I-TASSER results

I-TASSER results for job id Rv3519

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

Input Sequence in FASTA format

>protein (236 residues)
MPVSQHTIAGTVLTMPVRIRTANLHSAMFSVPADPAQRLIDYSGLRVCEYLPGKAIVMQM
LVRYVDGDLGRYHEYGTAIMVNPPGTQRRGPRALTRAAAFIHHLPVDQVFTLEAGRTIWG
FPKIMADFNVTDGRRFGFDVSADGRLIAGIEFSTGLPVPTLGWQMLKTYSHHDGVTREIP
WEMKVSGLRARLGGARLRLGDHPYAKELASLGLPKRALLSQSAANVEMTFGDGHPI

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MPVSQHTIAGTVLTMPVRIRTANLHSAMFSVPADPAQRLIDYSGLRVCEYLPGKAIVMQMLVRYVDGDLGRYHEYGTAIMVNPPGTQRRGPRALTRAAAFIHHLPVDQVFTLEAGRTIWGFPKIMADFNVTDGRRFGFDVSADGRLIAGIEFSTGLPVPTLGWQMLKTYSHHDGVTREIPWEMKVSGLRARLGGARLRLGDHPYAKELASLGLPKRALLSQSAANVEMTFGDGHPI
Prediction	CCCCCCHCCCCEEHCCEEEEEEEEEEEEEEHCHHHHHHHCCCCCCEEEEHCCCCEEEEEEEEEHCCCCCCCCEEEEEEEEHCCCCCCCCCCCCCCCCCCEEEEEHCCCHHHHHHCCCCCCCCCCEEEEEEHCCCEEEEEEEHCCEEEEEEEHCCCCCCCCCCCCCCCCEEHCCCEEEEEEEEEHCEEEEEHCCCEEEEHCCCCCHHHHHHCCCCCCEEEEEEHCCEEEEHCCCCCC
Conf.Score	98876555786676666887544899999969999998799888778887699769999999958999987658999998658998777754546667578887769856677655446999756768887588699999859979999998467788877776544456558856789999864457775576799987987656678769988847888876789997799779
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MPVSQHTIAGTVLTMPVRIRTANLHSAMFSVPADPAQRLIDYSGLRVCEYLPGKAIVMQMLVRYVDGDLGRYHEYGTAIMVNPPGTQRRGPRALTRAAAFIHHLPVDQVFTLEAGRTIWGFPKIMADFNVTDGRRFGFDVSADGRLIAGIEFSTGLPVPTLGWQMLKTYSHHDGVTREIPWEMKVSGLRARLGGARLRLGDHPYAKELASLGLPKRALLSQSAANVEMTFGDGHPI
Prediction	76464441453303010303403100000203273036115475041041243200000000103524212020000000023434444434424422020110203262013101411310241050415455433130345342102031544252344443313101314233331313143433434245040313723315305707134210011204403021435557
	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                 180                 200                 220

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCHCCCCEEHCCEEEEEEEEEEEEEEHCHHHHHHHCCCCCCEEEEHCCCCEEEEEEEEEHCCCCCCCCEEEEEEEEHCCCCCCCCCCCCCCCCCCEEEEEHCCCHHHHHHCCCCCCCCCCEEEEEEHCCCEEEEEEEHCCEEEEEEEHCCCCCCCCCCCCCCCCEEHCCCEEEEEEEEEHCEEEEEHCCCEEEEHCCCCCHHHHHHCCCCCCEEEEEEHCCEEEEHCCCCCC
MPVSQHTIAGTVLTMPVRIRTANLHSAMFSVPADPAQRLIDYSGLRVCEYLPGKAIVMQMLVRYVDGDLGRYHEYGTAIMVNPPGTQRRGPRALTRAAAFIHHLPVDQVFTLEAGRTIWGFPKIMADFNVTDGRRFGFDVSADGRLIAGIEFSTGLPVPTLGWQMLKTYSHHDGVTREIPWEMKVSGLRARLGGARLRLGDHPYAKELASLGLPKRALLSQSAANVEMTFGDGHPI

3bh3D

0.22

0.19

0.90

1.88

MUSTER

MPLTSPAFPPG----PYRFVNREYMIITYRTDPAAIEAVLP-EPLQMAE-----PVVRYEFIRMPDTGFGDYSESGQVIPVTFRGER----------GSYTLAMFLDDQPPLAGGRELWGFPKKAGKPRLEVQDTLVGSLDFGPVRIATGTMGYKLASLAEPNFLLKIIPHVDGSPRICELVRYHAIKGAWSAPGSLELHPHALA-PVAAL--PVLEVLSARHFVCDLTLDLGTVV

3bh3D

0.20

0.18

0.90

2.59

dPPAS

MPLTSPAFPPG----PYRFVNREYMIITYRTDPAAIEAVLP-EPLQMA-----EPVVRYEFIRMPDTGFGDYSESGQVIPVTFRG----------ERGSYTLAMFLDDQPPLAGGRELWGFPKKAGKPRLEVQDTLVGSLDFGPVRIATGTMGYKYASLAEPNFLLKIIPHVDGCELVRYHTTDVAIKGAWSAPGSLELHPHALA-PVAALPV--LEVLSARHFVCDLTLDLGTVV

3bh3D

0.20

0.18

0.90

3.78

wdPPAS

MPLTSPAFPPG----PYRFVNREYMIITYRTDPAAIEAVLPEP-LQMA-----EPVVRYEFIRMPDTGFGDYSESGQVIPVTFRG----------ERGSYTLAMFLDDQPPLAGGRELWGFPKKAGKPRLEVQDTLVGSLDFGPVRIATGTMGYKYASLAEPNFLLKIIPHVDGCELVRYHTTDVAIKGAWSAPGSLELHPHAL-APVAALPV--LEVLSARHFVCDLTLDLGTVV

3bh3D

0.22

0.19

0.90

2.32

wMUSTER

MPLTSPAFPPG----PYRFVNREYMIITYRTDPAAIEAVLP-EPLQMAE-----PVVRYEFIRMPDTGFGDYSESGQVIPVTFRGER----------GSYTLAMFLDDQPPLAGGRELWGFPKKAGKPRLEVQDTLVGSLDFGPVRIATGTMGYKLASLAEPNFLLKIIPHVDGSPRICELVRYHAIKGAWSAPGSLELHPHALAP-VAAL--PVLEVLSARHFVCDLTLDLGTVV

3bh3D

0.20

0.18

0.90

3.99

wPPAS

MPLTSPAFPPG----PYRFVNREYMIITYRTDPAAIEAVLPEP-LQM------EPVVRYEFIRMPDTGFGDYSESGQVIPVTFRG----------ERGSYTLAMFLDDQPPLAGGRELWGFPKKAGKPRLEVQDTLVGSLDFGPVRIATGTMGYKYASLAEPNFLLKIIPHVDGCELVRYHTTDVAIKGAWSAPGSLELHPHAL-APVAALPV--LEVLSARHFVCDLTLDLGTVV

3bh3D

0.20

0.18

0.90

8.49

dPPAS2

MPLTSPAFPPG----PYRFVNREYMIITYRTDPAAIEAVLP-EPLQMA-----EPVVRYEFIRMPDTGFGDYSESGQVIPVTFRG----------ERGSYTLAMFLDDQPPLAGGRELWGFPKKAGKPRLEVQDTLVGSLDFGPVRIATGTMGYKYASLAEPNFLLKIIPHVDGCELVRYHTTDVAIKGAWSAPGSLELHPHALA-PVAALPV--LEVLSARHFVCDLTLDLGTVV

3bh3D

0.21

0.19

0.90

3.24

PPAS

MPLTSPAFPPG----PYRFVNREYMIITYRTDPAAIEAVLP-EPLQMA-----EPVVRYEFIRMPDTGFGDYSESGQVIPVTFRG----------ERGSYTLAMFLDDQPPLAGGRELWGFPKKAGKPRLEVQDTLVGSLDFGPVRIATGTMGYKYASLAEPNFLLKIIPHVDGCELVRYHTTDVAIKGAWSAPGSLELHPHALA-PVAAL--PVLEVLSARHFVCDLTLDLGTVV

3bh3D

0.20

0.18

0.90

4.14

Env-PPAS

MPLTSPAFPPG----PYRFVNREYMIITYRTDPAAIEAVLPEP-LQMA-----EPVVRYEFIRMPDSTFGDYSESGQVIPVTFRG----------ERGSYTLAMFLDDQPPLAGGRELWGFPKKAGKPRLEVQDTLVGSLDFGPVRIATGTMGYKYASLAEPNFLLKIIPHVDGCELVRYHTTDVAIKGAWSAPGSLELHPHALA-PVAALPV--LEVLSARHFVCDLTLDLGTVV

3bh2A

0.20

0.18

0.90

1.79

MUSTER

TPLTSPAFPRG----PYKFHNREYFNIVYRTDMDALRKVVP-EPLEI-----DEPLVRFEIMAMHDTSLGCYTESGQAIPVSFNGVK----------GDYLHMMYLDNEPAIAVGRELSAYPKKLGYPKLFVSDTLVGTLDYGKLRVATATMGYKHKALDRPNYMLKIIPNYDGSPRICELINAKTVHEAWTGPTRLQLFDHAMA-PLNDL--PVKEIVSSSHILADIILPRAEVI

3bh2A

0.19

0.17

0.90

2.45

dPPAS

TPLTSPAFPRG----PYKFHNREYFNIVYRTDMDALRKVVPEP------LEIDEPLVRFEIMAMHDTGLGCYTESGQAIPVSFNG----------VKGDYLHMMYLDNEPAIAVGRELSAYPKKLGYPKLFVSDTLVGTLDYGKLRVATATMGYKHKALDRPNYMLKIIPNYDGSPRICELINAKTVHEAWTGPTRLQLFDHAMA-PLNDLPV--KEIVSSSHILADIILPRAEVI

(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=0.65

Estimated TM-score = 0.80±0.09

Estimated RMSD = 4.4±2.9Å

Download Model 2

C-score=-3.65

Download Model 3

C-score=-2.29

Download Model 4

C-score=-1.65

Download Model 5

C-score=-1.74

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	3bh3D	0.833	1.88	0.178	0.907
2	3bh2A	0.829	1.91	0.173	0.907
3	4zboA	0.815	2.18	0.181	0.911
4	3c8wA	0.806	2.05	0.181	0.890
5	4jm3A	0.802	2.29	0.164	0.907
6	3cmbB	0.792	2.97	0.185	0.936
7	1im0A	0.412	5.27	0.044	0.661
8	1qo8A	0.396	5.52	0.049	0.652
9	3dy5A	0.389	5.81	0.037	0.644
10	1d4cA	0.389	5.59	0.074	0.640

(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	0.34	10	3bh3B	PNH	Rep, Mult	22,72,111,121,123
2	0.14	4	4jm3B	EPE	Rep, Mult	19,64,72,111,114,115,119,123,228
3	0.03	1	3cmbA	NA	Rep, Mult	127,141,142,143,144
4	0.03	1	3cmbB	NA	Rep, Mult	127,128,129,139,140,141
5	0.03	1	1qd6D	HDS	Rep, Mult	22,62,72,74,75,76
6	0.03	1	3cmbD	PE8	Rep, Mult	18,26,62,68,118,181,183,230

	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	0.303	3bh3D	0.833	1.88	0.178	0.907	4.1.1.4	112,116,121,167
2	0.266	3c8wD	0.807	2.05	0.181	0.890	4.1.1.4	116,121
3	0.060	2j2mA	0.367	5.10	0.048	0.559	1.11.1.6	NA
4	0.060	1m7sA	0.365	5.35	0.061	0.572	1.11.1.6	NA
5	0.060	1qwlA	0.377	5.75	0.084	0.644	1.11.1.6	NA
6	0.060	1i78A	0.378	5.20	0.063	0.581	3.4.23.49	NA
7	0.060	3bh2D	0.828	1.92	0.178	0.907	4.1.1.4	69,116
8	0.060	1d4cA	0.389	5.59	0.074	0.640	1.3.99.1	198
9	0.060	1e93A	0.373	5.79	0.084	0.640	1.11.1.6	NA
10	0.060	1qo8D	0.395	5.51	0.049	0.652	1.3.99.1	NA
11	0.060	1e39A	0.389	5.58	0.064	0.644	1.3.99.1	NA
12	0.060	1w7cA	0.367	5.71	0.048	0.606	1.4.3.13	NA
13	0.060	1sy7A	0.377	5.71	0.061	0.640	1.11.1.6	NA
14	0.060	1si8A	0.364	5.28	0.033	0.568	1.11.1.6	NA
15	0.060	1rp5A	0.285	6.18	0.036	0.513	3.4.-.-	NA
16	0.060	1kwmA	0.373	6.30	0.063	0.665	3.4.17.2	NA
17	0.060	1cf9A	0.369	5.47	0.052	0.589	1.11.1.6	NA
18	0.060	3ej6A	0.363	5.41	0.029	0.572	1.11.1.6	NA
19	0.060	1sy7B	0.377	5.75	0.073	0.640	1.11.1.6	NA
20	0.060	1qo8A	0.396	5.52	0.049	0.652	1.3.99.1	NA
21	0.060	1u5uA	0.387	5.68	0.034	0.636	4.2.1.92	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	0.39	0.821	1.97	0.18	0.90	3c8wA	GO:0016829 GO:0047602
1	0.36	0.833	1.87	0.18	0.91	3bgtD	GO:0016829 GO:0016831 GO:0047602
2	0.32	0.829	1.91	0.17	0.91	3bh2A	GO:0016829 GO:0016831 GO:0047602
3	0.28	0.801	2.31	0.17	0.91	4jm3B	GO:0016829
4	0.27	0.815	2.18	0.18	0.91	4zboA	GO:0016829
5	0.25	0.802	2.90	0.19	0.94	3cmbB	GO:0016829
6	0.06	0.289	5.92	0.07	0.50	3c75H	GO:0016491 GO:0030058 GO:0030416 GO:0042597 GO:0052876 GO:0055114
7	0.06	0.311	5.89	0.01	0.53	3n2cA
8	0.06	0.285	6.07	0.05	0.50	4dg9A	GO:0000166 GO:0003824 GO:0008152
9	0.06	0.286	5.74	0.02	0.48	4dg8A	GO:0000166 GO:0003824 GO:0008152
10	0.06	0.277	5.72	0.04	0.47	1ln1A	GO:0005737 GO:0005829 GO:0006810 GO:0006869 GO:0008289 GO:0008525 GO:0015914 GO:0031210
11	0.06	0.281	5.98	0.06	0.49	2gc4A	GO:0016491 GO:0030058 GO:0030416 GO:0042597 GO:0052876 GO:0055114
12	0.06	0.307	6.12	0.04	0.53	4w5tA	GO:0000340 GO:0000932 GO:0000993 GO:0001047 GO:0003676 GO:0003723 GO:0003725 GO:0003727 GO:0003729 GO:0003743 GO:0004518 GO:0004519 GO:0004521 GO:0005634 GO:0005654 GO:0005737 GO:0005829 GO:0005844 GO:0005845 GO:0006351 GO:0006355 GO:0006412 GO:0006413 GO:0006417 GO:0007223 GO:0008022 GO:0009791 GO:0010501 GO:0010586 GO:0010628 GO:0016020 GO:0016442 GO:0016787 GO:0016891 GO:0030425 GO:0030529 GO:0031047 GO:0031054 GO:0035068 GO:0035087 GO:0035194 GO:0035196 GO:0035197 GO:0035198 GO:0035278 GO:0035279 GO:0035280 GO:0044822 GO:0045944 GO:0045947 GO:0046872 GO:0048015 GO:0060213 GO:0070551 GO:0070578 GO:0090502 GO:0090624 GO:0090625 GO:1900153
13	0.06	0.255	6.09	0.06	0.45	1etpA	GO:0005506 GO:0009055 GO:0020037 GO:0042597 GO:0046872 GO:0055114
14	0.06	0.220	5.74	0.02	0.36	2igfH
15	0.06	0.361	5.93	0.04	0.61	2iujA	GO:0006633 GO:0016491 GO:0016702 GO:0031408 GO:0046872 GO:0051213 GO:0055114
16	0.06	0.262	6.20	0.03	0.46	4pfeA	GO:0006091 GO:0008218 GO:0018298
17	0.06	0.295	5.79	0.08	0.49	1ss9A	GO:0016757 GO:0046872
18	0.06	0.226	5.83	0.05	0.38	2xraH

Consensus prediction of GO terms

Molecular Function	GO:0047602
GO-Score	0.73
Biological Processes
GO-Score
Cellular Component
GO-Score

(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.