I-TASSER results

I-TASSER results for job id Rv1505c

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

Input Sequence in FASTA format

>protein (221 residues)
MTKPLVIFGSGDIAQLAHYYFTRDSEYEVVAFTVDRDYASVSEFCGLPLVAFDEVAQRFP
PESHAMFVALAYAKLNGVRKEKYLAAKALGYELASYVSSHATVLNDGRIGENVFLLEDNT
IQPFVSIGNNVTLWSGNHIGHHSTIHDHCFLASHIVVSGGVVIEEQSFIGVNATLRDHIT
IGSRCVVGAGALLLGDADADGVYIGTKTERRPVPSTELRKI

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MTKPLVIFGSGDIAQLAHYYFTRDSEYEVVAFTVDRDYASVSEFCGLPLVAFDEVAQRFPPESHAMFVALAYAKLNGVRKEKYLAAKALGYELASYVSSHATVLNDGRIGENVFLLEDNTIQPFVSIGNNVTLWSGNHIGHHSTIHDHCFLASHIVVSGGVVIEEQSFIGVNATLRDHITIGSRCVVGAGALLLGDADADGVYIGTKTERRPVPSTELRKI
Prediction	CCCCEEEEHCCCHHHHHHHHHHHHCCCEEEEEHCCCCCCCCCEHCCEEHCCCHHHHHHCCCCCCEEEEEHCCCCCHHHHHHHHHHHHHHCCCCEEEHCCCEEHCCCEEHCCCCEHCCCCEHCCCEEHCCCCEHCCCCEHCCCCEHCCCCEHCCCCEHCCCEEHCCCCEHCCCEEHCCCEEHCCCCEHCCCEEEHCCCCCCEEEEEHCCEEHCCCHHHCCCC
Conf.Score	99768999588578999999999699759999959987677656685556886889876777878999877898769999999999998998658868967987985988984988997887995988996888997894797888986777995885986987995996885995994988996896775885567998799965657865774665579
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MTKPLVIFGSGDIAQLAHYYFTRDSEYEVVAFTVDRDYASVSEFCGLPLVAFDEVAQRFPPESHAMFVALAYAKLNGVRKEKYLAAKALGYELASYVSSHATVLNDGRIGENVFLLEDNTIQPFVSIGNNVTLWSGNHIGHHSTIHDHCFLASHIVVSGGVVIEEQSFIGVNATLRDHITIGSRCVVGAGALLLGDADADGVYIGTKTERRPVPSTELRKI
Prediction	86330000001100100010046365030000001454445541240200233620550476311000000236344103400530473715110100230302540401310201220301340401220301220301140402330201210301340302420201010101240400430000010001321454000000103426155741464
	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

CCCCEEEEHCCCHHHHHHHHHHHHCCCEEEEEHCCCCCCCCCEHCCEEHCCCHHHHHHCCCCCCEEEEEHCCCCCHHHHHHHHHHHHHHCCCCEEEHCCCEEHCCCEEHCCCCEHCCCCEHCCCEEHCCCCEHCCCCEHCCCCEHCCCCEHCCCCEHCCCEEHCCCCEHCCCEEHCCCEEHCCCCEHCCCEEEHCCCCCCEEEEEHCCEEHCCCHHHCCCC
MTKPLVIFGSGDIAQLAHYYFTRDSEYEVVAFTVDRDYASVSEFCGLPLVAFDEVAQRFPPESHAMFVALAYAKLNGVRKEKYLAAKALGYELASYVSSHATVLNDGRIGENVFLLEDNTIQPFVSIGNNVTLWSGNHIGHHSTIHDHCFLASHIVVSGGVVIEEQSFIGVNATLRDHITIGSRCVVGAGALLLGDADADGVYIGTKTERRPVPSTELRKI

4m98A

0.23

0.21

0.92

3.91

MUSTER

-NRKLAVIGAGGHGKVVAELAAALGTYGEIVFLDDRT---QGSVNGFPVIGTTLLLENSSPEQFDITVAVGN---NRIRRQITENAAALGFKLPVLIHPDATVSPSAIIGQGSVVMAKAVVQAGSVLKDGVIVNTAATVDHDCLLDAFVHISPGAHLSGNTRIGEESRIGTGACSRQQTTVGSGVTAGAGAVIVCDIPDGMTVAGNPAKPL----------

4m98A

0.23

0.21

0.92

6.04

dPPAS

-NRKLAVIGAGGHGKVVAELAAALGTYGEIVFLDDRT---QGSVNGFPVIGTLLLENSLSPEQFDITVAVGN---NRIRRQITENAAALGFKLPVLIHPDATVSPSAIIGQGSVVMAKAVVQAGSVLKDGVIVNTAATVDHDCLLDAFVHISPGAHLSGNTRIGEESRIGTGACSRQQTTVGSGVTAGAGAVIVCDIPDGMTVAGNPAKPL----------

4m98A

0.23

0.21

0.92

5.57

wdPPAS

-NRKLAVIGAGGHGKVVAELAAALGTYGEIVFLDDRT---QGSVNGFPVIGTTLLLENSSPEQFDITVAVGN---NRIRRQITENAAALGFKLPVLIHPDATVSPSAIIGQGSVVMAKAVVQAGSVLKDGVIVNTAATVDHDCLLDAFVHISPGAHLSGNTRIGEESRIGTGACSRQQTTVGSGVTAGAGAVIVCDIPDGMTVAGNPAKPL----------

4m98A

0.23

0.21

0.92

4.35

wMUSTER

--RKLAVIGAGGHGKVVAELAAALGTYGEIVFLDDRT---QGSVNGFPVIGTTLLLENSSPEQFDITVAVGN---NRIRRQITENAAALGFKLPVLIHPDATVSPSAIIGQGSVVMAKAVVQAGSVLKDGVIVNTAATVDHDCLLDAFVHISPGAHLSGNTRIGEESRIGTGACSRQQTTVGSGVTAGAGAVIVCDIPDGMTVAGNPAKPL----------

4m98A

0.23

0.21

0.92

4.76

wPPAS

-NRKLAVIGAGGHGKVVAELAAALGTYGEIVFLDDRT---QGSVNGFPVIGTTLLLENSSPEQFDITVAVGN---NRIRRQITENAAALGFKLPVLIHPDATVSPSAIIGQGSVVMAKAVVQAGSVLKDGVIVNTAATVDHDCLLDAFVHISPGAHLSGNTRIGEESRIGTGACSRQQTTVGSGVTAGAGAVIVCDIPDGMTVAGNPAKPL----------

4m98A

0.23

0.21

0.92

6.88

dPPAS2

-NRKLAVIGAGGHGKVVAELAAALGTYGEIVFLDDRT---QGSVNGFPVIGTTLLLENSSPEQFDITVAVGN---NRIRRQITENAAALGFKLPVLIHPDATVSPSAIIGQGSVVMAKAVVQAGSVLKDGVIVNTAATVDHDCLLDAFVHISPGAHLSGNTRIGEESRIGTGACSRQQTTVGSGVTAGAGAVIVCDIPDGMTVAGNPAKPL----------

4m98A

0.23

0.21

0.92

4.73

PPAS

-NRKLAVIGAGGHGKVVAELAAALGTYGEIVFLDDRT---QGSVNGFPVIGTTLLLENSSPEQFDITVAVGN---NRIRRQITENAAALGFKLPVLIHPDATVSPSAIIGQGSVVMAKAVVQAGSVLKDGVIVNTAATVDHDCLLDAFVHISPGAHLSGNTRIGEESRIGTGACSRQQTTVGSGVTAGAGAVIVCDIPDGMTVAGNPAKPL----------

4m98A

0.23

0.21

0.92

5.33

Env-PPAS

-NRKLAVIGAGGHGKVVAELAAALGTYGEIVFLDDRT---QGSVNGFPVIGTTLLLENSSPEQFDITVAVGN---NRIRRQITENAAALGFKLPVLIHPDATVSPSAIIGQGSVVMAKAVVQAGSVLKDGVIVNTAATVDHDCLLDAFVHISPGAHLSGNTRIGEESRIGTGACSRQQTTVGSGVTAGAGAVIVCDIPDGMTVAGNPAKPL----------

4m9cA

0.21

0.19

0.94

3.67

MUSTER

MTMIIGVYGASGFGKEVMPLVRQQFSKEQFAFIDDG--LSGTTLNGYPVLSYLDFISK-PADHKAVTIAIAN---SVVREKLVSLLEKDGVQHLAVQSTNTVILDEVEIGEGSLLCPFTCLTSNIKIGKFFHANIYSYVAHDCVIGDYVTFAPGAKCNGNIHIEDHAYIGTGAVIKQGLIIGKGAIVGMGAVVTKSVPAGVTVVGNPARILERK-------

4m9cA

0.21

0.19

0.94

5.37

dPPAS

MTMIIGVYGASGFGKEVMPLVRQQFSKEQFAFIDDG--LSGTTLNGYPVLSYLDFISK-PADHKAVTIAIAN---SVVREKLVSLLEKDGVQHLAVQSTNTVILDEVEIGEGSLLCPFTCLTSNIKIGKFFHANIYSYVAHDCVIGDYVTFAPGAKCNGNIHIEDHAYIGTGAVIKQGLIIGKGAIVGMGAVVTKSVPAGVTVVGNPARILERK-------

(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 3 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=1.38

Estimated TM-score = 0.90±0.06

Estimated RMSD = 2.8±2.1Å

Download Model 2

C-score=-0.32

Download Model 3

C-score=-3.16

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	4m98A	0.896	1.00	0.225	0.923
2	4ea7A	0.866	1.55	0.251	0.919
3	4m9cA	0.866	1.93	0.202	0.941
4	3bssA	0.798	1.53	0.194	0.842
5	1kgtA	0.611	3.18	0.110	0.733
6	5b04I	0.602	4.16	0.098	0.778
7	3fsyD	0.589	3.58	0.096	0.756
8	3r5aA	0.583	3.54	0.095	0.733
9	2ggoA	0.583	3.91	0.078	0.724
10	2rijA	0.576	3.63	0.097	0.729

(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	0.51	39	3bsyA	ACO	Rep, Mult	134,150,152,153,168,170,171,186,188,189,202,204,211
2	0.13	14	4j09A	III	Rep, Mult	138,140,141,156,158,159,174,176,192,193,207
3	0.06	5	4ea7A	JB2	Rep, Mult	8,11,12,13,33,34,35,53,70,71,78,82,150
4	0.03	4	2oi5B	ACO	Rep, Mult	128,129,144,146,147,164,165,182,184
5	0.03	2	4ea9A	JBT	Rep, Mult	8,11,12,13,33,34,35,53,70,71,78,82,134,150,153,168,170,171,188,189,204,211
6	0.03	4	4m99B	ACO	Rep, Mult	140,141,158,159,176,177,194,206,207,209
7	0.02	2	3mqgA	U5P	Rep, Mult	134,135,153,168,171
8	0.02	2	3r8yA	CA	Rep, Mult	122,140,141,159
9	0.02	3	2iu8A	UD1	Rep, Mult	141,142,159,160,177,178
10	0.01	1	3ectA	CA	Rep, Mult	172,190
11	0.01	1	3nz2C	MG	Rep, Mult	190,192,206
12	0.01	1	3mqgF	U5P	Rep, Mult	96,114,134
13	0.01	1	3mqhA	MJZ	Rep, Mult	132,150,170

	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	0.257	1ocxB	0.506	2.72	0.166	0.566	2.3.1.79	145,152,170,180,182,190,196
2	0.210	2ic7A	0.509	2.77	0.211	0.575	2.3.1.79	133
3	0.097	1ocxA	0.506	2.72	0.166	0.566	2.3.1.79	NA
4	0.060	1txgA	0.498	4.78	0.057	0.720	1.1.1.94	NA
5	0.060	1kruA	0.527	2.93	0.176	0.602	2.3.1.18	NA
6	0.060	3gvdI	0.517	4.74	0.143	0.729	2.3.1.30	NA
7	0.060	1u8xX	0.497	4.92	0.049	0.751	3.2.1.122	132,145,187
8	0.060	1v3wA	0.550	1.88	0.148	0.588	4.2.1.1	20
9	0.060	3d8vA	0.533	3.64	0.079	0.642	2.7.7.23,2.3.1.157	NA
10	0.060	1yp3C	0.499	3.77	0.139	0.620	2.7.7.27	NA
11	0.060	2iu8A	0.528	3.08	0.115	0.602	2.3.1.-	141
12	0.060	3cj8A	0.496	3.44	0.109	0.593	2.3.1.89	197
13	0.060	1s6yA	0.495	4.91	0.055	0.747	3.2.1.86	8,77
14	0.060	3mc4A	0.518	4.41	0.106	0.670	2.3.1.30	133,140
15	0.060	3eg4A	0.544	3.84	0.099	0.697	2.3.1.117	135
16	0.060	3fsyD	0.589	3.58	0.096	0.756	2.3.1.117	162
17	0.060	3hjjA	0.508	2.59	0.152	0.570	2.3.1.79	NA
18	0.060	1krvC	0.526	2.80	0.183	0.597	2.3.1.18	145,152,180,182,186,188,190,196
19	0.060	2vheA	0.820	1.51	0.199	0.864	2.7.7.23	141
20	0.060	3eh0A	0.556	3.59	0.090	0.661	2.3.1.-	141
21	0.060	1hm9B	0.541	3.85	0.155	0.674	2.3.1.157,2.7.7.23	128
22	0.060	1ssqD	0.527	4.05	0.108	0.679	2.3.1.30	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	0.39	0.876	1.60	0.24	0.93	4eaaA	GO:0016740
1	0.36	0.901	1.12	0.22	0.93	4m99A	GO:0016020 GO:0016021 GO:0016740
2	0.35	0.866	1.93	0.20	0.94	4m9cA	GO:0016740 GO:0016746
3	0.34	0.798	1.53	0.19	0.84	3bssA	GO:0006486 GO:0016740 GO:0016746 GO:0016747 GO:0018279
4	0.23	0.565	2.91	0.17	0.64	3t57A	GO:0005739 GO:0006629 GO:0008780 GO:0009245 GO:0016740 GO:0016746 GO:2001289
5	0.21	0.568	2.82	0.16	0.64	5depA	GO:0005737 GO:0006629 GO:0008610 GO:0008780 GO:0009245 GO:0016740 GO:0016746
6	0.18	0.490	2.38	0.11	0.54	4mfgA	GO:0016740 GO:0016746
7	0.17	0.562	2.73	0.16	0.63	4eqyA	GO:0005737 GO:0006629 GO:0008610 GO:0008780 GO:0009245 GO:0016740 GO:0016746
8	0.16	0.527	4.05	0.11	0.68	1ssqD	GO:0005737 GO:0006535 GO:0008652 GO:0009001 GO:0016740 GO:0016746 GO:0019344
9	0.16	0.544	3.66	0.10	0.69	3tk8A	GO:0005737 GO:0008652 GO:0008666 GO:0009085 GO:0009089 GO:0016740 GO:0016746 GO:0019877
10	0.15	0.509	2.77	0.21	0.57	2ic7A	GO:0008925 GO:0016407 GO:0016740 GO:0016746
11	0.15	0.548	1.90	0.16	0.59	4n27A	GO:0016740 GO:0046872
12	0.14	0.564	2.79	0.17	0.63	4e6tB	GO:0005737 GO:0006629 GO:0008610 GO:0008780 GO:0009245 GO:0016740 GO:0016746
13	0.14	0.551	1.85	0.15	0.59	2fkoA	GO:0046872
14	0.14	0.551	1.93	0.16	0.59	3r1wB
15	0.13	0.562	2.90	0.16	0.63	3r0sA	GO:0005737 GO:0006629 GO:0008610 GO:0008780 GO:0009245 GO:0016740 GO:0016746
16	0.12	0.557	3.30	0.13	0.65	3pmoA	GO:0006629 GO:0009245 GO:0016410 GO:0016740 GO:0016746 GO:0016747
17	0.12	0.562	2.89	0.16	0.63	1j2zA	GO:0005737 GO:0006629 GO:0008610 GO:0008780 GO:0009245 GO:0016740 GO:0016746
18	0.12	0.546	1.81	0.11	0.58	3ixcA	GO:0016740 GO:0046872
19	0.11	0.539	3.93	0.14	0.68	4e1kA	GO:0000287 GO:0000902 GO:0003824 GO:0003977 GO:0005737 GO:0006048 GO:0008152 GO:0008360 GO:0009103 GO:0009245 GO:0009252 GO:0016740 GO:0016746 GO:0016779 GO:0019134 GO:0046872 GO:0071555
20	0.11	0.544	3.84	0.10	0.70	3eg4A	GO:0005737 GO:0008652 GO:0008666 GO:0009085 GO:0009089 GO:0016740 GO:0016746 GO:0019877
21	0.10	0.534	3.61	0.12	0.66	3dk5A	GO:0000287 GO:0000902 GO:0003824 GO:0003977 GO:0005737 GO:0006048 GO:0008152 GO:0008360 GO:0009103 GO:0009245 GO:0009252 GO:0016740 GO:0016746 GO:0016779 GO:0019134 GO:0046872 GO:0071555

Consensus prediction of GO terms

Molecular Function	GO:0008374
GO-Score	0.47
Biological Processes	GO:0008654	GO:0046493	GO:0006040	GO:0009247	GO:1901271	GO:0018279
GO-Score	0.47	0.47	0.47	0.47	0.47	0.34
Cellular Component	GO:0043231	GO:0044444	GO:0016021
GO-Score	0.47	0.47	0.36

(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.