I-TASSER results

I-TASSER results for job id Rv3639c

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

Input Sequence in FASTA format

>protein (188 residues)
MAGLFTPPASGAATLQRAARDAAPDARWLLAVSDRNGIVSTSATTCNYPPAAKDSAQDGF
RHALAAAIAADIDEALRHGYGDLLELAYPLMSWPRRGVFGGPTPAPRGLATRQCPPRTVH
VDRVRPNGAERALRARFRPILRPQFTLGDGANGLPLAACTKTGAYVPHLPYSPIAVDPQP
SAGQQGPS

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MAGLFTPPASGAATLQRAARDAAPDARWLLAVSDRNGIVSTSATTCNYPPAAKDSAQDGFRHALAAAIAADIDEALRHGYGDLLELAYPLMSWPRRGVFGGPTPAPRGLATRQCPPRTVHVDRVRPNGAERALRARFRPILRPQFTLGDGANGLPLAACTKTGAYVPHLPYSPIAVDPQPSAGQQGPS
Prediction	CCCCCCCCCCCHHHHHHHHHHHCCHHHHHHHHHCCCCEEHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEHCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCEEEEHCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Conf.Score	99888899886578999999866567777776468875655555568998755556778999999999988999999857889998777755787787789999987765567998668887766886689999886555677766678888865566656677888877776556899887777899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MAGLFTPPASGAATLQRAARDAAPDARWLLAVSDRNGIVSTSATTCNYPPAAKDSAQDGFRHALAAAIAADIDEALRHGYGDLLELAYPLMSWPRRGVFGGPTPAPRGLATRQCPPRTVHVDRVRPNGAERALRARFRPILRPQFTLGDGANGLPLAACTKTGAYVPHLPYSPIAVDPQPSAGQQGPS
Prediction	74332334352333034226532441300010244422243434315234334542452133000211234135014422220140033023134412142433334423446134441414424264454513452431133523226325423011346542303302222131334354466458
	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

CCCCCCCCCCCHHHHHHHHHHHCCHHHHHHHHHCCCCEEHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEHCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCEEEEHCCCCCCCCCCCCCCCCCCCCCCCCCCCC
MAGLFTPPASGAATLQRAARDAAPDARWLLAVSDRNGIVSTSATTCNYPPAAKDSAQDGFRHALAAAIAADIDEALRHGYGDLLELAYPLMSWPRRGVFGGPTPAPRGLATRQCPPRTVHVDRVRPNGAERALRARFRPILRPQFTLGDGANGLPLAACTKTGAYVPHLPYSPIAVDPQPSAGQQGPS

3d0rB

0.20

0.99

0.62

MUSTER

IEGLFSSPGIGLIQLAWGFRTAGHDVLIAVA-EHADRAAAAGLEVVDVAPDYSQVAKDRFAETVATRPAIDLEEWGVQIAAVNRPLVDGTMAYRPDLVVYEQGATVGLLAADGVPAVQRNQSAWRTRGMHRSIASFLTDLMEPVATIESFPPSLLLEA-EPEGWFMRWVPYGGGAVLGDRLPPVPARP

3wadA1

0.15

0.98

0.60

dPPAS

MRVLMVFANRSMVPLAWALTTAHPDNVQAISDSGLTAVPVGNDLNIMAALTLNETTWQYIHDVFAQYSQIYEYMADSTMTADLVAHARQWQ--PDLVIWDALTYAGPIAAEAVGAPHVRMLFGLDQWGRMRDHFNRLTGERAADDRHDPLADWLATKGEPHGVAFTESLVTGTTTLAVAP-PWMSFPS

3tsaA1

0.21

0.16

0.80

0.50

wdPPAS

M--LVPLPYPTMVPLCWALQASPPELQATAHGA---GL--TTAGILRFPNPAFGQRDTEAGRQLWEQTASNVAQSSLDQLPEYLRLAEAW---P---LLVDVALIGRVLGGLDLP--LHRWGVDPTAGFSDRAHELLDPVCR-------GLTGLPTPELI---------------LDPCP-PSLQASD

3fbrA

0.20

0.18

0.87

0.52

wMUSTER

RVGELTKLANGAHTFK--------APEWL----SRYARLSLS-----LPLQRGNITSDAVFNFFDNLLSPIVRDRIVKRYHQ----PFDLLSEIGRDSVGAVTLIPEDETV---THPIMAWEKLTEARLEEVLTAYKADIPLGMISVA-GAQEKTALLRIGNDWCIPKTPTTPIGEIRQPNATLDLSQ

3tsaA1

0.21

0.17

0.79

0.52

wPPAS

M--LVPLPYPTMVPLCWALQASPPELQATAHGA---GL--TTAGILRFPNPAFGQRDTEAGRQLWEQTASNVAQSSLDQLPEYLRLAEAW---P---LLVDVC-ALIGLGGLDLP--LHRWGVDPTAGFSDRAHELLDPVCR-------GLTGLPTPELI---------------LDPCP-PSLQASD

3tsaA1

0.20

0.16

0.84

0.61

dPPAS2

MRVLVPLPYPTMVPLCWALQASPPELQATAHGA---GLTAGILRFPNPAFGQRDTEAGRQLWEQTASNVAQSSLDQLPEYLRLAEAWRPVL------LVDVCALIGRVLGGLLDLPVVLHRWGVDPTAFSDRAHELLDPVCRHH-----GLTGLPTPELI---------------LDPCP-PSLQASD

3wadA1

0.14

0.13

0.93

0.70

PPAS

M--LMVFANRSMVPLAWALTTAHPDNVQAISDSNDLNIMAALTLNETRPEKLTWQYIHDVFAQYSQIYEYMADSTMTADLVAHARQWQPLVIWA--LTYAGP------AAEAGAPHVRMLFGLDQWGRMRDHFNRLTGE--RAADDRHDPLADWLATKGEPHGVAFTESLVTGTTLAVAP-PWMSFPS

3it6B

0.29

0.26

0.89

0.69

Env-PPAS

MLCLTTDAAAEPAALERALRRAAAATFDRLDI-D--GSCSTNSSGAEIPPAQADEAVLRVCDDLCAQLQADVTVTVTGAEDDALVAARQIARDSKTALFGSPNWG-RGMAPITLDPDSVSFNGAAVHG-VGAPGAREVDLSDADIDLGVGDGQARIRTTDLSHAYVENSAYSS---------------

3tsaA

0.15

0.97

0.60

MUSTER

M--LVPLPYPTMVPLCWALQASGHEVLIAAPPELQATAHGAGLTILRFPNPAFGQRDTEAGRQLWEQTASNVAQSSLDQLPEYLRLAEAW---PSVLLVDVCALIGRVLGGLDLPVVLHRWGVDPTAGPFSDRAHELLGLPTPELILDPCPPSLQASD-APQGAPVQYVPYNGSGAFPAWGAARTSAR

3tsaA1

0.15

0.13

0.88

0.59

dPPAS

MRVLVVPLPYAMVPLCWALQASPPELQATAHGAGLT--TAGILRFPNPAFGQRDTEAGRQLWEQTASNVAQSSLDQLPEYLRLAEAWRPVL------LVDVCALIGRVLGGLLDLPVVLHRWGVDPTAFSDRAHELLDPVCR---HHGLTGLPTPELILDPCPPSL-QASDAPQGAP-----------

(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=-2.14

Estimated TM-score = 0.46±0.15

Estimated RMSD = 10.0±4.6Å

Download Model 2

C-score=-3.71

Download Model 3

C-score=-3.41

Download Model 4

C-score=-3.77

Download Model 5

C-score=-3.71

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	3tsaA1	0.653	3.24	0.127	0.840
2	2p6pA	0.626	3.61	0.146	0.846
3	2yjnA	0.625	3.93	0.103	0.878
4	4rieA	0.618	3.57	0.165	0.835
5	1rrvA	0.617	3.96	0.107	0.888
6	3otgA	0.612	4.13	0.090	0.888
7	4fzrA	0.611	3.56	0.106	0.819
8	3iaaA	0.607	4.17	0.064	0.899
9	3wadA1	0.601	4.01	0.105	0.851
10	4ambA	0.601	3.58	0.125	0.814

(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	0.07	4	2xquC	CVM	Rep, Mult	69,72
2	0.06	3	4m0kC	CA	Rep, Mult	130,134
3	0.04	2	1ey3A	DAK	Rep, Mult	134,137
4	0.04	2	1l7xB	700	Rep, Mult	45,47,74,78
5	0.04	2	1um0A	FMN	Rep, Mult	147,148
6	0.04	2	3luhB	5GP	Rep, Mult	138,142
7	0.02	1	5c2xB	CO3	Rep, Mult	77,140
8	0.02	1	1xi2A	CB1	Rep, Mult	99,145
9	0.02	1	1pn3A	III	Rep, Mult	8,9,12,72,103,104,134,137,156
10	0.02	1	1z62A	IAA	Rep, Mult	10,13,21,33,34
11	0.02	1	3ih1A	PYR	Rep, Mult	153,154
12	0.02	1	2atiA	IHU	Rep, Mult	24,25,26
13	0.02	1	2xquB	CVM	Rep, Mult	65,69
14	0.02	1	3pyoI	MG	Rep, Mult	140,143,144
15	0.02	1	1k77A	MG	Rep, Mult	176,177
16	0.02	1	4a8mR	ATP	Rep, Mult	123,125,149
17	0.02	1	3bd7A	CKB	Rep, Mult	55,59,60,63
18	0.02	1	4nhpA	2T8	Rep, Mult	132,136

	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	1gqtB	0.499	4.66	0.084	0.787	2.7.1.15	NA
2	0.060	1cjyA	0.501	5.29	0.043	0.856	3.1.1.4,3.1.1.5	NA
3	0.060	3beoA	0.522	4.48	0.094	0.787	5.1.3.14	NA
4	0.060	3f67A	0.498	4.83	0.057	0.793	3.1.1.-	NA
5	0.060	2oz5A	0.501	4.53	0.073	0.755	3.1.3.48	51,73,108,129
6	0.060	3dzcA	0.517	4.36	0.074	0.761	5.1.3.14	NA
7	0.060	1sb8A	0.503	4.96	0.069	0.787	5.1.3.7	NA
8	0.060	1rzuB	0.577	4.64	0.058	0.883	2.4.1.21	NA
9	0.060	2bfpD	0.499	4.22	0.070	0.734	1.5.1.33	NA
10	0.060	1f2dA	0.515	4.56	0.025	0.777	3.5.99.7	NA
11	0.060	2azdB	0.565	4.76	0.040	0.904	2.4.1.1	97
12	0.060	1f0kB	0.490	4.67	0.062	0.766	2.4.1.227	4,89
13	0.060	1e1yA	0.577	4.78	0.062	0.925	2.4.1.1	NA
14	0.060	1j33A	0.498	4.92	0.094	0.798	2.4.2.21	NA
15	0.060	2a9yA	0.502	4.54	0.057	0.761	2.7.1.20	NA
16	0.060	1ygpA	0.567	4.80	0.096	0.910	2.4.1.1	86
17	0.060	1gz5A	0.548	4.38	0.065	0.851	2.4.1.15	NA
18	0.060	2fv7A	0.503	4.29	0.109	0.766	2.7.1.15	NA
19	0.060	2r4uA	0.565	4.55	0.110	0.872	2.4.1.21	110

(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	0.09	0.626	3.61	0.15	0.85	2p6pA	GO:0016740
1	0.09	0.625	3.93	0.10	0.88	2yjnA	GO:0008152 GO:0016740 GO:0016757 GO:0016758 GO:0017000
2	0.08	0.617	3.96	0.11	0.89	1rrvA	GO:0005975 GO:0008152 GO:0016740 GO:0016757 GO:0016758 GO:0017000 GO:0030259 GO:0033072
3	0.08	0.652	3.23	0.13	0.84	3uykA	GO:0016740
4	0.08	0.618	3.57	0.17	0.84	4rieA	GO:0016740
5	0.08	0.627	4.17	0.10	0.91	3othA	GO:0005975 GO:0008152 GO:0016758 GO:0030259
6	0.08	0.623	3.42	0.11	0.82	4g2tA	GO:0008152 GO:0016758
7	0.07	0.582	3.69	0.07	0.81	3d0rB	GO:0046527
8	0.07	0.609	3.51	0.13	0.83	4rifB	GO:0016740
9	0.07	0.613	4.31	0.07	0.93	3rscA	GO:0008152 GO:0016758 GO:0016999
10	0.07	0.601	3.58	0.12	0.81	4ambB	GO:0008152 GO:0016740 GO:0016758 GO:0042802
11	0.07	0.582	4.14	0.11	0.84	1iirA	GO:0005975 GO:0008152 GO:0016740 GO:0016757 GO:0016758 GO:0017000 GO:0030259 GO:0033072
12	0.07	0.599	3.97	0.10	0.85	3wadB	GO:0008152 GO:0016740 GO:0016757 GO:0016758
13	0.07	0.588	3.88	0.07	0.85	2iyaA	GO:0000166 GO:0008152 GO:0016740 GO:0016757 GO:0016758 GO:0016999
14	0.07	0.580	4.32	0.12	0.88	4m7pA	GO:0008152 GO:0016740 GO:0016757 GO:0016758 GO:0016999 GO:0046677
15	0.07	0.546	3.89	0.12	0.78	4an4D	GO:0008152 GO:0016740 GO:0016758 GO:0042802
16	0.07	0.570	4.03	0.11	0.81	4leiA	GO:0016740 GO:0016757
17	0.07	0.539	4.11	0.11	0.79	4an4C	GO:0008152 GO:0016740 GO:0016758 GO:0042802
18	0.06	0.317	4.95	0.05	0.51	4pdeA	GO:0003824 GO:0005737 GO:0005829 GO:0006777 GO:0006810 GO:0016783 GO:0043546 GO:0097163

Consensus prediction of GO terms

Molecular Function	GO:0016740
GO-Score	0.35
Biological Processes	GO:0044249	GO:0016999
GO-Score	0.32	0.32
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.