D-I-TASSER Q7RTM1-D3

D-I-TASSER results for Q7RTM1-D3

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

Input Sequence in FASTA format

>Q7RTM1 (73 residues)
SEDIQTLRVVTVCNGNTMPLASSCPKSGGVARDVAPQGKDMPPAANGNVCMRESHDKEEE
KQEESSWGGSPSP

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| SEDIQTLRVVTVCNGNTMPLASSCPKSGGVARDVAPQGKDMPPAANGNVCMRESHDKEEEKQEESSWGGSPSP
Prediction	CCCCSSSSSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSCCCCCCCCCCCCCCCCCCCCCC
Confidence	9763278999994798530321125666534567877676886556860322467711101211367899999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| SEDIQTLRVVTVCNGNTMPLASSCPKSGGVARDVAPQGKDMPPAANGNVCMRESHDKEEEKQEESSWGGSPSP
Prediction	8752431301201336434133433664444554446657344335342134634456665556544564558
	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

CCCCSSSSSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSCCCCCCCCCCCCCCCCCCCCCC
SEDIQTLRVVTVCNGNTMPLASSCPKSGGVARDVAPQGKDMPPAANGNVCMRESHDKEEEKQEESSWGGSPSP

4nnzA2

0.11

3.96

0.51

CEthreader

RTQLPNLIMGFNVPSLLIGALLDGGYSARLASRLERGEELVAGAFVLSATPNVQKGKTLEQVEAGLWKQLDDL

1boyA1

0.09

0.08

3.12

0.57

EigenThreader

KPVNQVYTVQISTKSGDWKSKCDTECDLTDEIVKD----VKQTYLARVFSYPAGN---VESAGEPLYENSPEF

2kpyA

0.18

0.14

4.45

0.23

FFAS-3D

-----SCFCYFDCSKSPPGATPAPPGAAPPPAAGPADGGSPPPPADGG-------------SPPVDGGSPPPP

3bogA

0.08

3.21

1.12

SPARKS-K

-CKGADGAHGVGCPGTAGAAGSVGGPGCDGGGNGGNGNPGCAGGVGGAGGASGGTGVGGGSGTPKGADGAPGA

3r0xA

0.05

0.01

0.26

0.41

CNFpred

------VHCFFAEPTHSPCMLLGVY------------------------------------------------

7dhdA

0.12

0.10

3.36

0.83

DEthreader

-----------GFNK---ILVVCVNCRSPGERV-LQLPKTVLILMLGDIPDPYRQSKEAFVHAYQLIDAAW--

6tgbA1

0.10

3.52

0.66

MapAlign

--GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGTGGGGGGGGGGGGGGGG---

2mk0A

0.18

5.81

0.60

MUSTER

SQPSDCGEVIEECPIDACFLPKSDSARPPDCTAVGRPDCNVLPFPNNIGCPSMFTPSPDGSPPNCSPTMLPSP

3eh1A1

0.26

0.10

2.96

0.39

HHsearch

SKGERRIRVHTLCLPVVSSLADVYAG----V------------------------------------------

5e3pA1

0.00

0.97

0.46

CEthreader

--TTASATGIATLTSTVWYPEIGSTDQSALTPLEGVDEDRNVTRKIVTTTIDIDAAPTDTYDAWLRLHLLSHR

(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	0.642

(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	3nipA	0.52	3.76	0.030	0.904	model1_3nipA.pdb.gz
2	2x68A	0.52	3.83	0.014	0.904	model1_2x68A.pdb.gz
3	3qhbA	0.51	3.12	0.087	0.808	model1_3qhbA.pdb.gz
4	4rfqA	0.51	3.98	0.116	0.877	model1_4rfqA.pdb.gz
5	1rw0A	0.51	3.61	0.100	0.904	model1_1rw0A.pdb.gz
6	1t8hA	0.51	3.56	0.111	0.931	model1_1t8hA.pdb.gz
7	1rv9A	0.50	3.65	0.113	0.918	model1_1rv9A.pdb.gz
8	3nioA	0.49	3.83	0.061	0.877	model1_3nioA.pdb.gz
9	2a0mA	0.47	3.80	0.000	0.822	model1_2a0mA.pdb.gz
10	3m1rA	0.46	3.87	0.043	0.822	model1_3m1rA.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:0043169	0.53	cation 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:0042472	1.00	inner ear morphogenesis
GO:0009590	1.00	detection of gravity

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:0044424	1.00	intracellular part
GO:0016020	1.00	membrane
GO:0005737	0.53	cytoplasm

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	1af2A	0.486	3.42	0.075	0.904	3.5.4.5	NA
2	0.060	1t3cA	0.500	3.44	0.113	0.877	3.4.24.69	NA
3	0.060	1cttA	0.483	3.41	0.075	0.904	3.5.4.5	NA
4	0.060	1maaD	0.423	4.82	0.056	0.931	3.1.1.7	NA
5	0.060	1vq2A	0.476	3.53	0.048	0.836	3.5.4.12	50

	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	0.08	2v7jA	0.513	3.37	0.060	0.822	0.14	UUU	complex1.pdb.gz	22,28,29,46,47,49
2	0.01	2gm1D	0.440	4.47	0.139	0.904	0.13	ADP	complex2.pdb.gz	19,28,29
3	0.01	1q0bA	0.438	4.30	0.127	0.863	0.25	NAT	complex3.pdb.gz	60,63,67
4	0.01	2xaeB	0.462	4.11	0.041	0.877	0.16	2XA	complex4.pdb.gz	30,31,32
5	0.01	2uyiB	0.458	4.15	0.042	0.877	0.11	K02	complex5.pdb.gz	10,21,51
6	0.01	2d0uA	0.511	3.90	0.014	0.890	0.13	HEM	complex6.pdb.gz	31,34,66,67,68
7	0.01	2wogB	0.463	3.87	0.043	0.849	0.20	ZZD	complex7.pdb.gz	28,29,30,47,65,66
8	0.01	2fl6B	0.409	4.46	0.075	0.836	0.17	N5T	complex8.pdb.gz	30,47,51,65
9	0.01	3k5eB	0.451	4.34	0.041	0.877	0.24	K5E	complex9.pdb.gz	62,65,69
10	0.01	3bgvD	0.495	3.52	0.043	0.822	0.16	SAH	complex10.pdb.gz	21,33,47,48,49,52

	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.