C-I-TASSER CIT622

C-I-TASSER results for CIT622

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

Input Sequence in FASTA format

>JCVISYN3A_0593 (92 residues)
MLLDWSVDQNTQKIDVSKYKDEFVNNNVIDNSLIDDYFDNYSDLNPTPSIQPNPTPITNY
QDKPNKIKKKKLNQLIMSLKFLQIQKLINQKL

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MLLDWSVDQNTQKIDVSKYKDEFVNNNVIDNSLIDDYFDNYSDLNPTPSIQPNPTPITNYQDKPNKIKKKKLNQLIMSLKFLQIQKLINQKL
Prediction	CCCCCCCCCCCSSSSHHHHHHHHHCCCCCCHHHHHHHHHCHCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Confidence	97322235774243045555766313321125667775310127999887899978766566700788999999999999999999986219
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MLLDWSVDQNTQKIDVSKYKDEFVNNNVIDNSLIDDYFDNYSDLNPTPSIQPNPTPITNYQDKPNKIKKKKLNQLIMSLKFLQIQKLINQKL
Prediction	64342434553552415524551265532444214421552572544462545443145266445514554044103314333035215668
	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

                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCSSSSHHHHHHHHHCCCCCCHHHHHHHHHCHCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCC
MLLDWSVDQNTQKIDVSKYKDEFVNNNVIDNSLIDDYFDNYSDLNPTPSIQPNPTPITNYQDKPNKIKKKKLNQLIMSLKFLQIQKLINQKL

5yfpE1

0.11

3.90

0.99

SPARKS-K

--SLYELDPKKKLLKTDNFLGGLTVNEF-VQELSKDHRNDVLIDANTKNLPTNEKDQDAIREAIWKQLDPKPYIRTFESTLKELKNLNEETL

4j7oA3

0.21

0.15

4.85

0.54

FFAS-3D

--------------DFDTKKQAYINQGVVPTDI---------EAATNLGISYDPSKIDNNVEHDQKVRREKDKKAVIELYVSSINRGIKYK-

3s5hA1

0.11

0.10

3.50

0.27

HHpred

-----EITNL-TYEEFKEFYYKYNPKKVNNPNFVDQYLGQLDYSKYRD------DAVENYAQEQENLEKQELKKRIENFNEQEKEQVIKNF-

6f4aB

0.20

6.27

0.70

MUSTER

QIENSAPDQVEFRKVAWLRLKDMLYNQLLDKNLPAKINGYDPGLMETISPT-QPQHIIPHLVKMNKIKYEQFQYLLSSYYDCILNQEIIPSM

4ct4A

0.15

0.04

1.47

0.39

CNFpred

-----------------------------------------------------------------TLKNPEFNKMVLNETYRNIKVLLTSDK

1vt4I

0.22

0.21

6.51

0.51

HHsearch-2

KLHKYSLVESTISIP-SIYKVKLENEYALHRSIVDHYNIPK-TFDSDDLIPPY---LDQYSHIGHHLKNERMTLFRLDFRFLE-QKIRHDST

5yfpE4

0.14

0.13

4.46

0.99

Neff-PPAS

-----DINKTAGVVNLNFLKFISMSTEILDLLSISIKSIFLPLLNNSPEIKAQIIEMTNSQIQKMEILINIILQETITVISTKFSAILCKQ-

6eemA2

0.28

0.22

6.65

0.41

HHsearch

----------QNPLDP----DEFRRQMII--DFLADYYKNVEKYPVRSQVEPGPEPLTHWQS-PNAYGVANLRTFLKMAKH--FQGLIGMD-

2mmea

0.20

0.17

5.59

0.64

SP3

----MSVTVPDKDWTLSSLSETFDDGT---QTLQGQLTSALNALAENPS---NPQLLAEYQSKLSEYTLYRNAQSNTVKVIKDVDAAIIQNF

5ca8A2

0.22

0.18

5.82

0.53

PROSPECTOR2

-------DLPTQQILVAQFKDEIV------ESVFQEFLTKYQHHFKEVD---AAPDFEELGALFADLRQDAFEDYVYEQKRKKLRWLINDKL

(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	-2.14	0.46±0.15	8.3±4.5Å
	2	model2.pdb.gz	-2.93
	3	model3.pdb.gz	-5.88
	4	model4.pdb.gz	-5.88
	5	model5.pdb.gz	-6.38

(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	2b51A1	0.47	4.36	0.057	0.913	model1_2b51A1.pdb.gz
2	3k9vA	0.47	4.50	0.048	0.870	model1_3k9vA.pdb.gz
3	2nxxB	0.47	3.80	0.034	0.826	model1_2nxxB.pdb.gz
4	5gweA	0.47	4.36	0.048	0.859	model1_5gweA.pdb.gz
5	5b7iA1	0.47	4.43	0.084	0.880	model1_5b7iA1.pdb.gz
6	2zbzA	0.47	4.41	0.069	0.859	model1_2zbzA.pdb.gz
7	5fyfA	0.47	4.32	0.082	0.859	model1_5fyfA.pdb.gz
8	4q2cA	0.47	4.06	0.037	0.826	model1_4q2cA.pdb.gz
9	4yzfA1	0.47	4.12	0.090	0.848	model1_4yzfA1.pdb.gz
10	1f4tA	0.46	4.30	0.094	0.837	model1_1f4tA.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:0046914	0.37	transition metal ion binding
GO:0046906	0.37	tetrapyrrole 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:0044710	0.37	single-organism 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	0.67	intracellular 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	3b98A	0.443	4.37	0.033	0.859	5.3.99.4	NA
2	0.060	2f9qA	0.448	4.86	0.091	0.902	1.14.14.1	NA
3	0.060	3hf2A	0.415	4.63	0.073	0.837	1.14.14.1 1.6.2.4	NA
4	0.060	2z3tA	0.443	4.43	0.056	0.870	1.-.-.-	NA
5	0.060	1lgfA	0.455	4.54	0.044	0.880	1.14.-.-	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.	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