I-TASSER results

Input Sequence in FASTA format

>protein (89 residues)
MIGDQDSIAAVLNRLRRAQGQLAGVISMIEQGRDCRDVVTQLAAVSRALDRAGFKIVAAG
LKECVSGATASGAAPLSAAELEKLFLALA

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MIGDQDSIAAVLNRLRRAQGQLAGVISMIEQGRDCRDVVTQLAAVSRALDRAGFKIVAAGLKECVSGATASGAAPLSAAELEKLFLALA
Prediction	CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHC
Conf.Score	99998999999999999999999999999979995999999999999999999999999999999888875875899999999999979
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MIGDQDSIAAVLNRLRRAQGQLAGVISMIEQGRDCRDVVTQLAAVSRALDRAGFKIVAAGLKECVSGATASGAAPLSAAELEKLFLALA
Prediction	87445742650251044043215204401667540430030132034005401430044105400552376864653253035016528
	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

CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHC
MIGDQDSIAAVLNRLRRAQGQLAGVISMIEQGRDCRDVVTQLAAVSRALDRAGFKIVAAGLKECVSGATASGAAPLSAAELEKLFLALA

4m1pA

0.29

1.00

2.83

MUSTER

IPRTKEEIENIMKRLKRIEGQVRGVQKMVEDNRYCIDILVQISAIQAALRQVGMQLLERHANHCVAKAIREGSGEQSLRELMDVIKQFA

4m1pA

0.29

1.00

3.26

dPPAS

IPRTKEEIENIMKRLKRIEGQVRGVQKMVEDNRYCIDILVQISAIQAALRQVGMQLLERHANHCVAKAIREGSGEQSLRELMDVIKQFA

4m1pA

0.29

1.00

4.23

wdPPAS

IPRTKEEIENIMKRLKRIEGQVRGVQKMVEDNRYCIDILVQISAIQAALRQVGMQLLERHANHCVAKAIREGSGEQSLRELMDVIKQFA

4m1pA

0.29

1.00

3.27

wMUSTER

IPRTKEEIENIMKRLKRIEGQVRGVQKMVEDNRYCIDILVQISAIQAALRQVGMQLLERHANHCVAKAIREGSGEQSLRELMDVIKQFA

4m1pA

0.29

1.00

4.04

wPPAS

IPRTKEEIENIMKRLKRIEGQVRGVQKMVEDNRYCIDILVQISAIQAALRQVGMQLLERHANHCVAKAIREGSGEQSLRELMDVIKQFA

4m1pA

0.29

1.00

7.59

dPPAS2

IPRTKEEIENIMKRLKRIEGQVRGVQKMVEDNRYCIDILVQISAIQAALRQVGMQLLERHANHCVAKAIREGSGEQSLRELMDVIKQFA

4m1pA

0.29

1.00

3.34

PPAS

IPRTKEEIENIMKRLKRIEGQVRGVQKMVEDNRYCIDILVQISAIQAALRQVGMQLLERHANHCVAKAIREGSGEQSLRELMDVIKQFA

4m1pA

0.29

1.00

5.74

Env-PPAS

IPRTKEEIENIMKRLKRIEGQVRGVQKMVEDNRYCIDILVQISAIQAALRQVGMQLLERHANHCVAKAIREGSGEQSLRELMDVIKQFA

5lcyA

0.24

0.98

2.67

MUSTER

-PHSPEDKKRILTRVRRIRGQVEALERALESGEPCLAILQQIAAVRGASNGLMSEMVEIHLKDHLVSGETTPDRAVRMAEIGHLLRAY-

4adzA

0.29

0.28

0.97

2.98

dPPAS

---YHKQKAEHLKRLRRIEGQIRGLQRMVDEDVYCIDILTQVSASTKALQSFALQLLEEHLRHCVADAALKGGIDAKVEEATKAIGRLL

(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 1 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=1.40

Estimated TM-score = 0.91±0.06

Estimated RMSD = 1.2±1.2Å

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	4m1pA	0.924	1.07	0.292	1.000
2	4adzA	0.893	1.05	0.271	0.955
3	5lcyA	0.865	1.61	0.241	0.978
4	2hh7A	0.819	1.75	0.306	0.955
5	1ciiA	0.768	2.25	0.080	0.978
6	3rh3A	0.739	2.29	0.058	0.966
7	3ayfA	0.738	2.60	0.067	1.000
8	3ieeA	0.733	2.10	0.048	0.933
9	4dvyP	0.724	2.30	0.080	0.966
10	4d8mA	0.721	2.52	0.035	0.910

(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	0.38	168	2htnA	HEM	Rep, Mult	15,18,19,22,42,46,49,50,52,53
2	0.07	40	4zttF	O	Rep, Mult	14,17,48,51
3	0.06	30	3ri5D	IVM	Rep, Mult	22,25,29,38,41,42,45,49
4	0.03	15	2zg7X	PLL	Rep, Mult	25,38,42
5	0.03	15	5e1uA	RIR	Rep, Mult	26,29,35,38,39,42
6	0.02	9	1brrB	ARC	Rep, Mult	6,7,10,14,47,48,51
7	0.02	11	3kbkA	HG	Rep, Mult	17,21,44,48
8	0.02	10	4d2eB	78N	Rep, Mult	56,60,61,64
9	0.01	8	4h44A	CLA	Rep, Mult	22,25,26,29,38,45,49
10	0.01	5	1lghE	BCL	Rep, Mult	41,44,45,48
11	0.00	1	2uxuA	NAR	Rep, Mult	8,11,25,57,81,89
12	0.00	1	1g6uA	TFA	Rep, Mult	7,8,9
13	0.00	1	1xrpA	III	Rep, Mult	41,48,76,79,80,85
14	0.00	1	2vz2B	C15	Rep, Mult	50,51,54
15	0.00	2	2fmm9	III	Rep, Mult	3,4,5,6,11,12,15,17,18,24,25,28,29
16	0.00	1	2wm2A	CL	Rep, Mult	8,12,15,57
17	0.00	2	2hgu3	III	Rep, Mult	32,33,34,38,39,40,43

	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	0.181	1urfA	0.603	2.54	0.068	0.786	2.7.11.13	15,19
2	0.123	1fyjA	0.480	1.45	0.115	0.539	6.1.1.15,6.1.1.17	38
3	0.117	1vp7B	0.542	1.82	0.027	0.652	3.1.11.6	22
4	0.082	3cxhQ	0.532	2.64	0.063	0.697	1.10.2.2	45
5	0.067	1wcrA	0.643	1.98	0.075	0.753	2.7.1.69	NA
6	0.066	1a91A	0.541	2.60	0.118	0.764	3.6.3.14	NA
7	0.066	2w5jA	0.518	2.41	0.095	0.708	3.6.3.14	NA
8	0.066	1wu0A	0.467	2.52	0.103	0.629	3.6.3.14	NA
9	0.060	3no9A	0.665	2.51	0.096	0.933	4.2.1.2	NA
10	0.060	2fonB	0.637	3.29	0.057	0.966	1.3.3.6	NA
11	0.060	3csmA	0.664	3.02	0.080	0.899	5.4.99.5	NA
12	0.060	1ynnJ	0.398	3.68	0.012	0.618	2.7.7.6	38
13	0.060	1ynnD	0.616	2.57	0.068	0.786	2.7.7.6	NA
14	0.060	2zr3B	0.629	2.78	0.011	0.832	6.1.1.11	20
15	0.060	1csmA	0.668	2.87	0.080	0.888	5.4.99.5	NA
16	0.060	2vumA	0.709	3.16	0.067	0.944	2.7.7.6	NA
17	0.060	1dcnB	0.627	2.66	0.072	0.888	4.3.2.1	NA
18	0.060	1p49A	0.631	2.45	0.047	0.798	3.1.6.2	NA
19	0.060	2e9fB	0.670	2.64	0.110	0.921	4.3.2.1	NA
20	0.060	1yfmA	0.665	2.92	0.129	0.955	4.2.1.2	NA
21	0.060	1uzrB	0.670	3.01	0.071	0.955	1.17.4.1	NA
22	0.060	2fenD	0.654	3.38	0.148	0.944	5.5.1.2	NA
23	0.060	1i0aA	0.635	2.60	0.084	0.888	4.3.2.1	NA
24	0.060	3gtdA	0.650	3.37	0.102	0.989	4.2.1.2	NA
25	0.060	3gzhA	0.633	3.07	0.070	0.876	4.3.2.2	NA
26	0.060	1kkcX	0.642	3.34	0.057	0.978	1.15.1.1	27,34
27	0.060	3hm8A	0.634	3.35	0.057	0.921	2.7.1.1	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	0.54	0.907	1.15	0.29	0.98	4uigA	GO:0003677 GO:0006355 GO:0046872
1	0.47	0.924	1.07	0.29	1.00	4m1pA	GO:0003677 GO:0006355 GO:0046872
2	0.45	0.747	1.46	0.33	0.87	3aaiA	GO:0003677 GO:0006355 GO:0046872
3	0.33	0.819	1.75	0.31	0.96	2hh7A	GO:0003677 GO:0005507 GO:0005737 GO:0005886 GO:0006351 GO:0006355 GO:0010272 GO:0046688 GO:0046872 GO:0097077
4	0.20	0.768	2.25	0.08	0.98	1ciiA	GO:0005886 GO:0016020 GO:0016021 GO:0019835 GO:0042742 GO:0050829
5	0.20	0.612	2.41	0.04	0.79	3layJ	GO:0008270 GO:0042597
6	0.16	0.542	2.82	0.10	0.79	3k9aA
7	0.15	0.588	1.51	0.07	0.67	3p30A
8	0.08	0.407	1.79	0.01	0.46	4jppD	GO:0016032 GO:0019012 GO:0019028 GO:0046718
9	0.08	0.563	2.75	0.03	0.78	3wfvA	GO:0005198 GO:0016020 GO:0016021 GO:0016032 GO:0019012 GO:0019031 GO:0019062 GO:0020002 GO:0033644 GO:0039663 GO:0044174 GO:0044175 GO:0046718 GO:0055036
10	0.07	0.587	2.30	0.00	0.76	1s94B	GO:0000149 GO:0005484 GO:0005622 GO:0006886 GO:0016020 GO:0016021 GO:0016192 GO:0017157 GO:0061025
11	0.07	0.509	3.73	0.07	0.83	1a87A	GO:0005886 GO:0016020 GO:0016021 GO:0019835 GO:0042742 GO:0050829
12	0.07	0.454	3.18	0.01	0.66	1rh1A	GO:0005886 GO:0009405 GO:0016020 GO:0016021 GO:0019835 GO:0042742 GO:0050829
13	0.07	0.461	3.57	0.01	0.71	3eyjB	GO:0016020 GO:0016021 GO:0016032 GO:0019012 GO:0019031 GO:0019062 GO:0019064 GO:0019065 GO:0020002 GO:0033644 GO:0039654 GO:0039663 GO:0046718 GO:0046789 GO:0055036 GO:0075509 GO:0075512
14	0.07	0.416	4.74	0.07	0.84	3fewX	GO:0016020 GO:0016021 GO:0019835 GO:0050829
15	0.07	0.471	3.56	0.06	0.75	1ha0A	GO:0016020 GO:0016021 GO:0016032 GO:0019012 GO:0019031 GO:0019062 GO:0019064 GO:0019065 GO:0020002 GO:0033644 GO:0039654 GO:0039663 GO:0046718 GO:0046789 GO:0055036 GO:0075509 GO:0075512
16	0.07	0.478	3.69	0.06	0.72	4we8A	GO:0016020 GO:0016021 GO:0016032 GO:0019012 GO:0019031 GO:0019062 GO:0019064 GO:0019065 GO:0020002 GO:0033644 GO:0039654 GO:0039663 GO:0046718 GO:0046789 GO:0055036 GO:0075509 GO:0075512
17	0.07	0.413	4.39	0.03	0.78	4ggvA	GO:0004497 GO:0005506 GO:0016491 GO:0016705 GO:0020037 GO:0046872 GO:0055114
18	0.06	0.477	3.56	0.07	0.76	1u2zC	GO:0000077 GO:0000725 GO:0000781 GO:0003677 GO:0005634 GO:0006281 GO:0006289 GO:0006301 GO:0006348 GO:0006351 GO:0006355 GO:0008168 GO:0016568 GO:0016740 GO:0018024 GO:0031151 GO:0031493 GO:0031573 GO:0032259 GO:0034729 GO:0044783 GO:0051598 GO:0051726 GO:0070911
19	0.06	0.398	1.89	0.09	0.46	3tnuB	GO:0005198 GO:0005200 GO:0005634 GO:0005737 GO:0005739 GO:0005829 GO:0005882 GO:0005886 GO:0008544 GO:0016020 GO:0031581 GO:0045095 GO:0070062 GO:0097110
20	0.06	0.398	3.04	0.04	0.54	3pzlB	GO:0016787 GO:0016813 GO:0046872
21	0.06	0.377	4.47	0.03	0.71	1m7sA	GO:0004096 GO:0004601 GO:0006979 GO:0016491 GO:0020037 GO:0042597 GO:0042744 GO:0046872 GO:0055114 GO:0098869

Consensus prediction of GO terms

Molecular Function	GO:0003677	GO:0097077
GO-Score	0.91	0.33
Biological Processes	GO:0006355	GO:0042742	GO:0010272	GO:0046688
GO-Score	0.91	0.40	0.33	0.33
Cellular Component	GO:0005886	GO:0005737	GO:0031224
GO-Score	0.46	0.33	0.32

(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 Rv1766

[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]