C-I-TASSER CIT619

C-I-TASSER results for CIT619

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

Input Sequence in FASTA format

>JCVISYN3A_0520 (329 residues)
MNEKYPNLAKTMINMWNSRFSKTIHKRDEGFAINFSPIKIFSFLNSINRNSNKKLKIKEY
KNPNLNFWIYSLDNTKLAASIWLNEKQSNKWVIGVHGYNSNRLEVLYLVWHYQSLGYNIL
TFDFRNHGISDSNCITWGYKEKWDLISVINWLIKHYDVELIGLVGTSMGAFTTNYFLLTE
NELIKKANIKWAISDSSYMSVKNLLQRMIKDYSPKFLSNLSKDVLDDILEIYKNEYEVDL
TKLDFVDLITINTTYIPVLYIHNRLDKVTSYLDSFRMYQMKNNIENSFDNQIEIYDHGSH
HTKSIIEFENEYITKSLNFVKLHQKNHHN

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 320 \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| MNEKYPNLAKTMINMWNSRFSKTIHKRDEGFAINFSPIKIFSFLNSINRNSNKKLKIKEYKNPNLNFWIYSLDNTKLAASIWLNEKQSNKWVIGVHGYNSNRLEVLYLVWHYQSLGYNILTFDFRNHGISDSNCITWGYKEKWDLISVINWLIKHYDVELIGLVGTSMGAFTTNYFLLTENELIKKANIKWAISDSSYMSVKNLLQRMIKDYSPKFLSNLSKDVLDDILEIYKNEYEVDLTKLDFVDLITINTTYIPVLYIHNRLDKVTSYLDSFRMYQMKNNIENSFDNQIEIYDHGSHHTKSIIEFENEYITKSLNFVKLHQKNHHN
Prediction	CCCHHHHHHHHHHHHHHHHHHHHHHHHCCCSSSSSCCHHHHHHCCCCCCCCCCCCCHHHCCCCCSSSSSSCCCCCSSSSSSSSCCCCCCCSSSSSCCCCCCHHHHHHHHHHHHHHCCSSSSSCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCSSSSSSSCHCHHHHHHHHHHCCCCCCCCCSSSSSSCCCCCCHHHHHHHHHHHHCCHHHHHCHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHCCCCCSSSSSSCCCCCSCHHHHHHHHHHCCCCCCCCCCSSSSSSCCCCHHHHHHHCHHHHHHHHHHHHHHHHHHCCC
Confidence	98525899999887777777777765123446653434565421453458754568144189817999987999889999995799998489998798679899999999999909969997589888999976556630699999999999981799749999976117999999997343135776279998198799999999999973410111102578999999998874699100683327787549998899995899921879999999983574112675399996899713347753999999999999999851369
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 320 \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| MNEKYPNLAKTMINMWNSRFSKTIHKRDEGFAINFSPIKIFSFLNSINRNSNKKLKIKEYKNPNLNFWIYSLDNTKLAASIWLNEKQSNKWVIGVHGYNSNRLEVLYLVWHYQSLGYNILTFDFRNHGISDSNCITWGYKEKWDLISVINWLIKHYDVELIGLVGTSMGAFTTNYFLLTENELIKKANIKWAISDSSYMSVKNLLQRMIKDYSPKFLSNLSKDVLDDILEIYKNEYEVDLTKLDFVDLITINTTYIPVLYIHNRLDKVTSYLDSFRMYQMKNNIENSFDNQIEIYDHGSHHTKSIIEFENEYITKSLNFVKLHQKNHHN
Prediction	75652650142023323330022133333011011132201020342645465524266272442404040533220100002157524200000000011131013003101723000000000020406242333022014002200410274252430000000100000000003246334342010000000112024002410552224113301330042024203431413044131231440560400001010451503216203300520562463454311000430310300452253015203621551356368
	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                 200                 220                 240                 260                 280                 300                 320

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCHHHHHHHHHHHHHHHHHHHHHHHHCCCSSSSSCCHHHHHHCCCCCCCCCCCCCHHHCCCCCSSSSSSCCCCCSSSSSSSSCCCCCCCSSSSSCCCCCCHHHHHHHHHHHHHHCCSSSSSCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCSSSSSSSCHCHHHHHHHHHHCCCCCCCCCSSSSSSCCCCCCHHHHHHHHHHHHCCHHHHHCHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHCCCCCSSSSSSCCCCCSCHHHHHHHHHHCCCCCCCCCCSSSSSSCCCCHHHHHHHCHHHHHHHHHHHHHHHHHHCCC
MNEKYPNLAKTMINMWNSRFSKTIHKRDEGFAINFSPIKIFSFLNSINRNSNKKLKIKEYKNPNLNFWIYSLDNTKLAASIWLNEKQSNKWVIGVHGYNSNRLEVLYLVWHYQSLGYNILTFDFRNHGISDSNCITWGYKEKWDLISVINWLIKHYDVELIGLVGTSMGAFTTNYFLLTENELIKKANIKWAISDSSYMSVKNLLQRMIKDYSPKFLSNLSKDVLDDILEIYKNEYEVDLTKLDFVDLITINTTYIPVLYIHNRLDKVTSYLDSFRMYQMKNNIENSFDNQIEIYDHGSHHTKSIIEFENEYITKSLNFVKLHQKNHHN

5g59A

0.24

0.20

6.15

2.13

SPARKS-K

---------------------------------HHHHHHGYKMVNP--PRVVGNWTPKDLSFEYKDVEITTEDNVKLSGWWIDN--GSDKTVIPLHGYTSSRHYMRPVIEFLLKEGYNVLAFDFRAHGKSGGKYTTVGDKEILDLKAGVKWLKDNYPSKRIGVIGFSMGALVAIRGLSEV------KEICCGVADSPPIYLDKTGARGMKYFAK-----LPEWLYSFVKPFSELFSG--GRPINV--LNYTNSIKKPLFLIIGRRDTLVKVEEVQEFYERNKHVN----PNVELWVTDAPHVRTIQVFPEEWKSRVGEFLKRWMG----

5g59A

0.25

0.20

6.22

2.53

FFAS-3D

----HHHHGYKMVNP---------------------------------PRVVGNWTPKDLSFEYKDVEITTEDNVKLSGWWI--DNGSDKTVIPLHGYTSSRWAMRPVIEFLLKEGYNVLAFDFRAHGKSGGKYTTVGDKEILDLKAGVKWLKDNYKSKRIGVIGFSMGALVAIRGLSEVKE------ICCGVADSPPIYLDKTGARGMKYF-----AKLPEWLYSFVKPFSELFSGGR----PINVLNYTNSIKKPLFLIIGRRDTLVKVEEVQEFYERNKHV----NPNVELWVTDAPHVRTIQVFPEEWKSRVGEFLKRWM-----

5g59A

0.25

0.19

6.02

3.90

HHpred

----------------------------------------------NPPRVVGNWTPKDLSFEYKDVEITTEDNVKLSGWWIDN--GSDKTVIPLHGYTSSRAEHYMVIEFLLKEGYNVLAFDFRAHGKSGGKYTTVGDKEILDLKAGVKWLKDNPKSKRIGVIGFSMGALVAIRGLSEV------KEICCGVADSPPIYLDKTGARGMKYFKPEWLYSFVKPFS-------ELFSGGR--PINVLNYTNS--IKKPLFLIIGRRDTLVKVEEVQEFYEKHVN---P-NVELWVT--DAPHVRTIQVFPEEWKSRVGEFLKRWMG----

5g59A

0.25

0.20

6.23

2.10

MUSTER

---------------------------------HHHHHHGYKMVNPPRVVGN--WTPKDLSFEYKDVEITTEDNVKLSGWWIDN--GSDKTVIPLHGYTSSRHYMRPVIEFLLKEGYNVLAFDFRAHGKSGGKYTTVGDKEILDLKAGVKWLKDNYPSKRIGVIGFSMGALVAIRGLSEV------KEICCGVADSPPIYLDKTGARGMKYF-----AKLPEWLYSFVKPFSELFSGGR----PINVLNYTNSIKKPLFLIIGRRDTLVKVEEVQEFYERNKHVNP----NVELWVTDAPHVRTIQVFPEEWKSRVGEFLKRWMG----

5g59A

0.26

0.19

6.01

2.09

CNFpred

------------------------------------------------------WTPKDLSFEYKDVEITTEDNVKLSGWWIDNG--SDKTVIPLHGYTSSRWAMRPVIEFLLKEGYNVLAFDFRAHGKSGGKYTTVGDKEILDLKAGVKWLKDNYKSKRIGVIGFSMGALVAIRGLSEV------KEICCGVADSPPIYLDKTGARGMKYFA-----KLPEWLYSFVKPFSELFSGGR----PINVLNYTNSIKKPLFLIIGRRDTLVKVEEVQEFYERNKHVN----PNVELWVTDAPHVRTIQVFPEEWKSRVGEFLKRWMG----

4q3lA

0.13

0.10

3.36

0.38

HHsearch-2

-------------------------------------------------------------------SIFTYQEKDIYYEIDGTLDINSDVIVILNGIMMSTKSWDAFVENF-SKNHVLLRYDMFDQGQSSKIEESYTQIQVELLKNLLEHL----GIAQANIVGISYGASIALQFAAKYP-----TMIKRMVVANVVAKTSPWLKDWNETYYHIYSPQFLNDWMEKKELTRMIRLTKSAETHDVIKDLPN--IKTPTLIISSEEDYLTPPFEQKYLQEHLQ------NAELVSIPNC-GHAS-MYEVPKTFTALVLGFFGQTKLDYQI

5g59A

0.24

0.20

6.15

2.32

Neff-PPAS

---HHHHHGYKMVNP---------------------------------PRVVGNWTPKDLSFEYKDVEITTEDNVKLSGWWIDN--GSDKTVIPLHGYTSSEHYMRPVIEFLLKEGYNVLAFDFRAHGKSGGKYTTVGDKEILDLKAGVKWLKDNYPSKRIGVIGFSMGALVAIRGLSEVK------EICCGVADSPPIYLDKTGARGMKYFAK-----LPEWLYSFVKPFSELFSGGR----PINVLNYTNSIKKPLFLIIGRRDTLVKVEEVQEFYERNKHVNP----NVELWVTDAPHVRTIQVFPEEWKSRVGEFLKRWMG----

5g59A

0.24

0.20

6.15

0.62

HHsearch

--HHHHHHGYKM----------------------VNPPRVVGNWTP-----------KDLSFEYKDVEITTEDNVKLSGWWIDN--GSDKTVIPLHGYTSSRAEHYMVIEFLLKEGYNVLAFDFRAHGKSGGKYTTVGDKEILDLKAGVKWLKDNEKSKRIGVIGFSMGALVAIRGLSE-V-----KEICCGVADSPPIYLDKTGARGMKYFAK-LPEWLYS-FVK---PFSELFSGGR----PINVLNYTNSIKKPLFLIIGRRDTLVKVEEVQEFYERNKH--VNPNVELWVT--DAPHVRTIQVFPEEWKSRVGEFLKRWMG----

5g59A

0.24

0.20

6.15

2.22

PROSPECTOR2

HH--HHHHGYKMVNP---------------------------------PRVVGNWTPKDLSFEYKDVEITTEDNVKLSGWWI--DNGSDKTVIPLHGYTSSRWAMRPVIEFLLKEGYNVLAFDFRAHGKSGGKYTTVGDKEILDLKAGVKWLKDNYPSKRIGVIGFSMGALVAIRGLSE------VKEICCGVADSPPIYLDKTGARGMKYFAK-----LPEWLYSFVKPFSELFSGGR----PINVLNYTNSIKKPLFLIIGRRDTLVKVEEVQEFYERNKHV----NPNVELWVTDAPHVRTIQVFPEEWKSRVGEFLKRWM----G

5g59A

0.26

0.20

6.10

3.42

SAM

-------------------------------------------------RVVGNWTPKDLSFEYKDVEITTEDNVKLSGWWIDN--GSDKTVIPLHGYTSSRWAMRPVIEFLLKEGYNVLAFDFRAHGKSGGKYTTVGDKEILDLKAGVKWLKDNYPSKRIGVIGFSMGALVAIRGLSEV-----KE-ICCGVADSPPIYLDKTGARGMKYFAKLPEW----LYSFVKP---FSELFSGGRPINVLN--YTNSIKKPLFLIIGRRDTLVKVEEVQEFYERNKNPN------VELWVTDAPHVRTIQVFPEEWKSRVGEFLKRW------

(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	-0.36	0.67±0.13	7.2±4.2Å
	2	model2.pdb.gz	-1.09
	3	model3.pdb.gz	-2.33
	4	model4.pdb.gz	-3.13
	5	model5.pdb.gz	-3.75

(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	5g59A	0.81	0.80	0.242	0.818	model1_5g59A.pdb.gz
2	5l8sA	0.73	3.83	0.120	0.887	model1_5l8sA.pdb.gz
3	1ve6A	0.73	4.01	0.102	0.881	model1_1ve6A.pdb.gz
4	3azoA	0.72	4.11	0.104	0.887	model1_3azoA.pdb.gz
5	4hxeB	0.72	3.73	0.148	0.863	model1_4hxeB.pdb.gz
6	2ecfA	0.72	3.84	0.128	0.863	model1_2ecfA.pdb.gz
7	2bklB	0.72	4.31	0.085	0.897	model1_2bklB.pdb.gz
8	2xe4A	0.71	4.43	0.111	0.906	model1_2xe4A.pdb.gz
9	1h2xA	0.71	4.35	0.110	0.897	model1_1h2xA.pdb.gz
10	6eooA	0.71	4.08	0.129	0.878	model1_6eooA.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	0.99	hydrolase activity
GO:1901363	0.65	heterocyclic compound binding
GO:0097159	0.65	organic cyclic compound binding
GO:0005524	0.53	ATP 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:0071704	0.97	organic substance metabolic process
GO:0044238	0.96	primary metabolic process
GO:0009987	0.95	cellular process
GO:0044699	0.91	single-organism process
GO:0043170	0.86	macromolecule metabolic process
GO:0044237	0.85	cellular metabolic process
GO:0044710	0.84	single-organism metabolic process
GO:0006807	0.78	nitrogen compound metabolic process
GO:0044260	0.77	cellular macromolecule metabolic process
GO:0034641	0.77	cellular nitrogen compound metabolic process
GO:0044763	0.72	single-organism cellular process
GO:0006629	0.65	lipid metabolic process
GO:1901360	0.64	organic cyclic compound metabolic process
GO:0046483	0.64	heterocycle metabolic process
GO:0006725	0.64	cellular aromatic compound metabolic process
GO:0034660	0.63	ncRNA metabolic process
GO:1901564	0.58	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	0.90	membrane
GO:0005737	0.86	cytoplasm
GO:0005886	0.64	plasma membrane
GO:0044444	0.57	cytoplasmic part
GO:0044425	0.56	membrane part
GO:0016021	0.55	integral component of membrane
GO:0043226	0.52	organelle
GO:0043227	0.50	membrane-bounded organelle

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	0.271	1a8sA	0.596	3.10	0.162	0.675	1.11.1.10	167,196,266,301
2	0.257	1a88A	0.604	3.08	0.169	0.681	1.11.1.10	167,266,301
3	0.174	2h1iA	0.501	3.07	0.141	0.575	3.1.1.1	106,108,125,167
4	0.103	3hjuA	0.655	3.14	0.126	0.748	3.1.1.23	104,128,167
5	0.095	2jbwD	0.687	3.32	0.102	0.799	3.7.1.-	167,301

	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	0.42	2i3zA	0.703	3.89	0.116	0.857	0.63	LIR	complex1.pdb.gz	96,166,167,168,198,204,268
2	0.18	2hu5B	0.730	3.76	0.105	0.878	0.75	UUU	complex2.pdb.gz	97,98,167,168,201,209,268,269
3	0.17	3h0cA	0.701	3.88	0.120	0.857	0.64	PS4	complex3.pdb.gz	96,100,101,102,167,198,201,204,267
4	0.17	1tkrA	0.698	3.79	0.121	0.848	0.60	DFP	complex4.pdb.gz	96,167,168
5	0.17	1qfmA	0.713	4.37	0.110	0.897	0.64	SGL	complex5.pdb.gz	167,168,198,301

	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