I-TASSER results

I-TASSER results for job id Rv1861

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

Input Sequence in FASTA format

>protein (101 residues)
MDITATTEFSAMNLDGKTGIGWLGYIVIGGIAGWLASKIVKGGGSGILMNVVIGVVGAFG
AGLVLNALGVDVNHGGYWFTFFVALGGAVVLLWIVGMVRKT

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MDITATTEFSAMNLDGKTGIGWLGYIVIGGIAGWLASKIVKGGGSGILMNVVIGVVGAFGAGLVLNALGVDVNHGGYWFTFFVALGGAVVLLWIVGMVRKT
Prediction	CCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCC
Conf.Score	98545689999875678865899999999999999998647998456757889999999999999997987788746889999999999999999998669
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MDITATTEFSAMNLDGKTGIGWLGYIVIGGIAGWLASKIVKGGGSGILMNVVIGVVGAFGAGLVLNALGVDVNHGGYWFTFFVALGGAVVLLWIVGMVRKT
Prediction	75444344332444453331333312332331132043025454210110231123113303321331434343323231333133212212312432458
	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

CCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCC
MDITATTEFSAMNLDGKTGIGWLGYIVIGGIAGWLASKIVKGGGSGILMNVVIGVVGAFGAGLVLNALGVDVNHGGYWFTFFVALGGAVVLLWIVGMVRKT

4hzuS

0.23

0.98

1.00

wMUSTER

LLVGGASGFLIDILTGYPVFSLVIHGTQGLVVGWLLPRHHKGIRSPLLVGSLVMVIGYCLATTLLF--GWPAGLASIFGNVVQVGFGAGVTLSIVGPLTRL

3hzqA

0.15

0.12

0.79

1.13

wPPAS

M------EFALK-------LDLAIAVVMGAAFNKIICSLVE--------NIIMPLIGKIFGSFAKEWSFWGIKYGLFIQSVIDFIIIAFALFIFVKIANTK

4hzuS

0.16

0.99

1.62

dPPAS2

L-LVGGASGFLIDILTGYPVWCLFSLVIHGTQGLVVGWLLPRHHKGIRSMLLPLLVGSLVMVIGYCLATTLLFGASIFGNVVQVGFGAGVTLSIVGPLTRL

5a43A

0.09

1.00

1.19

PPAS

KSLWLLSTKFNSLFPNLPPGTLVVNLLAGLIIGTLAYFLRQPHLDPFWKLITTGLCGGLFSTFSVEVFALLQAGIWALTSVLVHVIGSLITALGFFIITIL

4hzuS

0.17

0.99

1.05

wPPAS

MTVLIAMTVALSILVVIPVGIYTSAILMGLLVGGASGFL-HKGIRSMLLPLLVGSLVMVIGYCLATTLLFGWPAGSIFGNVVQVGFGAGVTLSIVGPLTRL

5kbwA

0.17

1.00

1.37

dPPAS2

MFVVLVKDILFFLMKSGDPVGIAMNAVLGMSFVGIAGLIYNKSRATAIKGMIVATLFATAFALGLNALIVPLYFEALAFNLVKFGIDSVVTFFVYKKVSSI

4bwzA1

0.24

0.17

0.71

1.09

PPAS

------------------GAEHLLEIFYLLLAAQVCAFIFKRLNQP-------VVIGEVLAGVLVALLGLVHEG---EILEFLAELGLAPIFFAMVGVRL-

4bwzA1

0.25

0.17

0.68

1.03

wPPAS

------------------GAEHLLEIFYLLLAAQVCAFIFK----NQ------VVIGEVLAGVLVALLGLVHEG---EILEFLAELGLAPIFFAMVGVRL-

4huqS

0.13

0.98

1.35

dPPAS2

MLTAAVVDVIGTLMTGGPF--FIGFTVSAVLGSLIYAVFLYRQPVSWWRVIGASVLIALLVNTLLNTLWVTIMYQTALKELIVTPVQIVLVYLLLKSQVIQ

4hzuS

0.19

0.18

0.96

1.07

PPAS

L-LVGGASGFLIDILTGYPVWCLFSLVIHGTQGLVVGWLLPRHHKPLLVGSLVMVIGYCLATTLL---GWPAGLASIFGNVVQVGFGAGVTLSIVGPLTRL

(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=-1.23

Estimated TM-score = 0.56±0.15

Estimated RMSD = 6.5±3.9Å

Download Model 2

C-score=-4.01

Download Model 3

C-score=-2.81

Download Model 4

C-score=-4.32

Download Model 5

C-score=-4.07

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	4hzuS	0.815	1.92	0.168	1.000
2	5kbwA	0.750	2.34	0.140	0.990
3	3p5nA	0.728	2.44	0.130	0.990
4	3rlbA	0.716	2.67	0.120	0.990
5	4huqS	0.714	2.52	0.122	0.970
6	4m58A	0.699	2.73	0.062	0.960
7	5d0yA	0.687	2.72	0.073	0.951
8	4rfsS	0.686	2.87	0.140	0.990
9	4tkrA	0.684	2.86	0.112	0.970
10	4a01A	0.672	3.08	0.060	0.990

(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	0.10	4	2xquB	CVM	Rep, Mult	84,88
2	0.08	3	1ijdD	BCL	Rep, Mult	86,89
3	0.07	3	3rlbB	VIB	Rep, Mult	32,33,58,62,79,83,84
4	0.05	2	3aebC	EPH	Rep, Mult	25,63
5	0.02	1	3p5nA	RBF	Rep, Mult	29,32,33,36,57,61,87,88,91
6	0.02	1	2z4yA	252	Rep, Mult	34,38,60,64
7	0.02	1	3vi0A	UUU	Rep, Mult	7,26,49,56,60,61,63,64,72
8	0.02	1	4fe1F	CLA	Rep, Mult	23,27
9	0.02	1	2ciwA	MAN	Rep, Mult	98,101
10	0.02	1	4a01B	DMU	Rep, Mult	77,78,81
11	0.02	1	2r9rB	PGW	Rep, Mult	64,68
12	0.02	1	1g20B	SF4	Rep, Mult	55,56
13	0.02	1	2x2vH	DPV	Rep, Mult	31,39

	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	1hxgA	0.587	3.57	0.030	0.951	4.2.3.9,4.1.99.7	NA
2	0.060	2vn0A	0.577	3.03	0.030	0.832	1.14.14.1	NA
3	0.060	1w0eA	0.590	2.83	0.061	0.832	1.14.13.67,1.14.14.1	NA
4	0.060	3ckeD	0.542	4.27	0.041	0.960	4.2.3.9	NA
5	0.060	2f8zF	0.593	3.96	0.050	0.891	2.5.1.10,2.5.1.1	60
6	0.060	1jrpB	0.570	3.21	0.057	0.871	1.17.1.4	48
7	0.060	3npkA	0.589	3.30	0.051	0.891	2.5.1.10	NA
8	0.060	1uedA	0.588	2.96	0.069	0.842	1.14.-.-	NA
9	0.060	2f89F	0.591	3.84	0.060	0.871	2.5.1.1,2.5.1.10	NA
10	0.060	2f9qA	0.588	2.73	0.040	0.822	1.14.14.1	59
11	0.060	2d09A	0.572	3.06	0.052	0.802	1.14.-.-	NA
12	0.060	2j5cB	0.579	3.90	0.080	0.970	4.2.3.-	34,59
13	0.060	1n1zA	0.588	3.72	0.071	0.960	5.5.1.8	NA
14	0.060	1n6bA	0.564	3.11	0.040	0.832	1.14.14.1	59
15	0.060	1wmwA	0.588	3.15	0.062	0.871	2.5.1.-	NA
16	0.060	3ixzA	0.654	2.88	0.063	0.921	3.6.3.10	NA
17	0.060	1jroB	0.595	3.43	0.031	0.931	1.1.1.204	NA
18	0.060	1cptA	0.585	2.53	0.010	0.802	1.14.-.-	NA
19	0.060	2jjpA	0.580	3.05	0.061	0.852	1.14.-.-	39

(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	0.29	0.815	1.92	0.17	1.00	4hzuS	GO:0016020 GO:0016021
1	0.14	0.686	2.87	0.14	0.99	4rfsS	GO:0005215 GO:0006810 GO:0016020 GO:0016021
2	0.13	0.714	2.52	0.12	0.97	4huqS	GO:0005215 GO:0006810 GO:0016020 GO:0016021
3	0.12	0.699	2.73	0.06	0.96	4m58A	GO:0000041 GO:0016020 GO:0016021
4	0.11	0.728	2.44	0.13	0.99	3p5nA	GO:0005215 GO:0005886 GO:0006810 GO:0016020 GO:0016021 GO:0032217 GO:0032218
5	0.09	0.655	3.17	0.06	0.96	4z7fB	GO:0005215 GO:0006810 GO:0016020 GO:0016021
6	0.09	0.668	3.09	0.06	0.99	5d3mC	GO:0005215 GO:0006810 GO:0016020 GO:0016021
7	0.07	0.557	4.17	0.05	0.95	3b8cA	GO:0000166 GO:0000287 GO:0005524 GO:0005886 GO:0005887 GO:0006754 GO:0006810 GO:0006811 GO:0008553 GO:0015991 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0016887 GO:0046872 GO:0051453
8	0.07	0.716	2.82	0.11	0.99	4muuA	GO:0005886 GO:0015234 GO:0015888 GO:0016020 GO:0016021 GO:0071934
9	0.07	0.651	3.22	0.10	0.96	3a3yA	GO:0000166 GO:0005391 GO:0005524 GO:0006810 GO:0006811 GO:0006813 GO:0006814 GO:0010248 GO:0016020 GO:0016021 GO:0016787 GO:0046872 GO:0090662
10	0.07	0.551	4.05	0.07	0.95	1mhsA	GO:0000166 GO:0005524 GO:0005886 GO:0005887 GO:0006754 GO:0006810 GO:0006811 GO:0008553 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0016887 GO:0043231 GO:0046872 GO:0051453 GO:1902600
11	0.07	0.479	4.08	0.02	0.87	3w5bA	GO:0000166 GO:0005388 GO:0005509 GO:0005524 GO:0005783 GO:0005789 GO:0005793 GO:0006810 GO:0006811 GO:0006816 GO:0006942 GO:0016020 GO:0016021 GO:0016529 GO:0016787 GO:0031448 GO:0031673 GO:0031674 GO:0033017 GO:0045988 GO:0046872 GO:0048471 GO:0070588
12	0.07	0.624	3.21	0.10	0.97	4av6A	GO:0000287 GO:0004427 GO:0005509 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006814 GO:0009678 GO:0015081 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0030955 GO:0035725 GO:0042803 GO:0046872
13	0.07	0.672	3.08	0.06	0.99	4a01A	GO:0004427 GO:0005773 GO:0005774 GO:0006810 GO:0006811 GO:0009678 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0046872 GO:0055085
14	0.07	0.482	3.23	0.08	0.65	1flcB	GO:0001681 GO:0016020 GO:0016021 GO:0016032 GO:0016787 GO:0016788 GO:0019012 GO:0019031 GO:0019062 GO:0019064 GO:0020002 GO:0033644 GO:0039654 GO:0039663 GO:0046718 GO:0046789 GO:0055036
15	0.07	0.439	4.55	0.06	0.73	3rdpB	GO:0000166 GO:0004797 GO:0005524 GO:0006230 GO:0016301 GO:0016310 GO:0016740 GO:0071897
16	0.07	0.413	4.31	0.04	0.75	3r4cA	GO:0005737 GO:0016311 GO:0016787 GO:0016791 GO:0044283 GO:0046872
17	0.07	0.417	4.85	0.06	0.80	2rarA	GO:0005737 GO:0016311 GO:0016787 GO:0016791 GO:0044283 GO:0046872
18	0.07	0.711	2.65	0.11	0.99	4tkrB	GO:0005886 GO:0015234 GO:0015888 GO:0016020 GO:0016021 GO:0071934

Consensus prediction of GO terms

Molecular Function	GO:0005215
GO-Score	0.34
Biological Processes	GO:0006810
GO-Score	0.34
Cellular Component	GO:0016021
GO-Score	0.59

(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.