I-TASSER results

Input Sequence in FASTA format

>protein (99 residues)
MRTCVGCRKRGLAVELLRVVAVSTGNGNYAVIVDTATSLPGRGAWLHPLRQCAQQAIRRR
AFARALRIAGSPDTSAVVEYLESLGELEPPGNRTGSNRT

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MRTCVGCRKRGLAVELLRVVAVSTGNGNYAVIVDTATSLPGRGAWLHPLRQCAQQAIRRRAFARALRIAGSPDTSAVVEYLESLGELEPPGNRTGSNRT
Prediction	CCEEEHCCCCCCHHHCEEEEHCCCCCCCCEEEHCCCCCCCCCEEEEHCCHHHHHHHHHHCCHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCC
Conf.Score	976755588789766588998889998767997889999986799979999999999988577776687899999999999999877666555776679
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MRTCVGCRKRGLAVELLRVVAVSTGNGNYAVIVDTATSLPGRGAWLHPLRQCAQQAIRRRAFARALRIAGSPDTSAVVEYLESLGELEPPGNRTGSNRT
Prediction	734131245444473001001145465432021136353512002013436105303655204421635247415402520462376444674646658
	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

                   |                   |                   |                   |

Sec.Str
Seq

CCEEEHCCCCCCHHHCEEEEHCCCCCCCCEEEHCCCCCCCCCEEEEHCCHHHHHHHHHHCCHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCC
MRTCVGCRKRGLAVELLRVVAVSTGNGNYAVIVDTATSLPGRGAWLHPLRQCAQQAIRRRAFARALRIAGSPDTSAVVEYLESLGELEPPGNRTGSNRT

1g2rA

0.21

0.19

0.90

3.38

MUSTER

LRKSVVSNEVIDKRDLLRIVKNKEGQ----VFIDPTGKANGRGAYIKLDNAEALEAKKKKVFNRSFSMEVEESYDELIAYVDHKVKRRELGLE------

1g2rA

0.21

0.19

0.90

4.00

dPPAS

LRKSVVSNEVIDKRDLLRIVKNKEGQ----VFIDPTGKANGRGAYIKLDNAEALEAKKKKVFNRSFSMEVEESYDELIAYVDHKVKRRELGLE------

1g2rA

0.21

0.19

0.90

5.18

wdPPAS

LRKSVVSNEVIDKRDLLRIVKNKEGQ----VFIDPTGKANGRGAYIKLDNAEALEAKKKKVFNRSFSMEVEESYDELIAYVDHKVKRRELGLE------

1g2rA

0.21

0.19

0.90

4.30

wMUSTER

LRKSVVSNEVIDKRDLLRIVKNKEGQ----VFIDPTGKANGRGAYIKLDNAEALEAKKKKVFNRSFSMEVEESYDELIAYVDHKVKRRELGLE------

1g2rA

0.21

0.19

0.90

4.79

wPPAS

LRKSVVSNEVIDKRDLLRIVKNKEGQ----VFIDPTGKANGRGAYIKLDNAEALEAKKKKVFNRSFSMEVEESYDELIAYVDHKVKRRELG---LE---

1g2rA

0.21

0.19

0.90

9.80

dPPAS2

LRKSVVSNEVIDKRDLLRIVKNKEGQ----VFIDPTGKANGRGAYIKLDNAEALEAKKKKVFNRSFSMEVEESYDELIAYVDHKVKRRELGLE------

1g2rA

0.21

0.19

0.90

4.57

PPAS

LRKSVVSNEVIDKRDLLRIVKNKEGQ----VFIDPTGKANGRGAYIKLDNAEALEAKKKKVFNRSFSMEVEESYDELIAYVDHKVKRRELGLE------

1g2rA

0.21

0.19

0.90

3.99

Env-PPAS

LRKSVVSNEVIDKRDLLRIVKNKEGQ----VFIDPTGKANGRGAYIKLDNAEALEAKKKKVFNRSFSMEVEESYDELIAYVDHKVKRRELGLE------

1nq4A

0.13

0.11

0.87

0.83

MUSTER

-------MTLLTLSDLLTLLRECAGEEES---IDLGGDVEDVAF-LGYDSLALLNTVGR--IERDYGVQLGDDPRALIEMTNASLTGASPSAGGAARDK

2rp4A

0.14

0.10

0.72

0.90

dPPAS

----------------------DDSAAEWNVSRTPDGDY--RLAITCPNKEWLLQSIEGMIKEAAAEVLRNPNQENLRRHANKLLSLKKRAYELP----

(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 5 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=0.78

Estimated TM-score = 0.82±0.08

Estimated RMSD = 2.5±1.9Å

Download Model 2

C-score=-1.64

Download Model 3

C-score=-2.23

Download Model 4

C-score=-3.03

Download Model 5

C-score=-2.64

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	1g2rA	0.866	0.79	0.213	0.899
2	3gmeA	0.532	3.53	0.091	0.818
3	4aidA3	0.524	3.65	0.077	0.818
4	2fmlA2	0.523	3.77	0.060	0.828
5	2nn6C	0.521	3.94	0.068	0.828
6	4m5dA	0.521	4.16	0.111	0.849
7	2nn6A	0.520	4.20	0.099	0.869
8	2jssA	0.519	3.20	0.075	0.748
9	2v3qA	0.518	4.50	0.101	0.939
10	2br2P	0.514	3.80	0.114	0.818

(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	0.29	12	4up0A	ZN	Rep, Mult	4,7,47,52
2	0.12	5	3h1cR	III	Rep, Mult	45,47,53
3	0.09	2	1g2rA	SO4	Rep, Mult	2,18,43,45
4	0.02	1	1ibk4	III	Rep, Mult	15,72,76,83,85,86,87,88
5	0.02	1	1ibk9	III	Rep, Mult	18,19,44,46,56,57,58,59,60,61,62,63,70,74

	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	1e1yA	0.375	4.67	0.033	0.717	2.4.1.1	NA
2	0.060	1wdeA	0.477	4.04	0.102	0.798	2.1.1.98	5,69
3	0.060	2jg6A	0.482	3.62	0.081	0.727	3.2.2.20	NA
4	0.060	1r6lA	0.473	3.78	0.100	0.778	2.7.7.56	NA
5	0.060	1udoA	0.509	3.69	0.094	0.818	2.7.7.56	NA
6	0.060	3gpbA	0.423	4.42	0.120	0.798	2.4.1.1	NA
7	0.060	2wodA	0.503	3.71	0.058	0.758	3.2.2.24	64
8	0.060	2qllA	0.480	4.33	0.071	0.768	2.4.1.1	NA
9	0.060	1qi9B	0.483	4.27	0.057	0.818	1.11.1.10	NA
10	0.060	3cdjA	0.538	3.39	0.096	0.808	2.7.7.8	34
11	0.060	1s9cD	0.490	4.44	0.052	0.849	4.2.1.107	NA
12	0.060	1fa9A	0.376	4.74	0.065	0.727	2.4.1.1	NA
13	0.060	2pffB	0.476	4.42	0.082	0.849	2.3.1.86	25
14	0.060	1z1lA	0.333	4.42	0.020	0.626	3.1.4.17	NA
15	0.060	3fy4A	0.484	4.45	0.021	0.788	4.1.99.13	45
16	0.060	2a96B	0.480	4.03	0.063	0.768	3.1.3.2	47
17	0.060	2zuwC	0.486	3.98	0.067	0.768	2.4.1.211	NA
18	0.060	2nztA	0.466	3.99	0.100	0.727	2.7.1.1	NA
19	0.060	1dinA	0.474	4.07	0.107	0.849	3.1.1.45	7

(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	0.07	0.522	3.85	0.06	0.82	1e3pA	GO:0000175 GO:0000287 GO:0003676 GO:0003723 GO:0004654 GO:0005737 GO:0006396 GO:0006402 GO:0016740 GO:0016779 GO:0046872 GO:0090503
1	0.07	0.538	3.39	0.10	0.81	3cdjA	GO:0000175 GO:0000287 GO:0003676 GO:0003723 GO:0004654 GO:0005737 GO:0005829 GO:0006396 GO:0006402 GO:0009408 GO:0016020 GO:0016740 GO:0016779 GO:0035438 GO:0042802 GO:0046872 GO:0090503
2	0.07	0.514	3.80	0.11	0.82	2br2P	GO:0000175 GO:0000177 GO:0000178 GO:0004518 GO:0004527 GO:0005737 GO:0006401 GO:0016075 GO:0016787 GO:0016896 GO:0090305 GO:0090503
3	0.07	0.501	3.79	0.06	0.80	1oyrA	GO:0000049 GO:0004549 GO:0006364 GO:0008033 GO:0009022 GO:0016075 GO:0016740 GO:0016779 GO:0031125 GO:0090501
4	0.07	0.496	3.79	0.10	0.80	3dd6A	GO:0000049 GO:0004540 GO:0004549 GO:0008033 GO:0009022 GO:0016740 GO:0016779 GO:0090501
5	0.07	0.507	3.94	0.09	0.81	5c0wB	GO:0000176 GO:0000177 GO:0000178 GO:0000467 GO:0003723 GO:0005634 GO:0005730 GO:0005737 GO:0006364 GO:0016075 GO:0034427 GO:0034473 GO:0034475 GO:0034476 GO:0070478 GO:0070481 GO:0070651 GO:0071028 GO:0071038 GO:0071039 GO:0071042 GO:0071051
6	0.07	0.503	3.96	0.05	0.81	2pnzB	GO:0000178 GO:0005737 GO:0006401
7	0.07	0.524	3.65	0.08	0.82	4aidA	GO:0000175 GO:0000287 GO:0003676 GO:0003723 GO:0004654 GO:0005737 GO:0006396 GO:0006402 GO:0016740 GO:0016779 GO:0046872 GO:0090503
8	0.07	0.479	3.84	0.12	0.79	2nn6B	GO:0000175 GO:0000176 GO:0000177 GO:0000178 GO:0000460 GO:0000956 GO:0003723 GO:0004532 GO:0005634 GO:0005654 GO:0005730 GO:0005737 GO:0005829 GO:0006364 GO:0016075 GO:0017091 GO:0030307 GO:0031125 GO:0034427 GO:0034475 GO:0035327 GO:0043488 GO:0043928 GO:0045006 GO:0051607 GO:0071028 GO:0071044 GO:0071051 GO:0090503
9	0.07	0.531	3.50	0.11	0.82	3cdiA	GO:0000175 GO:0000287 GO:0003676 GO:0003723 GO:0004654 GO:0005737 GO:0005829 GO:0006396 GO:0006402 GO:0009408 GO:0016020 GO:0016740 GO:0016779 GO:0035438 GO:0042802 GO:0046872 GO:0090503
10	0.07	0.498	4.04	0.06	0.83	2nn6D	GO:0000175 GO:0000176 GO:0000177 GO:0000178 GO:0003723 GO:0004532 GO:0005634 GO:0005654 GO:0005730 GO:0005737 GO:0005829 GO:0006364 GO:0016075 GO:0031125 GO:0034427 GO:0034475 GO:0035327 GO:0043488 GO:0043928 GO:0045006 GO:0051607 GO:0071028 GO:0071051 GO:0090503
11	0.07	0.509	3.77	0.09	0.81	3krnA
12	0.07	0.508	3.67	0.10	0.82	1udnA	GO:0000049 GO:0004549 GO:0008033 GO:0009022 GO:0016075 GO:0016740 GO:0016779 GO:0090501
13	0.07	0.530	3.69	0.04	0.83	3u1kC	GO:0000175 GO:0000957 GO:0000958 GO:0000962 GO:0000964 GO:0000965 GO:0003676 GO:0003723 GO:0004518 GO:0004527 GO:0004654 GO:0005737 GO:0005739 GO:0005758 GO:0006396 GO:0006397 GO:0006401 GO:0006402 GO:0006810 GO:0008266 GO:0016020 GO:0016740 GO:0016779 GO:0016787 GO:0034046 GO:0034599 GO:0035198 GO:0035458 GO:0035927 GO:0035928 GO:0043457 GO:0043631 GO:0044822 GO:0045025 GO:0045926 GO:0051260 GO:0061014 GO:0070207 GO:0070584 GO:0071042 GO:0071850 GO:0090305 GO:0090503 GO:0097222 GO:2000627 GO:2000772
14	0.07	0.473	4.31	0.11	0.82	2wnrB	GO:0000175 GO:0000178 GO:0004518 GO:0004527 GO:0005737 GO:0006401 GO:0016787 GO:0016896 GO:0090305 GO:0090503
15	0.07	0.505	3.83	0.09	0.81	3hkmB	GO:0000176 GO:0000177 GO:0000178 GO:0003677 GO:0003690 GO:0003723 GO:0003727 GO:0004518 GO:0004527 GO:0004536 GO:0004540 GO:0005634 GO:0005730 GO:0006259 GO:0006364 GO:0016075 GO:0016787 GO:0031125 GO:0034427 GO:0034475 GO:0042802 GO:0071028 GO:0071051 GO:0090305 GO:0090501
16	0.07	0.506	3.85	0.10	0.81	3m85I	GO:0000178 GO:0005737 GO:0006401
17	0.07	0.496	3.82	0.07	0.80	2wp8B	GO:0000176 GO:0000177 GO:0000178 GO:0000467 GO:0003723 GO:0005634 GO:0005730 GO:0005737 GO:0006364 GO:0016075 GO:0034427 GO:0034473 GO:0034475 GO:0034476 GO:0070478 GO:0070481 GO:0070651 GO:0071028 GO:0071038 GO:0071039 GO:0071042 GO:0071051
18	0.07	0.476	4.05	0.03	0.81	2pnzA	GO:0000175 GO:0000178 GO:0004518 GO:0004527 GO:0005737 GO:0006401 GO:0016787 GO:0016896 GO:0090305 GO:0090503

Consensus prediction of GO terms

Molecular Function	GO:0016772	GO:0016896	GO:0008408
GO-Score	0.48	0.37	0.37
Biological Processes	GO:0090501
GO-Score	0.37
Cellular Component	GO:0044424
GO-Score	0.37

(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.

I-TASSER results for job id Rv2840c

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

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