I-TASSER results

Input Sequence in FASTA format

>protein (68 residues)
MLAGVRLTEFHERVALHFGAAYGSSVLLDHVLTGFDGRSAAQAIEDGVEPRDVWRALCAD
FDVPHDRW

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| MLAGVRLTEFHERVALHFGAAYGSSVLLDHVLTGFDGRSAAQAIEDGVEPRDVWRALCADFDVPHDRW
Prediction	CCCCCHHHHHHHHHHHHHCHHHHHHHHHHHCCCCCCCCCHHHHHHHCCCHHHHHHHHHHHHCCCCCCC
Conf.Score	99874489999999998664678888887555667998899999989999999999999989996559
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| MLAGVRLTEFHERVALHFGAAYGSSVLLDHVLTGFDGRSAAQAIEDGVEPRDVWRALCADFDVPHDRW
Prediction	75441444202520473136431432144231462644204402755350440042016427336748
	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

CCCCCHHHHHHHHHHHHHCHHHHHHHHHHHCCCCCCCCCHHHHHHHCCCHHHHHHHHHHHHCCCCCCC
MLAGVRLTEFHERVALHFGAAYGSSVLLDHVLTGFDGRSAAQAIEDGVEPRDVWRALCADFDVPHDRW

1dd4A1

0.23

0.16

0.69

1.29

dPPAS

KLTVSELAELVKKLEDKFGVTAAAPVAVAA--APVAGAAAGAAQEEKTE-------------------

3c4iA2

0.13

0.07

0.57

1.08

wdPPAS

----MNKAELIDVLTQKLGDRRQATAAVENVVD-----TIVRAVHKGD--------------------

4cgrA2

0.20

0.19

0.96

0.98

wMUSTER

LYAL-GAERWVRAVREALSPPEALERAVRHTLTPWE-RTLIRLAESSPALRKVWAEVCHSTEVQAAR-

1dd4A1

0.23

0.16

0.69

2.75

dPPAS2

KLTVSELAELVKKLEDKFGVTAAAPVAVAA--APVAGAAAGAAQEEKTE-------------------

1rqvA1

0.17

0.10

0.60

1.15

dPPAS

AMSVMDVVELISAMEEKFGVSAAAAVAVAA--------GPVEAAEEKTE-------------------

1dd4A1

0.23

0.16

0.69

1.03

wdPPAS

KLTVSELAELVKKLEDKFGVTAAAPVAVAA--APVAGAAAGAAQEEKTE-------------------

1rqvA1

0.17

0.10

0.60

2.58

dPPAS2

AMSVMDVVELISAMEEKFGVSAAAAVAVAA--------GPVEAAEEKTE-------------------

2w0yA2

0.13

0.12

0.90

1.06

dPPAS

AAQKATTSRLRDLLAGVRSADELESIVAAH--TGITALTDREVAKLRDAPGSISTILAERAGI-----

3c4iA2

0.13

0.07

0.57

2.04

dPPAS2

----MNKAELIDVLTQKLGDRRQATAAVENVVD-----TIVRAVHKGD--------------------

2n8oA

0.14

0.10

0.75

1.06

dPPAS

----MSWLNFLKYIAKYGKKAVSAAWKYKG--------KVLEWLNVGPTLEWVWQKLKKIAGL-----

(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=-1.88

Estimated TM-score = 0.49±0.15

Estimated RMSD = 7.1±4.1Å

Download Model 2

C-score=-2.86

Download Model 3

C-score=-3.35

Download Model 4

C-score=-3.48

Download Model 5

C-score=-2.11

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	2p82A	0.621	2.75	0.121	0.941
2	4rulA	0.601	3.10	0.131	0.882
3	3gn3A	0.599	2.79	0.076	0.926
4	1vw49	0.597	3.14	0.045	0.912
5	4cgyA	0.597	3.28	0.129	0.912
6	4xgcD	0.597	3.09	0.059	0.941
7	5d5hA3	0.591	3.27	0.048	0.912
8	3qnqA1	0.590	2.68	0.067	0.868
9	4oojA	0.590	2.78	0.046	0.912
10	3n3dA	0.585	2.53	0.032	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	0.09	5	5a43A	DMU	Rep, Mult	44,45,47,49
2	0.06	3	1yywA	RQA	Rep, Mult	12,15,16,19
3	0.04	2	4tnhH	CLA	Rep, Mult	10,14
4	0.04	2	3fofC	NUC	Rep, Mult	37,39
5	0.04	2	1jb0K	CLA	Rep, Mult	57,58,61
6	0.04	2	3ntlB	CA	Rep, Mult	2,5,6,7,8
7	0.04	2	2ez6A	RQA	Rep, Mult	5,7,8,11,12,15,19,25
8	0.04	2	3jcuL	CLA	Rep, Mult	14,18
9	0.02	1	1iw7P	MG	Rep, Mult	53,57
10	0.02	1	103mA	NBN	Rep, Mult	10,40,44
11	0.02	1	4bs1A	ADP	Rep, Mult	6,50,51,54
12	0.02	1	1h1lB	MG	Rep, Mult	62,66
13	0.02	1	4pj0h	CLA	Rep, Mult	7,10
14	0.02	1	3oyrB	IPE	Rep, Mult	14,26,27,30
15	0.02	1	3dvpA	III	Rep, Mult	49,50

	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	1di1A	0.541	3.46	0.047	0.926	4.2.3.9	31,39
2	0.060	3ff1A	0.540	3.18	0.034	0.853	5.3.1.9	NA
3	0.060	2gajB	0.579	3.26	0.108	0.926	5.99.1.2	NA
4	0.060	1xl7B	0.539	3.38	0.062	0.912	2.3.1.137	NA
5	0.060	3ipiA	0.537	3.06	0.048	0.853	2.5.1.-	NA
6	0.060	1nb8B	0.544	3.71	0.104	0.926	3.1.2.15	NA
7	0.060	1pjqB	0.547	2.86	0.133	0.882	4.99.1.4,1.3.1.76,2.1.1.107	36
8	0.060	2j5cB	0.537	3.33	0.049	0.868	4.2.3.-	NA
9	0.060	1bpxA	0.546	2.96	0.063	0.794	2.7.7.7	52
10	0.060	2debA	0.537	3.22	0.016	0.882	2.3.1.21	NA
11	0.060	1yykA	0.559	3.18	0.061	0.941	3.1.26.3	36
12	0.060	1dk3A	0.351	3.53	0.061	0.647	2.7.7.7	NA
13	0.060	3bicA	0.561	3.26	0.111	0.882	5.4.99.2	11
14	0.060	2gaiA	0.582	3.26	0.108	0.926	5.99.1.2	NA
15	0.060	1dgpA	0.542	3.45	0.047	0.926	4.2.3.9,4.1.99.7	NA
16	0.060	1yzeB	0.314	4.06	0.022	0.618	3.1.2.15	NA
17	0.060	3i4zA	0.538	2.81	0.050	0.838	2.5.1.34	NA
18	0.060	1zzgA	0.538	3.73	0.079	0.912	5.3.1.9	NA
19	0.060	1jmsA	0.537	3.08	0.150	0.809	2.7.7.31	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	0.11	0.495	2.28	0.08	0.71	2n8oA	GO:0005576 GO:0019835 GO:0042742
1	0.08	0.621	2.75	0.12	0.94	2p82A	GO:0000045 GO:0000422 GO:0004197 GO:0005737 GO:0005829 GO:0006501 GO:0006508 GO:0006612 GO:0006810 GO:0006914 GO:0008233 GO:0008234 GO:0015031 GO:0016485 GO:0016787 GO:0044804 GO:0051697
2	0.07	0.601	3.10	0.13	0.88	4rulA	GO:0000287 GO:0003677 GO:0003916 GO:0003917 GO:0005694 GO:0005829 GO:0006265 GO:0016853 GO:0046872
3	0.07	0.597	3.28	0.13	0.91	4cgyA	GO:0000731 GO:0000732 GO:0003677 GO:0003916 GO:0003917 GO:0005634 GO:0005654 GO:0005694 GO:0006260 GO:0006265 GO:0007126 GO:0008270 GO:0016605 GO:0016853 GO:0046872 GO:1901796
4	0.07	0.450	3.65	0.03	0.90	4ddtA	GO:0000166 GO:0000287 GO:0003676 GO:0003677 GO:0003916 GO:0003917 GO:0003918 GO:0004386 GO:0005524 GO:0006265 GO:0006268 GO:0008270 GO:0016787 GO:0016853 GO:0046872
5	0.07	0.493	3.92	0.08	0.91	2cd7A	GO:0004725 GO:0005737 GO:0016491 GO:0016787 GO:0030612 GO:0035335 GO:0046685 GO:0055114
6	0.07	0.468	3.31	0.09	0.78	5d5hA	GO:0000287 GO:0003677 GO:0003916 GO:0003917 GO:0005618 GO:0005829 GO:0005886 GO:0006265 GO:0016853 GO:0040007 GO:0046872 GO:0060701
7	0.07	0.427	3.85	0.10	0.72	1gl9B	GO:0000166 GO:0000287 GO:0003676 GO:0003677 GO:0003916 GO:0003917 GO:0003918 GO:0004386 GO:0005524 GO:0006265 GO:0006268 GO:0008270 GO:0016787 GO:0016853 GO:0046872
8	0.07	0.516	3.38	0.08	0.90	2d1iA	GO:0000045 GO:0000422 GO:0004175 GO:0004197 GO:0005737 GO:0005829 GO:0006501 GO:0006508 GO:0006612 GO:0006810 GO:0006914 GO:0008233 GO:0008234 GO:0015031 GO:0016236 GO:0016485 GO:0016787 GO:0044804 GO:0045732 GO:0051697
9	0.07	0.471	3.68	0.07	0.78	2a3lA	GO:0000166 GO:0003824 GO:0003876 GO:0005524 GO:0005634 GO:0005783 GO:0005829 GO:0008152 GO:0009117 GO:0009168 GO:0009737 GO:0009793 GO:0016020 GO:0016021 GO:0016787 GO:0019239 GO:0031090 GO:0031307 GO:0032264 GO:0043231 GO:0043424 GO:0046872
10	0.07	0.361	4.29	0.06	0.75	5dxlA	GO:0003824 GO:0003825 GO:0005992 GO:0009405 GO:0016740 GO:0016757 GO:0030448 GO:0031505 GO:0034605 GO:0043936
11	0.07	0.429	3.46	0.10	0.81	5cnjA	GO:0001641 GO:0004871 GO:0004930 GO:0005246 GO:0005622 GO:0005886 GO:0005887 GO:0007165 GO:0007186 GO:0007194 GO:0007196 GO:0007268 GO:0008066 GO:0014047 GO:0016020 GO:0016021 GO:0030054 GO:0030424 GO:0030425 GO:0042734 GO:0042995 GO:0043005 GO:0045202 GO:0051966
12	0.06	0.442	3.95	0.10	0.84	3e8xA	GO:0000166
13	0.06	0.408	3.66	0.04	0.78	2o5cA	GO:0000287 GO:0003677 GO:0003916 GO:0003917 GO:0006265 GO:0006310 GO:0016853 GO:0046872 GO:0051304
14	0.06	0.406	2.78	0.07	0.65	3wqyA	GO:0000049 GO:0000166 GO:0002161 GO:0003676 GO:0003723 GO:0004812 GO:0004813 GO:0005524 GO:0005737 GO:0006412 GO:0006419 GO:0006450 GO:0008270 GO:0016874 GO:0016876 GO:0043039 GO:0046872
15	0.06	0.393	3.34	0.12	0.66	2l6aA	GO:0000166 GO:0005524 GO:0005634 GO:0005737 GO:0006919 GO:0007165 GO:0008588 GO:0008656 GO:0009968 GO:0031953 GO:0032088 GO:0036336 GO:0043122 GO:0043124 GO:0043281 GO:0045345 GO:0045381 GO:0045409 GO:0045751 GO:0050710 GO:0050711 GO:0050718 GO:0050728 GO:0050729 GO:0070373 GO:0071345 GO:1901223
16	0.06	0.373	4.07	0.03	0.81	1mwuB	GO:0008658 GO:0046677
17	0.06	0.365	4.30	0.00	0.68	3qf2B	GO:0000166 GO:0002376 GO:0002674 GO:0002830 GO:0005524 GO:0005576 GO:0005634 GO:0005737 GO:0005783 GO:0005829 GO:0006351 GO:0006355 GO:0006915 GO:0006919 GO:0006952 GO:0006954 GO:0007165 GO:0008134 GO:0009595 GO:0032088 GO:0032611 GO:0032621 GO:0032736 GO:0032753 GO:0032754 GO:0042347 GO:0042834 GO:0043280 GO:0043565 GO:0044546 GO:0045087 GO:0045630 GO:0045944 GO:0050701 GO:0050713 GO:0050718 GO:0050727 GO:0050728 GO:0051092 GO:0051259 GO:0051607 GO:0061702 GO:0071222 GO:0072559 GO:2000321 GO:2000553
18	0.06	0.356	3.03	0.08	0.56	2dgtA	GO:0000166 GO:0003676 GO:0003723 GO:0005634 GO:0005730 GO:0006397 GO:0006417 GO:0007623 GO:0008270 GO:0008380 GO:0010628 GO:0032922 GO:0043153 GO:0044822 GO:0046872
19	0.06	0.370	4.31	0.08	0.71	4rs6A	GO:0000082 GO:0000166 GO:0000278 GO:0000785 GO:0004672 GO:0004674 GO:0004871 GO:0005524 GO:0005622 GO:0005737 GO:0005813 GO:0005814 GO:0005829 GO:0005856 GO:0006468 GO:0006977 GO:0007052 GO:0007093 GO:0007265 GO:0007613 GO:0010508 GO:0016301 GO:0016310 GO:0016740 GO:0018105 GO:0030425 GO:0032092 GO:0032403 GO:0032436 GO:0032486 GO:0042995 GO:0043008 GO:0043066 GO:0043123 GO:0045732 GO:0046599 GO:0048167 GO:0060291 GO:0060292 GO:0061000

Consensus prediction of GO terms

Molecular Function	GO:0043169	GO:0003676	GO:0016853
GO-Score	0.38	0.38	0.38
Biological Processes	GO:0071103	GO:0006259
GO-Score	0.38	0.38
Cellular Component	GO:0005829	GO:0005694	GO:0005576	GO:0016605
GO-Score	0.15	0.14	0.11	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 Rv2738c

[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]