D-I-TASSER Q6PIU1-D3

D-I-TASSER results for Q6PIU1-D3

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

Input Sequence in FASTA format

>Q6PIU1 (175 residues)
GRHSTGLRSLGMTITQCYEEVGLLLLFLSVGISIFSTVEYFAEQSIPDTTFTSVPCAWWW
ATTSMTTVGYGDIRPDTTTGKIVAFMCILSGILVLALPIAIINDRFSACYFTLKLKEAAV
RQREALKKLTKNIATDSYISVNLRDVYARSIMEMLRLKGRERASTRSSGGDDFWF

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| GRHSTGLRSLGMTITQCYEEVGLLLLFLSVGISIFSTVEYFAEQSIPDTTFTSVPCAWWWATTSMTTVGYGDIRPDTTTGKIVAFMCILSGILVLALPIAIINDRFSACYFTLKLKEAAVRQREALKKLTKNIATDSYISVNLRDVYARSIMEMLRLKGRERASTRSSGGDDFWF
Prediction	CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC
Confidence	9755689999999999999999999999999999999999997258987646257998887640146788887888743999999999999999999999999999999999999999999899999999875321023332678999988888666654177665225776679
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| GRHSTGLRSLGMTITQCYEEVGLLLLFLSVGISIFSTVEYFAEQSIPDTTFTSVPCAWWWATTSMTTVGYGDIRPDTTTGKIVAFMCILSGILVLALPIAIINDRFSACYFTLKLKEAAVRQREALKKLTKNIATDSYISVNLRDVYARSIMEMLRLKGRERASTRSSGGDDFWF
Prediction	8443411330130034024311112233333333332211101332555413311300110222233343344324233023202321333333323311311230243145344455445455415513751553542444245413641353264564545545664454213
	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                  80                 100                 120                 140                 160

                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC
GRHSTGLRSLGMTITQCYEEVGLLLLFLSVGISIFSTVEYFAEQSIPDTTFTSVPCAWWWATTSMTTVGYGDIRPDTTTGKIVAFMCILSGILVLALPIAIINDRFSACYFTLKLKEAAVRQREALKKLTKNIATDSYISVNLRDVYARSIMEMLRLKGRERASTRSSGGDDFWF

4ke2A

0.06

0.05

2.21

1.17

DEthreader

ITINAASAAAKSIAAAAAMAAKDTAAAAASAAAAAVASAAKALETINVK-------------------------AYAAATTANTAAAAAAATATTAAAAAAAKATIDNAAAAKAAAVATAVSDAAATAATAAAVAAATLEAAAAKAAATAVSAAAAAAAAAIAFAAAP-------

5u6oA2

0.09

0.07

2.64

1.06

SPARKS-K

--------------ASAVVRIFNLIGMMLLLCHWDGCLQFLVPLLQDFNEMVQYSYALFKAMSHMLCIGYGAQAPVSMSDLWITMLSMIVGATCYAMFVGHATALIQSLDS---SRRQYQEKYKQVEQYMSFHKLPADMRQKIHDYYEHRYQGKI--------------------

6xiwA

0.10

3.77

0.61

MapAlign

--FELPRTRITNILKRSGEQIWSVSIFLLFFLLLYGILGVQFGTFYGYSGFNEIGTSIFTVYEAASQEGWVFLMIDSWRSYFYFITLIFFLALVKNVFIAVIIETFAEIRVQFFHMFILSMVTVDVIVAASNQYDEFYLAEVAFTVLFDLEALLKIWCLGFTGYISSSLHKFELL

5vmsA

0.23

0.22

6.99

0.48

CEthreader

DRQGGTWRLLGSVVFIHRQELITTLYIGFLGLIFSSYFVYLAEKDAIDYQFGSYADALWWGVVTVTTIGYGDKVPQTWIGKTIASCFSVFAISFFALPAGILGSGFALKVQQKQRQKHFNRQIPAAASLIQTAWRCYAAENPDSATWKIEHHRAAIK----VIRRMQYFVAKKKF

5vmsA

0.22

7.02

1.05

MUSTER

DRQGGTWRLLGSVVFIHRQELITTLYIGFLGLIFSSYFVYLAEKDAGEYQFGSYADALWWGVVTVTTIGYGDKVPQTWIGKTIASCFSVFAISFFALPAGILGSGFALKVQQKQRQKHFNRQIPAAASLIQTAWRCYAAENPDSEHHRAAIKVIRRMQYFVAKKKFQQARKPYDV

5va1A

0.14

4.67

1.66

HHsearch

LRLVRVARKLDRYSEYGAAVLFLLMCTFALIAHWLACIWYAIGNMEQPSIKDKYVTALYFTFSSLTSVGFGNVSPNTNSEKIFSICVMLIGSLMYASIFGNVSAIIQRLYSGTARYH---TQMLRVREFIRFHQIPNPLRQRLEEYFQHAWSY---TNGIDMNAVLKGFPECLQA

4chvA1

0.22

0.17

5.42

1.99

FFAS-3D

----TFFPVLGRVLANEARNLIGVTTLFGVVLFAVALAAYVIERDIQPEKFGSIPQAMWWAVVTLSTTGYGDTIPQSFAGRVLAGAVMMSGIGIFGLWAGILATGFYQEVRRGDFV----RNWQLVAAVPLFQKLGPAVLVEIVRAL----------------------------

7bylA

0.20

6.39

1.13

EigenThreader

DRRGGTWKLLGSVVYAHSKELITAWYIGFLVLIFASFLVYLAEK-DANSDFSSYADSLWWGTITLTTIGYGDKTPHTWLGRVLAAGFALLGISFFALPAGILGSGFALKVQEQHRQKHFENLIQAAWRLYSTDMSMPAVKTVIRSIRILKFSAGHLDMLGRIKSLQTRVDQIVG-

5u6oA

0.08

3.12

0.81

CNFpred

IHQWEEIFHMTYDLASAVVRIFNLIGMMLLLCHWDGCLQFLVPLLQDDSWGKQYSYALFKAMSHMLCIGYGAQAPVSMSDLWITMLSMIVGATCYAMFVGHATALIQSL---DSSRRQYQEKYKQVEQYMSFHKLPADMRQKIHDYYEHRYQGKIFDEE----NILNELNDPLRE

6rw8A

0.09

0.07

2.82

1.00

DEthreader

-F--FNTLYDEDVNAGEKQAMDLYLSSSVLSTSGTALHMAAAAADLV----------------------------ALFNASAIGIEISASATRIAADKISQSEIYRRRRQEWEIQRNNAEAEIKQIDAQLATLAVR-REAAVLQKNYLETQQAQTQAQLAFLQSKFSNALYNWGR

(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	0.6684

(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	6xiwA	0.63	4.53	0.114	0.914	model1_6xiwA.pdb.gz
2	3syaA	0.62	3.73	0.110	0.829	model1_3syaA.pdb.gz
3	3jycA	0.61	3.63	0.105	0.783	model1_3jycA.pdb.gz
4	5twvA	0.60	3.48	0.083	0.771	model1_5twvA.pdb.gz
5	6c96A	0.60	4.72	0.118	0.903	model1_6c96A.pdb.gz
6	7bylA	0.60	3.95	0.203	0.794	model1_7bylA.pdb.gz
7	6nq0A	0.60	3.63	0.123	0.783	model1_6nq0A.pdb.gz
8	4chvA	0.59	3.95	0.173	0.811	model1_4chvA.pdb.gz
9	5vmsA	0.59	3.65	0.200	0.760	model1_5vmsA.pdb.gz
10	5x0mA	0.59	4.31	0.097	0.834	model1_5x0mA.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:0005261	1.00	cation channel activity
GO:0022843	0.99	voltage-gated cation channel activity
GO:0005267	0.99	potassium channel activity
GO:0005249	0.98	voltage-gated potassium channel activity
GO:0005251	0.95	delayed rectifier potassium channel 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:0006810	0.90	transport
GO:0006811	0.88	ion transport
GO:0006813	0.85	potassium ion transport
GO:0009987	0.83	cellular process
GO:0044763	0.75	single-organism cellular process
GO:0065007	0.72	biological regulation
GO:0050789	0.58	regulation of biological process
GO:0055085	0.55	transmembrane transport
GO:0034220	0.53	ion transmembrane transport
GO:0098662	0.50	inorganic cation transmembrane transport
GO:0071804	0.50	cellular potassium ion transport

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	0.98	membrane part
GO:0016021	0.92	integral component of membrane
GO:0044464	0.90	cell part
GO:0016020	0.58	membrane

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	3czoB	0.459	4.53	0.047	0.691	4.3.1.3	NA
2	0.060	3b8cB	0.521	4.93	0.040	0.840	3.6.3.6	NA
3	0.060	2nyfA	0.428	4.47	0.029	0.651	4.3.1.5	NA
4	0.060	2cseW	0.440	5.56	0.119	0.794	3.6.4.13	NA
5	0.060	3i9wA	0.486	4.24	0.100	0.709	2.7.13.3	90

	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	0.01	3ar3A	0.503	4.24	0.069	0.731	0.58	PTY	complex1.pdb.gz	83,86,90,94

	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.