I-TASSER results

I-TASSER results for job id Rv0340

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

Input Sequence in FASTA format

>protein (179 residues)
MANSLLDFVISLVRDPEAAARYAANPERSIAEAHLTDVTRADVNSLIPVVSDSLSMSEPI
GAAGGAHAGDRGNVWASGAATAALDAFAPHADAGVVQQHGAVGSVLNQPTPPGPGVTPTD
PRPFRAGPHETSALLTSAEIPDTTSEDGGLPTDHPAVWNHPVVDPHTVEPDHHGYDIHG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MANSLLDFVISLVRDPEAAARYAANPERSIAEAHLTDVTRADVNSLIPVVSDSLSMSEPIGAAGGAHAGDRGNVWASGAATAALDAFAPHADAGVVQQHGAVGSVLNQPTPPGPGVTPTDPRPFRAGPHETSALLTSAEIPDTTSEDGGLPTDHPAVWNHPVVDPHTVEPDHHGYDIHG
Prediction	CCHHHHHHHHHHHCCHHHHHHHHHCHHHHHHHHCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Conf.Score	97589999999968999999998699999999899999999999999887566777888887665566777763443444456777777788767777887665556777888888888887776677777655567888887666776667787766788777777888887777889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MANSLLDFVISLVRDPEAAARYAANPERSIAEAHLTDVTRADVNSLIPVVSDSLSMSEPIGAAGGAHAGDRGNVWASGAATAALDAFAPHADAGVVQQHGAVGSVLNQPTPPGPGVTPTDPRPFRAGPHETSALLTSAEIPDTTSEDGGLPTDHPAVWNHPVVDPHTVEPDHHGYDIHG
Prediction	75421140012014246104512641440056251450335304300310042242435444343344444432212231434244344424453354444324224444344443444444434244444344244551554424422231444223624224534454634345358
	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

CCHHHHHHHHHHHCCHHHHHHHHHCHHHHHHHHCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
MANSLLDFVISLVRDPEAAARYAANPERSIAEAHLTDVTRADVNSLIPVVSDSLSMSEPIGAAGGAHAGDRGNVWASGAATAALDAFAPHADAGVVQQHGAVGSVLNQPTPPGPGVTPTDPRPFRAGPHETSALLTSAEIPDTTSEDGGLPTDHPAVWNHPVVDPHTVEPDHHGYDIHG

3jbmA

0.08

0.07

0.80

1.02

dPPAS2

---------------------------------GTNDVHLSGMSRISQAVLPAGTGTDGYVVVDATIVPDLLP--RLGHAARIFQRYAVETLEFEIQPANTGGGYVAGFLPDPTDNDHTFDALQATRGAVVAKWWESRTVRPQYTRTLLWTSSGKEQRLTSPGRLILLCVGNNTDVVNV

2xgfA

0.14

0.13

0.95

1.19

PPAS

LME-----TFDKSAYPKLAVAY---PSGVIPDMGQTIKGKPSGRAVLSAEADGVKAHSHSASASSTDLGTKTT-SSFDYGTKGTNSTGGHTHSGSGSTSTNGEHSHYIEAWNGTGVGGNKMSSYAISYRAGGSNTNAAGNHSHTFSFGTSSAGDHSHSVGIGAHTHTVAIGSHGHTITV

5gaoE

0.16

0.15

0.92

1.01

dPPAS2

---------------AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

5gaoE

0.15

1.00

1.03

PPAS

AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

4ke2A

0.11

1.00

0.90

MUSTER

ASKAAVTAADAAAAAATIAASAASVAAATAADDAAASIATINAASAAAKSIAAAAMAAKDTAAAAASAAAAAVASAAKALETINVKAAYAAATTANTAAAAAAATATTAAAAAAAKATIDNAAAAKAAAVATAVSDAAATAATAAAVAAATLEAAAAKAAATAVSAAAAAAAAAIAFAA

2xgfA

0.11

0.97

0.84

dPPAS

LMEG------QTFDKSAYPKLAVAYPSGVIPDMRGQTIKGKPSGRAVLSAEADGVKAHSHSASASSTDLGTKTTSSFDYGTKGTNSTGGHTHSGSGSTSTNGEHSHYIEAWNGTGVGGNKMSSYAISYRAGGSNTNAAGNHSHTFSFGTSSAGDHSHSVGIGAHTHTVAIGSHGHTITV

4behA

0.16

0.09

0.59

0.70

wdPPAS

MAELACIYSALILHDDEVTVT-EDKINALIKAAGV-NVEPFWPGLFAKAIGSLICNVGAGGPAPAAGAAPAGGPAPSTAAAPAEEKKVEAKKEESEESDDDMGGLFD------------------------------------------------------------------------

2mu3A

0.13

0.96

0.92

wMUSTER

VANALASTLRTVLRSQQIASSVVQRAAQSLAS-TLG-VDGNNLARFAVQAVSRLPAGSDTSAYAQAFSSA---LFNAGVLNASIDTLGSRVLSALLNGVSSAAQGINVDSGSVQSDISSSSSFLSTSSSSASYSQASASSTSGAGYTGPSGPST-GPSGYPGPLGGGAPFGQSGFG--G

2xgfA

0.07

0.89

0.79

wPPAS

--SSY--WPSDALME----QTFDKSAYPKLAVA-YPS----DMRGQTIKGKPS-----GRAVLSAEADGVKAHSHSASASSTDLGTKTTSSFDYGTKGTNSTGGHTHSGSGSTSTNGEHSHYIEAWNGTGVGGNKMSSYAISYRAGGSNTNAAGNHSHTFS-FGTSSAGDHSHSVGIGA

2xgfA

0.12

0.10

0.87

0.99

dPPAS2

LME---------------GQTFDKSAYPKLAVAYPSGV-------IPDMRGQTIKGKPSGRAVLSAEADGVKAH--SHSASASSTDLGTKTTSSFDYGTKGTNSTGGHTHSGSGSTSTNGEHSHYIEAWNGTGVGGNKMSYAISYRAGGSNTNAAGNHSHTFSFGTSSAGDHHSVGIGA

(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=-3.94

Estimated TM-score = 0.29±0.09

Estimated RMSD = 14.5±3.7Å

Download Model 2

C-score=-4.86

Download Model 3

C-score=-5.00

Download Model 4

C-score=-3.32

Download Model 5

C-score=-5.00

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	2xgfA	0.784	2.68	0.127	0.950
2	4aurA	0.404	5.15	0.062	0.665
3	1ciiA	0.404	4.64	0.069	0.626
4	1vw1A	0.402	5.90	0.055	0.765
5	1sjjA	0.392	5.28	0.036	0.693
6	1n7uA	0.379	4.86	0.053	0.603
7	2v5yA	0.371	4.62	0.049	0.581
8	2w6dA	0.364	5.60	0.050	0.648
9	1e07A	0.358	5.79	0.037	0.659
10	4r04A	0.358	5.34	0.076	0.615

(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	0.10	5	3wmoJ	BCL	Rep, Mult	5,8,12
2	0.08	4	3cc9A	GRG	Rep, Mult	3,6
3	0.06	3	3h6tA	CYZ	Rep, Mult	5,6,19,22,28,29
4	0.04	2	3lsfE	PZI	Rep, Mult	15,19,20,23
5	0.04	2	3e3gB	SO4	Rep, Mult	14,40
6	0.04	2	2ps5B	MG	Rep, Mult	7,11,15
7	0.02	1	3g46A	XE	Rep, Mult	5,8,46,47,50
8	0.02	1	3s6lA	ZN	Rep, Mult	85,99
9	0.02	1	1nrjB	MG	Rep, Mult	33,35
10	0.02	1	4yfkC	4C6	Rep, Mult	6,10
11	0.02	1	2w6dB	CPL	Rep, Mult	1,2,3,6,31,32,34
12	0.02	1	2w6dA	GDP	Rep, Mult	37,38,39,40,51
13	0.02	1	3pmvA	557	Rep, Mult	49,50,51

	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	2pffB	0.287	5.32	0.061	0.508	2.3.1.86	NA
2	0.060	1nbwA	0.294	5.32	0.062	0.503	4.2.1.30	12,28,31
3	0.060	3b8eA	0.300	5.07	0.055	0.503	3.6.3.9	NA
4	0.060	2o6yA	0.258	4.97	0.028	0.413	4.3.1.-	NA
5	0.060	2v5yA	0.371	4.62	0.049	0.581	3.1.3.48	10,19
6	0.060	3c8xA	0.151	4.97	0.043	0.251	2.7.10.1	18,25
7	0.060	2dp5A	0.293	5.50	0.028	0.531	3.2.1.35	10,28,37
8	0.060	2g25A	0.216	4.77	0.030	0.341	1.2.4.1	NA
9	0.060	3errA	0.276	5.02	0.029	0.458	6.1.1.11	11,28
10	0.060	2nyfA	0.289	4.62	0.133	0.441	4.3.1.5	NA
11	0.060	2du3A	0.272	5.63	0.055	0.503	6.1.1.27	27,38
12	0.060	1mo7A	0.156	4.99	0.081	0.257	3.6.3.9	47
13	0.060	1sesA	0.201	5.41	0.051	0.341	6.1.1.11	NA
14	0.060	3czoB	0.219	5.52	0.011	0.402	4.3.1.3	NA
15	0.060	2vumA	0.248	5.36	0.048	0.430	2.7.7.6	NA
16	0.060	3hi7A	0.284	4.59	0.025	0.447	1.4.3.22	NA
17	0.060	2q3zA	0.278	5.33	0.009	0.497	2.3.2.13	NA
18	0.060	2ohyB	0.304	4.65	0.077	0.475	5.4.3.6	NA
19	0.060	2uv8G	0.284	5.41	0.069	0.514	2.3.1.86	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	0.15	0.784	2.68	0.13	0.95	2xgfA	GO:0005198 GO:0016032 GO:0019012 GO:0019062 GO:0046718
1	0.06	0.374	4.91	0.04	0.60	5iv5O	GO:0016032 GO:0019012 GO:0019062 GO:0046718 GO:0046872 GO:0098025
2	0.06	0.283	5.53	0.01	0.50	4aurA	GO:0005525
3	0.06	0.187	5.77	0.07	0.35	3cfoA	GO:0000166 GO:0003676 GO:0003677 GO:0003887 GO:0004518 GO:0004527 GO:0006260 GO:0008408 GO:0016740 GO:0016779 GO:0016787 GO:0039693 GO:0071897 GO:0090305
4	0.06	0.200	5.10	0.01	0.33	1m1cA	GO:0019012 GO:0019028
5	0.06	0.404	4.64	0.07	0.63	1ciiA	GO:0005886 GO:0016020 GO:0016021 GO:0019835 GO:0042742 GO:0050829
6	0.06	0.220	5.02	0.03	0.36	2ggmA	GO:0000086 GO:0000715 GO:0000717 GO:0005509 GO:0005622 GO:0005634 GO:0005654 GO:0005737 GO:0005813 GO:0005814 GO:0005829 GO:0005856 GO:0005929 GO:0006281 GO:0006289 GO:0006294 GO:0006974 GO:0007049 GO:0007067 GO:0007099 GO:0007283 GO:0008017 GO:0016925 GO:0031683 GO:0032391 GO:0032465 GO:0032795 GO:0036064 GO:0046872 GO:0051301 GO:0070911 GO:0071942
7	0.06	0.248	4.97	0.03	0.41	3o0zD	GO:0000139 GO:0000166 GO:0001726 GO:0003383 GO:0004672 GO:0004674 GO:0005524 GO:0005737 GO:0005794 GO:0005814 GO:0005829 GO:0005856 GO:0005886 GO:0006468 GO:0006915 GO:0006921 GO:0006939 GO:0007159 GO:0007165 GO:0007249 GO:0007266 GO:0016020 GO:0016301 GO:0016310 GO:0016525 GO:0016740 GO:0017048 GO:0017049 GO:0022614 GO:0030027 GO:0030036 GO:0030155 GO:0030866 GO:0032059 GO:0032060 GO:0032091 GO:0032956 GO:0032970 GO:0035509 GO:0035556 GO:0042995 GO:0043524 GO:0045616 GO:0046872 GO:0048010 GO:0048013 GO:0050900 GO:0050901 GO:0051451 GO:0051492 GO:0051493 GO:0051893 GO:0051894 GO:0090002 GO:1903140 GO:1903347 GO:2000114 GO:2000145
8	0.06	0.204	5.06	0.06	0.35	2j68A	GO:0000166 GO:0003924 GO:0005525 GO:0005886 GO:0008289 GO:0016020 GO:0016021 GO:0016787
9	0.06	0.204	4.77	0.03	0.33	2y51A	GO:0000166 GO:0008152 GO:0016491 GO:0016620 GO:0055114
10	0.06	0.189	4.69	0.03	0.31	3tnuB	GO:0005198 GO:0005200 GO:0005634 GO:0005737 GO:0005739 GO:0005829 GO:0005882 GO:0005886 GO:0008544 GO:0016020 GO:0031581 GO:0045095 GO:0070062 GO:0097110
11	0.06	0.148	5.08	0.01	0.25	1m7sA	GO:0004096 GO:0004601 GO:0006979 GO:0016491 GO:0020037 GO:0042597 GO:0042744 GO:0046872 GO:0055114 GO:0098869
12	0.06	0.218	5.21	0.06	0.37	4dcsA	GO:0000027 GO:0000166 GO:0003924 GO:0005525 GO:0005737 GO:0042254 GO:0043022
13	0.06	0.171	4.77	0.02	0.27	5d0uA	GO:0000166 GO:0003676 GO:0004386 GO:0005524 GO:0008026 GO:0016787
14	0.06	0.190	5.12	0.02	0.33	1rh1A	GO:0005886 GO:0009405 GO:0016020 GO:0016021 GO:0019835 GO:0042742 GO:0050829
15	0.06	0.165	4.71	0.01	0.26	3fk2A	GO:0000122 GO:0000977 GO:0001227 GO:0001843 GO:0003677 GO:0003714 GO:0005096 GO:0005525 GO:0005634 GO:0005737 GO:0005829 GO:0006351 GO:0006355 GO:0007165 GO:0007264 GO:0008360 GO:0010976 GO:0015629 GO:0030900 GO:0035024 GO:0043010 GO:0043116 GO:0043547 GO:0045892 GO:0051056
16	0.06	0.164	3.27	0.05	0.22	4hndA	GO:0000166 GO:0000287 GO:0002561 GO:0004430 GO:0005524 GO:0005739 GO:0005765 GO:0005768 GO:0005794 GO:0005829 GO:0005886 GO:0005887 GO:0006661 GO:0016020 GO:0016023 GO:0016301 GO:0016310 GO:0016740 GO:0030054 GO:0030425 GO:0030672 GO:0031083 GO:0031224 GO:0031410 GO:0031901 GO:0032403 GO:0035651 GO:0035838 GO:0042734 GO:0042995 GO:0043005 GO:0043025 GO:0043204 GO:0043231 GO:0043234 GO:0044231 GO:0045121 GO:0045202 GO:0046854 GO:0070382 GO:0098779
17	0.06	0.184	5.04	0.03	0.29	4ojjC	GO:0000290 GO:0000776 GO:0000932 GO:0001731 GO:0003682 GO:0003723 GO:0003729 GO:0005634 GO:0005737 GO:0006397 GO:0006417 GO:0006446 GO:0007049 GO:0007059 GO:0010494 GO:0022627 GO:0033962 GO:0045947 GO:0051301 GO:0061641 GO:1990726
18	0.06	0.155	5.60	0.06	0.28	4f8xA	GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0031176 GO:0045493

Consensus prediction of GO terms

Molecular Function	GO:0005198	GO:0003677	GO:0005525	GO:0046872	GO:0003887	GO:0008408
GO-Score	0.15	0.06	0.06	0.06	0.06	0.06
Biological Processes	GO:0030260	GO:0044650	GO:0019058
GO-Score	0.40	0.40	0.40
Cellular Component	GO:0019028	GO:0098025
GO-Score	0.06	0.06

(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.