I-TASSER results

I-TASSER results for job id Rv3129

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

Input Sequence in FASTA format

>protein (110 residues)
MVQGRTVLFRTAEGAKLFSAVAKCAVAFEADDHNVAEGWSVIVKVRAQVLTTDAGVREAE
RAQLLPWTATLKRHCVRVIPWEITGRHFRFGPEPDRSQTFACEASSHNQR

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MVQGRTVLFRTAEGAKLFSAVAKCAVAFEADDHNVAEGWSVIVKVRAQVLTTDAGVREAERAQLLPWTATLKRHCVRVIPWEITGRHFRFGPEPDRSQTFACEASSHNQR
Prediction	CCCCCEEEEHCCCCCHHHHHHCCCCEEEEHCCCCCCCCEEEEEEEEEEEHCCHHHHHHHHHCCCCCCCCCCCCEEEEEEEEEEEEEEEHCCCCCCCCCCCCCCCCCCCCC
Conf.Score	95698899995999747887559858998678889986589999988996899999999867998999888766999997688856787589998876555565545469
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MVQGRTVLFRTAEGAKLFSAVAKCAVAFEADDHNVAEGWSVIVKVRAQVLTTDAGVREAERAQLLPWTATLKRHCVRVIPWEITGRHFRFGPEPDRSQTFACEASSHNQR
Prediction	73555300000144240342266440000014345740000003140441457732440573524313635442002030540141314245526545423353554678
	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

CCCCCEEEEHCCCCCHHHHHHCCCCEEEEHCCCCCCCCEEEEEEEEEEEHCCHHHHHHHHHCCCCCCCCCCCCEEEEEEEEEEEEEEEHCCCCCCCCCCCCCCCCCCCCC
MVQGRTVLFRTAEGAKLFSAVAKCAVAFEADDHNVAEGWSVIVKVRAQVLTTDAGVREAERAQLLPWTATLKRHCVRVIPWEITGRHFRFGPEPDRSQTFACEASSHNQR

3fkhD

0.41

0.35

0.84

2.48

MUSTER

IVDKGAIYIRTAEGNKLFSNL-NHDVLFEADEVKDGKAWSVVVRATAEIVRKLDEIAYADTLELKPWIPTLKYNYVRIVPNEITGREFTLGEE-----------------

3fkhD

0.41

0.35

0.84

5.69

dPPAS

IVDKGAIYIRTAEGNKLFSN-LNHDVLFEADEVKDGKAWSVVVRATAEIVRKLDEIAYADTLELKPWIPTLKYNYVRIVPNEITGREFTLGEE-----------------

3fkhD

0.41

0.35

0.84

4.59

wdPPAS

IVDKGAIYIRTAEGNKLFSN-LNHDVLFEADEVKDGKAWSVVVRATAEIVRKLDEIAYADTLELKPWIPTLKYNYVRIVPNEITGREFTLGEE-----------------

3fkhD

0.41

0.35

0.84

2.83

wMUSTER

IVDKGAIYIRTAEGNKLFSNL-NHDVLFEADEVKDGKAWSVVVRATAEIVRKLDEIAYADTLELKPWIPTLKYNYVRIVPNEITGREFTLGEE-----------------

3fkhD

0.41

0.35

0.84

3.37

wPPAS

IVDKGAIYIRTAEGNKLFSNL-NHDVLFEADEVKDGKAWSVVVRATAEIVRKLDEIAYADTLELKPWIPTLKYNYVRIVPNEITGREFTLGEE-----------------

3fkhD

0.41

0.35

0.84

8.53

dPPAS2

IVDKGAIYIRTAEGNKLFSN-LNHDVLFEADEVKDGKAWSVVVRATAEIVRKLDEIAYADTLELKPWIPTLKYNYVRIVPNEITGREFTLGEE-----------------

3fkhD

0.41

0.35

0.84

3.27

PPAS

IVDKGAIYIRTAEGNKLFSN-LNHDVLFEADEVKDGKAWSVVVRATAEIVRKLDEIAYADTLELKPWIPTLKYNYVRIVPNEITGREFTLGEE-----------------

3fkhD

0.41

0.35

0.84

3.45

Env-PPAS

IVDKGAIYIRTAEGNKLFSNL-NHDVLFEADEVKDGKAWSVVVRATAEIVRKLDEIAYADTLELKPWIPTLKYNYVRIVPNEITGREFTLGEE-----------------

3cp3A

0.39

0.30

0.77

2.07

MUSTER

SAEQPRVYFRT--ATKLFSVNLNSDVLFEVDRFDE--GWSVVLKGNAYVVRDTEEARHADTLGLKPWLPTLKYNFVRIDVREVSGRAFV---------------------

3cp3A

0.40

0.31

0.77

4.72

dPPAS

SAEQPRVYFRT--ATKLFSVNLNSDVLFEVDRFD--EGWSVVLKGNAYVVRDTEEARHADTLGLKPWLPTLKYNFVRIDVREVSGRAFV---------------------

(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=0.07

Estimated TM-score = 0.72±0.11

Estimated RMSD = 4.0±2.7Å

Download Model 2

C-score=-1.15

Download Model 3

C-score=-0.63

Download Model 4

C-score=-3.36

Download Model 5

C-score=-3.74

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	3fkhD	0.784	1.26	0.413	0.836
2	2hq9B	0.671	1.99	0.184	0.791
3	3cp3A	0.660	2.00	0.357	0.764
4	4zkyA	0.650	2.29	0.102	0.782
5	4ybnA	0.643	2.52	0.083	0.809
6	1rfeA	0.639	3.05	0.122	0.855
7	3u0iA	0.634	2.09	0.165	0.727
8	2arzA	0.633	2.99	0.083	0.800
9	2fg9A	0.631	2.25	0.100	0.764
10	2furA	0.630	2.64	0.102	0.800

(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	0.24	3	2hq9A	FAD	Rep, Mult	38,40,41,42,84,85,86
2	0.18	3	2i02A	FMN	Rep, Mult	10,11,15,16,17,67,68
3	0.06	1	3hy8A	PO4	Rep, Mult	3,4,6,8,56
4	0.06	1	3in6B	FMN	Rep, Mult	42,46,81
5	0.06	1	1nrgA	PO4	Rep, Mult	10,11,67,68

	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	1x31B	0.467	4.87	0.151	0.791	1.5.3.1	41
2	0.060	1ddtA	0.426	4.83	0.119	0.764	2.4.2.36	NA
3	0.060	3hxxA	0.430	4.43	0.028	0.718	6.1.1.7	NA
4	0.060	1yiqA	0.433	4.05	0.085	0.691	1.1.99.-	NA
5	0.060	2zzgA	0.464	5.06	0.056	0.846	6.1.1.7	NA
6	0.060	1j5wB	0.455	4.98	0.075	0.855	6.1.1.14	NA
7	0.060	2jbvB	0.440	4.35	0.054	0.782	1.1.3.17	NA
8	0.060	1l0wB	0.462	3.52	0.091	0.718	6.1.1.12	NA
9	0.060	2a2jA	0.593	2.68	0.085	0.764	1.4.3.5	NA
10	0.060	1qtfA	0.430	3.97	0.056	0.654	3.4.21.-	NA
11	0.060	1si8A	0.438	4.38	0.064	0.736	1.11.1.6	NA
12	0.060	2g5fA	0.452	4.10	0.057	0.700	5.4.4.2	NA
13	0.060	2xalA	0.432	5.15	0.085	0.864	2.7.1.158	NA
14	0.060	1eqrA	0.447	3.77	0.034	0.709	6.1.1.12	NA
15	0.060	2nz2A	0.430	4.17	0.011	0.718	6.3.4.5	NA
16	0.060	2gewA	0.431	4.32	0.034	0.764	1.1.3.6	NA
17	0.060	1tuuA	0.428	3.85	0.080	0.673	2.7.2.1	NA
18	0.060	3c7cB	0.443	3.96	0.074	0.746	1.5.1.11	NA
19	0.060	1bdaA	0.320	5.35	0.033	0.664	3.4.21.68	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	0.787	1.41	0.41	0.85	3fkhD	GO:0010181 GO:0016491 GO:0055114
1	0.17	0.660	2.00	0.36	0.76	3cp3A	GO:0010181 GO:0016491 GO:0055114
2	0.14	0.643	3.06	0.12	0.86	1rfeA	GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
3	0.08	0.650	2.29	0.10	0.78	4zkyA	GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
4	0.08	0.662	2.17	0.10	0.79	2fg9A	GO:0000166 GO:0010181 GO:0016491 GO:0055114
5	0.07	0.637	2.23	0.14	0.77	2htiA	GO:0000166 GO:0010181 GO:0016491 GO:0055114
6	0.07	0.622	2.60	0.05	0.80	5bncA	GO:0010181 GO:0016491 GO:0055114
7	0.07	0.638	2.03	0.17	0.73	3u5wA	GO:0010181 GO:0016491 GO:0055114
8	0.07	0.642	2.68	0.10	0.82	2furA	GO:0010181 GO:0016491 GO:0055114
9	0.07	0.624	2.86	0.06	0.80	3tgvA	GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
10	0.07	0.643	2.52	0.08	0.81	4ybnA	GO:0010181 GO:0016491 GO:0055114
11	0.07	0.625	2.76	0.11	0.77	2x1kA	GO:0010181 GO:0016491 GO:0055114
12	0.07	0.604	2.53	0.15	0.75	2asfA	GO:0004733 GO:0005576 GO:0005618 GO:0010181 GO:0016491 GO:0042823 GO:0055114
13	0.07	0.601	2.68	0.08	0.75	5escA	GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
14	0.07	0.593	2.79	0.08	0.77	3dnhA	GO:0010181 GO:0016491 GO:0055114
15	0.07	0.577	2.77	0.13	0.71	2ou5A	GO:0000166 GO:0010181 GO:0016491 GO:0055114
16	0.07	0.608	2.32	0.09	0.75	3ec6A	GO:0000166 GO:0003677 GO:0010181 GO:0016491 GO:0055114
17	0.07	0.516	2.72	0.15	0.65	3r5lA	GO:0005618 GO:0005886 GO:0010181 GO:0016020 GO:0016491 GO:0055114 GO:0070967
18	0.07	0.551	3.47	0.17	0.74	3f7eA	GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
19	0.06	0.306	4.26	0.02	0.52	4k0vA	GO:0000165 GO:0000166 GO:0001525 GO:0001666 GO:0001725 GO:0001934 GO:0001935 GO:0001938 GO:0001958 GO:0002040 GO:0004672 GO:0004713 GO:0004714 GO:0004872 GO:0005088 GO:0005524 GO:0005576 GO:0005737 GO:0005856 GO:0005884 GO:0005886 GO:0005887 GO:0005902 GO:0005911 GO:0005925 GO:0006468 GO:0007165 GO:0007169 GO:0007267 GO:0007507 GO:0009925 GO:0009986 GO:0010033 GO:0010595 GO:0014068 GO:0016020 GO:0016021 GO:0016301 GO:0016310 GO:0016323 GO:0016324 GO:0016525 GO:0016740 GO:0018108 GO:0019838 GO:0030054 GO:0031100 GO:0032878 GO:0034446 GO:0035556 GO:0043066 GO:0043114 GO:0043434 GO:0043547 GO:0043552 GO:0043627 GO:0045121 GO:0045766 GO:0046777 GO:0048014 GO:0050728 GO:0050900 GO:0051259 GO:0051591 GO:0051894 GO:0051897 GO:0060216 GO:0060347 GO:0070374 GO:1902533 GO:2000251 GO:2000351 GO:2000352
20	0.06	0.273	3.36	0.02	0.37	3h0gK	GO:0001055 GO:0003677 GO:0003899 GO:0005634 GO:0005665 GO:0005829 GO:0006351 GO:0006366 GO:0016591 GO:0046983

Consensus prediction of GO terms

Molecular Function	GO:0010181	GO:0016641
GO-Score	0.60	0.41
Biological Processes	GO:0055114	GO:0009108	GO:0042822	GO:1901576
GO-Score	0.60	0.41	0.41	0.41
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.