_3kkrA.pdb.gz
6	1k6yB	0.77	1.62	0.196	0.933	model1_1k6yB.pdb.gz
7	1bl3C	0.77	1.65	0.196	0.933	model1_1bl3C.pdb.gz
8	1ex4A	0.75	1.74	0.179	0.933	model1_1ex4A.pdb.gz
9	3hpgB2	0.75	1.70	0.232	0.933	model1_3hpgB2.pdb.gz
10	4mq3A	0.72	1.81	0.179	0.933	model1_4mq3A.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:0003677	1.00	DNA binding
GO:0000981	1.00	RNA polymerase II transcription factor activity, sequence-specific DNA 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	0.90	cellular process
GO:0008152	0.79	metabolic process
GO:0071704	0.78	organic substance metabolic process
GO:0044238	0.78	primary metabolic process
GO:0044237	0.77	cellular metabolic process
GO:0043170	0.74	macromolecule metabolic process
GO:0044260	0.73	cellular macromolecule metabolic process
GO:0006139	0.72	nucleobase-containing compound metabolic process
GO:0065007	0.70	biological regulation
GO:0050789	0.68	regulation of biological process
GO:0090304	0.67	nucleic acid metabolic process
GO:0050794	0.67	regulation of cellular process
GO:0006259	0.62	DNA metabolic process
GO:1901576	0.58	organic substance biosynthetic process
GO:0044699	0.58	single-organism process
GO:0044249	0.58	cellular biosynthetic process
GO:0034654	0.57	nucleobase-containing compound biosynthetic process
GO:0031323	0.55	regulation of cellular metabolic process
GO:0016070	0.55	RNA metabolic process
GO:0009059	0.55	macromolecule biosynthetic process
GO:0080090	0.54	regulation of primary metabolic process
GO:0060255	0.54	regulation of macromolecule metabolic process
GO:0034645	0.54	cellular macromolecule biosynthetic process
GO:0006310	0.54	DNA recombination
GO:0065008	0.53	regulation of biological quality
GO:0048518	0.53	positive regulation of biological process
GO:0010468	0.53	regulation of gene expression
GO:0048522	0.52	positive regulation of cellular process
GO:0044419	0.52	interspecies interaction between organisms
GO:0075713	0.51	establishment of integrated proviral latency
GO:0031325	0.51	positive regulation of cellular metabolic process
GO:0030260	0.51	entry into host cell
GO:0010604	0.51	positive regulation of macromolecule metabolic process
GO:0006278	0.51	RNA-dependent DNA biosynthetic process
GO:0048519	0.50	negative regulation of biological process
GO:0044763	0.50	single-organism 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:0005737	1.00	cytoplasm
GO:0005654	1.00	nucleoplasm

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	3ig5A	0.567	3.41	0.083	0.967	6.3.2.2	NA
2	0.060	1ex4A	0.753	1.74	0.179	0.933	2.7.7.-	NA
3	0.060	3b9jJ	0.556	2.72	0.034	0.883	1.17.1.4 1.17.3.2	NA
4	0.060	1aa8B	0.554	3.00	0.034	0.900	1.4.3.3	NA
5	0.060	1g4wR	0.602	2.69	0.109	0.917	3.1.3.48	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:

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
	1	0.04	3ao5A	0.745	1.48	0.182	0.917	0.41	BBY	complex1.pdb.gz	45,46,48

	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, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.