I-TASSER results

I-TASSER results for job id Rv3180c

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

Input Sequence in FASTA format

>protein (144 residues)
MPLVYFDASAFVKLLTTETGSSLASALWDGCDAALSSRLAYPEVRAALAAAARNHDLTES
ELADAERDWEDFWAATRPVELTATVEQHAGHLARAHALRGADAVHLASALAVGDPGLVVA
VWDRRLHTGAHAAGCRVAPAQLDP

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MPLVYFDASAFVKLLTTETGSSLASALWDGCDAALSSRLAYPEVRAALAAAARNHDLTESELADAERDWEDFWAATRPVELTATVEQHAGHLARAHALRGADAVHLASALAVGDPGLVVAVWDRRLHTGAHAAGCRVAPAQLDP
Prediction	CCEEEEEHHHHHHHHHCCCCCHHHHHHHHHCCCEEHCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCEEEHCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCEEEEHCCHHHHHHHHHHCCEEHCCCCCC
Conf.Score	988998546889999769997999999986995786368899999999999986899999999999999999886656758999999999999985997778999999999899987999858899999999999686688899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MPLVYFDASAFVKLLTTETGSSLASALWDGCDAALSSRLAYPEVRAALAAAARNHDLTESELADAERDWEDFWAATRPVELTATVEQHAGHLARAHALRGADAVHLASALAVGDPGLVVAVWDRRLHTGAHAAGCRVAPAQLDP
Prediction	441000000000210262730640350057332100031031101000132245551447304401620462055043140345015302510562502100000000023255531100000430150047240512456468
	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                 140

                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCEEEEEHHHHHHHHHCCCCCHHHHHHHHHCCCEEHCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCEEEHCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCEEEEHCCHHHHHHHHHHCCEEHCCCCCC
MPLVYFDASAFVKLLTTETGSSLASALWDGCDAALSSRLAYPEVRAALAAAARNHDLTESELADAERDWEDFWAATRPVELTATVEQHAGHLARAHALRGADAVHLASALAVGDPGLVVAVWDRRLHTGAHAAGCRVAPAQLDP

2fe1A

0.28

0.25

0.90

2.31

MUSTER

M-ELVVDASAIAALYVPEERSEQAERAVSQAQELHTLDLAAYEVANDLWKHARRGLLREDEASNMLEELWEFFKALKVHS-YAEVLKDAFALALKHGVTVYDAAYVALAEKIG---GKLLTLDRQLAEKFPA----LVT-----

2fe1A

0.27

0.24

0.90

2.54

dPPAS

-MELVVDASAIAALYVPEERSEQAERAVSQAQELHTLDLAAYEVANDLWKHARRGLLREDEASNMLEELWEFFKALKVHS-YAEVLKDAFALALKHGVTVYDAAYVALAEKIGG---KLLTLDRQLAEKFPALVT---------

2fe1A

0.28

0.26

0.90

3.48

wdPPAS

M-ELVVDASAIAALYVPEERSEQAERAVSQAQELHTLDLAAYEVANDLWKHARRGLLREDEASNMLEELWEFFKAL-KVHSYAEVLKDAFALALKHGVTVYDAAYVALAEKIGG---KLLTLDRQLAEKFPA----LVT-----

2fe1A

0.27

0.24

0.90

2.70

wMUSTER

--ELVVDASAIAALYVPEERSEQAERAVSQAQELHTLDLAAYEVANDLWKHARRGLLREDEASNMLEELWEFFKALKVHS-YAEVLKDAFALALKHGVTVYDAAYVALAEKIG---GKLLTLDRQLAEKFPA----LVT-----

2fe1A

0.28

0.25

0.90

3.72

wPPAS

M-ELVVDASAIAALYVPEERSEQAERAVSQAQELHTLDLAAYEVANDLWKHARRGLLREDEASNMLEELWEFFKALKVHS-YAEVLKDAFALALKHGVTVYDAAYVALAEKIGG---KLLTLDRQLAEKFPA----LVT-----

2fe1A

0.28

0.25

0.90

6.91

dPPAS2

M-ELVVDASAIAALYVPEERSEQAERAVSQAQELHTLDLAAYEVANDLWKHARRGLLREDEASNMLEELWEFFKALKVHS-YAEVLKDAFALALKHGVTVYDAAYVALAEKIGG---KLLTLDRQLAEKFPAL-VT--------

2fe1A

0.27

0.24

0.90

3.20

PPAS

M-ELVVDASAIAALYVPEERSEQAERAVSQAQELHTLDLAAYEVANDLWKHARRGLLREDEASNMLEELWEFFKALKVHSY-AEVLKDAFALALKHGVTVYDAAYVALAEKIGG---KLLTLDRQLAEKFP--ALVT-------

2fe1A

0.27

0.24

0.90

4.30

Env-PPAS

M-ELVVDASAIAALYVPEERSEQAERAVSQAQELHTLDLAAYEVANDLWKHARRGLLREDEASNMLEELWEFFKALKVHSY-AEVLKDAFALALKHGVTVYDAAYVALAEKIGG---KLLTLDRQLAEKFP--ALVT-------

1v8pF

0.22

0.20

0.90

1.57

MUSTER

MAVYLVDASALYALAAHY---DKWIKHREK---LAILHLTIYEAGNALWKEARLGRV---DWAAASRHLKKVLSSFKVLEDPP--LDEVLRVAVERGLTFYDASYAYVAESSG---LVLVTQDRELLAKTKGADVETLLVRLAA

1v8pF

0.20

0.17

0.85

1.42

dPPAS

MAVYLVDASALYALAAH------YDKWIKHREKLAILHLTIYEAGNALWKEARLGRVDWAAASRHLKKVLSSF-----KVLEDPPLDEVLRVAVERGLTFYDASYAYVAESSGL---VLVTQDRELLAKT--------KGAIDV

(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=0.95

Estimated TM-score = 0.84±0.08

Estimated RMSD = 2.8±2.1Å

Download Model 2

C-score=-1.96

Download Model 3

C-score=0.91

Download Model 4

C-score=-4.77

Download Model 5

C-score=-4.73

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	2fe1A	0.873	0.85	0.262	0.903
2	1v8pF	0.726	2.62	0.206	0.854
3	2h1cA	0.724	2.38	0.156	0.882
4	4xgqA	0.713	2.17	0.172	0.847
5	3zvkA	0.685	2.72	0.095	0.868
6	3tndA	0.682	2.87	0.128	0.868
7	3dboB	0.665	2.50	0.183	0.833
8	3h87B	0.652	2.95	0.184	0.840
9	4chgA	0.643	2.97	0.176	0.819
10	1w8iA	0.643	2.91	0.133	0.819

(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	4	4xgqA	MG	Rep, Mult	7,8,43,101,102
2	0.08	4	2j5bB	TYE	Rep, Mult	5,7,8,102,105,121
3	0.06	3	2h1c0	III	Rep, Mult	38,39,42,45,46,49,50,80,81,82,83,86,87,89,90,93,94,104
4	0.05	2	2fe10	III	Rep, Mult	38,39,41,42,43,45,46,48,49,52,62,66,67,70,78,81,83,86,87,90,93,94,98,99,100,101,104
5	0.04	2	2h1cA	III	Rep, Mult	11,12,14,25,28,29,47,48,61,64,65,68,72,75
6	0.04	2	1tauA	ZN	Rep, Mult	7,9,102,123
7	0.04	2	3h87A	MG	Rep, Mult	102,123,127
8	0.02	1	2h1cA	MG	Rep, Mult	5,6,36,37,40
9	0.02	1	2h1cA	MG	Rep, Mult	45,49,66
10	0.02	1	2h1cA	MG	Rep, Mult	37,79,80,81,108
11	0.02	1	1v7pC	MN	Rep, Mult	7,9,21,123
12	0.02	1	1fx4A	MG	Rep, Mult	7,32

	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	2el7A	0.567	3.96	0.080	0.854	6.1.1.2	NA
2	0.060	3fnrA	0.592	4.40	0.092	0.972	6.1.1.19	NA
3	0.060	1irxB	0.574	4.18	0.038	0.896	6.1.1.6	123
4	0.060	2zufA	0.590	4.27	0.087	0.944	6.1.1.19	NA
5	0.060	1u0bB	0.556	4.37	0.065	0.896	6.1.1.16	NA
6	0.060	1li7B	0.529	4.67	0.072	0.875	6.1.1.16	NA
7	0.060	3a04A	0.555	4.23	0.083	0.868	6.1.1.2	43
8	0.060	2zueA	0.585	4.35	0.057	0.944	6.1.1.19	127
9	0.060	1ileA	0.544	4.37	0.065	0.896	6.1.1.5	NA
10	0.060	1wz2A	0.593	4.38	0.043	0.965	6.1.1.4	NA
11	0.060	2j5bA	0.557	4.14	0.061	0.861	6.1.1.1	NA
12	0.060	1ffyA	0.541	4.29	0.080	0.896	6.1.1.5	NA
13	0.060	2pidB	0.544	4.24	0.053	0.854	6.1.1.1	NA
14	0.060	1iq0A	0.574	4.25	0.108	0.903	6.1.1.19	105
15	0.060	2ct8A	0.540	4.57	0.110	0.910	6.1.1.10	NA
16	0.060	3d6vA	0.558	3.81	0.072	0.826	6.1.1.1	6,13,20
17	0.060	2cyaA	0.587	3.61	0.063	0.840	6.1.1.1	13
18	0.060	2ja2A	0.539	4.21	0.080	0.861	6.1.1.17	NA
19	0.060	1q11A	0.564	3.75	0.071	0.833	6.1.1.1	123

(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	0.36	0.873	0.85	0.26	0.90	2fe1A	GO:0000287 GO:0004518 GO:0004540 GO:0016787 GO:0046872 GO:0090305 GO:0090501
1	0.34	0.726	2.62	0.21	0.85	1v8pF	GO:0004518 GO:0004527 GO:0004540 GO:0016787 GO:0046872 GO:0090305 GO:0090501
2	0.30	0.665	2.50	0.18	0.83	3dboB	GO:0000287 GO:0004518 GO:0004521 GO:0004540 GO:0005576 GO:0016787 GO:0040007 GO:0040008 GO:0046872 GO:0090305 GO:0090501 GO:0090502
3	0.26	0.713	2.17	0.17	0.85	4xgqA	GO:0000287 GO:0004518 GO:0004540 GO:0016787 GO:0045926 GO:0046872 GO:0090305 GO:0090501
4	0.26	0.685	2.72	0.10	0.87	3zvkA	GO:0000287 GO:0004518 GO:0004540 GO:0016787 GO:0046872 GO:0090305 GO:0090501
5	0.26	0.723	2.66	0.15	0.90	2bsqA	GO:0000287 GO:0003677 GO:0004518 GO:0004540 GO:0016787 GO:0044001 GO:0046872 GO:0090305 GO:0090501
6	0.26	0.646	3.42	0.14	0.88	1y82A	GO:0000287 GO:0004518 GO:0004540 GO:0016787 GO:0046872 GO:0090305 GO:0090501
7	0.24	0.703	2.70	0.10	0.88	5ecdA	GO:0000287 GO:0004518 GO:0004519 GO:0004540 GO:0016787 GO:0046872 GO:0090305 GO:0090501
8	0.18	0.601	3.09	0.14	0.77	1o4wA	GO:0004518 GO:0004540 GO:0016787 GO:0046872 GO:0090305 GO:0090501
9	0.07	0.506	4.02	0.11	0.78	1q7tA	GO:0005886 GO:0008270 GO:0010125 GO:0016787 GO:0016811 GO:0019213 GO:0035595 GO:0046872
10	0.07	0.440	4.44	0.12	0.74	4almA	GO:0004318 GO:0006633 GO:0016491 GO:0047117 GO:0055114
11	0.06	0.425	5.07	0.03	0.79	3k6jA	GO:0003857 GO:0006631 GO:0016491 GO:0046872 GO:0055114
12	0.06	0.373	5.22	0.04	0.65	3x0uA	GO:0009405
13	0.06	0.341	5.18	0.04	0.63	3ozcA	GO:0003824 GO:0004645 GO:0005634 GO:0005737 GO:0005829 GO:0006139 GO:0006166 GO:0006738 GO:0009116 GO:0016740 GO:0016757 GO:0016763 GO:0017061 GO:0019509 GO:0032259 GO:0033574 GO:0043101 GO:0070062
14	0.06	0.355	4.78	0.07	0.61	4igbB	GO:0016020 GO:0016021
15	0.06	0.359	4.89	0.04	0.62	1zxjD
16	0.06	0.335	5.12	0.05	0.61	4e97B	GO:0003796 GO:0003824 GO:0008152 GO:0009253 GO:0016787 GO:0016798 GO:0016998 GO:0019076 GO:0019835 GO:0030430 GO:0042742
17	0.06	0.310	5.99	0.07	0.68	3r9cA	GO:0004497 GO:0005506 GO:0016491 GO:0016705 GO:0020037 GO:0046872 GO:0055114 GO:0070330
18	0.06	0.305	5.68	0.08	0.61	1n0eB	GO:0003677 GO:0003700 GO:0005737 GO:0006351 GO:0006355 GO:0009295

Consensus prediction of GO terms

Molecular Function	GO:0004540	GO:0000287	GO:0004519	GO:0004527
GO-Score	0.84	0.76	0.60	0.34
Biological Processes	GO:0090501	GO:0048519
GO-Score	0.84	0.53
Cellular Component	GO:0005576
GO-Score	0.30

(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.