I-TASSER results

I-TASSER results for job id Rv1813c

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

Input Sequence in FASTA format

>protein (143 residues)
MITNLRRRTAMAAAGLGAALGLGILLVPTVDAHLANGSMSEVMMSEIAGLPIPPIIHYGA
IAYAPSGASGKAWHQRTPARAEQVALEKCGDKTCKVVSRFTRCGAVAYNGSKYQGGTGLT
RRAAEDDAVNRLEGGRIVNWACN

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MITNLRRRTAMAAAGLGAALGLGILLVPTVDAHLANGSMSEVMMSEIAGLPIPPIIHYGAIAYAPSGASGKAWHQRTPARAEQVALEKCGDKTCKVVSRFTRCGAVAYNGSKYQGGTGLTRRAAEDDAVNRLEGGRIVNWACN
Prediction	CCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEHCCCCCEEEEHCCCCHHHHHHHHHHHHCCCCCEEEEEHCCEEEEEHCCCCCEEHCCCCHHHHHHHHHHHHCCCEEEEEHCC
Conf.Score	99864556678888899999999986467887778887777777788888998765468999869998689858999999999999996999988999986858999859865454568999999999999679889986569
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MITNLRRRTAMAAAGLGAALGLGILLVPTVDAHLANGSMSEVMMSEIAGLPIPPIIHYGAIAYAPSGASGKAWHQRTPARAEQVALEKCGDKTCKVVSRFTRCGAVAYNGSKYQGGTGLTRRAAEDDAVNRLEGGRIVNWACN
Prediction	74343444101112333332121012213343324443344334443463433333300000014433202024154465044302740446403011313301000234641120224335402530264047131341418
	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                 120                 140

                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEHCCCCCEEEEHCCCCHHHHHHHHHHHHCCCCCEEEEEHCCEEEEEHCCCCCEEHCCCCHHHHHHHHHHHHCCCEEEEEHCC
MITNLRRRTAMAAAGLGAALGLGILLVPTVDAHLANGSMSEVMMSEIAGLPIPPIIHYGAIAYAPSGASGKAWHQRTPARAEQVALEKCGDKTCKVVSRFTRCGAVAYNGSKYQGGTGLTRRAAEDDAVNRLEGGRIVNWACN

4b0aA1

0.11

0.99

0.76

MUSTER

-KTNLANEDEAYEAIFGGEFGSLEIGSYIGGDEARNSKDYTEHLPDAVDFEDEDELADDGIVPTLQN-IVATVTLGCRLDLKTVALHEYNPKRFAVIMRIRKTTALIFASGKMVVTGAKSEDDSKLASRKYARAAKFTDFKIQ

4b0aA1

0.10

0.99

0.67

dPPAS

-KTNLANEDEAYEAIFGGEFGSLEIGSYIGGDEARNSKDYTEHLPDAVDFEDEDELADDGIVPTLQN-IVATVTLGCRLDLKTVALHARNFAAVIMRIREPKTTALIFASGKMVVTGAKSEDDSKLASRKYARAAKFTDFKIQ

1ysdB

0.24

0.18

0.76

0.81

wdPPAS

GMASKWDQKGMDIAYEEALLGYKE------------------------GVPI------GGCLINKDGSLGRGHNMRFQKGGEISTLENCGRKDTTLYTTLSPCGAIIMYGIP-VVGENVNFKSKGEKYLQTR--GHEVVV-CK

1ay2A

0.07

0.06

0.86

0.75

wMUSTER

LMIVTARAQVSEAILLAEGQKSAVTEYYLNHGKWPENNTSAGVASPPSDIKG---KYVKEVEVKNGVVTATMLSSGVNNEIK----------GKKLSLWARRCGQPVTRTDDDTVADAKDGKEIDTKHLSTCFDAK-------

1ysdB

0.26

0.20

0.74

0.93

wPPAS

MVTGKGMDIAYEEALLGYKEG---------------------------GVPI------GGCLINKDGSLGRGHNMRFQKGGEISTLENCGRKDTTLYTTLSPCGAIIMYGIP-VVGENVNFKSKGEKYLQTR--GHEVVV-CK

3wmmA

0.14

0.05

0.34

0.89

dPPAS2

LILDPRRVLVSIVAFQIVLGLLIHMIVLSTDLNWLDDNIPVSYQALGKK----------------------------------------------------------------------------------------------

2mk4A

0.12

0.10

0.83

0.81

PPAS

VTMDGKQYSTIEV---------GQTYLIPDNGSKKRVARSLDSKVPQQTLRRGDVLMQGA-ASPELTVSGTLLVEADDASAKALATRH-------NFKQSSGGIALLEAKPG-------TDLNAIATKLKSEGVNVQIELSGA

4b0aA1

0.12

0.11

0.97

0.72

Env-PPAS

-KTNLANEDEAYEAIFGGEFGSLEIGSYIGGDEARNSKDYTEHLPDAVDFEDEDELADDGIVPTLQN-IVATVTLGCRLDLKTVALHARNKRFAAVIMRIRKTTALIFASGKMVVTGAKSEDDSKLASRKYAR--IIQKIGFA

5ed7A2

0.15

0.13

0.90

0.72

MUSTER

VLADAINGLFRDALAAGTTAEQLLMFDLLPPKDVPVGSDVQAQRLAVPGGVISPVAYLGAFL-------SVLYAGRGRMSAATHTARLTGVTS--LVLAVGDVDRLSAFDRGAAGAASRTRAAGYLDVLLTVRLARSQ-----

1zwtA

0.08

1.00

0.65

dPPAS

QSASDSNKSQNAISEVMSATSAINGLYIGQTSYSGTSAIPDNYKDTTNKKITNPFGGELNVGPANNNTYYLTLTRLDKAACVSLATLNLGTSAKGYGVNISGENNIFGNSADQAAKSTAITPAEAATACKNTDSTNKVTYFMK

(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=-2.23

Estimated TM-score = 0.45±0.15

Estimated RMSD = 9.6±4.6Å

Download Model 2

C-score=-3.54

Download Model 3

C-score=-3.88

Download Model 4

C-score=-3.70

Download Model 5

C-score=-4.54

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	4b0aA1	0.883	1.56	0.099	0.944
2	3axbA	0.497	4.14	0.080	0.776
3	1vokA	0.494	1.74	0.073	0.538
4	3gdnA	0.493	4.61	0.031	0.804
5	3q9tA	0.491	4.63	0.036	0.811
6	4uw2A	0.491	4.27	0.059	0.755
7	4r04A2	0.489	4.13	0.028	0.727
8	1mp9A	0.483	1.82	0.023	0.538
9	3fimB	0.482	4.55	0.028	0.790
10	3hjrA2	0.482	4.93	0.073	0.825

(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	0.14	12	1ngmE	QNA	Rep, Mult	70,97,99,102,104,106,116,117
2	0.09	8	1ngmE	QNA	Rep, Mult	70,106,108,110,112,114
3	0.07	6	1ytbA	QNA	Rep, Mult	70,72,97,99,104,106,108,110,112,114,116
4	0.05	4	1mp90	III	Rep, Mult	70,83,86,87,99,102,106,114,116
5	0.05	4	1k4yA	MAN	Rep, Mult	124,128
6	0.02	2	2raqA	CA	Rep, Mult	74,139
7	0.02	2	4ct4B	MG	Rep, Mult	120,121
8	0.01	1	1ju2A	UUU	Rep, Mult	64,66,67,116
9	0.01	1	2qieA	8CS	Rep, Mult	68,69,120,121
10	0.01	1	4il6R	HEM	Rep, Mult	128,132
11	0.01	1	3gl6A	ZN	Rep, Mult	89,94
12	0.01	1	1pcz0	III	Rep, Mult	78,80,82,83,86,87,99,104,106,108,109,110,114,116
13	0.01	1	1q9uA	ZN	Rep, Mult	142,143

	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	1vgmA	0.429	4.80	0.076	0.741	4.1.3.7	NA
2	0.060	1c0iA	0.453	4.49	0.047	0.727	1.4.3.3	NA
3	0.060	1coyA	0.468	5.05	0.061	0.832	1.1.3.6	NA
4	0.060	1msvB	0.449	4.23	0.058	0.671	4.1.1.50	NA
5	0.060	3eoqB	0.456	4.11	0.064	0.671	3.4.24.56	NA
6	0.060	1y56B	0.471	3.99	0.085	0.720	1.5.99.8	110
7	0.060	2jaeA	0.452	4.04	0.051	0.692	1.4.3.2	NA
8	0.060	1ng3A	0.474	3.99	0.055	0.699	1.4.3.19,1.5.3.-	NA
9	0.060	2g49A	0.406	3.85	0.044	0.601	3.4.24.56	NA
10	0.060	1qdlA	0.429	4.41	0.051	0.692	4.1.3.27	NA
11	0.060	1vrqB	0.473	4.35	0.085	0.741	1.5.3.1	NA
12	0.060	1vncA	0.459	4.61	0.041	0.762	1.11.1.10	75
13	0.060	1aa8B	0.455	4.24	0.016	0.713	1.4.3.3	NA
14	0.060	3hwoA	0.477	4.18	0.056	0.727	5.4.4.2	72,105
15	0.060	2qcuB	0.464	4.00	0.063	0.706	1.1.5.3	NA
16	0.060	1i7qA	0.448	4.63	0.066	0.699	4.1.3.27	NA
17	0.060	2ibpA	0.430	4.83	0.107	0.734	2.3.3.1	NA
18	0.060	1c0kA	0.453	4.58	0.048	0.734	1.4.3.3	104
19	0.060	1zovA	0.466	3.97	0.031	0.713	1.5.3.1	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	0.32	0.883	1.56	0.10	0.94	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
1	0.11	0.463	2.14	0.10	0.54	2z8uB	GO:0003677 GO:0003700 GO:0006351 GO:0006352 GO:0006355
2	0.10	0.488	1.84	0.09	0.54	5iy6P	GO:0000978 GO:0000979 GO:0001103 GO:0001939 GO:0001940 GO:0003677 GO:0003700 GO:0005634 GO:0005654 GO:0005669 GO:0005672 GO:0005719 GO:0005737 GO:0006351 GO:0006352 GO:0006355 GO:0006361 GO:0006362 GO:0006363 GO:0006366 GO:0006367 GO:0006368 GO:0006383 GO:0007283 GO:0008134 GO:0016032 GO:0019899 GO:0042795 GO:0044212 GO:0045120 GO:0045815 GO:0045893 GO:0070491 GO:1901796
3	0.10	0.491	1.80	0.08	0.54	3ociB	GO:0000126 GO:0000979 GO:0000983 GO:0001016 GO:0001102 GO:0001179 GO:0001186 GO:0003677 GO:0003682 GO:0003743 GO:0005634 GO:0005668 GO:0005669 GO:0006352 GO:0006356 GO:0006357 GO:0006413 GO:0008301 GO:0042790 GO:0051123 GO:0070893 GO:0070898 GO:1903357
4	0.07	0.483	1.82	0.02	0.54	1mp9A	GO:0003677 GO:0003700 GO:0006351 GO:0006352 GO:0006355
5	0.07	0.471	3.99	0.09	0.72	1y56B	GO:0000166 GO:0016491 GO:0055114
6	0.07	0.494	1.74	0.07	0.54	1vokA	GO:0003677 GO:0005634 GO:0006351 GO:0006352 GO:0006355
7	0.07	0.471	4.20	0.09	0.73	3ad7B	GO:0000166 GO:0008115 GO:0016491 GO:0046653 GO:0055114
8	0.07	0.467	2.66	0.12	0.57	1pczA	GO:0003677 GO:0003700 GO:0006351 GO:0006352 GO:0006355
9	0.06	0.491	4.63	0.04	0.81	3q9tA	GO:0016491 GO:0016614 GO:0050660 GO:0055114
10	0.06	0.321	5.90	0.05	0.71	3redA	GO:0000166 GO:0016491 GO:0016614 GO:0016829 GO:0050660 GO:0055114
11	0.06	0.289	6.13	0.03	0.62	3axbA	GO:0000166 GO:0016020 GO:0016021 GO:0016491 GO:0055114
12	0.06	0.309	5.19	0.04	0.57	4g65A	GO:0005886 GO:0006813 GO:0008324 GO:0015079 GO:0071805 GO:0098655
13	0.06	0.409	4.52	0.02	0.63	3e1tA
14	0.06	0.493	4.61	0.03	0.80	3gdnA	GO:0016491 GO:0016614 GO:0016829 GO:0046593 GO:0050660 GO:0050898 GO:0055114
15	0.06	0.479	4.92	0.06	0.83	3t37A	GO:0000166 GO:0016491 GO:0016614 GO:0050660 GO:0055114
16	0.06	0.458	4.50	0.03	0.74	2gb0B	GO:0005737 GO:0008115 GO:0016491 GO:0046653 GO:0055114
17	0.06	0.340	4.31	0.03	0.52	2po6G	GO:0005886 GO:0016020 GO:0016021 GO:0031295 GO:0050776 GO:0050852
18	0.06	0.495	4.33	0.06	0.78	5eb4A	GO:0016491 GO:0016614 GO:0016829 GO:0046593 GO:0050660 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0000979	GO:0001102	GO:0001179	GO:0001186	GO:0001016	GO:0003682	GO:0008301	GO:0001026	GO:0001075	GO:0032947	GO:0004402	GO:0017025
GO-Score	0.44	0.38	0.38	0.38	0.38	0.38	0.38	0.32	0.32	0.32	0.32	0.32
Biological Processes	GO:0070893	GO:0070898	GO:0042790	GO:0051123	GO:0006356	GO:0016568	GO:0006385	GO:0016573	GO:0006359
GO-Score	0.38	0.38	0.38	0.38	0.38	0.32	0.32	0.32	0.32
Cellular Component	GO:0005669	GO:0000126	GO:0000500	GO:0070860	GO:0005829
GO-Score	0.44	0.38	0.32	0.32	0.32

(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.