I-TASSER results

I-TASSER results for job id Rv3583c

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

Input Sequence in FASTA format

>protein (162 residues)
MIFKVGDTVVYPHHGAALVEAIETRTIKGEQKEYLVLKVAQGDLTVRVPAENAEYVGVRD
VVGQEGLDKVFQVLRAPHTEEPTNWSRRYKANLEKLASGDVNKVAEVVRDLWRRDQERGL
SAGEKRMLAKARQILVGELALAESTDDAKAETILDEVLAAAS

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MIFKVGDTVVYPHHGAALVEAIETRTIKGEQKEYLVLKVAQGDLTVRVPAENAEYVGVRDVVGQEGLDKVFQVLRAPHTEEPTNWSRRYKANLEKLASGDVNKVAEVVRDLWRRDQERGLSAGEKRMLAKARQILVGELALAESTDDAKAETILDEVLAAAS
Prediction	CCCCCCEEEEHCCCEEEEEEEEEEEEHCCEEEEEEEEEHCCCCEEEEEHCCCHHHHCCEHCCCHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCC
Conf.Score	999999699978975899999899886998888999999489959999677556659666599999999999868987666789899999999999979999999999999999757899967799999999999999999859999999999999998679
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MIFKVGDTVVYPHHGAALVEAIETRTIKGEQKEYLVLKVAQGDLTVRVPAENAEYVGVRDVVGQEGLDKVFQVLRAPHTEEPTNWSRRYKANLEKLASGDVNKVAEVVRDLWRRDQERGLSAGEKRMLAKARQILVGELALAESTDDAKAETILDEVLAAAS
Prediction	763444230003311002035045361564523102030467712010105416424034104573045006406766454464144025404620663404300400220142467562343144015303620140012037255740362047206658
	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                 160

                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCEEEEHCCCEEEEEEEEEEEEHCCEEEEEEEEEHCCCCEEEEEHCCCHHHHCCEHCCCHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCC
MIFKVGDTVVYPHHGAALVEAIETRTIKGEQKEYLVLKVAQGDLTVRVPAENAEYVGVRDVVGQEGLDKVFQVLRAPHTEEPTNWSRRYKANLEKLASGDVNKVAEVVRDLWRRDQERGLSAGEKRMLAKARQILVGELALAESTDDAKAETILDEVLAAAS

2lwjA

0.32

0.99

3.74

MUSTER

TSFKTGDKAVYPGQGVGEVMGIEHTEVAGQRQSFYVLRILENGMRIMIPINKVGSVGLREIISEEDVKQVYSILKEKDISVDTTWNRRYREYMEKIKTGSVFEIAEVLRDLYLLKGDKDLSFGERKMLDTARSLLIKELSLAKDCSEDEIESDLKKIFNLA-

2lwjA

0.32

0.99

4.60

dPPAS

TSFKTGDKAVYPGQGVGEVMGIEHTEVAGQRQSFYVLRILENGMRIMIPINKVGSVGLREIISEEDVKQVYSILKEKDISVDTTWNRRYREYMEKIKTGSVFEIAEVLRDLYLLKGDKDLSFGERKMLDTARSLLIKELSLAKDCSEDEIESDLKKIFNLA-

2lwjA

0.32

0.99

6.10

wdPPAS

TSFKTGDKAVYPGQGVGEVMGIEHTEVAGQRQSFYVLRILENGMRIMIPINKVGSVGLREIISEEDVKQVYSILKEKDISVDTTWNRRYREYMEKIKTGSVFEIAEVLRDLYLLKGDKDLSFGERKMLDTARSLLIKELSLAKDCSEDEIESDLKKIFNLA-

2lwjA

0.32

0.99

4.67

wMUSTER

TSFKTGDKAVYPGQGVGEVMGIEHTEVAGQRQSFYVLRILENGMRIMIPINKVGSVGLREIISEEDVKQVYSILKEKDISDSTTWNRRYREYMEKIKTGSVFEIAEVLRDLYLLKGDKDLSFGERKMLDTARSLLIKELSLAKDCSEDEIESDLKKIFNLA-

2lwjA

0.32

0.99

5.69

wPPAS

TSFKTGDKAVYPGQGVGEVMGIEHTEVAGQRQSFYVLRILENGMRIMIPINKVGSVGLREIISEEDVKQVYSILKEKDISDSTTWNRRYREYMEKIKTGSVFEIAEVLRDLYLLKGDKDLSFGERKMLDTARSLLIKELSLAKDCSEDEIESDLKKIFNLA-

2lwjA

0.32

0.99

9.37

dPPAS2

TSFKTGDKAVYPGQGVGEVMGIEHTEVAGQRQSFYVLRILENGMRIMIPINKVGSVGLREIISEEDVKQVYSILKEKDISVDTTWNRRYREYMEKIKTGSVFEIAEVLRDLYLLKGDKDLSFGERKMLDTARSLLIKELSLAKDCSEDEIESDLKKIFNLA-

2lwjA

0.32

0.99

4.79

PPAS

TSFKTGDKAVYPGQGVGEVMGIEHTEVAGQRQSFYVLRILENGMRIMIPINKVGSVGLREIISEEDVKQVYSILKEKDISVDTTWNRRYREYMEKIKTGSVFEIAEVLRDLYLLKGDKDLSFGERKMLDTARSLLIKELSLAKDCSEDEIESDLKKIFNLA-

2lwjA

0.32

0.99

4.39

Env-PPAS

TSFKTGDKAVYPGQGVGEVMGIEHTEVAGQRQSFYVLRILENGMRIMIPINKVGSVGLREIISEEDVKQVYSILKEKDIVDSTTWNRRYREYMEKIKTGSVFEIAEVLRDLYLLKGDKDLSFGERKMLDTARSLLIKELSLAKDCSEDEIESDLKKIFNLA-

4l5gA

0.24

0.23

0.98

3.71

MUSTER

-EFRPGDKVVLPPYGVGVVAGIAQRSVSGVSRAYYQVDFPGSRSKAYVPVEAPHSVGLRKALAPEEVPVILDLLKNGR-PLPKQWAARHRKTSEILADGNPYRIAQAGQLRAWEVE-RGLPDLDRQALRRAIHLLAEEVAQSLEITVQEAKRLFEEAWGEEL

4l5gA

0.24

0.23

0.98

4.51

dPPAS

-EFRPGDKVVLPPYGVGVVAGIAQRSVSGVSRAYYQVDFPGSRSKAYVPVEAPHSVGLRKALAPEEVPVILDLLKNGR-PLPKQWAARHRKTSEILADGNPYRIAQAGQLRAWEVE-RGLPDLDRQALRRAIHLLAEEVAQSLEITVQEAKRLFEEAWGEEL

(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 2 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=1.56

Estimated TM-score = 0.93±0.06

Estimated RMSD = 2.0±1.6Å

Download Model 2

C-score=-0.18

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	1ivsA	0.475	4.95	0.067	0.809
2	1ffyA	0.469	5.16	0.078	0.821
3	1x8rA	0.456	4.85	0.084	0.747
4	2d5bA	0.454	4.93	0.048	0.778
5	1lf9A	0.445	5.64	0.039	0.846
6	2cqtA	0.445	5.23	0.051	0.778
7	2nyzA	0.442	5.36	0.050	0.802
8	1jzsA	0.439	5.15	0.053	0.765
9	2pqcA	0.436	5.07	0.029	0.716
10	1xfiA	0.427	4.94	0.091	0.722

(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	0.09	4	2istA	BCT	Rep, Mult	106,109
2	0.09	4	3d4sA	CLR	Rep, Mult	108,128,132,135,136,140
3	0.05	2	1pkvA	RBF	Rep, Mult	6,9,10
4	0.05	2	3ny8A	CLR	Rep, Mult	108,135,136,139,140
5	0.02	1	3qfyB	BGC	Rep, Mult	99,106,111,130,131
6	0.02	1	3f1f2	MG	Rep, Mult	120,124
7	0.02	1	3iilA	MG	Rep, Mult	49,51
8	0.02	1	1bjyA	CTC	Rep, Mult	154,158
9	0.02	1	4ujmE	MG	Rep, Mult	109,113
10	0.02	1	2vhtB	ATP	Rep, Mult	29,31
11	0.02	1	4zdrA	TME	Rep, Mult	96,127
12	0.02	1	1pumA	GOL	Rep, Mult	6,7,75
13	0.02	1	2fkhB	CA	Rep, Mult	34,43
14	0.02	1	3mp8A	4BZ	Rep, Mult	90,94

	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	2qnoA	0.374	5.69	0.046	0.728	3.2.1.4	NA
2	0.060	2o15A	0.454	5.14	0.048	0.772	2.5.1.19	66,135,137
3	0.060	2esdA	0.404	5.15	0.058	0.728	1.2.1.9	137
4	0.060	2e8yA	0.393	5.94	0.067	0.802	3.2.1.41	110,155
5	0.060	1jxaA	0.427	5.29	0.046	0.765	2.6.1.16	NA
6	0.060	1gaxA	0.447	4.78	0.064	0.753	6.1.1.9	NA
7	0.060	2dkcA	0.386	5.51	0.048	0.704	5.4.2.3	12,15
8	0.060	1lf6A	0.427	4.97	0.040	0.735	3.2.1.3	NA
9	0.060	1wn1A	0.404	5.86	0.054	0.772	3.4.-.-	70
10	0.060	1d8yA	0.389	5.11	0.020	0.679	2.7.7.7	NA
11	0.060	1mosA	0.365	5.52	0.030	0.654	2.6.1.16	108
12	0.060	1a8hA	0.452	5.03	0.034	0.784	6.1.1.10	105
13	0.060	2vf4X	0.364	5.54	0.022	0.654	2.6.1.16	143
14	0.060	2pqdA	0.466	4.93	0.067	0.778	2.5.1.19	132
15	0.060	2cqsA	0.441	5.51	0.052	0.815	2.4.1.20	NA
16	0.060	1jroB	0.401	5.39	0.028	0.710	1.1.1.204	151
17	0.060	2fp0B	0.414	4.96	0.066	0.728	3.2.1.143	NA
18	0.060	2j08A	0.417	5.23	0.096	0.747	4.1.99.3	111
19	0.060	2e9bA	0.385	5.78	0.054	0.772	3.2.1.41	111,126

(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	0.14	0.469	5.16	0.08	0.82	1ffyA	GO:0000166 GO:0002161 GO:0004812 GO:0004822 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006428 GO:0006450 GO:0008270 GO:0016874 GO:0046872
1	0.07	0.469	5.19	0.08	0.83	5k0sC	GO:0000166 GO:0004812 GO:0004825 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006431 GO:0016874
2	0.07	0.482	5.08	0.07	0.81	3kflA	GO:0000166 GO:0000287 GO:0004812 GO:0004825 GO:0005524 GO:0005737 GO:0005829 GO:0006412 GO:0006418 GO:0006431 GO:0016874
3	0.07	0.468	4.76	0.05	0.78	2x1lA	GO:0000166 GO:0004812 GO:0004825 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006431 GO:0016874
4	0.07	0.444	4.98	0.09	0.77	1ileA	GO:0000166 GO:0002161 GO:0004812 GO:0004822 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006428 GO:0006450 GO:0008270 GO:0016874 GO:0046872
5	0.07	0.450	5.27	0.09	0.83	2x1lC	GO:0000166 GO:0004812 GO:0004825 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006431 GO:0016874
6	0.07	0.456	4.85	0.06	0.78	4qrdA	GO:0000049 GO:0000166 GO:0003723 GO:0004812 GO:0004825 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006431 GO:0016874
7	0.07	0.496	5.20	0.08	0.86	4eg6B	GO:0000166 GO:0004812 GO:0004825 GO:0005524 GO:0005737 GO:0005829 GO:0006412 GO:0006418 GO:0006431 GO:0016874
8	0.07	0.484	4.95	0.08	0.80	1rqgA	GO:0000049 GO:0000166 GO:0003723 GO:0004812 GO:0004825 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006431 GO:0016874 GO:0046872
9	0.07	0.452	5.03	0.03	0.78	1a8hA	GO:0000049 GO:0000166 GO:0003723 GO:0004812 GO:0004825 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006431 GO:0016874 GO:0046872
10	0.07	0.492	4.95	0.08	0.80	4ariA	GO:0000166 GO:0002161 GO:0004812 GO:0004823 GO:0005524 GO:0005737 GO:0005829 GO:0006412 GO:0006418 GO:0006429 GO:0006450 GO:0016874
11	0.07	0.439	4.94	0.09	0.76	1pg0A	GO:0000049 GO:0000166 GO:0003723 GO:0004812 GO:0004825 GO:0005524 GO:0005737 GO:0005829 GO:0006412 GO:0006418 GO:0006431 GO:0008270 GO:0016020 GO:0016874 GO:0046872
12	0.06	0.393	5.37	0.06	0.71	3pefA	GO:0000166 GO:0004616 GO:0016491 GO:0051287 GO:0055114
13	0.06	0.439	5.29	0.08	0.79	1wz2A	GO:0000166 GO:0002161 GO:0004812 GO:0004823 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006429 GO:0006450 GO:0016874
14	0.06	0.483	5.21	0.06	0.84	4dlpC	GO:0000166 GO:0004812 GO:0004825 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006431 GO:0016874
15	0.06	0.466	4.99	0.05	0.79	3ziuA	GO:0000166 GO:0004812 GO:0004823 GO:0005524 GO:0006418 GO:0006429 GO:0016874
16	0.06	0.378	5.47	0.06	0.71	4lhdA	GO:0003824 GO:0004375 GO:0005829 GO:0005960 GO:0006544 GO:0006546 GO:0016491 GO:0016594 GO:0019464 GO:0055114
17	0.06	0.315	5.70	0.07	0.59	1ml5f	GO:0003723 GO:0003735 GO:0005840 GO:0006412 GO:0019843 GO:0030529
18	0.06	0.459	4.90	0.09	0.74	2zueA	GO:0000166 GO:0004812 GO:0004814 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006420 GO:0016874

Consensus prediction of GO terms

Molecular Function	GO:0046914	GO:0052689	GO:0005524	GO:0004812
GO-Score	0.39	0.39	0.34	0.34
Biological Processes	GO:0065008	GO:0006448	GO:0006418
GO-Score	0.39	0.39	0.34
Cellular Component	GO:0005737
GO-Score	0.34

(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.