I-TASSER results

I-TASSER results for job id Rv0474

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

Input Sequence in FASTA format

>protein (140 residues)
MSSEEKLAAKVSTKASDVASDIGSFIRSQRETAHVSMRQLAERSGVSNPYLSQVERGLRK
PSADVLSQIAKALRVSAEVLYVRAGILEPSETSQVRDAIITDTAITERQKQILLDIYASF
THQNEATREECPSDPTPTDD

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MSSEEKLAAKVSTKASDVASDIGSFIRSQRETAHVSMRQLAERSGVSNPYLSQVERGLRKPSADVLSQIAKALRVSAEVLYVRAGILEPSETSQVRDAIITDTAITERQKQILLDIYASFTHQNEATREECPSDPTPTDD
Prediction	CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHCCCCCCHHHHHHHHHHHCCCHHHHHHCCCCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCC
Conf.Score	99877888876665778999999999999999899999999998999999999986999999999999999989998998864688887654789999997668999999999999999999756666678889888899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MSSEEKLAAKVSTKASDVASDIGSFIRSQRETAHVSMRQLAERSGVSNPYLSQVERGLRKPSADVLSQIAKALRVSAEVLYVRAGILEPSETSQVRDAIITDTAITERQKQILLDIYASFTHQNEATREECPSDPTPTDD
Prediction	76765644564654455035401530251067372215300741713442023114454413151033006227042430144374356744640350146257036722530250053026545556754466656478
	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

CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHCCCCCCHHHHHHHHHHHCCCHHHHHHCCCCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCC
MSSEEKLAAKVSTKASDVASDIGSFIRSQRETAHVSMRQLAERSGVSNPYLSQVERGLRKPSADVLSQIAKALRVSAEVLYVRAGILEPSETSQVRDAIITDTAITERQKQILLDIYASFTHQNEATREECPSDPTPTDD

1b0nA

0.29

0.21

0.73

1.97

MUSTER

--------------------MIGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNLTNPSIQFLEKVSAVLDVSVHTLLDEKHETLDSEWEKLVRDAMT-SGVSKKQFREFLDYQKWRKSQ-----------------

1b0nA

0.29

0.21

0.73

2.71

dPPAS

--------------------MIGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNLTNPSIQFLEKVSAVLDVSVHTLLDEKHETLDSEWEKLVRDAMT-SGVSKKQFREFLDYQKWRKSQ-----------------

1b0nA

0.28

0.21

0.73

3.12

wdPPAS

--------------------MIGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNQTNPSIQFLEKVSAVLDVSVHTLLDEKHETLDSEWEKLVRDAMT-SGVSKKQFREFLDYQKWRKSQ-----------------

1b0nA

0.29

0.21

0.73

2.28

wMUSTER

--------------------MIGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNLTNPSIQFLEKVSAVLDVSVHTLLDEKHETLDSEWEKLVRDAMT-SGVSKKQFREFLDYQKWRKSQ-----------------

1b0nA

0.28

0.21

0.73

2.81

wPPAS

--------------------MIGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNQTNPSIQFLEKVSAVLDVSVHTLLDEKHETLDSEWEKLVRDAMT-SGVSKKQFREFLDYQKWRKSQ-----------------

1b0nA

0.29

0.21

0.73

5.15

dPPAS2

--------------------MIGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNLTNPSIQFLEKVSAVLDVSVHTLLDEKHETLDSEWEKLVRDAMT-SGVSKKQFREFLDYQKWRKSQ-----------------

1b0nA

0.28

0.21

0.73

2.33

PPAS

--------------------MIGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNQTNPSIQFLEKVSAVLDVSVHTLLDEKHETLDSEWEKLVRDAMT-SGVSKKQFREFLDYQKWRKSQ-----------------

1b0nA

0.28

0.21

0.73

3.29

Env-PPAS

--------------------MIGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNQTNPSIQFLEKVSAVLDVSVHTLLDEKHETLDSEWEKLVRDAMTSG-VSKKQFREFLDYQKWRKSQ-----------------

3f51A

0.28

0.19

0.67

1.76

MUSTER

-------------PEPLLREALGAALRSFRADKGVTLRELAEASRVSPGYLSELERGRKEVSSELLASVCHALGASVADVLIEAAGSMALQAAQEDLARVLEWSHPQ---------------------------------

3f51A

0.28

0.19

0.67

2.48

dPPAS

-------------PEPLLREALGAALRSFRADKGVTLRELAEASRVSPGYLSELERGRKEVSSELLASVCHALGASVADVLIEAAGSMALQAAQEDLARVLEWSHPQ---------------------------------

(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=-1.00

Estimated TM-score = 0.59±0.14

Estimated RMSD = 6.7±4.0Å

Download Model 2

C-score=-2.66

Download Model 3

C-score=-1.12

Download Model 4

C-score=-1.74

Download Model 5

C-score=-1.42

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	1b0nA	0.676	1.36	0.294	0.721
2	3vk0A	0.560	2.09	0.216	0.629
3	3pxpA	0.543	3.41	0.137	0.721
4	3mxlA	0.529	4.95	0.086	0.879
5	1bucA	0.518	4.88	0.058	0.857
6	3lfpA	0.517	2.75	0.178	0.621
7	3ii9C	0.516	4.75	0.073	0.850
8	4o8bA	0.516	3.01	0.211	0.657
9	3oibA	0.514	4.86	0.095	0.857
10	4fyeA	0.512	4.64	0.068	0.850

(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	0.23	17	4iwrA	NUC	Rep, Mult	30,36,37,38,48,49,52,56,62
2	0.07	6	3p4tB	FAO	Rep, Mult	29,38,68,69,71
3	0.06	5	3dtuC	TRD	Rep, Mult	26,66,70,71,74
4	0.04	3	3s8qB	NUC	Rep, Mult	45,46,47,48,49,50,59,60,61,62,65
5	0.02	2	1zzcB	TRS	Rep, Mult	101,116,133,136,140
6	0.02	2	1zzcA	TRS	Rep, Mult	116,133,136,140
7	0.01	1	1b0nA	ZN	Rep, Mult	82,85
8	0.01	1	1y9qA	MED	Rep, Mult	63,67,102,117,119,130,133,140
9	0.01	1	2bnoB	HG	Rep, Mult	103,104,105,117,119
10	0.01	1	1b0nA	ZN	Rep, Mult	21,83
11	0.01	1	1b0nA	ZN	Rep, Mult	74,107
12	0.01	1	1b0n0	III	Rep, Mult	29,32,74,75,76,79,82,84,85,88,91,92,95,96,97,99,100,105,106,107,109,110,111,113,114,117,118,121
13	0.01	1	4i8tA	NUC	Rep, Mult	30,36,37,56

	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	3d9dA	0.401	4.87	0.076	0.671	1.7.3.1	NA
2	0.060	1ivhA	0.501	4.80	0.066	0.843	1.3.99.10	NA
3	0.060	1itzB	0.465	4.34	0.058	0.743	2.2.1.1	NA
4	0.060	2nyfA	0.469	4.77	0.055	0.829	4.3.1.5	51
5	0.060	2pfmA	0.461	4.79	0.072	0.807	4.3.2.2	NA
6	0.060	1qleA	0.451	5.09	0.046	0.786	1.9.3.1	25
7	0.060	1pg3B	0.473	5.55	0.043	0.921	6.2.1.1	42
8	0.060	1fftA	0.482	4.93	0.045	0.850	1.10.3.-	NA
9	0.060	1qw6A	0.473	4.64	0.025	0.786	1.14.13.39	NA
10	0.060	2ix6A	0.499	4.86	0.088	0.864	1.3.3.6	NA
11	0.060	2rioA	0.466	4.44	0.034	0.757	2.7.11.1	NA
12	0.060	2ix6E	0.500	4.86	0.088	0.864	1.3.3.6	NA
13	0.060	1itzA	0.464	4.44	0.057	0.750	2.2.1.1	44
14	0.060	2jifA	0.461	5.14	0.083	0.829	1.3.99.-	NA
15	0.060	1t9gC	0.480	5.06	0.086	0.836	1.3.99.3	78
16	0.060	1d0cA	0.476	4.55	0.085	0.786	1.14.13.39	NA
17	0.060	2fenD	0.482	4.84	0.064	0.807	5.5.1.2	55
18	0.060	1udyA	0.479	5.14	0.086	0.850	1.3.99.3	NA
19	0.060	3fbvD	0.461	4.29	0.089	0.743	2.7.11.1,	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	0.33	0.473	1.88	0.27	0.52	3f51A	GO:0003677 GO:0043565
1	0.28	0.485	1.93	0.25	0.54	2b5aA
2	0.25	0.509	2.95	0.17	0.64	4jqdE	GO:0003677 GO:0043565
3	0.24	0.464	2.44	0.22	0.53	4i6uA	GO:0003677 GO:0043565
4	0.23	0.560	2.09	0.22	0.63	3vk0A	GO:0003677 GO:0043565
5	0.23	0.676	1.36	0.29	0.72	1b0nA	GO:0003677 GO:0006351 GO:0006355 GO:0010629 GO:0030435 GO:0043565 GO:0046983
6	0.22	0.463	1.23	0.28	0.49	1y7yA	GO:0003677 GO:0043565
7	0.18	0.473	3.24	0.14	0.64	3ivpA	GO:0003677 GO:0043565
8	0.18	0.516	3.01	0.21	0.66	4o8bA	GO:0003677 GO:0043565
9	0.14	0.520	3.35	0.13	0.69	5d4z1	GO:0003677 GO:0043565
10	0.07	0.514	4.86	0.10	0.86	3oibA	GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
11	0.07	0.502	4.79	0.07	0.86	4m9aB	GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
12	0.07	0.506	2.45	0.17	0.58	1y9qA	GO:0003677 GO:0003700 GO:0006355 GO:0043565 GO:0046872
13	0.07	0.504	4.96	0.06	0.85	4w9uB	GO:0003995 GO:0004361 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
14	0.07	0.508	4.65	0.08	0.83	2pg0A	GO:0000166 GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
15	0.07	0.501	4.80	0.07	0.84	1ivhA	GO:0000062 GO:0003995 GO:0005739 GO:0005759 GO:0006552 GO:0008152 GO:0008470 GO:0009055 GO:0009083 GO:0016491 GO:0016627 GO:0033539 GO:0050660 GO:0052890 GO:0055088 GO:0055114
16	0.07	0.495	4.95	0.07	0.86	3x0yA	GO:0003995 GO:0008152 GO:0016627 GO:0050660 GO:0055114
17	0.07	0.480	5.16	0.07	0.86	3mddA	GO:0000062 GO:0001889 GO:0003995 GO:0005739 GO:0005759 GO:0005777 GO:0005978 GO:0006082 GO:0006111 GO:0006629 GO:0006631 GO:0006635 GO:0007507 GO:0008152 GO:0009055 GO:0009409 GO:0009437 GO:0009791 GO:0016491 GO:0016627 GO:0019254 GO:0033539 GO:0042594 GO:0050660 GO:0051791 GO:0052890 GO:0055007 GO:0055088 GO:0055114 GO:0070991
18	0.07	0.452	4.96	0.07	0.79	3r7kA	GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
19	0.07	0.482	5.16	0.09	0.86	1ukwA	GO:0000166 GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
20	0.07	0.483	5.13	0.07	0.86	2d29A	GO:0000166 GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
21	0.07	0.398	5.76	0.05	0.80	3pfdC	GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0043565
GO-Score	0.70
Biological Processes
GO-Score
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.