I-TASSER results

I-TASSER results for job id Rv0229c

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

Input Sequence in FASTA format

>protein (226 residues)
MRQPRRANAMGLALCIYIGSLLIYTPIHGETSRRHRRAGFKHGSYRIGHDDDQRHRQRGP
AASHVSASSTRRRRSRHAGRRTARGPRRSMALKYLLDTSVIKRLSRPAVRRAVEPLAEAG
AVARTQITDLEVGYSARNETEWQRLMVALSAFDLIESTASHHRRALGIQRLLAARSQRGR
KIPDLLIAAAGEEHGLVVLHYDADFDLIAAVTGQPCQWIVPAGTID

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MRQPRRANAMGLALCIYIGSLLIYTPIHGETSRRHRRAGFKHGSYRIGHDDDQRHRQRGPAASHVSASSTRRRRSRHAGRRTARGPRRSMALKYLLDTSVIKRLSRPAVRRAVEPLAEAGAVARTQITDLEVGYSARNETEWQRLMVALSAFDLIESTASHHRRALGIQRLLAARSQRGRKIPDLLIAAAGEEHGLVVLHYDADFDLIAAVTGQPCQWIVPAGTID
Prediction	CCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEHHHHHHHCCHHHHHHHHHHHHHCCEEHCHHHEHHHHHCCCCHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHCCEEEHCCCHHHHHHHHHCCCEEEEHCCCCCC
Conf.Score	9875566666678999887666534577877777666555677877877777656788887554566667788877777767888876544557754356787648589999999998798898355445666558999999999999987876558999999999999999997998889847799999999898799858779999998599879986888889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MRQPRRANAMGLALCIYIGSLLIYTPIHGETSRRHRRAGFKHGSYRIGHDDDQRHRQRGPAASHVSASSTRRRRSRHAGRRTARGPRRSMALKYLLDTSVIKRLSRPAVRRAVEPLAEAGAVARTQITDLEVGYSARNETEWQRLMVALSAFDLIESTASHHRRALGIQRLLAARSQRGRKIPDLLIAAAGEEHGLVVLHYDADFDLIAAVTGQPCQWIVPAGTID
Prediction	8543552402000001301100010102264455244332442344335665545656444444444454564455454445442544301030003000000034460252045116532001020010111230435620440352042022030345114212301220243424234120000000013160200110410420062261413111443548
	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                 160                 180                 200                 220

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEHHHHHHHCCHHHHHHHHHHHHHCCEEHCHHHEHHHHHCCCCHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHCCEEEHCCCHHHHHHHHHCCCEEEEHCCCCCC
MRQPRRANAMGLALCIYIGSLLIYTPIHGETSRRHRRAGFKHGSYRIGHDDDQRHRQRGPAASHVSASSTRRRRSRHAGRRTARGPRRSMALKYLLDTSVIKRLSRPAVRRAVEPLAEAGAVARTQITDLEVGYSARNETEWQRLMVALSAFDLIESTASHHRRALGIQRLLAARSQRGRKIPDLLIAAAGEEHGLVVLHYDADFDLIAAVTGQPCQWIVPAGTID

5sv2A

0.45

0.27

0.59

1.83

MUSTER

---------------------------------------------------------------------------------TTR---------YLLAKSAAYRAHLPAVRHRLEPLMERGLLARCGITDLEFGVSARSREDHRTLGTYRRDAEYVNTPDTVWVRAWEIQEALTDKGHRSVKIPDLIIAAVAEHHGIPVMHYDQDFERIAAITRQPVEWVVAPG---

5sv2A

0.44

0.26

0.59

2.31

dPPAS

------------------------------------------------------------------------------------------TTRYLLAKSAAYRAHLPAVRHRLEPLMERGLLARCGITDLEFGVSARSREDHRTLGTYRRDAEYVNTPDTVWVRAWEIQEALTDKGHRSVKIPDLIIAAVAEHHGIPVMHYDQDFERIAAITRQPVEWVVAPG---

5sv2A

0.44

0.26

0.59

3.20

wdPPAS

------------------------------------------------------------------------------------------TTRYLLAKSAAYRAHLPAVRHRLEPLMERGLLARCGITDLEFGVSARSREDHRTLGTYRRDAEYVNTPDTVWVRAWEIQEALTDKGHRSVKIPDLIIAAVAEHHGIPVMHYDQDFERIAAITRQPVEWVVAPG---

5sv2A

0.44

0.26

0.59

2.10

wMUSTER

------------------------------------------------------------------------------------------TTRYLLAKSAAYRAHLPAVRHRLEPLMERGLLARCGITDLEFGVSARSREDHRTLGTYRRDAEYVNTPDTVWVRAWEIQEALTDKGHRSVKIPDLIIAAVAEHHGIPVMHYDQDFERIAAITRQPVEWVVAPG---

5sv2A

0.44

0.26

0.59

2.95

wPPAS

------------------------------------------------------------------------------------------TTRYLLAKSAAYRAHLPAVRHRLEPLMERGLLARCGITDLEFGVSARSREDHRTLGTYRRDAEYVNTPDTVWVRAWEIQEALTDKGHRSVKIPDLIIAAVAEHHGIPVMHYDQDFERIAAITRQPVEWVVAPG---

5sv2A

0.44

0.26

0.59

4.70

dPPAS2

------------------------------------------------------------------------------------------TTRYLLAKSAAYRAHLPAVRHRLEPLMERGLLARCGITDLEFGVSARSREDHRTLGTYRRDAEYVNTPDTVWVRAWEIQEALTDKGHRSVKIPDLIIAAVAEHHGIPVMHYDQDFERIAAITRQPVEWVVAPG---

5sv2A

0.44

0.26

0.59

2.79

PPAS

------------------------------------------------------------------------------------------TTRYLLAKSAAYRAHLPAVRHRLEPLMERGLLARCGITDLEFGVSARSREDHRTLGTYRRDAEYVNTPDTVWVRAWEIQEALTDKGHRSVKIPDLIIAAVAEHHGIPVMHYDQDFERIAAITRQPVEWVVAPG---

5sv2A

0.44

0.26

0.59

3.02

Env-PPAS

------------------------------------------------------------------------------------------TTRYLLAKSAAYRAHLPAVRHRLEPLMERGLLARCGITDLEFGVSARSREDHRTLGTYRRDAEYVNTPDTVWVRAWEIQEALTDKGHRSVKIPDLIIAAVAEHHGIPVMHYDQDFERIAAITRQPVEWVVAPG---

3h87B

0.41

0.25

0.60

1.72

MUSTER

---------------------------------------------------------------------------------TDQ--------RWLIDKSALVRLTDSPDMEIWSNRIERGLVHITGVTRLEVGFSAECGEIARREFRPLSAMPVEYLTPRIEDRALEVQTLLADRGHRGPSIPDLLIAATAELSGLTVLHVDKDFDAIAALTGQKTERLTHRPP--

3h87B

0.41

0.24

0.60

2.17

dPPAS

-----------------------------------------------------------------------------------------TDQRWLIDKSALVRLTDSPDMEIWSNRIERGLVHITGVTRLEVGFSAECGEIARREFRPLSAMPVEYLTPRIEDRALEVQTLLADRGHRGPSIPDLLIAATAELSGLTVLHVDKDFDAIAALTGQKTERLTHRPP--

(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=-3.00

Estimated TM-score = 0.37±0.13

Estimated RMSD = 12.6±4.3Å

Download Model 2

C-score=-2.93

Download Model 3

C-score=-3.15

Download Model 4

C-score=-3.41

Download Model 5

C-score=-3.14

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	5sv2A	0.544	1.68	0.421	0.589
2	3h87B	0.521	2.31	0.403	0.593
3	4wbdA	0.518	4.52	0.058	0.761
4	4chgA	0.513	1.52	0.210	0.549
5	4j75A	0.500	5.01	0.054	0.770
6	1ct9A	0.499	4.96	0.057	0.765
7	3hzrA	0.498	5.13	0.069	0.774
8	3a04A	0.497	5.14	0.112	0.774
9	3tzeA	0.496	5.22	0.079	0.770
10	3kt8D	0.494	5.20	0.045	0.774

(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	0.17	4	3qe4A	4CF	Rep, Mult	95,96,125,128,183,187,191
2	0.14	3	4xgqA	MG	Rep, Mult	97,98,131,183,184
3	0.08	2	2cyb0	III	Rep, Mult	127,130,157,162,163,166,167,169,170,171,172,173,179,182,185
4	0.05	1	3h87A	MG	Rep, Mult	184,202,204
5	0.04	1	3h87B	IMD	Rep, Mult	118,119
6	0.04	1	2j5bA	TYE	Rep, Mult	94,97,182,186,190,200,202
7	0.04	1	2h1cA	III	Rep, Mult	101,102,104,105,110,113,114,135,140,141,144,151

	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	2zufA	0.421	4.31	0.040	0.597	6.1.1.19	NA
2	0.060	3focA	0.492	5.12	0.055	0.783	6.1.1.2	210
3	0.060	3c8zB	0.455	4.70	0.069	0.673	6.1.1.16	85,195
4	0.060	1q11A	0.463	4.95	0.067	0.704	6.1.1.1	98,108,130
5	0.060	1iq0A	0.417	4.63	0.063	0.611	6.1.1.19	102
6	0.060	1wq3A	0.454	5.27	0.030	0.721	6.1.1.1	NA
7	0.060	1vljB	0.418	5.16	0.047	0.628	1.1.1.-	NA
8	0.060	1tyaE	0.449	5.24	0.062	0.708	6.1.1.1	NA
9	0.060	2yxnA	0.453	5.28	0.030	0.721	6.1.1.1	NA
10	0.060	3i05B	0.489	5.17	0.079	0.770	6.1.1.2	205
11	0.060	3kt8D	0.494	5.20	0.045	0.774	6.1.1.2	NA
12	0.060	1c7sA	0.419	6.12	0.055	0.765	3.2.1.52	NA
13	0.060	1qbaA	0.419	6.08	0.066	0.757	3.2.1.52	97,113
14	0.060	2a0mA	0.420	5.36	0.048	0.673	3.5.3.8	NA
15	0.060	2ddtA	0.432	5.73	0.045	0.743	3.1.4.12	NA
16	0.060	2j5bA	0.474	4.78	0.067	0.708	6.1.1.1	NA
17	0.060	3ixzA	0.424	5.37	0.087	0.686	3.6.3.10	NA
18	0.060	2cybA	0.471	4.88	0.091	0.708	6.1.1.1	NA
19	0.060	2zueA	0.411	4.47	0.038	0.593	6.1.1.19	200

(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	0.40	0.456	2.64	0.22	0.53	3dboB	GO:0000287 GO:0004518 GO:0004521 GO:0004540 GO:0005576 GO:0016787 GO:0040007 GO:0040008 GO:0046872 GO:0090305 GO:0090501 GO:0090502
1	0.30	0.487	2.19	0.18	0.55	5ecdA	GO:0000287 GO:0004518 GO:0004519 GO:0004540 GO:0016787 GO:0046872 GO:0090305 GO:0090501
2	0.29	0.474	2.51	0.19	0.55	2bsqA	GO:0000287 GO:0003677 GO:0004518 GO:0004540 GO:0016787 GO:0044001 GO:0046872 GO:0090305 GO:0090501
3	0.25	0.530	1.51	0.20	0.57	4chgA	GO:0000287 GO:0001666 GO:0004518 GO:0004540 GO:0016787 GO:0040008 GO:0045926 GO:0046872 GO:0090305 GO:0090501
4	0.23	0.521	2.31	0.40	0.59	3h87B	GO:0000287 GO:0004518 GO:0004540 GO:0016787 GO:0017148 GO:0040008 GO:0046872 GO:0090305 GO:0090501
5	0.21	0.480	2.27	0.18	0.55	3zvkA	GO:0000287 GO:0004518 GO:0004540 GO:0016787 GO:0046872 GO:0090305 GO:0090501
6	0.19	0.459	3.24	0.10	0.58	1y82A	GO:0000287 GO:0004518 GO:0004540 GO:0016787 GO:0046872 GO:0090305 GO:0090501
7	0.18	0.477	2.47	0.20	0.54	4xgqA	GO:0000287 GO:0004518 GO:0004540 GO:0016787 GO:0045926 GO:0046872 GO:0090305 GO:0090501
8	0.09	0.474	4.78	0.07	0.71	2j5bA	GO:0000166 GO:0004812 GO:0004831 GO:0005524 GO:0006412 GO:0006418 GO:0016874 GO:0042802
9	0.07	0.489	5.17	0.08	0.77	3i05B	GO:0000166 GO:0004812 GO:0004830 GO:0005524 GO:0005737 GO:0005829 GO:0006412 GO:0006418 GO:0006436 GO:0016874
10	0.07	0.492	5.12	0.06	0.78	3focA	GO:0000166 GO:0004812 GO:0004830 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006436 GO:0016874
11	0.07	0.491	5.10	0.07	0.77	3hv0A	GO:0000166 GO:0004812 GO:0004830 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006436 GO:0016874
12	0.07	0.495	5.31	0.06	0.78	4jfaC	GO:0000166 GO:0004812 GO:0004830 GO:0005524 GO:0005737 GO:0006418 GO:0006436 GO:0016874
13	0.07	0.494	5.20	0.04	0.77	3kt8D	GO:0000166 GO:0004812 GO:0004830 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006436 GO:0016874
14	0.07	0.500	5.01	0.05	0.77	4j75A	GO:0000166 GO:0004812 GO:0004830 GO:0005524 GO:0005737 GO:0006418 GO:0006436 GO:0016874
15	0.07	0.485	4.66	0.08	0.70	2cyaA	GO:0000166 GO:0004812 GO:0004831 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006437 GO:0016874
16	0.07	0.497	5.14	0.11	0.77	3a04A	GO:0000166 GO:0004812 GO:0004830 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006436 GO:0016874
17	0.07	0.498	5.13	0.07	0.77	3hzrA	GO:0000166 GO:0004812 GO:0004830 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006436 GO:0016874
18	0.07	0.480	5.31	0.07	0.77	3jxeB	GO:0000166 GO:0004812 GO:0004830 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006436 GO:0016874
19	0.07	0.496	5.22	0.08	0.77	3tzeA	GO:0000166 GO:0004812 GO:0004830 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006436 GO:0016874
20	0.07	0.495	5.33	0.04	0.78	1r6tA	GO:0000166 GO:0001525 GO:0004812 GO:0004830 GO:0005524 GO:0005634 GO:0005737 GO:0005829 GO:0006412 GO:0006418 GO:0006436 GO:0008285 GO:0016874 GO:0045765 GO:0070062
21	0.07	0.473	4.91	0.10	0.70	2dlcX	GO:0000166 GO:0004812 GO:0004831 GO:0004832 GO:0005524 GO:0005634 GO:0005737 GO:0005829 GO:0006412 GO:0006418 GO:0006437 GO:0006438 GO:0016874
22	0.07	0.471	4.88	0.09	0.71	2cybA	GO:0000166 GO:0004812 GO:0004831 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006437 GO:0016874
23	0.07	0.473	4.53	0.10	0.69	3p0iA	GO:0000166 GO:0004812 GO:0004831 GO:0004832 GO:0005524 GO:0005829 GO:0006418 GO:0006438 GO:0016874
24	0.07	0.449	5.24	0.06	0.71	2ts1A	GO:0000166 GO:0003723 GO:0004812 GO:0004831 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006437 GO:0016874

Consensus prediction of GO terms

Molecular Function	GO:0000287	GO:0003676	GO:0004521
GO-Score	0.83	0.57	0.40
Biological Processes	GO:0040008	GO:0051815	GO:0044000	GO:0036293	GO:0006950	GO:2000113	GO:0032269	GO:0006417	GO:0034249	GO:0010629	GO:0090502
GO-Score	0.65	0.57	0.57	0.51	0.51	0.46	0.46	0.46	0.46	0.46	0.40
Cellular Component	GO:0005576
GO-Score	0.40

(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.