I-TASSER results

I-TASSER results for job id Rv0078A

[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)
MNAVESTLRRVAKDLTGLRQRWALVGGFAVSARSEPRFTRDVDIVVAVANDDAAESLVRQ
LLTQQYHLLASVEQDAARRLAAVRLGATADTAANVVVDLLFASCGIEPEIAEAAEEIEIL
PDLVAPVATTAHLIAMKLLARDDDRRPQDRSDLRALVDAASPQDIQDARKAIELITLRGF
HRDRDLAAEWTRLAAKW

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MNAVESTLRRVAKDLTGLRQRWALVGGFAVSARSEPRFTRDVDIVVAVANDDAAESLVRQLLTQQYHLLASVEQDAARRLAAVRLGATADTAANVVVDLLFASCGIEPEIAEAAEEIEILPDLVAPVATTAHLIAMKLLARDDDRRPQDRSDLRALVDAASPQDIQDARKAIELITLRGFHRDRDLAAEWTRLAAKW
Prediction	CCHHHHHHHHHHHHHHHHCCCEEEEEHHHHHHHCCCCCCCCEEEEHCCCCHHHHHHHHHHHHHHCCCCCCCCHHHHHCCEEEEEHCCCCCCCCCEEEEEEHCCCCCCHHHHHHCCEEEEHCCEEEEEHCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCHCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCC
Conf.Score	86899999999999999899889873778898788777897799985898789999999999988877666646655445677755666666667999997689999889875564677699889996999999999999876598788999999999855565999999999999756554544456777766569
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MNAVESTLRRVAKDLTGLRQRWALVGGFAVSARSEPRFTRDVDIVVAVANDDAAESLVRQLLTQQYHLLASVEQDAARRLAAVRLGATADTAANVVVDLLFASCGIEPEIAEAAEEIEILPDLVAPVATTAHLIAMKLLARDDDRRPQDRSDLRALVDAASPQDIQDARKAIELITLRGFHRDRDLAAEWTRLAAKW
Prediction	46413510440051057360300000020013103323030000003264573044015203744234352255413432321422342455350201000336524253135444243277140300215200311130346543430230033026324733152035015203245154445123403511476
	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

CCHHHHHHHHHHHHHHHHCCCEEEEEHHHHHHHCCCCCCCCEEEEHCCCCHHHHHHHHHHHHHHCCCCCCCCHHHHHCCEEEEEHCCCCCCCCCEEEEEEHCCCCCCHHHHHHCCEEEEHCCEEEEEHCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCHCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCC
MNAVESTLRRVAKDLTGLRQRWALVGGFAVSARSEPRFTRDVDIVVAVANDDAAESLVRQLLTQQYHLLASVEQDAARRLAAVRLGATADTAANVVVDLLFASCGIEPEIAEAAEEIEILPDLVAPVATTAHLIAMKLLARDDDRRPQDRSDLRALVDAASPQDIQDARKAIELITLRGFHRDRDLAAEWTRLAAKW

4ok0A

0.13

0.95

1.19

MUSTER

LSEQALNHEKLMRAIVKNLAPMVLKGETALYLG-LNRFSEDLDFDCHKKI--NLLGRVKSAIPNGIILNDIHIKKDTDSVGRYMVRYATKDNEEQTLKLEISYRDAP-----KESEVNVIEG--MRIAKIERIIDNKLCACFDRTKARDLFDLHFLAKHYEEHFNLDLASRLKDFSKDPIMDLEETALELGVMAQLI

4wqkA

0.12

0.11

0.86

1.39

dPPAS

-TTQVTLIHKILAAADERNLPLWIGGGWAIDARLVTRKHDDIDLTFPGERRGELEAIVEMLGGRVMEELDYGFLAEIGDELLDCEPAWWADEAYEIAEAPQGSCPEA--------AEGVIAGRPVRCNSWEAIIWDYFYYADEVPPTKHIESYRLACTSLGAEKVEVLRAAFRSRYAA-------------------

4wqkA

0.10

0.08

0.81

2.14

wdPPAS

-TTQVTLIHKILAAADERNLPLWIGGGWAIDAR-VTRKHDDIDLTF---PGERRGELEAIVEMLGGRVMEEL-----DYGFLAEI-------GDELLDCEP-EIAEAPQGSCPEAAEGVIAGRPVRCNSWEAIIWDYFYYADEVPPTKHIESYRLACTSLGAEKVEVLRAAFRSRYAA-------------------

4ok0A

0.15

0.14

0.93

1.42

wMUSTER

SENHEKLMRAIVKNLA--DTPMVLKGETALYLG-LNRFSEDLDFDCHKKIN--LLGRVKSAIPNGIILNDIHIKKDTDSVGRYMVRYATKDNQTLKLEISYRDAPK-------ESEVNVIEG--MRIAKIERIIDNKLCACFDRTKARDLFDLHFLAKHYEEHFNLDLASRLKDFSKDPIMDLEETALELGVMAQLI

4wqkA

0.12

0.10

0.80

2.09

wPPAS

-TTQVTLIHKILAAADERNLPLWIGGGWAIDAR-VTRKHDDIDLTF---PGERRGELEAIVEMLGGRVMEEL-----DYGFLAEI-------GDELLDCEP-AEAPQGSCPEAAE--GVIAGRPVRCNSWEAIIWDYFYYADEVPPTKHIESYRLACTSLGAEKVEVLRAAFRSRYAA-------------------

4wqkA

0.12

0.11

0.86

3.39

dPPAS2

-TTQVTLIHKILAAADERNLPLWIGGGWAIDARLVTRKHDDIDLTFPGERRGELEAIVEMLGGRVMEELDYGFLAEIGDELLDCEPAWWADEAYEIAEAPQGSCPEA--------AEGVIAGRPVRCNSWEAIIWDYFYYADEVPPTKHIESYRLACTSLGAEKVEVLRAAFRSRYAA-------------------

4wqkA

0.13

0.11

0.85

1.63

PPAS

-TTQVTLIHKILAAADERNLPLWIGGGWAIDAR-VTRKHDDIDLTFPGERRGELEAIVEMLGGRVMEELDYGFLAEIGDELLDCEPAWWADEAYEIAEAPQGSCPEAAE--------GVIAGRPVRCNSWEAIIWDYFYYADEVPPTKHIESYRLACTSLGAEKVEVLRAAFRSRYAA-------------------

4wqkA

0.13

0.11

0.86

1.56

Env-PPAS

-TTQVTLIHKILAAADERNLPLWIGGGWAIDARLVTRKHDDIDLTFPGERRGELEAIVEMLGGRVMEELDYGFLAEIGDELLDCEPAWWADEAYEIAEAPQGSCPEAAE--------GVIAGRPVRCNSWEAIIWDYFYYADEVPPTKHIESYRLACTSLGAEKVEVLRAAFRSRYAA-------------------

4wqkA

0.11

0.09

0.83

1.16

MUSTER

-TTQVTLIHKILAAADERNLPLWIGGGWAIDAR-VTRKHDDIDLTFPGERRGELEAIVEMLGGRVMEELD--------YGFLAEI-----GDELLDCEPAWWADAEAPQGSCPEAAEGVIAGRPVRCNSWEAIIWDYFYYADEVPPTKHIESYRLACTSLGAEKVEVLRAAFRSRYAA-------------------

4ok0A

0.14

0.96

1.15

dPPAS

LSEQALNHEKLMRAIVKNLAPMVLKGETALYLGYLNRFSEDLDFDCHKKI-NLLGRVKSAIPNGIILNDIHIKKDTDSVGRYMVRYATKDNKEEQTLKLEISYRDAPK-----ESEVNVIEG--MRIAKIERIIDNKLCACFDGEKARDLFDLHFLAKHYESKDPDKLVSDYLVDVKLDALLNQIMDLEETALELGV

(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=-0.72

Estimated TM-score = 0.62±0.14

Estimated RMSD = 6.8±4.1Å

Download Model 2

C-score=-2.57

Download Model 3

C-score=-3.18

Download Model 4

C-score=-3.86

Download Model 5

C-score=-3.68

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	4ok0A	0.762	2.98	0.148	0.929
2	4wqkA	0.672	2.74	0.124	0.802
3	4wseA	0.617	3.87	0.067	0.812
4	4p37A2	0.582	3.79	0.073	0.761
5	4e8iA	0.582	2.75	0.138	0.701
6	2gafD	0.576	4.15	0.056	0.807
7	2ewrA	0.560	3.35	0.128	0.716
8	4s3nA	0.537	4.89	0.098	0.833
9	4at7B	0.524	4.44	0.152	0.782
10	4xq7A	0.523	5.36	0.110	0.853

(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	0.47	19	3ercC	CA	Rep, Mult	27,41,43
2	0.05	2	5cfsA	APC	Rep, Mult	27,37,39,40,41,43,136,137,140,148,149
3	0.02	1	1zelA	NA	Rep, Mult	152,155,156
4	0.02	1	4xjeA	AMP	Rep, Mult	26,27,41,43,136,137,140,143,149
5	0.02	1	1fa0A	3AD	Rep, Mult	25,43,98,100

	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	0.080	1jmsA	0.463	4.80	0.083	0.690	2.7.7.31	98
2	0.060	1px5B	0.499	5.34	0.114	0.833	2.7.7.-	NA
3	0.060	2nomB	0.309	5.43	0.109	0.508	2.7.7.52	NA
4	0.060	3c66A	0.507	4.95	0.060	0.802	2.7.7.19	137
5	0.060	2q0cB	0.466	4.87	0.123	0.756	2.7.7.52	NA
6	0.060	2ytzA	0.454	4.86	0.053	0.736	2.1.1.32	29,43
7	0.060	2dr9A	0.490	4.78	0.109	0.772	2.7.7.21,2.7.7.25	29,43,98
8	0.060	2azdB	0.413	5.56	0.052	0.731	2.4.1.1	NA
9	0.060	3iv7A	0.440	5.18	0.081	0.706	1.3.1.32	NA
10	0.060	1ou5A	0.446	6.07	0.056	0.848	2.7.7.25	27,43,145,146
11	0.060	2q0eA	0.471	5.25	0.163	0.787	2.7.7.52	NA
12	0.060	1rrmA	0.449	5.25	0.064	0.736	1.1.1.77	NA
13	0.060	3dwbA	0.436	5.07	0.052	0.706	3.4.24.71	NA
14	0.060	2c4mC	0.443	5.65	0.091	0.751	2.4.1.1	NA
15	0.060	3hx0A	0.470	4.54	0.065	0.680	2.7.7.7,	98
16	0.060	3gpbA	0.419	5.87	0.065	0.772	2.4.1.1	NA
17	0.060	2gafD	0.576	4.15	0.056	0.807	2.7.7.19	43,98
18	0.060	1ahpA	0.413	5.61	0.057	0.736	2.4.1.1	NA
19	0.060	1fa9A	0.382	6.05	0.049	0.731	2.4.1.1	10

(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	0.17	0.595	2.72	0.14	0.71	4fo1A	GO:0046677
1	0.07	0.617	3.87	0.07	0.81	4wseA	GO:0000166 GO:0004652 GO:0005524 GO:0006351 GO:0006397 GO:0016740 GO:0019012
2	0.06	0.386	5.40	0.03	0.63	3kzwA	GO:0004177 GO:0005622 GO:0005737 GO:0006508 GO:0008233 GO:0008235 GO:0016787 GO:0019538 GO:0030145 GO:0046872
3	0.06	0.348	6.70	0.02	0.73	3loqA	GO:0000166 GO:0006950
4	0.06	0.299	5.47	0.05	0.52	2xtzA	GO:0000166 GO:0001789 GO:0003924 GO:0004871 GO:0005095 GO:0005525 GO:0005789 GO:0005834 GO:0005886 GO:0006571 GO:0007165 GO:0007186 GO:0008219 GO:0009094 GO:0009506 GO:0009738 GO:0009740 GO:0009749 GO:0009785 GO:0009788 GO:0009789 GO:0009845 GO:0010027 GO:0010119 GO:0010244 GO:0016020 GO:0016247 GO:0019001 GO:0031683 GO:0034260 GO:0042127 GO:0046872 GO:0071215 GO:0072593
5	0.06	0.356	5.34	0.07	0.59	1xgkA	GO:0001081 GO:0005634 GO:0005737 GO:0006351 GO:0006355 GO:0006808 GO:0016491 GO:0045892 GO:0051287 GO:0055114 GO:0070401 GO:0070402 GO:0070403 GO:0070404 GO:0070405 GO:0070406 GO:0090295
6	0.06	0.326	6.17	0.06	0.64	1k77A	GO:0008903 GO:0016853
7	0.06	0.325	5.66	0.04	0.56	1td9D	GO:0005737 GO:0006085 GO:0008152 GO:0008959 GO:0016407 GO:0016740 GO:0016746
8	0.06	0.355	6.15	0.07	0.67	2j3lB	GO:0000166 GO:0002161 GO:0004812 GO:0004827 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006433 GO:0006450 GO:0016874
9	0.06	0.325	5.27	0.04	0.54	3bwgB	GO:0003677 GO:0003700 GO:0006351 GO:0006355
10	0.06	0.344	6.15	0.03	0.65	1gpmA	GO:0000166 GO:0003921 GO:0003922 GO:0005524 GO:0005829 GO:0006164 GO:0006177 GO:0006541 GO:0016462 GO:0016874 GO:0042802
11	0.06	0.294	6.08	0.05	0.54	1tq5A	GO:0008127 GO:0016491 GO:0046872 GO:0051213 GO:0055114
12	0.06	0.345	5.35	0.04	0.59	5ap1A	GO:0000166 GO:0004672 GO:0004674 GO:0004712 GO:0004713 GO:0005524 GO:0005737 GO:0005819 GO:0006468 GO:0007051 GO:0007052 GO:0007093 GO:0007094 GO:0008284 GO:0010862 GO:0016020 GO:0016301 GO:0016310 GO:0016740 GO:0018108 GO:0051304
13	0.06	0.234	5.32	0.02	0.39	2hpvA	GO:0008752 GO:0009055 GO:0010181 GO:0016491 GO:0016652 GO:0016661 GO:0055114
14	0.06	0.275	5.97	0.04	0.51	1fnuA	GO:0005576 GO:0009405
15	0.06	0.315	5.68	0.03	0.55	1fsgA	GO:0000166 GO:0000310 GO:0004422 GO:0005737 GO:0006166 GO:0009116 GO:0016740 GO:0016757 GO:0032263 GO:0032264 GO:0032265 GO:0046872 GO:0052657
16	0.06	0.288	5.61	0.05	0.51	4pw7E	GO:0003677 GO:0004842 GO:0005634 GO:0005654 GO:0005720 GO:0006511 GO:0007049 GO:0008270 GO:0008283 GO:0010216 GO:0016567 GO:0016874 GO:0030154 GO:0042393 GO:0046872 GO:0051726 GO:0051865 GO:0061630 GO:0071158 GO:0090308
17	0.06	0.266	6.11	0.03	0.50	4ilsA	GO:0003824 GO:0006522 GO:0008784 GO:0016853 GO:0030170 GO:0030632
18	0.06	0.260	5.64	0.02	0.46	3gwyB	GO:0016787

Consensus prediction of GO terms

Molecular Function	GO:0036094	GO:1901265
GO-Score	0.37	0.37
Biological Processes	GO:0042221
GO-Score	0.34
Cellular Component	GO:0019012	GO:0009506	GO:0005834	GO:0005789
GO-Score	0.07	0.06	0.06	0.06

(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.