D-I-TASSER Q9C035-D2

D-I-TASSER results for Q9C035-D2

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

Input Sequence in FASTA format

>Q9C035 (74 residues)
DHCARHGEKLLLFCQEDGKVICWLCERSQEHRGHHTFLTEEVAREYQVKLQAALEMLRQK
QQEAEELEADIREE

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| DHCARHGEKLLLFCQEDGKVICWLCERSQEHRGHHTFLTEEVAREYQVKLQAALEMLRQKQQEAEELEADIREE
Prediction	CCCHHHCCSSSSSSCCCCSSSSCCCCCCCCCCCCCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Confidence	97532197323663348917800133575437974375999999999999999999999999999999999509
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| DHCARHGEKLLLFCQEDGKVICWLCERSQEHRGHHTFLTEEVAREYQVKLQAALEMLRQKQQEAEELEADIREE
Prediction	84476375405200451541002114417515512222044016524640462155045335515633553678
	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

CCCHHHCCSSSSSSCCCCSSSSCCCCCCCCCCCCCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
DHCARHGEKLLLFCQEDGKVICWLCERSQEHRGHHTFLTEEVAREYQVKLQAALEMLRQKQQEAEELEADIREE

5hau1z

0.11

0.09

3.42

1.00

DEthreader

-----M---K-VILLEPVQVDV-PGYARNYLPRLAVLNLKALEARIRAQAKRLAERKAEAERLKEILENDLKRH

5va4A

0.69

19.61

1.51

SPARKS-K

DHCAHHGEKLVLFCQQDGNVICWLCERSQEHRGHQTFLVEEVAQKYREKLQVALEMMRQKQKDAETECNQVAKR

5va4A

0.69

19.61

1.05

MapAlign

DHCAHHGEKLVLFCQQDGNVICWLCERSQEHRGHQTFLVEEVAQKYREKLQVALEMMRQKQKDAETECNQVAKR

5va4A

0.69

19.61

1.18

CEthreader

DHCAHHGEKLVLFCQQDGNVICWLCERSQEHRGHQTFLVEEVAQKYREKLQVALEMMRQKQKDAETECNQVAKR

5va4A

0.69

19.61

1.60

MUSTER

DHCAHHGEKLVLFCQQDGNVICWLCERSQEHRGHQTFLVEEVAQKYREKLQVALEMMRQKQKDAETECNQVAKR

5va4A

0.69

19.61

1.63

HHsearch

DHCAHHGEKLVLFCQQDGNVICWLCERSQEHRGHQTFLVEEVAQKYREKLQVALEMMRQKQKDAETECNQVAKR

5va4A

0.69

19.61

0.98

FFAS-3D

DHCAHHGEKLVLFCQQDGNVICWLCERSQEHRGHQTFLVEEVAQKYREKLQVALEMMRQKQKDAETECNQVAKR

4tn3A

0.89

25.08

0.92

EigenThreader

DHCARHGEKLLLFCQEDSKVICWLCKDSQEHRGHHTFLMEEVAQEYHVKLQTALEMLRQKQQEAEKLEADIREE

5eiuA

0.81

22.89

1.12

CNFpred

DHCARHGEKLLLFCQEDSKVICWLCERSQEHRGHHTFLMEEVAQEYHVKLQTALEMLRQKQQEAETERNQVAKR

5j8bz

0.13

0.11

3.76

1.00

DEthreader

-----M----KVILLEPVQVVD--V-KPGYARYLAVANLKALEARIRAQAKRLAERKAEAERLKEILENLSRIY

(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	0.6907

(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	4tn3A	0.74	2.91	0.730	0.973	model1_4tn3A.pdb.gz
2	5va4A	0.72	2.43	0.685	0.960	model1_5va4A.pdb.gz
3	6qajA	0.69	2.55	0.181	0.973	model1_6qajA.pdb.gz
4	6h3aA	0.68	2.40	0.219	0.987	model1_6h3aA.pdb.gz
5	4ypoA	0.64	3.00	0.083	0.919	model1_4ypoA.pdb.gz
6	5hau1z	0.64	2.38	0.125	0.865	model1_5hau1z.pdb.gz
7	1np3A	0.64	3.28	0.095	0.946	model1_1np3A.pdb.gz
8	2xqhA2	0.62	2.12	0.031	0.797	model1_2xqhA2.pdb.gz
9	1i36A	0.56	3.64	0.000	0.892	model1_1i36A.pdb.gz
10	2csvA	0.56	1.73	0.352	0.649	model1_2csvA.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	0.84	catalytic activity
GO:0016740	0.82	transferase activity
GO:0004842	0.81	ubiquitin-protein transferase activity
GO:0004871	0.70	signal transducer activity
GO:0004872	0.68	receptor activity
GO:0038023	0.67	signaling receptor activity
GO:0008329	0.65	signaling pattern recognition receptor 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	0.97	biological regulation
GO:0050789	0.97	regulation of biological process
GO:0050794	0.96	regulation of cellular process
GO:0048518	0.91	positive regulation of biological process
GO:0009987	0.90	cellular process
GO:0080090	0.89	regulation of primary metabolic process
GO:0060255	0.89	regulation of macromolecule metabolic process
GO:0031323	0.89	regulation of cellular metabolic process
GO:0048522	0.85	positive regulation of cellular process
GO:0065009	0.83	regulation of molecular function
GO:0010468	0.83	regulation of gene expression
GO:2001141	0.82	regulation of RNA biosynthetic process
GO:0044093	0.81	positive regulation of molecular function
GO:0006355	0.81	regulation of transcription, DNA-templated
GO:0071704	0.80	organic substance metabolic process
GO:0048583	0.80	regulation of response to stimulus
GO:0044238	0.80	primary metabolic process
GO:0044237	0.80	cellular metabolic process
GO:0043900	0.80	regulation of multi-organism process
GO:0044260	0.79	cellular macromolecule metabolic process
GO:0051090	0.77	regulation of sequence-specific DNA binding transcription factor activity
GO:0051091	0.76	positive regulation of sequence-specific DNA binding transcription factor activity
GO:0019538	0.76	protein metabolic process
GO:0002376	0.76	immune system process
GO:0051246	0.75	regulation of protein metabolic process
GO:0016567	0.75	protein ubiquitination
GO:0009966	0.75	regulation of signal transduction
GO:0032268	0.74	regulation of cellular protein metabolic process
GO:0080134	0.73	regulation of response to stress
GO:0048584	0.73	positive regulation of response to stimulus
GO:0031399	0.72	regulation of protein modification process
GO:0031347	0.72	regulation of defense response
GO:0009967	0.72	positive regulation of signal transduction
GO:0002682	0.71	regulation of immune system process
GO:0050776	0.70	regulation of immune response
GO:0032101	0.70	regulation of response to external stimulus
GO:0000209	0.70	protein polyubiquitination
GO:0051247	0.69	positive regulation of protein metabolic process
GO:1902531	0.68	regulation of intracellular signal transduction
GO:0051092	0.68	positive regulation of NF-kappaB transcription factor activity
GO:0045088	0.68	regulation of innate immune response
GO:0031325	0.68	positive regulation of cellular metabolic process
GO:1902533	0.67	positive regulation of intracellular signal transduction
GO:0032270	0.67	positive regulation of cellular protein metabolic process
GO:0031349	0.67	positive regulation of defense response
GO:0002831	0.67	regulation of response to biotic stimulus
GO:0002684	0.67	positive regulation of immune system process
GO:0001932	0.67	regulation of protein phosphorylation
GO:0045089	0.65	positive regulation of innate immune response
GO:0043123	0.65	positive regulation of I-kappaB kinase/NF-kappaB signaling
GO:0001934	0.65	positive regulation of protein phosphorylation
GO:0070534	0.63	protein K63-linked ubiquitination
GO:0002218	0.62	activation of innate immune response
GO:0043410	0.61	positive regulation of MAPK cascade
GO:0031664	0.61	regulation of lipopolysaccharide-mediated signaling pathway

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:0043226	0.92	organelle
GO:0043229	0.91	intracellular organelle
GO:0044444	0.88	cytoplasmic part
GO:0032991	0.79	macromolecular complex
GO:0043232	0.75	intracellular non-membrane-bounded organelle
GO:0030529	0.70	intracellular ribonucleoprotein complex
GO:0000932	0.68	cytoplasmic mRNA processing body

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	1qleD	0.461	1.63	0.048	0.527	1.9.3.1	NA
2	0.060	1t9gC	0.554	3.44	0.082	0.824	1.3.99.3	NA
3	0.060	1udyA	0.581	3.59	0.068	0.878	1.3.99.3	30
4	0.060	3dojA	0.577	3.32	0.027	0.865	1.1.1.79	NA
5	0.060	1x75B	0.365	2.30	0.027	0.419	5.99.1.3	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:

No Binding sites was predicted

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

	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.