I-TASSER results

I-TASSER results for job id Rv3541c

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

Input Sequence in FASTA format

>protein (129 residues)
MTVVGAVLPELKLYGDPTFIVSTALATRDFQDVHHDRDKAVAQGSKDIFVNILTDTGLVQ
RYVTDWAGPSALIKSIGLRLGVPWYAYDTVTFSGEVTAVNDGLITVKVVGRNTLGDHVTA
TVELSMRDS

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MTVVGAVLPELKLYGDPTFIVSTALATRDFQDVHHDRDKAVAQGSKDIFVNILTDTGLVQRYVTDWAGPSALIKSIGLRLGVPWYAYDTVTFSGEVTAVNDGLITVKVVGRNTLGDHVTATVELSMRDS
Prediction	CCCCCCCCCCEEEHCCHHHHHHHHHHHCCCCCCCCCHHHHHHHCCCCCEHCHHHHHHHHHHHHHHCCCCCEEEEEEEEEHCCCCCCCEEEEEEEEEEEEHCCEEEEEEEEEHCCCCEEEEEEEEEHCCC
Conf.Score	999986567678878999999999777899987689999998699997555568999999999985899748999999986788999899999999999899999999999689958999999997799
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MTVVGAVLPELKLYGDPTFIVSTALATRDFQDVHHDRDKAVAQGSKDIFVNILTDTGLVQRYVTDWAGPSALIKSIGLRLGVPWYAYDTVTFSGEVTAVNDGLITVKVVGRNTLGDHVTATVELSMRDS
Prediction	643345524636341445203300211423110020451056362642100112110200210252234512034140413220304130203030343565302030204256443020303030478
	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                 100                 120

                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCEEEHCCHHHHHHHHHHHCCCCCCCCCHHHHHHHCCCCCEHCHHHHHHHHHHHHHHCCCCCEEEEEEEEEHCCCCCCCEEEEEEEEEEEEHCCEEEEEEEEEHCCCCEEEEEEEEEHCCC
MTVVGAVLPELKLYGDPTFIVSTALATRDFQDVHHDRDKAVAQGSKDIFVNILTDTGLVQRYVTDWAGPSALIKSIGLRLGVPWYAYDTVTFSGEVTAVNDGLITVKVVGRNTLGDHVTATVELSMRDS

4w78B

1.00

0.98

4.53

MUSTER

MTVVGAVLPELKLYGDPTFIVSTALATRDFQDVHHDRDKAVAQGSKDIFVNILTDTGLVQRYVTDWAGPSALIKSIGLRLGVPWYAYDTVTFSGEVTAVNDGLITVKVVGRNTLGDHVTATVELSM---

4w78B

1.00

0.98

6.83

dPPAS

MTVVGAVLPELKLYGDPTFIVSTALATRDFQDVHHDRDKAVAQGSKDIFVNILTDTGLVQRYVTDWAGPSALIKSIGLRLGVPWYAYDTVTFSGEVTAVNDGLITVKVVGRNTLGDHVTATVELSM---

4w78B

1.00

0.98

6.17

wdPPAS

MTVVGAVLPELKLYGDPTFIVSTALATRDFQDVHHDRDKAVAQGSKDIFVNILTDTGLVQRYVTDWAGPSALIKSIGLRLGVPWYAYDTVTFSGEVTAVNDGLITVKVVGRNTLGDHVTATVELSM---

4w78B

1.00

0.97

5.62

wMUSTER

-TVVGAVLPELKLYGDPTFIVSTALATRDFQDVHHDRDKAVAQGSKDIFVNILTDTGLVQRYVTDWAGPSALIKSIGLRLGVPWYAYDTVTFSGEVTAVNDGLITVKVVGRNTLGDHVTATVELSM---

4w78B

1.00

0.98

5.55

wPPAS

MTVVGAVLPELKLYGDPTFIVSTALATRDFQDVHHDRDKAVAQGSKDIFVNILTDTGLVQRYVTDWAGPSALIKSIGLRLGVPWYAYDTVTFSGEVTAVNDGLITVKVVGRNTLGDHVTATVELSM---

4w78B

1.00

0.98

8.25

dPPAS2

MTVVGAVLPELKLYGDPTFIVSTALATRDFQDVHHDRDKAVAQGSKDIFVNILTDTGLVQRYVTDWAGPSALIKSIGLRLGVPWYAYDTVTFSGEVTAVNDGLITVKVVGRNTLGDHVTATVELSM---

4w78B

1.00

0.98

5.41

PPAS

MTVVGAVLPELKLYGDPTFIVSTALATRDFQDVHHDRDKAVAQGSKDIFVNILTDTGLVQRYVTDWAGPSALIKSIGLRLGVPWYAYDTVTFSGEVTAVNDGLITVKVVGRNTLGDHVTATVELSM---

4w78B

1.00

0.98

4.94

Env-PPAS

MTVVGAVLPELKLYGDPTFIVSTALATRDFQDVHHDRDKAVAQGSKDIFVNILTDTGLVQRYVTDWAGPSALIKSIGLRLGVPWYAYDTVTFSGEVTAVNDGLITVKVVGRNTLGDHVTATVELSM---

4rv2B

0.23

0.99

3.50

MUSTER

LRKVGDTLPERVITLTRGDLVNYAGVSGDLNPIHWDDEIAKQVGLDTAIAHGMLTMGLGGGYVTSWVGDPAAVTEYNVRFTAVVPVGAEITFNGRVKSVDAKLVTIAISATAG-GKKIFGRAVATARLA

1iq6B

0.20

0.19

0.98

5.04

dPPAS

SLEVGQKA-RLSKRFGAAEVAAFAALSEDFNPLHLDPAFAATTAFERPIVHGMLLASLFSGLLGQQPGKGSIYLGQSLSFKLPVFVGDEVTAEVEVTALRKPIATLTTRIFTQGGAAVTGEAVVKLP--

(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=1.98

Estimated TM-score = 0.99±0.04

Estimated RMSD = 0.8±0.8Å

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	4w78B	0.965	0.48	1.000	0.977
2	4rv2B	0.889	1.53	0.228	0.985
3	5cpgA	0.888	1.54	0.172	0.992
4	4v12A2	0.884	1.58	0.213	0.985
5	1iq6B	0.875	1.53	0.190	0.977
6	3k67A	0.847	1.84	0.200	0.969
7	4e3eA1	0.842	1.97	0.141	0.992
8	2bi0A1	0.840	1.93	0.118	0.985
9	4rljA	0.835	2.19	0.156	0.992
10	1q6wC	0.835	2.30	0.211	0.992

(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	0.22	8	4wnbB	4BN	Rep, Mult	31,43,52,80,81
2	0.09	5	1vpmB	COA	Rep, Mult	50,52,79,80,82,83,117
3	0.07	4	1wn3A	HXC	Rep, Mult	60,64,71,72,73,74,125
4	0.05	3	3kvuC	ACO	Rep, Mult	60,72,73,103,124,125
5	0.04	2	2q78B	MLC	Rep, Mult	79,116
6	0.04	2	2b3m0	III	Rep, Mult	11,13,17,18,19,22,23,25,26,27,28,29,30,31,35,39,53,54,56,57,58,60,61,64,65,70,71,72,73,74,75,76,77,78,79,80,127
7	0.03	2	3kvzF	ENV	Rep, Mult	25,30,49,51,52,53
8	0.02	1	3f5oB	UUU	Rep, Mult	51,78,79,80,81
9	0.02	1	2f410	III	Rep, Mult	51,53,56,57,73,74,75,76,77,78,79,80
10	0.02	1	1vpmA	COA	Rep, Mult	73,74,75,100,101,102,103,123,125
11	0.02	1	3f5oA	UUU	Rep, Mult	98,100,101,102,103,105

	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	0.401	1iq6B	0.875	1.53	0.190	0.977	4.2.1.17	29,34
2	0.194	2qq2C	0.696	2.23	0.124	0.806	3.1.2.2	91,93
3	0.185	2v1oE	0.651	1.91	0.126	0.736	3.1.2.2	93,95,97,121
4	0.180	1tbuB	0.601	2.35	0.063	0.698	3.1.2.2	54,91,119
5	0.151	1lo8A	0.671	1.97	0.070	0.775	3.1.2.23	91
6	0.067	1u1zB	0.662	2.77	0.073	0.830	4.2.1.-	NA
7	0.067	1z6bA	0.647	2.61	0.085	0.814	4.2.1.-	NA
8	0.067	1mkaA	0.647	2.96	0.090	0.845	4.2.1.60	50
9	0.060	2jfdA	0.345	5.42	0.071	0.682	2.3.1.85	28,58
10	0.060	3khpC	0.768	2.27	0.167	0.907	1.-.-.-	29,34,48
11	0.060	2pffB	0.774	2.42	0.080	0.946	2.3.1.86	15,57
12	0.060	3ir3A	0.754	2.60	0.202	0.915	4.2.1.-	NA
13	0.060	2vz8B	0.592	2.65	0.048	0.744	2.3.1.85	92
14	0.060	2hx5A	0.623	2.41	0.081	0.760	3.1.2.-	73
15	0.060	3el6A	0.578	3.15	0.047	0.798	4.2.1.61	22
16	0.060	2ortA	0.467	4.43	0.034	0.798	1.14.13.39	NA
17	0.060	3e7gC	0.494	4.56	0.072	0.837	1.14.13.39	NA
18	0.060	2vz9B	0.592	2.79	0.047	0.752	2.3.1.85	34
19	0.060	2aeyA	0.506	3.67	0.042	0.744	3.2.1.80	NA
20	0.060	2gllA	0.664	2.51	0.083	0.822	4.2.1.-	NA
21	0.060	1y7uA	0.666	2.41	0.127	0.791	3.1.2.20	67,122
22	0.060	3kvnX	0.492	3.78	0.066	0.698	3.1.1.1	52
23	0.060	2vkzG	0.816	2.24	0.141	0.977	2.3.1.38,3.1.2.14	NA
24	0.060	3khpA	0.753	2.41	0.139	0.922	1.-.-.-	29,34
25	0.060	3b7kC	0.660	1.74	0.118	0.744	3.1.2.1	NA
26	0.060	2vz8A	0.591	2.88	0.047	0.760	2.3.1.85	34
27	0.060	2cf2C	0.648	2.94	0.090	0.845	2.3.1.85	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	0.32	0.835	2.30	0.21	0.99	1q6wC
1	0.32	0.875	1.53	0.19	0.98	1iq6B	GO:0004312 GO:0005835 GO:0006629 GO:0006631 GO:0006633 GO:0016829 GO:0055114
2	0.31	0.888	1.54	0.17	0.99	5cpgA	GO:0004312 GO:0005835 GO:0006633 GO:0016829 GO:0055114
3	0.29	0.829	2.10	0.17	0.98	2c2iA	GO:0004300 GO:0006629 GO:0006631 GO:0006633 GO:0016829 GO:0018812
4	0.28	0.843	2.07	0.15	1.00	4rltA	GO:0005886 GO:0019171 GO:0040007
5	0.28	0.810	2.37	0.19	0.98	4ffuI	GO:0016491 GO:0055114
6	0.26	0.847	1.84	0.20	0.97	3k67A	GO:0004312 GO:0005835 GO:0006633 GO:0055114
7	0.25	0.754	2.60	0.20	0.91	3ir3A	GO:0005730 GO:0005737 GO:0005739 GO:0006629 GO:0006631 GO:0016829
8	0.25	0.765	2.14	0.17	0.89	1s9cD	GO:0000038 GO:0001649 GO:0003857 GO:0005102 GO:0005739 GO:0005777 GO:0005778 GO:0005782 GO:0006629 GO:0006631 GO:0006635 GO:0006699 GO:0008209 GO:0008210 GO:0016020 GO:0016491 GO:0016508 GO:0016616 GO:0016829 GO:0016853 GO:0033540 GO:0033989 GO:0036109 GO:0036111 GO:0036112 GO:0042803 GO:0043231 GO:0044594 GO:0055114 GO:0060009
9	0.21	0.662	2.77	0.07	0.83	1u1zB	GO:0005737 GO:0006629 GO:0006633 GO:0009245 GO:0016829 GO:0016836 GO:0019171 GO:0047451
10	0.16	0.728	2.14	0.17	0.84	4oobA	GO:0004312 GO:0005835 GO:0005886 GO:0006631 GO:0006633 GO:0018812 GO:0019171 GO:0055114
11	0.16	0.770	1.88	0.12	0.88	1pn4D	GO:0003824 GO:0005777 GO:0006629 GO:0006631 GO:0006635 GO:0008152 GO:0016491 GO:0016616 GO:0016829 GO:0016853 GO:0055114
12	0.15	0.758	1.86	0.12	0.87	1pn4C	GO:0003824 GO:0005777 GO:0006629 GO:0006631 GO:0006635 GO:0008152 GO:0016491 GO:0016616 GO:0016829 GO:0016853 GO:0055114
13	0.15	0.787	2.18	0.16	0.92	3kh8A
14	0.15	0.770	2.12	0.18	0.89	1s9cG	GO:0000038 GO:0001649 GO:0003857 GO:0005102 GO:0005739 GO:0005777 GO:0005778 GO:0005782 GO:0006629 GO:0006631 GO:0006635 GO:0006699 GO:0008209 GO:0008210 GO:0016020 GO:0016491 GO:0016508 GO:0016616 GO:0016829 GO:0016853 GO:0033540 GO:0033989 GO:0036109 GO:0036111 GO:0036112 GO:0042803 GO:0043231 GO:0044594 GO:0055114 GO:0060009
15	0.15	0.767	2.16	0.19	0.89	3omlA	GO:0003824 GO:0004300 GO:0005777 GO:0006629 GO:0006631 GO:0006635 GO:0008152 GO:0016491 GO:0016616 GO:0016829 GO:0033540 GO:0042803 GO:0055114 GO:0080023
16	0.14	0.768	2.27	0.17	0.91	3khpC
17	0.14	0.753	2.41	0.14	0.92	3khpA
18	0.06	0.301	4.74	0.06	0.54	1kzqA	GO:0016020 GO:0020003
19	0.06	0.274	4.79	0.09	0.48	4mxmA	GO:0003677 GO:0006351 GO:0006355

Consensus prediction of GO terms

Molecular Function	GO:0016836	GO:0004312
GO-Score	0.58	0.53
Biological Processes	GO:0006633	GO:0055114
GO-Score	0.66	0.53
Cellular Component	GO:0071944	GO:0005835	GO:0016020
GO-Score	0.57	0.53	0.43

(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.