I-TASSER results

I-TASSER results for job id Rv2081c

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

Input Sequence in FASTA format

>protein (146 residues)
MFANAGLSPFVAIWTARAASLYTSHNFWCAAAVSAAVYVGSAVVPAAVAGPLFVGRVSAT
IKAAAPSTTAAIATLATAANGQLRERGGAGGWVGVHCPVVGGGGVGHPRKAIAAAVSVHS
TCMPAAFGGHLGLGDRSRSVSLSGTP

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MFANAGLSPFVAIWTARAASLYTSHNFWCAAAVSAAVYVGSAVVPAAVAGPLFVGRVSATIKAAAPSTTAAIATLATAANGQLRERGGAGGWVGVHCPVVGGGGVGHPRKAIAAAVSVHSTCMPAAFGGHLGLGDRSRSVSLSGTP
Prediction	CCCCCCCCCEEEEEHCHHHHHHCCCCCEEEEEEEEEEEHCCCCCCCCCCCCEEEEEEEEEEEHCCCCHHHHHHHHHHHHCCCEHCCCCCCCEEEEHCCEHCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCEEEHCCCC
Conf.Score	98876787556676534554444566445444457777655445443346656666656765457754778888887756865556788766777665556888888656666666435555654446665678776657757899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MFANAGLSPFVAIWTARAASLYTSHNFWCAAAVSAAVYVGSAVVPAAVAGPLFVGRVSATIKAAAPSTTAAIATLATAANGQLRERGGAGGWVGVHCPVVGGGGVGHPRKAIAAAVSVHSTCMPAAFGGHLGLGDRSRSVSLSGTP
Prediction	73453413110000124234123433110000030022123231221232212223132304433443312122123235341354343311020301222233333334111212423430232233322222444453526658
	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

                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCEEEEEHCHHHHHHCCCCCEEEEEEEEEEEHCCCCCCCCCCCCEEEEEEEEEEEHCCCCHHHHHHHHHHHHCCCEHCCCCCCCEEEEHCCEHCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCEEEHCCCC
MFANAGLSPFVAIWTARAASLYTSHNFWCAAAVSAAVYVGSAVVPAAVAGPLFVGRVSATIKAAAPSTTAAIATLATAANGQLRERGGAGGWVGVHCPVVGGGGVGHPRKAIAAAVSVHSTCMPAAFGGHLGLGDRSRSVSLSGTP

3g98A

0.15

0.11

0.75

0.91

MUSTER

---------------MKEENV--------DFTLHYGVFEEVEPEELRNLADMLRQRTKKDVVFIASRKGDKI-NFVIGVSKEISDKVNAKEVIREVGKVLKGGGGGRADLAQGGGKAP--DKFPEAVKLLKEI--------LSG--

4opeA2

0.22

0.18

0.84

0.73

dPPAS

TQTPAQEPPYVCALSARAERLH-------EHTARTAEFLGRAAHPAAVAATLLTREPAHRLAVVFDTVDDLADALEDHLAGA----GSPRVLTGTASRAAAPATGRTAPELAEAWVR----------GAPVAAPAGAPRVSLPG--

4opeA2

0.24

0.19

0.81

0.61

wdPPAS

TQTPAQEPPYVCALSARAERLH-------EHTARTAEFLGRAAHPAAVAATLLTREPAHRLAVVFDTVDDLADALEDHLAGA----GSPRVLTGT-----AAPATGRTAPELAEAWV----------GAPVAAPAGAPRVSLPG--

5ak1A

0.14

0.97

0.60

wMUSTER

KRSTKSGGPYTTIATNITSTNYTDTGYYYVVSAVSNGVETLNSAEAILQYPKLTGTVIGTQGSWNNIGNTIHKAFDGDLNTFFDGPTANGCWLGLDF----GEGVRNVITQIKFCPRSGYEQRIGGIANKEDFSDAVTLFTITSLP

4tktA2

0.23

0.18

0.79

0.56

wPPAS

---HRG-ETVVVVLSAFEERLR-------ESAGRLRDALRKERWSPDIA--LQVGR-EATARFAVSTLPALVDALDACALGS----GLPAG-------AYFNP---GFQETAVRWARRGKPAPLAEAGLAVRLGPKPRKVAL---P

4opeA2

0.22

0.18

0.84

0.67

dPPAS2

TQTPAQEPPYVCALSARAERLH-------EHTARTAEFLGRAAHPAAVAATLLTREPAHRLAVVFDTVDDLADALEDHLAGA----GSPRVLTGTASRAAAPATGRTAPELAEAWVR----------GAPVAAPAGAPRVSLPG--

4opeA2

0.23

0.19

0.83

0.70

PPAS

TQTPAQEPPYVCALSARAERLH-------EHTARTAEFLGRAAHPAAVAATLLTREPAHRLAVVFDTVDDLADALEDHLAGA----GSPRVLTGTASRAAAPATGRTAPELAEAWVR----------GAPV-PAGAPR-VSLPG--

1u7iA

0.20

0.17

0.84

0.78

Env-PPAS

--HSARVRPFLFQGVQAAANFYLSL-FD-DAEILQIQRYGAE--GPGPEG--SVLKALFRLG---DQS---V--HCIDSHVRHAFDFTPAFSFFVDCESN------AQIERLAEALSDGGKALPLGFSQRFALADRSWQLNLAG--

2qo3B3

0.20

0.18

0.87

0.69

MUSTER

TTAHDG-RPVPLVVSARTAALRAQ-----AAQI-AELLERPDADLAGVGLGLATTRHEHRAAVVASTREEAVRGLREIAAG----AATADAVVEGVTE----VDGDLSAFLRSMATA-HVSGVDIRWDVAL---PGAAPFALPTYP

4qyrA2

0.18

0.16

0.86

0.61

dPPAS

-------APQAIVLSARDDRLRATAGRL-RDFLDRARRDGHAPDLADLAFTLQVGREAERRLGFVVGSDDVLGTLDRFFAGD----EPSGWHTGGIRR--GVRREAEQAPEVTRALHDGRLDRVTALGAPVAHTGERRA-------

(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=-2.01

Estimated TM-score = 0.47±0.15

Estimated RMSD = 9.1±4.6Å

Download Model 2

C-score=-3.67

Download Model 3

C-score=-3.68

Download Model 4

C-score=-2.57

Download Model 5

C-score=-3.84

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	4opeA	0.628	3.21	0.202	0.849
2	2qo3B	0.613	3.78	0.140	0.884
3	4tktA	0.605	3.63	0.180	0.856
4	4na1A	0.603	3.73	0.138	0.863
5	4z37A	0.602	3.77	0.123	0.870
6	5elpC	0.595	3.74	0.134	0.843
7	3tzwA	0.594	3.56	0.126	0.829
8	4kc5A3	0.594	3.80	0.133	0.849
9	4wkyA	0.590	3.76	0.111	0.863
10	5erbA	0.581	4.05	0.099	0.870

(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	0.09	5	4z90F	4LE	Rep, Mult	69,72
2	0.05	3	4f8hB	LMD	Rep, Mult	69,70,73
3	0.04	2	2gwnA	ZN	Rep, Mult	62,96,130
4	0.04	2	4z10C	RCO	Rep, Mult	75,76
5	0.04	2	1woqB	PO4	Rep, Mult	40,41,144,145
6	0.02	1	3k89A	GOL	Rep, Mult	103,104,105
7	0.02	1	2vc2B	180	Rep, Mult	49,50,51,133,134,135,136
8	0.02	1	2wse1	CLA	Rep, Mult	32,40
9	0.02	1	3sbmA	ACT	Rep, Mult	37,41,47,48
10	0.02	1	2o011	CLA	Rep, Mult	134,135
11	0.02	1	1esoA	ZN	Rep, Mult	107,119,130,135
12	0.02	1	1rmgA	MAN	Rep, Mult	120,121
13	0.02	1	1ybqA	ZN	Rep, Mult	96,119
14	0.02	1	3mjlB	2AI	Rep, Mult	96,107
15	0.02	1	2nqaA	III	Rep, Mult	79,80,81
16	0.02	1	1l5gB	UUU	Rep, Mult	10,12,14,58,60
17	0.02	1	3sqgD	M43	Rep, Mult	10,11,12,13,109,112
18	0.02	1	2qo3B	CER	Rep, Mult	53,127,131
19	0.02	1	1l5gB	III	Rep, Mult	54,55,56,58,60

	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	1e6vA	0.415	5.15	0.063	0.774	2.8.4.1	NA
2	0.060	3lw6A	0.416	4.71	0.090	0.719	2.4.1.133	NA
3	0.060	3g87A	0.436	4.69	0.065	0.781	2.3.1.39	NA
4	0.060	2vkzG	0.472	4.98	0.066	0.849	2.3.1.38,3.1.2.14	NA
5	0.060	1djgB	0.400	5.30	0.076	0.747	3.1.4.11	NA
6	0.060	2c2nA	0.448	4.95	0.092	0.815	2.3.1.39	NA
7	0.060	3ezoA	0.412	4.78	0.094	0.719	2.3.1.39	NA
8	0.060	2qj3B	0.467	4.72	0.094	0.815	2.3.1.39	NA
9	0.060	2vz8A	0.468	4.37	0.117	0.753	2.3.1.85	62
10	0.060	2g9xC	0.396	4.76	0.068	0.664	2.7.11.22,2.7.1.37	NA
11	0.060	2jfdA	0.374	5.62	0.067	0.753	2.3.1.85	130,131
12	0.060	3exeA	0.370	5.62	0.076	0.740	1.2.4.1	NA
13	0.060	2pffB	0.481	5.04	0.072	0.877	2.3.1.86	50,94
14	0.060	1cjyA	0.419	5.16	0.054	0.774	3.1.1.4,3.1.1.5	NA
15	0.060	2vz9B	0.470	4.34	0.117	0.753	2.3.1.85	NA
16	0.060	2h1yB	0.460	4.73	0.079	0.801	2.3.1.39	NA
17	0.060	1fhvA	0.415	4.98	0.046	0.712	4.2.1.113	NA
18	0.060	3jrqA	0.409	4.43	0.056	0.637	3.1.3.16	52,54
19	0.060	1zefA	0.418	5.06	0.048	0.726	3.1.3.1	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	0.07	0.634	3.17	0.20	0.85	4opeA	GO:0003824 GO:0008152 GO:0016874 GO:0031177
1	0.07	0.605	3.63	0.18	0.86	4tktA	GO:0003824 GO:0008152 GO:0031177
2	0.07	0.595	3.74	0.13	0.84	5elpC	GO:0003824 GO:0008152 GO:0031177
3	0.07	0.613	3.78	0.14	0.88	2qo3B	GO:0003824 GO:0008152 GO:0016491 GO:0016740 GO:0016746 GO:0017000 GO:0031177 GO:0033068 GO:0047879 GO:0048037 GO:0055114
4	0.07	0.603	3.73	0.14	0.86	4na1A	GO:0003824 GO:0005737 GO:0008152 GO:0016740 GO:0016746 GO:0016874 GO:0017000 GO:0031177
5	0.07	0.602	3.77	0.12	0.87	4z37A	GO:0003824 GO:0008152 GO:0031177
6	0.07	0.580	4.02	0.14	0.86	4qyrA	GO:0003824 GO:0008152 GO:0031177
7	0.07	0.594	3.80	0.13	0.85	4kc5A	GO:0003824 GO:0008152 GO:0031177
8	0.07	0.596	4.09	0.11	0.90	5erbB	GO:0003824 GO:0008152 GO:0031177
9	0.07	0.591	3.80	0.10	0.86	4wkyA	GO:0003824 GO:0008152 GO:0031177
10	0.07	0.564	4.10	0.13	0.85	4zdnA	GO:0003824 GO:0008152 GO:0031177
11	0.07	0.566	4.00	0.08	0.85	4mz0B	GO:0003824 GO:0008152 GO:0016740 GO:0031177 GO:0046872
12	0.07	0.583	3.82	0.13	0.84	5e5nB	GO:0003824 GO:0005737 GO:0008152 GO:0016491 GO:0016740 GO:0016746 GO:0017000 GO:0031177 GO:0055114
13	0.07	0.580	3.82	0.13	0.84	5e5nC	GO:0003824 GO:0005737 GO:0008152 GO:0016491 GO:0016740 GO:0016746 GO:0017000 GO:0031177 GO:0055114
14	0.07	0.562	3.17	0.12	0.77	5elpA	GO:0003824 GO:0008152 GO:0031177
15	0.06	0.384	5.08	0.06	0.70	3lrfA	GO:0003824 GO:0004315 GO:0008152 GO:0016740 GO:0016746
16	0.06	0.391	5.18	0.07	0.71	4b7vA	GO:0003824 GO:0006633 GO:0008152 GO:0016740 GO:0016746 GO:0016747 GO:0033817
17	0.06	0.392	5.20	0.07	0.71	4qavA	GO:0003824 GO:0006633 GO:0008152 GO:0016740 GO:0016746 GO:0016747 GO:0033817
18	0.06	0.391	4.97	0.06	0.69	4ls8A	GO:0003824 GO:0006629 GO:0006631 GO:0006633 GO:0008152 GO:0016740 GO:0016746 GO:0016747 GO:0033817

Consensus prediction of GO terms

Molecular Function	GO:0019842	GO:0033218	GO:0072341
GO-Score	0.59	0.59	0.59
Biological Processes	GO:0055114	GO:0033068
GO-Score	0.07	0.07
Cellular Component	GO:0005737
GO-Score	0.07

(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.