I-TASSER results

I-TASSER results for job id Rv3183

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

Input Sequence in FASTA format

>protein (109 residues)
MTMARNWRDIRADAVAQGRVDLQRAAVAREEMRDAVLAHRLAEIRKALGHARQADVAALM
GVSQARVSKLESGDLSHTELGTLQAYVAALGGHLRIVAEFGENTVELTA

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MTMARNWRDIRADAVAQGRVDLQRAAVAREEMRDAVLAHRLAEIRKALGHARQADVAALMGVSQARVSKLESGDLSHTELGTLQAYVAALGGHLRIVAEFGENTVELTA
Prediction	CCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCEEEEEEEHCCCEEEHCC
Conf.Score	9988899999999987547999999999999999999999999999996998999999989998999999868999875799999999989889999997996577589
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MTMARNWRDIRADAVAQGRVDLQRAAVAREEMRDAVLAHRLAEIRKALGHARQADVAALMGVSQARVSKLESGDLSHTELGTLQAYVAALGGHLRIVAEFGENTVELTA
Prediction	8764442640355246656544642552454145223634035105636434154006427354530240154647514041033105213440402040577726158
	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

CCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCEEEEEEEHCCCEEEHCC
MTMARNWRDIRADAVAQGRVDLQRAAVAREEMRDAVLAHRLAEIRKALGHARQADVAALMGVSQARVSKLESGDLSHTELGTLQAYVAALGGHLRIVAEFGENTVELTA

3vk0A

0.22

0.17

0.81

1.62

MUSTER

----------------KLTLPAELP---DEQDLRAVLAYNMRLFRVNKGWS-QEELARQCGLDRTYVSAVERKRW-NIALSNIEKMAAALGVAAYQLLLPPQERLKLMT

1y7yA

0.25

0.16

0.63

1.48

dPPAS

---------------------------HDHYADLVKFGQRLRELRTAKGLS-QETLAFLSGLDRSYVGGVERGQR-NVSLVNILKLATALDIEPRELF-----------

3dnvB

0.21

0.14

0.65

2.18

wdPPAS

---------------------------FQKIYSPTQLANAMKLVRQQNGWT-QSELAKKIGIKQATISNFENNP-DNTTLTTFFKILQSLELSMTLCDAK---------

3vk0A

0.23

0.18

0.80

2.07

wMUSTER

LTLP-----------AELPDEQD---------LRAVLAYNMRLFRVNKGWS-QEELARQCGLDRTYVSAVERKR-WNIALSNIEKMAAALGVAAYQLLLPPQERLKLMT

3dnvB

0.21

0.14

0.65

2.33

wPPAS

---------------------------FQKIYSPTQLANAMKLVRQQNGWT-QSELAKKIGIKQATISNFENNP-DNTTLTTFFKILQSLELSMTLC----DAK-----

1y7yA

0.25

0.16

0.63

3.14

dPPAS2

---------------------------HDHYADLVKFGQRLRELRTAKGLS-QETLAFLSGLDRSYVGGVERGQR-NVSLVNILKLATALDIEPRELF-----------

3dnvB

0.21

0.14

0.65

1.89

PPAS

---------------------------FQKIYSPTQLANAMKLVRQQNGWT-QSELAKKIGIKQATISNFENNP-DNTTLTTFFKILQSLELSMTLC----DAK-----

3dnvB

0.21

0.14

0.65

2.15

Env-PPAS

---------------------------FQKIYSPTQLANAMKLVRQQNGWT-QSELAKKIGIKQATISNFENNPD-NTTLTTFFKILQSLELSMTLC----DAK-----

2b5aA

0.25

0.17

0.70

1.53

MUSTER

MIN--------------------------EIEIKRKFGRTLKKIRTQKGVS-QEELADLAGLHRTYISEVERGDRN-ISLINIHKICAALDIPATFFRKMEEEN-----

3dnvB

0.21

0.14

0.65

1.45

dPPAS

---------------------------FQKIYSPTQLANAMKLVRQQNGWT-QSELAKKIGIKQATISNFENNP-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=-1.18

Estimated TM-score = 0.57±0.15

Estimated RMSD = 6.5±4.0Å

Download Model 2

C-score=-2.45

Download Model 3

C-score=-2.74

Download Model 4

C-score=-2.72

Download Model 5

C-score=-4.19

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	3vk0A	0.639	2.28	0.218	0.780
2	2b5aA	0.571	2.61	0.237	0.688
3	3g5gJ	0.570	2.06	0.133	0.670
4	3f51A	0.562	2.22	0.203	0.679
5	2kpjA	0.558	2.46	0.156	0.697
6	1y9qA	0.553	2.51	0.243	0.670
7	3pxpA	0.548	2.94	0.192	0.697
8	1y7yA	0.548	1.80	0.246	0.633
9	5anzA	0.541	4.18	0.090	0.872
10	3eusA	0.539	2.21	0.247	0.651

(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	0.31	8	5k98P	NUC	Rep, Mult	45,53,64,65,68,72
2	0.07	2	1b0nA	ZN	Rep, Mult	36,102
3	0.04	1	1b0nA	ZN	Rep, Mult	33,99
4	0.03	1	1zz7B	UUU	Rep, Mult	34,74,77,85
5	0.03	1	3e62A	5B1	Rep, Mult	55,56,59,60,87
6	0.03	1	2z55B	UUU	Rep, Mult	60,61,62
7	0.03	1	2ofy0	III	Rep, Mult	33,37,79,80,81,83,93,94,95,97,99

	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	3dqwA	0.515	4.07	0.064	0.853	2.7.10.2	NA
2	0.060	3dsiA	0.509	4.28	0.038	0.890	4.2.1.92	NA
3	0.060	3brbB	0.512	3.65	0.108	0.780	2.7.10.1	66
4	0.060	1mqbB	0.515	3.75	0.075	0.807	2.7.10.1,2.7.1.112	55,57
5	0.060	2gqgA	0.517	3.78	0.065	0.835	2.7.10.2	55,57
6	0.060	1p4oB	0.515	3.76	0.087	0.798	2.7.10.1,2.7.1.112	NA
7	0.060	2vwxA	0.504	3.68	0.053	0.780	2.7.10.1	55,57
8	0.060	3e62A	0.523	3.92	0.031	0.853	2.7.10.2	55,57
9	0.060	2dq7X	0.521	4.02	0.064	0.853	2.7.10.2	66
10	0.060	2hz0B	0.500	3.63	0.089	0.780	2.7.10.2	NA
11	0.060	3gvuA	0.501	3.57	0.117	0.771	2.7.10.2	NA
12	0.060	2qi8A	0.506	4.05	0.089	0.807	2.7.10.2	55
13	0.060	3d7uA	0.520	3.64	0.089	0.817	2.7.10.2	55,57
14	0.060	1yolA	0.503	3.84	0.067	0.789	2.7.10.2,2.7.1.112	37
15	0.060	3fxxA	0.510	3.92	0.097	0.817	2.7.10.1	55,57
16	0.060	1uedA	0.511	4.34	0.041	0.862	1.14.-.-	NA
17	0.060	1d0kA	0.527	4.18	0.050	0.881	4.2.2.-	NA
18	0.060	1yvjA	0.517	4.08	0.093	0.844	2.7.10.2	55,57
19	0.060	2helA	0.504	4.10	0.099	0.817	2.7.10.1	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	0.29	0.579	2.31	0.13	0.69	4i6uA	GO:0003677 GO:0043565
1	0.27	0.562	2.22	0.20	0.68	3f51A	GO:0003677 GO:0043565
2	0.26	0.480	1.97	0.27	0.58	1sq8A	GO:0003677 GO:0006351 GO:0006355 GO:0043565
3	0.24	0.510	2.33	0.19	0.62	4ghjB	GO:0003677 GO:0043565
4	0.24	0.487	2.70	0.17	0.63	2ef8A	GO:0003677 GO:0043565
5	0.23	0.476	2.01	0.21	0.58	2gzuA	GO:0003677 GO:0043565
6	0.23	0.488	2.69	0.21	0.62	4yg1A	GO:0000985 GO:0003677 GO:0006351 GO:0006355 GO:0043565 GO:0045892
7	0.23	0.537	3.00	0.23	0.71	3f6wA	GO:0003677 GO:0043565
8	0.22	0.639	2.28	0.22	0.78	3vk0A	GO:0003677 GO:0043565
9	0.21	0.539	2.21	0.25	0.65	3eusA	GO:0003677 GO:0043565
10	0.19	0.538	1.83	0.19	0.63	4jqdE	GO:0003677 GO:0043565
11	0.18	0.571	2.61	0.24	0.69	2b5aA
12	0.17	0.557	2.22	0.18	0.67	5d4z1	GO:0003677 GO:0043565
13	0.16	0.514	1.91	0.17	0.62	2ewtA	GO:0003677 GO:0043565
14	0.16	0.518	2.29	0.23	0.65	4o8bA	GO:0003677 GO:0043565
15	0.15	0.512	2.82	0.15	0.65	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
16	0.14	0.548	1.80	0.25	0.63	1y7yA	GO:0003677 GO:0043565
17	0.11	0.478	2.73	0.11	0.61	4ybaB	GO:0003677 GO:0043565
18	0.07	0.527	2.58	0.15	0.67	3b7hA	GO:0003677 GO:0043565
19	0.07	0.570	2.48	0.25	0.69	1y9qA	GO:0003677 GO:0003700 GO:0006355 GO:0043565 GO:0046872
20	0.07	0.536	2.20	0.16	0.62	1b0nA	GO:0003677 GO:0006351 GO:0006355 GO:0010629 GO:0030435 GO:0043565 GO:0046983
21	0.07	0.499	3.01	0.18	0.67	3kxaA	GO:0003677 GO:0043565

Consensus prediction of GO terms

Molecular Function	GO:0043565
GO-Score	0.78
Biological Processes	GO:1903506	GO:2000112	GO:0010468
GO-Score	0.52	0.52	0.52
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.