D-I-TASSER Q5SY68-D1

D-I-TASSER results for Q5SY68-D1

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

Input Sequence in FASTA format

>Q5SY68 (101 residues)
MNIPLGEKVMLDIVAMFRQYSGDDGRMDMPGLVNLMKENFPNFLSGCEKSDMDYLSNALE
KKDDNKDKKVNYSEFLSLLGDITIDHHKIMHGVAPCSGGSQ

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MNIPLGEKVMLDIVAMFRQYSGDDGRMDMPGLVNLMKENFPNFLSGCEKSDMDYLSNALEKKDDNKDKKVNYSEFLSLLGDITIDHHKIMHGVAPCSGGSQ
Prediction	CCCCHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCCCCCSCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC
Confidence	98678999999999999998289999799999999999989997512557989999999996168999646999999999999999999825678988999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MNIPLGEKVMLDIVAMFRQYSGDDGRMDMPGLVNLMKENFPNFLSGCEKSDMDYLSNALEKKDDNKDKKVNYSEFLSLLGDITIDHHKIMHGVAPCSGGSQ
Prediction	86656235104300410241045745042730351046304520554674446103500650173575403041003000300220044127554567448
	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

                   |                   |                   |                   |                   |

SS
Seq

CCCCHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCCCCCSCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC
MNIPLGEKVMLDIVAMFRQYSGDDGRMDMPGLVNLMKENFPNFLSGCEKSDMDYLSNALEKKDDNKDKKVNYSEFLSLLGDITIDHHKIMHGVAPCSGGSQ

1juoA

0.10

0.09

3.27

1.33

DEthreader

GNFKELWAVLNGWRQHFISFDTDSGTVDPQELQKALTTMGF-RL------SPQAVNSIAKRYS-T-NGKITFDDYIACCVKLRALTDSFRRRDT-AQ----

1psrA

0.53

0.52

15.16

1.41

SPARKS-K

-SNTQAERSIIGMIDMFHKYTRRDDKIDKPSLLTMMKENFPNFLSACDKKGTNYLADVFEKKDKNEDKKIDFSEFLSLLGDIATDYHKQSHGAAPCSGGSQ

1psrA

0.53

0.52

15.16

1.54

MUSTER

-SNTQAERSIIGMIDMFHKYTRRDDKIDKPSLLTMMKENFPNFLSACDKKGTNYLADVFEKKDKNEDKKIDFSEFLSLLGDIATDYHKQSHGAAPCSGGSQ

1psrA

0.53

0.52

15.16

1.69

FFAS-3D

-SNTQAERSIIGMIDMFHKYTRRDDKIDKPSLLTMMKENFPNFLSACDKKGTNYLADVFEKKDKNEDKKIDFSEFLSLLGDIATDYHKQSHGAAPCSGGSQ

3siaA

0.06

0.05

2.21

1.17

DEthreader

SYFMAMYKFMELAYNLFVMNARRSGTLEPHEILPALQQLFY--I------NQRTSLLLHRLFA--MA-FCDLNCWIAICAFAAQTRSAYQMIFMNYGPM--

6zdyA

0.17

5.52

1.26

SPARKS-K

-APSQMERSITTIIDTFHQYSRHPDTLSKKEFRQMVEAQLATFMKKEKR-NEALINDIMEDLDTNQDNQLSFEECMMLMAKLIFACHEKLHENNPRGHGHS

2jnfA

0.08

0.07

2.76

0.63

MapAlign

----LSSNQVKLLETAFRDFETPSGRVSTDQIGIILE-VL-GIQ-----QTKSTIRQLIDEFDPFGNGDIDFDSFKIIGARFLREILAELDETLSSEDLDA

1ozoA

0.29

0.27

8.13

0.34

CEthreader

--MTELEAAMGMIIDVFSRYSGSTQTLTKGELKVLMEKELPGFL--QSGKDKDAVDKLLKDLDANGDAQVDFSEFIVFVAAITSASHKYFEKTGLK-----

1bt6A

0.25

0.23

7.05

1.33

MUSTER

--PSQMEHAMETMMFTFHKFAGDKGYLTKEDLRVLMEKEFPGFLENQK--DPLAVDKIMKDLDQCRDGKVGFQSFFSLIAGLTIACNDYFVVHMK------

6zdyA

0.17

5.51

0.75

HHsearch

-APSQMERSITTIIDTFHQYSKEHDTLSKKEFRQMVEAQLATFMKK--ERNEALINDIMEDLDTNQDNQLSFEECMMLMAKLIFACHEKLHENNPRGHGHS

(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	0.7304

(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	1psrA	0.88	1.61	0.531	0.970	model1_1psrA.pdb.gz
2	1xk4L	0.78	1.76	0.258	0.881	model1_1xk4L.pdb.gz
3	6zdyA	0.77	2.24	0.170	0.911	model1_6zdyA.pdb.gz
4	1bt6A	0.76	1.82	0.253	0.881	model1_1bt6A.pdb.gz
5	1mr8A	0.75	1.90	0.230	0.861	model1_1mr8A.pdb.gz
6	2y5iA	0.74	2.23	0.223	0.871	model1_2y5iA.pdb.gz
7	1juoA	0.73	2.41	0.087	0.881	model1_1juoA.pdb.gz
8	1qxpB3	0.73	2.41	0.097	0.911	model1_1qxpB3.pdb.gz
9	1k9kA	0.72	2.15	0.233	0.842	model1_1k9kA.pdb.gz
10	1ij5A	0.72	2.92	0.108	0.911	model1_1ij5A.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:0046872	0.90	metal ion binding
GO:0005509	0.89	calcium ion binding
GO:0008270	0.65	zinc ion binding
GO:0005102	0.61	receptor binding
GO:0050786	0.60	RAGE receptor binding
GO:0042802	0.55	identical protein binding
GO:0042803	0.53	protein homodimerization 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:0065007	0.92	biological regulation
GO:0050789	0.92	regulation of biological process
GO:0050794	0.90	regulation of cellular process
GO:0009987	0.90	cellular process
GO:0044699	0.82	single-organism process
GO:0044763	0.78	single-organism cellular process
GO:0050896	0.75	response to stimulus
GO:0006950	0.70	response to stress
GO:0006952	0.68	defense response
GO:0002376	0.68	immune system process
GO:0048518	0.67	positive regulation of biological process
GO:0048522	0.66	positive regulation of cellular process
GO:0080090	0.59	regulation of primary metabolic process
GO:0060255	0.59	regulation of macromolecule metabolic process
GO:0031323	0.59	regulation of cellular metabolic process
GO:0006955	0.59	immune response
GO:0023051	0.58	regulation of signaling
GO:0010646	0.58	regulation of cell communication
GO:0009605	0.58	response to external stimulus
GO:0045087	0.57	innate immune response
GO:0043207	0.57	response to external biotic stimulus
GO:0023056	0.57	positive regulation of signaling
GO:0010647	0.57	positive regulation of cell communication
GO:0051707	0.56	response to other organism
GO:0048869	0.56	cellular developmental process
GO:0009966	0.55	regulation of signal transduction
GO:1902533	0.54	positive regulation of intracellular signal transduction
GO:0051246	0.54	regulation of protein metabolic process
GO:0042742	0.54	defense response to bacterium
GO:0031325	0.53	positive regulation of cellular metabolic process
GO:0030154	0.53	cell differentiation
GO:0065008	0.52	regulation of biological quality
GO:0032270	0.52	positive regulation of cellular protein metabolic process
GO:0008152	0.52	metabolic process
GO:0032101	0.51	regulation of response to external stimulus
GO:0030216	0.51	keratinocyte differentiation
GO:0051179	0.50	localization
GO:0042221	0.50	response to chemical
GO:0032103	0.50	positive regulation of response to external stimulus
GO:0007165	0.50	signal transduction

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	0.96	intracellular part
GO:0043226	0.90	organelle
GO:0043227	0.88	membrane-bounded organelle
GO:0043229	0.85	intracellular organelle
GO:0043231	0.80	intracellular membrane-bounded organelle
GO:0005737	0.80	cytoplasm
GO:0005634	0.79	nucleus
GO:0044444	0.71	cytoplasmic part
GO:0044421	0.69	extracellular region part
GO:0016020	0.58	membrane
GO:0031988	0.57	membrane-bounded vesicle
GO:0070062	0.56	extracellular exosome

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	0.066	3bowB	0.709	2.56	0.075	0.891	3.4.22.53	NA
2	0.060	3letA	0.527	3.19	0.030	0.782	2.7.7.-	NA
3	0.060	2c9oA	0.536	3.45	0.048	0.822	3.6.4.12	NA
4	0.060	1f6wA	0.520	4.31	0.074	0.881	3.1.1.13 3.1.1.3	NA
5	0.060	1aknA	0.516	4.16	0.106	0.871	3.1.1.13 3.1.1.3	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:

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	0.38	1psr0	0.881	1.61	0.531	0.970	1.54	III	complex1.pdb.gz	2,3,4,6,7,9,10,11,14,16,25,39,40,41,42,43,72,76,80,83,84,86,87,90,91
	2	0.10	1nx1A	0.685	2.74	0.097	0.891	1.44	CA	complex2.pdb.gz	22,24,26,31,69

	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.