I-TASSER results

I-TASSER results for job id Rv1139c

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

Input Sequence in FASTA format

>protein (166 residues)
MYYLLILAVVFERLAELVVAQRNARWSFAQGGKEFGRPHYVVMVILHTALLLGCVVEPWA
LHRPFIPWLGWPMLAVVVASQGLRWWCVKSLGKRWNTRVIVLPHATLVRRGPYRWMRHPN
YVAVVAEGFALPLVHTAWLTALVFTLANATLLTVRLRVENSVLGYI

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MYYLLILAVVFERLAELVVAQRNARWSFAQGGKEFGRPHYVVMVILHTALLLGCVVEPWALHRPFIPWLGWPMLAVVVASQGLRWWCVKSLGKRWNTRVIVLPHATLVRRGPYRWMRHPNYVAVVAEGFALPLVHTAWLTALVFTLANATLLTVRLRVENSVLGYI
Prediction	HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEHCCCEEHCCCCCCCCCCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Conf.Score	6779999999999999999998689999888734366655899999999999999998766777655899999999999999999999998885557999969978867776333369589999999999999985799999999999999999999999999869
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MYYLLILAVVFERLAELVVAQRNARWSFAQGGKEFGRPHYVVMVILHTALLLGCVVEPWALHRPFIPWLGWPMLAVVVASQGLRWWCVKSLGKRWNTRVIVLPHATLVRRGPYRWMRHPNYVAVVAEGFALPLVHTAWLTALVFTLANATLLTVRLRVENSVLGYI
Prediction	3332323313333321121034124303653043234711200022133333322321323544333123332222233133323200320354121403236715112411123212321202233331210233132102133333230012104202510666
	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

HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEHCCCEEHCCCCCCCCCCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
MYYLLILAVVFERLAELVVAQRNARWSFAQGGKEFGRPHYVVMVILHTALLLGCVVEPWALHRPFIPWLGWPMLAVVVASQGLRWWCVKSLGKRWNTRVIVLPHATLVRRGPYRWMRHPNYVAVVAEGFALPLVHTAWLTALVFTLANATLLTVRLRVENSVLGYI

4a2nB

0.18

0.17

0.99

2.22

MUSTER

CFIVMFIIWVFVRKVYGTRAMKNKSK-KKVRPNFEKSLVFLNFIGMVFLPLTAVFSSLDSFNINLPDSIRLFALIVTFLNIGLFTKIHKDLGNNWSAILEIKDGHKLVKEGIYKNIRHPMYAHLWLWVITQGIILSNWVVLIFGIVAWAILYFIRVPKEEELLIEE

4a2nB

0.18

1.00

2.14

dPPAS

CFIVMFIIWVFVRKVYGTRAMKNKSKKKVRPNFEKSLVFLNFIGMVFLPLTAVFSSYLDSFNINLPDSIRLFALIVTFLNIGLFTKIHKDLGNNWSAILEIKDGHKLVKEGIYKNIRHPMYAHLWLWVITQGIILSNWVVLIFGIVAWAILYFIRVPKEEELLIEE

4a2nB

0.18

1.00

4.40

wdPPAS

CFIVMFIIWVFVRKVYGTRAMKNKSKKKVRPNFEKSLVFLNFIGMVFLPLTAVFSSYLDSFNINLPDSIRLFALIVTFLNIGLFTKIHKDLGNNWSAILEIKDGHKLVKEGIYKNIRHPMYAHLWLWVITQGIILSNWVVLIFGIVAWAILYFIRVPKEEELLIEE

4a2nB

0.18

0.17

0.99

2.90

wMUSTER

CFIVMFIIWVFVRKVYGTRAMKNKSK-KKVRPNFEKSLVFLNFIGMVFLPLTAVFSSLDSFNINLPDSIRLFALIVTFLNIGLFTKIHKDLGNNWSAILEIKDGHKLVKEGIYKNIRHPMYAHLWLWVITQGIILSNWVVLIFGIVAWAILYFIRVPKEEELLIEE

4a2nB

0.19

0.18

0.98

5.39

wPPAS

CFIVMFIIWVFVRKVYGTRAMKNKSKKKVRPNFEK----FLNFIGMVFLPLTAVFSSLDSFNINLPDSIRLFALIVTFLNIGLFTKIHKDLGNNWSAILEIKDGHKLVKEGIYKNIRHPMYAHLWLWVITQGIILSNWVVLIFGIVAWAILYFIRVPKEEELLIEE

4a2nB

0.18

0.99

6.16

dPPAS2

CFIVMFIIWVFVRKVYGTRAMKNKSKKKVRPNFEKSLV-FLNFIGMVFLPLTAVFSSLDSFNINLPDSIRLFALIVTFLNIGLFTKIHKDLGNNWSAILEIKDGHKLVKEGIYKNIRHPMYAHLWLWVITQGIILSNWVVLIFGIVAWAILYFIRVPKEEELLIEE

4a2nB

0.18

0.99

3.66

PPAS

CFIVMFIIWVFVRKVYGTRAMKNKSKKKVRPNFEKSL-VFLNFIGMVFLPLTAVFSSLDSFNINLPDSIRLFALIVTFLNIGLFTKIHKDLGNNWSAILEIKDGHKLVKEGIYKNIRHPMYAHLWLWVITQGIILSNWVVLIFGIVAWAILYFIRVPKEEELLIEE

4a2nB

0.18

0.99

3.98

Env-PPAS

CFIVMFIIWVFVRKVYGTRAMKNKSKKKVRPNFEKSL-VFLNFIGMVFLPLTAVFSSLDSFNINLPDSIRLFALIVTFLNIGLFTKIHKDLGNNWSAILEIKDGHKLVKEGIYKNIRHPMYAHLWLWVITQGIILSNWVVLIFGIVAWAILYFIRVPKEEELLIEE

4quvA2

0.13

0.08

0.61

1.10

MUSTER

----------------------------------------------------------------LPVWGIIAIVALNLAGYAIFRGANIQKHGKPAKYIKTKQGSLLLTSGWWGIARHMNYFGDLMIALSWCLPAAGSPIPYFHIVYFTILLLHREKRDDAMCLAK

4quvA2

0.13

0.08

0.61

1.08

dPPAS

----------------------------------------------------------------LPVWGIIAIVALNLAGYAIFRGANIQKHGKPAKYIKTKQGSLLLTSGWWGIARHMNYFGDLMIALSWCLPAAGSPIPYFHIVYFTILLLHREKRDDAMCLAK

(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=1.24

Estimated TM-score = 0.88±0.07

Estimated RMSD = 2.6±1.9Å

Download Model 2

C-score=-1.02

Download Model 3

C-score=-3.95

Download Model 4

C-score=-4.85

Download Model 5

C-score=-4.96

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	4a2nB	0.963	0.89	0.182	0.994
2	4quvA	0.655	3.80	0.107	0.885
3	2jswA	0.612	4.15	0.045	0.910
4	2mgyA	0.587	4.15	0.063	0.855
5	4djiA	0.586	4.37	0.081	0.855
6	1r0dA	0.586	4.34	0.083	0.885
7	3ay5A2	0.563	4.14	0.070	0.831
8	2msvA	0.562	4.19	0.036	0.819
9	1syyA	0.555	4.19	0.079	0.807
10	3l1lA	0.546	4.80	0.091	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	0.19	2	4a2nB	SAH	Rep, Mult	91,95,96,99,100,101,105,107,108,113,118,119,120,121,159,163
2	0.15	3	1m57G	PEH	Rep, Mult	66,68,69,76,128,132,133
3	0.10	2	3omnC	TRD	Rep, Mult	97,152,155,159
4	0.06	1	4a2nB	CDL	Rep, Mult	78,82,86,89
5	0.05	1	3fyeA	DMU	Rep, Mult	143,144,147,148,151
6	0.05	1	1m57A	PEH	Rep, Mult	77,78,79,80,83,87,122,123

	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	1smsA	0.515	4.38	0.055	0.771	1.17.4.1	NA
2	0.060	1occA	0.510	4.76	0.108	0.837	1.9.3.1	NA
3	0.060	2v8tA	0.491	4.82	0.054	0.789	1.11.1.6	NA
4	0.060	3ee4A	0.535	4.63	0.034	0.837	1.17.4.1	144
5	0.060	1xvgC	0.519	4.36	0.053	0.813	1.14.13.25	51
6	0.060	3es3A	0.490	4.24	0.031	0.735	1.16.3.1	NA
7	0.060	1biqB	0.511	4.57	0.067	0.825	1.17.4.1	NA
8	0.060	2ix6A	0.502	5.28	0.057	0.849	1.3.3.6	NA
9	0.060	1krqA	0.489	4.09	0.047	0.717	1.16.3.1	133
10	0.060	1jk0A	0.522	4.28	0.049	0.771	1.17.4.1	NA
11	0.060	3hf1B	0.506	4.26	0.049	0.765	1.17.4.1	NA
12	0.060	1yrqI	0.501	5.25	0.056	0.885	1.12.2.1	NA
13	0.060	2r42A	0.481	4.75	0.062	0.741	2.7.1.36	NA
14	0.060	1iduA	0.484	5.24	0.067	0.825	1.11.1.10	NA
15	0.060	1h2aL	0.496	5.28	0.063	0.879	1.12.2.1	16
16	0.060	1mfrW	0.492	4.19	0.038	0.735	1.16.3.1	NA
17	0.060	1qleA	0.495	4.91	0.083	0.813	1.9.3.1	NA
18	0.060	1vncA	0.485	5.33	0.080	0.825	1.11.1.10	NA
19	0.060	2frvD	0.492	5.26	0.088	0.879	1.12.2.1	63

(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	0.42	0.963	0.89	0.18	0.99	4a2nB	GO:0004671 GO:0006481 GO:0016020 GO:0016021
1	0.20	0.655	3.80	0.11	0.89	4quvA	GO:0000166 GO:0006696 GO:0016020 GO:0016021 GO:0016126 GO:0016491 GO:0016628 GO:0050613 GO:0050661 GO:0055114
2	0.09	0.514	4.58	0.06	0.83	5cnvH	GO:0004748 GO:0005506 GO:0005737 GO:0005829 GO:0005971 GO:0006260 GO:0009186 GO:0009263 GO:0015949 GO:0016491 GO:0042802 GO:0046872 GO:0055114
3	0.07	0.612	4.15	0.04	0.91	2jswA	GO:0001726 GO:0003779 GO:0005178 GO:0005200 GO:0005737 GO:0005815 GO:0005856 GO:0005886 GO:0005925 GO:0007016 GO:0007044 GO:0007155 GO:0009986 GO:0016020 GO:0017166 GO:0030054 GO:0030274 GO:0030866 GO:0032403 GO:0032587 GO:0042995 GO:0051015 GO:0070062 GO:0070527
4	0.07	0.596	4.38	0.08	0.89	1r0dA	GO:0003779 GO:0005543 GO:0005737 GO:0005856 GO:0005905 GO:0006897 GO:0006898 GO:0006915 GO:0012505 GO:0016020 GO:0030136 GO:0030276 GO:0030665 GO:0031410 GO:0035091 GO:0043231 GO:0048471 GO:0072583
5	0.07	0.587	4.15	0.06	0.86	2mgyA	GO:0005497 GO:0005737 GO:0005739 GO:0005741 GO:0006694 GO:0006810 GO:0006811 GO:0006821 GO:0006869 GO:0007268 GO:0007568 GO:0008347 GO:0008503 GO:0010042 GO:0010266 GO:0010823 GO:0010940 GO:0014012 GO:0016020 GO:0016021 GO:0030325 GO:0031397 GO:0031965 GO:0031966 GO:0032570 GO:0032720 GO:0033574 GO:0042493 GO:0043065 GO:0043231 GO:0044325 GO:0045019 GO:0048265 GO:0048266 GO:0048678 GO:0050810 GO:0051901 GO:0051928 GO:0060242 GO:0060252 GO:0060253 GO:0070062 GO:0071222 GO:0071294 GO:0071476 GO:0072655 GO:0072656 GO:0098794 GO:0099565 GO:1903147 GO:1903579 GO:2000379
6	0.07	0.586	4.37	0.08	0.86	4djiA	GO:0003333 GO:0005886 GO:0005887 GO:0006810 GO:0006865 GO:0015171 GO:0015179 GO:0015297 GO:0015807 GO:0016020 GO:0016021 GO:0051454 GO:1902475
7	0.07	0.433	5.02	0.12	0.72	3gi9C	GO:0003333 GO:0005886 GO:0005887 GO:0015171 GO:0015179 GO:0015297 GO:0015807 GO:0016020 GO:0016021 GO:1902475
8	0.07	0.534	4.21	0.07	0.82	5duoA	GO:0005886 GO:0006810 GO:0008289 GO:0016020 GO:0016021 GO:0033013 GO:0046906
9	0.07	0.562	4.19	0.04	0.82	2msvA	GO:0000166 GO:0004672 GO:0005524 GO:0005737 GO:0005829 GO:0005886 GO:0006468 GO:0012501 GO:0016020 GO:0019901 GO:0032403 GO:0070207 GO:0070266
10	0.07	0.542	4.11	0.03	0.80	2rccA	GO:0004748 GO:0006260 GO:0009186 GO:0016491 GO:0046872 GO:0055114
11	0.07	0.504	4.78	0.08	0.81	3ob6B	GO:0003333 GO:0005886 GO:0005887 GO:0006810 GO:0006865 GO:0015171 GO:0015179 GO:0015181 GO:0015297 GO:0015807 GO:0016020 GO:0016021 GO:0051454 GO:1902475 GO:1903826
12	0.07	0.558	4.23	0.08	0.82	4m1hB	GO:0004748 GO:0005971 GO:0006260 GO:0009186 GO:0009263 GO:0016491 GO:0046872 GO:0055114
13	0.07	0.517	4.60	0.04	0.81	3lrbA	GO:0003333 GO:0005886 GO:0006810 GO:0006865 GO:0015171 GO:0015297 GO:0016020 GO:0016021
14	0.07	0.528	4.23	0.03	0.84	4rymA	GO:0005886 GO:0006810 GO:0016020 GO:0016021 GO:0033013 GO:0046906
15	0.07	0.534	4.42	0.03	0.80	4dr0B	GO:0004748 GO:0005971 GO:0006260 GO:0009186 GO:0009263 GO:0016491 GO:0046872 GO:0055114
16	0.07	0.516	4.20	0.04	0.77	1h0nA	GO:0004748 GO:0005634 GO:0005737 GO:0005971 GO:0006260 GO:0009186 GO:0009262 GO:0009263 GO:0016491 GO:0046872 GO:0051259 GO:0051290 GO:0055114
17	0.07	0.471	4.39	0.04	0.76	2bq1I	GO:0004748 GO:0005971 GO:0006260 GO:0009186 GO:0009263 GO:0016491 GO:0046872 GO:0055114
18	0.07	0.507	4.38	0.06	0.77	4djnA	GO:0001822 GO:0003014 GO:0004748 GO:0005634 GO:0005654 GO:0005737 GO:0005739 GO:0005971 GO:0006260 GO:0006264 GO:0006281 GO:0006974 GO:0006979 GO:0009186 GO:0009200 GO:0009263 GO:0014075 GO:0015949 GO:0016491 GO:0046872 GO:0055114 GO:0070062 GO:1902254

Consensus prediction of GO terms

Molecular Function	GO:0004671	GO:0050662	GO:0000166	GO:0016628
GO-Score	0.42	0.39	0.39	0.39
Biological Processes	GO:0006481	GO:0016129	GO:0016126	GO:0008204	GO:0097384	GO:0044108	GO:1902653
GO-Score	0.42	0.39	0.39	0.39	0.39	0.39	0.39
Cellular Component	GO:0016021	GO:0044424
GO-Score	0.54	0.43

(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.