I-TASSER results

I-TASSER results for job id Rv0039c

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

Input Sequence in FASTA format

>protein (115 residues)
MFLAGVLCMCAAAASALFGSWSLCHTPTADPTALALRAMAPTQLAAAVMLAAGGVVAVAA
PGHTALMVVIVCIAGAVGTLAAGSWQSAQYALRRETASPTANCVGSCAVCTQACH

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MFLAGVLCMCAAAASALFGSWSLCHTPTADPTALALRAMAPTQLAAAVMLAAGGVVAVAAPGHTALMVVIVCIAGAVGTLAAGSWQSAQYALRRETASPTANCVGSCAVCTQACH
Prediction	CCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCHHHHHHHHHHHHCCEEEEHCCCCCEEEEEEHHHHHHHHHHHHCHHHHHHHHHHHHCCCCCCCCCCCCCCEEEHCC
Conf.Score	9556899999999999988888746899998898888755699999999986777998768996898875666667888765568899999997567777788787655566659
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MFLAGVLCMCAAAASALFGSWSLCHTPTADPTALALRAMAPTQLAAAVMLAAGGVVAVAAPGHTALMVVIVCIAGAVGTLAAGSWQSAQYALRRETASPTANCVGSCAVCTQACH
Prediction	4331123131223322031211013355453343114313344222103133423110233443100000003322302022222432432144564464451453124134428
	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

                   |                   |                   |                   |                   |

Sec.Str
Seq

CCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCHHHHHHHHHHHHCCEEEEHCCCCCEEEEEEHHHHHHHHHHHHCHHHHHHHHHHHHCCCCCCCCCCCCCCEEEHCC
MFLAGVLCMCAAAASALFGSWSLCHTPTADPTALALRAMAPTQLAAAVMLAAGGVVAVAAPGHTALMVVIVCIAGAVGTLAAGSWQSAQYALRRETASPTANCVGSCAVCTQACH

5ezmA

0.17

0.98

0.83

MUSTER

SWGKQLIGMAIVAACGLLASPVVATLNANHIPNSFYRAYAVWVAVAFVVMLLGIAVARLLLRRGVLPSVAVYAMGMYLGFTV-ALLGHETVGRPASGADIAP-QKLTPEMPLYGV

5ezmA3

0.19

0.16

0.83

0.66

dPPAS

SWGKQLIGMAIVAACGLLASPVVATLNANHIPNSFYRAYAVWVAVAFVVMLLGIAVARLLLRRGVLPSVAVYAMGMYLGFTV-ALLGHETVGRPAS-------------------

5a6eB

0.13

0.10

0.74

wdPPAS

QVLILICTLLCLVFTGTCGIQHLERAGEK------LSLFKSFYFCIVTFSTVGG-----VTPKIWPLLVVIMICVALVVLPLQFEELVYLWMERQK-------------------

5ezmA3

0.22

0.17

0.80

0.83

wMUSTER

SWGKQLIGMAIVAACGLLASPVVATLNANHIPNSFYRAYAVWVAVAFVVMLLGIAVALLRRG----------VLPSVAVYAMGMYLGFTVALLGHETGRPAS-------------

5a6eB

0.13

0.10

0.73

0.79

wPPAS

QVLILICTLLCLVFTGTCGIQHLERAGEK------LSLFKSFYFCIVTFSTVGG------TPKIWPLLVVIMICVALVVLPLQFEELVYLWMERQK-------------------

5ezmA3

0.19

0.16

0.83

0.73

dPPAS2

SWGKQLIGMAIVAACGLLASPVVATLNANHIPNSFYRAYAVWVAVAFVVMLLGIAVARLLLRRGVLPSVAVYAMGMYLGFTV-ALLGHETVGRPAS-------------------

5a6eB

0.13

0.10

0.74

0.84

PPAS

QVLILICTLLCLVFTGTCGIQHLERAGEK------LSLFKSFYFCIVTFSTVGG-----VTPKIWPLLVVIMICVALVVLPLQFEELVYLWMERQK-------------------

1ys3B

0.17

1.00

0.75

Env-PPAS

VDITDLLDRAAHDAARIYPDLDVSLVPSPTCIPAGLRLAVDNAIANAVKHGGATLVQLSAVSSRAGVEIAIDVEGERQVVFEGLALVAQQAQLHTASLENSPLGGARLVLRLPGP

4or2A2

0.09

0.97

0.76

MUSTER

IIAIAFSCLGILVTLFVTLIFVLYR--DTPVVKSSSREL-CYIILAGIFLGYVCPFTLIAKPTTTSCYLQRLLVGLSSAMCYSALVTKTNRIARILARKPRFMSAAQVIIASILI

5a6eB

0.12

0.10

0.77

0.61

dPPAS

QVLILICTLLCLVFTGTCGIQHLERAGEKLS-------LFKSFYFCIVTFSTVGYGDVTPKIWPSQLLVVIMICVALVVLPLQFEELVYLWMERQK-------------------

(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=-3.09

Estimated TM-score = 0.37±0.12

Estimated RMSD = 11.2±4.6Å

Download Model 2

C-score=-3.69

Download Model 3

C-score=-3.79

Download Model 4

C-score=-4.38

Download Model 5

C-score=-3.26

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	1c3cA3	0.657	3.55	0.115	0.948
2	2e9fB	0.649	3.52	0.097	0.939
3	2pfmA3	0.646	3.48	0.097	0.948
4	1yfeA3	0.641	3.43	0.124	0.948
5	3e04D	0.641	3.40	0.062	0.948
6	1vdkA3	0.639	3.40	0.080	0.939
7	1yo7A	0.638	2.99	0.097	0.896
8	1x8zA	0.636	2.71	0.111	0.861
9	4akvA	0.635	2.96	0.055	0.835
10	2c9kA	0.635	3.23	0.018	0.913

(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	0.09	6	3qvdA	FE	Rep, Mult	13,16,47
2	0.08	6	3bl5C	ZN	Rep, Mult	103,107,110,114
3	0.07	5	4am2B	HEM	Rep, Mult	14,17,18,21,41,45,48,51
4	0.06	4	2wieE	CVM	Rep, Mult	40,43
5	0.04	3	3gvyC	HEM	Rep, Mult	14,21,48,49,51,52
6	0.04	3	1kyoE	SMA	Rep, Mult	114,115
7	0.04	3	1i490	III	Rep, Mult	5,9,12,16,19,22,23,26,32,36,50,73,74,77,78,80,81,84,88,89,91,92
8	0.03	2	1y8oA	RED	Rep, Mult	39,42,84
9	0.03	2	5da5A	GOA	Rep, Mult	19,43
10	0.01	1	1y8nA	RED	Rep, Mult	50,83,84
11	0.01	1	3wmgA	DMU	Rep, Mult	78,82
12	0.01	1	5d91A	8K6	Rep, Mult	85,86

	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	2fenD	0.625	3.72	0.126	0.957	5.5.1.2	NA
2	0.060	2q8gA	0.582	3.69	0.028	0.930	2.7.11.2	NA
3	0.060	1jqoA	0.613	3.10	0.031	0.844	4.1.1.31	NA
4	0.060	1o9iA	0.574	3.37	0.055	0.835	1.11.1.6	45,48
5	0.060	2ix6E	0.578	3.77	0.066	0.922	1.3.3.6	83
6	0.060	2frvD	0.577	3.66	0.078	0.878	1.12.2.1	NA
7	0.060	2pnrB	0.617	3.34	0.056	0.913	2.7.11.2	NA
8	0.060	1frvB	0.580	3.48	0.078	0.870	1.12.2.1	72
9	0.060	1yqwR	0.594	3.56	0.058	0.887	1.12.2.1	NA
10	0.060	1mhyB	0.594	3.53	0.085	0.870	1.14.13.25	47,49
11	0.060	1h2aL	0.543	3.69	0.078	0.844	1.12.2.1	72
12	0.060	1yfmA	0.574	3.11	0.070	0.765	4.2.1.2	NA
13	0.060	1yrqI	0.593	3.56	0.067	0.887	1.12.2.1	31,32,44,83
14	0.060	2htnG	0.519	3.64	0.086	0.791	1.16.3.1	NA
15	0.060	3bhgA	0.572	4.07	0.072	0.930	4.3.2.2	NA
16	0.060	2o6yA	0.501	4.14	0.071	0.870	4.3.1.-	NA
17	0.060	1c3cA	0.657	3.55	0.115	0.948	4.3.2.2	NA
18	0.060	1jqnA	0.597	3.37	0.086	0.887	4.1.1.31	NA
19	0.060	1k62B	0.586	3.33	0.038	0.861	4.3.2.1	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	0.16	0.494	3.79	0.07	0.80	3gzhA	GO:0003824 GO:0004018 GO:0006164 GO:0006188 GO:0006189 GO:0009152 GO:0016829 GO:0044208 GO:0070626
1	0.14	0.453	1.65	0.10	0.52	4gycB	GO:0004871 GO:0005886 GO:0006935 GO:0007165 GO:0009881 GO:0016020 GO:0016021 GO:0018298 GO:0050896
2	0.07	0.554	3.39	0.03	0.79	3r6qF	GO:0003824 GO:0006099 GO:0006531 GO:0008797 GO:0016829
3	0.07	0.574	3.11	0.07	0.77	1yfmA	GO:0003824 GO:0004333 GO:0005737 GO:0005739 GO:0005759 GO:0005829 GO:0006099 GO:0006106 GO:0006108 GO:0016829 GO:0045239 GO:0051262
4	0.07	0.559	3.40	0.05	0.80	3gtdA	GO:0003824 GO:0004333 GO:0005737 GO:0006099 GO:0006106 GO:0008152 GO:0016829 GO:0045239
5	0.07	0.544	3.59	0.04	0.81	1yfeA	GO:0003824 GO:0004333 GO:0005737 GO:0005829 GO:0006099 GO:0006106 GO:0006108 GO:0006979 GO:0008152 GO:0016829 GO:0045239 GO:0051262
6	0.07	0.607	3.99	0.06	0.97	4eeiB	GO:0000166 GO:0003824 GO:0004018 GO:0009152 GO:0016829 GO:0070626
7	0.07	0.516	3.48	0.04	0.77	2pfmA	GO:0003824 GO:0004018 GO:0006164 GO:0006189 GO:0009152 GO:0016829 GO:0044208 GO:0070626
8	0.07	0.641	3.64	0.10	0.97	2x75A	GO:0003824 GO:0004018 GO:0006164 GO:0006189 GO:0009152 GO:0016829 GO:0044208 GO:0070626
9	0.07	0.577	3.75	0.08	0.88	1dofA	GO:0003824 GO:0004018 GO:0006163 GO:0009152 GO:0016829 GO:0051262 GO:0070626
10	0.07	0.546	3.47	0.06	0.80	4hgvA	GO:0003824 GO:0004333 GO:0005737 GO:0006099 GO:0006106 GO:0016829 GO:0045239
11	0.07	0.500	3.66	0.06	0.77	3c8tA	GO:0003824 GO:0016853 GO:0047472
12	0.07	0.511	3.65	0.06	0.78	2qgaC	GO:0000166 GO:0003824 GO:0004018 GO:0006164 GO:0006188 GO:0006189 GO:0009152 GO:0016829 GO:0044208 GO:0070626
13	0.07	0.523	3.43	0.03	0.77	3bhgA	GO:0003824 GO:0004018 GO:0006164 GO:0006188 GO:0006189 GO:0009152 GO:0016829 GO:0044208 GO:0070626
14	0.07	0.657	3.55	0.12	0.95	1c3cA	GO:0003824 GO:0004018 GO:0006163 GO:0006164 GO:0006189 GO:0009152 GO:0016829 GO:0044208 GO:0051262 GO:0070626
15	0.07	0.586	3.33	0.04	0.86	1k62B	GO:0000050 GO:0003824 GO:0004056 GO:0005737 GO:0005829 GO:0006475 GO:0006526 GO:0006527 GO:0008652 GO:0016829 GO:0042450 GO:0051262 GO:0070062
16	0.07	0.581	3.90	0.07	0.90	1f1oA	GO:0003824 GO:0004018 GO:0006164 GO:0006167 GO:0006189 GO:0009152 GO:0016829 GO:0044208 GO:0051262 GO:0070626
17	0.07	0.515	3.99	0.04	0.82	4nleA	GO:0003824 GO:0004018 GO:0006164 GO:0006189 GO:0009152 GO:0016829 GO:0044208 GO:0070626
18	0.07	0.541	4.37	0.05	0.86	4mx2B	GO:0000166 GO:0003824 GO:0004018 GO:0006164 GO:0006188 GO:0006189 GO:0009152 GO:0016829 GO:0044208 GO:0070626
19	0.07	0.588	3.41	0.05	0.86	1yisA	GO:0003824 GO:0004018 GO:0006163 GO:0006164 GO:0006189 GO:0016829 GO:0044208 GO:0051262 GO:0070626

Consensus prediction of GO terms

Molecular Function	GO:0016842
GO-Score	0.33
Biological Processes	GO:0009060	GO:0006082	GO:0046040	GO:0006167
GO-Score	0.38	0.38	0.33	0.33
Cellular Component	GO:0005886	GO:0016021	GO:0045239	GO:0005759	GO:0005829
GO-Score	0.14	0.14	0.13	0.07	0.07

(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.