I-TASSER results

I-TASSER results for job id Rv3702c

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

Input Sequence in FASTA format

>protein (233 residues)
MCRHLGWLGAQVAVSSLVLDPPQGLRVQSYAPRRQKHGLMNADGWGVGFFDGAIPRRWRS
PAPLWGDTSFHSVAPALRSHCILAAVRSATVGMPIEVSATPPFTDGHWLLAHNGVVDRAV
LPAGPAAESVCDSAILAATIFAHGLDALGDTIVKVGAADPNARLNILAANGSRLIATTWG
DTLSILRRADGVVLASEPYDDDSGWGDVPDRHLVEVTQKGVTLTALDRAKGPR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MCRHLGWLGAQVAVSSLVLDPPQGLRVQSYAPRRQKHGLMNADGWGVGFFDGAIPRRWRSPAPLWGDTSFHSVAPALRSHCILAAVRSATVGMPIEVSATPPFTDGHWLLAHNGVVDRAVLPAGPAAESVCDSAILAATIFAHGLDALGDTIVKVGAADPNARLNILAANGSRLIATTWGDTLSILRRADGVVLASEPYDDDSGWGDVPDRHLVEVTQKGVTLTALDRAKGPR
Prediction	CCCEEEEEHCCCCCHHHHHCCCHHHHHHHHHHHHHCCCCCCCCCCEEEEEHCCEEEEEHCCCCCCCCHHHHHHHHHCCCCEEEEEEHCCCCCCCCCCCCCCCCCCCCEEEEHCCCCCCCHHHHCCCCCCCCHHHHHHHHHHHHCHHHHHHHHHHHHHHCCCCEEEEEEHCCCEEEEEHCCCCEEEEHCCCEEEEHCCCCCCCCCEEHCCCCEEEEEHCCEEEEEHCCCCCCCC
Conf.Score	99689999598545567654665689987778765567767888589999899899994675445696899999867788799998667899887655689865697899977887874566567566788579999999985778999999999986666558999978999999987998799995998999866789999879859998999999979999889998999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MCRHLGWLGAQVAVSSLVLDPPQGLRVQSYAPRRQKHGLMNADGWGVGFFDGAIPRRWRSPAPLWGDTSFHSVAPALRSHCILAAVRSATVGMPIEVSATPPFTDGHWLLAHNGVVDRAVLPAGPAAESVCDSAILAATIFAHGLDALGDTIVKVGAADPNARLNILAANGSRLIATTWGDTLSILRRADGVVLASEPYDDDSGWGDVPDRHLVEVTQKGVTLTALDRAKGPR
Prediction	73100001044340441024134002420343444542343442210000257301212423302626305500640413000000010134443443001113443200001130552446644325030000000000143225102400430272253000000002442300002230000033750000000012647413504631001026750413417576568
	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                 180                 200                 220

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCEEEEEHCCCCCHHHHHCCCHHHHHHHHHHHHHCCCCCCCCCCEEEEEHCCEEEEEHCCCCCCCCHHHHHHHHHCCCCEEEEEEHCCCCCCCCCCCCCCCCCCCCEEEEHCCCCCCCHHHHCCCCCCCCHHHHHHHHHHHHCHHHHHHHHHHHHHHCCCCEEEEEEHCCCEEEEEHCCCCEEEEHCCCEEEEHCCCCCCCCCEEHCCCCEEEEEHCCEEEEEHCCCCCCCC
MCRHLGWLGAQVAVSSLVLDPPQGLRVQSYAPRRQKHGLMNADGWGVGFFDGAIPRRWRSPAPLWGDTSFHSVAPALRSHCILAAVRSATVGMPIEVSATPPFTDGHWLLAHNGVVDRAVLPAGPAAESVCDSAILAATIFAHGLDALGDTIVKVGAADPNARLNILAANGSRLIATTWGDTLSILRRADGVVLASEPYDDDSGWGDVPDRHLVEVTQKGVTLTALDRAKGPR

4zfjA

0.71

0.69

0.97

3.98

MUSTER

-CRHVAWLGAPRSLADLVLDPPQGLLVQSYAPRRQK-HGLNADGWGAGFFDDGVARRWRSDKPLWGDASFASVAPALRSRCVVAAVRSATIG-SIEPSASAPFSDGQWLLSHNGLVARGVLPLTGAAESTVDSAILAALIFSRGLDALGATIAEVGELDPNARLNILAANGSRLLATTWGDTLSVLRRPDGVVLASEPYDDDPGWSDIPDRHLVDVRDAHVVVTPLSSH----

4zfjA

0.70

0.68

0.97

8.01

dPPAS

-CRHVAWLGAPRSLADLVLDPPQGLLVQSYAP-RRQKHGLNADGWGAGFFDDGVARRWRSDKPLWGDASFASVAPALRSRCVVAAVRSATIG-SIEPSASAPFSDGQWLLSHNGLVARGVLPLTGAAESTVDSAILAALIFSRGLDALGATIAEVGELDPNARLNILAANGSRLLATTWGDTLSVLRRPDGVVLASEPYDDDPGWSDIPDRHLVDVRDAHVVVTPLSSH----

4zfjA

0.68

0.66

0.97

7.32

wdPPAS

-CRHVAWLGAPRSLADLVLDPPQGLLVQSYAP-RRQKHGLNADGWGAGFFDDGVARRWRSDKPLWGDASFASVAPALRSRCVVAAVRSATIGSIEPSASAP-FSDGQWLLSHNGLVARGVLPLTGAAESTVDSAILAALIFSRGLDALGATIAEVGELDPNARLNILAANGSRLLATTWGDTLSVLRRPDGVVLASEPYDDDPGWSDIPDRHLVDVRDAHVVVTPLSSH----

4zfjA

0.69

0.67

0.97

5.48

wMUSTER

--RHVAWLGAPRSLADLVLDPPQGLLVQSYAPRRQK-HGLNADGWGAGFFDDGVARRWRSDKPLWGDASFASVAPALRSRCVVAAVRSATIGSIEPSAS-APFSDGQWLLSHNGLVARGVLPLTGAAESTVDSAILAALIFSRGLDALGATIAEVGELDPNARLNILAANGSRLLATTWGDTLSVLRRPDGVVLASEPYDDDPGWSDIPDRHLVDVRDAHVVVTPLSSH----

4zfjA

0.68

0.66

0.97

6.13

wPPAS

-CRHVAWLGAPRSLADLVLDPPQGLLVQSYAP-RRQKHGLNADGWGAGFFDDGVARRWRSDKPLWGDASFASVAPALRSRCVVAAVRSATIGSIEPSASAP-FSDGQWLLSHNGLVARGVLPLTGAAESTVDSAILAALIFSRGLDALGATIAEVGELDPNARLNILAANGSRLLATTWGDTLSVLRRPDGVVLASEPYDDDPGWSDIPDRHLVDVRDAHVVVTPLSSH----

4zfjA

0.70

0.68

0.97

14.40

dPPAS2

-CRHVAWLGAPRSLADLVLDPPQGLLVQSYAP-RRQKHGLNADGWGAGFFDDGVARRWRSDKPLWGDASFASVAPALRSRCVVAAVRSATIG-SIEPSASAPFSDGQWLLSHNGLVARGVLPLTGAAESTVDSAILAALIFSRGLDALGATIAEVGELDPNARLNILAANGSRLLATTWGDTLSVLRRPDGVVLASEPYDDDPGWSDIPDRHLVDVRDAHVVVTPLSSH----

4zfjA

0.69

0.67

0.97

5.23

PPAS

-CRHVAWLGAPRSLADLVLDPPQGLLVQSYAPRR-QKHGLNADGWGAGFFDDGVARRWRSDKPLWGDASFASVAPALRSRCVVAAVRSATIGSIEPS-ASAPFSDGQWLLSHNGLVARGVLPLTGAAESTVDSAILAALIFSRGLDALGATIAEVGELDPNARLNILAANGSRLLATTWGDTLSVLRRPDGVVLASEPYDDDPGWSDIPDRHLVDVRDAHVVVTPLSSH----

4zfjA

0.69

0.67

0.97

6.70

Env-PPAS

-CRHVAWLGAPRSLADLVLDPPQGLLVQSYAPRR-QKHGLNADGWGAGFFDDGVARRWRSDKPLWGDASFASVAPALRSRCVVAAVRSATIGSIE-PSASAPFSDGQWLLSHNGLVARGVLPLTGAAESTVDSAILAALIFSRGLDALGATIAEVGELDPNARLNILAANGSRLLATTWGDTLSVLRRPDGVVLASEPYDDDPGWSDIPDRHLVDVRDAHVVVTPLSSH----

2j6hA1

0.20

0.19

0.92

2.72

MUSTER

-CGIVGAIAQR-DVAEILLEGLRRLEYRGYDSA------------GLAVVDEGHMTRLRRLGKV---QMLAQAAEELHGGTGIAHTRWATHGEPSEVNA-HPHVSEHIVVVHNGIIENHLKARGYTFVSETDTEVIAHLVNWELKQTLREAVLRAIPQLRGAYGTVIMDHPDTLLAARSGSPLVIGLGMGENFIASDQLPVTRRFIFLEEGDIAEITRRSVNIFDKTGAEVKR

2j6hA1

0.20

0.19

0.92

4.62

dPPAS

-CGIVGAIAQ-RDVAEILLEGLRRLEYRGYDSA------------GLAVVDEGHMTRLRRLGKV---QMLAQAAEELHGGTGIAHTRWATHGEPSEVNA-HPHVSEHIVVVHNGIIENHLKARGYTFVSETDTEVIAHLVNWELKQTLREAVLRAIPQLRGAYGTVIMDHPDTLLAARSGSPLVIGLGMGENFIASDQLPVTRRFIFLEEGDIAEITRRSVNIFDKTGAEVKR

(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=1.91

Estimated TM-score = 0.99±0.04

Estimated RMSD = 2.0±1.6Å

Download Model 2

C-score=-1.22

Download Model 3

C-score=-2.23

Download Model 4

C-score=-3.40

Download Model 5

C-score=1.99

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	4zfjA	0.945	0.97	0.704	0.966
2	2j6hA	0.816	2.12	0.189	0.910
3	1ecgB1	0.778	2.47	0.196	0.893
4	1gph12	0.768	2.74	0.189	0.897
5	1te5A	0.740	2.89	0.216	0.858
6	1llwA	0.735	3.48	0.147	0.914
7	2vdcA1	0.729	3.45	0.134	0.910
8	3mdnA	0.721	2.12	0.237	0.798
9	1ct9A	0.649	2.33	0.130	0.738
10	1jgtB	0.594	3.09	0.127	0.721

(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	0.76	32	1eccA	ONL	Rep, Mult	2,87,88,90,91,101,113,114,132,133

	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	0.305	1gmsG	0.812	2.19	0.203	0.910	2.6.1.16	162,180,196
2	0.060	1ofdA	0.739	3.39	0.163	0.906	1.4.7.1	30
3	0.060	1wp6A	0.422	5.96	0.058	0.730	3.2.1.98	NA
4	0.060	2gl9D	0.387	3.88	0.117	0.511	3.5.1.26	92,114
5	0.060	2r7oA	0.427	5.90	0.061	0.755	2.7.7.48	NA
6	0.060	1ecfB	0.779	2.44	0.199	0.893	2.4.2.14	113,114
7	0.060	1seoD	0.389	3.81	0.092	0.511	3.4.19.5	84,92,114
8	0.060	1w9xA	0.417	6.09	0.077	0.730	3.2.1.1	NA
9	0.060	1hn0A	0.422	5.46	0.041	0.691	4.2.2.20	87
10	0.060	2a8jB	0.546	5.08	0.046	0.828	3.4.25.-	113
11	0.060	1mc1B	0.601	2.97	0.133	0.721	6.3.3.4	149,156,179
12	0.060	2gl9C	0.208	4.91	0.021	0.313	3.5.1.26	NA
13	0.060	2vdcA	0.729	3.44	0.134	0.910	1.4.1.13	NA
14	0.060	1aorB	0.447	5.87	0.066	0.764	1.2.7.5	NA
15	0.060	1gph1	0.768	2.74	0.189	0.897	2.4.2.14	NA
16	0.060	1ea0A	0.729	3.44	0.134	0.910	1.4.1.13	NA
17	0.060	2vf4X	0.312	5.98	0.044	0.545	2.6.1.16	NA
18	0.060	1mosA	0.316	6.04	0.055	0.558	2.6.1.16	73
19	0.060	1jqnA	0.458	5.79	0.057	0.790	4.1.1.31	NA
20	0.060	1jxaA	0.803	2.30	0.198	0.910	2.6.1.16	143

(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	0.75	0.947	1.11	0.73	0.97	4zfkB	GO:0006541 GO:0016787 GO:0016811 GO:0052699 GO:0052704
1	0.40	0.779	2.44	0.20	0.89	1ecfB	GO:0000287 GO:0004044 GO:0005737 GO:0005829 GO:0006164 GO:0006189 GO:0006541 GO:0009113 GO:0009116 GO:0016740 GO:0016757 GO:0042802 GO:0046872
2	0.27	0.737	2.10	0.21	0.82	3mdnD	GO:0006541 GO:0016740
3	0.25	0.649	2.33	0.13	0.74	1ct9A	GO:0000166 GO:0004066 GO:0004071 GO:0005524 GO:0005737 GO:0005829 GO:0006529 GO:0006541 GO:0008652 GO:0009063 GO:0016597 GO:0016874 GO:0042802 GO:0042803 GO:0070981
4	0.16	0.804	2.32	0.21	0.91	4amvA	GO:0004360 GO:0005737 GO:0005829 GO:0005975 GO:0006002 GO:0006048 GO:0006541 GO:0008483 GO:0016740 GO:0030246 GO:1901137
5	0.15	0.768	2.74	0.19	0.90	1gph1	GO:0000287 GO:0003824 GO:0004044 GO:0006164 GO:0006189 GO:0006541 GO:0008152 GO:0009113 GO:0009116 GO:0016740 GO:0016757 GO:0046872 GO:0051536 GO:0051539
6	0.13	0.740	2.89	0.22	0.86	1te5A
7	0.06	0.362	6.27	0.06	0.67	4mhbA	GO:0016491 GO:0055114
8	0.06	0.359	6.21	0.02	0.65	1iyxA	GO:0000015 GO:0000287 GO:0004634 GO:0005576 GO:0005737 GO:0006096 GO:0009986 GO:0016829 GO:0046872
9	0.06	0.358	6.11	0.04	0.65	4mksA	GO:0000015 GO:0000287 GO:0004634 GO:0005576 GO:0005737 GO:0006096 GO:0009986 GO:0016829 GO:0046872
10	0.06	0.365	5.89	0.05	0.64	4z17A	GO:0000015 GO:0000287 GO:0004634 GO:0005576 GO:0005737 GO:0006096 GO:0009986 GO:0016829 GO:0046872
11	0.06	0.314	6.23	0.04	0.57	4qwvA	GO:0000160 GO:0005737 GO:0006865 GO:0006935 GO:0046872 GO:0097588
12	0.06	0.370	5.99	0.05	0.66	3zlfA	GO:0000015 GO:0000287 GO:0004634 GO:0005576 GO:0005737 GO:0006096 GO:0009405 GO:0009986 GO:0016829 GO:0046872
13	0.06	0.312	6.22	0.05	0.54	3fj1A	GO:0005975 GO:0030246
14	0.06	0.361	6.22	0.06	0.66	1e9iD	GO:0000015 GO:0000287 GO:0004634 GO:0005576 GO:0005737 GO:0005829 GO:0005856 GO:0006096 GO:0009986 GO:0016020 GO:0016829 GO:0042802 GO:0046872
15	0.06	0.346	6.37	0.04	0.65	4ywsB	GO:0000015 GO:0000287 GO:0004634 GO:0005576 GO:0005737 GO:0006096 GO:0009986 GO:0016829 GO:0046872
16	0.06	0.304	6.36	0.05	0.56	2cb0B	GO:0005975 GO:0008483 GO:0016740 GO:0030246
17	0.06	0.319	5.70	0.05	0.54	3fkjA	GO:0004360 GO:0005975 GO:0006002 GO:0006047 GO:0016853 GO:0030246
18	0.06	0.320	5.66	0.03	0.52	2zj3A	GO:0004360 GO:0005829 GO:0005975 GO:0006002 GO:0006042 GO:0006047 GO:0006048 GO:0006112 GO:0006541 GO:0008483 GO:0009744 GO:0016597 GO:0016740 GO:0030246 GO:0032868 GO:0032869 GO:0032922 GO:0036498 GO:0045719 GO:0048511 GO:0051289 GO:0070062 GO:1901137

Consensus prediction of GO terms

Molecular Function	GO:0016811	GO:0042802	GO:0032559	GO:0046983	GO:0016211	GO:0031406	GO:0032550	GO:0035639	GO:0016884	GO:0004044	GO:0000287	GO:0070548
GO-Score	0.75	0.55	0.49	0.49	0.49	0.49	0.49	0.49	0.49	0.40	0.40	0.32
Biological Processes	GO:0006541	GO:0052704	GO:0006529	GO:0070982	GO:0009116	GO:0006189	GO:0009113	GO:0046349	GO:0009226	GO:0006047
GO-Score	0.93	0.75	0.49	0.49	0.40	0.40	0.40	0.32	0.32	0.32
Cellular Component	GO:0005829
GO-Score	0.62

(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.