I-TASSER results

Input Sequence in FASTA format

>protein (63 residues)
MRKSKKTRDQLLRELRNAYEGGASIRNLAATTGRSYGSIHSMLRESGTTMRGRGGPNRRS
RPR

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| MRKSKKTRDQLLRELRNAYEGGASIRNLAATTGRSYGSIHSMLRESGTTMRGRGGPNRRSRPR
Prediction	CCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHCCCHCCCCCCCCCCCCC
Conf.Score	998878999999999999985977899999979957899999999899555689998888889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| MRKSKKTRDQLLRELRNAYEGGASIRNLAATTGRSYGSIHSMLRESGTTMRGRGGPNRRSRPR
Prediction	763457425511540374166343134106534432320241045362513743446556578
	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

CCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHCCCHCCCCCCCCCCCCC
MRKSKKTRDQLLRELRNAYEGGASIRNLAATTGRSYGSIHSMLRESGTTMRGRGGPNRRSRPR

2m8eA

0.18

0.16

0.87

1.10

MUSTER

MGKSKEISQDLRKKIVDLHKSGSSLGAISKRLKVPRSSVQTIVRKY-----KHHGTTQHH---

2r0qC2

0.11

0.08

0.75

1.00

dPPAS

PNAKDPQKRVIYHRVVEMLEEGQAISKIAKEVNITRQTVYRIKHDNG----------------

4a0xA1

0.13

0.10

0.71

1.00

wdPPAS

LKLKKDKRREAIRQQIDS----ITDHELSDLFQVSIQTIRLDRTYLNIP--------------

2lvsA

0.24

0.19

0.81

0.90

wMUSTER

YRQHRRLTEEELATIRELYLKGATVYEIARQLGRPESTIYYALKKLGLKLE------------

5fmfV2

0.19

0.17

0.90

1.00

wPPAS

--SIRMPKKEILDYLFKLFDE--SLKGLKERTRQPEAHLKECLDKVAT-LVKKG-PYAFKRPE

2r0qC2

0.11

0.08

0.75

1.32

dPPAS2

PNAKDPQKRVIYHRVVEMLEEGQAISKIAKEVNITRQTVYRIKHDNG----------------

3eetA1

0.21

0.97

1.11

PPAS

-YFEQPAYLRVAGDLRKKIVDGSSQARIREEYGVSDTVALEARKVLGL-VEGRSGTYVRERPV

4p96A1

0.16

1.00

1.26

Env-PPAS

VIKAKSPAGFAEKYIIESIWNGRAERELSELIGVTLREVLQRLARDGWLTIQHGKPTKNQFME

3eetA1

0.22

0.21

0.95

1.07

MUSTER

FEQP--AYLRVAGDLRKKIVDGSSQARIREEYGVSDTVALEARKVLGL-VEGRSGTYVRERPV

5fmfV2

0.11

0.97

0.99

dPPAS

--SIRMPKKEILDYLFKLFDEYDSLKGLKERTRQPEAHLKECLDKVATLVKKGPYAFKYTLRP

(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=-1.22

Estimated TM-score = 0.56±0.15

Estimated RMSD = 5.5±3.5Å

Download Model 2

C-score=-3.06

Download Model 3

C-score=-3.30

Download Model 4

C-score=-2.50

Download Model 5

C-score=-4.23

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	1j5yA	0.691	2.52	0.186	0.936
2	4rgwA	0.689	2.36	0.148	0.952
3	3iuoB	0.685	2.97	0.049	0.952
4	4d0pA2	0.683	2.59	0.119	0.936
5	1fokA4	0.682	2.66	0.048	0.952
6	5i0pA	0.679	2.77	0.131	0.968
7	4d10B2	0.677	2.82	0.079	0.952
8	4a0xA	0.675	2.27	0.085	0.825
9	3nfhA	0.660	2.43	0.148	0.936
10	3f8fA	0.658	2.69	0.111	0.968

(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	0.24	25	4on0A	NUC	Rep, Mult	9,12,35,37,38,41,42,45
2	0.07	8	2e1cA	NUC	Rep, Mult	24,25,26,36,37,40
3	0.06	7	3dk4A	GSH	Rep, Mult	15,18,19
4	0.04	5	2h27A	NUC	Rep, Mult	19,24,25,40,44,45,47
5	0.03	3	3foeA	NUC	Rep, Mult	11,32,34,35,38
6	0.03	4	2ve9B	NUC	Rep, Mult	24,25,26,36
7	0.03	3	1zt9A	TRP	Rep, Mult	12,15,38,42,47
8	0.01	1	3bdnB	NUC	Rep, Mult	34,35,37,51,52,53,54,57
9	0.01	1	1smyF	MG	Rep, Mult	51,55
10	0.01	1	2xquA	CVM	Rep, Mult	8,12
11	0.01	1	3v2cM	MG	Rep, Mult	53,54
12	0.01	1	3x01A	AMP	Rep, Mult	10,14
13	0.01	1	5gm1A	SAH	Rep, Mult	19,20

	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	2ewnA	0.616	2.38	0.164	0.857	6.3.4.15	NA
2	0.060	2ip2A	0.566	2.86	0.190	0.857	2.1.1.-	NA
3	0.060	3dbmA	0.441	3.64	0.083	0.746	4.2.1.92	NA
4	0.060	3hxxA	0.566	2.54	0.115	0.809	6.1.1.7	26
5	0.060	1l3sA	0.570	3.16	0.095	0.857	2.7.7.7	NA
6	0.060	2q2eA	0.581	3.32	0.161	0.936	5.99.1.3	NA
7	0.060	1mj9A	0.633	2.92	0.095	0.984	2.3.1.48	10
8	0.060	2wuzA	0.509	3.01	0.037	0.841	1.14.13.70	NA
9	0.060	3l4dB	0.497	3.00	0.033	0.825	1.14.13.70	NA
10	0.060	1d8yA	0.589	2.69	0.075	0.794	2.7.7.7	14
11	0.060	2gaiA	0.562	3.08	0.067	0.952	5.99.1.2	NA
12	0.060	1cyfA	0.566	3.81	0.063	0.952	1.11.1.5	NA
13	0.060	1leaA	0.592	2.45	0.102	0.873	3.4.21.88	14,26,29
14	0.060	3ilwA	0.575	3.54	0.129	0.968	5.99.1.3	NA
15	0.060	3c46B	0.582	2.87	0.089	0.809	2.7.7.6	17
16	0.060	2zo4A	0.643	2.63	0.136	0.936	3.-.-.-	NA
17	0.060	2e18B	0.579	2.48	0.115	0.746	6.3.1.5	16,22,59
18	0.060	2rc4A	0.558	2.99	0.035	0.905	2.3.1.48,	NA
19	0.060	3k9fA	0.619	3.29	0.113	0.968	5.99.1.-	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	0.21	0.582	2.18	0.10	0.73	1fseB	GO:0003677 GO:0006351 GO:0006355
1	0.21	0.560	3.25	0.10	0.98	5k1yB	GO:0003700 GO:0006355
2	0.14	0.706	2.31	0.15	0.94	1j5yA	GO:0003677 GO:0006351 GO:0006355 GO:0036094 GO:0046872
3	0.11	0.689	2.36	0.15	0.95	5furG	GO:0000166 GO:0002039 GO:0003677 GO:0003713 GO:0004402 GO:0004674 GO:0005524 GO:0005634 GO:0005654 GO:0005669 GO:0006351 GO:0006352 GO:0006355 GO:0006366 GO:0006367 GO:0006368 GO:0006974 GO:0007049 GO:0008134 GO:0016032 GO:0016301 GO:0016310 GO:0016573 GO:0016740 GO:0016746 GO:0017025 GO:0018105 GO:0018107 GO:0032436 GO:0043565 GO:0044212 GO:0045944 GO:0046777 GO:0051123 GO:0060261 GO:0070577 GO:0071339 GO:1901796
4	0.10	0.704	2.88	0.05	0.97	3iuoB	GO:0000166 GO:0003676 GO:0003824 GO:0004003 GO:0004386 GO:0005524 GO:0005622 GO:0006260 GO:0006281 GO:0006310 GO:0008026 GO:0009432 GO:0032508 GO:0043140 GO:0044237
5	0.09	0.681	2.72	0.05	0.95	1fokA	GO:0003677 GO:0004518 GO:0004519 GO:0004536 GO:0009036 GO:0009307 GO:0016787 GO:0090305
6	0.08	0.630	2.95	0.10	0.92	1ufmA	GO:0000338 GO:0005634 GO:0005654 GO:0005737 GO:0005829 GO:0008021 GO:0008180 GO:0010388 GO:0019784 GO:0030054 GO:0031410 GO:0045202 GO:0070062
7	0.08	0.633	2.96	0.08	0.97	4d10C	GO:0000715 GO:0001701 GO:0005634 GO:0005654 GO:0005737 GO:0006283 GO:0006511 GO:0007165 GO:0008180 GO:0009416 GO:0010388
8	0.07	0.575	3.22	0.08	0.95	3txmA	GO:0000502 GO:0005838 GO:0005875 GO:0008541 GO:0043161
9	0.07	0.580	2.51	0.05	0.86	4pdxA	GO:0016787 GO:0018741 GO:0030288 GO:0046983
10	0.07	0.582	3.19	0.08	0.95	3jcoP	GO:0000502 GO:0006511 GO:0008180 GO:0008541 GO:0010388 GO:0031595 GO:0034515 GO:0043161
11	0.07	0.531	2.35	0.19	0.73	2l4aA	GO:0003677 GO:0003700 GO:0005622 GO:0005829 GO:0006351 GO:0006355 GO:0009098 GO:0042802 GO:0043201 GO:0043565
12	0.07	0.572	2.62	0.12	0.90	4oy2A	GO:0001075 GO:0003682 GO:0004402 GO:0005634 GO:0005669 GO:0005829 GO:0006351 GO:0006355 GO:0006366 GO:0016568 GO:0016573 GO:0016740 GO:0016746 GO:0017025 GO:0032947 GO:0051123
13	0.07	0.630	2.88	0.10	0.97	3jckF	GO:0000502 GO:0005198 GO:0005634 GO:0005829 GO:0006511 GO:0008541 GO:0034515 GO:0043248
14	0.07	0.538	3.32	0.05	0.90	1q1hA	GO:0003677 GO:0006351 GO:0006352 GO:0006355 GO:0006367 GO:0043565
15	0.07	0.580	2.98	0.07	0.94	4d10D	GO:0000338 GO:0000715 GO:0005634 GO:0005654 GO:0005737 GO:0005829 GO:0006283 GO:0008021 GO:0008180 GO:0010388 GO:0019784 GO:0030054 GO:0031410 GO:0045202 GO:0070062
16	0.07	0.515	3.40	0.06	0.94	4rb3C	GO:0003677 GO:0003700 GO:0006355 GO:0046872
17	0.07	0.418	3.15	0.04	0.73	3hjzA	GO:0003824 GO:0004801 GO:0005737 GO:0005975 GO:0006098 GO:0016740
18	0.07	0.433	4.06	0.07	0.79	4r0vA	GO:0016491 GO:0046872 GO:0051536 GO:0051539 GO:0055114
19	0.07	0.449	3.39	0.05	0.81	4flbA	GO:0005654 GO:0016591 GO:0042795
20	0.07	0.433	2.91	0.06	0.67	4ijcA	GO:0005737 GO:0005829 GO:0016491 GO:0044262 GO:0045290 GO:0055114
21	0.06	0.422	3.49	0.05	0.83	4wvyA	GO:0000166 GO:0003678 GO:0004386 GO:0005524 GO:0005634 GO:0006281 GO:0006351 GO:0006355 GO:0006974 GO:0016568 GO:0016787 GO:0032508 GO:0043141

Consensus prediction of GO terms

Molecular Function	GO:0001071	GO:0003677	GO:0032550	GO:0035639	GO:0032559
GO-Score	0.41	0.40	0.40	0.40	0.40
Biological Processes	GO:0006355
GO-Score	0.52
Cellular Component	GO:0071339	GO:0005669
GO-Score	0.11	0.11

(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 Rv1473A

[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]