C-I-TASSER CIT621

C-I-TASSER results for CIT621

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

Input Sequence in FASTA format

>JCVISYN3A_0546 (78 residues)
LSGLKHFAKALNINYKDIIVFGDNHNDIEMVKGVKQGYCVENGVDELKKVAFEVCDSLEN
DGVAKKIEQIIKEVQNQK

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| LSGLKHFAKALNINYKDIIVFGDNHNDIEMVKGVKQGYCVENGVDELKKVAFEVCDSLENDGVAKKIEQIIKEVQNQK
Prediction	CHHHHHHHHHHCCCHHHSSSSCCCCHHHHHHHHCCCSSSCCCCCHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHCCC
Confidence	769999999969998886764697101999997495677578889999974802598611179999999999702469
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| LSGLKHFAKALNINYKDIIVFGDNHNDIEMVKGVKQGYCVENGVDELKKVAFEVCDSLENDGVAKKIEQIIKEVQNQK
Prediction	440043017427053620000024710240043033120151037403620531063255400030044005636878
	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

                   |                   |                   |

SS
Seq

CHHHHHHHHHHCCCHHHSSSSCCCCHHHHHHHHCCCSSSCCCCCHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHCCC
LSGLKHFAKALNINYKDIIVFGDNHNDIEMVKGVKQGYCVENGVDELKKVAFEVCDSLENDGVAKKIEQIIKEVQNQK

3gygA3

0.26

0.24

7.53

3.10

SPARKS-K

NEIVTFMLEKYNLNTERAIAFGDSGNDVRMLQTVGNGYLLKNATQEAKNLHNLITDSEYSKGITNTLKKLIGFM----

1rkqA2

0.36

0.33

9.92

1.66

FFAS-3D

-TGVKSLADVLGIKPEEIMAIGDQENDIAMIEYAGVGVAVDNAIPSVKEVANFVTKSNLEDGVAFAIEKYVLN-----

4hgnA

0.18

5.85

1.13

HHpred

IHDYRNFRDKYGLSDDEILYMGDDVPDIEVMRECGLPCCPKDAVPEVKSVAKYISYADGGRGCGRDVVEQVLKAHGKW

1nf2A2

0.25

0.24

7.55

1.89

MUSTER

GKALRFLRERMNWKKEEIVVFGDNENDLFMFEEAGLRVAMENAIEKVKEASDIVTLTNNDSGVSYVLERISTDCLD--

4zevA

0.26

0.24

7.51

1.28

CNFpred

FEGVKEICKYYNISLNNALAMGDGENDIEMLSGLTHSVGVHNASEKVKNSAAYVGPSNNEHAISHVLKTFCDI-----

2b30A

0.28

0.27

8.22

0.69

HHsearch-2

YTGINYLLKHYNISNDQVLVVGDAENDIAMLSNFKYSFAVANATDSAKSHAKCVLVSHREGAVAYLLKKVFDLK----

1nf2A2

0.25

0.24

7.55

2.25

Neff-PPAS

GKALRFLRERMNWKKEEIVVFGDNENDLFMFEEAGLRVAMENAIEKVKEASDIVTLTNNDSGVSYVLERISTDCLD--

2b30A

0.28

0.27

8.22

1.49

HHsearch

YTGINYLLKHYNISNDQVLVVGDAENDIAMLSNFKYSFAVANATDSAKSHAKCVLVSHREGAVAYLLKKVFDLK----

1rlmA1

0.19

6.19

0.98

PROSPECTOR2

ANGISRLLKRWDLSPQNVVAIGDSGNDAEMLKMARYSFAMGNAAENIKQIARYATDDNNHEGALNVIQAVLDNTYPFN

4qjbA

0.27

0.24

7.47

1.05

SAM

FEGVKEICKYYNISLNNALAMGDGENDIEMLSGLTHSVGVHNASEKVKNSAAYVGPSNNEHAISHVLKTF--------

(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 C-I-TASSER

Click to view	Rank^a	Download	C-score^b	Estimated TM-score^c	Estimated RMSD^c
	1	model1.pdb.gz	1.01	0.85±0.08	1.6±1.4Å

(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	1rkqA	0.89	0.80	0.356	0.936	model1_1rkqA.pdb.gz
2	4um5A	0.88	1.39	0.273	0.987	model1_4um5A.pdb.gz
3	2ravA1	0.87	1.08	0.219	0.936	model1_2ravA1.pdb.gz
4	3r4cA1	0.87	1.10	0.288	0.936	model1_3r4cA1.pdb.gz
5	3mn1A	0.87	1.46	0.195	0.987	model1_3mn1A.pdb.gz
6	4navD	0.87	1.45	0.091	0.987	model1_4navD.pdb.gz
7	3l7yA2	0.86	1.15	0.288	0.936	model1_3l7yA2.pdb.gz
8	3n1uA	0.85	1.58	0.234	0.987	model1_3n1uA.pdb.gz
9	4qjbA	0.85	1.10	0.260	0.936	model1_4qjbA.pdb.gz
10	4hgnA	0.85	1.68	0.195	0.987	model1_4hgnA.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	1.00	catalytic activity
GO:0016787	0.94	hydrolase activity
GO:0016791	0.93	phosphatase activity
GO:1901363	0.73	heterocyclic compound binding
GO:0097159	0.73	organic cyclic compound binding
GO:0046872	0.67	metal ion 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:0008152	1.00	metabolic process
GO:0044710	0.99	single-organism metabolic process
GO:0009058	0.99	biosynthetic process
GO:0044711	0.98	single-organism biosynthetic process
GO:0044281	0.98	small molecule metabolic process
GO:0044283	0.97	small molecule biosynthetic process
GO:0009987	0.95	cellular process
GO:0044237	0.90	cellular metabolic process
GO:0071704	0.81	organic substance metabolic process
GO:0044238	0.79	primary metabolic process
GO:0006807	0.74	nitrogen compound metabolic process
GO:0034641	0.71	cellular nitrogen compound metabolic process
GO:0006796	0.64	phosphate-containing compound metabolic process
GO:1901564	0.59	organonitrogen compound metabolic process
GO:0016311	0.54	dephosphorylation
GO:1901360	0.53	organic cyclic compound metabolic process
GO:0046483	0.53	heterocycle metabolic process
GO:0044763	0.53	single-organism cellular process
GO:0006725	0.53	cellular aromatic compound metabolic process
GO:0044260	0.52	cellular macromolecule metabolic process
GO:0006139	0.51	nucleobase-containing 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:0044424	1.00	intracellular part
GO:0005737	0.96	cytoplasm
GO:0044444	0.59	cytoplasmic part

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	0.099	3ewiB	0.845	1.86	0.179	0.987	2.7.7.43	29,32,34,57
2	0.067	2r8zP	0.836	1.65	0.169	0.987	3.1.3.45	51,54
3	0.067	1k1eK	0.872	1.46	0.117	0.987	3.1.3.45	54
4	0.060	1vj0A	0.628	2.38	0.081	0.897	1.1.1.1	NA
5	0.060	2gmwB	0.691	2.10	0.203	0.872	3.1.3.-	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:

Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
1	0.16	2r8zA	0.844	1.60	0.169	0.987	0.57	PO4	complex1.pdb.gz	21,22,23,39,40
2	0.16	3i6bB	0.840	1.62	0.169	0.987	0.54	PO4	complex2.pdb.gz	22,24,40,41,42,62
3	0.05	3e81A	0.847	1.69	0.154	0.974	0.59	UUU	complex3.pdb.gz	63,66,67
4	0.04	3ar7A	0.701	2.32	0.143	0.897	0.59	PTY	complex4.pdb.gz	62,66,70
5	0.03	3namA	0.697	2.05	0.143	0.872	0.62	NA	complex5.pdb.gz	31,32,34,35,37,53

	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