I-TASSER results

Input Sequence in FASTA format

>protein (91 residues)
MSVENSQIREPPPLPPVLLEVWPVIAVGALAWLVAAVAAFVVPGLASWRPVTVAGLATGL
LGTTIFVWQLAAARRGARGAQAGLETYLDPK

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MSVENSQIREPPPLPPVLLEVWPVIAVGALAWLVAAVAAFVVPGLASWRPVTVAGLATGLLGTTIFVWQLAAARRGARGAQAGLETYLDPK
Prediction	CCCCCCCCCCCCCCCHHHCCCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHCCCCCCCCC
Conf.Score	9988877899998886776898746689999999999999738876467645678889999999999999999987767877545667889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MSVENSQIREPPPLPPVLLEVWPVIAVGALAWLVAAVAAFVVPGLASWRPVTVAGLATGLLGTTIFVWQLAAARRGARGAQAGLETYLDPK
Prediction	7555677446346125314733210011232333123111103444332100230331133332123113312433453145415554678
	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

CCCCCCCCCCCCCCCHHHCCCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHCCCCCCCCC
MSVENSQIREPPPLPPVLLEVWPVIAVGALAWLVAAVAAFVVPGLASWRPVTVAGLATGLLGTTIFVWQLAAARRGARGAQAGLETYLDPK

5d92D2

0.18

0.14

0.79

1.15

wMUSTER

SLNKGLFAAIFLPIARLLWGVSPVTVVGTLGVMAGALIFYPMGQ-------LFWGTVVITVFVFSDIIDGLMARLLFRE------------

5jhfA

0.15

0.11

0.74

0.95

wPPAS

MNSENTIV-RVAGRARNFVDPLKFLERDRSLWSSVSKLD-------------WKRLSREF--PEHFIRKRSYALF-AKHLKL-LE------

5d92D2

0.16

0.12

0.76

1.35

dPPAS2

---SGSLNKYARGLFAAIFLPSPVTVVGTLGVMAGALIFYPMGQL------FWGTVVITVFVFSDIIDGLMARLLFRE-------------

5d92D2

0.17

0.13

0.76

1.01

PPAS

---SGSLNKYARGLFAAIFLPSPVTVVGTLGVMAGALIFYPMGQ-------LFWGTVVITVFVFSDIIDGLMARLLFRE------------

4yzfA2

0.15

0.12

0.80

1.02

wMUSTER

LFKPPKYH---PDVPYVKRVKTWRMHLFTGIQIICLAVLWVVKSTP-------ASLALPFVLILTVPLRRVLLPL-----NVELQ-CLD--

2mmuA

0.12

0.07

0.55

0.95

wPPAS

--------------SVWFV---SLFIGLMLIGLIWLMVFQLLGPWN-----YAIAFAFMITGLLLTMRWH-------------LE------

2mmuA

0.08

0.04

0.55

1.34

dPPAS2

--------------SVWFV---SLFIGLMLIGLIWLMVFQLLGPWN-----YAIAFAFMITGLLLTMRWHLE-------------------

5d92D2

0.15

0.11

0.71

0.95

wPPAS

SLNKYAR-----GLFAAIFLP-PVTVVGTLGVMAGALIFYPMGQ-------LFWGTVVITVFVFSDIIDGLMARLFRE-------------

2mp8A

0.14

0.09

0.65

1.20

dPPAS2

-------------------------LTANLSYAAKKVIDIINTGSAVATIIALVTAVVGLITAGIVATAKSLIKKYGAKYAAAW-------

1spfA

0.28

0.10

0.35

1.15

dPPAS2

--------LRIPCCPKRLL----VVVVVVVLVVVVIVGALLMGL-----------------------------------------------

(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=-2.00

Estimated TM-score = 0.48±0.15

Estimated RMSD = 8.0±4.4Å

Download Model 2

C-score=-3.62

Download Model 3

C-score=-2.54

Download Model 4

C-score=-5.00

Download Model 5

C-score=-3.41

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	5d92D	0.669	2.58	0.071	0.923
2	4o6mA	0.656	2.68	0.118	0.934
3	4xhjA	0.624	3.02	0.072	0.912
4	1o5hA	0.623	3.05	0.125	0.879
5	2bkpA1	0.623	2.54	0.095	0.813
6	5cwmA	0.621	2.80	0.080	0.824
7	3eb7A	0.620	2.77	0.090	0.835
8	1ciyA	0.617	2.33	0.067	0.813
9	4hnwA	0.617	2.77	0.033	0.857
10	1dlcA1	0.616	3.31	0.012	0.945

(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	0.11	6	2vxiA	HEM	Rep, Mult	33,36,37,40,52,56,59,60,62,66
2	0.06	3	1vctA	NA	Rep, Mult	69,79,83,84
3	0.06	3	5c65B	37X	Rep, Mult	17,27,58,61
4	0.06	3	4ryoA	MPG	Rep, Mult	34,51,58
5	0.04	2	3dhhB	BML	Rep, Mult	26,29,83,84,87
6	0.04	2	2o014	CLA	Rep, Mult	61,66,69
7	0.02	1	4il6x	CLA	Rep, Mult	59,60
8	0.02	1	2wscB	CLA	Rep, Mult	25,28,32,33
9	0.02	1	1xm2B	SO4	Rep, Mult	20,52,53,54,55,56,59,60
10	0.02	1	1q0kA	THJ	Rep, Mult	31,58,61
11	0.02	1	3ic3D	BGC	Rep, Mult	74,78
12	0.02	1	1q90M	BCR	Rep, Mult	52,56
13	0.02	1	4fe1B	CLA	Rep, Mult	22,23
14	0.02	1	2wilA	UUU	Rep, Mult	2,5

	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	0.117	1cxzB	0.480	2.84	0.029	0.637	2.7.11.13	39
2	0.060	1hxgA	0.603	2.89	0.105	0.835	4.2.3.9,4.1.99.7	NA
3	0.060	1rx0A	0.568	3.56	0.022	0.901	1.3.99.-	NA
4	0.060	1fziA	0.614	3.29	0.057	0.835	1.14.13.25	NA
5	0.060	1biqB	0.574	3.90	0.068	0.912	1.17.4.1	NA
6	0.060	3g61A	0.571	3.18	0.045	0.813	3.6.3.44	NA
7	0.060	2cqsA	0.559	3.25	0.115	0.857	2.4.1.20	NA
8	0.060	2pfdB	0.606	3.45	0.056	0.912	2.1.2.5,4.3.1.4	76
9	0.060	1ca1A	0.585	3.29	0.078	0.901	3.1.4.3	NA
10	0.060	1l2aE	0.584	3.40	0.072	0.901	3.2.1.4	NA
11	0.060	2uw1B	0.595	3.74	0.067	0.945	1.14.99.6	NA
12	0.060	2o36A	0.575	2.97	0.068	0.813	3.4.24.15	55
13	0.060	1mhyD	0.594	3.70	0.044	0.923	1.14.13.25	NA
14	0.060	2vuxB	0.588	3.56	0.103	0.901	1.17.4.1	NA
15	0.060	2jg0A	0.571	3.39	0.080	0.868	3.2.1.28	NA
16	0.060	3im1A	0.572	3.45	0.012	0.879	3.6.4.13	NA
17	0.060	3hf1B	0.568	3.98	0.100	0.956	1.17.4.1	NA
18	0.060	1jkuA	0.568	3.65	0.033	0.824	1.11.1.6	NA
19	0.060	3n2oA	0.581	3.72	0.061	0.879	4.1.1.19	87
20	0.060	1siqA	0.564	3.79	0.033	0.956	1.3.99.7	31

(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	0.10	0.663	2.66	0.06	0.92	5d92B	GO:0000166 GO:0008654 GO:0016020 GO:0016021 GO:0016740 GO:0016780 GO:0046872
1	0.09	0.590	2.96	0.02	0.90	4o6mB	GO:0000166 GO:0008654 GO:0016020 GO:0016021 GO:0016740 GO:0016780 GO:0046872
2	0.09	0.610	2.47	0.08	0.78	1t72A	GO:0005315 GO:0005436 GO:0005737 GO:0005886 GO:0006810 GO:0006817 GO:0010629 GO:0015321 GO:0030643 GO:0035435 GO:0035725 GO:0042803 GO:0044341 GO:0045936 GO:0055085 GO:2000186
3	0.09	0.642	3.03	0.09	0.91	1o5hA	GO:0003824 GO:0016829 GO:0030412 GO:0044237
4	0.08	0.623	2.54	0.10	0.81	2bkpA	GO:0006813 GO:0008324 GO:0098655
5	0.07	0.598	2.77	0.04	0.82	4mndA	GO:0003824 GO:0008152 GO:0008654 GO:0016020 GO:0016021 GO:0016740 GO:0016779 GO:0016780 GO:0046872
6	0.07	0.585	3.27	0.14	0.89	3phf1	GO:0016020 GO:0016021 GO:0019012 GO:0019031 GO:0019064 GO:0020002 GO:0033644 GO:0039663 GO:0046718 GO:0055036
7	0.07	0.624	3.02	0.07	0.91	4xhjA	GO:0016020 GO:0016021 GO:0019012 GO:0019031 GO:0019064 GO:0020002 GO:0033644 GO:0039663 GO:0044174 GO:0044175 GO:0046718 GO:0055036
8	0.07	0.591	2.90	0.15	0.86	2xqyA	GO:0016020 GO:0016021 GO:0019012 GO:0019031 GO:0019064 GO:0020002 GO:0033644 GO:0039663 GO:0046718 GO:0055036
9	0.07	0.473	3.18	0.05	0.70	2pfdA	GO:0000139 GO:0003824 GO:0005542 GO:0005737 GO:0005783 GO:0005793 GO:0005794 GO:0005814 GO:0005829 GO:0005856 GO:0006547 GO:0007010 GO:0008017 GO:0008152 GO:0016740 GO:0016829 GO:0019215 GO:0019556 GO:0019557 GO:0030407 GO:0030409 GO:0030412 GO:0030868 GO:0035999 GO:0044237 GO:0070062
10	0.07	0.529	3.46	0.06	0.79	4uvkA	GO:0000755 GO:0003682 GO:0005634 GO:0005829 GO:0006473 GO:0007064 GO:0009847 GO:0031505 GO:0031618 GO:0031934 GO:0034990 GO:1990707
11	0.07	0.589	3.27	0.09	0.89	3m1cA	GO:0016020 GO:0016021 GO:0019012 GO:0019031 GO:0019064 GO:0020002 GO:0033644 GO:0039663 GO:0044174 GO:0044175 GO:0046718 GO:0055036
12	0.07	0.480	3.90	0.06	0.76	3at7A
13	0.07	0.453	3.14	0.01	0.66	4k3vB	GO:0006810 GO:0007155 GO:0030001 GO:0046872
14	0.06	0.407	4.32	0.03	0.74	3r4iA	GO:0003824 GO:0008815 GO:0016829 GO:0046872
15	0.06	0.485	2.66	0.10	0.65	1rhgB	GO:0005125 GO:0005130 GO:0005576 GO:0005615 GO:0006955 GO:0007275 GO:0008083 GO:0008284 GO:0014068 GO:0019221 GO:0019899 GO:0030838 GO:0030851 GO:0032092 GO:0033138 GO:0042993 GO:0045639 GO:0045944 GO:0050731 GO:0051897 GO:0071222 GO:0071345 GO:1901215 GO:2000251
16	0.06	0.350	3.93	0.09	0.64	3wwpA	GO:0016829 GO:0046872
17	0.06	0.408	2.32	0.04	0.54	2y4uA	GO:0004860 GO:0005737 GO:0005783 GO:0005788 GO:0005790 GO:0005829 GO:0006417 GO:0006986 GO:0016020 GO:0019901 GO:0031205 GO:0036494 GO:0036498 GO:0043066 GO:0051087 GO:0051603 GO:0051607 GO:0051787 GO:0070062 GO:0070417 GO:1903561 GO:1903912 GO:1904030
18	0.06	0.555	3.47	0.06	0.78	2ah6B

Consensus prediction of GO terms

Molecular Function	GO:0036094	GO:1901265	GO:0043169	GO:0016772
GO-Score	0.37	0.37	0.37	0.37
Biological Processes	GO:0090407	GO:0006644	GO:0044249	GO:0008610
GO-Score	0.37	0.37	0.37	0.37
Cellular Component	GO:0016021	GO:0005737	GO:0005886
GO-Score	0.18	0.09	0.09

(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 Rv0879c

[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]