I-TASSER results

I-TASSER results for job id Rv0807

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

Input Sequence in FASTA format

>protein (129 residues)
MSARDRVDPAKTRQVVLALADWLRDETLPAPDTDVLAAAVRLTARTLAALAPGASVEVRI
PPFAAVQCISGPRHTRGTPPNVVQTDPRTWLLVATGLSGVAQARGSGALQLSGSRAGEIE
AWLPLVDLG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MSARDRVDPAKTRQVVLALADWLRDETLPAPDTDVLAAAVRLTARTLAALAPGASVEVRIPPFAAVQCISGPRHTRGTPPNVVQTDPRTWLLVATGLSGVAQARGSGALQLSGSRAGEIEAWLPLVDLG
Prediction	CCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCEEEEHCCCCEEEEHCCCCCCCCCCCCCEEHCCHHHHHHHHHCCCCHHHHHHHCCEEEEHCCCHHHHHHCCCEHCC
Conf.Score	998778999999999999999997778899998999999999999999979998589876996689985898889999976677899999999877998999988789588854545688648765589
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MSARDRVDPAKTRQVVLALADWLRDETLPAPDTDVLAAAVRLTARTLAALAPGASVEVRIPPFAAVQCISGPRHTRGTPPNVVQTDPRTWLLVATGLSGVAQARGSGALQLSGSRAGEIEAWLPLVDLG
Prediction	756546442550340042035126567465252630130022005303751544300020133000101623634643323021222400010012324165037534041324205403421332538
	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

CCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCEEEEHCCCCEEEEHCCCCCCCCCCCCCEEHCCHHHHHHHHHCCCCHHHHHHHCCEEEEHCCCHHHHHHCCCEHCC
MSARDRVDPAKTRQVVLALADWLRDETLPAPDTDVLAAAVRLTARTLAALAPGASVEVRIPPFAAVQCISGPRHTRGTPPNVVQTDPRTWLLVATGLSGVAQARGSGALQLSGSRAGEIEAWLPLVDLG

4nssA

0.67

0.59

0.88

3.95

MUSTER

--------PAKTLEAVSAVADWLRDPQRESPARAQLAEAVRLTARTLAAVAPGASVEVRVPPFVAVQCISG-----GTPPNVVETDARTWLLLATGLLDIADA--GASVQMSGSRAAEVAHWLPVVRID

4nssA

0.67

0.59

0.88

4.74

dPPAS

--------PAKTLEAVSAVADWLRDPQRESPARAQLAEAVRLTARTLAAVAPGASVEVRVPPFVAVQCISG-----GTPPNVVETDARTWLLLATGLLDIADA--GASVQMSGSRAAEVAHWLPVVRID

4nssA

0.67

0.59

0.88

6.01

wdPPAS

--------PAKTLEAVSAVADWLRDPQRESPARAQLAEAVRLTARTLAAVAPGASVEVRVPPFVAVQCISG-----GTPPNVVETDARTWLLLATGLLDIADA--GASVQMSGSRAAEVAHWLPVVRID

4nssA

0.67

0.59

0.88

4.75

wMUSTER

--------PAKTLEAVSAVADWLRDPQRESPARAQLAEAVRLTARTLAAVAPGASVEVRVPPFVAVQCISG-----GTPPNVVETDARTWLLLATGLLDIADA--GASVQMSGSRAAEVAHWLPVVRID

4nssA

0.67

0.59

0.88

5.28

wPPAS

--------PAKTLEAVSAVADWLRDPQRESPARAQLAEAVRLTARTLAAVAPGASVEVRVPPFVAVQCISG-----GTPPNVVETDARTWLLLATGLLDIADA--GASVQMSGSRAAEVAHWLPVVRID

4nssA

0.67

0.59

0.88

8.75

dPPAS2

--------PAKTLEAVSAVADWLRDPQRESPARAQLAEAVRLTARTLAAVAPGASVEVRVPPFVAVQCISG-----GTPPNVVETDARTWLLLATGLLDIADA--GASVQMSGSRAAEVAHWLPVVRID

4nssA

0.67

0.59

0.88

5.04

PPAS

--------PAKTLEAVSAVADWLRDPQRESPARAQLAEAVRLTARTLAAVAPGASVEVRVPPFVAVQCISG-----GTPPNVVETDARTWLLLATGLLDIADA--GASVQMSGSRAAEVAHWLPVVRID

4nssA

0.67

0.59

0.88

5.47

Env-PPAS

--------PAKTLEAVSAVADWLRDPQRESPARAQLAEAVRLTARTLAAVAPGASVEVRVPPFVAVQCISG-----GTPPNVVETDARTWLLLATGLLDIADA--GASVQMSGSRAAEVAHWLPVVRID

4jgxA

0.13

0.12

0.92

1.02

MUSTER

-SL--KVDGFTSSIIFDVIRDGLNDPSQAK-QKAESIKKANAIIVFNLKNKAGKTESWYLDLKNDGDVGKGNKSPKGDADIQLTLSDDHFQQLVEGKANAQRLFMTGKLKVKGN--VMKAAAI----EG

4jgxA

0.11

0.10

0.92

0.87

dPPAS

---SLKVDGFTSSIIFDVIRDGLNDPSQAK-QKAESIKKANAIIVFNLKNKAGKTESWYLDLKNDGDVGKGNKSPKGDADIQLTLSDDHFQQLVEGKANAQRLFMTGKLKVKGN--VMKAAAIEG----

(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=0.66

Estimated TM-score = 0.80±0.09

Estimated RMSD = 3.2±2.2Å

Download Model 2

C-score=-0.64

Download Model 3

C-score=0.72

Download Model 4

C-score=0.54

Download Model 5

C-score=-4.93

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	4nssA	0.871	0.52	0.675	0.884
2	3ssmA	0.624	3.68	0.120	0.907
3	2i00C	0.595	4.18	0.080	0.899
4	2hv2A1	0.573	4.42	0.109	0.899
5	3r1kA	0.573	4.28	0.081	0.884
6	3n7zA	0.568	4.50	0.105	0.884
7	2ozgA	0.562	4.20	0.089	0.868
8	1c44A	0.561	3.25	0.122	0.729
9	3sxnA	0.558	4.41	0.106	0.884
10	2qztB	0.554	3.02	0.143	0.705

(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	0.08	4	3r1bC	TB2	Rep, Mult	39,43
2	0.06	3	4jgxA	PLM	Rep, Mult	47,58,93,94,100,121
3	0.06	3	2ps1A	PRP	Rep, Mult	85,86,90,92,95,96,98,99
4	0.04	2	4ujwE	MG	Rep, Mult	41,42,45
5	0.04	2	1iktA	OXN	Rep, Mult	58,90,93,94,100,101,104,116,117,120,122
6	0.04	2	2c11A	CU	Rep, Mult	57,74
7	0.04	2	1uthB	SCN	Rep, Mult	48,51,52,56
8	0.04	2	3wqtD	MG	Rep, Mult	32,34
9	0.02	1	3l26B	MG	Rep, Mult	79,80
10	0.02	1	1lh0A	ORO	Rep, Mult	49,57,58,120
11	0.02	1	3bpxA	SAL	Rep, Mult	37,41
12	0.02	1	3ku4B	SO4	Rep, Mult	113,114,115
13	0.02	1	3gyyB	ZN	Rep, Mult	86,89
14	0.02	1	1zkjA	ZN	Rep, Mult	34,74

	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	0.066	1c44A	0.561	3.25	0.122	0.729	2.3.1.176	109
2	0.060	1qcdA	0.476	4.68	0.073	0.830	2.4.2.7	48,85
3	0.060	1f2dA	0.468	4.90	0.050	0.868	3.5.99.7	85,118
4	0.060	3i58A	0.509	4.96	0.096	0.915	2.1.1.-	NA
5	0.060	1jlrA	0.474	4.08	0.088	0.760	2.4.2.9	NA
6	0.060	1o5oD	0.491	4.07	0.085	0.775	2.4.2.9	48,50,117
7	0.060	1v9sB	0.470	4.25	0.087	0.760	2.4.2.9	67
8	0.060	2qyoA	0.431	4.80	0.024	0.752	2.1.1.46	NA
9	0.060	3ezoA	0.468	4.14	0.057	0.736	2.3.1.39	NA
10	0.060	2ps1A	0.521	3.88	0.053	0.814	2.4.2.10	NA
11	0.060	1i5eB	0.496	3.94	0.073	0.744	2.4.2.9	48,117,123
12	0.060	1kywC	0.478	4.64	0.070	0.861	2.1.1.68	NA
13	0.060	2p1zB	0.507	4.18	0.139	0.814	2.4.2.10	NA
14	0.060	1g2qA	0.485	3.92	0.100	0.760	2.4.2.7	NA
15	0.060	2e55A	0.501	4.19	0.077	0.775	2.4.2.9	NA
16	0.060	1xtvG	0.498	4.18	0.097	0.775	2.4.2.9	45,85
17	0.060	1nt4A	0.471	3.95	0.061	0.705	3.1.3.10	13,38,43
18	0.060	2cuyA	0.478	4.11	0.057	0.736	2.3.1.39	NA
19	0.060	1lh0A	0.507	4.17	0.118	0.806	2.4.2.10	NA
20	0.060	2ehjA	0.487	4.20	0.063	0.760	2.4.2.9	95,103

(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	0.25	0.624	3.58	0.12	0.90	3ssmB	GO:0000287 GO:0008168 GO:0008171 GO:0016740 GO:0017000 GO:0032259 GO:0046872 GO:0051289 GO:0102302
1	0.23	0.619	3.71	0.12	0.91	3ssoB	GO:0000287 GO:0008168 GO:0008171 GO:0016740 GO:0017000 GO:0032259 GO:0046872 GO:0051289 GO:0102302
2	0.12	0.535	3.20	0.13	0.69	1iktA	GO:0000038 GO:0001649 GO:0003857 GO:0005102 GO:0005739 GO:0005777 GO:0005778 GO:0005782 GO:0006629 GO:0006631 GO:0006635 GO:0006699 GO:0008209 GO:0008210 GO:0016020 GO:0016491 GO:0016508 GO:0016616 GO:0016829 GO:0016853 GO:0033540 GO:0033989 GO:0036109 GO:0036111 GO:0036112 GO:0042803 GO:0043231 GO:0044594 GO:0055114 GO:0060009
3	0.07	0.595	4.18	0.08	0.90	2i00C	GO:0008080 GO:0016740
4	0.07	0.586	4.17	0.10	0.88	2hv2B	GO:0008080
5	0.07	0.577	4.41	0.10	0.89	3n7zB	GO:0008080 GO:0016740
6	0.07	0.570	4.30	0.09	0.88	5ebvA	GO:0008080 GO:0016740 GO:0030649 GO:0034069 GO:0044119 GO:0044121 GO:0052035 GO:0052040 GO:0052164 GO:0052167
7	0.07	0.563	4.45	0.08	0.90	2ozgA	GO:0008080 GO:0016740
8	0.07	0.544	4.33	0.09	0.87	4my0C	GO:0008080 GO:0016740
9	0.07	0.557	4.22	0.11	0.87	4qb9A	GO:0008080
10	0.07	0.561	3.25	0.12	0.73	1c44A	GO:0003824 GO:0005737 GO:0005739 GO:0005777 GO:0006810 GO:0006869 GO:0008152 GO:0008289 GO:0016740 GO:0016746 GO:0016747 GO:0033814
11	0.07	0.541	3.48	0.10	0.72	1pz4A
12	0.06	0.390	4.93	0.05	0.66	4yzeA	GO:0000976 GO:0003677 GO:0003700 GO:0005829 GO:0006351 GO:0006355 GO:0045892
13	0.06	0.308	4.97	0.03	0.57	1tz9A	GO:0006064 GO:0008927 GO:0016829
14	0.06	0.315	5.54	0.03	0.66	3mjfA	GO:0000166 GO:0000287 GO:0003824 GO:0004637 GO:0005524 GO:0006164 GO:0006189 GO:0009113 GO:0016874 GO:0030145 GO:0046872
15	0.06	0.363	5.02	0.04	0.66	3ezsA	GO:0003824 GO:0009058 GO:0030170
16	0.06	0.340	4.97	0.03	0.63	4qusB	GO:0004596 GO:0006474 GO:0008080 GO:0016740 GO:0016746 GO:0016747 GO:0031248
17	0.06	0.339	4.89	0.05	0.60	2cy2A	GO:0008080 GO:0016740
18	0.06	0.346	4.74	0.03	0.60	4yr9A	GO:0003824 GO:0005739 GO:0006567 GO:0008743 GO:0016491 GO:0019518 GO:0050662 GO:0055114
19	0.06	0.353	5.00	0.13	0.67	3ec4A	GO:0008080 GO:0016740 GO:0016747
20	0.06	0.337	4.55	0.08	0.56	3a5zC	GO:0000166 GO:0004812 GO:0004824 GO:0005524 GO:0005737 GO:0005829 GO:0006418 GO:0006430 GO:0016874 GO:0016880 GO:0043687 GO:0052868 GO:0071915 GO:0072581
21	0.06	0.318	5.07	0.04	0.59	2ge3A	GO:0008080 GO:0016740

Consensus prediction of GO terms

Molecular Function	GO:0008171	GO:0000287	GO:0102302
GO-Score	0.42	0.42	0.42
Biological Processes	GO:0051289	GO:0017000	GO:0032259
GO-Score	0.42	0.42	0.42
Cellular Component	GO:0005739	GO:0005782	GO:0005778
GO-Score	0.12	0.12	0.12

(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.