I-TASSER results

I-TASSER results for job id Rv0786c

[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)
MHVGDELPLAELTVRAVGGCHAVIHPEIPVIENISYLVGDSKHRARLMHPGDALFVPGEQ
VDVLATPAAAPWMKISEAVDYLRAVAPARAVPIHQAIVAPDARGIYYGRLTEMTTTDFQV
LPEESAVTF

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MHVGDELPLAELTVRAVGGCHAVIHPEIPVIENISYLVGDSKHRARLMHPGDALFVPGEQVDVLATPAAAPWMKISEAVDYLRAVAPARAVPIHQAIVAPDARGIYYGRLTEMTTTDFQVLPEESAVTF
Prediction	CCCCEEEEHCCEEEEEHCCCCCCCCCCCCCCCCEEEEHCCCCCCCEEHCCCCCCCCCCCCEEEEEHCCCCCCCCHHHHHHHHHHHCCCEEEEHCCCCCCCHHHHHHHHHHHHHCCCCEEHCCCCCCCCC
Conf.Score	999878999688999986765555788888787799988888986898588788889876579998588988899999999999799868874333357545788999999867875898699865569
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MHVGDELPLAELTVRAVGGCHAVIHPEIPVIENISYLVGDSKHRARLMHPGDALFVPGEQVDVLATPAAAPWMKISEAVDYLRAVAPARAVPIHQAIVAPDARGIYYGRLTEMTTTDFQVLPEESAVTF
Prediction	864545151360404233542130237234162000002346554300001112324755030000023233342440041045142530130030113550341034205724655144046645365
	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

CCCCEEEEHCCEEEEEHCCCCCCCCCCCCCCCCEEEEHCCCCCCCEEHCCCCCCCCCCCCEEEEEHCCCCCCCCHHHHHHHHHHHCCCEEEEHCCCCCCCHHHHHHHHHHHHHCCCCEEHCCCCCCCCC
MHVGDELPLAELTVRAVGGCHAVIHPEIPVIENISYLVGDSKHRARLMHPGDALFVPGEQVDVLATPAAAPWMKISEAVDYLRAVAPARAVPIHQAIVAPDARGIYYGRLTEMTTTDFQVLPEESAVTF

3x2xA

0.19

0.97

1.64

MUSTER

MHIGGSYLFDFGRVKMTPAVHGSGILDIYGGNPSGFLITI--EGKKIYHAGDTGLTAEENVDVAFLPIGGNFMDVEDAVRAAVMIKPKKVVPMHYGTWELI-VELFKKKVEEK-GVECVILEPGESLEL

3x2xA

0.19

0.98

2.12

dPPAS

MHIGGSYLFDFGRVKMTPAVHGSGILDIYGGNPSGFLI--TIEGKKIYHAGDTGLTAEENVDVAFLPIGGNFMDVEDAVRAAVMIKPKKVVPMHYGTLIFADVELFKKKVEEK-GVECVILEPGESLEL

3x2xA

0.19

0.98

2.52

wdPPAS

MHIGGSYLFDFGRVKMTPAVHGSGILDIYGGNPSGFLI--TIEGKKIYHAGDTGLTREENVDVAFLPIGGNFMDVEDAVRAAVMIKPKKVVPMHYGTWELIDVELFKKKVEEK-GVECVILEPGESLEL

3x2xA

0.19

0.98

2.13

wMUSTER

MHIGGSYLFDFGRVKMTPAVHGSGILDIYGGNPSGFLITI--EGKKIYHAGDTGLTREENVDVAFLPIGGNFMDVEDAVRAAVMIKPKKVVPMHYGTWEFADVELFKKKVEEK-GVECVILEPGESLEL

3x2xA

0.19

0.98

2.40

wPPAS

MHIGGSYLFDFGRVKMTPAVHGSGILDIYGGNPSGFLI--TIEGKKIYHAGDTGLTREENVDVAFLPIGGNFMDVEDAVRAAVMIKPKKVVPMHYGTWEFADVELFKKKVEEK-GVECVILEPGESLEL

3x2xA

0.19

0.98

5.69

dPPAS2

MHIGGSYLFDFGRVKMTPAVHGSGILDIYGGNPSGFLI--TIEGKKIYHAGDTGLTREENVDVAFLPIGGNFMDVEDAVRAAVMIKPKKVVPMHYGTLIFADVELFKKKVEEK-GVECVILEPGESLEL

3x2xA

0.19

0.98

2.06

PPAS

MHIGGSYLFDFGRVKMTPAVHGSGILDIYGGNPSGFLI--TIEGKKIYHAGDTGLTREENVDVAFLPIGGNFMDVEDAVRAAVMIKPKKVVPMHYGTLIFADVELFKKKVEEK-GVECVILEPGESLEL

3x2xA

0.19

0.98

2.29

Env-PPAS

MHIGGSYLFDFGRVKMTPAVHGSGILDIYGGNPSGFLI--TIEGKKIYHAGDTGLTREENVDVAFLPIGGNFMDVEDAVRAAVMIKPKKVVPMHYGTLIFADVELFKKKVEEK-GVECVILEPGESLEL

1vjnA

0.14

0.12

0.89

1.43

MUSTER

IDRPGAYTVNGVKIKGVETFHD--------GKNIVFVFEG--EGIKVCHLGDLGHVLTGEIDVLLVPVGGTYIGPKEAKEVADLLNAKVIIPHYKTKYLKFNLLPVDDFLKLFDS----YERVGNILEL

3kl7A

0.19

0.17

0.91

1.89

dPPAS

LKNGDTDTSISYKIEAVPAYNTTPGRDHPRHRDNGYIL--TFDGLRVYIAGDTEDIPEKDIDIAFLPVNQPYTTVSQAAKAARF-SPKILYPYHYGDTK---IGELKDALKD-SGIDVRIRELQ-----

(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=0.60

Estimated TM-score = 0.79±0.09

Estimated RMSD = 3.3±2.3Å

Download Model 2

C-score=-5.00

Download Model 3

C-score=-4.63

Download Model 4

C-score=-2.30

Download Model 5

C-score=0.68

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	3x2xA	0.886	1.44	0.183	0.977
2	4qn9A	0.813	2.23	0.190	0.977
3	3bv6B	0.809	2.42	0.150	0.977
4	4jo0A	0.771	2.64	0.089	0.954
5	3af5A	0.764	2.07	0.110	0.915
6	2ycbA	0.764	2.07	0.076	0.915
7	2xr1A	0.759	2.10	0.102	0.915
8	4ojvA	0.753	2.79	0.094	0.961
9	5a0tA	0.751	2.18	0.111	0.907
10	2i7vA1	0.749	2.36	0.110	0.915

(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	0.27	10	3x2zA	NI	Rep, Mult	52,94
2	0.17	8	2hxtA	MG	Rep, Mult	47,49,65,91,124
3	0.04	2	3iemB	SSU	Rep, Mult	14,16,39,46,57,58,59,60
4	0.02	1	2uwfA	CA	Rep, Mult	62,117
5	0.02	1	3rpcA	ZN	Rep, Mult	21,52
6	0.02	1	3kl7A	ZN	Rep, Mult	28,52

	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	0.060	2hsaA	0.589	4.11	0.040	0.938	1.3.1.42	NA
2	0.060	1aknA	0.579	4.53	0.079	0.961	3.1.1.13,3.1.1.3	NA
3	0.060	2cbnA	0.725	2.49	0.151	0.922	3.1.26.11	23,33
4	0.060	1gonA	0.602	4.19	0.078	0.922	3.2.1.21	NA
5	0.060	1p9eA	0.617	3.86	0.091	0.907	3.1.8.1	68
6	0.060	2dkfA	0.738	2.02	0.150	0.876	3.1.-.-	NA
7	0.060	1od0B	0.594	4.25	0.031	0.915	3.2.1.21	NA
8	0.060	1b1yA	0.584	4.44	0.047	0.961	3.2.1.2	52,59
9	0.060	1q45B	0.601	4.43	0.085	0.977	1.3.1.42	NA
10	0.060	2pbgA	0.585	3.96	0.023	0.922	3.2.1.85	NA
11	0.060	2z1sA	0.581	4.31	0.085	0.922	3.2.1.21	NA
12	0.060	1icpA	0.599	4.18	0.104	0.930	1.3.1.42	122
13	0.060	1cb7B	0.586	4.26	0.074	0.922	5.4.99.1	NA
14	0.060	1f6wA	0.575	4.21	0.071	0.922	3.1.1.13,3.1.1.3	NA
15	0.060	1tr1D	0.597	4.18	0.085	0.922	3.2.1.21	NA
16	0.060	1z41A	0.604	4.13	0.062	0.938	1.6.99.1,1.-.-.-	NA
17	0.060	2jieA	0.579	4.31	0.085	0.922	3.2.1.21	NA
18	0.060	2i7vA	0.749	2.36	0.110	0.915	3.1.27.-	NA
19	0.060	1qoxM	0.597	4.21	0.054	0.922	3.2.1.21	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	0.24	0.814	2.22	0.19	0.98	4qn9B	GO:0001523 GO:0004620 GO:0005737 GO:0006629 GO:0008270 GO:0009395 GO:0016020 GO:0016042 GO:0016787 GO:0042622 GO:0046872 GO:0070062 GO:0070290
1	0.21	0.791	2.35	0.13	0.95	2wylA	GO:0005737 GO:0016787 GO:0019854 GO:0030145 GO:0035460 GO:0052689
2	0.20	0.886	1.44	0.18	0.98	3x2xA	GO:0016787
3	0.16	0.809	2.42	0.15	0.98	3bv6B	GO:0046872
4	0.16	0.761	2.36	0.20	0.88	3kl7A	GO:0016787 GO:0046872
5	0.13	0.719	2.92	0.14	0.93	3rpcA	GO:0046872
6	0.11	0.711	2.34	0.14	0.86	1vjnA	GO:0016787
7	0.07	0.610	3.64	0.09	0.92	2p4zB	GO:0016787 GO:0046872
8	0.07	0.619	3.97	0.07	0.91	4xukA	GO:0016787
9	0.07	0.771	2.64	0.09	0.95	4jo0A	GO:0046872
10	0.07	0.514	3.86	0.08	0.77	5evdA	GO:0008270 GO:0008800 GO:0016787 GO:0017001 GO:0042597 GO:0046677 GO:0046872
11	0.07	0.426	4.62	0.19	0.69	4le6A	GO:0004063 GO:0016311 GO:0016787 GO:0046872
12	0.07	0.519	4.68	0.04	0.88	4dgqA	GO:0004601 GO:0016491 GO:0016691 GO:0055114 GO:0098869
13	0.07	0.521	3.96	0.05	0.77	4g36B	GO:0000166 GO:0003824 GO:0004497 GO:0005524 GO:0005777 GO:0008152 GO:0008218 GO:0016491 GO:0046872 GO:0047077 GO:0055114
14	0.07	0.749	2.36	0.11	0.91	2i7vA	GO:0000398 GO:0003723 GO:0004518 GO:0004519 GO:0004521 GO:0005634 GO:0005654 GO:0005847 GO:0006369 GO:0006378 GO:0006379 GO:0006397 GO:0006398 GO:0006406 GO:0008409 GO:0016787 GO:0030529 GO:0031124 GO:0046872 GO:0090305 GO:0090502
15	0.07	0.766	2.06	0.08	0.91	2ycbB	GO:0003676 GO:0003723 GO:0046872
16	0.07	0.750	2.40	0.11	0.91	2i7tA	GO:0000398 GO:0003723 GO:0004518 GO:0004519 GO:0004521 GO:0005634 GO:0005654 GO:0005847 GO:0006369 GO:0006378 GO:0006379 GO:0006397 GO:0006398 GO:0006406 GO:0008409 GO:0016787 GO:0030529 GO:0031124 GO:0046872 GO:0090305 GO:0090502
17	0.07	0.468	4.67	0.07	0.81	4p7cA	GO:0002098 GO:0006400 GO:0008033 GO:0016300 GO:0016740 GO:0016765 GO:0030488
18	0.07	0.502	4.47	0.03	0.84	4rt6A	GO:0005576 GO:0006810

Consensus prediction of GO terms

Molecular Function	GO:0008081	GO:0046914	GO:0016298
GO-Score	0.49	0.49	0.49
Biological Processes	GO:0006644	GO:0044242	GO:0046434	GO:0016101	GO:0046395	GO:0019852	GO:0042365
GO-Score	0.49	0.49	0.49	0.49	0.41	0.41	0.41
Cellular Component	GO:0001750	GO:1903561	GO:0031988	GO:0060170	GO:0005737
GO-Score	0.49	0.49	0.49	0.49	0.40

(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.