I-TASSER results

I-TASSER results for job id Rv1154c

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

Input Sequence in FASTA format

>protein (213 residues)
MEFPLITANSLSSKTWRAMPRAYVAVASFSGGLVQSGMAKFAAFLRGVNVGGVNLKMAEV
ATALTDAGFCNVRTILASGNVLLESTCGAAEVREKTEATLRERFGYDAWALIYDVDTVRT
IVTAYPFECELEGYQSYVTFVADAAILDELSALADTAGPDENISRGPDPLGVLYWQVPKG
STLDSTIGQTMGKKRYKSSTTTRNLRTLAKVLR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MEFPLITANSLSSKTWRAMPRAYVAVASFSGGLVQSGMAKFAAFLRGVNVGGVNLKMAEVATALTDAGFCNVRTILASGNVLLESTCGAAEVREKTEATLRERFGYDAWALIYDVDTVRTIVTAYPFECELEGYQSYVTFVADAAILDELSALADTAGPDENISRGPDPLGVLYWQVPKGSTLDSTIGQTMGKKRYKSSTTTRNLRTLAKVLR
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEHCCHCCCCCCCCHHHHHHHHHHHCCCCCEEEEHCCCEEEHCCCCHHHHHHHHHHHHHHHHCCCCCEEEHCHHHHHHHHHHCCCCCCCCCCEEEEEEHCCCCCHHHHHHHHHCCCCCCEEEEHCCCEEEEEEEHCCCCCCCCCHHHHHHHHHCCCCCEHCHHHHHHHHHC
Conf.Score	988765566667665555555556766677776667888699998446689997787999999999899885577545879998699999999999999999979998689868999999999799976789876899996899999999999876889978999767659999997588776675566776655589754336899999979
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MEFPLITANSLSSKTWRAMPRAYVAVASFSGGLVQSGMAKFAAFLRGVNVGGVNLKMAEVATALTDAGFCNVRTILASGNVLLESTCGAAEVREKTEATLRERFGYDAWALIYDVDTVRTIVTAYPFECELEGYQSYVTFVADAAILDELSALADTAGPDENISRGPDPLGVLYWQVPKGSTLDSTIGQTMGKKRYKSSTTTRNLRTLAKVLR
Prediction	771322314314543043134233534544442355604100000001134354140640251047251640312041210103174437402520251047416140210023372035007613346655622100000255143730550475735513022055310000010246443414023420444162400011230032128
	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

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEHCCHCCCCCCCCHHHHHHHHHHHCCCCCEEEEHCCCEEEHCCCCHHHHHHHHHHHHHHHHCCCCCEEEHCHHHHHHHHHHCCCCCCCCCCEEEEEEHCCCCCHHHHHHHHHCCCCCCEEEEHCCCEEEEEEEHCCCCCCCCCHHHHHHHHHCCCCCEHCHHHHHHHHHC
MEFPLITANSLSSKTWRAMPRAYVAVASFSGGLVQSGMAKFAAFLRGVNVGGVNLKMAEVATALTDAGFCNVRTILASGNVLLESTCGAAEVREKTEATLRERFGYDAWALIYDVDTVRTIVTAYPFECELEGYQSYVTFVADAAILDELSALADTAGPDENISRGPDPLGVLYWQVPKGSTLDSTIGQTMGKKRYKSSTTTRNLRTLAKVLR

2hiyD

0.22

0.18

0.83

2.62

MUSTER

-----------------------------------SNATRYALLVRGINVGGKNKVVAELRQELTNLGLEKVESYINSGNIFFTSIDSKAQLVEKLETFFAVHYPFIQSFSLLSLEDFEAELENLPAWWSRDLARKDFLFYTEGLDVDQVIATVESELKDEVLYFGKL--GIFWGKFSEESYSKTAYHKYLLKVPFYRHITIRNAKTFDKIGQ

2hiyD

0.20

0.16

0.83

3.63

dPPAS

-----------------------------------SNATRYALLVRGINVGGKNKVVAELRQELTNLGLEKVESYINSGNIFFTSIDSKAQLVEKLETFFAVHYPFIQSFSLLSLEDFEAELENLPAWWSRDLARKDFLFYTEGLDVDQVIATVESLELKDEVLYFGKL-GIFWGKFSEESYSKTAYHKYLLKVPFYRHITIRNAKTFDKIGQ

2hiyD

0.22

0.18

0.83

4.26

wdPPAS

-----------------------------------SNATRYALLVRGINVGGKNKVVAELRQELTNLGLEKVESYINSGNIFFTSIDSKAQLVEKLETFFAVHYPFIQSFSLLSLEDFEAELENLPAWWSRDLARKDFLFYTEGLDVDQVIATVESELKDEVLYFGKL--GIFWGKFSEESYSKTAYHKYLLKVPFYRHITIRNAKTFDKIGQ

2hiyD

0.21

0.17

0.82

3.08

wMUSTER

------------------------------------NATRYALLVRGINVGGKNKVVAELRQELTNLGLEKVESYINSGNIFFTSIDSKAQLVEKLETFFAVHYPFIQSFSLLSLEDFEAELENLPAWWSRDLARKDFLFYTEGLDVDQVIATVESELKDEVLYFGKL--GIFWGKFSEESYSKTAYHKYLLKVPFYRHITIRNAKTFDKIGQ

2hiyD

0.22

0.18

0.83

4.53

wPPAS

-----------------------------------SNATRYALLVRGINVGGKNKVVAELRQELTNLGLEKVESYINSGNIFFTSIDSKAQLVEKLETFFAVHYPFIQSFSLLSLEDFEAELENLPAWWSRDLARKDFLFYTEGLDVDQVIATVESELKDEVLYFGKL--GIFWGKFSEESYSKTAYHKYLLKVPFYRHITIRNAKTFDKIGQ

2hiyD

0.22

0.18

0.83

8.50

dPPAS2

-----------------------------------SNATRYALLVRGINVGGKNKVVAELRQELTNLGLEKVESYINSGNIFFTSIDSKAQLVEKLETFFAVHYPFIQSFSLLSLEDFEAELENLPAWWSRDLARKDFLFYTEGLDVDQVIATVESELKDEVLYFGKL--GIFWGKFSEESYSKTAYHKYLLKVPFYRHITIRNAKTFDKIGQ

2hiyD

0.22

0.18

0.83

3.94

PPAS

-----------------------------------SNATRYALLVRGINVGGKNKVVAELRQELTNLGLEKVESYINSGNIFFTSIDSKAQLVEKLETFFAVHYPFIQSFSLLSLEDFEAELENLPAWWSRDLARKDFLFYTEGLDVDQVIATVESELKDEVLYFGKL--GIFWGKFSEESYSKTAYHKYLLKVPFYRHITIRNAKTFDKIGQ

2hiyD

0.22

0.18

0.83

4.38

Env-PPAS

-----------------------------------SNATRYALLVRGINVGGKNKVVAELRQELTNLGLEKVESYINSGNIFFTSIDSKAQLVEKLETFFAVHYPFIQSFSLLSLEDFEAELENLPAWWSRDLARKDFLFYTEGLDVDQVIATVESELKDEVLYFGKL--GIFWGKFSEESYSKTAYHKYLLKVPFYRHITIRNAKTFDKIGQ

2hiyD1

0.29

0.11

0.37

1.12

MUSTER

-----------------------------------SNATRYALLVRGINVGGKNKVVAELRQELTNLGLEKVESYINSGNIFFTSIDSKAQLVEKLETFFAVHYPFIQSFSLL----------------------------------------------------------------------------------------------------

2hiyD1

0.29

0.11

0.37

1.96

dPPAS

-----------------------------------SNATRYALLVRGINVGGKNKVVAELRQELTNLGLEKVESYINSGNIFFTSIDSKAQLVEKLETFFAVHYPFIQSFSLL----------------------------------------------------------------------------------------------------

(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=-0.46

Estimated TM-score = 0.65±0.13

Estimated RMSD = 6.4±3.9Å

Download Model 2

C-score=-1.85

Download Model 3

C-score=-1.52

Download Model 4

C-score=-0.94

Download Model 5

C-score=-3.69

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	2hiyD	0.809	0.82	0.210	0.826
2	4k0eA	0.501	4.38	0.044	0.723
3	2j8sA	0.473	4.64	0.069	0.700
4	3zphA	0.467	5.23	0.040	0.775
5	3k07A	0.452	4.46	0.069	0.648
6	2ptzA	0.445	5.33	0.079	0.728
7	3qtpA	0.445	5.37	0.066	0.718
8	3dsiA	0.443	5.51	0.082	0.761
9	3otrA	0.443	5.47	0.061	0.723
10	3danA	0.442	5.66	0.077	0.770

(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	0.05	4	2qv6C	CA	Rep, Mult	44,45,79,200
2	0.05	4	3h8aC	III	Rep, Mult	42,79,82,83
3	0.04	3	4dh9F	NUC	Rep, Mult	39,41,92,93,97,100,109,111,112,113,114
4	0.04	3	3aodC	RFP	Rep, Mult	42,43,44,80,113
5	0.04	3	3dsjA	HEM	Rep, Mult	60,61,64,65,68,95,96,111
6	0.04	3	3t51A	CU	Rep, Mult	44,80,138
7	0.02	2	3dsiA	T24	Rep, Mult	92,93,96,97,100,108,109
8	0.02	2	3fgvB	UNL	Rep, Mult	138,173,202
9	0.02	2	2ptz0	III	Rep, Mult	8,9,54,56,60,73,74,82,84
10	0.02	2	3h8aA	III	Rep, Mult	42,44,47,95,102
11	0.02	2	3dbmA	HO2	Rep, Mult	60,64,104,110
12	0.02	2	1tkoB	FE	Rep, Mult	94,97
13	0.02	2	3dsiB	HEM	Rep, Mult	79,80,204,207,208
14	0.01	1	3pm0A	HEM	Rep, Mult	48,49,56,110,111
15	0.01	1	3gr3A	FMN	Rep, Mult	77,78,79,80,191
16	0.01	1	3ecaA	ASP	Rep, Mult	80,130
17	0.01	1	2xctS	CPF	Rep, Mult	46,47
18	0.01	1	3damA	HEM	Rep, Mult	18,22,25,84,85,92,209,210
19	0.01	1	3pm0A	BHF	Rep, Mult	118,121,169,205,208,209,213
20	0.01	1	3fcsC	IMD	Rep, Mult	156,185

	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	2frvD	0.432	5.96	0.033	0.765	1.12.2.1	209
2	0.060	2psnC	0.432	5.54	0.036	0.728	4.2.1.11	NA
3	0.060	2ptwA	0.437	5.45	0.069	0.718	4.2.1.11	2
4	0.060	2f9qA	0.423	6.00	0.093	0.789	1.14.14.1	81
5	0.060	2w0aA	0.423	5.95	0.059	0.775	1.14.13.70	NA
6	0.060	3hf2A	0.426	5.84	0.036	0.761	1.14.14.1,1.6.2.4	NA
7	0.060	2akzA	0.440	5.55	0.063	0.732	4.2.1.11	NA
8	0.060	1nb7A	0.424	4.83	0.050	0.638	3.4.21.98	NA
9	0.060	1e9xA	0.425	5.67	0.048	0.747	1.14.13.70	NA
10	0.060	1yrqI	0.425	5.67	0.049	0.742	1.12.2.1	82
11	0.060	3k9vA	0.425	5.83	0.065	0.761	1.14.13.-	NA
12	0.060	2vn0A	0.429	5.62	0.071	0.761	1.14.14.1	140
13	0.060	1jpzB	0.430	5.92	0.054	0.770	1.14.14.1,1.6.2.4	NA
14	0.060	1pdyA	0.439	5.58	0.046	0.728	4.2.1.11	2
15	0.060	1iyxA	0.438	5.65	0.056	0.732	4.2.1.11	NA
16	0.060	1uwkA	0.433	5.30	0.053	0.714	4.2.1.49	170
17	0.060	1w0eA	0.344	6.17	0.054	0.624	1.14.13.67,1.14.14.1	NA
18	0.060	3hfwA	0.425	4.79	0.058	0.653	3.2.2.19	NA
19	0.060	2pa6A	0.439	5.36	0.068	0.718	4.2.1.11	2

(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	0.07	0.493	4.39	0.04	0.72	4k0eC	GO:0005215 GO:0006810 GO:0006812 GO:0008324 GO:0016020 GO:0016021 GO:0098655
1	0.07	0.501	4.38	0.04	0.72	4k0eA	GO:0005215 GO:0006810 GO:0006812 GO:0008324 GO:0016020 GO:0016021 GO:0098655
2	0.07	0.462	4.82	0.04	0.69	2v50D	GO:0005215 GO:0005886 GO:0006810 GO:0006855 GO:0015238 GO:0016020 GO:0016021 GO:0046677
3	0.07	0.503	4.28	0.05	0.71	4k0eB	GO:0005215 GO:0006810 GO:0006812 GO:0008324 GO:0016020 GO:0016021 GO:0098655
4	0.07	0.477	4.78	0.06	0.73	3w9iF	GO:0005215 GO:0005886 GO:0006810 GO:0006855 GO:0015238 GO:0016020 GO:0016021 GO:0046677
5	0.07	0.431	5.05	0.03	0.65	3d9bA	GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0006855 GO:0015238 GO:0015307 GO:0016020 GO:0016021 GO:0042493 GO:0042802 GO:0046618
6	0.06	0.434	4.76	0.07	0.64	4dnrA	GO:0005215 GO:0005375 GO:0005507 GO:0005886 GO:0006810 GO:0006811 GO:0006812 GO:0006825 GO:0006878 GO:0008324 GO:0010272 GO:0010273 GO:0015080 GO:0015673 GO:0015679 GO:0016020 GO:0016021 GO:0046688 GO:0060003 GO:1902601
7	0.06	0.433	4.97	0.07	0.68	5en5C	GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0006855 GO:0015238 GO:0015307 GO:0016020 GO:0016021 GO:0042493 GO:0042802 GO:0046618
8	0.06	0.422	5.00	0.06	0.63	4r86B	GO:0005215 GO:0006810 GO:0016020 GO:0016021
9	0.06	0.437	5.20	0.06	0.72	4mt1A	GO:0005215 GO:0006810 GO:0016020 GO:0016021
10	0.06	0.439	4.97	0.06	0.67	3nogA	GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0006855 GO:0015238 GO:0015307 GO:0016020 GO:0016021 GO:0042493 GO:0042802 GO:0046618
11	0.06	0.370	5.56	0.05	0.63	4i0wD	GO:0004252 GO:0006508 GO:0008233 GO:0008236 GO:0016787
12	0.06	0.400	5.71	0.05	0.69	3i6sA	GO:0004252 GO:0005618 GO:0006508 GO:0008233 GO:0008236 GO:0016787
13	0.06	0.314	6.06	0.02	0.54	3wxvA	GO:0004872 GO:0005886 GO:0006629 GO:0006631 GO:0007186 GO:0009755 GO:0010633 GO:0010719 GO:0010906 GO:0016020 GO:0016021 GO:0019216 GO:0019395 GO:0019901 GO:0030308 GO:0031226 GO:0033210 GO:0033211 GO:0042593 GO:0042802 GO:0046426 GO:0046427 GO:0046628 GO:0046872 GO:0046982 GO:0055100 GO:0097003 GO:1901223
14	0.06	0.307	6.17	0.08	0.58	3qvjA	GO:0006807 GO:0036361
15	0.06	0.289	4.76	0.08	0.45	4phtY	GO:0006810 GO:0008565 GO:0009276 GO:0015031 GO:0016021
16	0.06	0.289	6.07	0.05	0.50	3qivA
17	0.06	0.284	5.68	0.07	0.49	3lwkA	GO:0005212 GO:0007601 GO:0043010
18	0.06	0.291	3.77	0.05	0.39	3jb9Y	GO:0000166 GO:0000387 GO:0000974 GO:0003676 GO:0003723 GO:0005634 GO:0005681 GO:0006397 GO:0007049 GO:0008380 GO:0017070 GO:0036002 GO:0045292 GO:0046872 GO:0071006 GO:0071007

Consensus prediction of GO terms

Molecular Function	GO:0015075
GO-Score	0.37
Biological Processes	GO:0034220
GO-Score	0.37
Cellular Component	GO:0031224
GO-Score	0.46

(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.