I-TASSER results

I-TASSER results for job id Rv0138

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

Input Sequence in FASTA format

>protein (167 residues)
MSASEFSRAELAAAFEKFEKTVARAAATRDWDCWVQHYTPDVEYIEHAAGIMRGRQRVRA
WIQETMTTFPGSHMVAFPSLWSVIDESTGRIICELDNPMLDPGDGSVISATNISIITYAG
NGQWCRQEDIYNPLRFLRAAMKWCRKAQELGTLDEDAARWMRRHGGP

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MSASEFSRAELAAAFEKFEKTVARAAATRDWDCWVQHYTPDVEYIEHAAGIMRGRQRVRAWIQETMTTFPGSHMVAFPSLWSVIDESTGRIICELDNPMLDPGDGSVISATNISIITYAGNGQWCRQEDIYNPLRFLRAAMKWCRKAQELGTLDEDAARWMRRHGGP
Prediction	CCCCCCCHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHCCCCEEEHCCCCCCHCCHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEHCCCCEEEEEEHCCCCCCCCCCCEEHCCEEEEEHCCCCCEEEEHHHCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCC
Conf.Score	99999999999999999999999988658858888856788678657777557999999999998656788655556655799968975899999767889999985555668999986898745653445778999999999999999878999999999987899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MSASEFSRAELAAAFEKFEKTVARAAATRDWDCWVQHYTPDVEYIEHAAGIMRGRQRVRAWIQETMTTFPGSHMVAFPSLWSVIDESTGRIICELDNPMLDPGDGSVISATNISIITYAGNGQWCRQEDIYNPLRFLRAAMKWCRKAQELGTLDEDAARWMRRHGGP
Prediction	86657143620450054035104504646304300620043030323331304127202610353054234341232233111034730300020223356357143141431000301253303303121213402510440053056245147604501674758
	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

CCCCCCCHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHCCCCEEEHCCCCCCHCCHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEHCCCCEEEEEEHCCCCCCCCCCCEEHCCEEEEEHCCCCCEEEEHHHCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCC
MSASEFSRAELAAAFEKFEKTVARAAATRDWDCWVQHYTPDVEYIEHAAGIMRGRQRVRAWIQETMTTFPGSHMVAFPSLWSVIDESTGRIICELDNPMLDPGDGSVISATNISIITYAGNGQWCRQEDIYNPLRFLRAAMKWCRKAQELGTLDEDAARWMRRHGGP

2rfrA

0.12

0.11

0.87

1.55

MUSTER

LTNARLRLLEDREEIRELIARYGPLADSGDAEALSELWVEDGEYAVVGFATAKGRAAIAALIDQTHRALADGCAHFLGPATVTVEGDTATARCHSVVFRCVSGTFGSHRVSANRWTFRRTPAGWRAVRRENALLD---------------G--SAAARALLQF----

5aifA

0.11

0.08

0.74

1.94

dPPAS

MT------------PIETVTAFIAHWNSGDMEAMYDLCAEDVVWHNIPMEPIAGKPAMRAAVEGFMANVSQ---CDWQVHAIAANGA--TVLTERTDGFTFT-NGRRATIRVMGTFECDAERRIIAWRDYFDMLEFQREFAG-------------------------

5aifA

0.12

0.09

0.74

2.41

wdPPAS

MT--------PIETVTAFIAHWNSG----DMEAMYDLCAEDVVWHNIPMEPIAGKPAMRAAVEGFMANVSQCD---WQVHAIAANGA--TVLTERTDGFTFT-NGRRATIRVMGTFECDAERRIIAWRDYFDMLEFQREFAG-------------------------

2rfrA

0.12

0.10

0.87

1.78

wMUSTER

LTNARLRLLEDREEIRELIARYGPLADSGDAEALSELWVEDGEYAVVGFATAKGRAAIAALIDGQTHALADGCAHFLGPATVTVEGDTATARCHSVVFRC-VSGTFGSHRVSANRWTFRTPAGWRAVRRENALLD---------------G--SAAARALLQF----

5aifA

0.11

0.08

0.74

2.23

wPPAS

MT--------PIETVTAFIAHWNSG----DMEAMYDLCAEDVVWHNIPMEPIAGKPAMRAAVEGFMANVSQCD---WQVHAIAANGA--TVLTERTDGFTFT-NGRRATIRVMGTFECDAERRIIAWRDYFD------------------------MLEFQREFAG-

5aifA

0.12

0.09

0.74

3.50

dPPAS2

MT--------PIETVTAFIAHWNSG----DMEAMYDLCAEDVVWHNIPMEPIAGKPAMRAAVEGFMANVSQ---CDWQVHAIAANGA--TVLTERTDGFTFT-NGRRATIRVMGTFECDAERRIIAWRDYFDMLEFQREFAG-------------------------

5aifA

0.11

0.08

0.74

1.77

PPAS

MT--------PIETVTAFIAHWNSG----DMEAMYDLCAEDVVWHNIPMEPIAGKPAMRAAVEGFMANVSQCD---WQVHAIAANGA--TVLTERTDGFTFT-NGRRATIRVMGTFECDAERRIIAWRDYFD------------------------MLEFQREFAG-

5aifA

0.11

0.08

0.74

2.11

Env-PPAS

MT--------PIETVTAFIAHWNSG----DMEAMYDLCAEDVVWHNIPMEPIAGKPAMRAAVEGFMANVS---QCDWQVHAIAANGA--TVLTERTDGFTFT-NGRRATIRVMGTFECDAERRIIAWRDYFD------------------------MLEFQREFAG-

3a76A

0.14

0.12

0.87

1.52

MUSTER

MS--DLDRLASRAAIQDLYSDKLIAVDKRQEGRLASIWWDDAEWTIEGIGTYKGPEGALDLANNVWPMFHECIHYGTNLRLEFVSADKVNGIGDVLLLGNLVEGNQSILIAAVFTDEYERDGVWKFSKRNACTNYFTPL----------AGIH----------FAPP

5cxoA

0.10

0.08

0.77

1.78

dPPAS

MQD--------EQKRKEIVAEYFRKVNEGDVDAIVEMFTENATIEDPVGKDREGRAAQREYFNSNVTAEVTIEPGHL---SAGQDGKSVAVALAAEMTNILDPNRTRVKINAVDVFTLTPEGKIDSMRVFWGMTDIGVW----------------------------

(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=-0.65

Estimated TM-score = 0.63±0.13

Estimated RMSD = 6.3±3.9Å

Download Model 2

C-score=-2.40

Download Model 3

C-score=-3.59

Download Model 4

C-score=-3.33

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	2chcA	0.748	2.41	0.118	0.892
2	6stdA	0.728	2.63	0.089	0.874
3	3ef8A	0.704	2.53	0.079	0.832
4	4gb5A	0.694	2.29	0.089	0.808
5	3a76A	0.692	2.29	0.112	0.802
6	2rfrA	0.684	3.00	0.127	0.838
7	3b8lA	0.682	2.14	0.128	0.778
8	3rgaA	0.680	2.90	0.077	0.838
9	3soyA	0.668	2.12	0.090	0.760
10	2gbwB	0.662	2.80	0.086	0.808

(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	0.43	105	5stdB	UNN	Rep, Mult	26,46,48,61,62,65,95,97,99,110,112,114,127,129,131
2	0.04	10	2inxA	FFP	Rep, Mult	18,22,46,95,112,114,127,129
3	0.02	6	4xbtC	3ZQ	Rep, Mult	46,65,97,99,110,131
4	0.02	5	5bvbB	DOG	Rep, Mult	23,26,34,46,61,62,65,69,73,95,108,112,131,137
5	0.01	2	1oh00	III	Rep, Mult	12,16,47,48,79,80,81,82,83,84,85,90,92,94,95,110,111,113,115,131,132,133,134,135,136
6	0.01	2	3juqA	AJD	Rep, Mult	31,34,58,61,62,65,69,73,112,129
7	0.01	2	4xbyC	3ZS	Rep, Mult	26,44,62,127
8	0.00	1	3f8hA	CA	Rep, Mult	30,32
9	0.00	1	2bmo0	III	Rep, Mult	17,21,24,25,28,29,30,31,32,33,36,37,72,74,75,76,77,78,96,98,100,105,107

	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	0.188	1hkxA	0.602	2.90	0.099	0.766	2.7.11.17	17,25
2	0.163	3e99A	0.631	2.80	0.098	0.772	1.14.12.10	18,24
3	0.162	1o7hB	0.656	2.71	0.070	0.802	1.14.12.12	26,37
4	0.137	3gzxB	0.651	2.82	0.112	0.802	1.14.12.18	NA
5	0.113	4stdA	0.727	2.64	0.089	0.874	4.2.1.94	44
6	0.111	1e3vB	0.628	2.51	0.109	0.754	5.3.3.1	38
7	0.096	1buqA	0.594	2.65	0.097	0.731	5.3.3.1	NA
8	0.060	1kb0A	0.449	4.61	0.021	0.707	1.1.99.-	96
9	0.060	8choA	0.640	1.93	0.106	0.725	5.3.3.1	25,35,59
10	0.060	3ecqB	0.452	5.01	0.067	0.784	3.2.1.97	34
11	0.060	3i4zA	0.448	4.59	0.097	0.737	2.5.1.34	131
12	0.060	1z45A	0.454	4.98	0.021	0.743	5.1.3.2,5.1.3.3	109,111
13	0.060	1j0mA	0.466	5.26	0.071	0.814	4.2.2.12	58
14	0.060	1i8qA	0.467	5.30	0.081	0.808	4.2.2.1	NA
15	0.060	2d0vA	0.497	4.55	0.055	0.743	1.1.99.8	NA
16	0.060	1sa3A	0.453	4.39	0.031	0.701	3.1.21.4	NA
17	0.060	1kitA	0.445	4.98	0.071	0.719	3.2.1.18	NA
18	0.060	1kv9A	0.455	4.54	0.064	0.695	1.1.99.-	96
19	0.060	3elqB	0.448	4.56	0.048	0.689	2.8.2.22	NA
20	0.060	1cb8A	0.453	5.22	0.069	0.772	4.2.2.5	126
21	0.060	2ux0A	0.599	2.94	0.077	0.760	2.7.11.17	46
22	0.060	1nu3B	0.631	2.50	0.119	0.749	3.3.2.8	NA
23	0.060	1lrwC	0.498	4.65	0.062	0.749	1.1.99.8	NA
24	0.060	3en1B	0.649	2.87	0.112	0.802	1.14.12.3,1.14.12.11	NA
25	0.060	2wyhA	0.446	5.00	0.051	0.749	3.2.1.24	21
26	0.060	2v7oA	0.315	5.09	0.028	0.533	2.7.11.17	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	0.26	0.636	2.28	0.12	0.75	5cxoB	GO:0016787
1	0.24	0.673	2.63	0.11	0.81	4l8pA	GO:0016829 GO:0033988
2	0.23	0.692	2.27	0.11	0.80	3a76B	GO:0009636 GO:0016829 GO:0042597
3	0.23	0.679	2.64	0.10	0.81	4r9kC	GO:0016787 GO:0018744
4	0.20	0.616	2.70	0.18	0.75	1z1sA	GO:0017000
5	0.20	0.727	2.64	0.09	0.87	4stdA	GO:0006582 GO:0016829 GO:0030411 GO:0042438 GO:0043581
6	0.19	0.647	2.46	0.12	0.77	4xbxC	GO:0016787 GO:0018744
7	0.19	0.635	2.43	0.10	0.75	3t8nB	GO:0004769 GO:0006629 GO:0008202 GO:0016853
8	0.17	0.609	2.47	0.09	0.74	2bngC	GO:0004301 GO:0005886 GO:0016787 GO:0033963 GO:0097176
9	0.17	0.656	2.79	0.11	0.80	4l8oA	GO:0016829 GO:0033988
10	0.16	0.590	3.03	0.10	0.74	4cdlA	GO:0004769 GO:0006629 GO:0008202 GO:0016853
11	0.15	0.641	2.37	0.14	0.76	3wmdB	GO:0016853
12	0.14	0.594	2.65	0.10	0.73	1buqA	GO:0004769 GO:0005622 GO:0006629 GO:0006810 GO:0008202 GO:0016853
13	0.06	0.343	5.10	0.04	0.57	2r2iA	GO:0001750 GO:0005509 GO:0005886 GO:0007601 GO:0007602 GO:0008048 GO:0030249 GO:0031282 GO:0031284 GO:0046872 GO:0050896 GO:0071277
14	0.06	0.385	5.41	0.06	0.69	5d80B	GO:0000166 GO:0000221 GO:0000329 GO:0003677 GO:0004518 GO:0004519 GO:0005524 GO:0005773 GO:0005774 GO:0006314 GO:0006810 GO:0006811 GO:0007035 GO:0012505 GO:0015991 GO:0015992 GO:0016020 GO:0016539 GO:0016787 GO:0016820 GO:0030908 GO:0033178 GO:0044267 GO:0046034 GO:0046961 GO:0090305
15	0.06	0.306	5.51	0.03	0.53	3alnA	GO:0000165 GO:0000166 GO:0004672 GO:0004674 GO:0004702 GO:0004713 GO:0005524 GO:0005634 GO:0005737 GO:0005829 GO:0006468 GO:0006915 GO:0007165 GO:0007254 GO:0009611 GO:0016301 GO:0016310 GO:0016740 GO:0018108 GO:0035897 GO:0038095 GO:0071260 GO:2000672
16	0.06	0.308	5.43	0.05	0.55	3bvcA	GO:0046872
17	0.06	0.297	5.47	0.03	0.55	3csqD	GO:0003824 GO:0006508 GO:0008152 GO:0008233 GO:0008237 GO:0016787 GO:0016798 GO:0019012 GO:0019076 GO:0019835 GO:0042742 GO:0046718 GO:0046872 GO:0071555 GO:0098023
18	0.06	0.348	5.77	0.02	0.65	2refA	GO:0003824 GO:0008080 GO:0008152 GO:0016740 GO:0031177
19	0.06	0.248	5.10	0.01	0.42	3qz6A	GO:0003824 GO:0046872
20	0.06	0.269	5.13	0.03	0.46	1xx6A	GO:0000166 GO:0004797 GO:0005524 GO:0005737 GO:0006259 GO:0008270 GO:0009157 GO:0016301 GO:0016310 GO:0016740 GO:0046872 GO:0071897

Consensus prediction of GO terms

Molecular Function	GO:0016836	GO:0004301
GO-Score	0.49	0.45
Biological Processes	GO:0042221	GO:0044249	GO:0016999
GO-Score	0.46	0.40	0.40
Cellular Component	GO:0044464
GO-Score	0.38

(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.