I-TASSER results

I-TASSER results for job id Rv2011c

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

Input Sequence in FASTA format

>protein (143 residues)
MSDEIARLVADVFELAGLLRRSGEVVAAREGHTQARWQLLSVVSDRALTVPQAARRLGVT
RQGVQRVANDLVVCGLAELRHNPDHRTSPLLVLTENGRRVLQAITERAIVVNNRLADAVD
PAALQATRDSLRRMIVALKAERP

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MSDEIARLVADVFELAGLLRRSGEVVAAREGHTQARWQLLSVVSDRALTVPQAARRLGVTRQGVQRVANDLVVCGLAELRHNPDHRTSPLLVLTENGRRVLQAITERAIVVNNRLADAVDPAALQATRDSLRRMIVALKAERP
Prediction	CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCEEHCCCCCCCCEEEEEHCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCC
Conf.Score	98679999999999999999999999998899999999999999689999999999999878899999999998997877898889668898799999999999999999999999799999999999999999999975799
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MSDEIARLVADVFELAGLLRRSGEVVAAREGHTQARWQLLSVVSDRALTVPQAARRLGVTRQGVQRVANDLVVCGLAELRHNPDHRTSPLLVLTENGRRVLQAITERAIVVNNRLADAVDPAALQATRDSLRRMIVALKAERP
Prediction	76441240032024004203420452157361333013002103745242430043151444303410430275421413523733223204016403500540353045014302761456015203500530263056758
	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

CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCEEHCCCCCCCCEEEEEHCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCC
MSDEIARLVADVFELAGLLRRSGEVVAAREGHTQARWQLLSVVSDRALTVPQAARRLGVTRQGVQRVANDLVVCGLAELRHNPDHRTSPLLVLTENGRRVLQAITERAIVVNNRLADAVDPAALQATRDSLRRMIVALKAERP

3gfiA

0.14

1.00

2.40

MUSTER

SNENRIQIMSTIAKIYRAMSRELNRRLGELNLSYLDFLVLRATSDGPKTMAYLANRYFVTQSAITASVDKLEEMGLVVRVRDREDRRKILIEITEKGLETFNKGIEIYKKLANEVTGDLSEDEVILVLDKISKILKRIEEISQ

4xrfA

0.12

0.99

2.68

dPPAS

-MTHIDKIQALAFSIGKKMQTELLEQMQATGLTPPQFYILKILDHYGSRATTLAKKMYVKPSAITVMIDRLIDQELVERYHDKDDRRVVIIELTKKGKARVEEAMTARNEHIAKYFSHLELQEREDLLRLFEKLETIICGTQ-

4xrfA

0.13

0.99

2.84

wdPPAS

MTH-IDKIQALAFSIGKKMQTELLEQMQATGLTPPQFYILKILDHYGSRATTLAKKMYVKPSAITVMIDRLIDQELVERYHDKDDRRVVIIELTKKGKARVEEAMTARNEHIAKYFSHLELQEREDLLRLFEKLETIICGTQ-

3gfiA

0.14

0.99

2.72

wMUSTER

-NENRIQIMSTIAKIYRAMSRELNRRLGELNLSYLDFLVLRATSDGPKTMAYLANRYFVTQSAITASVDKLEEMGLVVRVRDREDRRKILIEITEKGLETFNKGIEIYKKLANEVTGDLSEDEVILVLDKISKILKRIEEISQ

4xrfA

0.13

0.99

3.01

wPPAS

MTH-IDKIQALAFSIGKKMQTELLEQMQATGLTPPQFYILKILDHYASRATTLAKKMYVKPSAITVMIDRLIDQELVERYHDKDDRRVVIIELTKKGKARVEEAMTARNEHIAKYFSHLELQEREDLLRLFEKLETIICGTQ-

4xrfA

0.13

0.99

3.70

dPPAS2

MTH-IDKIQALAFSIGKKMQTELLEQMQATGLTPPQFYILKILDHYGSRATTLAKKMYVKPSAITVMIDRLIDQELVERYHDKDDRRVVIIELTKKGKARVEEAMTARNEHIAKYFSHLELQEREDLLRLFEKLETIICGTQ-

4xrfA

0.13

0.99

2.80

PPAS

MTH-IDKIQALAFSIGKKMQTELLEQMQATGLTPPQFYILKILDHYASRATTLAKKMYVKPSAITVMIDRLIDQELVERYHDKDDRRVVIIELTKKGKARVEEAMTARNEHIAKYFSHLELQEREDLLRLFEKLETIICGTQ-

4xrfA

0.13

0.99

3.59

Env-PPAS

MTH-IDKIQALAFSIGKKMQTELLEQMQATGLTPPQFYILKILDHYASRATTLAKKMYVKPSAITVMIDRLIDQELVERYHDKDDRRVVIIELTKKGKARVEEAMTARNEHIAKYFSHLELQEREDLLRLFEKLETIICGTQ-

4xrfA

0.13

0.99

2.36

MUSTER

MTH-IDKIQALAFSIGKKMQTELLEQMQATGLTPPQFYILKILDHYASRATTLAKKMYVKPSAITVMIDRLIDQELVERYHDKDDRRVVIIELTKKGKARVEEAMTARNEHIAKYFSHLELQEREDLLRLFEKLETIICGTQ-

3gfiA

0.14

1.00

2.67

dPPAS

SNENRIQIMSTIAKIYRAMSRELNRRLGELNLSYLDFLVLRATSDGPKTMAYLANRYFVTQSAITASVDKLEEMGLVVRVRDREDRRKILIEITEKGLETFNKGIEIYKKLANEVTGDLSEDEVILVLDKISKILKRIEEISQ

(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 3 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=0.19

Estimated TM-score = 0.74±0.11

Estimated RMSD = 4.3±2.9Å

Download Model 2

C-score=-0.18

Download Model 3

C-score=0.29

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	4xrfA	0.898	1.55	0.135	0.979
2	3zplA	0.819	2.70	0.154	0.993
3	3zmdA	0.788	2.61	0.138	0.965
4	4fhtA	0.784	2.35	0.188	0.923
5	5e1wA	0.774	2.83	0.099	0.965
6	4b8xA	0.756	2.77	0.209	0.909
7	5eriA	0.751	3.14	0.092	0.986
8	3hrmB	0.750	2.34	0.117	0.895
9	2nnnA	0.743	2.43	0.156	0.895
10	2pexB	0.738	2.69	0.133	0.888

(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	0.19	15	3zplA	NUC	Rep, Mult	24,49,50,51,61,62,65,66,79,87,88,89
2	0.18	13	3q5fA	NUC	Rep, Mult	20,33,35,59,60,62,63,66,85,86,87
3	0.10	9	4llnC	NUC	Rep, Mult	17,21,49,50,62,65,79,87,89
4	0.04	3	4xrfA	ISQ	Rep, Mult	9,12,131
5	0.02	2	3bpxB	SAL	Rep, Mult	6,9,10,13,17
6	0.02	2	3gf2A	SAL	Rep, Mult	34,38,41,108
7	0.02	2	3kp2B	PNN	Rep, Mult	60,62,63,66,70
8	0.02	2	3bpxA	SAL	Rep, Mult	38,41,45,56,57
9	0.02	2	3bpv0	III	Rep, Mult	11,12,14,15,17,18,19,20,22,23,24,25,34,56,57,58,59,118,120,123,124,125
10	0.02	2	5cyvA	WCA	Rep, Mult	19,20,23,34,35,38,57,59,108,112
11	0.01	1	2yr2B	ZN	Rep, Mult	82,84
12	0.01	1	3bpxB	NA	Rep, Mult	33,35,36,70
13	0.01	1	1z910	III	Rep, Mult	1,6,19,23,34,37,38,41,42,45,57,58,104,105,123,124
14	0.01	1	3gezA	CA	Rep, Mult	140,141
15	0.01	1	2fbhA	ZN	Rep, Mult	26,27,28,29
16	0.01	1	3echB	III	Rep, Mult	3,5,6,7,9,10,12,13,15,16,19,20,23,34,35,38,108,112
17	0.01	1	3fm5C	MG	Rep, Mult	129,132
18	0.01	1	2fnp0	III	Rep, Mult	11,12,13,15,16,17,18,21,22,23,26,34,37,38,41,58,105,106,109
19	0.01	1	3bpxA	SAL	Rep, Mult	13,17
20	0.01	1	3hsrC	BT6	Rep, Mult	19,23,115

	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	2e7zA	0.473	5.01	0.067	0.867	4.2.1.71	NA
2	0.060	3fofA	0.459	4.17	0.064	0.720	5.99.1.-	NA
3	0.060	1s76D	0.372	5.06	0.056	0.671	2.7.7.6	NA
4	0.060	1lwtA	0.496	4.52	0.096	0.832	3.6.3.14	122
5	0.060	3k9fA	0.476	4.37	0.109	0.748	5.99.1.-	NA
6	0.060	1fp1D	0.468	3.31	0.075	0.615	2.1.1.-	NA
7	0.060	1gw6A	0.458	5.57	0.086	0.895	3.3.2.6	NA
8	0.060	2rc4A	0.494	4.06	0.083	0.720	2.3.1.48,	106
9	0.060	1cy7A	0.509	4.10	0.105	0.762	5.99.1.2	NA
10	0.060	2gaiA	0.523	4.03	0.104	0.769	5.99.1.2	NA
11	0.060	3gwqA	0.467	4.81	0.099	0.818	4.3.1.18	NA
12	0.060	2rgrA	0.498	4.43	0.085	0.762	5.99.1.3	NA
13	0.060	2yvwA	0.461	4.53	0.092	0.727	2.5.1.7	NA
14	0.060	1fokA	0.593	4.00	0.096	0.804	3.1.21.4	NA
15	0.060	1dfaA	0.420	5.02	0.091	0.748	3.6.3.14,3.6.1.34	NA
16	0.060	1vfsA	0.457	4.48	0.067	0.755	5.1.1.1	NA
17	0.060	1in5A	0.467	2.26	0.133	0.531	3.6.4.12	NA
18	0.060	2gajB	0.522	4.05	0.104	0.769	5.99.1.2	NA
19	0.060	1wydB	0.458	4.68	0.043	0.748	6.1.1.12	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	0.45	0.735	2.71	0.15	0.93	3f3xA	GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0044212
1	0.43	0.898	1.55	0.14	0.98	4xrfA	GO:0003677 GO:0003700 GO:0006351 GO:0006355
2	0.35	0.698	3.27	0.14	0.92	3bpxA	GO:0003677 GO:0003700 GO:0006351 GO:0006355
3	0.33	0.632	3.18	0.16	0.85	1jgsA	GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0009408 GO:0044212 GO:0045892 GO:0046677 GO:0071236
4	0.32	0.742	2.80	0.14	0.93	3nqoA	GO:0003677 GO:0003700 GO:0006351 GO:0006355
5	0.32	0.766	2.55	0.19	0.93	4fhtB	GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0044212
6	0.31	0.819	2.69	0.15	0.99	3zplE	GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0044212
7	0.31	0.738	2.69	0.13	0.89	2pexB	GO:0003677 GO:0003700 GO:0006351 GO:0006355
8	0.29	0.752	2.70	0.16	0.92	3q5fA	GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0009405
9	0.28	0.779	2.85	0.14	0.96	3zmdC	GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0044212
10	0.28	0.594	3.95	0.09	0.91	4kdpA	GO:0003677 GO:0003700 GO:0006351 GO:0006355
11	0.28	0.659	3.40	0.16	0.94	3cjnA	GO:0003677 GO:0003700 GO:0006351 GO:0006355
12	0.27	0.749	2.43	0.15	0.90	2nnnA	GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0044212
13	0.27	0.666	3.15	0.20	0.91	2nyxB	GO:0003677 GO:0003700 GO:0005886 GO:0006351 GO:0006355 GO:0044212
14	0.27	0.622	3.41	0.16	0.90	4yifB	GO:0003677 GO:0003700 GO:0006351 GO:0006355
15	0.27	0.728	2.85	0.08	0.90	3bjaA	GO:0003677 GO:0003700 GO:0006351 GO:0006355
16	0.26	0.625	3.07	0.11	0.83	3oopA	GO:0003677 GO:0003700 GO:0006351 GO:0006355
17	0.26	0.676	3.29	0.19	0.92	3e6mD	GO:0003677 GO:0003700 GO:0006351 GO:0006355
18	0.26	0.561	4.13	0.17	0.81	3tgnB	GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0046872
19	0.26	0.697	3.22	0.09	0.94	4em0B	GO:0003677 GO:0003700 GO:0006351 GO:0006355
20	0.24	0.657	3.40	0.17	0.92	1s3jA	GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0006367 GO:0044212
21	0.24	0.638	3.39	0.10	0.91	4aijB	GO:0003677 GO:0003700 GO:0006351 GO:0006355
22	0.23	0.693	2.90	0.16	0.85	3boqB	GO:0003677 GO:0003700 GO:0006351 GO:0006355
23	0.22	0.730	3.17	0.15	0.96	5cyvB	GO:0003677 GO:0003700 GO:0006351 GO:0006355
24	0.22	0.567	4.10	0.18	0.85	2ethA	GO:0003677 GO:0003700 GO:0006351 GO:0006355
25	0.19	0.654	3.35	0.15	0.90	3g3zA	GO:0003677 GO:0003700 GO:0006351 GO:0006355
26	0.15	0.542	2.99	0.16	0.66	2a61A	GO:0003677 GO:0003700 GO:0006351 GO:0006355
27	0.15	0.452	2.21	0.08	0.52	2zkzC	GO:0003677 GO:0003700 GO:0006351 GO:0006355
28	0.13	0.697	3.08	0.12	0.90	2fbiA	GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0010124 GO:0044212 GO:0045892
29	0.12	0.654	3.29	0.16	0.85	3gfiA	GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0046872
30	0.12	0.721	2.88	0.09	0.94	2fxaB	GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0030435 GO:0045892
31	0.10	0.658	3.12	0.16	0.89	3mexA	GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0034763 GO:0042802 GO:0044212 GO:0045892 GO:0050709

Consensus prediction of GO terms

Molecular Function	GO:0003700	GO:0044212
GO-Score	0.91	0.63
Biological Processes	GO:0045892	GO:0071236	GO:0009408
GO-Score	0.33	0.33	0.33
Cellular Component
GO-Score

(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.