I-TASSER results

I-TASSER results for job id Rv3763

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

Input Sequence in FASTA format

>protein (159 residues)
MKRGLTVAVAGAAILVAGLSGCSSNKSTTGSGETTTAAGTTASPGAASGPKVVIDGKDQN
VTGSVVCTTAAGNVNIAIGGAATGIAAVLTDGNPPEVKSVGLGNVNGVTLGYTSGTGQGN
ASATKDGSHYKITGTATGVDMANPMSPVNKSFEIEVTCS

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MKRGLTVAVAGAAILVAGLSGCSSNKSTTGSGETTTAAGTTASPGAASGPKVVIDGKDQNVTGSVVCTTAAGNVNIAIGGAATGIAAVLTDGNPPEVKSVGLGNVNGVTLGYTSGTGQGNASATKDGSHYKITGTATGVDMANPMSPVNKSFEIEVTCS
Prediction	CCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEHCCEHCCCCCCEEEEEHCCEEEEEHCCCCCEEEEEHCCCCCCEEEEEEHCCCCCEEEEEHCCCCCCEEEEEEHCCEEEEEEEEEEHCCCCCCCCCCEEEEEEEEHC
Conf.Score	986589999999999999754679999888888877888887777888658999777757887668997598999997789985999988999976899975566886787757888766899996998999999998668999875556799999759
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MKRGLTVAVAGAAILVAGLSGCSSNKSTTGSGETTTAAGTTASPGAASGPKVVIDGKDQNVTGSVVCTTAAGNVNIAIGGAATGIAAVLTDGNPPEVKSVGLGNVNGVTLGYTSGTGQGNASATKDGSHYKITGTATGVDMANPMSPVNKSFEIEVTCS
Prediction	763310000011100010000014566555454444444444544566514030214537355414044453322030345441010203565403042040453312312234445535150335664130303041334743644354605051518
	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                 140

                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEHCCEHCCCCCCEEEEEHCCEEEEEHCCCCCEEEEEHCCCCCCEEEEEEHCCCCCEEEEEHCCCCCCEEEEEEHCCEEEEEEEEEEHCCCCCCCCCCEEEEEEEEHC
MKRGLTVAVAGAAILVAGLSGCSSNKSTTGSGETTTAAGTTASPGAASGPKVVIDGKDQNVTGSVVCTTAAGNVNIAIGGAATGIAAVLTDGNPPEVKSVGLGNVNGVTLGYTSGTGQGNASATKDGSHYKITGTATGVDMANPMSPVNKSFEIEVTCS

4xinA

0.34

0.24

0.71

2.16

MUSTER

-------------------------------------------AQLSSTASVTVDGKDRNFH-IVTCRQLEWRRMIDIGADFSGAKVAVDNAQPPVVESVHIQNLSGFSGMYSRG-GSGSADMSMTGDKFTISGTADGYKTDKPGEPATATFKIVVTC-

4xinA

0.33

0.23

0.71

2.47

dPPAS

-------------------------------------------AQLSSTASVTVDGKDRNFH-IVTCRQLEWRRMIDIGADFSGAKVAVDNAQPPVVESVHIQNLSGFSGMYSRGGS-GSADMSMTGDKFTISGTADGYKTDKPGEPATATFKIVVTC-

4xinA

0.33

0.23

0.71

3.38

wdPPAS

-------------------------------------------AQLSSTASVTVDGKDRNF-HIVTCRQLEWRRMIDIGADFSGAKVAVDNAQPPVVESVHIQNLSGFSGMYSRGGS-GSADMSMTGDKFTISGTADGYKTDKPGEPATATFKIVVTC-

4xinA

0.34

0.24

0.70

2.65

wMUSTER

--------------------------------------------QLSSTASVTVDGKDRNFH-IVTCRQLEWRRMIDIGADFSGAKVAVDNAQPPVVESVHIQNLSGFSGMYSRG-GSGSADMSMTGDKFTISGTADGYKTDKPGEPATATFKIVVTC-

4xinA

0.33

0.23

0.71

3.80

wPPAS

-------------------------------------------AQLSSTASVTVDGKDRNF-HIVTCRQLEWRRMIDIGADFSGAKVAVDNAQPPVVESVHIQNLSGFSGMYSRGGS-GSADMSMTGDKFTISGTADGYKTDKPGEPATATFKIVVTC-

4xinA

0.33

0.23

0.71

5.08

dPPAS2

-------------------------------------------AQLSSTASVTVDGKDRNFH-IVTCRQLEWRRMIDIGADFSGAKVAVDNAQPPVVESVHIQNLSGFSGMYSRGGS-GSADMSMTGDKFTISGTADGYKTDKPGEPATATFKIVVTC-

4xinA

0.34

0.24

0.71

3.29

PPAS

-------------------------------------------AQLSSTASVTVDGKDRNF-HIVTCRQLEWRRMIDIGADFSGAKVAVDNAQPPVVESVHIQNLSGFSGMYSRG-GSGSADMSMTGDKFTISGTADGYKTDKPGEPATATFKIVVTC-

4xinA

0.34

0.24

0.71

3.79

Env-PPAS

-------------------------------------------AQLSSTASVTVDGKDRNFH-IVTCRQLEWRRMIDIGADFSGAKVAVDNAQPPVVESVHIQNLSGFSGMYSRG-GSGSADMSMTGDKFTISGTADGYKTDKPGEPATATFKIVVTC-

4zjmA

0.94

0.63

0.67

1.95

MUSTER

--------------------------------------------------PVVIDGKDQNVTGSVVCTTAAGNVNIAIGGAATGIAAVLTDGNPPEV-SVGLGNVNGVTLGYTSGTGQG-NASATDGSHYKITGTATGVDMANPMSPVN-SFEIEVTCS

4zjmA

0.94

0.63

0.67

2.23

dPPAS

--------------------------------------------------PVVIDGKDQNVTGSVVCTTAAGNVNIAIGGAATGIAAVLTDGNPPEV-SVGLGNVNGVTLGYTSGTGQG-NASATDGSHYKITGTATGVDMANPMSPVN-SFEIEVTCS

(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=-1.70

Estimated TM-score = 0.51±0.15

Estimated RMSD = 8.6±4.5Å

Download Model 2

C-score=-2.29

Download Model 3

C-score=-2.54

Download Model 4

C-score=-2.13

Download Model 5

C-score=-2.77

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	4xinA	0.680	1.24	0.327	0.711
2	4zjmA	0.577	1.93	0.961	0.648
3	4xhfA	0.511	4.84	0.056	0.824
4	4p6vC	0.506	5.01	0.075	0.849
5	2f1tA	0.505	3.89	0.071	0.698
6	3lwxA	0.500	4.70	0.052	0.786
7	1p4tA	0.489	3.54	0.055	0.685
8	1r0uA	0.479	3.98	0.063	0.673
9	3dzmA	0.475	3.79	0.083	0.679
10	1s5lo	0.473	3.84	0.050	0.679

(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	0.10	5	4jwmA	MG	Rep, Mult	55,58,153
2	0.04	2	3hsvB	ZN	Rep, Mult	51,56,155
3	0.04	2	1q9lC	MG	Rep, Mult	53,55,56,151,153
4	0.04	2	2ervB	CXE	Rep, Mult	68,75,76,87,98,100
5	0.04	2	1l6mA	DBS	Rep, Mult	53,121,132,134,152,154
6	0.04	2	3d5dH	MG	Rep, Mult	115,122,134
7	0.02	1	3kv7B	ACT	Rep, Mult	51,129,155
8	0.02	1	4fd8A	MA4	Rep, Mult	66,132
9	0.02	1	2oi6B	GP1	Rep, Mult	129,143
10	0.02	1	2ervB	CXE	Rep, Mult	74,87,88,89,98,113
11	0.02	1	3ca0A	UUU	Rep, Mult	106,107,144,145,155
12	0.02	1	2z7cC	ARG	Rep, Mult	135,149,151
13	0.02	1	3fcsC	IMD	Rep, Mult	88,90,130,144
14	0.02	1	3rckX	1FP	Rep, Mult	48,158
15	0.02	1	3hpeB	ERU	Rep, Mult	50,52,62,76,78,87,100,102,152,154
16	0.02	1	3dwrA	0PA	Rep, Mult	77,79,99,101

	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	1y9mA	0.433	5.46	0.064	0.786	3.2.1.80	NA
2	0.060	2pfrA	0.402	5.25	0.051	0.704	2.3.1.5	NA
3	0.060	3fg3A	0.352	5.29	0.092	0.641	4.2.1.92,1.13.11.40	NA
4	0.060	2vgrD	0.444	4.50	0.047	0.698	1.3.7.2	NA
5	0.060	1a4gA	0.435	4.71	0.048	0.717	3.2.1.18	NA
6	0.060	1tlbA	0.463	4.60	0.068	0.748	1.3.3.3	126
7	0.060	1usrA	0.428	5.36	0.106	0.786	3.2.1.18	83,130
8	0.060	2x4mA	0.449	3.91	0.067	0.660	3.4.23.48	120,133,135
9	0.060	1e93A	0.321	5.51	0.070	0.598	1.11.1.6	NA
10	0.060	1qwlA	0.431	4.58	0.044	0.698	1.11.1.6	NA
11	0.060	3ej6D	0.422	4.93	0.049	0.685	1.11.1.6	52
12	0.060	2vfbA	0.427	4.33	0.067	0.679	2.3.1.5	NA
13	0.060	2ow6A	0.444	5.28	0.052	0.780	3.2.1.114	140
14	0.060	2ijaA	0.453	4.77	0.059	0.736	2.3.1.5	140
15	0.060	2ebsB	0.433	5.01	0.075	0.748	3.2.1.150	89
16	0.060	2zxlA	0.469	4.34	0.036	0.717	1.3.1.80	78
17	0.060	1i7qA	0.428	4.79	0.047	0.685	4.1.3.27	NA
18	0.060	2pqtA	0.451	4.67	0.059	0.730	2.3.1.5	NA
19	0.060	1ncaN	0.359	5.00	0.090	0.616	3.2.1.18	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	0.55	0.587	2.03	0.96	0.67	4zjmE	GO:0005618 GO:0005886 GO:0006810 GO:0009405 GO:0009986 GO:0016020 GO:0030430 GO:0044117 GO:0046789 GO:0052157 GO:0052553 GO:0097691
1	0.09	0.428	3.94	0.10	0.64	2n2lA	GO:0009279 GO:0016021
2	0.08	0.403	4.44	0.06	0.64	2n6pA	GO:0009279 GO:0016021 GO:0019867 GO:0055085
3	0.07	0.501	5.14	0.06	0.84	4xa7A	GO:0000166 GO:0005886 GO:0006810 GO:0006811 GO:0006814 GO:0009276 GO:0010181 GO:0016020 GO:0016021 GO:0016491 GO:0016655 GO:0055114
4	0.07	0.507	4.41	0.06	0.77	3lwxA	GO:0005506 GO:0005886 GO:0006810 GO:0006811 GO:0006814 GO:0009276 GO:0010181 GO:0016020 GO:0016021 GO:0016491 GO:0016655 GO:0055114
5	0.07	0.514	5.15	0.05	0.86	4xhfB	GO:0005886 GO:0006120 GO:0006810 GO:0006811 GO:0006814 GO:0008137 GO:0009276 GO:0010181 GO:0016020 GO:0016021 GO:0016491 GO:0016655 GO:0055114
6	0.07	0.506	5.01	0.07	0.85	4p6vC	GO:0005886 GO:0006810 GO:0006811 GO:0006814 GO:0009276 GO:0010181 GO:0016020 GO:0016021 GO:0016491 GO:0016655 GO:0055114
7	0.07	0.447	3.94	0.05	0.67	2mhlA	GO:0016021 GO:0019867
8	0.07	0.489	3.54	0.06	0.69	1p4tA	GO:0015288 GO:0016020 GO:0016021 GO:0055085
9	0.07	0.437	4.20	0.07	0.64	2ge4A	GO:0000746 GO:0005198 GO:0006810 GO:0006811 GO:0006974 GO:0009279 GO:0009597 GO:0015288 GO:0016020 GO:0016021 GO:0019867 GO:0034220 GO:0046718 GO:0046930
10	0.07	0.475	3.79	0.08	0.68	3dzmA	GO:0046872
11	0.06	0.385	5.40	0.04	0.71	2wqkA	GO:0000166 GO:0005737 GO:0008252 GO:0008253 GO:0016311 GO:0016787 GO:0046872
12	0.06	0.360	4.99	0.05	0.62	4v0mF	GO:0005113 GO:0005119 GO:0005813 GO:0005930 GO:0034464 GO:0035058 GO:0036064 GO:0042384 GO:0061512
13	0.06	0.371	5.58	0.06	0.70	2j3lB	GO:0000166 GO:0002161 GO:0004812 GO:0004827 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006433 GO:0006450 GO:0016874
14	0.06	0.358	5.04	0.06	0.64	4v0mB	GO:0005113 GO:0005119 GO:0005813 GO:0005930 GO:0034464 GO:0035058 GO:0036064 GO:0042384 GO:0061512
15	0.06	0.391	4.26	0.06	0.60	2mlhA	GO:0009279 GO:0015288 GO:0016020 GO:0016021 GO:0019867 GO:0055085
16	0.06	0.305	5.65	0.03	0.60	4evwA	GO:0003743 GO:0006413
17	0.06	0.359	5.40	0.07	0.67	1yxmA	GO:0005102 GO:0005739 GO:0005777 GO:0005778 GO:0006629 GO:0006631 GO:0006633 GO:0008670 GO:0016491 GO:0019166 GO:0033306 GO:0043231 GO:0044255 GO:0055114
18	0.06	0.306	5.83	0.05	0.58	3khyA	GO:0000166 GO:0000287 GO:0005524 GO:0005622 GO:0005737 GO:0006082 GO:0006085 GO:0008152 GO:0008776 GO:0016301 GO:0016310 GO:0016740 GO:0016774 GO:0046872

Consensus prediction of GO terms

Molecular Function	GO:0046789
GO-Score	0.56
Biological Processes	GO:0006810	GO:0052157	GO:0044117	GO:0009405
GO-Score	0.61	0.56	0.56	0.56
Cellular Component	GO:0005886	GO:0097691	GO:0009986	GO:0005618	GO:0030430	GO:0031224	GO:0044462	GO:0019867	GO:0030313
GO-Score	0.61	0.56	0.56	0.56	0.56	0.42	0.32	0.32	0.32

(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.