I-TASSER results

I-TASSER results for job id Rv2375

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

Input Sequence in FASTA format

>protein (105 residues)
MIFKGVREGKPYPEHGLSYRDWSQIPPQQIRLDELVTTTTVLALDRLLSEDSTFYGDLFP
HAVKWRGTTYLEDGLHRAVRAALRNRTVLHARVFDMDASPGGRRS

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MIFKGVREGKPYPEHGLSYRDWSQIPPQQIRLDELVTTTTVLALDRLLSEDSTFYGDLFPHAVKWRGTTYLEDGLHRAVRAALRNRTVLHARVFDMDASPGGRRS
Prediction	CCCCCCCCCCCCCCCCCCHHHHHCCCCCCEEHHHHEEHHHHHHHHHHHHHCCCCHHHHHCEEEEHCCEEEEEHCHHHHHHHHHHHCCEEEEEEEEHCCCCCCCCC
Conf.Score	977544679999988999778656999644345534455577899998756654444444468885879874448999999998596789999865578887789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MIFKGVREGKPYPEHGLSYRDWSQIPPQQIRLDELVTTTTVLALDRLLSEDSTFYGDLFPHAVKWRGTTYLEDGLHRAVRAALRNRTVLHARVFDMDASPGGRRS
Prediction	631442576432363424464037134441415413434431404401464232223011100425341213320230033115634212020131434454668
	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

CCCCCCCCCCCCCCCCCCHHHHHCCCCCCEEHHHHEEHHHHHHHHHHHHHCCCCHHHHHCEEEEHCCEEEEEHCHHHHHHHHHHHCCEEEEEEEEHCCCCCCCCC
MIFKGVREGKPYPEHGLSYRDWSQIPPQQIRLDELVTTTTVLALDRLLSEDSTFYGDLFPHAVKWRGTTYLEDGLHRAVRAALRNRTVLHARVFDMDASPGGRRS

2o3dA

0.18

0.14

0.80

1.10

dPPAS2

----MAPRGRYGP------------PSRRVVVSGLPPSGSWQDLKDHMRE----AGDVYADVYR-DGTGVVEFVRKEDMTYAVRKHETAYIRVKVDGPRSPSYGR

4id9A1

0.39

0.13

0.34

1.07

dPPAS2

--------------------------------------------------------------------MILVTGVGRAVVAALRTQGR-TVRGFDLRPSGTGGEE

2o90A

0.18

0.17

0.93

0.74

MUSTER

MVF--IEQLSVITTIGVY--DWEQTIEQKLVFDEMAWDNRKAAKS---VADCLSYADIAETVVSHEGARFVERVAEEVAELLLARFNSVRIKLSKPGAVARAANV

1wf1A

0.13

0.11

0.87

0.92

dPPAS

LKLQASNVTNKNDPKSINSRVFGNLNTALV---------KKSDVETIFSK----YGRV-AGCSVHKGYAFVQYSNERHARAAVLGENVLAGQTLDINMAGEPKPD

1wf1A

0.14

0.11

0.81

0.74

wdPPAS

LKLQASNVTNKNDPKSINSR--GNLNTALV---------KKSDVETIFSK----YGRV--GCSVHKGYAFVQ---ERHARAAVLGENVLAGQTLDINMAGEPKPD

4f0lA

0.17

0.16

0.94

0.75

wMUSTER

YGMAGLAERRGPSAD--SFWSWREMYKFALTMPEQAEAVALRLYVDMLEAGFTRVGEFYLHH-DCDGTPYMADRIAAAATTA---GLTLLPVFYAHSGFGGAAAN

2o90A

0.18

0.15

0.86

0.56

wPPAS

MVF--IEQ---ITTIGV---DWEQTIEQKLVFD--IE---AWDNRKAAKSDDCLYADIAETVVSHEGARFVER-AEEVAELLLARFNSVRIKLSKPGAVARAA-N

4mjsA

0.34

0.21

0.62

1.00

dPPAS2

-------------------------PHMRVRLDILITSVDTTTFQDLCEE----VRDMCPLTLKWVD----SEGLEEAFRLACQGREVLIIHVFPSIP-------

2o90A

0.17

0.16

0.94

0.76

PPAS

MVF--IEQLSVITTIGVY--DWEQTIEQKLVFDEMAWDNRKAAKSDDVAD--CLYADIAETVVSHEGARFVERVAEEVAELLLARFNSVRIKLSKPGAVARAANV

2o90A

0.17

0.16

0.94

0.71

Env-PPAS

MVF--IEQLSVITTIGVY--DWEQTIEQKLVFDEMAWDNRKAAKSDDVAD--CLYADIAETVVSHEGARFVERVAEEVAELLLARFNSVRIKLSKPGAVARAANV

(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=-2.50

Estimated TM-score = 0.42±0.14

Estimated RMSD = 9.5±4.6Å

Download Model 2

C-score=-3.15

Download Model 3

C-score=-4.83

Download Model 4

C-score=-3.74

Download Model 5

C-score=-2.66

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	2ebfX3	0.489	3.87	0.054	0.781
2	2fknB1	0.484	4.17	0.071	0.848
3	1hr6A	0.483	4.46	0.098	0.857
4	4z24A	0.476	4.32	0.060	0.848
5	1kb9B2	0.475	4.22	0.068	0.819
6	1uwkA	0.469	4.50	0.053	0.867
7	2g47B3	0.468	4.08	0.044	0.771
8	3t2bA	0.465	4.38	0.052	0.867
9	2exuA	0.464	3.66	0.029	0.724
10	3h1kB	0.464	4.15	0.078	0.800

(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	1gzmA	C8E	Rep, Mult	44,47
2	0.06	3	3tuvA	ATP	Rep, Mult	49,60,61,78,81
3	0.06	3	3srbA	28S	Rep, Mult	47,48
4	0.06	3	3h44B	III	Rep, Mult	45,50,61,62,63,65,66
5	0.04	2	3mkvA	ZN	Rep, Mult	10,61,90
6	0.04	2	3i8hS	MG	Rep, Mult	37,39
7	0.04	2	2a69F	MG	Rep, Mult	83,84
8	0.04	2	1ajcA	ZN	Rep, Mult	57,61,90,92
9	0.02	1	3e4aA	III	Rep, Mult	45,61,62
10	0.02	1	3zk1E	DMU	Rep, Mult	38,42
11	0.02	1	3sxnD	COA	Rep, Mult	57,58
12	0.02	1	3r4iB	CA	Rep, Mult	72,95
13	0.02	1	1kyzC	SAH	Rep, Mult	16,33,35,41,57,58,59,63,64,65,66,70

	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	1uwkA	0.469	4.50	0.053	0.867	4.2.1.49	NA
2	0.060	1elsA	0.430	4.75	0.063	0.848	4.2.1.11	NA
3	0.060	1hr7A	0.481	4.47	0.098	0.857	3.4.24.64	70
4	0.060	2vvmA	0.442	4.50	0.063	0.819	1.4.3.4	NA
5	0.060	2qv6D	0.442	4.25	0.073	0.781	3.5.4.29	95
6	0.060	1hr6A	0.483	4.46	0.098	0.857	3.4.24.64	45
7	0.060	1ezvB	0.472	4.29	0.082	0.829	1.10.2.2	NA
8	0.060	1iriA	0.466	3.85	0.067	0.752	5.3.1.9	NA
9	0.060	1q2lA	0.440	4.31	0.061	0.771	3.4.24.55	NA
10	0.060	1o5wC	0.447	4.51	0.010	0.829	1.4.3.4	NA
11	0.060	2hfuA	0.443	4.17	0.032	0.762	2.7.1.36	NA
12	0.060	3h1kB	0.464	4.15	0.078	0.800	1.10.2.2	NA
13	0.060	3cxhM	0.481	4.17	0.063	0.829	1.10.2.2	NA
14	0.060	2ew9A	0.445	3.60	0.151	0.695	3.6.3.4	48,71
15	0.060	2pa6B	0.442	4.70	0.030	0.848	4.2.1.11	NA
16	0.060	1x87A	0.446	4.71	0.030	0.857	4.2.1.49	93
17	0.060	2gmhA	0.441	4.65	0.040	0.838	1.5.5.1	7,78
18	0.060	1ebgA	0.443	4.74	0.063	0.848	4.2.1.11	NA
19	0.060	1u7lA	0.448	4.44	0.100	0.819	3.6.3.14	71

(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	0.11	0.313	4.37	0.03	0.55	1be3A	GO:0003824 GO:0004222 GO:0005739 GO:0005743 GO:0005750 GO:0006122 GO:0008270 GO:0009060 GO:0016020 GO:0016485 GO:0046872 GO:0055114 GO:0070469
1	0.07	0.469	4.50	0.05	0.87	1uwkA	GO:0005737 GO:0006547 GO:0006548 GO:0016153 GO:0016829 GO:0019556 GO:0019557
2	0.07	0.440	4.32	0.07	0.78	1sqbB	GO:0003824 GO:0004222 GO:0005654 GO:0005739 GO:0005743 GO:0005750 GO:0006122 GO:0006508 GO:0008270 GO:0009060 GO:0016020 GO:0016485 GO:0043209 GO:0046872 GO:0055114 GO:0070062 GO:0070469
3	0.06	0.389	4.74	0.03	0.77	3l70A	GO:0003824 GO:0005739 GO:0005743 GO:0006122 GO:0008121 GO:0031625 GO:0043209 GO:0046872 GO:1902600
4	0.06	0.484	4.10	0.06	0.82	3cx5B	GO:0003824 GO:0004222 GO:0005739 GO:0005743 GO:0005750 GO:0006122 GO:0006508 GO:0008121 GO:0009060 GO:0016020 GO:0030061 GO:0046872 GO:0055114 GO:0070469 GO:1902600
5	0.06	0.361	5.21	0.09	0.78	1hr6D	GO:0003824 GO:0004222 GO:0005739 GO:0005750 GO:0005759 GO:0006122 GO:0006508 GO:0006626 GO:0006627 GO:0008233 GO:0008237 GO:0008270 GO:0009060 GO:0016787 GO:0017087 GO:0046872
6	0.06	0.355	5.40	0.06	0.79	3amiA	GO:0003824 GO:0046872
7	0.06	0.449	4.23	0.10	0.75	3eoqB	GO:0003824 GO:0006508 GO:0008233 GO:0046872
8	0.06	0.375	4.52	0.06	0.70	2dt9A	GO:0000166 GO:0004072 GO:0005524 GO:0008152 GO:0008652 GO:0009085 GO:0009088 GO:0009089 GO:0016301 GO:0016310 GO:0016597 GO:0016740 GO:0019877
9	0.06	0.424	4.42	0.05	0.79	3cx5A	GO:0003824 GO:0004222 GO:0005739 GO:0005743 GO:0005750 GO:0006122 GO:0008121 GO:0008270 GO:0009060 GO:0016020 GO:0016485 GO:0046872 GO:0055114 GO:0070469 GO:1902600
10	0.06	0.483	4.46	0.10	0.86	1hr6A	GO:0003824 GO:0004222 GO:0005739 GO:0005743 GO:0005759 GO:0006508 GO:0006626 GO:0006627 GO:0008233 GO:0008237 GO:0008270 GO:0016787 GO:0017087 GO:0046872
11	0.06	0.403	4.76	0.03	0.78	3amjB	GO:0003824 GO:0046872
12	0.06	0.387	4.22	0.06	0.68	1kkjA	GO:0003824 GO:0004372 GO:0005737 GO:0006544 GO:0006545 GO:0006563 GO:0006730 GO:0008652 GO:0016740 GO:0019264 GO:0030170 GO:0035999
13	0.06	0.331	5.05	0.09	0.70	1aohB	GO:0000272 GO:0004553 GO:0005576 GO:0005975 GO:0030245 GO:0030246 GO:0030248 GO:0071555
14	0.06	0.447	4.13	0.04	0.82	3hdiA	GO:0003824 GO:0004222 GO:0006508 GO:0008233 GO:0046872
15	0.06	0.350	4.64	0.07	0.65	2ohhA	GO:0009055 GO:0010181 GO:0016491 GO:0046872 GO:0055114
16	0.06	0.484	4.17	0.07	0.85	2fknB	GO:0005737 GO:0006547 GO:0006548 GO:0016153 GO:0016829 GO:0019556 GO:0019557
17	0.06	0.482	3.83	0.04	0.75	2ebfX	GO:0001907 GO:0004620 GO:0005543 GO:0005576 GO:0005737 GO:0016020 GO:0016021 GO:0020002 GO:0033644 GO:1990216
18	0.06	0.335	5.27	0.02	0.72	2fskB	GO:0000166 GO:0005524

Consensus prediction of GO terms

Molecular Function	GO:0008237	GO:0004175	GO:0046914
GO-Score	0.45	0.45	0.34
Biological Processes	GO:0042775	GO:0006508	GO:0051604
GO-Score	0.55	0.34	0.34
Cellular Component	GO:0005746	GO:0045275	GO:0098800
GO-Score	0.45	0.45	0.45

(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.