I-TASSER results

I-TASSER results for job id Rv0543c

[Click on result.tar.bz2 to download the tarball file including all modelling results listed on this page]

Input Sequence in FASTA format

>protein (100 residues)
MNRFLTSIVAWLRAGYPEGIPPTDSFAVLALLCRRLSHDEVKAVANELMRLGDFDQIDIG
VVITHFTDELPSPEDVERVRARLAAQGWPLDDVRDREEHA

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MNRFLTSIVAWLRAGYPEGIPPTDSFAVLALLCRRLSHDEVKAVANELMRLGDFDQIDIGVVITHFTDELPSPEDVERVRARLAAQGWPLDDVRDREEHA
Prediction	CCHHHHHHHHHHHHCCCCCCCCCCCCEEEEEHCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCC
Conf.Score	9789999999999758899999998557887489999999999999999879999999999999998689999999999999998588889999998999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MNRFLTSIVAWLRAGYPEGIPPTDSFAVLALLCRRLSHDEVKAVANELMRLGDFDQIDIGVVITHFTDELPSPEDVERVRARLAAQGWPLDDVRDREEHA
Prediction	7452153004203322274237641100000044503562044004302763614554034103502754246731530253146441304436688778
	Values range from 0 (buried residue) to 8 (highly exposed residue)

Predicted Normalized B-facotr

(B-factor is a value to indicate the extent of the inherent thermal mobility of residues/atoms in proteins. In I-TASSER, this value is deduced from threading template proteins from the PDB in combination with the sequence profiles derived from sequence databases. The reported B-factor profile in the figure below corresponds to the normalized B-factor of the target protein, defined by B=(B'-u)/s, where B' is the raw B-factor value, u and s are respectively the mean and standard deviation of the raw B-factors along the sequence. (Click here to read more about predicted normalized B-factor)

Top 10 threading templates used by I-TASSER

Rank

PDB
Hit

Iden1

Iden2

Cov

Norm.
Zscore

Download
Align.

                  20                  40                  60                  80                 100

                   |                   |                   |                   |                   |

Sec.Str
Seq

CCHHHHHHHHHHHHCCCCCCCCCCCCEEEEEHCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCC
MNRFLTSIVAWLRAGYPEGIPPTDSFAVLALLCRRLSHDEVKAVANELMRLGDFDQIDIGVVITHFTDELPSPEDVERVRARLAAQGWPLDDVRDREEHA

2kvcA

1.00

3.34

MUSTER

MNRFLTSIVAWLRAGYPEGIPPTDSFAVLALLCRRLSHDEVKAVANELMRLGDFDQIDIGVVITHFTDELPSPEDVERVRARLAAQGWPLDDVRDREEHA

2kvcA

1.00

4.14

dPPAS

MNRFLTSIVAWLRAGYPEGIPPTDSFAVLALLCRRLSHDEVKAVANELMRLGDFDQIDIGVVITHFTDELPSPEDVERVRARLAAQGWPLDDVRDREEHA

2kvcA

1.00

4.26

wdPPAS

MNRFLTSIVAWLRAGYPEGIPPTDSFAVLALLCRRLSHDEVKAVANELMRLGDFDQIDIGVVITHFTDELPSPEDVERVRARLAAQGWPLDDVRDREEHA

2kvcA

1.00

3.87

wMUSTER

MNRFLTSIVAWLRAGYPEGIPPTDSFAVLALLCRRLSHDEVKAVANELMRLGDFDQIDIGVVITHFTDELPSPEDVERVRARLAAQGWPLDDVRDREEHA

2kvcA

1.00

4.36

wPPAS

MNRFLTSIVAWLRAGYPEGIPPTDSFAVLALLCRRLSHDEVKAVANELMRLGDFDQIDIGVVITHFTDELPSPEDVERVRARLAAQGWPLDDVRDREEHA

2kvcA

1.00

8.35

dPPAS2

MNRFLTSIVAWLRAGYPEGIPPTDSFAVLALLCRRLSHDEVKAVANELMRLGDFDQIDIGVVITHFTDELPSPEDVERVRARLAAQGWPLDDVRDREEHA

2kvcA

1.00

4.09

PPAS

MNRFLTSIVAWLRAGYPEGIPPTDSFAVLALLCRRLSHDEVKAVANELMRLGDFDQIDIGVVITHFTDELPSPEDVERVRARLAAQGWPLDDVRDREEHA

2kvcA

1.00

5.08

Env-PPAS

MNRFLTSIVAWLRAGYPEGIPPTDSFAVLALLCRRLSHDEVKAVANELMRLGDFDQIDIGVVITHFTDELPSPEDVERVRARLAAQGWPLDDVRDREEHA

2lkyA

0.60

1.00

3.03

MUSTER

VNAFLAKIAAWLNAGYPEGVPGPDRVPLLALLTRRLTNDEIKAIAEDLEKRAHFDHIDIGVLITQMTDEMPREEDIERVRRHLALQGWPLDDPRDGEEPD

3ol3A

0.39

0.37

0.94

3.94

dPPAS

TTTFMDNVLGWLHKGYPEGVPPKDYFALLALLKRSLTEDEVVRAAQAILRSSPVTDDDIRNAVHQIIEKEPTAEEINQVAARLASVGWPLAVPV------

(a)	Iden1 is the number of template residues identical to query divided by number of aligned residues.
(b)	Iden2 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.
(e)	Download Align. list the threading program used to identify the template provide the 3D structure of aligned regions of threading templates.

Top 3 final models predicted by I-TASSER

(For each target, I-TASSER simulations generate a large ensemble of structural conformations, called decoys. To select the final models, I-TASSER uses the SPICKER program to cluster all the decoys based on the pair-wise structure similarity, and reports up to five models which corresponds to the five largest structure clusters. The confidence of each model is quantitatively measured by C-score that is calculated based on the significance of threading template alignments and the convergence parameters of the structure assembly simulations. C-score is typically in the range of [-5, 2], where a C-score of higher value signifies a model with a high confidence and vice-versa. TM-score and RMSD are estimated based on C-score and protein length following the correlation observed between these qualities. Since the top 5 models are ranked by the cluster size, it is possible that the lower-rank models have a higher C-score in rare cases. Although the first model has a better quality in most cases, it is also possible that the lower-rank models have a better quality than the higher-rank models as seen in our benchmark tests. If the I-TASSER simulations converge, it is possible to have less than 5 clusters generated. This is usually an indication that the models have a good quality because of the converged simulations.)

More about C-score

Local structure accuracy of first model

Download Model 1

C-score=1.22

Estimated TM-score = 0.88±0.07

Estimated RMSD = 1.7±1.5Å

Download Model 2

C-score=-1.54

Download Model 3

C-score=-1.56

Proteins structureally close to the target in PDB (as identified by TM-align

(After the structure assembly simulation, I-TASSER uses the TM-align structural alignment program to match the first I-TASSER model to all structures in the PDB library. This section reports the top 10 proteins from the PDB that have the closest structural similarity, i.e. the highest TM-score, to the predicted I-TASSER model. Due to the structural similarity, these proteins often have similar function to the target. However, users are encouraged to use the data in the next section 'Predicted function using COACH' to infer the function of the target protein, since COACH has been extensively trained to derive biological functions from multi-source of sequence and structure features which has on average a higher accuracy than the function annotations derived only from the global structure comparison.)

Top 10 Identified stuctural analogs in PDB

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov
1	2kvcA	0.946	0.91	1.000	1.000
2	2lkyA	0.724	2.40	0.550	0.910
3	1w3tA	0.599	3.43	0.076	0.920
4	2r91A	0.598	3.41	0.033	0.920
5	3b4uB	0.597	3.54	0.086	0.930
6	2nuyA	0.595	3.35	0.098	0.910
7	4xcvA	0.593	2.88	0.143	0.840
8	2j6iA	0.593	2.77	0.083	0.840
9	4xa8A1	0.591	2.90	0.179	0.840
10	4weqA2	0.590	2.98	0.118	0.850

(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 function using COACH

(This section reports biological annotations of the target protein by COACH based on the I-TASSER structure prediction. COACH is a meta-server approach that combines multiple function annotation results from the COFACTOR, TM-SITE and S-SITE programs.)

Ligand binding sites

Rank	C-score	Cluster size	PDB Hit	Lig Name	Download Complex	Ligand Binding Site Residues
1	0.12	3	1dwsA	CMO	Rep, Mult	32,54,83
2	0.08	2	3ol3B	IOD	Rep, Mult	48,51,58
3	0.08	2	1o0sA	TTN	Rep, Mult	4,7,8,34,40
4	0.07	3	4il9E	UNL	Rep, Mult	9,16
5	0.05	2	1uvxA	XE	Rep, Mult	11,12,15,32,83
6	0.05	2	3dc2A	SER	Rep, Mult	16,20,21,22,23,24,25,48
7	0.05	2	1smyF	MG	Rep, Mult	28,79,82
8	0.04	1	3ol3B	IOD	Rep, Mult	43,50,66
9	0.04	1	3ol3B	IOD	Rep, Mult	39,40,43
10	0.02	1	4rkuL	CLA	Rep, Mult	5,8,16
11	0.02	1	3cuzA	MG	Rep, Mult	27,75
12	0.02	1	1xzcA	PMB	Rep, Mult	5,9,44,47,48

	Download the all possible binding ligands and detailed prediction summary.
	Download the templates clustering results.
(a)	C-score is the confidence score of the prediction. C-score ranges [0-1], where a higher score indicates a more reliable prediction.
(b)	Cluster size is the total number of templates in a cluster.
(c)	Lig Name is name of possible binding ligand. Click the name to view its information in the BioLiP database.
(d)	Rep is a single complex structure with the most representative ligand in the cluster, i.e., the one listed in the Lig Name column. Mult is the complex structures with all potential binding ligands in the cluster.

Enzyme Commission (EC) numbers and active sites

Rank	Cscore^EC	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov	EC Number	Active Site Residues
1	0.060	3ga0A	0.586	2.84	0.107	0.840	1.1.1.-	NA
2	0.060	2fssA	0.595	2.76	0.083	0.840	1.2.1.2	NA
3	0.060	1f7bA	0.574	3.65	0.031	0.950	4.1.3.3	NA
4	0.060	3ba1A	0.559	2.90	0.120	0.830	1.1.1.237	22,53
5	0.060	3gg9A	0.570	2.83	0.074	0.810	1.1.1.95	NA
6	0.060	1dxyA	0.560	2.95	0.048	0.830	1.1.1.-	NA
7	0.060	1gdhA	0.582	2.81	0.096	0.830	1.1.1.29	NA
8	0.060	3noeA	0.557	3.84	0.095	0.950	4.2.1.52	35
9	0.060	1f5zA	0.576	3.62	0.021	0.950	4.1.3.3	83
10	0.060	2wkjA	0.576	3.67	0.083	0.950	4.1.3.3	NA
11	0.060	2dldA	0.571	2.72	0.049	0.810	1.1.1.28	13
12	0.060	1w37A	0.600	3.45	0.076	0.920	4.1.2.20	NA
13	0.060	1wwkA	0.569	2.93	0.098	0.820	1.1.1.95	NA
14	0.060	1o0sA	0.563	3.64	0.112	0.880	1.1.1.38	NA
15	0.060	2ehhA	0.560	3.70	0.074	0.930	4.2.1.52	NA
16	0.060	3n7uA	0.559	3.26	0.024	0.840	1.2.1.2	32,45
17	0.060	2yxgA	0.558	3.86	0.125	0.960	4.2.1.52	NA
18	0.060	2nuwA	0.583	3.43	0.097	0.930	4.1.2.14	NA
19	0.060	1ygyA	0.577	2.91	0.145	0.830	1.1.1.95	13

(a)	Cscore^EC is the confidence score for the 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.

Gene Ontology (GO) terms

Rank	Cscore^GO	TM-score	RMSD^a	IDEN^a	Cov	PDB Hit	Associated GO Terms
Homologous GO templates in PDB
0	0.18	0.568	3.77	0.08	0.95	1xkyA	GO:0003824 GO:0005737 GO:0008152 GO:0008652 GO:0008840 GO:0009085 GO:0009089 GO:0016829 GO:0019877
1	0.18	0.577	3.58	0.09	0.94	3na8A	GO:0003824 GO:0008152 GO:0016829 GO:0046872
2	0.07	0.581	3.55	0.09	0.95	5c54A	GO:0003824 GO:0008152 GO:0008747 GO:0016829
3	0.07	0.579	3.56	0.12	0.95	5hwjA	GO:0003824 GO:0008152 GO:0016052 GO:0016829 GO:0019394 GO:0042838 GO:0047448
4	0.07	0.577	3.41	0.06	0.93	1xxxA	GO:0003824 GO:0005737 GO:0005886 GO:0008152 GO:0008652 GO:0008840 GO:0009085 GO:0009089 GO:0016829 GO:0019877 GO:0040007
5	0.07	0.600	3.45	0.08	0.92	1w37A	GO:0003824 GO:0005975 GO:0008152 GO:0008674 GO:0008675 GO:0016829
6	0.07	0.583	3.43	0.10	0.93	2nuwA	GO:0003824 GO:0005975 GO:0008152 GO:0008674 GO:0008675 GO:0016829
7	0.07	0.570	3.38	0.14	0.91	3g0sA	GO:0003824 GO:0005737 GO:0008152 GO:0008652 GO:0008840 GO:0009085 GO:0009089 GO:0016829 GO:0019877
8	0.07	0.571	3.68	0.08	0.95	3e96B	GO:0003824 GO:0008152 GO:0016829
9	0.07	0.579	3.52	0.09	0.93	4xkyD	GO:0003824 GO:0008152 GO:0016829
10	0.07	0.587	3.61	0.06	0.95	3cprA	GO:0003824 GO:0005737 GO:0008152 GO:0008652 GO:0008840 GO:0009085 GO:0009089 GO:0016829 GO:0019877
11	0.07	0.576	3.62	0.02	0.95	1f5zA	GO:0003824 GO:0005737 GO:0005975 GO:0008152 GO:0008747 GO:0016829
12	0.07	0.598	3.41	0.03	0.92	2r91A	GO:0003824 GO:0005975 GO:0008152 GO:0008675 GO:0016829 GO:0061677
13	0.07	0.597	3.54	0.09	0.93	3b4uB	GO:0003824 GO:0008152 GO:0016829
14	0.07	0.571	3.55	0.09	0.91	3d0cA	GO:0003824 GO:0008152 GO:0016829
15	0.07	0.580	3.60	0.07	0.95	5afdA	GO:0003824 GO:0005737 GO:0008152 GO:0008747 GO:0016829
16	0.07	0.558	3.88	0.12	0.97	4i7uB	GO:0003824 GO:0005737 GO:0008152 GO:0008652 GO:0008840 GO:0009085 GO:0009089 GO:0016829 GO:0019877
17	0.07	0.570	3.77	0.04	0.96	4amaC	GO:0003824 GO:0005737 GO:0005975 GO:0008152 GO:0008747 GO:0016829 GO:0019262
18	0.07	0.559	3.77	0.10	0.95	4icnA	GO:0003824 GO:0005737 GO:0008152 GO:0008652 GO:0008840 GO:0009085 GO:0009089 GO:0016829 GO:0019877

Consensus prediction of GO terms

Molecular Function	GO:0016836	GO:0043169
GO-Score	0.48	0.35
Biological Processes	GO:0046451	GO:0043650	GO:0009085
GO-Score	0.48	0.48	0.48
Cellular Component	GO:0044424
GO-Score	0.48

(a)	Cscore^GO is a combined measure for evaluating global and local similarity between query and template protein. It's range is [0-1] and higher values indicate more confident predictions.
(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.
(f)	The second table shows a consensus GO terms amongst the top scoring templates. The GO-Score associated with each prediction is defined as the average weight of the GO term, where the weights are assigned based on Cscore^GO of the template.

[Click on result.tar.bz2 to download the tarball file including all modelling results listed on this page]

Please cite the following articles when you use the I-TASSER server:
1.	J Yang, R Yan, A Roy, D Xu, J Poisson, Y Zhang. The I-TASSER Suite: Protein structure and function prediction. Nature Methods, 12: 7-8, 2015.
2.	J Yang, Y Zhang. I-TASSER server: new development for protein structure and function predictions, Nucleic Acids Research, 43: W174-W181, 2015.
3.	A Roy, A Kucukural, Y Zhang. I-TASSER: a unified platform for automated protein structure and function prediction. Nature Protocols, 5: 725-738, 2010.
4.	Y Zhang. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, 9: 40, 2008.