I-TASSER results

I-TASSER results for job id Rv0611c

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

Input Sequence in FASTA format

>protein (127 residues)
MPDRPQHPTASRQSSMVSWNHGAAGWLHCVQCGSATNPTACLDWLPPIHARSGPMYAEHD
VVVLTRDVPDKSLIAGDVGAVVGRYAAGGYEVDFTAANGCTVAVVTLAGDDIRPRRRREI
PHVREVA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MPDRPQHPTASRQSSMVSWNHGAAGWLHCVQCGSATNPTACLDWLPPIHARSGPMYAEHDVVVLTRDVPDKSLIAGDVGAVVGRYAAGGYEVDFTAANGCTVAVVTLAGDDIRPRRRREIPHVREVA
Prediction	CCCCCCCCCCCCCCCCEHCCCCCCCEEEEEHCCCCCCCCCEHCCCCCCCCCCCCCCHHHEEEEHCCCCCCCCCCCCEEEEEEEEHCCCCEEEEEHCCCCCEEEEEHCCHHHHEHCCCCCCCCCCCCC
Conf.Score	9988888875445554444566654566665477888764444566544467666544447876467776689988678999997799789999869996899986697884435645665443469
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MPDRPQHPTASRQSSMVSWNHGAAGWLHCVQCGSATNPTACLDWLPPIHARSGPMYAEHDVVVLTRDVPDKSLIAGDVGAVVGRYAAGGYEVDFTAANGCTVAVVTLAGDDIRPRRRREIPHVREVA
Prediction	8674474444545533241443121111014135444341014133413345430051132020344147550443210000111576200010125534220113045730441476313413738
	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

CCCCCCCCCCCCCCCCEHCCCCCCCEEEEEHCCCCCCCCCEHCCCCCCCCCCCCCCHHHEEEEHCCCCCCCCCCCCEEEEEEEEHCCCCEEEEEHCCCCCEEEEEHCCHHHHEHCCCCCCCCCCCCC
MPDRPQHPTASRQSSMVSWNHGAAGWLHCVQCGSATNPTACLDWLPPIHARSGPMYAEHDVVVLTRDVPDKSLIAGDVGAVVGRYAAGGYEVDFTAANGCTVAVVTLAGDDIRPRRRREIPHVREVA

4r5oA4

0.17

0.14

0.83

0.78

MUSTER

QPKGPYHPTIGSETENIIYLVSTDGAIYKYILGDSDSLKA-----PFIAAESG--------VSITAP-LQLNQQSGELYVTYTEERKDESKIVVYSKDGKVLHTVDCGESVPSQILFNN--------

4r5oA4

0.13

0.11

0.83

0.86

dPPAS

KGPYHSSPTIGSETENIIYLVSTDGAIYKYILGDSDSLKA-----PFIAAESG---------VSITAPLQLNQQSGELYVTYTEERKDESKIVVYSKDGKVLHTVDCGESVPSQILFNN--------

4of8A2

0.14

0.11

0.80

0.71

wdPPAS

VP--PEAPKIT-QGDVIYATEDRKVEIECVSVGG--KPAAEITWI-----DGLGNVLTDNIEYTVIPLPDQRRF--TAKSVLRLTPKKEFSCQAQNTADRTYRSAKI---RVEVKY-----------

1l0qA

0.14

0.13

0.96

0.73

wMUSTER

TPDGTKVYVANFDSSISVID-TVTN--SVIDTVKVEAAPSGIAVNPEAYVTNVDKYFNTVSIDTGTNKITARIPVGPDPAGIAVTPDGKKVYVALSFN--TVSVIDTATNTITATAVGKNPYASGQF

2e9wB2

0.26

0.18

0.69

0.72

wPPAS

--TKPE--------ILTYDR-LVNGMLQCVAAG---FPEPTIDWYPGCSASVLPV----DVQTLNSSGPPFG--KLVVQSSID-FKHNGVECKAYNDVGKTSAYFNFA-------------------

3zf7r1

0.17

0.06

0.38

0.83

dPPAS2

----AVNRLSGMKHSAESWGRAVARIPRIHGGGTSMSGAGAF----GNMCRGGRMF-----------------------------------------------------------------------

2e9wB2

0.25

0.17

0.69

0.80

PPAS

----------TKPEILTYDRLVN-GMLQCVAAG---FPEPTIDWCPGCSASVLPV----DVQTLNSSGPPFG--KLVVQSSIDSFKHNGVECKAYNDVGKTSAYFNFA-------------------

2aklA

0.20

0.17

0.86

0.96

Env-PPAS

MVS--TLPPCPQCNSEYTYEDGA--LLVCPECASPNEAATASDDGKVIKDSVGNVLQDGDTITVIKDLKVKGVKVGTKVKNI-RLVDGDHDIDCK-IDG--IGAMKLKSEFVRKVGS----------

3bg1D2

0.13

0.94

0.71

MUSTER

PPSKPNYISGGCDNLIKLWKEEEDGQWKEEQKLEASDWVRDVAWAPSI-GLPTSTI--QDRVFI--TCDDASSNT-WSPKLLHKFNDVVWHVSWS-ITANILAVSG-GDNKVTLWKESVDGQWVCIS

3zf7r1

0.12

0.05

0.40

0.74

dPPAS

----AVNRLSGMKHSAESWGRAVARIPRIHGGGTSMSGAGAFGNMCRGGRMFAPT------------------------------------------------------------------------

(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=-3.78

Estimated TM-score = 0.30±0.10

Estimated RMSD = 13.2±4.1Å

Download Model 2

C-score=-3.85

Download Model 3

C-score=-3.96

Download Model 4

C-score=-4.40

Download Model 5

C-score=-4.21

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	1ddiA	0.440	4.64	0.084	0.772
2	4g1bA	0.440	4.39	0.073	0.748
3	3mdoA	0.437	4.39	0.040	0.724
4	4qi3A	0.435	4.87	0.049	0.772
5	5acfA	0.433	4.81	0.106	0.787
6	1gvhA	0.432	4.62	0.091	0.764
7	1cqxA	0.432	4.45	0.037	0.732
8	4p6vF	0.427	4.82	0.046	0.764
9	4eh1A	0.427	4.63	0.074	0.748
10	3elqB	0.426	5.14	0.065	0.795

(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	0.21	9	4wqkA	MG	Rep, Mult	91,93
2	0.05	2	2yyeA	APC	Rep, Mult	83,103,104,105,106
3	0.05	2	1h9mA	MOO	Rep, Mult	105,106,108
4	0.02	1	4twfF	BR7	Rep, Mult	32,93
5	0.02	1	3e2vA	MG	Rep, Mult	28,67
6	0.02	1	2ofwC	MG	Rep, Mult	39,67
7	0.02	1	4b5wA	CA	Rep, Mult	67,71
8	0.02	1	3knkF	MG	Rep, Mult	118,120,121,123
9	0.02	1	1iiiB	BME	Rep, Mult	80,82
10	0.02	1	3eqnA	ZN	Rep, Mult	58,59
11	0.02	1	3eqnA	ZN	Rep, Mult	7,88

	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	1jb9A	0.425	4.58	0.078	0.748	1.18.1.2	NA
2	0.060	2zodB	0.327	5.89	0.036	0.717	2.7.9.3	83
3	0.060	1yq3A	0.404	4.93	0.072	0.740	1.3.5.1	NA
4	0.060	1cneA	0.415	4.80	0.113	0.748	1.7.1.1,1.6.6.1	NA
5	0.060	3ladB	0.410	4.88	0.076	0.772	1.8.1.4	10
6	0.060	2eixA	0.413	4.89	0.028	0.748	1.6.2.2	NA
7	0.060	3mmpG	0.416	4.95	0.041	0.779	2.7.7.48	94
8	0.060	2a8xA	0.407	4.99	0.058	0.787	1.8.1.4	NA
9	0.060	1tllA	0.426	4.92	0.042	0.772	1.14.13.39	NA
10	0.060	1f20A	0.425	4.93	0.016	0.779	1.14.13.39	110
11	0.060	1cqxB	0.432	4.68	0.055	0.764	1.14.12.17	43,82
12	0.060	1bx0A	0.412	4.83	0.106	0.756	1.18.1.2	NA
13	0.060	1cqxA	0.432	4.45	0.037	0.732	1.14.12.17	56
14	0.060	1i7pA	0.409	4.81	0.093	0.732	1.6.2.2	NA
15	0.060	1ddgB	0.439	4.55	0.083	0.779	1.8.1.2	NA
16	0.060	1ddgA	0.438	4.67	0.076	0.779	1.8.1.2	NA
17	0.060	1f0xA	0.413	4.92	0.020	0.756	1.1.1.28	30
18	0.060	2cndA	0.408	4.53	0.077	0.717	1.7.1.1	45,79,85
19	0.060	3ladA	0.398	4.98	0.074	0.772	1.8.1.4	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	0.07	0.438	4.67	0.08	0.78	1ddgA	GO:0000103 GO:0004783 GO:0008652 GO:0009337 GO:0010181 GO:0016491 GO:0019344 GO:0042602 GO:0050660 GO:0055114 GO:0070814
1	0.07	0.426	5.12	0.07	0.79	4dqkA	GO:0003824 GO:0003958 GO:0004497 GO:0005506 GO:0005737 GO:0008152 GO:0010181 GO:0016491 GO:0016705 GO:0016712 GO:0020037 GO:0042802 GO:0046872 GO:0055114 GO:0070330
2	0.07	0.421	4.76	0.08	0.76	2b5oA	GO:0004324 GO:0009579 GO:0016020 GO:0016491 GO:0030089 GO:0042651 GO:0055114
3	0.06	0.428	4.95	0.05	0.77	3w5hA	GO:0004128 GO:0005737 GO:0005739 GO:0005741 GO:0005783 GO:0005789 GO:0006629 GO:0006694 GO:0006695 GO:0008202 GO:0008203 GO:0016020 GO:0016126 GO:0016491 GO:0050660 GO:0055114 GO:0071949
4	0.06	0.423	4.77	0.06	0.76	2r6hC	GO:0000166 GO:0005886 GO:0006810 GO:0006811 GO:0006814 GO:0009055 GO:0016020 GO:0016021 GO:0016491 GO:0016655 GO:0046872 GO:0051536 GO:0051537 GO:0055114
5	0.06	0.421	4.51	0.09	0.73	2piaA	GO:0009055 GO:0016491 GO:0046872 GO:0051536 GO:0051537 GO:0055114
6	0.06	0.427	4.63	0.07	0.75	4eh1A	GO:0004155 GO:0005344 GO:0005623 GO:0006810 GO:0006879 GO:0008941 GO:0009636 GO:0015671 GO:0016491 GO:0019825 GO:0020037 GO:0046872 GO:0051409 GO:0055114 GO:0071949
7	0.06	0.395	4.55	0.04	0.69	1qfjA	GO:0005829 GO:0006810 GO:0006811 GO:0006979 GO:0008047 GO:0016491 GO:0030091 GO:0042602 GO:0043085 GO:0047138 GO:0052873 GO:0052875 GO:0055072 GO:0055114 GO:0071949
8	0.06	0.413	4.74	0.05	0.76	3vo2A	GO:0000166 GO:0004324 GO:0016491 GO:0055114
9	0.06	0.412	4.83	0.11	0.76	1bx0A	GO:0004324 GO:0009507 GO:0009535 GO:0009536 GO:0009570 GO:0009579 GO:0015979 GO:0016020 GO:0016491 GO:0055114
10	0.06	0.417	4.79	0.03	0.76	2rc5A	GO:0000166 GO:0004324 GO:0016491 GO:0046872 GO:0055114
11	0.06	0.421	4.62	0.04	0.74	1gawB	GO:0000166 GO:0016491 GO:0055114
12	0.06	0.409	4.81	0.09	0.73	1i7pA	GO:0004128 GO:0005737 GO:0005739 GO:0005741 GO:0005743 GO:0005783 GO:0005789 GO:0005811 GO:0006629 GO:0006694 GO:0006695 GO:0008202 GO:0008203 GO:0016020 GO:0016126 GO:0016208 GO:0016491 GO:0043531 GO:0050660 GO:0051287 GO:0055114 GO:0070062 GO:0071949
13	0.06	0.413	4.89	0.03	0.75	2eixA	GO:0000166 GO:0004128 GO:0016020 GO:0016021 GO:0016491 GO:0055114
14	0.06	0.415	4.67	0.06	0.75	1qgaA	GO:0004324 GO:0009507 GO:0009535 GO:0009536 GO:0009570 GO:0009579 GO:0015979 GO:0016020 GO:0016491 GO:0055114
15	0.06	0.413	4.49	0.03	0.72	3jqpD	GO:0000166 GO:0004324 GO:0008937 GO:0009055 GO:0016491 GO:0020011 GO:0042802 GO:0055114
16	0.06	0.410	4.94	0.08	0.76	1qfyA	GO:0004324 GO:0009507 GO:0009535 GO:0009536 GO:0009570 GO:0009579 GO:0015979 GO:0016020 GO:0016491 GO:0055114
17	0.06	0.406	5.04	0.06	0.76	1tvcA	GO:0004497 GO:0006730 GO:0009055 GO:0015049 GO:0015050 GO:0015947 GO:0016491 GO:0046872 GO:0051536 GO:0051537 GO:0055114
18	0.06	0.425	4.58	0.08	0.75	3lvbA	GO:0000166 GO:0004324 GO:0016491 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0003824
GO-Score	0.40
Biological Processes	GO:0044710
GO-Score	0.57
Cellular Component	GO:0005741	GO:0016021	GO:0005886	GO:0005789	GO:0030089	GO:0009337
GO-Score	0.07	0.07	0.07	0.07	0.07	0.07

(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.