C-I-TASSER CIT618

C-I-TASSER results for CIT618

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

Input Sequence in FASTA format

>JCVISYN3A_0521 (138 residues)
MFFKKKKNFFKQNEQDQDQIELELTDSDIFEQESPVLKDSYTQTSNQFNQNHQTNTSNMN
QTDMNKSPINTYVFSPMKFSEVQSIVDTLLDQKVVVVDFKNLDDNKAKRFKDFLSGVLYI
KKGEYIRLNENIYKFIIN

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MFFKKKKNFFKQNEQDQDQIELELTDSDIFEQESPVLKDSYTQTSNQFNQNHQTNTSNMNQTDMNKSPINTYVFSPMKFSEVQSIVDTLLDQKVVVVDFKNLDDNKAKRFKDFLSGVLYIKKGEYIRLNENIYKFIIN
Prediction	CCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSSCCCHHHHHHHHHHHHCCCSSSSSCCCCCHHHHHHHHHHHHCCSSSSCCSSSSSCCCSSSSSCC
Confidence	962789998089876543222234444210012454445445555555555566754333356778852899983498899999999998199699977899989987889766142266423799963968999269
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MFFKKKKNFFKQNEQDQDQIELELTDSDIFEQESPVLKDSYTQTSNQFNQNHQTNTSNMNQTDMNKSPINTYVFSPMKFSEVQSIVDTLLDQKVVVVDFKNLDDNKAKRFKDFLSGVLYIKKGEYIRLNENIYKFIIN
Prediction	643542362044446444444463656744557554467644555554565555644445445565541300013054172045005304763000000541467303100010100010140325402730000118
	Values range from 0 (buried residue) to 8 (highly exposed residue)

Predicted contact map used in C-I-TASSER simulation

C-I-TASSER simulation is guided by consensus contact map (upper left triangle) derived based on confidence scores of TripletRes (lower right triangle), ResTriplet, ResPRE, and NeBcon. In the contact map, the axes mark the residue indexes along the sequence, while each dot represents a residue pair with predicted contact. No dot is close to the diagonal, because C-I-TASSER does not consider contacts for residue pairs separated by <6 residues.

Top 10 threading templates used by C-I-TASSER

Rank

PDB
hit

ID1

ID2

Cov

Norm.
Zscore

Download
alignment

                  20                  40                  60                  80                 100                 120

                   |                   |                   |                   |                   |                   |

SS
Seq

CCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSSCCCHHHHHHHHHHHHCCCSSSSSCCCCCHHHHHHHHHHHHCCSSSSCCSSSSSCCCSSSSSCC
MFFKKKKNFFKQNEQDQDQIELELTDSDIFEQESPVLKDSYTQTSNQFNQNHQTNTSNMNQTDMNKSPINTYVFSPMKFSEVQSIVDTLLDQKVVVVDFKNLDDNKAKRFKDFLSGVLYIKKGEYIRLNENIYKFIIN

3zihA

0.30

0.15

4.62

2.03

SPARKS-K

-------------------------------------------------------------------SSKVVLSEPRVYAEAQEIADHLKNRRAVVVNLQRIQHDQAKRIVDFLSGTVYAIGGDIQRIGSDIFLCTPD

3ziiA

0.29

0.14

4.41

1.41

FFAS-3D

---------------------------------------------------------------------KVVLSEPRVYAEAQEIADHLKNRRAVVVNLQRIQHDQAKRIVDFLSKTVYAIGGDIQRIGSDIFLCTPD

3zihA

0.30

0.15

4.62

2.19

HHpred

-------------------------------------------------------------------SSKVVLSEPRVYAEAQEIADHLKNRRAVVVNLQRIQHDQAKRIVDFLSGTVYAIGGDIQRIGSDIFLCTPD

3zihA

0.30

0.15

4.62

1.98

MUSTER

-------------------------------------------------------------------SSKVVLSEPRVYAEAQEIADHLKNRRAVVVNLQRIQHDQAKRIVDFLSGTVYAIGGDIQRIGSDIFLCTPD

3zihA

0.31

0.15

4.60

1.37

CNFpred

----------------------------------------------------------------------VVLSEPRVYAEAQEIADHLKNRRAVVVNLQRIQHDQAKRIVDFLSGTVYAIGGDIQRIGSDIFLCTPD

3zihA

0.30

0.15

4.62

2.33

HHsearch-2

-------------------------------------------------------------------SSKVVLSEPRVYAEAQEIADHLKNRRAVVVNLQRIQHDQAKRIVDFLSGTVYAIGGDIQRIGSDIFLCTPD

3zihA

0.30

0.15

4.62

2.64

Neff-PPAS

--------------------------------------------------------------------SKVVLSEPRVYAEAQEIADHLKNRRAVVVNLQRIQHDQAKRIVDFLSGTVYAIGGDIQRIGSDIFLCTPD

3zihA

0.30

0.15

4.62

3.90

HHsearch

-------------------------------------------------------------------SSKVVLSEPRVYAEAQEIADHLKNRRAVVVNLQRIQHDQAKRIVDFLSGTVYAIGGDIQRIGSDIFLCTP-

3zihA

0.30

0.15

4.62

0.98

PROSPECTOR2

-------------------------------------------------------------------SSKVVLSEPRVYAEAQEIADHLKNRRAVVVNLQRIQHDQAKRIVDFLSGTVYAIGGDIQRIGSDIFLCTPD

3zihA

0.30

0.15

4.61

1.01

SAM

--------------------------------------------------------------------SKVVLSEPRVYAEAQEIADHLKNRRAVVVNLQRIQHDQAKRIVDFLSGTVYAIGGDIQRIGSDIFLCTP-

(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 5 final models from C-I-TASSER

Click to view	Rank^a	Download	C-score^b	Estimated TM-score^c	Estimated RMSD^c
	1	model1.pdb.gz	-0.94	0.60±0.14	6.6±4.0Å
	2	model2.pdb.gz	-1.66
	3	model3.pdb.gz	-2.70
	4	model4.pdb.gz	-2.70
	5	model5.pdb.gz	-3.77

(a)	C-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 C-score, calculated based on significance of threading template alignments and convergence of C-I-TASSER simulations. C-score is typically in the range of [-5, 2], with higher C-score signifies higher model confidence.
(c)	Model TM-score and RMSD are estimated based on C-score and protein length for the first model.

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	6uqvA	0.57	4.36	0.120	0.913	model1_6uqvA.pdb.gz
2	4atnA	0.56	4.23	0.084	0.855	model1_4atnA.pdb.gz
3	5xtuA	0.55	4.49	0.076	0.899	model1_5xtuA.pdb.gz
4	3kvnX1	0.55	4.46	0.073	0.877	model1_3kvnX1.pdb.gz
5	2oo3A	0.55	4.36	0.101	0.848	model1_2oo3A.pdb.gz
6	2ei9A	0.55	3.82	0.056	0.804	model1_2ei9A.pdb.gz
7	3opnA	0.50	4.69	0.076	0.848	model1_3opnA.pdb.gz
8	1ej0A	0.50	4.22	0.068	0.804	model1_1ej0A.pdb.gz
9	3hp7A2	0.49	4.77	0.074	0.862	model1_3hp7A2.pdb.gz
10	1kxzA	0.47	4.52	0.090	0.761	model1_1kxzA.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:1901363	0.56	heterocyclic compound binding
GO:0097159	0.56	organic cyclic compound binding
GO:0042802	0.54	identical protein 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:0000917	1.00	barrier septum assembly
GO:0044260	0.92	cellular macromolecule metabolic process
GO:0044238	0.92	primary metabolic process
GO:0034641	0.92	cellular nitrogen compound metabolic process
GO:0016070	0.76	RNA metabolic process
GO:0034660	0.67	ncRNA metabolic process
GO:1901564	0.52	organonitrogen compound metabolic 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:0044464	1.00	cell part
GO:0044424	0.97	intracellular part
GO:0016020	0.87	membrane
GO:0005886	0.86	plasma membrane
GO:0005737	0.83	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	2frxA	0.532	4.25	0.067	0.841	2.1.1.-	NA
2	0.060	2o3hA	0.537	4.17	0.063	0.819	4.2.99.18	NA
3	0.060	2hsaA	0.550	4.54	0.063	0.848	1.3.1.42	NA
4	0.060	1ktbA	0.539	4.17	0.044	0.812	3.2.1.49	39,98
5	0.060	3i4eA	0.542	4.28	0.031	0.826	4.1.3.1	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	0.01	3h55A	0.541	4.15	0.037	0.812	0.44	GLA	complex1.pdb.gz	118,119,135

	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.	Chengxin Zhang, S M Mortuza, Baoji He, Yanting Wang, and Yang Zhang. "Template-based and free modeling of I-TASSER and QUARK pipelines using predicted contact maps in CASP12." Proteins: Structure, Function, and Bioinformatics (2017). doi: 10.1002/prot.25414