I-TASSER results

Input Sequence in FASTA format

>protein (104 residues)
MFGQWEFDVSPTGGIAVASTEVEHFAGSQHEVDTAEVPSAAWGWSRIDHRTWHIVGLCIF
GFLLAMLRGNHVGHVEDWFLITFAAVVLFVLARDLWGRRRGWIR

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MFGQWEFDVSPTGGIAVASTEVEHFAGSQHEVDTAEVPSAAWGWSRIDHRTWHIVGLCIFGFLLAMLRGNHVGHVEDWFLITFAAVVLFVLARDLWGRRRGWIR
Prediction	CCCCCCHCCCCCCCEEEHCCCEEHCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEHHHHHHHHHHHHHHCCCCCCEEEEEEHHHHHHHHHHHHHHHHHHHCCCCC
Conf.Score	98876555568876677656545578888898845588645666778997456558999999999997688887666654788999999999999875467689
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MFGQWEFDVSPTGGIAVASTEVEHFAGSQHEVDTAEVPSAAWGWSRIDHRTWHIVGLCIFGFLLAMLRGNHVGHVEDWFLITFAAVVLFVLARDLWGRRRGWIR
Prediction	74452524244431330133422446744651444423314121243444112121232133122003223433121110133233213212321145455348
	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

CCCCCCHCCCCCCCEEEHCCCEEHCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEHHHHHHHHHHHHHHCCCCCCEEEEEEHHHHHHHHHHHHHHHHHHHCCCCC
MFGQWEFDVSPTGGIAVASTEVEHFAGSQHEVDTAEVPSAAWGWSRIDHRTWHIVGLCIFGFLLAMLRGNHVGHVEDWFLITFAAVVLFVLARDLWGRRRGWIR

5ezmA3

0.12

0.11

0.88

0.74

MUSTER

SPRSWGKQLIGMAIVAACGLLASPVVAT---LNANHIPNSFY----RAYAVWVAVAFVVMLLGIAVAR-LRRGVLPSV-MGMYLGFTVALLGHETVGRPAS---

3zifN

0.14

0.12

0.87

0.90

dPPAS

GSVQDKTGSNMLGGVVLPPNSQAHRTETVGTEATRDNLHAEGARRPEDQTPYMILVEDSLGGLKRRMD-----------LLEESNQQLLATLNRLRTGLAA---

4od4A2

0.13

0.10

0.73

0.76

wdPPAS

SL--W-FDT------SIMDIDFDRSHGLG---------SALLG----PKGALAASLAMHAAAVALFIA--GLG----IATVSTALTALVIILVQAMAWLGRVKE

4od4A2

0.14

0.11

0.75

wMUSTER

SL--W-FDT------SIMDIDFDRSHGLG---------SALLG----PKGALAASLAMHAAAVALFIAGYGLG----IATVSTALTALVIILVQAMAWLGRVKE

4od4A2

0.19

0.12

0.67

0.72

wPPAS

SL--WDFDRS---GL---SI-----------------P-ALLG----PKGALAASLAMHAAAVALFIAGYGLG----IATVSTALTALVIILVQAMAWLGRVKE

2lzlA

0.23

0.10

0.41

0.98

dPPAS2

------------------------LPAEEELVEADEAGSV-------------YAGILSYGVGFFLFI------------LVVAAVTLCRLR------------

2o013

0.10

0.09

0.89

0.79

PPAS

----WYGEI---GRFAMLGA----APEILGKAGLIPAETTYTYWADNYTLFVLEMALMGFAEHRRLQDWYNPGSMGKQYFGRLAMLAILGYFIQGLVTGVGPYQ

2xzmG1

0.14

0.12

0.88

0.86

Env-PPAS

LFGKWNYD-----EVKIQDPCFQNYIACTTTKSQVFVPHTAGRYQVKKFRKTQCP-IVERLIGTLMFHGRNAGKK-------ALCIKVVKNAFEIIHLVTGRVG

1ticB2

0.13

0.12

0.95

0.74

MUSTER

IITTFTSLLSDTNGVLRSDKQVFRGTNSFRSADIVFNFSDYKPVKGAKHAGFLSSYEQVYFPVVQEQLTAHPTY--KVIVTGLGGAQALLAGMDLYQREP---R

5d92D2

0.12

0.09

0.75

0.89

dPPAS

----------------SGSLNKYARGLFAAIFLPIARLLADWG---VSPDAVTVVGTLGVMAGALIFYPMGQ-------LFWGTVVITVFVFSDIIDGLMARLL

(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=-2.80

Estimated TM-score = 0.39±0.13

Estimated RMSD = 10.2±4.6Å

Download Model 2

C-score=-3.02

Download Model 3

C-score=-3.67

Download Model 4

C-score=-3.32

Download Model 5

C-score=-3.41

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	3kp9A	0.551	3.35	0.110	0.808
2	4a01A	0.533	4.26	0.072	0.817
3	3wiqA	0.528	3.45	0.058	0.788
4	4av3A	0.525	4.12	0.071	0.827
5	1h54B	0.523	3.66	0.081	0.788
6	5sy1A	0.521	3.57	0.030	0.817
7	2x68A	0.521	4.15	0.062	0.875
8	1otwA	0.517	4.20	0.000	0.885
9	3ayfA2	0.517	3.75	0.020	0.846
10	2wnhA	0.516	4.21	0.031	0.856

(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	0.07	3	4uc1B	Z0P	Rep, Mult	56,63,88,89,92,95
2	0.07	3	4qi1B	MPG	Rep, Mult	59,62,89,96
3	0.05	2	3oadD	LPO	Rep, Mult	33,34,43,45
4	0.05	2	2gpjA	CA	Rep, Mult	69,74,76
5	0.05	2	4resG	17F	Rep, Mult	88,89
6	0.05	2	1vd5A	GLY	Rep, Mult	63,86
7	0.02	1	3as3A	I5I	Rep, Mult	5,50,76
8	0.02	1	5d56B	78M	Rep, Mult	84,87,91
9	0.02	1	3madA	PO4	Rep, Mult	70,71
10	0.02	1	3a6eA	MN	Rep, Mult	23,33,74,76
11	0.02	1	1pprM	PID	Rep, Mult	80,84
12	0.02	1	4u5tA	3CG	Rep, Mult	93,100
13	0.02	1	4gbgA	EAC	Rep, Mult	22,23
14	0.02	1	2fxfA	CA	Rep, Mult	76,77

	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	1nt4A	0.503	4.05	0.043	0.846	3.1.3.10	60
2	0.060	1rsrB	0.490	4.24	0.049	0.875	1.17.4.1	80
3	0.060	2j2fA	0.491	4.02	0.080	0.817	1.14.19.2,1.14.99.6	NA
4	0.060	2wnhA	0.516	4.21	0.031	0.856	3.1.3.8	36,50
5	0.060	3ckyC	0.516	4.17	0.083	0.865	1.1.1.291	34
6	0.060	1js4A	0.495	4.19	0.070	0.817	3.2.1.4	NA
7	0.060	1otwA	0.517	4.20	0.000	0.885	1.3.3.11	83
8	0.060	1w6jA	0.482	4.13	0.056	0.769	5.4.99.7	61
9	0.060	2f6dA	0.491	3.37	0.036	0.750	3.2.1.3	41
10	0.060	1mhyD	0.490	4.02	0.030	0.856	1.14.13.25	NA
11	0.060	2uw1B	0.491	3.89	0.080	0.808	1.14.99.6	94
12	0.060	1dkpA	0.508	4.33	0.043	0.837	3.1.3.2,3.1.3.26	20
13	0.060	2vn7A	0.487	3.77	0.042	0.760	3.2.1.3	92
14	0.060	2pfdB	0.490	3.30	0.036	0.740	2.1.2.5,4.3.1.4	67
15	0.060	3g17G	0.485	4.31	0.034	0.808	1.1.1.169	NA
16	0.060	2i9pB	0.510	4.35	0.060	0.875	1.1.1.31	58,63,91
17	0.060	1fziA	0.493	3.88	0.020	0.837	1.14.13.25	82
18	0.060	3kv4A	0.503	3.86	0.069	0.798	1.14.11.27	35,56
19	0.060	2vn4A	0.485	3.92	0.032	0.769	3.2.1.3	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	0.523	3.66	0.08	0.79	1h54B	GO:0003824 GO:0005975 GO:0030246
1	0.07	0.555	3.26	0.10	0.81	4nv2A	GO:0016020 GO:0016021 GO:0016491 GO:0048038 GO:0055114
2	0.07	0.530	3.38	0.08	0.78	3wirA	GO:0003824 GO:0005975 GO:0016740 GO:0016757 GO:0030246 GO:0033831
3	0.07	0.533	4.26	0.07	0.82	4a01A	GO:0004427 GO:0005773 GO:0005774 GO:0006810 GO:0006811 GO:0009678 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0046872 GO:0055085
4	0.06	0.473	3.69	0.05	0.75	3qdeA	GO:0003824 GO:0005975 GO:0016740 GO:0016757 GO:0030246 GO:0047738
5	0.06	0.419	3.92	0.08	0.69	3l0iC	GO:0000166 GO:0003824 GO:0005085 GO:0005524 GO:0005576 GO:0005622 GO:0006612 GO:0008152 GO:0008289 GO:0009405 GO:0016020 GO:0016740 GO:0016779 GO:0017137 GO:0018117 GO:0018260 GO:0033644 GO:0043087 GO:0043547 GO:0044161 GO:0044162 GO:0044600 GO:0070273 GO:0070733
6	0.06	0.525	4.13	0.07	0.83	4av3B	GO:0000287 GO:0004427 GO:0005509 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006814 GO:0009678 GO:0015081 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0030955 GO:0035725 GO:0042803 GO:0046872
7	0.06	0.426	4.05	0.07	0.72	3l0mA	GO:0000166 GO:0003824 GO:0005085 GO:0005524 GO:0005576 GO:0005622 GO:0006612 GO:0008152 GO:0008289 GO:0009405 GO:0016020 GO:0016740 GO:0016779 GO:0017137 GO:0018117 GO:0018260 GO:0033644 GO:0043087 GO:0043547 GO:0044161 GO:0044162 GO:0044600 GO:0070273 GO:0070733
8	0.06	0.368	4.82	0.07	0.68	4dg8A	GO:0000166 GO:0003824 GO:0008152
9	0.06	0.494	3.59	0.03	0.79	4av6A	GO:0000287 GO:0004427 GO:0005509 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006814 GO:0009678 GO:0015081 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0030955 GO:0035725 GO:0042803 GO:0046872
10	0.06	0.405	4.32	0.09	0.76	5bv7A	GO:0004607 GO:0004623 GO:0005576 GO:0005615 GO:0006629 GO:0006644 GO:0006656 GO:0008202 GO:0008203 GO:0008374 GO:0016740 GO:0016746 GO:0030301 GO:0034186 GO:0034364 GO:0034372 GO:0034375 GO:0034435 GO:0042157 GO:0042158 GO:0042632 GO:0043691 GO:0046470 GO:0046688 GO:0051384 GO:0070062 GO:0090107
11	0.06	0.336	4.58	0.02	0.62	1z81A	GO:0000413 GO:0003755 GO:0006457 GO:0016853
12	0.06	0.337	3.82	0.02	0.52	2wlkA	GO:0005242 GO:0005244 GO:0006810 GO:0006811 GO:0006813 GO:0016020 GO:0016021 GO:0034765 GO:0071805
13	0.06	0.332	4.95	0.07	0.67	4gmvB	GO:0005737 GO:0005856 GO:0005886 GO:0007165 GO:0016020 GO:0030027 GO:0030175 GO:0031252 GO:0042995 GO:0048675
14	0.06	0.363	3.98	0.00	0.58	1vipA	GO:0004623 GO:0005509 GO:0005576 GO:0006629 GO:0016042 GO:0016787 GO:0046872
15	0.06	0.311	4.15	0.11	0.53	2ipaB	GO:0004725 GO:0016491 GO:0016787 GO:0030612 GO:0035335 GO:0046685 GO:0055114
16	0.06	0.332	4.15	0.00	0.60	3k5pA	GO:0004617 GO:0006564 GO:0008152 GO:0016491 GO:0016597 GO:0016616 GO:0051287 GO:0055114
17	0.06	0.279	5.20	0.01	0.60	2q1zB	GO:0003677 GO:0006351 GO:0006355 GO:0046872
18	0.06	0.312	4.34	0.01	0.56	2lrcA	GO:0000103 GO:0005737 GO:0006457 GO:0006662 GO:0015035 GO:0016671 GO:0034599 GO:0045454 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0030246	GO:0016491	GO:0033831	GO:0009678	GO:0047738	GO:0048038	GO:0004427	GO:0046872
GO-Score	0.18	0.07	0.07	0.07	0.07	0.07	0.07	0.07
Biological Processes	GO:0044238
GO-Score	0.32
Cellular Component	GO:0016021	GO:0005774
GO-Score	0.13	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 Rv2876

[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]