I-TASSER results

I-TASSER results for job id Rv2468c

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

Input Sequence in FASTA format

>protein (167 residues)
MTHRSSRLEVGPVARGDVATIEHAELPPGWVLTTSGRISGVTEPGELSVHYPFPIADLVA
LDDALTYSSRACQVRFAIYLGDLGRDTAARAREILGKVPTPDNAVLLAVSPNQCAIEVVY
GSQVRGRGAESAAPLGVAAASSAFEQGELVDGLISAIRVLSAGIAPG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MTHRSSRLEVGPVARGDVATIEHAELPPGWVLTTSGRISGVTEPGELSVHYPFPIADLVALDDALTYSSRACQVRFAIYLGDLGRDTAARAREILGKVPTPDNAVLLAVSPNQCAIEVVYGSQVRGRGAESAAPLGVAAASSAFEQGELVDGLISAIRVLSAGIAPG
Prediction	CCCCCCCCCCCCCCCCCEHCCCCCCCCCCEEEHCCCEEEEHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCEEEEEEHCCCCCCHHHHHHHHHHHCCCCCCEEEEEEHCCCCEEEEEHCCHHHHCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCC
Conf.Score	99876554567777765555676678875788656656655567777778999999999999999999998594899998589999999999999868888887999995687769999786688758979999999999999986986889999999999856889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MTHRSSRLEVGPVARGDVATIEHAELPPGWVLTTSGRISGVTEPGELSVHYPFPIADLVALDDALTYSSRACQVRFAIYLGDLGRDTAARAREILGKVPTPDNAVLLAVSPNQCAIEVVYGSQVRGRGAESAAPLGVAAASSAFEQGELVDGLISAIRVLSAGIAPG
Prediction	75444552643414525144254771431202033331232442563446340447205303501530465240300020142455125203500570473430000001364320101124404731446304200430252056341240014004302742668
	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

                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCCCCCCEHCCCCCCCCCCEEEHCCCEEEEHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCEEEEEEHCCCCCCHHHHHHHHHHHCCCCCCEEEEEEHCCCCEEEEEHCCHHHHCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCC
MTHRSSRLEVGPVARGDVATIEHAELPPGWVLTTSGRISGVTEPGELSVHYPFPIADLVALDDALTYSSRACQVRFAIYLGDLGRDTAARAREILGKVPTPDNAVLLAVSPNQCAIEVVYGSQVRGRGAESAAPLGVAAASSAFEQGELVDGLISAIRVLSAGIAPG

2lt2A

0.16

0.12

0.73

2.02

MUSTER

---------------------------------------------MSKIEEFLTAEEEKAIVDAIRDAEKNTSGEIRVHLEKSEIDVFDRAMDVFHNLKKLQNGVLIYVAVEDKTFVIYGDKGINDVVSDDFWDTTRNAIQLQFKQGNFKQGLVDGIEKAGMALAPW

2lt2A

0.16

0.11

0.73

2.61

dPPAS

---------------------------------------------MSKIEEFLTAEEEKAIVDAIRDAEKNTSGEIRVHLEKSEIDVFDRAMDVFHNLKKLQNGVLIYVAVEDKTFVIYGDKGINDVVSDDFWDTTRNAIQLQFKQGNFKQGLVDGIEKAGMALAKY

2lt2A

0.16

0.11

0.72

3.20

wdPPAS

---------------------------------------------MSKIEEFLTAEEEKAIVDAIRDAEKNTSGEIRVHL-TSEIDVFDRAMDVFHNLKKLQNGVLIYVAVEDKTFVIYGDKGINDVVSDDFWDTTRNAIQLQFKQGNFKQGLVDGIEKAGMALAKY

2lt2A

0.15

0.11

0.72

2.47

wMUSTER

----------------------------------------------SKIEEFLTAEEEKAIVDAIRDAEKNTSGEIRVHLEKSEIDVFDRAMDVFHNLKKLQNGVLIYVAVEDKTFVIYGDKGINDVVSDDFWDTTRNAIQLQFKQGNFKQGLVDGIEKAGMALKKD

2lt2A

0.16

0.12

0.73

3.35

wPPAS

---------------------------------------------MSKIEEFLTAEEEKAIVDAIRDAEKNTSGEIRVHLEKSEIDVFDRAMDVFHNLKKLQNGVLIYVAVEDKTFVIYGDKGINDVVSDDFWDTTRNAIQLQFKQGNFKQGLVDGIEKAGMALAPW

2lt2A

0.16

0.11

0.73

6.64

dPPAS2

---------------------------------------------MSKIEEFLTAEEEKAIVDAIRDAEKNTSGEIRVHLEKSEIDVFDRAMDVFHNLKKLQNGVLIYVAVEDKTFVIYGDKGINDVVSDDFWDTTRNAIQLQFKQGNFKQGLVDGIEKAGMALAKY

2lt2A

0.16

0.12

0.73

2.84

PPAS

---------------------------------------------MSKIEEFLTAEEEKAIVDAIRDAEKNTSGEIRVHLEKSEIDVFDRAMDVFHNLKKLQNGVLIYVAVEDKTFVIYGDKGINDVVSDDFWDTTRNAIQLQFKQGNFKQGLVDGIEKAGMALAPW

2lt2A

0.16

0.12

0.73

2.86

Env-PPAS

---------------------------------------------MSKIEEFLTAEEEKAIVDAIRDAEKNTSGEIRVHLEKSEIDVFDRAMDVFHNLKKLQNGVLIYVAVEDKTFVIYGDKGINDVVSDDFWDTTRNAIQLQFKQGNFKQGLVDGIEKAGMALAPW

2kw7A

0.11

0.10

0.85

1.90

MUSTER

-----------------MRVYKPEDVPNVQLADSTRLVTDEA--------GLLSNAQEEVMNGRLRAIRSSHAVEFAVVTLPSDAPLEDFTLKLARQWGKNNNGLLLVLVLDQRRVRFETGYGLEGYLPGLLSRIIHDRMIPHFRSGNYAEGLSEGVLAVQQVLDEH

2kw7A

0.11

0.10

0.85

2.14

dPPAS

-----------------MRVYKPEDVPNVQLADSTRLVTDE--------AGLLSNAQEEVMNGRLRAIRSSHAVEFAVVTLPSDAPLEDFTLKLARQWGKNNNGLLLVLVLDQRRVRFETGYGLEGYLPGLLSRIIHDRMIPHFRSGNYAEGLSEGVLAVQQVLDGS

(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=-0.82

Estimated TM-score = 0.61±0.14

Estimated RMSD = 6.7±4.0Å

Download Model 2

C-score=-2.00

Download Model 3

C-score=-0.60

Download Model 4

C-score=-0.99

Download Model 5

C-score=-4.87

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	2kw7A	0.744	1.99	0.120	0.850
2	3ptjA	0.699	2.16	0.118	0.814
3	2lt2A	0.690	1.32	0.156	0.731
4	2kptA	0.622	2.28	0.106	0.725
5	1gytL	0.529	4.87	0.057	0.868
6	1ua4A	0.528	4.23	0.061	0.778
7	5aexA	0.526	5.17	0.042	0.886
8	4zi6A2	0.525	5.01	0.063	0.880
9	2ewbA	0.524	4.87	0.038	0.862
10	4af8A	0.523	4.82	0.079	0.874

(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	0.06	3	3jruB	CO3	Rep, Mult	133,134,135,136,160
2	0.06	3	3e7lC	ZN	Rep, Mult	148,151
3	0.04	2	1cgpA	CMP	Rep, Mult	157,161
4	0.04	2	3qmeA	CYH	Rep, Mult	78,106,107,117,120,153,157,160
5	0.04	2	3b7aA	EOH	Rep, Mult	78,108,109,116,153,156,157,160
6	0.02	1	2wl3A	CA	Rep, Mult	111,151
7	0.02	1	4oa3A	CA	Rep, Mult	69,75
8	0.02	1	2qtgA	MTH	Rep, Mult	116,118
9	0.02	1	3kzwD	NA	Rep, Mult	69,72,158,161,162
10	0.02	1	3pvhA	CA	Rep, Mult	16,34,35,81
11	0.02	1	1gk9B	EDO	Rep, Mult	103,105,107
12	0.02	1	4h6pC	FMN	Rep, Mult	120,161
13	0.02	1	5pgmE	ALA	Rep, Mult	130,132,133
14	0.02	1	3fltA	CA	Rep, Mult	145,148
15	0.02	1	3pw9A	SER	Rep, Mult	31,32,33,58
16	0.02	1	3o7uA	ZN	Rep, Mult	50,93
17	0.02	1	3a0bX	CLA	Rep, Mult	149,152,153,156
18	0.02	1	4ro2B	GLY	Rep, Mult	154,157

	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	0.066	3g98A	0.452	2.77	0.064	0.563	6.1.1.7	NA
2	0.060	1obrA	0.481	5.03	0.032	0.826	3.4.17.18	NA
3	0.060	1gytA	0.529	4.86	0.057	0.868	3.4.11.1	158
4	0.060	1gc5A	0.479	4.17	0.051	0.713	2.7.1.147	NA
5	0.060	3ifeA	0.509	5.34	0.044	0.916	3.4.11.4	88
6	0.060	3fedA	0.495	5.10	0.033	0.868	3.4.17.21	NA
7	0.060	2veoB	0.510	4.61	0.048	0.808	3.1.1.3	61
8	0.060	2qb7A	0.507	4.16	0.071	0.749	3.6.1.11	NA
9	0.060	3ij3A	0.506	5.10	0.057	0.874	3.4.11.1	NA
10	0.060	1jjfA	0.480	4.81	0.045	0.790	3.2.1.8	63
11	0.060	1e5tA	0.488	5.30	0.078	0.844	3.4.21.26	NA
12	0.060	1r3nA	0.476	5.36	0.081	0.868	3.5.1.6	NA
13	0.060	2hb6A	0.516	5.00	0.070	0.874	3.4.11.1	158
14	0.060	3d68C	0.478	5.07	0.068	0.820	3.4.17.20	NA
15	0.060	1jqgA	0.487	5.14	0.095	0.820	3.4.17.1	NA
16	0.060	1ua4A	0.528	4.23	0.061	0.778	2.7.1.147	120
17	0.060	1fnoA	0.485	5.47	0.063	0.892	3.4.11.4	126
18	0.060	2ewbA	0.524	4.87	0.038	0.862	3.4.11.1,3.4.11.5	NA
19	0.060	1wb4B	0.479	4.69	0.065	0.784	3.2.1.8	97
20	0.060	3ic1A	0.478	5.17	0.071	0.832	3.5.1.18	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	0.26	0.690	1.32	0.16	0.73	2lt2A	GO:0046872
1	0.23	0.705	2.16	0.12	0.82	3ptjA	GO:0003993 GO:0009507 GO:0009534 GO:0009535 GO:0009536 GO:0009579 GO:0010206 GO:0016020 GO:0016021 GO:0016311 GO:0031977
2	0.23	0.522	4.89	0.04	0.86	3jruA	GO:0004177 GO:0005622 GO:0005737 GO:0006508 GO:0008233 GO:0008235 GO:0016787 GO:0019538 GO:0030145 GO:0046872
3	0.20	0.744	1.99	0.12	0.85	2kw7A	GO:0016020 GO:0016021
4	0.07	0.452	2.77	0.06	0.56	3g98A	GO:0000049 GO:0000166 GO:0003676 GO:0003723 GO:0004812 GO:0004813 GO:0005524 GO:0005737 GO:0005829 GO:0006400 GO:0006412 GO:0006419 GO:0008270 GO:0016597 GO:0016874 GO:0016876 GO:0043039 GO:0046872
5	0.07	0.528	4.23	0.06	0.78	1ua4A	GO:0000287 GO:0004340 GO:0005737 GO:0005975 GO:0006006 GO:0006096 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0043843 GO:0046872 GO:0051156
6	0.07	0.499	5.11	0.07	0.87	4ksiA	GO:0004177 GO:0005622 GO:0005737 GO:0006508 GO:0008233 GO:0008235 GO:0009507 GO:0009536 GO:0016787 GO:0019538 GO:0030145 GO:0046872
7	0.07	0.523	3.24	0.06	0.65	3drwA	GO:0000287 GO:0005737 GO:0005975 GO:0006000 GO:0006096 GO:0008443 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0043844 GO:0046835 GO:0046872
8	0.07	0.464	5.46	0.06	0.81	4efdA	GO:0004177 GO:0005622 GO:0005737 GO:0006508 GO:0008235 GO:0019538 GO:0030145
9	0.07	0.485	4.55	0.04	0.73	5ck7A	GO:0005576 GO:0005783 GO:0005975 GO:0006096 GO:0016020 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0043843 GO:0046872
10	0.07	0.486	3.85	0.04	0.67	4b8rA	GO:0000287 GO:0004340 GO:0005737 GO:0005975 GO:0006006 GO:0006096 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0043843 GO:0046872 GO:0051156
11	0.07	0.456	4.23	0.05	0.68	1l2lA	GO:0000287 GO:0004340 GO:0005737 GO:0005975 GO:0006006 GO:0006096 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0043843 GO:0046872 GO:0051156
12	0.06	0.516	5.00	0.07	0.87	2hb6A	GO:0004177 GO:0005622 GO:0005737 GO:0006508 GO:0008233 GO:0008235 GO:0016787 GO:0019538 GO:0030145 GO:0040009 GO:0042802 GO:0046662 GO:0046872
13	0.06	0.410	4.68	0.04	0.63	1xl7B	GO:0005102 GO:0005739 GO:0005777 GO:0006091 GO:0006629 GO:0006631 GO:0006635 GO:0006810 GO:0008458 GO:0009437 GO:0010243 GO:0015908 GO:0015936 GO:0016740 GO:0016746 GO:0042493 GO:0043231 GO:0051791
14	0.06	0.391	4.45	0.02	0.62	3k4oA	GO:0000166 GO:0004349 GO:0005524 GO:0005737 GO:0006561 GO:0008299 GO:0016301 GO:0016310 GO:0016740 GO:0102043
15	0.06	0.518	4.99	0.06	0.86	3peiA	GO:0004177 GO:0005622 GO:0005737 GO:0006508 GO:0008233 GO:0008235 GO:0016787 GO:0019538 GO:0030145 GO:0046872
16	0.06	0.524	4.87	0.04	0.86	2ewbA	GO:0004177 GO:0005622 GO:0005634 GO:0005654 GO:0005737 GO:0005739 GO:0005925 GO:0006508 GO:0008233 GO:0008235 GO:0016787 GO:0019538 GO:0030145 GO:0046872 GO:0070062
17	0.06	0.392	4.79	0.07	0.65	1gqoB	GO:0003855 GO:0008652 GO:0009073 GO:0009423 GO:0016829
18	0.06	0.506	5.10	0.06	0.87	3ij3A	GO:0004177 GO:0005622 GO:0005737 GO:0006508 GO:0008233 GO:0008235 GO:0016787 GO:0019538 GO:0030145 GO:0046872
19	0.06	0.499	5.04	0.07	0.85	3h8eA	GO:0004177 GO:0005622 GO:0005737 GO:0006508 GO:0008233 GO:0008235 GO:0016787 GO:0019538 GO:0030145 GO:0046872

Consensus prediction of GO terms

Molecular Function	GO:0016791	GO:0008238	GO:0046914	GO:0008237
GO-Score	0.46	0.46	0.46	0.46
Biological Processes	GO:0030091	GO:0009765	GO:0006796
GO-Score	0.46	0.46	0.46
Cellular Component	GO:0055035	GO:0009534	GO:0016021
GO-Score	0.46	0.46	0.39

(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.