I-TASSER results

I-TASSER results for job id Rv2035

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

Input Sequence in FASTA format

>protein (162 residues)
MTRPRTDAIHHHVVVNAPIERAFAVFTTRFGDFKPREHNLLAIPITETVFECHAGGHIYD
RGVDGSVCKWARVLVYEPPSRVLFTWDIGPTWRPETDLAKTSEVEVRFTAQSAETTRVDL
EHRHLDRHGPGWESVADGVDSEAGWPLYLRRYTDLLCIQVQP

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MTRPRTDAIHHHVVVNAPIERAFAVFTTRFGDFKPREHNLLAIPITETVFECHAGGHIYDRGVDGSVCKWARVLVYEPPSRVLFTWDIGPTWRPETDLAKTSEVEVRFTAQSAETTRVDLEHRHLDRHGPGWESVADGVDSEAGWPLYLRRYTDLLCIQVQP
Prediction	CCCCCCCEEEEEEEHCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEEHCCCCEEEEEHCCCCCEEEEEEEEEEHCCCEEEEEEHCCCCCCCCCCCCCCEEEEEEEEEHCCCEEEEEEEEHCCCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCC
Conf.Score	999999859999999699999999999998886788877766665589998579979999879996787899999969958999986688887778888757999999996699699999997566677755778887655565899999999999977999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MTRPRTDAIHHHVVVNAPIERAFAVFTTRFGDFKPREHNLLAIPITETVFECHAGGHIYDRGVDGSVCKWARVLVYEPPSRVLFTWDIGPTWRPETDLAKTSEVEVRFTAQSAETTRVDLEHRHLDRHGPGWESVADGVDSEAGWPLYLRRYTDLLCIQVQP
Prediction	856565550322030503263014001440450234644244443340302242102001315534413203023143443010203244534444545430302030245367313030214305534662542354253551033005302510465468
	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

CCCCCCCEEEEEEEHCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEEHCCCCEEEEEHCCCCCEEEEEEEEEEHCCCEEEEEEHCCCCCCCCCCCCCCEEEEEEEEEHCCCEEEEEEEEHCCCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCC
MTRPRTDAIHHHVVVNAPIERAFAVFTTRFGDFKPREHNLLAIPITETVFECHAGGHIYDRGVDGSVCKWARVLVYEPPSRVLFTWDIGPTWRPETDLAKTSEVEVRFTAQSAETTRVDLEHRHLDRHGPGWESVADGVDSEAGWPLYLRRYTDLLCIQVQP

2gkcA

0.24

0.23

0.95

2.57

MUSTER

---NYDPFVRHSVTVKADRKTAFKTFLEGFPEWWPNNFRTTKVGAP--LGVDKKGGRWYEIDEQGEEHTFGLIRKVDEPDTLVIGWRLNGFGRI--DPDNSSEFTVTFVADGQKKTRVDVEHTHFDRMGTKHAKRVRN-GMDKGWPTILQSFQDKIDEEGAK

2gkcA

0.23

0.22

0.95

3.16

dPPAS

---NYDPFVRHSVTVKADRKTAFKTFLEGFPEWWPNNFRTTKVGAP--LGVDKKGGRWYEIDEQGEEHTFGLIRKVDEPDTLVIGWRLNGFGRID--PDNSSEFTVTFVADGQKKTRVDVEHTHFDRMGT-KHAKRVRNGMDKGWPTILQSFQDKIDEEGAK

2gkcA

0.23

0.22

0.95

3.89

wdPPAS

---NYDPFVRHSVTVKADRKTAFKTFLEGFPEWWPNNFRTTKVGAP--LGVDKKGGRWYEIDEQGEEHTFGLIRKVDEPDTLVIGWRLNGFGRID--PDNSSEFTVTFVADGQKKTRVDVEHTHFDRMG-TKHAKRVRNGMDKGWPTILQSFQDKIDEEGAK

2gkcA

0.24

0.23

0.94

3.38

wMUSTER

----YDPFVRHSVTVKADRKTAFKTFLEGFPEWWPNNFRTTKVGAPL--GVDKKGGRWYEIDEQGEEHTFGLIRKVDEPDTLVIGWRLNGFGRI--DPDNSSEFTVTFVADGQKKTRVDVEHTHFDRMGTKHAKRVRN-GMDKGWPTILQSFQDKIDEEGAK

2gkcA

0.23

0.22

0.95

4.11

wPPAS

---NYDPFVRHSVTVKADRKTAFKTFLEGFPEWWPNNFRT--TKVGAPLGVDKKGGRWYEIDEQGEEHTFGLIRKVDEPDTLVIGWRLNGFG--RIDPDNSSEFTVTFVADGQKKTRVDVEHTHFDRMGT-KHAKRVRNGMDKGWPTILQSFQDKIDEEGAK

2gkcA

0.23

0.22

0.95

5.13

dPPAS2

---NYDPFVRHSVTVKADRKTAFKTFLEGFPEWWPNNFRTTKVGAP--LGVDKKGGRWYEIDEQGEEHTFGLIRKVDEPDTLVIGWRLNGFGRID--PDNSSEFTVTFVADGQKKTRVDVEHTHFDRMGT-KHAKRVRNGMDKGWPTILQSFQDKIDEEGAK

2gkcA

0.24

0.23

0.95

3.81

PPAS

---NYDPFVRHSVTVKADRKTAFKTFLEGFPEWWPNNFRTTKVGAP--LGVDKKGGRWYEIDEQGEEHTFGLIRKVDEPDTLVIGWRLNGFGRI--DPDNSSEFTVTFVADGQKKTRVDVEHTHFDRMGT-KHAKRVRNGMDKGWPTILQSFQDKIDEEGAK

2gkcA

0.24

0.23

0.95

3.77

Env-PPAS

---NYDPFVRHSVTVKADRKTAFKTFLEGFPEWWPNNFRTTKVGAP--LGVDKKGGRWYEIDEQGEEHTFGLIRKVDEPDTLVIGWRLNGFGRI--DPDNSSEFTVTFVADGQKKTRVDVEHTHFDRMGT-KHAKRVRNGMDKGWPTILQSFQDKIDEEGAK

2l9pA

0.16

0.15

0.95

2.53

MUSTER

MTEKKKNKIIFTRTFSAPINKVFDAYRELFEQWFHPQ----DASVTVYDFNATKGGSAFYAIPQMISYTIAEYLQVDAPYYIEYLDYFATSKGEKDTSMPGMHITLNFEEV-KGKTTVTSTSTF---PTESAAQQAIDMGVETGMNSTLNQLEKLLNQKLEH

2l9pA

0.16

0.15

0.95

2.80

dPPAS

MTIKKKNKIIFTRTFSAPINKVFDAYRELFEQWFHPQ----DASVTVYDFNATKGGSAFYAIPQMISYTIAEYLQVDAPYYIEYLDYFATSKGEKDTSMPGMHITLNFEE-VKGKTTVTSTSTF---PTESAAQQAIDMGVETGMNSTLNQLEKLLNQKLEH

(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 3 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=0.55

Estimated TM-score = 0.79±0.09

Estimated RMSD = 3.8±2.6Å

Download Model 2

C-score=-1.18

Download Model 3

C-score=0.57

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	2gkcA	0.845	1.82	0.227	0.951
2	2ldkA	0.691	3.48	0.118	0.901
3	3uidA	0.687	3.17	0.099	0.889
4	1xuvA	0.683	3.07	0.177	0.889
5	3q64A	0.654	3.38	0.137	0.846
6	3pu2A	0.645	3.10	0.167	0.840
7	3otlA	0.641	3.59	0.131	0.846
8	3ni8A	0.641	3.18	0.162	0.827
9	2l9pA	0.638	3.83	0.132	0.876
10	3ie5B	0.637	3.86	0.098	0.889

(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	0.35	16	4n3eB	2AN	Rep, Mult	11,13,15,22,26,106,118,120,148,149,152
2	0.05	2	2l65A	UUU	Rep, Mult	68,69,70,90,91,92,141,143,144,145
3	0.04	2	3n0qA	FES	Rep, Mult	52,72,74,83,104,105,106
4	0.02	1	2flhA	ZEA	Rep, Mult	24,27,28,78,79
5	0.02	1	2gkdA	NUC	Rep, Mult	92,138,139
6	0.02	1	2gkdA	NUC	Rep, Mult	132,135,136
7	0.02	1	1txcA	2AN	Rep, Mult	149,152,153,156
8	0.02	1	2l65A	MRP	Rep, Mult	70,141,143,144,145

	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	1kizA	0.460	5.38	0.063	0.821	4.2.3.6	NA
2	0.060	2b1xA	0.594	4.19	0.066	0.901	1.14.12.12	NA
3	0.060	1duvG	0.459	4.58	0.034	0.710	2.1.3.3	NA
4	0.060	1dgjA	0.470	5.18	0.051	0.833	1.2.-.-	121
5	0.060	2e1qA	0.475	5.49	0.044	0.858	1.17.3.2,1.17.1.4	NA
6	0.060	3claA	0.461	5.25	0.029	0.790	2.3.1.28	151
7	0.060	1dpbA	0.457	5.20	0.086	0.809	2.3.1.12	NA
8	0.060	1ffuB	0.472	4.81	0.057	0.821	1.2.99.2	NA
9	0.060	2wodA	0.465	4.88	0.037	0.809	3.2.2.24	20,29
10	0.060	1vlbA	0.460	5.37	0.063	0.827	1.2.99.7	55
11	0.060	2ii4A	0.459	5.29	0.056	0.815	2.3.1.168	NA
12	0.060	3l60A	0.452	5.26	0.063	0.809	2.3.1.12	NA
13	0.060	1z01A	0.602	4.11	0.053	0.895	1.14.13.61	32
14	0.060	3b9jJ	0.380	5.21	0.015	0.660	1.17.1.4,1.17.3.2	155
15	0.060	2oa6D	0.459	5.19	0.081	0.809	4.2.3.9	30
16	0.060	3hfwA	0.464	4.72	0.091	0.802	3.2.2.19	NA
17	0.060	2vq5A	0.566	4.11	0.099	0.852	4.2.1.78	56
18	0.060	2ihwA	0.459	5.30	0.056	0.821	2.3.1.168	122
19	0.060	1ciaA	0.460	5.30	0.029	0.790	2.3.1.28	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	0.27	0.620	3.57	0.20	0.84	2leqA	GO:0006950
1	0.25	0.628	2.92	0.16	0.78	1x53A	GO:0001671 GO:0005737 GO:0005783 GO:0005829 GO:0005913 GO:0006950 GO:0032781 GO:0051087 GO:0070062 GO:0098609 GO:0098641
2	0.24	0.625	3.55	0.18	0.83	3rd6A	GO:0006950
3	0.23	0.664	3.22	0.17	0.87	3pu2B	GO:0006950
4	0.23	0.638	3.83	0.13	0.88	2l9pA	GO:0006950
5	0.22	0.626	2.90	0.17	0.78	2m89A	GO:0006950
6	0.22	0.652	3.58	0.13	0.86	3otlA	GO:0006950
7	0.22	0.692	3.11	0.17	0.91	1xuvA	GO:0006950
8	0.22	0.667	3.32	0.14	0.86	3q64A	GO:0006950
9	0.22	0.641	3.18	0.16	0.83	3ni8A	GO:0006950
10	0.19	0.637	3.78	0.11	0.90	2lf2A	GO:0006950
11	0.18	0.691	3.48	0.12	0.90	2ldkA	GO:0006950
12	0.18	0.592	2.94	0.22	0.76	4fpwA	GO:0006950
13	0.18	0.687	3.17	0.10	0.89	3uidA	GO:0006950
14	0.18	0.655	3.61	0.14	0.87	3putB	GO:0006950
15	0.18	0.599	3.07	0.15	0.77	2lcgA	GO:0006950
16	0.17	0.629	3.58	0.11	0.86	1xfsA	GO:0006950
17	0.17	0.619	3.44	0.16	0.83	1z94B	GO:0006950
18	0.16	0.592	3.18	0.21	0.78	2luzA	GO:0006950
19	0.16	0.557	3.73	0.14	0.79	2l8oA	GO:0006950
20	0.16	0.613	3.21	0.16	0.80	2lghA	GO:0006950
21	0.16	0.618	3.33	0.13	0.80	2nn5A	GO:0006950
22	0.15	0.586	3.09	0.19	0.75	3q6aB	GO:0006950
23	0.15	0.570	3.41	0.20	0.77	1xn5A	GO:0006950
24	0.15	0.621	3.61	0.09	0.85	2il5A	GO:0006950
25	0.14	0.626	3.27	0.17	0.82	3eliA	GO:0006950
26	0.13	0.627	3.37	0.17	0.83	3q63F	GO:0006950
27	0.10	0.543	4.20	0.12	0.81	2kewA	GO:0006950

Consensus prediction of GO terms

Molecular Function	GO:0045296	GO:0060590	GO:0008047	GO:0098632
GO-Score	0.50	0.50	0.50	0.50
Biological Processes	GO:0006950	GO:0051345	GO:0043462	GO:0007155
GO-Score	0.75	0.50	0.50	0.50
Cellular Component	GO:0031988	GO:0005912	GO:0012505	GO:0005911	GO:1903561	GO:0043231	GO:0044444
GO-Score	0.50	0.50	0.50	0.50	0.50	0.50	0.50

(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.