C-I-TASSER CIT624

C-I-TASSER results for CIT624

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

Input Sequence in FASTA format

>JCVISYN3A_0548 (181 residues)
MNKRKINIVLYQPEIAQNVGAIMRTCVAINARLHIIEPLGFIFDDRHLSRPSANEYKYVD
CIRYDDWNDFITKHPNITLFCLSRYGQKPISDFDFSKINDNVYLVFGKESTGIAKPILKE
HYNTTFRIPMISETRSLNIANTVGIASYEVLRQWDYLDLVKYETQKGKDYILSERWKGIE
E

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MNKRKINIVLYQPEIAQNVGAIMRTCVAINARLHIIEPLGFIFDDRHLSRPSANEYKYVDCIRYDDWNDFITKHPNITLFCLSRYGQKPISDFDFSKINDNVYLVFGKESTGIAKPILKEHYNTTFRIPMISETRSLNIANTVGIASYEVLRQWDYLDLVKYETQKGKDYILSERWKGIEE
Prediction	CCCCCSSSSSSCCCCCCCHHHHHHHHHHHCCSSSSSCCCCCCCCCCCSSSCCCCHHHCCCSSSSCCHHHHHHHCCCCCSSSSSCCCCCCSSSSSSCCCCCCSSSSSCCCCCCCCHHHHHHCCCCSSSSCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHCCCCCC
Confidence	9999869998277589718899999999899699968999878781011011781552977998999999998199949999748897413355036999979998699999999999847880798169989961479999999999999971977640034100122211221266569
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MNKRKINIVLYQPEIAQNVGAIMRTCVAINARLHIIEPLGFIFDDRHLSRPSANEYKYVDCIRYDDWNDFITKHPNITLFCLSRYGQKPISDFDFSKINDNVYLVFGKESTGIAKPILKEHYNTTFRIPMISETRSLNIANTVGIASYEVLRQWDYLDLVKYETQKGKDYILSERWKGIEE
Prediction	8754101000120423421310031013140400003434043324402300020034041231430440066157320000024074313313046374200000133444125601662044204414376230130000000000001003405404624454155203646166478
	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                 140                 160                 180

                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCSSSSSSCCCCCCCHHHHHHHHHHHCCSSSSSCCCCCCCCCCCSSSCCCCHHHCCCSSSSCCHHHHHHHCCCCCSSSSSCCCCCCSSSSSSCCCCCCSSSSSCCCCCCCCHHHHHHCCCCSSSSCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHCCCCCC
MNKRKINIVLYQPEIAQNVGAIMRTCVAINARLHIIEPLGFIFDDRHLSRPSANEYKYVDCIRYDDWNDFITKHPNITLFCLSRYGQKPISDFDFSKINDNVYLVFGKESTGIAKPILKEHYNTTFRIPMISETRSLNIANTVGIASYEVLRQWDYLDLVKYETQKGKDYILSERWKGIEE

4pzkA

0.40

0.35

10.28

5.61

SPARKS-K

----GVHVVLYQPEIPANTGNIARTCAATGTELHLIRPLGFSTDDKMLKRAGLDYWQHVKITYYDSIEEFYEKNKDGEFFYLTKYGEKAHTAFDYSKREKDYYFVFGRETNGLPANVIEENFDHCLRIPMTDKVRSLNLSNTAAILIYEAFRQQNYPGLDLEI------------------

4pzkA

0.40

0.35

10.26

3.13

FFAS-3D

----GVHVVLYQPEIPANTGNIARTCAATGTELHLIRPLGFSTDDKMLKRAGLDYWQHVKITYYDSIEEFYEKNKDGEFFYLTKYGEKAHTAFDYSKREKDYYFVFGRETNGLPANVIEENFDHCLRIPMTDKVRSLNLSNTAAILIYEAFRQQNYPGLD---------------------

4pzkA

0.40

0.35

10.28

6.49

HHpred

----GVHVVLYQPEIPANTGNIARTCAATGTELHLIRPLGFSTDDKMLKRAGLDYWQHVKITYYDSIEEFYEKNKDGEFFYLTKYGEKAHTAFDYSKREKDYYFVFGRETNGLPANVIEENFDHCLRIPMTDKVRSLNLSNTAAILIYEAFRQQNYPGLDLEI------------------

4pzkA

0.40

0.35

10.28

4.52

MUSTER

----GVHVVLYQPEIPANTGNIARTCAATGTELHLIRPLGFSTDDKMLKRAGLDYWQHVKITYYDSIEEFYEKNKDGEFFYLTKYGEKAHTAFDYSKREKDYYFVFGRETNGLPANVIEENFDHCLRIPMTDKVRSLNLSNTAAILIYEAFRQQNYPGLDLEI------------------

4pzkA

0.40

0.35

10.26

2.63

CNFpred

----GVHVVLYQPEIPANTGNIARTCAATGTELHLIRPLGFSTDDKMLKRAGLDYWQHVKITYYDSIEEFYEKNKDGEFFYLTKYGEKAHTAFDYSKREKDYYFVFGRETNGLPANVIEENFDHCLRIPMTDKVRSLNLSNTAAILIYEAFRQQNYPGLD---------------------

1ipaA

0.21

0.17

5.45

1.26

HHsearch-2

PSPDALILVAVGLEKPGNLGAVLRSADAAGAEAVLVAG-GVDLYSPQVIRNSTGVVFSLRTL-AASESEVLDWIKNLPLVATTPHAEALYWEANLRP---PVAIAVGPEHEGLRAAWLE-AAQTQVRIPMQGQADSLNVSVSAALLLYEALRQRLL-------------------------

4pzkA

0.40

0.35

10.28

4.57

Neff-PPAS

----GVHVVLYQPEIPANTGNIARTCAATGTELHLIRPLGFSTDDKMLKRAGLDYWQHVKITYYDSIEEFYEKNKDGEFFYLTKYGEKAHTAFDYSKREKDYYFVFGRETNGLPANVIEENFDHCLRIPMTDKVRSLNLSNTAAILIYEAFRQQNYPGLDLEI------------------

4pzkA

0.38

0.33

9.66

1.99

HHsearch

----GVHVVLYQPEIPANTGNIARTCAATGTELHLIRPLGFSTDDKMLKRAGLDYWQHVKITYYDSIEEFYEKNKDGEFFYLTKYGEKA---HTAFDYSKDYYFVFGRETNGLPANVIEENFDHCLRIPMTDKVRSLNLSNTAAILIYEAFRQQNYPGLDLEI------------------

1j85a

0.37

0.32

9.51

2.47

PROSPECTOR2

M----LDIVLYEPEIPQNTGNIIRLCANTGFRLHLIEPLGFTWDDKRLRRSGLDYHEFAEIKRHKTFEAFLESEKPKRLFALTTKGCPAHSQVKF---KLGDYLMFGPETRGIPMSILEMPMEQKIRIPMTANSRSMNLSNSVAVTVYEAWRQLGYKGA-------------------VNL

4pzkA

0.41

0.35

10.25

2.70

SAM

----GVHVVLYQPEIPANTGNIARTCAATGTELHLIRPLGFSTDDKMLKRAGLDYWQHVKITYYDSIEEFYEKNKDGEFFYLTKYGEKAHTAFDYSKREKDYYFVFGRETNGLPANVIEENFDHCLRIPMTDKVRSLNLSNTAAILIYEAFRQQNYPGL----------------------

(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	1.05	0.86±0.07	3.1±2.2Å
	2	model2.pdb.gz	-1.17
	3	model3.pdb.gz	-1.93
	4	model4.pdb.gz	-3.53
	5	model5.pdb.gz	-4.03

(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	4pzkA	0.87	0.41	0.396	0.878	model1_4pzkA.pdb.gz
2	1j85A	0.80	1.64	0.396	0.851	model1_1j85A.pdb.gz
3	3e5yA	0.79	1.35	0.329	0.840	model1_3e5yA.pdb.gz
4	3l8uA	0.78	1.32	0.359	0.823	model1_3l8uA.pdb.gz
5	4x3mA	0.72	2.43	0.222	0.823	model1_4x3mA.pdb.gz
6	2ha8A	0.71	2.68	0.173	0.829	model1_2ha8A.pdb.gz
7	1zjrA	0.71	2.78	0.177	0.845	model1_1zjrA.pdb.gz
8	3gyqA2	0.71	2.75	0.248	0.840	model1_3gyqA2.pdb.gz
9	3ic6A	0.70	2.79	0.202	0.834	model1_3ic6A.pdb.gz
10	4cnfA	0.69	2.31	0.217	0.790	model1_4cnfA.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:0008168	1.00	methyltransferase activity
GO:0003723	1.00	RNA binding
GO:0008757	0.69	S-adenosylmethionine-dependent methyltransferase activity
GO:0008173	0.69	RNA methyltransferase activity
GO:0008175	0.54	tRNA methyltransferase 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:0001510	1.00	RNA methylation
GO:0034660	0.96	ncRNA metabolic process
GO:0034470	0.95	ncRNA processing
GO:0006399	0.88	tRNA metabolic process
GO:0006400	0.85	tRNA modification
GO:0030488	0.83	tRNA methylation
GO:0002128	0.79	tRNA nucleoside ribose methylation
GO:0002132	0.75	wobble position uridine ribose methylation
GO:0002131	0.75	wobble position cytosine ribose methylation

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:0044444	0.99	cytoplasmic part
GO:0005737	0.92	cytoplasm
GO:0005829	0.68	cytosol

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	0.326	1v2xA	0.728	2.59	0.196	0.840	2.1.1.34	21,25,107,109,112,128,137
2	0.257	1zjrA	0.710	2.78	0.177	0.845	2.1.1.34	21,25,28,112,145
3	0.229	3gyqA	0.705	2.75	0.248	0.840	2.1.1.66	14
4	0.060	1w9pA	0.521	3.65	0.034	0.696	3.2.1.14	NA
5	0.060	1yq2A	0.517	4.71	0.051	0.823	3.2.1.23	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	0.79	1mxiA	0.800	1.57	0.396	0.851	1.56	SAH	complex1.pdb.gz	82,83,84,106,107,108,109,111,112,127,128,130,136,137,139,142
	2	0.07	3n4j0	0.806	1.36	0.357	0.851	1.35	III	complex2.pdb.gz	21,24,28,30,52,54,90,91,128,129,130,131,134,135,136,137,138,140,141,144,145,148,149,151,152,156,158,159,160

	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