I-TASSER results

I-TASSER results for job id Rv2514c

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

Input Sequence in FASTA format

>protein (153 residues)
MLYSFDTSAILNGRRDLFRPAVFRSLWGRVEDAISAGQIRSVDEVQRELARRDDDAKRWA
DGQTGLFCPLDEQIQQAARHILRLHPNMVRQGGRRSAADPFVIALAMVNNATVVTQETAS
GNIEKPRIPDVCDALGVPWLTLMGYIEAQGWTF

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MLYSFDTSAILNGRRDLFRPAVFRSLWGRVEDAISAGQIRSVDEVQRELARRDDDAKRWADGQTGLFCPLDEQIQQAARHILRLHPNMVRQGGRRSAADPFVIALAMVNNATVVTQETASGNIEKPRIPDVCDALGVPWLTLMGYIEAQGWTF
Prediction	CEEEEEHHHHHHHHHHCCCCHHCHHHHHHHHHHHHHCCEEEEHHHHHHHHHCCHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCEEEHCCCCCCCCCCCCCHHHHHHHCCCCCCHHHHHHHHCCCC
Conf.Score	948986457788888768744567999999999876987864889999998987899998555544567899999999999997688888756667765999999999897899855678887889866899988998679999999979989
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MLYSFDTSAILNGRRDLFRPAVFRSLWGRVEDAISAGQIRSVDEVQRELARRDDDAKRWADGQTGLFCPLDEQIQQAARHILRLHPNMVRQGGRRSAADPFVIALAMVNNATVVTQETASGNIEKPRIPDVCDALGVPWLTLMGYIEAQGWTF
Prediction	531000000002035532336203200520362266420100430250046435403521663442125434402410430252345236545646200000001032461100020355664641302300672604112123104537166
	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

                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CEEEEEHHHHHHHHHHCCCCHHCHHHHHHHHHHHHHCCEEEEHHHHHHHHHCCHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCEEEHCCCCCCCCCCCCCHHHHHHHCCCCCCHHHHHHHHCCCC
MLYSFDTSAILNGRRDLFRPAVFRSLWGRVEDAISAGQIRSVDEVQRELARRDDDAKRWADGQTGLFCPLDEQIQQAARHILRLHPNMVRQGGRRSAADPFVIALAMVNNATVVTQETASGNIEKPRIPDVCDALGVPWLTLMGYIEAQGWTF

3zvkA

0.17

0.14

0.82

1.76

MUSTER

MIYMLGTNICVYAINKHP-----DSYYNNLELLAKNNTIAISSIVLAELQYGKEQNQSKLDISRLEIIDFS---AKCTFYYGELRTELEQKGLIIGNNDLLIASHAIAENATLVTNNIKEFKR----IP------NLILENWDK---------

3zvkA

0.15

0.12

0.80

2.04

dPPAS

MIYMLGTNICVYAINKHP-----DSYYNNLELLAKNNTIAISSIVLAELQYGKKEQNQSKLDIFLSRLEIIDFSAKCTFYYGELRTELEQKGLIIGNNDLLIASHAIAENATLVTNNIKEFKRIPNK--------------------------

3zvkA

0.15

0.12

0.82

3.32

wdPPAS

MIYMLGTNICVYAINKHP-----DSYYNNLELLAKNNTIAISSIVLAELQYGVEQNQSKLDISRLEIIDFS---AKCTFYYGELRTELEQKGLIIGNNDLLIASHAIAENATLVTNNIKEFKRPNLILENWDK--------------------

2h1cA

0.18

0.15

0.82

1.95

wMUSTER

-MILLDTNVISEPLRPQPN----ERVVAWLDSLILED-VYLSAITVAELRLGKNVLHERLEQSAGRILPFDEPVAAIYAQIRSYAKTH---GKEIAAADGYIAATAKQHSLTVATRDTGSFFAADVAV-----------FNPWHL--------

3zvkA

0.18

0.15

0.82

3.11

wPPAS

MIYMLGTNICVYAINKHP-----DSYYNNLELLAKNNTIAISSIVLAELQYGVEQNQSKLDISRLEIIDFS---AKCTFYYGELRTELEQKGLIIGNNDLLIASHAIAENATLVTNNIKEFK----RIP------NLI-LENWD--K------

3zvkA

0.16

0.12

0.78

7.57

dPPAS2

MIYMLGTNICVYAINKHP-----DSYYNNLELLAKNNTIAISSIVLAELQYGKEQNQSKLDISRLEIIDFS---AKCTFYYGELRTELEQKGLIIGNNDLLIASHAIAENATLVTNNIKEFKRPNLIL-------------------------

3zvkA

0.15

0.12

0.82

2.30

PPAS

MIYMLGTNICVYAINKHP-----DSYYNNLELLAKNNTIAISSIVLAELQYGKEQNQSKLDISRLEIIDFS---AKCTFYYGELRTELEQKGLIIGNNDLLIASHAIAENATLVTNNIKEFKRPNLILENWDK--------------------

3zvkA

0.17

0.14

0.82

2.51

Env-PPAS

MIYMLGTNICVYAINKHP-----DSYYNNLELLAKNNTIAISSIVLAELQYGKEQNQSKLDISRLEIIDFS---AKCTFYYGELRTELEQKGLIIGNNDLLIASHAIAENATLVTNNIKEFK----RIP------NLILENWDK---------

2h1cA

0.18

0.15

0.82

1.71

MUSTER

M-ILLDTNVISEPLRPQPN----ERVVAWLDSLILED-VYLSAITVAELRLGKNVLHERLEQSAGRILPFD---EPVAAIYAQIRSYAKTHGKEIAAADGYIAATAKQHSLTVATRD-----------TGSFFAADVAVFNPWHL--------

3tndA

0.16

0.13

0.82

1.89

dPPAS

LKFMLDTNICIFTIKNKP-----ASVRERFNLNQ--GKMCISSVTLMELIYGMPERNLAVIEGFVSRIDVLDYDAAAATHTGQIRAELARQGRPVGPFDQMIAGHARSRGLIIVTNNTREFEVGGLRTEDWS---------------------

(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=0.09

Estimated TM-score = 0.73±0.11

Estimated RMSD = 4.6±3.0Å

Download Model 2

C-score=-3.17

Download Model 3

C-score=-3.35

Download Model 4

C-score=-2.27

Download Model 5

C-score=-2.58

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	3zvkA	0.739	1.77	0.159	0.824
2	3tndA	0.711	1.98	0.161	0.810
3	2h1cA	0.682	2.43	0.159	0.824
4	3h87B	0.675	2.61	0.116	0.817
5	5sv2A	0.666	2.69	0.117	0.830
6	4xgqA	0.664	2.60	0.131	0.797
7	4chgA	0.648	2.56	0.185	0.791
8	1w8iA	0.643	3.01	0.108	0.824
9	3dboB	0.638	2.49	0.172	0.758
10	1y82A	0.619	3.20	0.113	0.810

(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	0.17	6	4xgqA	MG	Rep, Mult	6,7,48,98,99
2	0.11	5	2bsq1	III	Rep, Mult	43,44,47,50,51,75,78,79,81,82,85,86,101
3	0.04	2	2bq8X	ZN	Rep, Mult	48,54
4	0.04	2	3qe4B	4CF	Rep, Mult	4,5,6,42,45,106,109
5	0.04	2	2h1cA	III	Rep, Mult	10,11,13,14,15,16,26,30,31,55,58,63
6	0.02	1	2fe10	III	Rep, Mult	43,44,46,47,48,50,57,58,61,68,78,79,82,85,86,96,98,101
7	0.02	1	2xblA	M7P	Rep, Mult	48,52
8	0.02	1	1bofA	MG	Rep, Mult	8,152
9	0.02	1	2h1cA	MG	Rep, Mult	4,5,40,41,45
10	0.02	1	2h1cA	MG	Rep, Mult	41,68,69,70,105
11	0.02	1	3h87A	MG	Rep, Mult	99,117

	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	3afhA	0.560	4.51	0.056	0.889	6.1.1.17	11,122
2	0.060	2j5bA	0.580	4.15	0.068	0.863	6.1.1.1	NA
3	0.060	2a4mC	0.555	4.19	0.035	0.856	6.1.1.2	6,124
4	0.060	2ja2A	0.562	4.55	0.090	0.895	6.1.1.17	NA
5	0.060	3fi0G	0.562	4.08	0.071	0.850	6.1.1.2	125
6	0.060	2el7A	0.565	4.09	0.069	0.869	6.1.1.2	NA
7	0.060	3n9iA	0.565	4.02	0.069	0.856	6.1.1.2	15
8	0.060	2yy5B	0.574	4.13	0.041	0.876	6.1.1.2	NA
9	0.060	3fnrA	0.574	4.43	0.068	0.882	6.1.1.19	NA
10	0.060	2x1lA	0.568	4.51	0.048	0.915	6.1.1.10	NA
11	0.060	2zufA	0.569	4.67	0.061	0.948	6.1.1.19	NA
12	0.060	3fhjD	0.570	4.00	0.076	0.863	6.1.1.2	NA
13	0.060	2o5rA	0.551	4.43	0.063	0.869	6.1.1.17	NA
14	0.060	2cycB	0.583	4.13	0.055	0.863	6.1.1.1	5
15	0.060	2yy5D	0.574	4.12	0.041	0.876	6.1.1.2	NA
16	0.060	1euqA	0.549	4.56	0.061	0.882	6.1.1.18	NA
17	0.060	1r6tA	0.559	3.99	0.063	0.843	6.1.1.2	105
18	0.060	1u0bB	0.563	4.47	0.047	0.889	6.1.1.16	NA
19	0.060	3kt8D	0.568	4.04	0.055	0.856	6.1.1.2	50

(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	0.36	0.739	1.77	0.16	0.82	3zvkA	GO:0000287 GO:0004518 GO:0004540 GO:0016787 GO:0046872 GO:0090305 GO:0090501
1	0.24	0.673	2.66	0.20	0.82	4chgA	GO:0000287 GO:0001666 GO:0004518 GO:0004540 GO:0016787 GO:0040008 GO:0045926 GO:0046872 GO:0090305 GO:0090501
2	0.23	0.638	2.49	0.17	0.76	3dboB	GO:0000287 GO:0004518 GO:0004521 GO:0004540 GO:0005576 GO:0016787 GO:0040007 GO:0040008 GO:0046872 GO:0090305 GO:0090501 GO:0090502
3	0.23	0.664	2.60	0.13	0.80	4xgqA	GO:0000287 GO:0004518 GO:0004540 GO:0016787 GO:0045926 GO:0046872 GO:0090305 GO:0090501
4	0.23	0.692	2.60	0.15	0.85	2bsqA	GO:0000287 GO:0003677 GO:0004518 GO:0004540 GO:0016787 GO:0044001 GO:0046872 GO:0090305 GO:0090501
5	0.22	0.648	3.28	0.12	0.86	1y82A	GO:0000287 GO:0004518 GO:0004540 GO:0016787 GO:0046872 GO:0090305 GO:0090501
6	0.22	0.675	2.61	0.12	0.82	3h87B	GO:0000287 GO:0004518 GO:0004540 GO:0016787 GO:0017148 GO:0040008 GO:0046872 GO:0090305 GO:0090501
7	0.21	0.564	2.83	0.17	0.71	2lcqA	GO:0000287 GO:0003723 GO:0004518 GO:0004519 GO:0004540 GO:0016787 GO:0019843 GO:0042254 GO:0046872 GO:0090305 GO:0090501
8	0.21	0.702	2.17	0.15	0.81	5ecdA	GO:0000287 GO:0004518 GO:0004519 GO:0004540 GO:0016787 GO:0046872 GO:0090305 GO:0090501
9	0.18	0.570	4.01	0.06	0.86	3prhA	GO:0000166 GO:0004812 GO:0004830 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006436 GO:0016874
10	0.17	0.651	3.04	0.11	0.84	1w8iA	GO:0000287 GO:0004518 GO:0004540 GO:0016787 GO:0046872 GO:0090305 GO:0090501
11	0.13	0.580	4.15	0.07	0.86	2j5bA	GO:0000166 GO:0004812 GO:0004831 GO:0005524 GO:0006412 GO:0006418 GO:0016874 GO:0042802
12	0.12	0.647	3.30	0.13	0.86	1ye5B	GO:0000287 GO:0004518 GO:0004540 GO:0016787 GO:0046872 GO:0090305 GO:0090501
13	0.07	0.586	4.19	0.05	0.87	2cycA	GO:0000166 GO:0004812 GO:0004831 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006437 GO:0016874
14	0.07	0.592	3.73	0.07	0.86	3p0iA	GO:0000166 GO:0004812 GO:0004831 GO:0004832 GO:0005524 GO:0005829 GO:0006418 GO:0006438 GO:0016874
15	0.07	0.574	4.13	0.04	0.88	2yy5B	GO:0000166 GO:0004812 GO:0004830 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006436 GO:0016874
16	0.07	0.578	4.09	0.08	0.86	4nx2A	GO:0000166 GO:0004812 GO:0004831 GO:0004832 GO:0005524 GO:0005737 GO:0005829 GO:0006412 GO:0006418 GO:0006437 GO:0006438 GO:0016874
17	0.07	0.594	3.90	0.05	0.87	3vgjB	GO:0000166 GO:0004812 GO:0004831 GO:0005524 GO:0006412 GO:0006418 GO:0006437 GO:0016874 GO:0044164 GO:0046789
18	0.07	0.577	3.92	0.06	0.86	3tzlB	GO:0000166 GO:0004812 GO:0004830 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006436 GO:0016874
19	0.07	0.570	4.00	0.08	0.86	3fhjD	GO:0000166 GO:0004812 GO:0004830 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006436 GO:0016874

Consensus prediction of GO terms

Molecular Function	GO:0004540	GO:0000287	GO:0004519	GO:0003676
GO-Score	0.78	0.78	0.46	0.45
Biological Processes	GO:0090501	GO:0036293	GO:0006950	GO:0051815	GO:0044000	GO:0045926
GO-Score	0.78	0.49	0.49	0.45	0.45	0.42
Cellular Component	GO:0005576
GO-Score	0.23

(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.