I-TASSER results

I-TASSER results for job id Rv2390c

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

Input Sequence in FASTA format

>protein (185 residues)
MAIFGRGHGASEPGGTGEPAETPGRGRLTRSVIGWVGAVAVVVSLAGSGWCGWVLFEKHQ
TDVAAGQALQAARSYVVKLATMDCERIDHNMRDILEGSTGEFKDKYGKSSAHLRQLLADN
RVATHGTVVAASVKSATTNKVVVLMFIDQSVSNRNSPTPQIDRSRIKVIMDKVNGRWLAS
KVELL

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MAIFGRGHGASEPGGTGEPAETPGRGRLTRSVIGWVGAVAVVVSLAGSGWCGWVLFEKHQTDVAAGQALQAARSYVVKLATMDCERIDHNMRDILEGSTGEFKDKYGKSSAHLRQLLADNRVATHGTVVAASVKSATTNKVVVLMFIDQSVSNRNSPTPQIDRSRIKVIMDKVNGRWLASKVELL
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCEEEEEEEEEEEEEEHCCEEEEEEEEEEEEEHCCCCCCCEEEEEEEEEEEEHCCEEEEHCCEHC
Conf.Score	99888999888888888887788888764579999999999999999999988754566789999999999999999998689776899999999859989999999999999999998597899999999999986998999999999998589988756678999999998998998756669
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MAIFGRGHGASEPGGTGEPAETPGRGRLTRSVIGWVGAVAVVVSLAGSGWCGWVLFEKHQTDVAAGQALQAARSYVVKLATMDCERIDHNMRDILEGSTGEFKDKYGKSSAHLRQLLADNRVATHGTVVAASVKSATTNKVVVLMFIDQSVSNRNSPTPQIDRSRIKVIMDKVNGRWLASKVELL
Prediction	74444656556666656655654654433221000000000001112111110122445434532540252035002302103373055115303721246026404622650353057472424041330003333753020000011314457476454432103010344744020452457
	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

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCEEEEEEEEEEEEEEHCCEEEEEEEEEEEEEHCCCCCCCEEEEEEEEEEEEHCCEEEEHCCEHC
MAIFGRGHGASEPGGTGEPAETPGRGRLTRSVIGWVGAVAVVVSLAGSGWCGWVLFEKHQTDVAAGQALQAARSYVVKLATMDCERIDHNMRDILEGSTGEFKDKYGKSSAHLRQLLADNRVATHGTVVAASVKSATTNKVVVLMFIDQSVSNRNSPTPQIDRSRIKVIMDKVNGRWLASKVELL

4xzzA

0.10

0.98

0.71

MUSTER

FVTNYPNLYDTLKKRTGHGMPLNGDRNELN-IAIENPLLSSYDKVLKGEKAFLITYEDKFFPSTKEELSMILSSLFQWKEAWARGDFERYMRFYNPNFTRYDGMKFNAFKEYKKRVFAKNE-KKNIAFSSINVIPYSQNKRLFYVVFDQDYKAYQHNKLSSSNSQKELYIEIENNQVSIIMEK--

5d9rA

0.12

0.08

0.69

dPPAS

-----------------------------------------------------SEALPRMDARTAENIVSKWQKIKSLAFGPDHR-----IEMLPEVLDGRMLKIWTDRAAETAQLGLVYDYTLLKLSVDSVTVSADGTRALVEATLEESACLSDLVHPEVRTYTTRYEVFWSKSGWKITEGSVL

5d9rA

0.12

0.08

0.63

1.27

wdPPAS

---------------------------------------------------------SEADARTAENIVSKWQKIKSLAFGPDHR-----IEMLPEVLDGRMLKIWTDRAAETAQL-----TLLKLSVDSVTVSA-DGTRALVEATLEESACLSDLVHPEVRTYTTRYEVFWSKSGWKITEGSVL

4v1ai

0.09

0.98

0.87

wMUSTER

LVIPHERLERPIHLACTAGIFDAPEGDARISSLSKEGLAQRAERLKKNVASQLSIRKIRESDPKIKDFPEKAKDIFIEAHLC----NNSDHDRLHTLVTENCFPDMVWDIRYKTVRWSFVESLEPPQVVQVRCSSLMNQYGQVTVRMHTRQTLAYGQEDVPRDVLEYVVFEKHYGSWRMHGIIPP

5d9rA

0.15

0.09

0.59

1.39

wPPAS

----------------------------------------------------------------SEALARTAENIVSKWQK-DHR-----IEMLPEVLDGRMLKIWTDRAAETAQL-----TLLKLSVDSVTVSA-DGTRALVEATLEESACLSDLVHPEVRTYTTRYEVFWSKSGWKITEGSVL

4ke2A

0.08

0.05

0.64

1.10

dPPAS2

AAASAAAAAVASAAKALETINVKAAYAAATTANTAAAAAAATATTAAAAAAAKATIDNAAAAKAAAVATAVSDAAATAATA-----AAVAAATLEAAAAKAAATAVSAAAAAAAAAIAFAAAP--------------------------------------------------------------

5cnlA

0.08

0.05

0.66

1.16

PPAS

------------------------------------------------------------GGPDRAQLAVWANEAIIATYTFDYKNYQQQKEIAKYFSADGWIAYSKALNQSLPEVVQKNAYFVNAVATEPPKLITLDPTHWQAIPILVVYKNPQYE--QKQNLKVVLGFTVASPGQGVRGFSVT

5d9rA

0.12

0.08

0.69

1.16

Env-PPAS

-----------------------------------------------------SEALPRMDARTAENIVSKWQKIKSLAFGPDHR-----IEMLPEVLDGRMLKIWTDRAAETAQLGLVYDYTLLKLSVDSVTVSADGTRALVEATLEESACLSDLVHPEVRTYTTRYEVFWSKSGWKITEGSVL

4xgtA

0.08

0.94

0.69

MUSTER

MVDDKLEPETARAIVVGNQDKLNSAFHLGYNMVLNLLRI------ISPEYMLERCFFQFQNAASVPQLERELISLQQERDAIIIPD----ESIVKDY--YGVRQQLEEYNKDMVFVIQHPQNCLGFEGRLIHIKSPSGVDYGWGVLIKHIQRNGQPPYPEQESYVLDVLLKVSDFNPKTRGEGPM

5cnlA

0.08

0.05

0.66

0.69

dPPAS

------------------------------------------------------------GGPDRAQLAVWANEAIIATYTFDYKNYQQQKEIAKYFSADGWIAYSKALNQSLPEVVQKNAYFVNAVATEPPKLITLDPTHWQAIPILVVYKNPQYE--QKQNLKVVLGFTVASPGQGVRGFSVT

(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=-2.96

Estimated TM-score = 0.38±0.13

Estimated RMSD = 12.0±4.4Å

Download Model 2

C-score=-3.70

Download Model 3

C-score=-3.91

Download Model 4

C-score=-3.69

Download Model 5

C-score=-4.45

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	2fxtA	0.575	3.56	0.039	0.741
2	3gzxB	0.570	3.00	0.075	0.719
3	2bmqB	0.568	3.37	0.066	0.730
4	3rgaA	0.564	3.89	0.066	0.773
5	2cc3A	0.562	2.46	0.115	0.654
6	1wqlB	0.561	2.86	0.093	0.697
7	4o3vA	0.555	2.54	0.083	0.649
8	4xzzA	0.549	3.98	0.048	0.762
9	3en1B	0.548	3.03	0.047	0.686
10	4jf8A	0.545	2.50	0.107	0.643

(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	0.11	6	3ov4B	EQU	Rep, Mult	75,79,109,147,149,151,162,166,182
2	0.07	4	4fcmA	III	Rep, Mult	66,67,70,71,74,96,97,175,176,177,178
3	0.04	2	2fhyA	A37	Rep, Mult	99,100
4	0.04	2	2yr2B	ZN	Rep, Mult	83,85
5	0.04	2	1gy60	III	Rep, Mult	101,130,132,133,134,135,136,137,138,142,144,165,167,169,171,181,182,183
6	0.04	2	3hx8D	IMD	Rep, Mult	73,128,143,166,168,179
7	0.02	1	3ov4A	EQU	Rep, Mult	75,79,124,149,151
8	0.02	1	4akyA	4LL	Rep, Mult	79,82,106,109,113,149,164,184
9	0.02	1	1jn5B	III	Rep, Mult	136,137,138,139,140,141,170,171,172,177
10	0.02	1	2axtl	UNK	Rep, Mult	42,45
11	0.02	1	3ujmA	EPE	Rep, Mult	96,175,177,178
12	0.02	1	3k7tA	GP7	Rep, Mult	23,24
13	0.02	1	2byoA	ZN	Rep, Mult	125,148
14	0.02	1	3a52A	MG	Rep, Mult	127,129
15	0.02	1	3m4gC	ZN	Rep, Mult	180,181
16	0.02	1	1hkxA	TBR	Rep, Mult	61,64,133,134,135

	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	3e99A	0.502	2.93	0.078	0.616	1.14.12.10	NA
2	0.066	4stdA	0.526	2.77	0.092	0.643	4.2.1.94	125
3	0.060	3gzxB	0.570	3.00	0.075	0.719	1.14.12.18	146
4	0.060	1g72A	0.423	4.37	0.067	0.627	1.1.99.8	NA
5	0.060	1gpeB	0.427	5.83	0.064	0.784	1.1.3.4	72,74
6	0.060	1o7hB	0.573	3.42	0.051	0.735	1.14.12.12	95
7	0.060	2h1nA	0.428	5.77	0.045	0.773	3.4.24.-	NA
8	0.060	1wmwA	0.423	4.66	0.048	0.665	2.5.1.-	NA
9	0.060	1galA	0.385	5.74	0.064	0.708	1.1.3.4	48
10	0.060	2v7oA	0.358	5.60	0.050	0.627	2.7.11.17	85
11	0.060	1rsrB	0.459	3.66	0.056	0.622	1.17.4.1	NA
12	0.060	1cf3A	0.424	5.99	0.069	0.800	1.1.3.4	NA
13	0.060	1hkxA	0.529	3.37	0.096	0.670	2.7.11.17	NA
14	0.060	2ux0A	0.537	3.10	0.113	0.659	2.7.11.17	100,178
15	0.060	1lrwC	0.425	4.23	0.075	0.622	1.1.99.8	96
16	0.060	1uzrB	0.444	3.96	0.056	0.632	1.17.4.1	106
17	0.060	1e3vB	0.455	2.72	0.048	0.551	5.3.3.1	75,106
18	0.060	8choA	0.455	2.49	0.059	0.540	5.3.3.1	76
19	0.060	3en1B	0.548	3.03	0.047	0.686	1.14.12.3,1.14.12.11	70,86,129
20	0.060	1buqA	0.459	2.40	0.059	0.546	5.3.3.1	75
21	0.060	1biqB	0.458	3.66	0.064	0.622	1.17.4.1	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	0.20	0.547	2.41	0.12	0.64	4akzA	GO:0005886 GO:0009405 GO:0016020 GO:0016021 GO:0030255 GO:0042802
1	0.16	0.460	2.50	0.11	0.55	4ec6A	GO:0016020 GO:0016021
2	0.13	0.540	2.47	0.14	0.63	4lsoA	GO:0005886 GO:0006810 GO:0009405 GO:0016020 GO:0016021 GO:0030255
3	0.12	0.555	2.51	0.08	0.65	4o3vB	GO:0016020 GO:0016021
4	0.12	0.561	2.86	0.09	0.70	1wqlB	GO:0003824 GO:0006725 GO:0051213 GO:0055114
5	0.11	0.544	2.65	0.11	0.64	4nhfA	GO:0016020 GO:0016021 GO:0030255
6	0.11	0.545	2.50	0.11	0.64	4jf8A	GO:0016020 GO:0016021 GO:0030255
7	0.10	0.526	2.99	0.11	0.66	2ckfB	GO:0003824 GO:0006725 GO:0051213 GO:0055114
8	0.10	0.541	3.01	0.07	0.68	1uliD	GO:0003824 GO:0006725 GO:0016491 GO:0018687 GO:0019439 GO:0051213 GO:0055114
9	0.09	0.546	3.27	0.04	0.69	2cw9A	GO:0000166 GO:0005524 GO:0005739 GO:0005743 GO:0005759 GO:0006626 GO:0006810 GO:0015031 GO:0016020 GO:0030150 GO:0051087
10	0.07	0.534	2.41	0.13	0.63	4meiA	GO:0016020 GO:0030255
11	0.07	0.562	2.46	0.12	0.65	2cc3A	GO:0005886 GO:0016020 GO:0016021 GO:0030255 GO:0042802 GO:0043684
12	0.07	0.575	3.56	0.04	0.74	2fxtA	GO:0000166 GO:0001405 GO:0005524 GO:0005739 GO:0005743 GO:0006626 GO:0006810 GO:0015031 GO:0016020 GO:0030150 GO:0030674 GO:0051087
13	0.07	0.570	3.00	0.07	0.72	3gzxB	GO:0003824 GO:0006725 GO:0016491 GO:0018687 GO:0019439 GO:0051213 GO:0055114
14	0.07	0.570	3.34	0.07	0.73	2bmoB	GO:0003824 GO:0006725 GO:0055114
15	0.07	0.572	3.43	0.05	0.74	1eg9B	GO:0003824 GO:0006725 GO:0016491 GO:0018625 GO:0019439 GO:0051213 GO:0055114
16	0.07	0.566	3.99	0.07	0.78	4rzmB	GO:0016853 GO:0017000
17	0.07	0.548	3.03	0.05	0.69	3en1B	GO:0003824 GO:0006725 GO:0016491 GO:0018619 GO:0018624 GO:0019439 GO:0042184 GO:0042203 GO:0051213 GO:0055114
18	0.07	0.533	2.67	0.10	0.64	2b1xB	GO:0003824 GO:0006725 GO:0051213 GO:0055114
19	0.07	0.532	3.23	0.08	0.67	5aewF	GO:0003824 GO:0006725 GO:0016491 GO:0018687 GO:0019439 GO:0051213 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0005515
GO-Score	0.41
Biological Processes	GO:0009405	GO:0030255
GO-Score	0.31	0.31
Cellular Component	GO:0016021	GO:0005886
GO-Score	0.49	0.31

(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.