I-TASSER results

Input Sequence in FASTA format

>protein (61 residues)
MSLVSVAPELVVTAVPDVARIGSSIGAPDTAAAARPTTSVLAAGADEVSADVVALFGWVA
R

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| MSLVSVAPELVVTAVPDVARIGSSIGAPDTAAAARPTTSVLAAGADEVSADVVALFGWVAR
Prediction	CCEEEHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCC
Conf.Score	9677644689999999988999999999998755555555467664899999999998689
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| MSLVSVAPELVVTAVPDVARIGSSIGAPDTAAAARPTTSVLAAGADEVSADVVALFGWVAR
Prediction	7433433243133114314413432443343223442341343343310321043235458
	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

                   |                   |                   |

Sec.Str
Seq

CCEEEHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCC
MSLVSVAPELVVTAVPDVARIGSSIGAPDTAAAARPTTSVLAAGADEVSADVVALFGWVAR

2g38C

0.30

0.26

0.87

0.95

MUSTER

-------PEALTVAATEVRRIRDRAIQSDAQVAPMTTA-VRPPAADLVSEKAATFLVEYAR

2g38C

0.30

0.26

0.87

0.89

dPPAS

-------PEALTVAATEVRRIRDRAIQSDAQVAPMTTA-VRPPAADLVSEKAATFLVEYAR

2g38C

0.30

0.26

0.87

1.93

wdPPAS

-------PEALTVAATEVRRIRDRAIQSDAQVAPMTTA-VRPPAADLVSEKAATFLVEYAR

2g38C

0.30

0.26

0.87

1.23

wMUSTER

-------PEALTVAATEVRRIRDRAIQSDAQVAPMTTA-VRPPAADLVSEKAATFLVEYAR

2g38C

0.30

0.26

0.87

1.65

wPPAS

-------PEALTVAATEVRRIRDRAIQSDAQVAPMTTA-VRPPAADLVSEKAATFLVEYAR

2g38C

0.30

0.26

0.87

1.50

dPPAS2

-------PEALTVAATEVRRIRDRAIQSDAQVAPMTTA-VRPPAADLVSEKAATFLVEYAR

2g38C

0.30

0.26

0.87

1.07

PPAS

-------PEALTVAATEVRRIRDRAIQSDAQVAPMTTA-VRPPAADLVSEKAATFLVEYAR

2b3tA1

0.12

0.11

0.93

1.30

Env-PPAS

MEY----QHWLREAISQLQASESPRRDAEILLEHVTRTFILAFGETQLTDEQCQQLDALLT

4yxxA1

0.13

0.11

0.85

0.93

MUSTER

-----VSLEQALKILKVAAELGTTVEEAVKRALKLKTKL----VSLEQALKILEVAAELGT

4eijA

0.17

0.16

0.95

0.81

dPPAS

---VISANEIMDLLRGMDARLQHLEQKVDKVLAQGSMVTQIKNELSTVKTTLATIEGMMAT

(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=-0.79

Estimated TM-score = 0.61±0.14

Estimated RMSD = 4.5±3.0Å

Download Model 2

C-score=-2.57

Download Model 3

C-score=-3.64

Download Model 4

C-score=-2.88

Download Model 5

C-score=-5.00

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	2j69A	0.768	1.84	0.066	1.000
2	1dlcA	0.761	1.61	0.034	0.967
3	3zrwA	0.758	1.79	0.034	0.902
4	1f5nA2	0.757	1.86	0.034	0.934
5	5azoA	0.755	1.72	0.067	0.902
6	3kb9A	0.752	2.30	0.082	0.967
7	5h3wA	0.749	1.65	0.051	0.902
8	3eb7A	0.746	1.58	0.017	0.967
9	5j65A1	0.736	2.02	0.066	1.000
10	3ggzD	0.735	1.38	0.073	0.869

(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	0.09	70	2q7rA	3CS	Rep, Mult	18,19,21,22,23,25
2	0.09	72	4uxzC	79M	Rep, Mult	29,32,33,36
3	0.08	65	5lsjG	III	Rep, Mult	12,13,16,17,19
4	0.08	66	4y281	CLA	Rep, Mult	13,16,17,20,21
5	0.06	48	4tt3G	III	Rep, Mult	27,28,31,32,35
6	0.05	43	1hjbA	NUC	Rep, Mult	7,8,11,12,14,15,18
7	0.04	34	1sumB	FE	Rep, Mult	23,24,27
8	0.03	26	2bbhA	DMU	Rep, Mult	11,15,18,19,22
9	0.03	21	4rdaB	SGN	Rep, Mult	33,34,37
10	0.02	21	1jnmA	NUC	Rep, Mult	7,8,11,15
11	0.01	8	4tt0B	IOD	Rep, Mult	4,6,11,14
12	0.00	1	1ujw1	III	Rep, Mult	40,42,43,44,51,52,53,54,55,57,58,60
13	0.00	1	2xqsA	CVM	Rep, Mult	48,52,55
14	0.00	1	2g380	III	Rep, Mult	10,17,21,24,28,32,36,38,40,41,42,43,44,45,46,47,48,49,52,55,56,59,60
15	0.00	1	2x2vA	DPV	Rep, Mult	43,47
16	0.00	1	2wieC	CVM	Rep, Mult	2,3

	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	0.223	2jwaA	0.511	1.87	0.048	0.639	2.7.10.1	26
2	0.172	3e7kH	0.570	2.43	0.080	0.705	2.7.11.1	18
3	0.164	1qleD	0.494	1.12	0.025	0.557	1.9.3.1	20
4	0.159	1xtcC	0.518	1.67	0.000	0.639	2.4.2.36	18,20
5	0.118	1wt6B	0.579	2.14	0.085	0.689	2.7.11.1	NA
6	0.113	3brvC	0.478	2.20	0.024	0.607	2.7.11.10	NA
7	0.102	1k1fA	0.579	2.02	0.045	0.721	2.7.11.1	61
8	0.067	2w5jA	0.606	2.04	0.038	0.869	3.6.3.14	NA
9	0.060	3kb9A	0.752	2.30	0.082	0.967	4.2.3.37	NA
10	0.060	2pfmA	0.680	2.20	0.033	0.902	4.3.2.2	NA
11	0.060	2iukB	0.643	2.61	0.051	0.967	1.13.11.12	NA
12	0.060	1i0aA	0.681	2.16	0.067	0.902	4.3.2.1	NA
13	0.060	1x75B	0.477	2.89	0.091	0.705	5.99.1.3	32,55
14	0.060	1f1oA	0.660	2.27	0.017	0.902	4.3.2.2	NA
15	0.060	2p0mB	0.671	2.43	0.069	0.951	1.13.11.33	NA
16	0.060	1no3A	0.679	2.32	0.033	0.984	1.13.11.12	NA
17	0.060	1y2mB	0.660	2.41	0.034	0.951	4.3.1.24	NA
18	0.060	3i39X	0.664	2.02	0.098	0.869	1.2.99.2	40,53,55
19	0.060	3f9mA	0.670	2.20	0.038	0.836	2.7.1.2	NA
20	0.060	1tj7A	0.687	2.18	0.033	0.902	4.3.2.1	NA
21	0.060	1b8fA	0.668	2.44	0.053	0.934	4.3.1.3	NA
22	0.060	2p0mA	0.663	2.48	0.069	0.951	1.13.11.33	NA
23	0.060	1dofA	0.672	2.29	0.050	0.902	4.3.2.2	NA
24	0.060	1k62B	0.693	2.13	0.067	0.902	4.3.2.1	NA
25	0.060	2zr3B	0.669	2.09	0.070	0.853	6.1.1.11	30,54
26	0.060	2iukA	0.683	2.35	0.033	0.984	1.13.11.12	NA
27	0.060	1c3cA	0.722	2.09	0.033	0.902	4.3.2.2	NA

(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	0.14	0.589	1.98	0.00	0.70	2x7rC	GO:0002223 GO:0005198 GO:0016020 GO:0016021 GO:0016032 GO:0019012 GO:0019031 GO:0019062 GO:0019064 GO:0019082 GO:0020002 GO:0030683 GO:0033644 GO:0039654 GO:0039663 GO:0044174 GO:0044175 GO:0046718 GO:0055036 GO:0075509 GO:0075512
1	0.14	0.589	1.60	0.12	0.67	2ocyA	GO:0005085 GO:0005829 GO:0005934 GO:0005935 GO:0006810 GO:0006887 GO:0006914 GO:0015031 GO:0030133 GO:0031410 GO:0043547 GO:0070273
2	0.11	0.624	2.29	0.14	0.82	2j68A	GO:0000166 GO:0003924 GO:0005525 GO:0005886 GO:0008289 GO:0016020 GO:0016021 GO:0016787
3	0.10	0.648	2.67	0.05	0.89	4aurA	GO:0005525
4	0.09	0.597	1.88	0.04	0.70	3vp9B	GO:0000122 GO:0000123 GO:0000433 GO:0001191 GO:0001198 GO:0005634 GO:0006351 GO:0006355 GO:0007070 GO:0008023 GO:0016584 GO:0017053 GO:0033588 GO:0035955 GO:0036033 GO:0042393 GO:0042826 GO:0043486 GO:0080025 GO:2000217 GO:2000531 GO:2001020
5	0.09	0.761	1.61	0.03	0.97	1dlcA	GO:0005102 GO:0006952 GO:0009405 GO:0030435
6	0.08	0.661	1.80	0.08	0.90	3l4qC	GO:0001678 GO:0005634 GO:0005925 GO:0005942 GO:0006810 GO:0007165 GO:0008134 GO:0008286 GO:0010506 GO:0014065 GO:0015031 GO:0016303 GO:0030833 GO:0032869 GO:0034976 GO:0035014 GO:0036092 GO:0036312 GO:0042993 GO:0043551 GO:0045785 GO:0045944 GO:0046854 GO:0046935 GO:0046982 GO:0051492 GO:0090003 GO:2001275
7	0.07	0.718	1.97	0.02	0.95	4moaA	GO:0005102 GO:0006952 GO:0009405 GO:0030435
8	0.07	0.570	2.72	0.03	0.72	3vp8B	GO:0000122 GO:0000123 GO:0000433 GO:0001191 GO:0001198 GO:0005634 GO:0006351 GO:0006355 GO:0007070 GO:0008023 GO:0016584 GO:0017053 GO:0033588 GO:0035955 GO:0036033 GO:0042393 GO:0042826 GO:0043486 GO:0080025 GO:2000217 GO:2000531 GO:2001020
9	0.07	0.679	2.24	0.03	0.97	4d8mA	GO:0009405 GO:0030435
10	0.07	0.657	2.00	0.06	0.90	1i5pA	GO:0005102 GO:0006952 GO:0009405 GO:0030435
11	0.07	0.729	1.66	0.07	0.97	1ciyA	GO:0005102 GO:0006952 GO:0009405 GO:0030435
12	0.07	0.733	1.63	0.07	0.97	4w8jA	GO:0005102 GO:0006952 GO:0009405 GO:0030435
13	0.07	0.746	1.58	0.02	0.97	3eb7A	GO:0005102 GO:0006952 GO:0009405 GO:0030435
14	0.07	0.537	3.15	0.08	0.97	3w6nB	GO:0000166 GO:0000266 GO:0001836 GO:0003374 GO:0003924 GO:0005525 GO:0005737 GO:0005739 GO:0005741 GO:0005777 GO:0005794 GO:0005829 GO:0005874 GO:0005903 GO:0005905 GO:0006897 GO:0006921 GO:0008289 GO:0010821 GO:0012501 GO:0012505 GO:0015630 GO:0016020 GO:0016559 GO:0016787 GO:0030054 GO:0030672 GO:0031410 GO:0031625 GO:0032459 GO:0042802 GO:0042803 GO:0043065 GO:0043231 GO:0043234 GO:0043653 GO:0045202 GO:0048471 GO:0050714 GO:0051289 GO:0060047 GO:0061025 GO:0070266 GO:0070584 GO:0070585 GO:0090141 GO:0090149 GO:0090200 GO:1900063 GO:1903146 GO:1903578 GO:2001244
15	0.07	0.734	1.70	0.05	0.97	1ji6A	GO:0005102 GO:0006952 GO:0009405 GO:0030435
16	0.07	0.492	3.13	0.03	0.80	2v57B	GO:0003677 GO:0006351 GO:0006355
17	0.07	0.702	2.07	0.12	0.98	3x0uA	GO:0009405
18	0.07	0.613	2.65	0.02	0.92	2c9kA	GO:0005102 GO:0006952 GO:0009405 GO:0030435
19	0.07	0.484	3.30	0.07	0.87	4h1uA	GO:0000166 GO:0000266 GO:0001836 GO:0003374 GO:0003924 GO:0005525 GO:0005737 GO:0005739 GO:0005741 GO:0005777 GO:0005794 GO:0005829 GO:0005874 GO:0005903 GO:0005905 GO:0006897 GO:0006921 GO:0008289 GO:0010821 GO:0012501 GO:0012505 GO:0015630 GO:0016020 GO:0016559 GO:0016787 GO:0030054 GO:0030672 GO:0031410 GO:0031625 GO:0032459 GO:0042802 GO:0042803 GO:0043065 GO:0043231 GO:0043234 GO:0043653 GO:0045202 GO:0048471 GO:0050714 GO:0051289 GO:0060047 GO:0061025 GO:0070266 GO:0070584 GO:0070585 GO:0090141 GO:0090149 GO:0090200 GO:1900063 GO:1903146 GO:1903578 GO:2001244

Consensus prediction of GO terms

Molecular Function	GO:0035639	GO:0032550	GO:0032561
GO-Score	0.39	0.39	0.39
Biological Processes	GO:0075512	GO:0019064	GO:0002223	GO:0019082	GO:0019062	GO:0030683	GO:0039654	GO:0006914	GO:0043547	GO:0006887	GO:0015031	GO:0001198	GO:0000433	GO:0007070	GO:0043486	GO:2000531	GO:2000217	GO:2001020	GO:0035955	GO:0016584
GO-Score	0.14	0.14	0.14	0.14	0.14	0.14	0.14	0.14	0.14	0.14	0.14	0.09	0.09	0.09	0.09	0.09	0.09	0.09	0.09	0.09
Cellular Component	GO:0031224
GO-Score	0.38

(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 Rv2371

[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]