I-TASSER results

I-TASSER results for job id Rv2923c

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

Input Sequence in FASTA format

>protein (137 residues)
MTQLWVERTGTRRYIGRSTRGAQVLVGSEDVDGVFTPGELLKIALAACSGMASDQPLARR
LGDDYQAVVKVSGAADRDQERYPLIEETMELDLSGLTEDEKERLLVVINRAVELACTVGR
TLKSGTTVNLEVVDVGA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MTQLWVERTGTRRYIGRSTRGAQVLVGSEDVDGVFTPGELLKIALAACSGMASDQPLARRLGDDYQAVVKVSGAADRDQERYPLIEETMELDLSGLTEDEKERLLVVINRAVELACTVGRTLKSGTTVNLEVVDVGA
Prediction	CCEEEEEEHCCCEEEEHCCCCCEEEHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEEEEHCCCCCCCEEEEEEEEEEHCCCCHHHHHHHHHHHHHHHHHCCCHHHHHCCCCEEEEEEEHCCC
Conf.Score	95899999869689999699969996899999999999999999976577679999999689875899999998746888865899999999789999999999999999998789588875688679999997589
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MTQLWVERTGTRRYIGRSTRGAQVLVGSEDVDGVFTPGELLKIALAACSGMASDQPLARRLGDDYQAVVKVSGAADRDQERYPLIEETMELDLSGLTEDEKERLLVVINRAVELACTVGRTLKSGTTVNLEVVDVGA
Prediction	74504053336341404265424040344766542211100120323110110230054363625604030414446477414404030304054156731520350064127440312312557150413045478
	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

                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCEEEEEEHCCCEEEEHCCCCCEEEHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEEEEHCCCCCCCEEEEEEEEEEHCCCCHHHHHHHHHHHHHHHHHCCCHHHHHCCCCEEEEEEEHCCC
MTQLWVERTGTRRYIGRSTRGAQVLVGSEDVDGVFTPGELLKIALAACSGMASDQPLARRLGDDYQAVVKVSGAADRDQERYPLIEETMELDLSGLTEDEKERLLVVINRAVELACTVGRTLKSGTTVNLEVVDVGA

1ml8A

0.20

0.19

0.96

3.57

MUSTER

M-QARVKWVEGLTFLGESASGHQILMDGNSGDKAPSPMEMVLMAAGGCSAIDVVSILQKGRQDVVDCEVKLTSERR--ERLFTHINLHFIVTGRDLK---DAAVARAVDLSAEKYCSVALMLEKAVNITHSYEVVAA

1ml8A

0.19

0.18

0.96

5.35

dPPAS

-MQARVKWVEGLTFLGESASGHQILMDGNSGDKAPSPMEMVLMAAGGCSAIDVVSILQKGRQDVVDCEVKLTSERR--ERLFTHINLHFIVTGRDLK---DAAVARAVDLSAEKYCSVALMLEKAVNITHSYEVVAA

1ml8A

0.20

0.19

0.96

5.40

wdPPAS

M-QARVKWVEGLTFLGESASGHQILMDGNSGDKAPSPMEMVLMAAGGCSAIDVVSILQKGRQDVVDCEVKLTSERR--ERLFTHINLHFIVTGRDLK---DAAVARAVDLSAEKYCSVALMLEKAVNITHSYEVVAA

1ml8A

0.19

0.18

0.95

4.40

wMUSTER

--QARVKWVEGLTFLGESASGHQILMDGNSGDKAPSPMEMVLMAAGGCSAIDVVSILQKGRQDVVDCEVKLTSERR--ERLFTHINLHFIVTGRDLK---DAAVARAVDLSAEKYCSVALMLEKAVNITHSYEVVAA

1ml8A

0.20

0.19

0.96

5.17

wPPAS

M-QARVKWVEGLTFLGESASGHQILMDGNSGDKAPSPMEMVLMAAGGCSAIDVVSILQKGRQDVVDCEVKLTSER--RERLFTHINLHFIVTGRDLK---DAAVARAVDLSAEKYCSVALMLEKAVNITHSYEVVAA

1ml8A

0.20

0.19

0.96

8.79

dPPAS2

M-QARVKWVEGLTFLGESASGHQILMDGNSGDKAPSPMEMVLMAAGGCSAIDVVSILQKGRQDVVDCEVKLTSERR--ERLFTHINLHFIVTGRDLK---DAAVARAVDLSAEKYCSVALMLEKAVNITHSYEVVAA

1ml8A

0.20

0.19

0.96

4.71

PPAS

M-QARVKWVEGLTFLGESASGHQILMDGNSGDKAPSPMEMVLMAAGGCSAIDVVSILQKGRQDVVDCEVKLTSER--RERLFTHINLHFIVTGRDLK---DAAVARAVDLSAEKYCSVALMLEKAVNITHSYEVVAA

1ml8A

0.20

0.19

0.96

4.79

Env-PPAS

M-QARVKWVEGLTFLGESASGHQILMDGNSGDKAPSPMEMVLMAAGGCSAIDVVSILQKGRQDVVDCEVKLTSER--RERLFTHINLHFIVTGRDLK---DAAVARAVDLSAEKYCSVALMLEKAVNITHSYEVVAA

2e8fA

0.17

0.15

0.93

3.02

MUSTER

K-EVELELSSEATFLSKTSIG-EITAG----EKGLNPMELLLVSIGSCSGVDVYHILKKKRQEVKDIKIFLKGKRRKHPKIYEEIEIKYVAVG-KVE---EKALEQAVKLSTEKYCSVLAMVKPSTNLKISWEVKWE

2e8fA

0.16

0.15

0.93

4.34

dPPAS

VKEVELELSSEATFLSKTSIGEITAG-----EKGLNPMELLLVSIGSCSGVDVYHILKKKRQEVKDIKIFLKGKRREKPKIYEEIEIKYVAVG----KVEEKALEQAVKLSTEKYCSVLAMVKPSTNLKISWEVKWE

(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=1.67

Estimated TM-score = 0.95±0.05

Estimated RMSD = 1.5±1.4Å

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	1ml8A	0.936	0.66	0.191	0.956
2	2e8fA	0.871	1.25	0.156	0.934
3	1lqlC	0.826	1.89	0.154	0.949
4	2onfA	0.803	1.98	0.164	0.934
5	2d7vA	0.795	2.06	0.159	0.920
6	2pn2A	0.775	1.99	0.153	0.905
7	1vlaA	0.766	2.47	0.173	0.927
8	2oplB	0.741	2.02	0.141	0.861
9	1nyeD	0.739	2.59	0.156	0.934
10	1ukkA	0.723	2.59	0.192	0.912

(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	0.40	6	3lusA	MCO	Rep, Mult	48,51,52,117
2	0.11	2	2onfB	COA	Rep, Mult	51,56,59,61,106,110,113,114,116
3	0.10	2	2onfA	COA	Rep, Mult	31,39,79,80

	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	1x54A	0.536	3.90	0.080	0.766	6.1.1.22	NA
2	0.060	1mhyB	0.517	4.49	0.069	0.825	1.14.13.25	117,121
3	0.060	1nyeD	0.739	2.59	0.156	0.934	1.11.1.15	39,46,48,52
4	0.060	2obvA	0.547	2.77	0.070	0.715	2.5.1.6	20,42
5	0.060	2zzgA	0.520	3.97	0.070	0.818	6.1.1.7	44
6	0.060	3ixzA	0.538	4.15	0.054	0.876	3.6.3.10	NA
7	0.060	1bbuA	0.513	3.99	0.049	0.737	6.1.1.6	NA
8	0.060	2dplA	0.524	3.97	0.079	0.745	6.3.5.2	NA
9	0.060	2ajqA	0.547	4.11	0.122	0.818	2.7.7.7	NA
10	0.060	2dr9A	0.518	3.90	0.081	0.723	2.7.7.21,2.7.7.25	NA
11	0.060	1wydB	0.547	4.10	0.112	0.781	6.1.1.12	NA
12	0.060	1xvgC	0.541	4.35	0.067	0.825	1.14.13.25	117
13	0.060	1b8aA	0.538	4.13	0.072	0.774	6.1.1.12	NA
14	0.060	3e9hA	0.511	4.14	0.074	0.745	6.1.1.6	NA
15	0.060	3b8eA	0.535	4.44	0.044	0.912	3.6.3.9	NA
16	0.060	3c66A	0.500	3.11	0.057	0.686	2.7.7.19	NA
17	0.060	3b7wA	0.503	4.27	0.068	0.839	6.2.1.2	NA
18	0.060	2jifA	0.504	4.38	0.017	0.781	1.3.99.-	NA
19	0.060	3i7fA	0.527	4.08	0.055	0.766	6.1.1.12	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	0.43	0.872	1.24	0.16	0.93	2e8cA
1	0.40	0.936	0.66	0.19	0.96	1ml8A
2	0.40	0.766	2.47	0.17	0.93	1vlaA
3	0.34	0.736	2.55	0.20	0.92	1ukkA	GO:0004601 GO:0006979 GO:0098869
4	0.32	0.775	1.99	0.15	0.91	2pn2A
5	0.31	0.716	2.82	0.13	0.91	3i07B	GO:0006979 GO:0009636 GO:0046872
6	0.30	0.826	1.89	0.15	0.95	1lqlC	GO:0004601 GO:0005737 GO:0016491 GO:0055114 GO:0098869
7	0.30	0.739	2.59	0.16	0.93	1nyeD	GO:0004601 GO:0005737 GO:0005829 GO:0006972 GO:0006979 GO:0016209 GO:0016491 GO:0033194 GO:0051920 GO:0055114 GO:0098869
8	0.30	0.721	2.49	0.13	0.91	4mh4A	GO:0006979
9	0.29	0.795	2.06	0.16	0.92	2d7vA
10	0.26	0.741	2.02	0.14	0.86	2oplB
11	0.24	0.706	2.92	0.15	0.93	1uspA	GO:0006979
12	0.24	0.813	2.00	0.16	0.95	2onfA
13	0.06	0.391	4.81	0.08	0.69	3d36B
14	0.06	0.365	5.43	0.07	0.69	4i8pA	GO:0000166 GO:0008152 GO:0016491 GO:0016620 GO:0019145 GO:0033737 GO:0055114
15	0.06	0.317	5.62	0.08	0.62	2e7yA	GO:0016787 GO:0034414 GO:0042781 GO:0046872
16	0.06	0.322	5.51	0.04	0.65	3islA	GO:0003824 GO:0004760 GO:0005777 GO:0006144 GO:0008453 GO:0008483 GO:0016740 GO:0019265
17	0.06	0.301	4.97	0.06	0.52	1hcfA	GO:0005102 GO:0005166 GO:0005576 GO:0005788 GO:0007169 GO:0007267 GO:0007402 GO:0007616 GO:0008052 GO:0008083 GO:0008344 GO:0008544 GO:0016023 GO:0042490 GO:0043524 GO:0045664 GO:0048812 GO:0060384 GO:0060548 GO:0061193
18	0.06	0.329	4.99	0.06	0.57	1i82A	GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0016052 GO:0016787 GO:0016798 GO:0030246 GO:0031176 GO:0045493
19	0.06	0.298	5.11	0.05	0.55	4es6A	GO:0004852 GO:0006779 GO:0006782 GO:0016829 GO:0033014
20	0.06	0.356	4.48	0.07	0.59	3pm6A	GO:0003824 GO:0004332 GO:0005975 GO:0006096 GO:0008270 GO:0016829 GO:0016832 GO:0046872
21	0.06	0.354	4.72	0.10	0.62	5aecA	GO:0004497 GO:0016491 GO:0016705 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0004601
GO-Score	0.34
Biological Processes	GO:0098869	GO:0006979
GO-Score	0.34	0.34
Cellular Component
GO-Score

(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.