I-TASSER results

I-TASSER results for job id Rv3675

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

Input Sequence in FASTA format

>protein (125 residues)
MFTLLVSWLLVACVPGLLMLATLGLGRLERFLARDTVTATDVAEFLEQAEAVDVHTLARN
GMPEALDYLHRRQARRITDSPPLGSGAGPRYAGPLFVTDLDSPVEPPRHGQPNPQFRTAR
HANHV

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MFTLLVSWLLVACVPGLLMLATLGLGRLERFLARDTVTATDVAEFLEQAEAVDVHTLARNGMPEALDYLHRRQARRITDSPPLGSGAGPRYAGPLFVTDLDSPVEPPRHGQPNPQFRTARHANHV
Prediction	CCCEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCHHHHHHHHHHCCHHHHHHHHHHCHCCCCCCCCCCCCCCCCCCCCCEHCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Conf.Score	95335599999999999999999999999865445799999999999768677888888686789999887555456677777778888667885664677888777777889888898888899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MFTLLVSWLLVACVPGLLMLATLGLGRLERFLARDTVTATDVAEFLEQAEAVDVHTLARNGMPEALDYLHRRQARRITDSPPLGSGAGPRYAGPLFVTDLDSPVEPPRHGQPNPQFRTARHANHV
Prediction	63233133331333133213313114303530574514673045116525574144136532350154145454544574445665444444444244526345434454444561554535658
	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

                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCHHHHHHHHHHCCHHHHHHHHHHCHCCCCCCCCCCCCCCCCCCCCCEHCCCCCCCCCCCCCCCCCCCCCCCCCCCC
MFTLLVSWLLVACVPGLLMLATLGLGRLERFLARDTVTATDVAEFLEQAEAVDVHTLARNGMPEALDYLHRRQARRITDSPPLGSGAGPRYAGPLFVTDLDSPVEPPRHGQPNPQFRTARHANHV

2mi2A

0.17

0.14

0.79

0.81

MUSTER

MFDIGFSELLLVFIIGLVVLLPVAVKTVAGWIRALRSLATTVNELTQELKLQEFQDSLKKVEKASLTNLTPELKASMDELRQAAESMKRSYVA-------NDPLEH-------------------

4behB

0.11

0.10

0.86

0.75

dPPAS

---------AMRYVASYLLAALGG---------NSSPSAKDIKKILDSVGDDRLNKVISELNGKNIEDVIAQGIGKLASVPAGGAVAVSAAPGSAAPAAGSAPAAAEEKKDEKKEESEESDDDMG

4behB

0.11

0.10

0.85

0.81

wdPPAS

----AMR------VASYLLAALGG---------NSSPSAKDIKKILDSVDDDRLNKVISELNGKNIEDVIAQGIGKLASVPAGGAVAVSAAPGSAAPAAGSAPAAAEEKKDEKKEESEESDDDMG

5fvmA

0.17

0.98

0.77

wMUSTER

WHELWYEGLEDASRQFFTEKMFATLEPLHEMLKRGPETQNSFGRDLNDA-YEWVLNYKRTKLNQAWDIYYNV-FRRISRKLPQLQTLDLQHVSPKLSAAKDLELAVPGTYHAGKPIVRTHFEPVF

2mi2A

0.19

0.13

0.69

0.91

wPPAS

MFLVFIIGLVVL-LPVAVKTVAGWIRALRSLATTVQLKLQEFQDSLKKVEKASLTNLTPE-LKASMDELRQA-AESMKRSYVAND-----------------PLE---H----------------

4behB

0.12

0.10

0.82

0.91

dPPAS2

-------------VASYLLAALGG---------NSSPSAKDIKKILDSVGDDRLNKVISELNGKNIEDVIAQGIGKLASVPAGGAVAVSAAPGSAAPAAGSAPAAAEEKKDEKKEESEESDDDMG

4behB

0.11

0.10

0.84

0.94

PPAS

-----------------AMVASYLLAALGG---NSSPSAKDIKKILDSVDDDRLNKVISELNGKNIEDVIAQGIGKLASVPAGGAVAVSAAPGSAAPAAGSAPAAAEEKKDEKKEESEESDDDMG

4behB

0.11

0.10

0.84

0.85

Env-PPAS

-----------------AMVASYLLAALGG---NSSPSAKDIKKILDSVDDDRLNKVISELNGKNIEDVIAQGIGKLASVPAGGAVAVSAAPGSAAPAAGSAPAAAEEKKDEKKEESEESDDDMG

4yt2A2

0.12

0.10

0.83

0.78

MUSTER

M----GSLVTAVALSGVLDYYTVGRKII-------NAPKKMIEQQVIMTLQTMASLVETSGIEGMVKALNPELLIRSASSMKLLDRQKD----DAALEILQNLDETLKAEVEKAEIKPT------

3pntA1

0.12

0.09

0.70

0.68

dPPAS

--------------------ERDLFEKKFKEIKDKWVTDKQADEFIETADKYADKAVQSAVASRAEYYRYVSRKYQYTASGDTPGANSLNIPGCQTWSGKHIENSESE-----------------

(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=-2.28

Estimated TM-score = 0.45±0.14

Estimated RMSD = 9.4±4.6Å

Download Model 2

C-score=-3.60

Download Model 3

C-score=-4.98

Download Model 4

C-score=-4.30

Download Model 5

C-score=-4.37

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	4behB	0.750	1.74	0.112	0.856
2	1ivsA	0.480	5.01	0.078	0.880
3	3vwaA	0.472	4.81	0.093	0.864
4	5fwkA	0.469	4.84	0.026	0.880
5	1gkuB3	0.465	3.50	0.071	0.680
6	1cy8A3	0.465	3.50	0.025	0.672
7	5egiA	0.461	3.84	0.059	0.704
8	3ixzA	0.460	4.59	0.050	0.840
9	5eikA	0.459	4.00	0.074	0.704
10	3kdpA	0.458	4.68	0.041	0.832

(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	5d56E	78M	Rep, Mult	11,14,18
2	0.06	3	1w5cD	CLA	Rep, Mult	16,19,20,28
3	0.06	3	2w6dA	GDP	Rep, Mult	41,42,44,45,58
4	0.04	2	1e7cA	HLT	Rep, Mult	32,38,41,45
5	0.04	2	1zzhB	ZN	Rep, Mult	47,50
6	0.04	2	4bntD	36E	Rep, Mult	6,10
7	0.04	2	1izlC	III	Rep, Mult	13,16,17,20
8	0.02	1	2o012	CLA	Rep, Mult	57,61,64
9	0.02	1	1e7aB	PFL	Rep, Mult	10,54,57,58
10	0.02	1	1gzmA	C8E	Rep, Mult	17,20
11	0.02	1	1xz3A	ICF	Rep, Mult	17,21,66
12	0.02	1	1xrmA	III	Rep, Mult	66,69
13	0.02	1	2w6dB	CPL	Rep, Mult	38,42,43,46,57,58,60

	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	1zd3A	0.397	5.32	0.074	0.800	3.3.2.10	17
2	0.060	3gpbA	0.416	4.56	0.037	0.680	2.4.1.1	NA
3	0.060	3b8cA	0.434	4.93	0.111	0.824	3.6.3.6	NA
4	0.060	3ilwA	0.405	2.97	0.088	0.568	5.99.1.3	NA
5	0.060	3btaA	0.410	5.51	0.033	0.824	3.4.24.69	NA
6	0.060	3ixzA	0.460	4.59	0.050	0.840	3.6.3.10	NA
7	0.060	1mhsA	0.436	5.29	0.067	0.824	3.6.3.6	NA
8	0.060	1w36C	0.436	4.79	0.068	0.776	3.1.11.5	59
9	0.060	3b8eA	0.464	4.78	0.057	0.856	3.6.3.9	NA
10	0.060	7reqB	0.419	4.58	0.035	0.752	5.4.99.2	NA
11	0.060	3c5vA	0.411	3.96	0.047	0.624	3.1.1.-	NA
12	0.060	1gl9B	0.351	5.08	0.074	0.688	5.99.1.3	NA
13	0.060	3hkzJ	0.433	3.93	0.088	0.696	2.7.7.6	24,55
14	0.060	1ddtA	0.427	4.46	0.056	0.712	2.4.2.36	NA
15	0.060	1hm9B	0.402	5.46	0.033	0.832	2.3.1.157,2.7.7.23	19,61
16	0.060	1x75B	0.405	4.30	0.094	0.680	5.99.1.3	NA
17	0.060	1cqzB	0.390	5.38	0.041	0.800	3.3.2.10,3.3.2.3	NA
18	0.060	1eulA	0.448	5.16	0.076	0.896	3.6.3.8	NA
19	0.060	1ojnA	0.410	4.25	0.054	0.672	4.2.2.1	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	0.25	0.750	1.74	0.11	0.86	4behB	GO:0000184 GO:0002181 GO:0003735 GO:0005622 GO:0005829 GO:0005840 GO:0005925 GO:0006364 GO:0006412 GO:0006413 GO:0006414 GO:0006614 GO:0016020 GO:0019083 GO:0022625 GO:0030529 GO:0030687 GO:0070062 GO:0070180
1	0.06	0.330	5.21	0.07	0.66	1a8hA	GO:0000049 GO:0000166 GO:0003723 GO:0004812 GO:0004825 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006431 GO:0016874 GO:0046872
2	0.06	0.365	5.63	0.02	0.79	1gaxA	GO:0000166 GO:0002161 GO:0004812 GO:0004832 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006438 GO:0006450 GO:0016874 GO:0046872
3	0.06	0.351	5.49	0.03	0.72	4ariA	GO:0000166 GO:0002161 GO:0004812 GO:0004823 GO:0005524 GO:0005737 GO:0005829 GO:0006412 GO:0006418 GO:0006429 GO:0006450 GO:0016874
4	0.06	0.299	5.66	0.02	0.64	1rqgA	GO:0000049 GO:0000166 GO:0003723 GO:0004812 GO:0004825 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006431 GO:0016874 GO:0046872
5	0.06	0.280	5.31	0.07	0.55	4dlpC	GO:0000166 GO:0004812 GO:0004825 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006431 GO:0016874
6	0.06	0.302	5.82	0.04	0.70	3kflA	GO:0000166 GO:0000287 GO:0004812 GO:0004825 GO:0005524 GO:0005737 GO:0005829 GO:0006412 GO:0006418 GO:0006431 GO:0016874
7	0.06	0.328	5.50	0.04	0.69	2ct8A	GO:0000166 GO:0004812 GO:0004825 GO:0005524 GO:0005737 GO:0005829 GO:0006412 GO:0006418 GO:0006431 GO:0016874 GO:0046872
8	0.06	0.290	4.91	0.06	0.53	3mi6D	GO:0003824 GO:0004553 GO:0004557 GO:0005975
9	0.06	0.358	4.92	0.05	0.67	1ffyA	GO:0000166 GO:0002161 GO:0004812 GO:0004822 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006428 GO:0006450 GO:0008270 GO:0016874 GO:0046872
10	0.06	0.341	5.00	0.09	0.66	4mw1B	GO:0000166 GO:0004812 GO:0004825 GO:0005524 GO:0005737 GO:0005829 GO:0006412 GO:0006418 GO:0006431 GO:0016874
11	0.06	0.324	2.64	0.13	0.42	3a1yA	GO:0003735 GO:0005622 GO:0005840 GO:0006412 GO:0006414 GO:0030529
12	0.06	0.344	5.20	0.04	0.69	5ah5A	GO:0000166 GO:0002161 GO:0004812 GO:0004823 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006429 GO:0006450 GO:0016874
13	0.06	0.328	5.46	0.05	0.66	1wz2A	GO:0000166 GO:0002161 GO:0004812 GO:0004823 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006429 GO:0006450 GO:0016874
14	0.06	0.293	4.76	0.04	0.53	1u0bB	GO:0000166 GO:0004812 GO:0004817 GO:0005524 GO:0005737 GO:0005829 GO:0006412 GO:0006418 GO:0006423 GO:0008270 GO:0016874 GO:0046872
15	0.06	0.367	5.60	0.03	0.79	1ileA	GO:0000166 GO:0002161 GO:0004812 GO:0004822 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006428 GO:0006450 GO:0008270 GO:0016874 GO:0046872
16	0.06	0.305	4.85	0.02	0.55	5efrA	GO:0009279 GO:0016020 GO:0016021 GO:0019867 GO:0071709
17	0.06	0.299	2.81	0.14	0.40	4v6iBv	GO:0002181 GO:0003735 GO:0005622 GO:0005737 GO:0005840 GO:0006414 GO:0022625 GO:0030295 GO:0030529 GO:0030687 GO:0032147 GO:0070180
18	0.06	0.251	5.13	0.03	0.49	3o0aB	GO:0000166 GO:0002161 GO:0004812 GO:0004823 GO:0005524 GO:0005737 GO:0005829 GO:0006412 GO:0006418 GO:0006429 GO:0006450 GO:0016874

Consensus prediction of GO terms

Molecular Function	GO:0019843	GO:0005198	GO:0032550	GO:0016876	GO:0035639	GO:0032559	GO:0043169
GO-Score	0.49	0.49	0.47	0.47	0.47	0.47	0.36
Biological Processes	GO:0016072	GO:0000956	GO:0034470	GO:0019080	GO:0042254	GO:0045047	GO:0032774	GO:0006613	GO:0043039	GO:0006412
GO-Score	0.49	0.49	0.49	0.49	0.49	0.49	0.49	0.49	0.47	0.42
Cellular Component	GO:0031988	GO:0015934	GO:0030684	GO:1903561	GO:0022626	GO:0005924
GO-Score	0.49	0.49	0.49	0.49	0.49	0.49

(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.