I-TASSER results

I-TASSER results for job id Rv2771c

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

Input Sequence in FASTA format

>protein (150 residues)
MRRLLIVHHTPSPHMQEMFEAVVSGATDPEIEGVEVVRRPALTVSPIEMLEADGYLLGTP
ANLGYISGALKHAFDVCYYLCLDTTRGRSFGAYIHGNEGTEGAERAVDAITTGLGWVQAA
ETVVVMGKPSKADIEACWNLGATVAAQLMG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MRRLLIVHHTPSPHMQEMFEAVVSGATDPEIEGVEVVRRPALTVSPIEMLEADGYLLGTPANLGYISGALKHAFDVCYYLCLDTTRGRSFGAYIHGNEGTEGAERAVDAITTGLGWVQAAETVVVMGKPSKADIEACWNLGATVAAQLMG
Prediction	CCEEEEEEHCCCCHHHHHHHHHHHHHHHHCCCCEEEEEEHCCCCCHHHHHHCCEEEHCCCCCCCCCCHHHHHHHHHHHHHHHCCCHCEEEEEEEHCCCCCCHHHHHHHHHHHHHCCEEHCCCEEEHCCCCHHHHHHHHHHHHHHHHHHCC
Conf.Score	988999996899599999999999998758887899998656699999987997999589999877678999999987665578644579999976899867999999999976988867868996789999999999999999999859
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MRRLLIVHHTPSPHMQEMFEAVVSGATDPEIEGVEVVRRPALTVSPIEMLEADGYLLGTPANLGYISGALKHAFDVCYYLCLDTTRGRSFGAYIHGNEGTEGAERAVDAITTGLGWVQAAETVVVMGKPSKADIEACWNLGATVAAQLMG
Prediction	543000011033310330051015106657156030332426514262035020000000132140344035204312432364241210000001233232024104301652414312430304431476116303600440153158
	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

                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCEEEEEEHCCCCHHHHHHHHHHHHHHHHCCCCEEEEEEHCCCCCHHHHHHCCEEEHCCCCCCCCCCHHHHHHHHHHHHHHHCCCHCEEEEEEEHCCCCCCHHHHHHHHHHHHHCCEEHCCCEEEHCCCCHHHHHHHHHHHHHHHHHHCC
MRRLLIVHHTPSPHMQEMFEAVVSGATDPEIEGVEVVRRPALTVSPIEMLEADGYLLGTPANLGYISGALKHAFDVCYYLCLDTTRGRSFGAYIHGNEGTEGAERAVDAITTGLGWVQAAETVVVMGKPSKADIEACWNLGATVAAQLMG

2ohiA2

0.18

0.17

0.96

2.64

MUSTER

DERVTVIYDTMHGSTRKMAHAIAEGAMSEG---VDVRVYCLHEDDVKDILESGAIALGAPTIYDEPYPSVGDLLMYLRGLKFNRTLTRKALVFGSMGGNGG-ATGTMKELLAEAGFDVAC-EEEVYYVPTGDELDACFEAGRKLAAEIR-

2ohiA2

0.17

0.96

3.09

dPPAS

DERVTVIYDTMHGSTRKMAHAIAEGAMSEGV---DVRVYCLHEDDVKDILESGAIALGAPTIYDEPYPSVGDLLMYLRGLKFNRTLTRKALVFGSMGGNGG-ATGTMKELLAEAGFDVAC-EEEVYYVPTGDELDACFEAGRKLAAEIR-

2ohiA2

0.19

0.18

0.96

3.31

wdPPAS

DERVTVIYDTMHGSTRKMAHAIAEGAMSEG---VDVRVYCLHEDDVKDILESGAIALGAPTIYDEPYPSVGDLLMYLRGLKFNRTLTRKALVFGSMGGN-GGATGTMKELLAEAGFDVAC-EEEVYYVPTGDELDACFEAGRKLAAEIR-

2ohiA2

0.19

0.18

0.96

3.12

wMUSTER

DERVTVIYDTMHGSTRKMAHAIAEGAMSEG---VDVRVYCLHEDDVKDILESGAIALGAPTIYDEPYPSVGDLLMYLRGLKFNRTLTRKALVFGSMGGN-GGATGTMKELLAEAGFDVA-CEEEVYYVPTGDELDACFEAGRKLAAEIR-

2ohiA2

0.19

0.18

0.96

3.61

wPPAS

DERVTVIYDTMHGSTRKMAHAIAEGAMSEG---VDVRVYCLHEDDVKDILESGAIALGAPTIYDEPYPSVGDLLMYLRGLKFNRTLTRKALVFGSMGGN-GGATGTMKELLAEAGFDVAC-EEEVYYVPTGDELDACFEAGRKLAAEIR-

2ohiA2

0.17

0.96

5.59

dPPAS2

DERVTVIYDTMHGSTRKMAHAIAEGAMSEGV---DVRVYCLHEDDVKDILESGAIALGAPTIYDEPYPSVGDLLMYLRGLKFNRTLTRKALVFGSMGGNGG-ATGTMKELLAEAGFDVAC-EEEVYYVPTGDELDACFEAGRKLAAEIR-

4d02A2

0.17

0.16

0.96

3.31

PPAS

EDRITIFYDTMSNNTRMMADAIAQGIAETDP-RVAVKIFNVARSDLTNVFRSKGVLVGTSTMNNVMMPKIAGLVEEMTGLRFRNKRASAFGSHGWSGG----AVDRLSTRLQDAGFEMS-LSLKAKWRPDQDALKLCREHGREIARQWAL

4d02A2

0.17

0.16

0.96

3.65

Env-PPAS

EDRITIFYDTMSNNTRMMADAIAQGIAETDP-RVAVKIFNVARSDLTNVFRSKGVLVGTSTMNNVMMPKIAGLVEEMTGLRFRNKRASAFGSHGWSGG----AVDRLSTRLQDAGFEMS-LSLKAKWRPDQDALKLCREHGREIARQWAL

1e5dA2

0.18

0.17

0.95

2.60

MUSTER

TNKVVIFYDSMWHSTEKMARVLAESFRDE---GCTVKLMWCKACHMSEISDAGAVIVGSPTHNNGILPYVAGTLQYIKGLRPQNK---IGGAFGSFGWS-GESTKVLAEWLTGMGFDMPATPVKVKNVPTHADYEQLKTMAQTIARALKA

1e5dA2

0.18

0.17

0.95

3.09

dPPAS

TNKVVIFYDSMWHSTEKMARVLAESFRDEGC---TVKLMWCKACHMSEISDAGAVIVGSPTHNNGILPYVAGTLQYIKGLRPQNKIGGAFGSFGWS----GESTKVLAEWLTGMGFDMPATPVKVKNVPTHADYEQLKTMAQTIARALKA

(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 1 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=1.05

Estimated TM-score = 0.86±0.07

Estimated RMSD = 2.7±2.0Å

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	2ohiA	0.926	0.93	0.194	0.960
2	1e5dA2	0.905	1.09	0.182	0.953
3	4d02A2	0.904	1.23	0.160	0.960
4	2q9uA	0.901	1.31	0.139	0.960
5	1ycgA	0.894	1.30	0.217	0.953
6	4la4A	0.879	1.91	0.196	0.987
7	1ydgE	0.872	1.93	0.129	0.980
8	2r97A	0.871	1.90	0.211	0.980
9	1zwlA	0.864	1.90	0.158	0.973
10	2zkiE	0.849	2.06	0.185	0.973

(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	0.67	72	1rljA	FMN	Rep, Mult	10,11,12,13,14,15,60,61,62,63,64,95,96,97,98,99,100,101,127
2	0.02	3	1bu5A	SO4	Rep, Mult	10,11,12,13,14,15,60,95
3	0.02	3	1yrhG	FMN	Rep, Mult	75,78
4	0.01	1	1ag9A	BTB	Rep, Mult	17,21,128
5	0.01	1	3b6jB	AMP	Rep, Mult	124,125,126,135,139,142
6	0.01	2	2ohjE	FE	Rep, Mult	81
7	0.01	1	3hlyB	CA	Rep, Mult	139,143
8	0.01	1	1ycfA	ZN	Rep, Mult	20,24

	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	0.325	2rg1B	0.878	1.80	0.211	0.980	1.6.5.2	53
2	0.266	3hr4A	0.770	2.45	0.113	0.940	1.14.13.39	10,96
3	0.219	1cb7A	0.604	3.17	0.113	0.827	5.4.99.1	37,47,52,56
4	0.069	2kyrA	0.507	2.65	0.104	0.640	2.7.1.69	21,36
5	0.068	3lwzA	0.586	3.61	0.057	0.820	4.2.1.10	47
6	0.068	1bdjA	0.569	3.58	0.091	0.807	2.7.13.3	NA
7	0.067	1uqrK	0.595	3.38	0.098	0.820	4.2.1.10	NA
8	0.067	1uqrD	0.582	3.69	0.033	0.820	4.2.1.10	NA
9	0.067	1y80A	0.590	2.99	0.095	0.773	2.1.1.13	NA
10	0.067	1h0rA	0.584	3.47	0.081	0.813	4.2.1.10	NA
11	0.067	2uygL	0.586	3.51	0.073	0.813	4.2.1.10	47
12	0.067	2r25B	0.581	3.00	0.061	0.767	2.7.13.3	NA
13	0.067	2uygA	0.587	3.46	0.073	0.813	4.2.1.10	NA
14	0.067	1gqoB	0.574	3.61	0.032	0.820	4.2.1.10	NA
15	0.066	2fewB	0.452	3.29	0.096	0.627	2.7.1.69	NA
16	0.066	1be1A	0.534	3.81	0.059	0.793	5.4.99.1	14
17	0.066	1b1aA	0.529	3.62	0.138	0.767	5.4.99.1	NA
18	0.066	2r48A	0.471	2.70	0.151	0.600	2.7.1.69	5,134
19	0.060	1cp2A	0.666	3.33	0.121	0.920	1.18.6.1	NA
20	0.060	2z9dB	0.780	2.39	0.129	0.933	1.7.1.6	41,75
21	0.060	1ha3B	0.658	3.65	0.084	0.953	3.1.5.1	NA
22	0.060	2ag5A	0.663	3.52	0.094	0.920	1.1.1.30	NA
23	0.060	1sevA	0.659	3.11	0.076	0.873	1.1.1.37	NA
24	0.060	1f20A	0.444	4.36	0.042	0.707	1.14.13.39	43
25	0.060	1llcA	0.659	3.04	0.093	0.860	1.1.1.27	NA
26	0.060	2bd0A	0.689	3.52	0.070	0.953	1.1.1.153	NA
27	0.060	1zemA	0.667	3.45	0.116	0.913	1.1.1.9	NA
28	0.060	1t0iA	0.783	2.60	0.139	0.960	1.5.1.29	69,71,75
29	0.060	1tllA	0.770	2.61	0.112	0.953	1.14.13.39	NA
30	0.060	3f9iB	0.665	3.50	0.087	0.920	1.1.1.100	89
31	0.060	1smkA	0.648	3.20	0.076	0.873	1.1.1.37	58,60
32	0.060	3gdfA	0.668	3.71	0.064	0.933	1.1.1.138	70
33	0.060	1iy8A	0.668	3.53	0.071	0.927	1.1.1.-	NA
34	0.060	2qx9B	0.791	2.49	0.130	0.953	1.10.99.2	71,80,112
35	0.060	2hq1A	0.659	3.55	0.080	0.907	1.1.1.100	89
36	0.060	1ycfA	0.891	1.33	0.217	0.953	1.7.99.7	NA
37	0.060	1cp2B	0.671	3.29	0.114	0.920	1.18.6.1	41,47,57,74,103

(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	0.39	0.879	1.75	0.27	0.98	2arkA	GO:0009055 GO:0010181 GO:0055114
1	0.39	0.844	1.94	0.21	0.95	3d7nA	GO:0009055 GO:0010181 GO:0016491 GO:0055114
2	0.35	0.871	1.85	0.22	0.98	2rg1A	GO:0000166 GO:0003955 GO:0005829 GO:0006979 GO:0010181 GO:0016020 GO:0016491 GO:0042802 GO:0045892 GO:0050660 GO:0050661 GO:0051287 GO:0055114
3	0.34	0.875	1.86	0.21	0.98	3b6iA	GO:0000166 GO:0003955 GO:0005829 GO:0006979 GO:0010181 GO:0016020 GO:0016491 GO:0042802 GO:0045892 GO:0050660 GO:0050661 GO:0051287 GO:0055114
4	0.32	0.922	0.97	0.19	0.96	2ohhA	GO:0009055 GO:0010181 GO:0016491 GO:0046872 GO:0055114
5	0.31	0.812	1.88	0.18	0.92	4heqA	GO:0009055 GO:0010181 GO:0055114
6	0.30	0.891	1.33	0.22	0.95	1ycfA	GO:0009055 GO:0010181 GO:0016491 GO:0046872 GO:0055114
7	0.29	0.813	1.66	0.18	0.91	2faxA	GO:0009055 GO:0010181 GO:0055114
8	0.28	0.867	1.89	0.16	0.98	2a5lB	GO:0000166 GO:0003955 GO:0009055 GO:0010181 GO:0016491 GO:0045892 GO:0050660 GO:0050661 GO:0051287 GO:0055114
9	0.28	0.809	2.04	0.21	0.93	3kapA	GO:0009055 GO:0010181 GO:0055114
10	0.27	0.905	1.09	0.18	0.95	1e5dA	GO:0009055 GO:0010181 GO:0016491 GO:0022904 GO:0046872 GO:0055114
11	0.27	0.804	1.64	0.19	0.89	2fz5A	GO:0009055 GO:0010181 GO:0055114
12	0.27	0.810	2.03	0.22	0.93	3f6rA	GO:0009055 GO:0010181 GO:0055114
13	0.26	0.881	1.84	0.20	0.99	4lafA	GO:0003955 GO:0010181 GO:0016491 GO:0019439 GO:0045892 GO:0046196 GO:0050660 GO:0050661 GO:0051287 GO:0055114
14	0.26	0.901	1.31	0.14	0.96	2q9uA	GO:0000166 GO:0009055 GO:0010181 GO:0016491 GO:0046872 GO:0055114
15	0.26	0.812	1.98	0.20	0.93	1akqA	GO:0009055 GO:0010181 GO:0055114
16	0.26	0.788	2.42	0.10	0.95	1czhA	GO:0009055 GO:0010181 GO:0055114
17	0.25	0.783	2.36	0.10	0.95	3esxB	GO:0009055 GO:0010106 GO:0010181 GO:0055114
18	0.24	0.770	2.42	0.13	0.93	2mokA	GO:0005737 GO:0005829 GO:0009055 GO:0010181 GO:0055114
19	0.22	0.904	1.23	0.16	0.96	4d02A	GO:0005506 GO:0005737 GO:0009055 GO:0010181 GO:0016491 GO:0016661 GO:0016966 GO:0042802 GO:0046210 GO:0046872 GO:0051289 GO:0055114 GO:0071731
20	0.21	0.765	2.62	0.21	0.93	3hlyC	GO:0010181 GO:0016491 GO:0055114
21	0.15	0.792	2.42	0.04	0.93	4dikA	GO:0009055 GO:0010181 GO:0016491 GO:0046872 GO:0055114
22	0.13	0.784	2.49	0.12	0.95	2wc1A	GO:0009055 GO:0009399 GO:0010181 GO:0055114
23	0.07	0.527	4.76	0.06	0.93	3e4dA	GO:0016787 GO:0018738 GO:0046294 GO:0046872 GO:0052689
24	0.07	0.524	3.82	0.07	0.75	3devA	GO:0003676 GO:0046872
25	0.07	0.469	4.41	0.07	0.77	3a4yA	GO:0003723 GO:0004518 GO:0004519 GO:0005737 GO:0006364 GO:0016787 GO:0046872 GO:0090305
26	0.07	0.457	4.72	0.07	0.77	4f4hB	GO:0000166 GO:0003952 GO:0005524 GO:0006807 GO:0008795 GO:0009435 GO:0016810 GO:0016874
27	0.07	0.474	4.53	0.07	0.76	2ycbB	GO:0003676 GO:0003723 GO:0046872
28	0.07	0.464	4.80	0.08	0.78	3b9nB	GO:0000166 GO:0004497 GO:0016705 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0010181	GO:0009055	GO:0050661	GO:0051287	GO:0042802	GO:0050660	GO:0003955	GO:0046872
GO-Score	0.89	0.75	0.57	0.57	0.57	0.57	0.57	0.32
Biological Processes	GO:0055114	GO:0006979	GO:0045892
GO-Score	0.89	0.57	0.57
Cellular Component	GO:0016020	GO:0005829
GO-Score	0.57	0.57

(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.