I-TASSER results

I-TASSER results for job id Rv3422c

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

Input Sequence in FASTA format

>protein (168 residues)
MSREGIRRRPKARAGLTGGGTATLPRVEDTLTLGSRLGEQLCAGDVVVLSGPLGAGKTVL
AKGIAMAMDVEGPITSPTFVLARMHRPRRPGTPAMVHVDVYRLLDHNSADLLSELDSLDL
DTDLEDAVVVVEWGEGLAERLSQRHLDVRLERVSHSDTRIATWSWGRS

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MSREGIRRRPKARAGLTGGGTATLPRVEDTLTLGSRLGEQLCAGDVVVLSGPLGAGKTVLAKGIAMAMDVEGPITSPTFVLARMHRPRRPGTPAMVHVDVYRLLDHNSADLLSELDSLDLDTDLEDAVVVVEWGEGLAERLSQRHLDVRLERVSHSDTRIATWSWGRS
Prediction	CCCCCCCCCCCCCCCCCCCEEEEHCCHHHHHHHHHHHHHHCCCCEEEEEHCCCCCCHHHHHHHHHHHHCCCCCCCCCCEEEEEEHCCCCCCCCCEEEEEEHCCCCCHHHHHHCCHHHHCCCCCCCCEEEEEHCCCCCCCCCCCCCEEEEEEEHCCCCEEEEEEHCCCC
Conf.Score	987776667776667788769998999999999999999889996999986899888899999999989999999996666788668889998589999766999577887684676587544589599998887754569987589999995899789999986899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MSREGIRRRPKARAGLTGGGTATLPRVEDTLTLGSRLGEQLCAGDVVVLSGPLGAGKTVLAKGIAMAMDVEGPITSPTFVLARMHRPRRPGTPAMVHVDVYRLLDHNSADLLSELDSLDLDTDLEDAVVVVEWGEGLAERLSQRHLDVRLERVSHSDTRIATWSWGRS
Prediction	755643564454445144523040532720250053006205632000020422112220020004424376704001110243152546541200000001044363133122232142333254000000005404720264204035533787412112143478
	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

                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCCCCCCCCEEEEHCCHHHHHHHHHHHHHHCCCCEEEEEHCCCCCCHHHHHHHHHHHHCCCCCCCCCCEEEEEEHCCCCCCCCCEEEEEEHCCCCCHHHHHHCCHHHHCCCCCCCCEEEEEHCCCCCCCCCCCCCEEEEEEEHCCCCEEEEEEHCCCC
MSREGIRRRPKARAGLTGGGTATLPRVEDTLTLGSRLGEQLCAGDVVVLSGPLGAGKTVLAKGIAMAMDVEGPITSPTFVLARMHRPRRPGTPAMVHVDVYRLLDHNSADLLSELDSLDLDTDLEDAVVVVEWGEGLAERLSQRHLDVRLERVSHSDTRIATWSWGRS

1htwA

0.25

0.21

0.85

3.03

MUSTER

----------------MESLTQYIPDEFSMLRFGKKFAEILEKAIMVYLNGDLGAGKTTLTRGMLQGIGHQGNVKSPTYTLVEEYNI---AGKMIYHFDLYRLADPEELEFMGIRDYFN-----TDSICLIEWSEKGQGILPEADILVNIDYYDDA-RNIELIAQTNL

1htwA

0.25

0.21

0.85

4.18

dPPAS

----------------MESLTQYIPDEFSMLRFGKKFAEILEKAIMVYLNGDLGAGKTTLTRGMLQGIGHQGNVKSPTYTLVEEYNI---AGKMIYHFDLYRLADPEELEFMGIRDYF-----NTDSICLIEWSEKGQGILPEADILVNIDYYDDA-RNIELIAQTNL

1htwA

0.25

0.21

0.85

4.69

wdPPAS

----------------MESLTQYIPDEFSMLRFGKKFAEILEKAIMVYLNGDLGAGKTTLTRGMLQGIGHQGNVKSPTYTLVEEYNI---AGKMIYHFDLYRLADPEELEFMGIRDYFN-----TDSICLIEWSEKGQGILPEADILVNIDYYDDA-RNIELIAQTNL

1htwA

0.25

0.21

0.85

3.78

wMUSTER

-----------------ESLTQYIPDEFSMLRFGKKFAEILEKAIMVYLNGDLGAGKTTLTRGMLQGIGHQGNVKSPTYTLVEEYNI---AGKMIYHFDLYRLADPEELEFMGIRDYFN-----TDSICLIEWSEKGQGILPEADILVNIDYYDD-ARNIELIAQTNL

1htwA

0.25

0.21

0.85

4.75

wPPAS

----------------MESLTQYIPDEFSMLRFGKKFAEILEKAIMVYLNGDLGAGKTTLTRGMLQGIGHQGNVKSPTYTLVEEYNI---AGKMIYHFDLYRLADPEELEFMGIRDYFN-----TDSICLIEWSEKGQGILPEADILVNIDYYDDA-RNIELIAQTNL

1htwA

0.25

0.21

0.85

10.27

dPPAS2

----------------MESLTQYIPDEFSMLRFGKKFAEILEKAIMVYLNGDLGAGKTTLTRGMLQGIGHQGNVKSPTYTLVEEYNI---AGKMIYHFDLYRLADPEELEFMGIRDYF-----NTDSICLIEWSEKGQGILPEADILVNIDYYDDA-RNIELIAQTNL

1htwA

0.25

0.21

0.85

4.09

PPAS

----------------MESLTQYIPDEFSMLRFGKKFAEILEKAIMVYLNGDLGAGKTTLTRGMLQGIGHQGNVKSPTYTLVEEYNI---AGKMIYHFDLYRLADPEELEFMGIRDYFN-----TDSICLIEWSEKGQGILPEADILVNIDYYDDA-RNIELIAQTNL

1htwA

0.25

0.21

0.85

4.34

Env-PPAS

----------------MESLTQYIPDEFSMLRFGKKFAEILEKAIMVYLNGDLGAGKTTLTRGMLQGIGHQGNVKSPTYTLVEEYNI---AGKMIYHFDLYRLADPEELEFMGIRDYF-----NTDSICLIEWSEKGQGILPEADILVNIDYYDDA-RNIELIAQTNL

2qgzA

0.14

0.12

0.91

0.78

MUSTER

IQLVSLPKSYRHIH---SDIDVNNASRMEAFSAILDFVEQYAEQKGLYLYGDMGIGKSYLLAAMAHELSEKKGVS--HFPFAIDVKNAISKEVPVLILDDIGAVRDEVLQVI--LQYR----MLEELPTFFT-FADLERKWAWQAKRV-MERVRYLAREFHL--EGAN

4nkrA

0.15

0.10

0.67

0.75

dPPAS

-------------------------------------------FPIVQVVGFQNSGKTTFIERILEKASEQGLNL---GCLKHHDRYQAAGADVTAVEGAGVRRLWDLTRLIELYQFLETD------CLLIE----GFKKAPYPKVVILLEALKTVNTIAIIYRKKEH

(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=-0.09

Estimated TM-score = 0.70±0.12

Estimated RMSD = 5.2±3.3Å

Download Model 2

C-score=-0.67

Download Model 3

C-score=-3.22

Download Model 4

C-score=-3.50

Download Model 5

C-score=-3.56

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	1htwA	0.815	1.17	0.252	0.851
2	3cmuA	0.582	4.12	0.145	0.827
3	3hr8A1	0.573	4.08	0.127	0.816
4	4nh0A1	0.570	4.06	0.121	0.798
5	1ubgA	0.570	4.05	0.120	0.804
6	1xp8A	0.569	4.11	0.145	0.809
7	2iutA	0.568	4.51	0.079	0.833
8	1xu4A	0.566	4.03	0.098	0.804
9	3ozxA	0.566	4.40	0.070	0.845
10	5aj3g	0.565	4.06	0.105	0.786

(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	0.33	9	3cmvE	ANP	Rep, Mult	52,53,54,55,56,57,58,59
2	0.26	3	1htwA	ADP	Rep, Mult	26,27,30,54,55,56,57,58,59,132,156,158
3	0.13	2	1htwA	MG	Rep, Mult	58,132
4	0.05	1	1htwA	NA	Rep, Mult	48,49,50,131,132,133,134
5	0.04	1	1htwA	MG	Rep, Mult	51,52

	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	3cioA	0.511	4.79	0.099	0.816	2.7.10.2	23
2	0.060	1hv8A	0.520	4.40	0.114	0.762	3.6.4.13	NA
3	0.060	2r9vA	0.548	4.02	0.095	0.774	3.6.3.14	NA
4	0.060	2gblA	0.541	4.42	0.083	0.792	2.7.11.1	54,56
5	0.060	3fdbA	0.511	4.66	0.053	0.827	3.-.-.-	NA
6	0.060	1iayA	0.523	4.63	0.067	0.833	4.4.1.14	NA
7	0.060	2db3A	0.524	4.86	0.074	0.809	3.6.4.13	NA
8	0.060	3gqbA	0.531	4.33	0.132	0.792	3.6.3.14	NA
9	0.060	1kmhB	0.530	4.17	0.096	0.774	3.6.3.14	115,138
10	0.060	1k7hA	0.521	4.93	0.098	0.869	3.1.3.1	NA
11	0.060	1pq3A	0.508	4.58	0.063	0.804	3.5.3.1	NA
12	0.060	1esmA	0.512	3.88	0.067	0.744	2.7.1.33	101
13	0.060	3fvqB	0.527	4.17	0.152	0.774	3.6.3.30	83,103
14	0.060	2aebA	0.514	4.54	0.089	0.804	3.5.3.1	69
15	0.060	3gmzA	0.515	4.57	0.082	0.809	3.5.3.1	119
16	0.060	2qi9D	0.523	4.16	0.169	0.756	3.6.3.33	60,104,112,130
17	0.060	2awnA	0.502	4.53	0.123	0.768	3.6.3.19	NA
18	0.060	2c9oC	0.565	4.00	0.153	0.798	3.6.1.-	NA
19	0.060	3b9pA	0.534	4.38	0.160	0.780	3.6.4.3	56,58

(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	0.41	0.815	1.17	0.25	0.85	1htwA	GO:0000166 GO:0002949 GO:0005524 GO:0005737 GO:0008033 GO:0046872
1	0.35	0.572	4.13	0.12	0.81	2g88A	GO:0000166 GO:0003677 GO:0003697 GO:0005524 GO:0006259 GO:0006281 GO:0006310 GO:0006974 GO:0008094 GO:0009432
2	0.20	0.602	4.18	0.16	0.86	3cmvA	GO:0000150 GO:0000166 GO:0000400 GO:0000730 GO:0003677 GO:0003684 GO:0003690 GO:0003697 GO:0004520 GO:0005524 GO:0005737 GO:0005829 GO:0006259 GO:0006281 GO:0006310 GO:0006312 GO:0006974 GO:0008094 GO:0009432 GO:0010212 GO:0042148 GO:0048870
3	0.07	0.602	4.18	0.16	0.86	3cmvG	GO:0000150 GO:0000166 GO:0000400 GO:0000730 GO:0003677 GO:0003684 GO:0003690 GO:0003697 GO:0004520 GO:0005524 GO:0005737 GO:0005829 GO:0006259 GO:0006281 GO:0006310 GO:0006312 GO:0006974 GO:0008094 GO:0009432 GO:0010212 GO:0042148 GO:0048870
4	0.07	0.556	4.31	0.12	0.81	1szpA	GO:0000150 GO:0000166 GO:0000228 GO:0000400 GO:0000709 GO:0000722 GO:0000724 GO:0000730 GO:0000794 GO:0003677 GO:0003690 GO:0003697 GO:0004520 GO:0005524 GO:0005634 GO:0005654 GO:0005694 GO:0006259 GO:0006281 GO:0006310 GO:0006974 GO:0007131 GO:0008094 GO:0010212 GO:0030491 GO:0042148 GO:0042802 GO:0045002 GO:0070192 GO:1990426
5	0.07	0.566	4.03	0.10	0.80	1xu4A	GO:0000166 GO:0003677 GO:0003684 GO:0005524 GO:0006259 GO:0006281 GO:0006310 GO:0006974 GO:0008094
6	0.07	0.570	4.11	0.13	0.81	1mo4A	GO:0000150 GO:0000166 GO:0000287 GO:0000400 GO:0000725 GO:0000730 GO:0003677 GO:0003690 GO:0003697 GO:0004518 GO:0004519 GO:0004520 GO:0005524 GO:0005737 GO:0005829 GO:0006259 GO:0006281 GO:0006310 GO:0006312 GO:0006314 GO:0006974 GO:0008094 GO:0009432 GO:0009650 GO:0010212 GO:0016539 GO:0016787 GO:0016887 GO:0030145 GO:0042148 GO:0046677 GO:0090305
7	0.07	0.569	4.11	0.14	0.81	1xp8A	GO:0000150 GO:0000166 GO:0000400 GO:0000730 GO:0003677 GO:0003684 GO:0003690 GO:0003697 GO:0004520 GO:0005524 GO:0005737 GO:0005829 GO:0006259 GO:0006281 GO:0006302 GO:0006310 GO:0006312 GO:0006974 GO:0008094 GO:0009432 GO:0010212 GO:0042148
8	0.07	0.542	4.25	0.08	0.79	4hyyA	GO:0000150 GO:0000166 GO:0000400 GO:0000730 GO:0000781 GO:0000794 GO:0001541 GO:0001556 GO:0003677 GO:0003690 GO:0003697 GO:0004520 GO:0005524 GO:0005634 GO:0005654 GO:0005694 GO:0006259 GO:0006281 GO:0006312 GO:0007049 GO:0007126 GO:0007129 GO:0007131 GO:0007141 GO:0007276 GO:0007283 GO:0007286 GO:0007292 GO:0008094 GO:0010212 GO:0042148 GO:0051321 GO:0070192
9	0.07	0.573	4.08	0.13	0.82	3hr8A	GO:0000150 GO:0000166 GO:0000400 GO:0000730 GO:0003677 GO:0003684 GO:0003690 GO:0003697 GO:0004520 GO:0005524 GO:0005737 GO:0005829 GO:0006259 GO:0006281 GO:0006310 GO:0006312 GO:0006974 GO:0008094 GO:0009432 GO:0010212 GO:0042148
10	0.07	0.565	4.02	0.08	0.80	3ew9A	GO:0000166 GO:0003677 GO:0003684 GO:0005524 GO:0006259 GO:0006281 GO:0006310 GO:0006974 GO:0008094
11	0.07	0.546	4.11	0.10	0.76	2w0mA	GO:0000150 GO:0000400 GO:0000730 GO:0003690 GO:0003697 GO:0004520 GO:0005524 GO:0006312 GO:0008094 GO:0010212 GO:0042148 GO:0046872
12	0.07	0.549	4.47	0.14	0.79	1xmvA	GO:0000150 GO:0000166 GO:0000400 GO:0000730 GO:0003677 GO:0003684 GO:0003690 GO:0003697 GO:0004520 GO:0005524 GO:0005737 GO:0005829 GO:0006259 GO:0006281 GO:0006310 GO:0006312 GO:0006974 GO:0008094 GO:0009432 GO:0010212 GO:0042148 GO:0048870
13	0.07	0.527	4.43	0.10	0.78	4xgcE	GO:0000166 GO:0000808 GO:0003677 GO:0005524 GO:0005634 GO:0005664 GO:0006260 GO:0006261 GO:0006270 GO:0006342 GO:0007052 GO:0007076 GO:0046331
14	0.07	0.548	4.04	0.16	0.80	2cvfA	GO:0000166 GO:0003677 GO:0003684 GO:0005524 GO:0006281 GO:0006310 GO:0006974 GO:0008094 GO:0016887
15	0.07	0.550	4.53	0.07	0.83	2zucB	GO:0000150 GO:0000166 GO:0000400 GO:0000730 GO:0003677 GO:0003684 GO:0003690 GO:0003697 GO:0004520 GO:0005524 GO:0006259 GO:0006281 GO:0006310 GO:0006312 GO:0006974 GO:0008094 GO:0010212 GO:0042148
16	0.07	0.501	4.54	0.08	0.78	3t15A	GO:0000166 GO:0005524 GO:0009507 GO:0009536 GO:0009570
17	0.07	0.522	4.45	0.14	0.78	1z47A	GO:0000166 GO:0005215 GO:0005524 GO:0006810 GO:0016820 GO:0016887 GO:0043190 GO:0055085
18	0.07	0.502	4.58	0.06	0.73	3io5B	GO:0000166 GO:0003677 GO:0003697 GO:0005524 GO:0006259 GO:0006260 GO:0006281 GO:0006310 GO:0006974 GO:0008094

Consensus prediction of GO terms

Molecular Function	GO:0005524	GO:0003697	GO:0008094	GO:0046872	GO:0004520	GO:0000150	GO:0003690	GO:0000400
GO-Score	0.73	0.55	0.55	0.41	0.30	0.30	0.30	0.30
Biological Processes	GO:0009432	GO:0051674	GO:0040011	GO:0006928	GO:0002949	GO:0042148	GO:0000730	GO:0010212
GO-Score	0.52	0.51	0.51	0.51	0.41	0.30	0.30	0.30
Cellular Component	GO:0044444
GO-Score	0.51

(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.