I-TASSER results

I-TASSER results for job id Rv2306A

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

Input Sequence in FASTA format

>protein (197 residues)
MTDNECPADSRRRHVLRLALFAGILLGLFYLVAVARVIHVDGVRSAIVVATGPIAPLAYV
VVSAALGALFVPGPILAAGSGVLFGPLLDTFVTLPAFSAGAQAGMTPRRCWVSIAPIASM
HRSNGADCGRWSVSASSPASRMRWPRTPSGRSEFRCGRWSLGRSSGRRHGCSSTPRWARR
SPTCRRRWFTRRSRCGA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MTDNECPADSRRRHVLRLALFAGILLGLFYLVAVARVIHVDGVRSAIVVATGPIAPLAYVVVSAALGALFVPGPILAAGSGVLFGPLLDTFVTLPAFSAGAQAGMTPRRCWVSIAPIASMHRSNGADCGRWSVSASSPASRMRWPRTPSGRSEFRCGRWSLGRSSGRRHGCSSTPRWARRSPTCRRRWFTRRSRCGA
Prediction	CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCEEEEHCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEHCCCCCEEEEHCCCCCCEEEEEHCEHHHHHCCCHCCCCCCCCCCCCCCCHHHHHHHHHCCCCC
Conf.Score	99888887665458999999999999998764345565457899999999665455689999999999876555555443343558999999999999999999999999998666777665566555655655456765456554566645555544444444465445556875445687545555554445589
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MTDNECPADSRRRHVLRLALFAGILLGLFYLVAVARVIHVDGVRSAIVVATGPIAPLAYVVVSAALGALFVPGPILAAGSGVLFGPLLDTFVTLPAFSAGAQAGMTPRRCWVSIAPIASMHRSNGADCGRWSVSASSPASRMRWPRTPSGRSEFRCGRWSLGRSSGRRHGCSSTPRWARRSPTCRRRWFTRRSRCGA
Prediction	85567555553343001001210222210011001202427412510261044132310010121312323213333332133333332222232332331131033333010032255545553341230232144423434144354343434223221143444445136425135544404441134456258
	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

                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCEEEEHCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEHCCCCCEEEEHCCCCCCEEEEEHCEHHHHHCCCHCCCCCCCCCCCCCCCHHHHHHHHHCCCCC
MTDNECPADSRRRHVLRLALFAGILLGLFYLVAVARVIHVDGVRSAIVVATGPIAPLAYVVVSAALGALFVPGPILAAGSGVLFGPLLDTFVTLPAFSAGAQAGMTPRRCWVSIAPIASMHRSNGADCGRWSVSASSPASRMRWPRTPSGRSEFRCGRWSLGRSSGRRHGCSSTPRWARRSPTCRRRWFTRRSRCGA

4mt1A2

0.20

0.18

0.87

1.50

MUSTER

I-------SYMGMSINVLTMFAMILVIGIVDDAIVVVENVERIKEATKKAMGQI-SGAVIGITAVLISVFVPLAMFSGAAGNIYKQFALTMASSIAFSAFLALTLTPALCA-------------TGFFGWFNKKFDSWTHGY---EGRVAKVLRKTFRMMVGLAVVGVFLFMRLPT--SFLPTLYGLAVAAVFLVLA

2j8sA3

0.19

0.18

0.94

0.70

dPPAS

FSIN-----------TLTMFGMVLAIGLLVDDAIVVVENAEEPKEATRKSMGQI-QGALVGIAMVLSAVFVPMAFFGGSTGAIYRQFSITIVSAMALSVLVALILTPALCATMLKPIAKGDHGKKGFFGWFNRMFEKSTHHYTDSVGGILRSTGRYLVLYLIIVVGMAYLFVRLPSSFNQAPSLYAISLIVVFLCLA

4mt1A2

0.21

0.18

0.88

1.36

wdPPAS

I--------YMGMSINVLTMFAMILVIGIVDDAIVVVENVERPKEATKKAMGQISGAV-IGITAVLISVFVPLAMFSGAAGNIYKQFALTMASSIAFSAFLALTLTPALCA-------------TGFFGWFNKKFDSWTHGYEGRVAKVLRKTFRMMVVYIGLAVVGVFLFMRLPT--SFLPTEGSQTLILYGLAVA

4mt1A2

0.21

0.19

0.88

1.02

wMUSTER

I-------SYMGMSINVLTMFAMILVIGIVDDAIVVVENVERIKEATKKAMGQI-SGAVIGITAVLISVFVPLAMFSGAAGNIYKQFALTMASSIAFSAFLALTLTPALCA-------------TGFFGWFNKKFDSWTHGYEGRVAKVLRKTFRMMVVYIGLAVVGVFLFMRLPT--SFLPTEGSQTLILYGLAVA

4mt1A2

0.22

0.19

0.86

1.65

wPPAS

I------------SINVLTMFAMILVIGIVDDAIVVVENVERPKEATKKAMGQI-SGAVIGITAVLISVFVPLAMFSGAAGNIYKQFALTMASSIAFSAFLALTLTPALCA-------------TGFFGWFNKKFDSWTHGYEGRVAKVLRKTFRMMVVYIGLAVVGVFLFMRLPT--SFLPTEGSQTLILYGLAVA

4mt1A2

0.21

0.18

0.85

1.70

dPPAS2

M------------SINVLTMFAMILVIGIVDDAIVVVENVERIKEATKKAMGQI-SGAVIGITAVLISVFVPLAMFSGAAGNIYKQFALTMASSIAFSAFLALTLTPALCA-------------TGFFGWFNKKFDSWTHGY---EGRVAKVLRKTFRMMVGLAVVMRLPTSFLPTEGSQTLILYGLAVAAVFLVLA

4mt1A2

0.20

0.17

0.85

1.17

PPAS

I------------SINVLTMFAMILVIGIVDDAIVVVENVERIKEATKKAMGQI-SGAVIGITAVLISVFVPLAMFSGAAGNIYKQFALTMASSIAFSAFLALTLTPALCA-------------TGFFGWFNKKFDSWTHGY---EGRVAKVLRKTFRMLAVVGVFMRLPTSFLPTEGSQTLILYGLAVAAVFLVLA

4mt1A2

0.20

0.17

0.88

1.18

Env-PPAS

I-----SYMGM--SINVLTMFAMILVIGIVDDAIVVVENVERIKEATKKAMGQI-SGAVIGITAVLISVFVPLAMFSGAAGNIYKQFALTMASSIAFSAFLALTLTPALCA-------------TGFFGWFNKKFDSWTHGY---EGRVAKVLRKTFRMLAVVGVFMRLPTSFLPTEGSQTLILYGLAVAAVFLVLA

2j8sA3

0.19

0.18

0.91

1.45

MUSTER

L------------SINTLTMFGMVLAIGLLVD-IVVVENAEEPKEATRKSMGQI-QGALVGIAMVLSAVFVPMAFFGGSTGAIYRQFSITIVSAMALSVLVALILTPALCATMLKPIAKGDHGKKGFFGWFNRMFEKSTHHYT---DSVGGILRSTGRYYLIIVVGMAYLFVRLPSSFNQAPSLYAISLIVVFLCAA

4mt1A2

0.22

0.19

0.87

0.70

dPPAS

MS------------INVLTMFAMILVIGIVDDAIVVVENVERIKEATKKAMGQI-SGAVIGITAVLISVFVPLAMFSGAAGNIYKQFALTMASSIAFSAFLALTLTPALCA-------------TGFFGWFNKKFDSWTHGYEGRVAKVLRKTFRMMVVYIGLAVVMRLPTSFLPTEGSQTLILYGLAVAAVFLVLA

(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=-0.40

Estimated TM-score = 0.66±0.13

Estimated RMSD = 6.2±3.8Å

Download Model 2

C-score=-4.48

Download Model 3

C-score=-3.30

Download Model 4

C-score=-1.21

Download Model 5

C-score=-1.10

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	2j8sA	0.893	2.08	0.184	0.995
2	4mt1A2	0.848	1.96	0.191	0.929
3	3k07A2	0.777	2.40	0.113	0.898
4	3jd8A3	0.733	3.06	0.072	0.914
5	4k0eA	0.731	2.60	0.094	0.868
6	3aqpA2	0.711	3.02	0.076	0.873
7	3mktA	0.463	4.69	0.053	0.695
8	1st6A	0.461	5.16	0.059	0.761
9	4iggA	0.460	4.39	0.042	0.665
10	3gi9C	0.459	4.91	0.066	0.726

(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	0.06	3	2v50E	LMT	Rep, Mult	11,71,74,75,85,89
2	0.06	3	5c65B	37X	Rep, Mult	34,62,91,94
3	0.04	2	2c4wA	IMD	Rep, Mult	81,84
4	0.04	2	5ezmA	MPG	Rep, Mult	60,99
5	0.04	2	3aodA	MIY	Rep, Mult	66,67,72,93
6	0.04	2	2q6hA	CXX	Rep, Mult	35,54,58,59,62,95
7	0.04	2	3kziL	PL9	Rep, Mult	25,26,28
8	0.02	1	4xk8L	CLA	Rep, Mult	32,66
9	0.02	1	2j8rB	AZI	Rep, Mult	71,81
10	0.02	1	1k6dA	MG	Rep, Mult	14,24
11	0.02	1	2wieA	CVM	Rep, Mult	34,38
12	0.02	1	3f3aA	TRP	Rep, Mult	29,32,35,36,58
13	0.02	1	2gwwA	III	Rep, Mult	8,86,89,97,100
14	0.02	1	3gjcA	BOG	Rep, Mult	28,31
15	0.02	1	5l8gV	CA	Rep, Mult	70,88,91
16	0.02	1	2ljcB	RIM	Rep, Mult	61,64
17	0.02	1	3t34A	MG	Rep, Mult	45,90

	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	1dquA	0.419	5.64	0.061	0.731	4.1.3.1	39
2	0.060	2gtqA	0.418	5.73	0.065	0.741	3.4.11.2	NA
3	0.060	3ebgA	0.423	5.59	0.047	0.746	3.4.11.-	NA
4	0.060	1e3pA	0.454	5.31	0.062	0.751	2.7.7.8	26,29,34
5	0.060	2cycA	0.409	5.60	0.044	0.695	6.1.1.1	NA
6	0.060	1igwC	0.421	5.96	0.027	0.787	4.1.3.1	NA
7	0.060	2e7zA	0.426	5.48	0.033	0.731	4.2.1.71	NA
8	0.060	1jqnA	0.434	4.97	0.038	0.690	4.1.1.31	NA
9	0.060	3c46B	0.384	5.38	0.032	0.645	2.7.7.6	68
10	0.060	3bicA	0.424	4.40	0.039	0.619	5.4.99.2	NA
11	0.060	1oqzB	0.419	5.83	0.067	0.766	3.5.1.93	NA
12	0.060	2dlcX	0.409	5.49	0.031	0.675	6.1.1.1	59
13	0.060	1biqB	0.407	4.88	0.041	0.650	1.17.4.1	NA
14	0.060	1xdpA	0.447	4.92	0.053	0.706	2.7.4.1	96,97
15	0.060	1f8mA	0.408	6.10	0.063	0.766	4.1.3.1	99
16	0.060	1xmeA	0.415	5.02	0.055	0.665	1.9.3.1	NA
17	0.060	5acnA	0.437	5.82	0.056	0.782	4.2.1.3	NA
18	0.060	1ut9A	0.410	5.66	0.051	0.701	3.2.1.4	NA
19	0.060	2cycB	0.412	5.54	0.050	0.701	6.1.1.1	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	0.22	0.897	2.01	0.18	0.99	3d9bA	GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0006855 GO:0015238 GO:0015307 GO:0016020 GO:0016021 GO:0042493 GO:0042802 GO:0046618
1	0.22	0.886	2.17	0.17	0.99	3w9iF	GO:0005215 GO:0005886 GO:0006810 GO:0006855 GO:0015238 GO:0016020 GO:0016021 GO:0046677
2	0.19	0.856	2.20	0.19	0.97	3nogA	GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0006855 GO:0015238 GO:0015307 GO:0016020 GO:0016021 GO:0042493 GO:0042802 GO:0046618
3	0.18	0.819	2.39	0.15	0.94	2v50D	GO:0005215 GO:0005886 GO:0006810 GO:0006855 GO:0015238 GO:0016020 GO:0016021 GO:0046677
4	0.13	0.731	2.60	0.09	0.87	4k0eA	GO:0005215 GO:0006810 GO:0006812 GO:0008324 GO:0016020 GO:0016021 GO:0098655
5	0.11	0.702	3.16	0.09	0.89	4dnrA	GO:0005215 GO:0005375 GO:0005507 GO:0005886 GO:0006810 GO:0006811 GO:0006812 GO:0006825 GO:0006878 GO:0008324 GO:0010272 GO:0010273 GO:0015080 GO:0015673 GO:0015679 GO:0016020 GO:0016021 GO:0046688 GO:0060003 GO:1902601
6	0.10	0.502	2.60	0.10	0.58	4k0eB	GO:0005215 GO:0006810 GO:0006812 GO:0008324 GO:0016020 GO:0016021 GO:0098655
7	0.07	0.743	2.43	0.09	0.86	4k0eC	GO:0005215 GO:0006810 GO:0006812 GO:0008324 GO:0016020 GO:0016021 GO:0098655
8	0.06	0.848	1.96	0.19	0.93	4mt1A	GO:0005215 GO:0006810 GO:0016020 GO:0016021
9	0.06	0.313	5.28	0.05	0.52	3wxvA	GO:0004872 GO:0005886 GO:0006629 GO:0006631 GO:0007186 GO:0009755 GO:0010633 GO:0010719 GO:0010906 GO:0016020 GO:0016021 GO:0019216 GO:0019395 GO:0019901 GO:0030308 GO:0031226 GO:0033210 GO:0033211 GO:0042593 GO:0042802 GO:0046426 GO:0046427 GO:0046628 GO:0046872 GO:0046982 GO:0055100 GO:0097003 GO:1901223
10	0.06	0.330	4.26	0.03	0.47	4ni5B	GO:0016491 GO:0055114
11	0.06	0.301	5.74	0.03	0.52	1vknA	GO:0003942 GO:0005737 GO:0006526 GO:0008652 GO:0016491 GO:0016620 GO:0046983 GO:0051287 GO:0055114
12	0.06	0.267	5.98	0.01	0.50	4r86B	GO:0005215 GO:0006810 GO:0016020 GO:0016021
13	0.06	0.294	5.71	0.03	0.53	4i0wD	GO:0004252 GO:0006508 GO:0008233 GO:0008236 GO:0016787
14	0.06	0.260	5.28	0.02	0.43	1h6eA	GO:0005048 GO:0005215 GO:0005739 GO:0005765 GO:0005829 GO:0005886 GO:0005905 GO:0006810 GO:0006886 GO:0006897 GO:0007018 GO:0008289 GO:0015031 GO:0016020 GO:0016192 GO:0019886 GO:0030122 GO:0030131 GO:0030666 GO:0030669 GO:0035615 GO:0036020 GO:0042059 GO:0043195 GO:0044325 GO:0048013 GO:0050690 GO:0050750 GO:0060071 GO:0070062 GO:0072583 GO:1903077
15	0.06	0.307	5.13	0.03	0.50	3ge6A	GO:0000166 GO:0016491 GO:0055114
16	0.06	0.236	5.11	0.05	0.40	2fi7A	GO:0009297 GO:0043683 GO:0046903
17	0.06	0.281	5.68	0.04	0.50	1texD	GO:0016740
18	0.06	0.244	5.28	0.04	0.41	4mkmA	GO:0016020 GO:0016021 GO:0046872

Consensus prediction of GO terms

Molecular Function	GO:0042802	GO:0015307
GO-Score	0.37	0.37
Biological Processes	GO:0006855	GO:0046618	GO:0046677
GO-Score	0.60	0.37	0.36
Cellular Component	GO:0005887
GO-Score	0.37

(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.