I-TASSER results

Input Sequence in FASTA format

>protein (59 residues)
MGILDKVKNLLSQNADKVETVINKAGEFVDEQTQGNYSDAIHKLHDAASNVVGMSDQQS

Predicted Secondary Structure

Sequence	20 40 \| \| MGILDKVKNLLSQNADKVETVINKAGEFVDEQTQGNYSDAIHKLHDAASNVVGMSDQQS
Prediction	CCHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCCCC
Conf.Score	98899999999977899999999999999998799657778999999999978999999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 \| \| MGILDKVKNLLSQNADKVETVINKAGEFVDEQTQGNYSDAIHKLHDAASNVVGMSDQQS
Prediction	64335404621763563045015401531375264424741451353047327587878
	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

                   |                   |

Sec.Str
Seq

CCHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCCCC
MGILDKVKNLLSQNADKVETVINKAGEFVDEQTQGNYSDAIHKLHDAASNVVGMSDQQS

4tqlA

0.14

0.98

0.84

MUSTER

EKLLEKLKQIMQEAKQKMEKLLKQLKEEMKKMKE-KMEKLLKEMKQRMEEVKKKMDDEL

2n8oA

0.14

0.12

0.86

1.01

dPPAS

MSWLNFLKYIAKYGKKAVSAAWKYKGKVLEWLNVGP---TLEWVWQKLKKIAGL-----

2n8oA

0.14

0.12

0.86

1.16

wdPPAS

MSWLNFLKYIAKYGKKAVSAAWKYKGKVLEWLNVGP---TLEWVWQKLKKIAGL-----

4uicA7

0.15

0.14

0.90

1.18

wMUSTER

M-KAREAQDAVKANLDKAKAALDQVNQYVSKVTDA-FKAELQKAAQDAKAAYEAA----

2n8oA

0.14

0.12

0.86

1.13

wPPAS

MSWLNFLKYIAKYGKKAVSAAWKYKGKVLEWLNVGP---TLEWVWQKLKKIAGL-----

2n8oA

0.14

0.12

0.86

1.46

dPPAS2

MSWLNFLKYIAKYGKKAVSAAWKYKGKVLEWLNVGP---TLEWVWQKLKKIAGL-----

2n8oA

0.14

0.12

0.86

1.19

PPAS

MSWLNFLKYIAKYGKKAVSAAWKYKGKVLEWLNVGP---TLEWVWQKLKKIAGL-----

1pgyA

0.19

0.15

0.80

1.04

Env-PPAS

-ALVDEVKDMEIARLMSLGLSIEEATEFYENDV--TYERYLEILKSKQKE---------

4tqlA1

0.14

0.98

0.69

MUSTER

IELLEKLKQIMQEAKQKMEKLLKQLKEEMKKMKE-KMEKLLKEMKQRMEEVKKKMDDEL

4uicA7

0.15

0.14

0.92

0.95

dPPAS

MKAREAQDAVKAGNLDKAKAALDQVNQYVSKVTDA-FKAELQKAAQDAKAAYEAA----

(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=-0.76

Estimated TM-score = 0.62±0.14

Estimated RMSD = 4.4±2.9Å

Download Model 2

C-score=-1.81

Download Model 3

C-score=-3.99

Download Model 4

C-score=-4.48

Download Model 5

C-score=-4.57

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	4wzxA	0.828	1.41	0.085	1.000
2	1oxzA	0.824	1.36	0.119	1.000
3	3e1qL	0.810	2.14	0.051	1.000
4	1wrdA	0.804	1.62	0.085	1.000
5	1yd8G	0.801	1.41	0.190	0.983
6	4hwdD	0.800	1.22	0.143	0.949
7	1tkpA	0.799	2.05	0.068	1.000
8	1sofA	0.796	2.19	0.051	1.000
9	1jgcA	0.794	2.22	0.102	1.000
10	2vxxB	0.793	2.21	0.051	1.000

(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	0.25	177	3is7K	HEM	Rep, Mult	19,22,23,26,42,46,49,50,52,53
2	0.06	41	3wqjA	22B	Rep, Mult	23,26,29,30,38,41,42,45,46
3	0.05	42	4pj0I	CLA	Rep, Mult	44,45,47,48,51,52
4	0.05	35	3wmmB	CRT	Rep, Mult	36,37,40,41,44
5	0.04	31	3m4oA	C7P	Rep, Mult	43,44,47
6	0.03	22	3nozX	PLL	Rep, Mult	29,38,42,45
7	0.03	21	4qpqF	NUC	Rep, Mult	36,37,38,39
8	0.03	24	2rccB	ZN	Rep, Mult	18,48,51
9	0.03	22	1gwgA	IOD	Rep, Mult	33,34,35,38
10	0.02	14	5i50B	NUC	Rep, Mult	41,44,45,48
11	0.01	5	3is7A	HEM	Rep, Mult	7,8,11,15,19,22,23
12	0.01	11	3kbkA	HG	Rep, Mult	21,25,44,48
13	0.00	2	1hvvA	TAR	Rep, Mult	26,29,30
14	0.00	3	1tkoB	FE	Rep, Mult	30,34
15	0.00	2	3j000	PEV	Rep, Mult	23,27
16	0.00	1	3k2sB	POV	Rep, Mult	1,4

	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	0.184	1cxzB	0.706	2.06	0.056	0.848	2.7.11.13	22,24
2	0.167	1urfA	0.641	1.65	0.051	0.797	2.7.11.13	21
3	0.145	1fyjA	0.584	1.78	0.130	0.746	6.1.1.15,6.1.1.17	26,40
4	0.136	3eabA	0.668	1.91	0.070	0.966	3.6.4.3	11
5	0.131	2jpnA	0.593	2.17	0.151	0.898	3.6.4.12	13,19,29,47
6	0.129	1r1bA	0.537	2.48	0.104	0.814	6.1.1.15,6.1.1.17	18
7	0.067	3c90A	0.700	2.15	0.068	0.881	3.6.1.31	25,29
8	0.066	1yxbG	0.645	1.96	0.055	0.797	3.6.1.31	18,24
9	0.060	1o9iA	0.740	2.44	0.068	1.000	1.11.1.6	NA
10	0.060	2a7wK	0.672	1.87	0.054	0.814	3.6.1.31	NA
11	0.060	1vp7B	0.708	2.03	0.056	0.881	3.1.11.6	38
12	0.060	1f7uA	0.717	2.20	0.138	0.983	6.1.1.19	8
13	0.060	1y0vD	0.733	2.28	0.121	0.983	4.6.1.1	NA
14	0.060	2v8tA	0.731	2.29	0.085	1.000	1.11.1.6	NA
15	0.060	1hn0A	0.734	2.10	0.034	1.000	4.2.2.20	NA
16	0.060	3iayA	0.702	2.36	0.103	0.966	2.7.7.7	NA
17	0.060	3e6sF	0.702	2.57	0.051	0.983	1.16.3.1	NA
18	0.060	2htnG	0.803	2.18	0.051	1.000	1.16.3.1	4
19	0.060	1yq3A	0.704	2.00	0.035	0.966	1.3.5.1	NA
20	0.060	1eumE	0.707	2.84	0.034	1.000	1.16.3.1	24
21	0.060	2epoA	0.716	1.94	0.088	0.966	3.2.1.52	NA
22	0.060	2ct8A	0.694	2.40	0.068	1.000	6.1.1.10	5
23	0.060	2fbnA	0.765	1.80	0.070	0.966	5.2.1.8	8,16
24	0.060	3es3A	0.729	2.42	0.102	0.983	1.16.3.1	NA
25	0.060	1r76A	0.700	2.31	0.103	0.983	4.2.2.2	NA
26	0.060	1r03A	0.732	2.36	0.051	0.983	1.16.3.1	11
27	0.060	2f4eA	0.327	3.43	0.074	0.644	5.2.1.8	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	0.33	0.559	2.87	0.09	0.97	1jigA	GO:0005737 GO:0006879 GO:0006950 GO:0008199 GO:0016491 GO:0016722 GO:0046872 GO:0055114
1	0.27	0.781	2.29	0.09	1.00	3gvyB	GO:0004322 GO:0005623 GO:0006826 GO:0006879 GO:0008199 GO:0046872 GO:0055114
2	0.25	0.803	2.19	0.05	1.00	1bcfA	GO:0004322 GO:0005506 GO:0005829 GO:0005886 GO:0006826 GO:0006879 GO:0006880 GO:0008199 GO:0016020 GO:0016491 GO:0020037 GO:0042802 GO:0046872 GO:0055114
3	0.25	0.828	1.41	0.09	1.00	4wzxA	GO:0000166 GO:0000407 GO:0004672 GO:0004674 GO:0005524 GO:0005737 GO:0006468 GO:0006914 GO:0016301 GO:0016310 GO:0016740 GO:0045879 GO:0045880 GO:0046777 GO:0090398 GO:0097542
4	0.25	0.737	1.89	0.05	1.00	2cptA	GO:0000166 GO:0000920 GO:0000922 GO:0005524 GO:0005634 GO:0005737 GO:0005768 GO:0005813 GO:0005829 GO:0006810 GO:0006813 GO:0006914 GO:0006997 GO:0007032 GO:0007033 GO:0007049 GO:0007080 GO:0008022 GO:0008568 GO:0010008 GO:0010824 GO:0010971 GO:0015031 GO:0016020 GO:0016197 GO:0016787 GO:0016887 GO:0019058 GO:0019076 GO:0030301 GO:0031122 GO:0031902 GO:0032510 GO:0033993 GO:0036258 GO:0039702 GO:0042623 GO:0042802 GO:0042803 GO:0043162 GO:0048524 GO:0050792 GO:0051261 GO:0051301 GO:0060548 GO:0061738 GO:0070062 GO:0090543 GO:0090611 GO:1901673 GO:1902188 GO:1903542 GO:1903543 GO:1903724 GO:1903902 GO:1904903
5	0.25	0.679	1.80	0.06	0.76	4djgA	GO:0003779 GO:0005737 GO:0005856 GO:0007015 GO:0010119
6	0.23	0.786	2.19	0.05	1.00	3bknA	GO:0004322 GO:0005623 GO:0006826 GO:0006879 GO:0008199 GO:0046872 GO:0055114
7	0.21	0.694	1.28	0.02	0.78	1z0jB	GO:0000011 GO:0005768 GO:0005829 GO:0005886 GO:0006810 GO:0006895 GO:0006896 GO:0006897 GO:0007596 GO:0008270 GO:0010008 GO:0010009 GO:0015031 GO:0016020 GO:0016197 GO:0017137 GO:0031901 GO:0034058 GO:0034498 GO:0043231 GO:0046872 GO:0070062 GO:0090160 GO:1903358
8	0.20	0.559	2.63	0.09	0.97	2wtlA	GO:0004322 GO:0005576 GO:0005829 GO:0005886 GO:0006826 GO:0006879 GO:0008199 GO:0010039 GO:0016491 GO:0033214 GO:0046872 GO:0055114
9	0.18	0.795	2.19	0.05	1.00	2fkzA	GO:0004322 GO:0005623 GO:0006826 GO:0006879 GO:0008199 GO:0016491 GO:0046872 GO:0055114
10	0.18	0.712	1.34	0.04	0.80	1u7mA
11	0.18	0.674	1.16	0.06	0.73	1ec5A
12	0.17	0.783	2.28	0.07	1.00	3fvbA	GO:0004322 GO:0005623 GO:0006826 GO:0006879 GO:0008199 GO:0046872 GO:0055114
13	0.15	0.824	1.36	0.12	1.00	1oxzA	GO:0005622 GO:0005654 GO:0005768 GO:0005794 GO:0006810 GO:0006886 GO:0010008 GO:0015031 GO:0016020 GO:0016192 GO:0030131 GO:0043231 GO:0044267 GO:0045732 GO:1901998
14	0.15	0.794	2.22	0.10	1.00	1jgcA	GO:0004322 GO:0005623 GO:0006826 GO:0006879 GO:0008199 GO:0016491 GO:0046872 GO:0055114
15	0.15	0.736	2.42	0.09	0.97	1nf6F	GO:0004322 GO:0005623 GO:0006826 GO:0006879 GO:0006880 GO:0008199 GO:0016491 GO:0046872 GO:0055114
16	0.13	0.678	1.43	0.00	0.80	3r2hA	GO:0004322 GO:0005623 GO:0006826 GO:0006879 GO:0006880 GO:0008199 GO:0016491 GO:0046872 GO:0055114
17	0.13	0.698	2.45	0.09	1.00	2hz8A
18	0.13	0.775	2.21	0.07	1.00	4am2A	GO:0004322 GO:0005623 GO:0006826 GO:0006879 GO:0008199 GO:0016491 GO:0046872 GO:0055114
19	0.13	0.613	1.53	0.04	0.73	1u7jA
20	0.12	0.806	2.18	0.09	1.00	4e6kA	GO:0004322 GO:0005623 GO:0006826 GO:0006879 GO:0006880 GO:0008199 GO:0046872 GO:0055114
21	0.12	0.558	3.20	0.09	0.97	4ll8A	GO:0000146 GO:0000166 GO:0003774 GO:0003779 GO:0005516 GO:0005524 GO:0005933 GO:0005934 GO:0006810 GO:0007533 GO:0008298 GO:0016459 GO:0031941 GO:0048309 GO:0051015 GO:0051028
22	0.11	0.801	1.41	0.19	0.98	1yd8G	GO:0005622 GO:0005768 GO:0005794 GO:0005802 GO:0006810 GO:0006886 GO:0010008 GO:0015031 GO:0016020 GO:0016192 GO:0030131 GO:0030306 GO:0044267 GO:0045732
23	0.11	0.804	1.62	0.09	1.00	1wrdA	GO:0005622 GO:0005737 GO:0005768 GO:0005769 GO:0005829 GO:0006810 GO:0006886 GO:0006897 GO:0015031 GO:0016020 GO:0016197 GO:0030276 GO:0070062

Consensus prediction of GO terms

Molecular Function	GO:0008199	GO:0046906	GO:0016773	GO:0042623	GO:0046983	GO:0004322	GO:0042802	GO:0005524
GO-Score	0.63	0.50	0.50	0.49	0.49	0.45	0.44	0.43
Biological Processes	GO:0055114	GO:0006464	GO:0006796	GO:0009967	GO:0008589	GO:0033554	GO:0009968	GO:0007569	GO:0051651	GO:0097577	GO:0051301	GO:0046755	GO:0010941	GO:0006511	GO:0045921	GO:0008333	GO:1901992	GO:1903541	GO:0000070	GO:0090169	GO:1903902	GO:0051310	GO:0015918	GO:1902186	GO:0043624	GO:0036257	GO:0032509	GO:0010389	GO:0045184	GO:1903722	GO:0046601	GO:1902751	GO:0007088	GO:0015672	GO:0090307	GO:1904896	GO:0010033	GO:0045920	GO:0006826	GO:0006914
GO-Score	0.63	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.49	0.49	0.49	0.49	0.49	0.49	0.49	0.49	0.49	0.49	0.49	0.49	0.49	0.49	0.49	0.49	0.49	0.49	0.49	0.49	0.49	0.49	0.49	0.49	0.49	0.49	0.49	0.49	0.45	0.43
Cellular Component	GO:0071944	GO:0044441	GO:0030496	GO:0010008	GO:0005819	GO:0031988	GO:0005770	GO:1903561	GO:0005815	GO:0005829
GO-Score	0.50	0.50	0.49	0.49	0.49	0.49	0.49	0.49	0.49	0.44

(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 Rv0909

[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]