I-TASSER results

I-TASSER results for job id Rv1152

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

Input Sequence in FASTA format

>protein (121 residues)
MELRDWLRVDVKAGKPLFDQLRTQVIDGVRAGALPPGTRLPTVRDLAGQLGVAANTVARA
YRELESAAIVETRGRFGTFISRFDPTDAAMAAAAKEYVGVARALGLTKSDAMRYLTHVPD
D

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MELRDWLRVDVKAGKPLFDQLRTQVIDGVRAGALPPGTRLPTVRDLAGQLGVAANTVARAYRELESAAIVETRGRFGTFISRFDPTDAAMAAAAKEYVGVARALGLTKSDAMRYLTHVPDD
Prediction	CCCCCCEEHCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHCCEEEHCCCEEEHCCCCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCC
Conf.Score	9987765765899986899999999999998999999568859999999899999999999999998988997887589858865689999999999999999899999999999999769
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MELRDWLRVDVKAGKPLFDQLRTQVIDGVRAGALPPGTRLPTVRDLAGQLGVAANTVARAYRELESAAIVETRGRFGTFISRFDPTDAAMAAAAKEYVGVARALGLTKSDAMRYLTHVPDD
Prediction	8725420402473732003101520362046351556553343241075371334004401530374220313443121025556645414640451054047371447202510561278
	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

                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCEEHCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHCCEEEHCCCEEEHCCCCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCC
MELRDWLRVDVKAGKPLFDQLRTQVIDGVRAGALPPGTRLPTVRDLAGQLGVAANTVARAYRELESAAIVETRGRFGTFISRFDPTDAAMAAAAKEYVGVARALGLTKSDAMRYLTHVPDD

4hamA

0.25

0.98

2.36

MUSTER

---SNAFTINTKSQLPIYEQIVQKIKEQVVKGVLQEGEKILSIREFASRIGVNPNTVSKAYQELERQEVIITVKGKGTFIANQTKKLAETRTKLKETILDLVYLGVNIEEIHKLADEYSQD

4r1hA

0.25

0.23

0.92

3.99

dPPAS

----------FDDSKPIYKQIVHYIHTEIVTGTYEAGDKLLSVRELATKLEVNPTTIQRAYAELEETEIIYTVRGTGKYLTEDEQLENDIAKQLTENFISESKLGINKEKIIAWVKKVEEV

4hamA

0.25

0.98

3.92

wdPPAS

---SNAFTINTKSQLPIYEQIVQKIKEQVVKGVLQEGEKILSIREFASRIGVNPNTVSKAYQELERQEVIITVKGKGTFIANQTKKLAETRTKLKETILDLVYLGVNIEEIHKLADEYSQD

4hamA

0.26

0.25

0.97

2.78

wMUSTER

NA----FTINTKSQLPIYEQIVQKIKEQVVKGVLQEGEKILSIREFASRIGVNPNTVSKAYQELERQEVIITVKGKGTFIANQTKKLAETRTKLKETILDLVYLGVNIEEIHKLADEYSQD

4r1hA

0.25

0.23

0.91

3.47

wPPAS

----------FDDSKPIYKQIVHYIHTEIVTGTYEAGDKLLSVRELATKLEVNPTTIQRAYAELEETEIIYTVRGTGKYLTEDEQLENDIAKQLTENFISESKLGINKEKIIAWVKKVE-E

4r1hA

0.25

0.23

0.92

5.82

dPPAS2

----------FDDSKPIYKQIVHYIHTEIVTGTYEAGDKLLSVRELATKLEVNPTTIQRAYAELEETEIIYTVRGTGKYLTEDEQLENDIAKQLTENFISESKLGINKEKIIAWVKKVEEV

4r1hA

0.25

0.23

0.91

3.19

PPAS

----------FDDSKPIYKQIVHYIHTEIVTGTYEAGDKLLSVRELATKLEVNPTTIQRAYAELEETEIIYTVRGTGKYLTEDEQLENDIAKQLTENFISESKLGINKEKIIAWVKKVE-E

4r1hA

0.25

0.23

0.91

3.94

Env-PPAS

----------FDDSKPIYKQIVHYIHTEIVTGTYEAGDKLLSVRELATKLEVNPTTIQRAYAELEETEIIYTVRGTGKYLTEDEQLENDIAKQLTENFISESKLGINKEKIIAWVKKVE-E

4r1hA

0.25

0.23

0.91

2.24

MUSTER

----------FDDSKPIYKQIVHYIHTEIVTGTYEAGDKLLSVRELATKLEVNPTTIQRAYAELEETEIIYTVRGTGKYLTEDEQLENDIAKQLTENFISESKLGINKEKIIAWVKKV-EE

4hamA

0.25

0.98

3.98

dPPAS

---SNAFTINTKSQLPIYEQIVQKIKEQVVKGVLQEGEKILSIREFASRIGVNPNTVSKAYQELERQEVIITVKGKGTFIANQTKKLAETRTKLKETILDLVYLGVNIEEIHKLADEYSQD

(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=0.74

Estimated TM-score = 0.81±0.09

Estimated RMSD = 2.9±2.1Å

Download Model 2

C-score=-4.72

Download Model 3

C-score=0.33

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	4hamA	0.805	2.45	0.254	0.975
2	4r1hA	0.730	2.74	0.245	0.901
3	3neuA	0.712	2.46	0.290	0.860
4	3tqnA	0.694	2.08	0.184	0.810
5	2wv0D	0.687	3.51	0.219	0.917
6	3by6E	0.674	2.86	0.226	0.851
7	2ek5C	0.647	2.55	0.198	0.785
8	4p96A	0.624	3.24	0.174	0.868
9	3ic7A	0.623	3.07	0.208	0.802
10	4mgrA	0.603	2.66	0.165	0.719

(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	0.33	19	5d4rA	NUC	Rep, Mult	16,17,18,52,53,55,56,73,74,75,76
2	0.22	6	4u0yD	NUC	Rep, Mult	16,17,18,52,53,56,59
3	0.13	8	4h0eB	NUC	Rep, Mult	42,43,54,58,72,73,74,75,77
4	0.05	2	1hw2B	QNA	Rep, Mult	42,43,44,54,58,72
5	0.02	2	2d45B	QNA	Rep, Mult	53,56,59,63,67
6	0.02	1	2du9A	MPD	Rep, Mult	98,101,102,106,108
7	0.01	1	3f6v0	III	Rep, Mult	20,23,26,80,82,83,84,87,90,92,95
8	0.01	1	3f8fA	DM1	Rep, Mult	19,26,87,90,91,94

	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	3kx2B	0.523	4.19	0.121	0.835	3.6.4.13	23,48,55
2	0.060	1f1oA	0.421	4.37	0.088	0.719	4.3.2.2	65
3	0.060	1k4jA	0.482	3.90	0.043	0.736	2.3.1.184	NA
4	0.060	1yleA	0.481	4.47	0.063	0.818	2.3.1.109	NA
5	0.060	2vwbA	0.540	4.25	0.113	0.876	3.4.24.57	NA
6	0.060	3mcqA	0.498	4.45	0.092	0.826	2.7.4.16	17
7	0.060	3enhA	0.511	4.12	0.084	0.818	3.4.24.57	NA
8	0.060	2v9yA	0.486	4.20	0.056	0.810	6.3.3.1	NA
9	0.060	1ofdA	0.410	4.66	0.072	0.719	1.4.7.1	NA
10	0.060	2ip2A	0.496	4.19	0.121	0.802	2.1.1.-	NA
11	0.060	2zodB	0.477	4.64	0.073	0.843	2.7.9.3	14
12	0.060	3lk5A	0.487	4.05	0.078	0.777	2.5.1.1	17,65,78
13	0.060	1n0hA	0.500	4.27	0.075	0.860	2.2.1.6	37
14	0.060	2btuA	0.503	4.19	0.064	0.826	6.3.3.1	9
15	0.060	2ewgA	0.486	4.39	0.073	0.793	2.5.1.10	30
16	0.060	3fofA	0.476	4.92	0.051	0.851	5.99.1.-	NA
17	0.060	1fp2A	0.519	4.16	0.110	0.793	2.1.1.150	NA
18	0.060	1wmwA	0.480	4.44	0.065	0.793	2.5.1.-	30
19	0.060	1w07B	0.482	4.10	0.079	0.752	1.3.3.6	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	0.744	2.42	0.28	0.89	3neuA	GO:0003677 GO:0003700 GO:0006351 GO:0006355
1	0.42	0.735	2.38	0.22	0.88	4r1hA	GO:0003677 GO:0003700 GO:0006351 GO:0006355
2	0.42	0.806	2.44	0.25	0.98	4hamA	GO:0003677 GO:0003700 GO:0006351 GO:0006355
3	0.38	0.674	2.86	0.23	0.85	3by6E	GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0006367
4	0.35	0.635	3.11	0.20	0.82	3ic7A	GO:0003677 GO:0003700 GO:0006351 GO:0006355
5	0.33	0.654	2.54	0.20	0.79	2ek5C	GO:0003677 GO:0003700 GO:0006351 GO:0006355
6	0.30	0.567	1.93	0.22	0.64	5d4sB	GO:0003677 GO:0003700 GO:0005737 GO:0006351 GO:0006355
7	0.29	0.728	2.36	0.16	0.85	3tqnB	GO:0003677 GO:0003700 GO:0006351 GO:0006355
8	0.26	0.528	3.37	0.24	0.74	1v4rA	GO:0003677 GO:0003700 GO:0006351 GO:0006355
9	0.13	0.505	3.07	0.17	0.64	2hs5A	GO:0003677 GO:0003700 GO:0006351 GO:0006355
10	0.07	0.606	2.67	0.16	0.73	4mgrC	GO:0003677 GO:0003700 GO:0003824 GO:0006351 GO:0006355 GO:0008483 GO:0009058 GO:0016740 GO:0030170
11	0.07	0.553	3.82	0.15	0.81	3fmsA	GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0046872
12	0.07	0.602	2.64	0.18	0.72	4u0vA	GO:0003677 GO:0003700 GO:0006351 GO:0006355
13	0.07	0.587	2.18	0.17	0.69	4wwcA	GO:0003677 GO:0003700 GO:0006351 GO:0006355
14	0.07	0.557	3.08	0.15	0.72	3c7jA	GO:0003700 GO:0006355
15	0.07	0.532	3.05	0.13	0.68	3bwgB	GO:0003677 GO:0003700 GO:0006351 GO:0006355
16	0.07	0.512	2.74	0.17	0.61	4tv7B	GO:0003677 GO:0003700 GO:0003824 GO:0006351 GO:0006355 GO:0008483 GO:0009058 GO:0016740 GO:0030170
17	0.07	0.489	2.19	0.19	0.57	4zs8B	GO:0003677 GO:0003700 GO:0005737 GO:0006351 GO:0006355
18	0.07	0.474	2.82	0.18	0.59	2di3A	GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0046872
19	0.07	0.452	3.80	0.12	0.63	2h09A	GO:0003677 GO:0003700 GO:0005737 GO:0006351 GO:0006355 GO:0045892 GO:0046914 GO:0046983 GO:2000144

Consensus prediction of GO terms

Molecular Function	GO:0003677	GO:0003700
GO-Score	0.92	0.92
Biological Processes	GO:0006355	GO:0006367
GO-Score	0.92	0.38
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.