I-TASSER results

I-TASSER results for job id Rv3902c

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

Input Sequence in FASTA format

>protein (176 residues)
MTIGVDLSTDLQDWIRLSGMNMIQGSETNDGRTILWNKGGEVRYFIDRLAGWYVITSSDR
MSREGYEFAAASMSVIEKYLYGYFGGSVRSERELPAIRAPFQPEELMPEYSIGTMTFAGR
QRDTLIDSSGTVVAITAADRLVELSHYLDVSVNVIKDSFLDSEGKPLFTLWKDYKG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MTIGVDLSTDLQDWIRLSGMNMIQGSETNDGRTILWNKGGEVRYFIDRLAGWYVITSSDRMSREGYEFAAASMSVIEKYLYGYFGGSVRSERELPAIRAPFQPEELMPEYSIGTMTFAGRQRDTLIDSSGTVVAITAADRLVELSHYLDVSVNVIKDSFLDSEGKPLFTLWKDYKG
Prediction	CCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCEEEHCCCCCEEEEEEEHCCEEEEEEHCCCCCCEEEEHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCEHCCCCCCCCCCCCEHCCCCCEEHCCCCCHHHHHHHHHCCCHHHHHHHHHCCCCCHHHHHHHHCCC
Conf.Score	99877668899999999798545676678985899869987899999849889999866799875788757889999999999999999987998655888855579984544566655444544468887676577756888889888999999999859999745565554589
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MTIGVDLSTDLQDWIRLSGMNMIQGSETNDGRTILWNKGGEVRYFIDRLAGWYVITSSDRMSREGYEFAAASMSVIEKYLYGYFGGSVRSERELPAIRAPFQPEELMPEYSIGTMTFAGRQRDTLIDSSGTVVAITAADRLVELSHYLDVSVNVIKDSFLDSEGKPLFTLWKDYKG
Prediction	76542513540241033142323434446423121224724220104355321211315547444331211323201310123004313663714304232537421541424444443344422444543324344354023003115241730361103462420130155268
	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                 160

                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCEEEHCCCCCEEEEEEEHCCEEEEEEHCCCCCCEEEEHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCEHCCCCCCCCCCCCEHCCCCCEEHCCCCCHHHHHHHHHCCCHHHHHHHHHCCCCCHHHHHHHHCCC
MTIGVDLSTDLQDWIRLSGMNMIQGSETNDGRTILWNKGGEVRYFIDRLAGWYVITSSDRMSREGYEFAAASMSVIEKYLYGYFGGSVRSERELPAIRAPFQPEELMPEYSIGTMTFAGRQRDTLIDSSGTVVAITAADRLVELSHYLDVSVNVIKDSFLDSEGKPLFTLWKDYKG

4o6gA

0.99

0.98

3.38

MUSTER

VTIGVDLSTDLQDWIRLSGMNMIQGSETNDGRTILWNKGGEVRYFIDRLAGWYVITSSDRMSREGYEFAAASMSVIEKYLYGYFGGSVRSERELPAIRAPFQPEELMPEYSIGTMTFAGRQRDTLIDSSGTVVAITAADRLVELSHYLDVSVNVIKDSFLDSEGKPLFTLWKD---

4o6gA

0.99

0.98

3.97

dPPAS

VTIGVDLSTDLQDWIRLSGMNMIQGSETNDGRTILWNKGGEVRYFIDRLAGWYVITSSDRMSREGYEFAAASMSVIEKYLYGYFGGSVRSERELPAIRAPFQPEELMPEYSIGTMTFAGRQRDTLIDSSGTVVAITAADRLVELSHYLDVSVNVIKDSFLDSEGKPLFTLWKD---

4o6gA

0.99

0.98

5.87

wdPPAS

VTIGVDLSTDLQDWIRLSGMNMIQGSETNDGRTILWNKGGEVRYFIDRLAGWYVITSSDRMSREGYEFAAASMSVIEKYLYGYFGGSVRSERELPAIRAPFQPEELMPEYSIGTMTFAGRQRDTLIDSSGTVVAITAADRLVELSHYLDVSVNVIKDSFLDSEGKPLFTLWKD---

4o6gA

0.99

0.98

4.20

wMUSTER

VTIGVDLSTDLQDWIRLSGMNMIQGSETNDGRTILWNKGGEVRYFIDRLAGWYVITSSDRMSREGYEFAAASMSVIEKYLYGYFGGSVRSERELPAIRAPFQPEELMPEYSIGTMTFAGRQRDTLIDSSGTVVAITAADRLVELSHYLDVSVNVIKDSFLDSEGKPLFTLWKD---

4o6gA

0.99

0.98

6.67

wPPAS

VTIGVDLSTDLQDWIRLSGMNMIQGSETNDGRTILWNKGGEVRYFIDRLAGWYVITSSDRMSREGYEFAAASMSVIEKYLYGYFGGSVRSERELPAIRAPFQPEELMPEYSIGTMTFAGRQRDTLIDSSGTVVAITAADRLVELSHYLDVSVNVIKDSFLDSEGKPLFTLWKD---

4o6gA

0.99

0.98

9.27

dPPAS2

VTIGVDLSTDLQDWIRLSGMNMIQGSETNDGRTILWNKGGEVRYFIDRLAGWYVITSSDRMSREGYEFAAASMSVIEKYLYGYFGGSVRSERELPAIRAPFQPEELMPEYSIGTMTFAGRQRDTLIDSSGTVVAITAADRLVELSHYLDVSVNVIKDSFLDSEGKPLFTLWKD---

4o6gA

0.99

0.98

5.46

PPAS

VTIGVDLSTDLQDWIRLSGMNMIQGSETNDGRTILWNKGGEVRYFIDRLAGWYVITSSDRMSREGYEFAAASMSVIEKYLYGYFGGSVRSERELPAIRAPFQPEELMPEYSIGTMTFAGRQRDTLIDSSGTVVAITAADRLVELSHYLDVSVNVIKDSFLDSEGKPLFTLWKD---

4o6gA

0.99

0.98

5.45

Env-PPAS

VTIGVDLSTDLQDWIRLSGMNMIQGSETNDGRTILWNKGGEVRYFIDRLAGWYVITSSDRMSREGYEFAAASMSVIEKYLYGYFGGSVRSERELPAIRAPFQPEELMPEYSIGTMTFAGRQRDTLIDSSGTVVAITAADRLVELSHYLDVSVNVIKDSFLDSEGKPLFTLWKD---

4o6gA2

1.00

0.51

1.26

MUSTER

------------------------------------------------------------------------------------GGSVRSERELPAIRAPFQPEELMPEYSIGTMTFAGRQRDTLIDSSGTVVAITAADRLVELSHYLDVSVNVIKDSFLDSEGKPLFTLWKD---

4o6gA2

1.00

0.51

1.65

dPPAS

------------------------------------------------------------------------------------GGSVRSERELPAIRAPFQPEELMPEYSIGTMTFAGRQRDTLIDSSGTVVAITAADRLVELSHYLDVSVNVIKDSFLDSEGKPLFTLWKD---

(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=1.93

Estimated TM-score = 0.99±0.04

Estimated RMSD = 1.5±1.3Å

Download Model 2

C-score=-5.00

Download Model 3

C-score=-5.00

Download Model 4

C-score=-5.00

Download Model 5

C-score=-5.00

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	4o6gA	0.977	0.39	0.994	0.983
2	5annA	0.480	4.85	0.090	0.778
3	4q1vA2	0.473	4.88	0.065	0.756
4	2btoB	0.464	5.26	0.057	0.744
5	4fffA	0.463	5.01	0.050	0.750
6	2yhgA	0.461	5.05	0.041	0.773
7	2vawA	0.460	5.04	0.078	0.727
8	5cskA	0.460	4.99	0.086	0.750
9	3fmwC	0.460	5.70	0.048	0.830
10	4a01A	0.459	5.28	0.047	0.773

(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	0.07	4	1izlM	CLA	Rep, Mult	79,82
2	0.06	3	3jcuD	CLA	Rep, Mult	73,76,80
3	0.04	2	4bs1A	ADP	Rep, Mult	81,152,153,156
4	0.04	2	2gyiB	MG	Rep, Mult	143,146
5	0.04	2	2buqA	CAQ	Rep, Mult	108,110
6	0.04	2	3jcuL	CLA	Rep, Mult	80,84
7	0.02	1	1tyeA	UUU	Rep, Mult	112,133,141
8	0.02	1	3bpxA	SAL	Rep, Mult	74,78
9	0.02	1	3da3A	MG	Rep, Mult	151,153
10	0.02	1	2vdnA	III	Rep, Mult	74,80,144,145
11	0.02	1	3wctD	OXY	Rep, Mult	44,68,79,83
12	0.02	1	1gzmB	C8E	Rep, Mult	79,125
13	0.02	1	2vc2A	180	Rep, Mult	45,54,71,77
14	0.02	1	5tglA	HEE	Rep, Mult	62,128
15	0.02	1	2iubD	MG	Rep, Mult	94,95,100,156
16	0.02	1	3ao1B	BZX	Rep, Mult	85,89,95
17	0.02	1	4flfA	XXH	Rep, Mult	8,10
18	0.02	1	1tyeC	CA	Rep, Mult	47,49,53,55

	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	1ethA	0.433	4.97	0.038	0.727	3.1.1.3	NA
2	0.060	1hplA	0.417	5.05	0.032	0.693	3.1.1.3	82,144
3	0.060	1utwF	0.445	5.33	0.049	0.773	3.2.1.26	NA
4	0.060	1eutA	0.432	5.44	0.050	0.750	3.2.1.18	NA
5	0.060	2bfgA	0.422	4.91	0.085	0.682	3.2.1.37	NA
6	0.060	2zofA	0.433	5.26	0.068	0.739	3.4.13.18	NA
7	0.060	2icyB	0.425	5.62	0.069	0.773	2.7.7.9	9
8	0.060	2e1pA	0.439	4.75	0.038	0.710	3.4.21.62	13
9	0.060	1euuA	0.427	5.32	0.065	0.739	3.2.1.18	33
10	0.060	1ygaA	0.426	5.09	0.060	0.699	5.1.3.3	NA
11	0.060	2g8sA	0.429	5.15	0.067	0.722	1.1.5.-	NA
12	0.060	1pn0C	0.443	5.42	0.065	0.790	1.14.13.7	NA
13	0.060	1wqlA	0.443	5.32	0.052	0.812	1.14.12.-	NA
14	0.060	1w27A	0.429	5.20	0.043	0.722	4.3.1.24	NA
15	0.060	1g72A	0.427	5.36	0.057	0.756	1.1.99.8	NA
16	0.060	1uliC	0.432	5.42	0.052	0.801	1.14.12.18	NA
17	0.060	1z01A	0.426	5.44	0.060	0.744	1.14.13.61	NA
18	0.060	2dkiA	0.422	5.74	0.066	0.778	1.14.13.23	NA
19	0.060	1zxvA	0.428	4.57	0.080	0.682	3.4.24.83	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	0.469	5.14	0.05	0.78	3pigB	GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798
1	0.07	0.476	4.83	0.07	0.76	4q1vA	GO:0006508 GO:0008236 GO:0016787 GO:0046872
2	0.06	0.410	4.93	0.05	0.65	3ugfB	GO:0004553 GO:0004564 GO:0004575 GO:0005975 GO:0008152 GO:0016020 GO:0016021 GO:0016740 GO:0016787 GO:0016798
3	0.06	0.409	5.25	0.04	0.70	2ac1A	GO:0004553 GO:0004564 GO:0004575 GO:0005576 GO:0005618 GO:0005886 GO:0005975 GO:0008152 GO:0009611 GO:0016787 GO:0016798 GO:0048046 GO:0080167
4	0.06	0.396	4.85	0.03	0.65	3kf5A	GO:0004553 GO:0004564 GO:0004575 GO:0005975 GO:0008152 GO:0016787 GO:0016798
5	0.06	0.480	4.85	0.09	0.78	5annA	GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798
6	0.06	0.400	5.34	0.05	0.69	4eqvA	GO:0004553 GO:0004564 GO:0004575 GO:0005576 GO:0005737 GO:0005975 GO:0005987 GO:0008152 GO:0010147 GO:0016787 GO:0016798 GO:0034484 GO:0051670 GO:1902927
7	0.06	0.395	5.44	0.07	0.72	2bklB	GO:0004252 GO:0006508 GO:0008236 GO:0070008
8	0.06	0.423	5.07	0.07	0.70	2gbcA	GO:0002020 GO:0002709 GO:0004177 GO:0004252 GO:0005102 GO:0005518 GO:0005576 GO:0005783 GO:0005794 GO:0005886 GO:0006508 GO:0007155 GO:0008233 GO:0008236 GO:0008239 GO:0008284 GO:0009986 GO:0010716 GO:0016020 GO:0016021 GO:0016324 GO:0016787 GO:0030027 GO:0030054 GO:0030139 GO:0031258 GO:0031295 GO:0042277 GO:0042803 GO:0042995 GO:0043542 GO:0045121 GO:0051234 GO:0071438
9	0.06	0.412	5.17	0.03	0.70	3ldkA	GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798
10	0.06	0.410	5.52	0.04	0.70	4wjlB	GO:0005886 GO:0006508 GO:0008236 GO:0008239 GO:0015459 GO:0016020 GO:0016021 GO:0072659 GO:0090004 GO:1901379
11	0.06	0.404	5.15	0.06	0.67	4bp8A	GO:0004252 GO:0006508 GO:0008236 GO:0070008
12	0.06	0.385	5.00	0.08	0.61	3munA	GO:0004252 GO:0006508 GO:0008236 GO:0070008
13	0.06	0.368	5.67	0.02	0.67	2aj8A	GO:0001618 GO:0001662 GO:0001666 GO:0002020 GO:0004177 GO:0004252 GO:0005102 GO:0005576 GO:0005765 GO:0005886 GO:0005925 GO:0006508 GO:0007155 GO:0008233 GO:0008236 GO:0008239 GO:0008284 GO:0009986 GO:0010716 GO:0016020 GO:0016021 GO:0016324 GO:0016787 GO:0030027 GO:0030054 GO:0030139 GO:0031258 GO:0031295 GO:0033632 GO:0035641 GO:0036343 GO:0042110 GO:0042802 GO:0042803 GO:0042995 GO:0043542 GO:0045121 GO:0046581 GO:0046718 GO:0070062 GO:0071438
14	0.06	0.418	5.19	0.07	0.72	1xfdA	GO:0005886 GO:0006508 GO:0008076 GO:0008236 GO:0008239 GO:0009986 GO:0015459 GO:0016020 GO:0016021 GO:0043025 GO:0043268 GO:0070062 GO:0072659 GO:1901379
15	0.06	0.386	5.29	0.04	0.67	1y4wA	GO:0000272 GO:0004553 GO:0005576 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0051669
16	0.06	0.422	4.96	0.05	0.70	2addA	GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0051669
17	0.06	0.372	4.88	0.06	0.59	2d5lA	GO:0004177 GO:0006508 GO:0008233 GO:0008236 GO:0016787
18	0.06	0.391	5.12	0.05	0.65	3o4jC	GO:0005737 GO:0006508 GO:0008236 GO:0016787

Consensus prediction of GO terms

Molecular Function	GO:0090599
GO-Score	0.36
Biological Processes	GO:0044238	GO:0071704
GO-Score	0.41	0.38
Cellular Component	GO:0005618	GO:0048046	GO:0005886	GO:0016021
GO-Score	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.