I-TASSER results

Input Sequence in FASTA format

>protein (53 residues)
MCTMPKLWRAFMAGRPLGSTFTPRQPTGAAPNHVRALDDSIDPSSAPAARAAL

Predicted Secondary Structure

Sequence	20 40 \| \| MCTMPKLWRAFMAGRPLGSTFTPRQPTGAAPNHVRALDDSIDPSSAPAARAAL
Prediction	CCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCHHHHHHHC
Conf.Score	99858999999979999988888898999874443444689987558988879
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 \| \| MCTMPKLWRAFMAGRPLGSTFTPRQPTGAAPNHVRALDDSIDPSSAPAARAAL
Prediction	74534413412344443654244544444346314324551547524445458
	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

                   |                   |

Sec.Str
Seq

CCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCHHHHHHHC
MCTMPKLWRAFMAGRPLGSTFTPRQPTGAAPNHVRALDDSIDPSSAPAARAAL

1z9iA

0.20

0.17

0.83

0.88

MUSTER

HIVRKRTLRRLLQE---RELVEPLTPSGEAPNLLRILKE------TEFKKIKV

2kkeA

0.29

0.23

0.79

0.82

dPPAS

-----------MVGRRPGGGLKDTKPVVVRPDEIEALKSRVPANSAYIRRIIL

2kkeA

0.29

0.23

0.79

0.89

wdPPAS

-----------MVGRRPGGGLKDTKPVVVRPDEIEALKSRVPANSAYIRRIIL

4b29A

0.22

0.21

0.94

0.78

wMUSTER

WHEALPEFRAFAT--PEDLRWADRPAH-ALPDHLTRDPGHASDQSQPLRDALV

2kkeA

0.32

0.25

0.77

0.76

wPPAS

-----------MVGRRPGGGLKDTKPVVVRPDEIEALKSRV-PASAYIRRIIL

2kkeA

0.32

0.25

0.77

0.86

dPPAS2

-----------MVGRRPGGGLKDTKPVVVRPDEIEALKSRV-PASAYIRRIIL

2kkeA

0.32

0.25

0.77

0.89

PPAS

-----------MVGRRPGGGLKDTKPVVVRPDEIEALKSRV-PASAYIRRIIL

1yr1A1

0.28

0.21

0.75

0.93

Env-PPAS

---GSEWRRAYVYDR---QTFFPLLENGRLLKQ-EGTKTA--PSDAPVL----

1d6gA

0.29

0.25

0.85

0.83

MUSTER

---MDVVDSLLVNG----SNITPPCELGLENETLFCLDQP-RPSKQPAQVILL

1z9iA

0.19

0.17

0.89

0.81

dPPAS

HIVRKRTLRRLLQE---RELVEPLTPSGEAPNQALLR---ILKETEFKKIKVL

(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=-2.18

Estimated TM-score = 0.46±0.15

Estimated RMSD = 7.2±4.2Å

Download Model 2

C-score=-3.16

Download Model 3

C-score=-2.41

Download Model 4

C-score=-2.81

Download Model 5

C-score=-4.62

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	3gniA2	0.566	2.60	0.059	0.868
2	1dl2A2	0.560	3.14	0.043	0.849
3	3opbA3	0.543	3.28	0.078	0.924
4	2wb9A	0.533	2.67	0.043	0.868
5	1nxcA	0.532	3.25	0.020	0.924
6	4knhA	0.532	3.28	0.100	0.887
7	5ijnD	0.531	3.11	0.100	0.887
8	3gq2A	0.529	2.93	0.039	0.906
9	1xqrA2	0.528	3.31	0.078	0.924
10	3w3tA	0.527	3.01	0.061	0.868

(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	0.26	11	4yweD	CA	Rep, Mult	38,42
2	0.09	4	4db8B	MG	Rep, Mult	4,8,48
3	0.04	2	4y18B	III	Rep, Mult	6,9
4	0.04	2	2gl7D	III	Rep, Mult	22,26,29,33,37
5	0.04	2	3fr3B	GDS	Rep, Mult	24,26,27,52
6	0.02	1	4evtA	URE	Rep, Mult	4,37,41
7	0.02	1	1yklG	DHB	Rep, Mult	28,31
8	0.02	1	2wduB	GDS	Rep, Mult	33,37,49,53

	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	2dchX	0.479	3.32	0.146	0.849	3.1.-.-	NA
2	0.060	1zl9A	0.495	3.45	0.039	0.943	2.5.1.18	NA
3	0.060	1r5aA	0.491	3.01	0.065	0.868	2.5.1.18	NA
4	0.060	3f6fA	0.485	3.41	0.083	0.906	2.5.1.18	NA
5	0.060	2gaiA	0.476	3.59	0.063	0.830	5.99.1.2	NA
6	0.060	1tu8D	0.473	2.93	0.082	0.924	2.5.1.18	NA
7	0.060	1nxcA	0.532	3.25	0.020	0.924	3.2.1.113	NA
8	0.060	1j0mA	0.469	3.23	0.083	0.887	4.2.2.12	11,20
9	0.060	2gajB	0.469	3.47	0.082	0.849	5.99.1.2	19
10	0.060	1zl9B	0.489	3.47	0.039	0.943	2.5.1.18	NA
11	0.060	2hnlA	0.478	3.53	0.163	0.887	2.5.1.18	NA
12	0.060	1fo2A	0.526	2.65	0.000	0.774	3.2.1.113	NA
13	0.060	2nppC	0.476	2.86	0.047	0.774	3.1.3.16	NA
14	0.060	1dq3A	0.485	3.02	0.083	0.868	1.17.4.1	NA
15	0.060	2ljrA	0.491	3.68	0.157	0.962	2.5.1.18	NA
16	0.060	1f1sA	0.489	3.44	0.041	0.924	4.2.2.1	NA
17	0.060	1fmiA	0.529	2.88	0.000	0.792	3.2.1.113	NA
18	0.060	1i8qA	0.488	3.43	0.041	0.924	4.2.2.1	NA
19	0.060	1pn9B	0.482	3.35	0.021	0.906	2.5.1.18	12

(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	0.16	0.533	2.67	0.04	0.87	2wb9A	GO:0004364 GO:0016740
1	0.07	0.516	3.08	0.02	0.89	3nowA	GO:0007525 GO:0031034 GO:0034605 GO:0045824 GO:0050829 GO:0061077
2	0.07	0.460	3.25	0.13	0.85	3isoA	GO:0016740 GO:0046872
3	0.07	0.487	2.60	0.16	0.85	4w66A	GO:0016740
4	0.07	0.474	3.33	0.14	0.92	13gsA	GO:0000302 GO:0002674 GO:0004364 GO:0005615 GO:0005622 GO:0005634 GO:0005737 GO:0005739 GO:0005829 GO:0005886 GO:0006469 GO:0006749 GO:0006805 GO:0007417 GO:0008144 GO:0008152 GO:0008432 GO:0009636 GO:0009890 GO:0010804 GO:0014003 GO:0016740 GO:0019207 GO:0031100 GO:0031667 GO:0031982 GO:0032355 GO:0032691 GO:0032720 GO:0032869 GO:0032872 GO:0032873 GO:0032930 GO:0033591 GO:0035726 GO:0035730 GO:0035731 GO:0035732 GO:0043066 GO:0043124 GO:0043200 GO:0043295 GO:0043407 GO:0043409 GO:0043508 GO:0045471 GO:0046689 GO:0048147 GO:0051771 GO:0070026 GO:0070062 GO:0070372 GO:0070373 GO:0070664 GO:0071222 GO:0071364 GO:0071385 GO:0071460 GO:0071638 GO:0097057 GO:1901687 GO:2001237
5	0.07	0.464	3.24	0.07	0.83	4q5qA	GO:0004364 GO:0005737 GO:0008152 GO:0016740
6	0.07	0.461	3.54	0.14	0.94	1fheA	GO:0004364 GO:0005737 GO:0016740
7	0.07	0.471	3.05	0.20	0.92	1yq1A	GO:0016740
8	0.07	0.450	3.40	0.10	0.91	1pd21	GO:0000287 GO:0001516 GO:0004364 GO:0004667 GO:0005509 GO:0005737 GO:0006629 GO:0006631 GO:0006633 GO:0006693 GO:0016740 GO:0016853 GO:0042803 GO:2000255
9	0.07	0.478	3.53	0.16	0.89	2hnlA	GO:0004364 GO:0016740
10	0.07	0.532	3.25	0.02	0.92	1nxcA	GO:0000139 GO:0004571 GO:0005509 GO:0005737 GO:0005783 GO:0005793 GO:0005794 GO:0006486 GO:0006491 GO:0008152 GO:0016020 GO:0016021 GO:0016787 GO:0016798 GO:0046872 GO:0070062
11	0.07	0.450	3.71	0.10	0.94	4ec0B	GO:0000287 GO:0001516 GO:0004364 GO:0004667 GO:0005509 GO:0005737 GO:0005829 GO:0006629 GO:0006631 GO:0006633 GO:0006693 GO:0007165 GO:0007626 GO:0016740 GO:0016853 GO:0019371 GO:0042803 GO:0046872 GO:1901687 GO:2000255
12	0.07	0.454	3.59	0.15	0.91	4q5rA	GO:0004364 GO:0016740
13	0.07	0.473	3.32	0.14	0.92	2gsrA	GO:0004364 GO:0005634 GO:0005737 GO:0005739 GO:0008152 GO:0016740
14	0.07	0.495	3.45	0.04	0.94	1zl9A	GO:0004364 GO:0016740 GO:0045087
15	0.07	0.445	3.60	0.10	0.92	1u3iA	GO:0004364 GO:0016740
16	0.07	0.471	3.14	0.10	0.92	5d73A	GO:0004364 GO:0008152 GO:0016740
17	0.07	0.460	3.61	0.08	0.96	3w8sA	GO:0016740
18	0.07	0.427	3.63	0.02	0.91	2dc5A	GO:0004364 GO:0005102 GO:0005737 GO:0006749 GO:0008152 GO:0010880 GO:0016529 GO:0016740 GO:0018916 GO:0019899 GO:0042178 GO:0042803 GO:0043295 GO:0060315 GO:0060316 GO:0070062 GO:0070458 GO:0071313

Consensus prediction of GO terms

Molecular Function	GO:0016765
GO-Score	0.42
Biological Processes	GO:1901687	GO:0050829	GO:0032930	GO:0045471	GO:0032355	GO:0000302	GO:0031100	GO:0034605	GO:0032869	GO:0043200	GO:0046689	GO:0007525	GO:0071385	GO:0051771	GO:0070373	GO:0045824	GO:0031034	GO:0061077	GO:0043124	GO:0006749	GO:0014003	GO:0071460	GO:0010804	GO:2001237	GO:0032720	GO:0035732	GO:0033591	GO:0002674	GO:0009636	GO:0032691	GO:0070664	GO:0071638	GO:0048147	GO:0035726	GO:0071222	GO:0043508	GO:0071364	GO:0006805
GO-Score	0.07	0.07	0.07	0.07	0.07	0.07	0.07	0.07	0.07	0.07	0.07	0.07	0.07	0.07	0.07	0.07	0.07	0.07	0.07	0.07	0.07	0.07	0.07	0.07	0.07	0.07	0.07	0.07	0.07	0.07	0.07	0.07	0.07	0.07	0.07	0.07	0.07	0.07
Cellular Component	GO:0005886	GO:0005615	GO:0005829	GO:0070062	GO:0005634	GO:0005739	GO:0097057
GO-Score	0.07	0.07	0.07	0.07	0.07	0.07	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.

I-TASSER results for job id Rv3613c

[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]