I-TASSER results

Input Sequence in FASTA format

>protein (63 residues)
MKTNPRYGPAFYSVMTVLFLALFVLNVCTHGSTLGLISTGGLAVLMGYIGYRGWSGKRHI
NRQ

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| MKTNPRYGPAFYSVMTVLFLALFVLNVCTHGSTLGLISTGGLAVLMGYIGYRGWSGKRHINRQ
Prediction	CCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEHCCCEEEEHCCEEEEHHHHHHCCCCC
Conf.Score	999986458899999999999999986678855666545874666565344444444344479
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| MKTNPRYGPAFYSVMTVLFLALFVLNVCTHGSTLGLISTGGLAVLMGYIGYRGWSGKRHINRQ
Prediction	865545333213323333223210020034332211133332120223333332235445778
	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

                   |                   |                   |

Sec.Str
Seq

CCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEHCCCEEEEHCCEEEEHHHHHHCCCCC
MKTNPRYGPAFYSVMTVLFLALFVLNVCTHGSTLGLISTGGLAVLMGYIGYRGWSGKRHINRQ

4pgrA

0.16

1.00

0.91

MUSTER

KKDLSFLWSFLLVAVLALAVVGIFNIFSPLNSAAMMYSVIGTIVFSLYILYDLNQIKHRHITE

1wazA

0.20

0.14

0.73

0.87

dPPAS

--------------TPVLVILLGVVGLSALTGYLDYVLLPALAIFIGLTIYAIQRKRQAD---

2l9uA

0.24

0.14

0.60

0.81

wdPPAS

GRT---HLTMALTVIAGLVVIFMMLGG----TFL------------------YWRGRRHHHHH

4jc95

0.39

0.25

0.65

0.82

wMUSTER

MIFDPRR------VFVAQGVFLFLLAVMIH---LILLSTPS------YN----WL---EISAA

4jc95

0.39

0.24

0.60

0.83

wPPAS

MIFDPR-------VFVAQGVFLFLLAVMIH-----LLSTPS------YN----WL---EISAA

1wazA

0.20

0.14

0.73

0.93

dPPAS2

--------------TPVLVILLGVVGLSALTGYLDYVLLPALAIFIGLTIYAIQRKRQAD---

1wazA

0.20

0.14

0.73

1.00

PPAS

--------------TPVLVILLGVVGLSALTGYLDYVLLPALAIFIGLTIYAIQRKRQAD---

3vseA1

0.13

1.00

0.85

Env-PPAS

MKINKGKETKYFNGYPLIEEEDIYQDHLKEGDIFQIVTDKSQYVATAYHKGLGWVLTYDKAQE

3madA

0.18

0.17

0.95

0.86

MUSTER

SQSNPLWTAKFEAEVVAMTAHML--GDAAGGTVCGTVTSGG-SLLLAMKTYRDWARATKGITA

4cjdA1

0.12

0.11

0.90

0.82

dPPAS

---PPSTDEIAKAALVGVYNNTQDINGFKVGDTIYDIENG---QPKGRPATEDDVKADDFGGL

(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=-2.53

Estimated TM-score = 0.42±0.14

Estimated RMSD = 8.3±4.5Å

Download Model 2

C-score=-3.06

Download Model 3

C-score=-3.15

Download Model 4

C-score=-4.80

Download Model 5

C-score=-3.18

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	4k1cA	0.597	2.55	0.049	0.873
2	5cwqA	0.587	2.83	0.148	0.857
3	4p3eC	0.583	2.43	0.077	0.809
4	2nq2A	0.583	3.22	0.081	0.921
5	1gntA	0.579	3.10	0.100	0.889
6	1oa0A	0.578	3.39	0.063	0.952
7	3dpgA2	0.577	3.42	0.097	0.889
8	3eo2A	0.577	2.83	0.113	0.825
9	1fx7A	0.574	3.05	0.033	0.841
10	4p3gA	0.574	2.87	0.074	0.841

(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	0.13	13	2q7mF	2CS	Rep, Mult	15,17,18,19,21
2	0.10	11	4xk8L	III	Rep, Mult	24,27,28
3	0.08	8	1s5lT	CLA	Rep, Mult	20,23
4	0.06	6	5e7cH	CLA	Rep, Mult	11,14,15,18
5	0.04	4	1sqpE	PLX	Rep, Mult	7,10
6	0.03	3	3q4gA	CA	Rep, Mult	39,41
7	0.02	2	2dyrQ	PGV	Rep, Mult	10,13
8	0.02	2	5d56B	78M	Rep, Mult	13,16,20
9	0.01	1	3f1f8	MG	Rep, Mult	56,57,58,59,60
10	0.01	1	1cnoA	HEC	Rep, Mult	48,58
11	0.01	1	1c0wB	QNA	Rep, Mult	8,11,52
12	0.01	1	3ff6A	RCP	Rep, Mult	39,42,45
13	0.01	1	1px7B	CA	Rep, Mult	2,6
14	0.01	1	3nwyB	GTP	Rep, Mult	32,40,41,43,44,45,52,59,62
15	0.01	1	2k3mA	MTN	Rep, Mult	28,58
16	0.01	1	2x6pB	ZN	Rep, Mult	26,30

	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	3dojA	0.540	3.30	0.048	0.841	1.1.1.79	NA
2	0.060	4matA	0.548	3.50	0.032	0.873	3.4.11.18	NA
3	0.060	3l24A	0.555	3.07	0.067	0.841	3.1.8.2,3.4.13.9,3.1.8.1	NA
4	0.060	1wy2A	0.552	3.16	0.018	0.841	3.4.13.9	NA
5	0.060	1q2rA	0.540	2.83	0.080	0.778	2.4.2.29	NA
6	0.060	2b3lA	0.554	3.38	0.017	0.857	3.4.11.18	NA
7	0.060	1y1nA	0.534	3.31	0.082	0.889	3.4.11.18	27
8	0.060	1y5xD	0.544	3.11	0.077	0.794	2.4.2.29	NA
9	0.060	3dpgA	0.577	3.42	0.097	0.889	3.1.21.4	NA
10	0.060	1cevA	0.545	3.30	0.127	0.873	3.5.3.1	NA
11	0.060	2aebA	0.555	3.43	0.107	0.889	3.5.3.1	NA
12	0.060	1chmA	0.557	2.63	0.017	0.825	3.5.3.3	NA
13	0.060	1myrA	0.540	2.32	0.083	0.762	3.2.1.147	35,44
14	0.060	3gzkA	0.543	3.55	0.016	0.825	3.2.1.4	NA
15	0.060	3bkkA	0.568	2.42	0.060	0.794	3.4.15.1	51
16	0.060	2jifA	0.541	3.00	0.056	0.809	1.3.99.-	NA
17	0.060	1pq3A	0.542	3.33	0.071	0.873	3.5.3.1	NA
18	0.060	3bllA	0.536	3.05	0.078	0.809	2.4.2.29	NA
19	0.060	1pv9A	0.539	3.00	0.058	0.809	3.4.13.9	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	0.597	2.55	0.05	0.87	4k1cA	GO:0000324 GO:0000329 GO:0005773 GO:0005774 GO:0006810 GO:0006811 GO:0006812 GO:0006816 GO:0006828 GO:0006874 GO:0008324 GO:0015085 GO:0015369 GO:0015386 GO:0016020 GO:0016021 GO:0046872 GO:0055085 GO:0070588 GO:0071805 GO:0098655
1	0.07	0.574	3.17	0.10	0.89	1e1dA	GO:0003824 GO:0005737 GO:0016491 GO:0016661 GO:0046872 GO:0050418 GO:0051536 GO:0051539 GO:0055114
2	0.07	0.580	2.78	0.07	0.84	4p3gA	GO:0003723 GO:0005047 GO:0005737 GO:0005786 GO:0006614 GO:0008312 GO:0030529 GO:0030942
3	0.07	0.574	2.99	0.07	0.89	4g1uA	GO:0005215 GO:0005886 GO:0006810 GO:0006811 GO:0016020 GO:0016021 GO:0055072
4	0.07	0.581	3.39	0.06	0.95	1gnlA	GO:0003824 GO:0005737 GO:0016491 GO:0016661 GO:0046872 GO:0050418 GO:0051536 GO:0051539 GO:0055114
5	0.07	0.497	2.98	0.05	0.81	4dblA	GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0015235 GO:0015420 GO:0015889 GO:0016020 GO:0016021 GO:0035461 GO:0043190
6	0.07	0.564	2.53	0.08	0.81	4p3fB	GO:0003723 GO:0005047 GO:0005634 GO:0005730 GO:0005737 GO:0005783 GO:0005786 GO:0005829 GO:0005840 GO:0005925 GO:0006614 GO:0008312 GO:0030529 GO:0030942 GO:0042493 GO:0044822 GO:0045047
7	0.07	0.564	3.13	0.07	0.89	4kjrA	GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006812 GO:0006816 GO:0008324 GO:0015297 GO:0015369 GO:0016020 GO:0016021 GO:0055085 GO:0070588
8	0.07	0.577	3.42	0.10	0.89	3dpgA	GO:0003677 GO:0009036 GO:0009307 GO:0046872
9	0.07	0.437	4.09	0.09	0.84	5euhA	GO:0016020 GO:0016021
10	0.07	0.482	3.20	0.05	0.75	1cfrA	GO:0003677 GO:0004518 GO:0004519 GO:0009036 GO:0009307 GO:0016787 GO:0046872 GO:0090305
11	0.07	0.499	3.23	0.06	0.73	1knvB	GO:0003677 GO:0004519 GO:0009036 GO:0009307 GO:0090305
12	0.07	0.423	3.95	0.07	0.78	4hz5A	GO:0000287 GO:0003677 GO:0003918 GO:0005524 GO:0005694 GO:0006265 GO:0007059 GO:0016853 GO:0046872
13	0.06	0.429	3.32	0.04	0.76	3j6b1	GO:0003735 GO:0005739 GO:0005762 GO:0005840 GO:0030529 GO:0032543
14	0.06	0.376	3.88	0.05	0.73	4o50A	GO:0003824 GO:0004807 GO:0005829 GO:0006094 GO:0006096 GO:0006098 GO:0008152 GO:0016853 GO:0019563 GO:0046166
15	0.06	0.583	3.22	0.08	0.92	2nq2A	GO:0005215 GO:0005886 GO:0006810 GO:0016020 GO:0016021
16	0.06	0.331	2.46	0.05	0.44	4b0aA	GO:0000126 GO:0000500 GO:0000979 GO:0001016 GO:0001026 GO:0001075 GO:0001102 GO:0001179 GO:0001186 GO:0003677 GO:0003682 GO:0004402 GO:0005634 GO:0005654 GO:0005669 GO:0005829 GO:0006351 GO:0006352 GO:0006355 GO:0006356 GO:0006359 GO:0006366 GO:0006383 GO:0006385 GO:0008301 GO:0016568 GO:0016573 GO:0016740 GO:0016746 GO:0017025 GO:0032947 GO:0042790 GO:0051123 GO:0070860 GO:0070893 GO:0070898
17	0.06	0.438	3.74	0.00	0.73	1zp3B	GO:0004489 GO:0005829 GO:0006555 GO:0006730 GO:0008652 GO:0009086 GO:0016491 GO:0035999 GO:0046654 GO:0051289 GO:0055114 GO:0071949
18	0.06	0.372	3.89	0.10	0.68	1jj7A	GO:0000166 GO:0002250 GO:0002376 GO:0002474 GO:0002481 GO:0002485 GO:0002489 GO:0002591 GO:0005524 GO:0005739 GO:0005783 GO:0005789 GO:0006810 GO:0006952 GO:0015031 GO:0015197 GO:0015440 GO:0015833 GO:0016020 GO:0016021 GO:0016032 GO:0016887 GO:0019060 GO:0019885 GO:0023029 GO:0030176 GO:0042270 GO:0042287 GO:0042288 GO:0042605 GO:0042626 GO:0042803 GO:0042825 GO:0043231 GO:0043531 GO:0043657 GO:0046967 GO:0046978 GO:0046979 GO:0046980 GO:0046982 GO:0055085

Consensus prediction of GO terms

Molecular Function	GO:0043169
GO-Score	0.37
Biological Processes	GO:0055114	GO:0006874	GO:0006614	GO:0055072	GO:0006828	GO:0070588	GO:0071805
GO-Score	0.13	0.07	0.07	0.07	0.07	0.07	0.07
Cellular Component	GO:0044424
GO-Score	0.37

(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.

I-TASSER results for job id Rv2806

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

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