I-TASSER results

I-TASSER results for job id Rv2021c

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

Input Sequence in FASTA format

>protein (101 residues)
MAMTLRDMDAVRPVNREAVDRHKARMRDEVRAFRLRELRAAQSLTQVQVAALAHIRQSRV
SSIENGDIGSAQVNTLRKYVSALGGELDITVRLGDETFTLA

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MAMTLRDMDAVRPVNREAVDRHKARMRDEVRAFRLRELRAAQSLTQVQVAALAHIRQSRVSSIENGDIGSAQVNTLRKYVSALGGELDITVRLGDETFTLA
Prediction	CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCEEEEEEEHCCCEEHCC
Conf.Score	99899999998558989999999999999999999999999899999999998999899999986999998789999999998998999999899657769
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MAMTLRDMDAVRPVNREAVDRHKARMRDEVRAFRLRELRAAQSLTQVQVAALAHIRQSRVSSIENGDIGSAQVNTLRKYVSALGGELDITVRLGDETFTLA
Prediction	77442640376347556325524541453324430351067473315400642725453024025464761305203310521434040205157762618
	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

                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCEEEEEEEHCCCEEHCC
MAMTLRDMDAVRPVNREAVDRHKARMRDEVRAFRLRELRAAQSLTQVQVAALAHIRQSRVSSIENGDIGSAQVNTLRKYVSALGGELDITVRLGDETFTLA

3vk0A

0.20

0.17

0.85

1.83

MUSTER

LTLP-----AELPDEQD---------LRAVLAYNMRLFRVNKGWSQEELARQCGLDRTYVSAVERKRW-NIALSNIEKMAAALGVAAYQLLLPPQERLKLM

1y7yA

0.29

0.20

0.68

1.98

dPPAS

---------------------HDHYADLVKFGQRLRELRTAKGLSQETLAFLSGLDRSYVGGVERGQ-RNVSLVNILKLATALDIEPRELF----------

1y7yA

0.29

0.20

0.68

2.46

wdPPAS

---------------------HDHYADLVKFGQRLRELRTAKGLSQETLAFLSGLDRSYVGGVERGQ-RNVSLVNILKLATALDIEPRELF----------

3vk0A

0.20

0.17

0.85

2.37

wMUSTER

LTLP-----AELPDEQD---------LRAVLAYNMRLFRVNKGWSQEELARQCGLDRTYVSAVERKR-WNIALSNIEKMAAALGVAAYQLLLPPQERLKLM

3vk0A

0.17

0.15

0.85

2.41

wPPAS

LTLP--------AELP------DEQDLRAVLAYNMRLFRVNKGWSQEELARQCGLDRTYVSAVERKR-WNIALSNIEKMAAALGVAAYQLLLPPQERLKLM

1y7yA

0.29

0.20

0.68

3.98

dPPAS2

---------------------HDHYADLVKFGQRLRELRTAKGLSQETLAFLSGLDRSYVGGVERGQ-RNVSLVNILKLATALDIEPRELF----------

3dnvB

0.20

0.14

0.70

2.04

PPAS

---------------------FQKIYSPTQLANAMKLVRQQNGWTQSELAKKIGIKQATISNFENNP-DNTTLTTFFKILQSLELSMTLC----DAK----

2gzuA

0.18

0.12

0.65

2.36

Env-PPAS

-----------------------------MIINNLKLIREKKKISQSELAALLEVSRQTINGIEKNKY-NPSLQLALKIAYYLNTPLEDIFQWQPE-----

2b5aA

0.21

0.16

0.76

1.83

MUSTER

MI--------------------NEIEIKRKFGRTLKKIRTQKGVSQEELADLAGLHRTYISEVERGDR-NISLINIHKICAALDIPASTFFRKMEEEN---

3dnvB

0.18

0.13

0.70

1.91

dPPAS

---------------------FQKIYSPTQLANAMKLVRQQNGWTQSELAKKIGIKQATISNFENNP-DNTTLTTFFKILQSLELSMTLCDAK--------

(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=-1.20

Estimated TM-score = 0.57±0.15

Estimated RMSD = 6.4±3.9Å

Download Model 2

C-score=-1.18

Download Model 3

C-score=-1.54

Download Model 4

C-score=-3.52

Download Model 5

C-score=-4.33

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	2b5aA	0.678	1.43	0.187	0.743
2	1y7yA	0.648	0.90	0.290	0.683
3	3f51A	0.639	2.46	0.179	0.752
4	3g5gJ	0.635	1.95	0.133	0.733
5	3vk0A	0.624	2.31	0.174	0.762
6	1y9qA	0.614	1.81	0.216	0.693
7	3pxpA	0.608	2.67	0.158	0.743
8	2ofyA	0.606	1.82	0.215	0.693
9	1b0nA	0.594	1.82	0.200	0.683
10	3eusA	0.594	2.42	0.241	0.733

(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	0.73	60	4iwrA	NUC	Rep, Mult	39,45,46,47,57,58,61,65,72
2	0.02	3	3qyxB	QNA	Rep, Mult	56,59,70,72,75
3	0.02	3	2ofy0	III	Rep, Mult	27,31,71,72,73,74,76,86,87,88,91
4	0.01	1	1y7y0	III	Rep, Mult	24,25,27,28,31,69,70,71,72,73,76,87,91
5	0.01	1	1b0nA	ZN	Rep, Mult	30,93
6	0.01	1	1b0nA	ZN	Rep, Mult	84

	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	1tj7A	0.495	3.51	0.053	0.762	4.3.2.1	NA
2	0.060	1occA	0.484	3.42	0.063	0.733	1.9.3.1	NA
3	0.060	1z6fA	0.485	3.49	0.098	0.733	3.4.16.4	48
4	0.060	1dw9A	0.494	3.06	0.110	0.703	4.2.1.104	77
5	0.060	2pnrF	0.492	4.03	0.074	0.802	2.7.11.2	NA
6	0.060	3no9A	0.483	3.85	0.086	0.762	4.2.1.2	52
7	0.060	2pnrB	0.494	4.13	0.074	0.812	2.7.11.2	NA
8	0.060	2e9fB	0.515	3.78	0.064	0.792	4.3.2.1	NA
9	0.060	1b26A	0.489	4.60	0.074	0.861	1.4.1.3	NA
10	0.060	2yyjA	0.505	4.19	0.050	0.822	1.14.13.3	NA
11	0.060	1hwxA	0.477	4.65	0.040	0.871	1.4.1.3	74
12	0.060	1yfmA	0.498	3.66	0.021	0.772	4.2.1.2	NA
13	0.060	1y8pA	0.486	4.09	0.074	0.802	2.7.11.2	NA
14	0.060	2ix6E	0.510	4.03	0.081	0.832	1.3.3.6	NA
15	0.060	1jswB	0.496	3.69	0.087	0.752	4.3.1.1	86
16	0.060	1u8vA	0.483	3.85	0.032	0.812	5.3.3.3	NA
17	0.060	1b3bE	0.489	4.58	0.085	0.852	1.4.1.3	80
18	0.060	1k62B	0.502	3.55	0.053	0.772	4.3.2.1	86
19	0.060	1dofA	0.489	3.74	0.064	0.762	4.3.2.2	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	0.34	0.590	2.29	0.15	0.70	1adrA	GO:0003677 GO:0006351 GO:0006355 GO:0043565
1	0.31	0.678	1.43	0.19	0.74	2b5aA
2	0.31	0.641	2.20	0.13	0.74	4i6uA	GO:0003677 GO:0043565
3	0.30	0.639	2.46	0.18	0.75	3f51A	GO:0003677 GO:0043565
4	0.30	0.574	2.57	0.24	0.69	4ghjB	GO:0003677 GO:0043565
5	0.27	0.518	2.06	0.24	0.61	1sq8A	GO:0003677 GO:0006351 GO:0006355 GO:0043565
6	0.24	0.549	2.54	0.19	0.69	4yg1A	GO:0000985 GO:0003677 GO:0006351 GO:0006355 GO:0043565 GO:0045892
7	0.24	0.624	2.31	0.17	0.76	3vk0A	GO:0003677 GO:0043565
8	0.23	0.522	1.86	0.17	0.62	2gzuA	GO:0003677 GO:0043565
9	0.23	0.591	1.79	0.20	0.68	2ewtA	GO:0003677 GO:0043565
10	0.22	0.529	1.59	0.13	0.61	3bs3A	GO:0003677 GO:0043565
11	0.22	0.554	2.10	0.18	0.67	3omtA	GO:0003677 GO:0043565
12	0.21	0.547	2.80	0.11	0.69	2jvlA	GO:0003677 GO:0043565
13	0.20	0.594	2.42	0.24	0.73	3eusA	GO:0003677 GO:0043565
14	0.20	0.534	2.59	0.22	0.69	2ef8A	GO:0003677 GO:0043565
15	0.19	0.525	2.83	0.19	0.65	4ybaB	GO:0003677 GO:0043565
16	0.19	0.568	2.17	0.17	0.67	4jqdE	GO:0003677 GO:0043565
17	0.18	0.548	2.62	0.21	0.69	3ivpA	GO:0003677 GO:0043565
18	0.16	0.555	2.58	0.14	0.67	1x57A	GO:0003677 GO:0003700 GO:0003713 GO:0004402 GO:0005516 GO:0005622 GO:0005634 GO:0005669 GO:0005730 GO:0005737 GO:0006351 GO:0006355 GO:0007275 GO:0008168 GO:0019216 GO:0030154 GO:0043388 GO:0043565 GO:0044822 GO:0045446 GO:0045893 GO:0070062
19	0.15	0.648	0.90	0.29	0.68	1y7yA	GO:0003677 GO:0043565
20	0.14	0.531	3.01	0.21	0.71	3mlfA	GO:0003677 GO:0043565
21	0.13	0.545	2.46	0.16	0.68	2wusR	GO:0003677 GO:0016020 GO:0016021
22	0.11	0.570	2.59	0.26	0.71	3b7hA	GO:0003677 GO:0043565
23	0.07	0.633	1.79	0.22	0.71	1y9qA	GO:0003677 GO:0003700 GO:0006355 GO:0043565 GO:0046872
24	0.07	0.594	1.82	0.20	0.68	1b0nA	GO:0003677 GO:0006351 GO:0006355 GO:0010629 GO:0030435 GO:0043565 GO:0046983
25	0.07	0.561	1.89	0.21	0.65	2qfcA	GO:0003677 GO:0043565
26	0.07	0.544	2.78	0.25	0.67	3kxaA	GO:0003677 GO:0043565

Consensus prediction of GO terms

Molecular Function	GO:0043565
GO-Score	0.78
Biological Processes	GO:0006355
GO-Score	0.34
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.