I-TASSER results

I-TASSER results for job id Rv0887c

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

Input Sequence in FASTA format

>protein (152 residues)
MAINVEPALSPHLVVDDAASAIDFYVKAFDAVELGRVPGPDGKLIHAALRINGFTVMLND
DVPQMCGGKSMTPTSLGGTPVTIHLTVTDVDAKFQRALNAGATVVTALEDQLWGDRYGVV
ADPFGHHWSLGQPVREVNMDEIQAAMSSQGDG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MAINVEPALSPHLVVDDAASAIDFYVKAFDAVELGRVPGPDGKLIHAALRINGFTVMLNDDVPQMCGGKSMTPTSLGGTPVTIHLTVTDVDAKFQRALNAGATVVTALEDQLWGDRYGVVADPFGHHWSLGQPVREVNMDEIQAAMSSQGDG
Prediction	CCCCCCCCHCEEEEHCCHHHHHHHHHHHHCCEEEEEHCCCCCEEEEEEEEHCCCEEEHCCCCCCCCCCCCCCCCCCCCCCEEEEEHCCCHHHHHHHHHHHCCEEEHCCCCCCCCCCCEEEHCCCCCEEEEEHCCCCCCHHHHHHHHHHHCCC
Conf.Score	99888886545888768899999999997988998876999958999999799589866789766788999987779986799998598899999999989967655677887766578878999868866557779999999999998599
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MAINVEPALSPHLVVDDAASAIDFYVKAFDAVELGRVPGPDGKLIHAALRINGFTVMLNDDVPQMCGGKSMTPTSLGGTPVTIHLTVTDVDAKFQRALNAGATVVTALEDQLWGDRYGVVADPFGHHWSLGQPVREVNMDEIQAAMSSQGDG
Prediction	76454413020100043044014103502404131204247120000003246030000021242475614417434133000101043013104302724154433266002110303041333130332133561446304501663488
	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

CCCCCCCCHCEEEEHCCHHHHHHHHHHHHCCEEEEEHCCCCCEEEEEEEEHCCCEEEHCCCCCCCCCCCCCCCCCCCCCCEEEEEHCCCHHHHHHHHHHHCCEEEHCCCCCCCCCCCEEEHCCCCCEEEEEHCCCCCCHHHHHHHHHHHCCC
MAINVEPALSPHLVVDDAASAIDFYVKAFDAVELGRVPGPDGKLIHAALRINGFTVMLNDDVPQMCGGKSMTPTSLGGTPVTIHLTVTDVDAKFQRALNAGATVVTALEDQLWGDRYGVVADPFGHHWSLGQPVREVNMDEIQAAMSSQGDG

3itwB

0.30

0.25

0.83

3.24

MUSTER

------SHMVVELAYTDPDRAVDWLVRVFGFRLLLRQPAI-GTIRHADLDTGGGIVMVRRTGEPY-----TVSCAGGHTCKQVIVWVSDVDEHFMRSTAAGADIVQPLQDKPWGLRQYLVRDLEGHLWEFTRGAVAMT--------------

3itwB

0.30

0.25

0.83

7.84

dPPAS

------SHMVVELAYTDPDRAVDWLVRVFGFRLLLRQPAI-GTIRHADLDTGGGIVMVRRTGEPYTVSCAG-----GHTCKQVIVWVSDVDEHFMRSTAAGADIVQPLQDKPWGLRQYLVRDLEGHLWEFTRGAVAMT--------------

3itwB

0.30

0.25

0.83

5.67

wdPPAS

------SHMVVELAYTDPDRAVDWLVRVFGFRLLLRQPA-IGTIRHADLDTGGGIVMVRRTGEPYTVSCAG-----GHTCKQVIVWVSDVDEHFMRSTAAGADIVQPLQDKPWGLRQYLVRDLEGHLWEFTRGAVAMT--------------

3itwB

0.32

0.26

0.82

3.47

wMUSTER

-------HMVVELAYTDPDRAVDWLVRVFGFRLLLRQPAI-GTIRHADLDTGGGIVMVRRTGEPY------TVSCAGGTCKQVIVWVSDVDEHFMRSTAAGADIVQPLQDKPWGLRQYLVRDLEGHLWEFTRGAVAMT--------------

3itwB

0.32

0.26

0.82

3.47

wPPAS

------SHMVVELAYTDPDRAVDWLVRVFGFRLLLRQP-AIGTIRHADLDTGGGIVMVRRTGEPY------TVSCAGGTCKQVIVWVSDVDEHFMRSTAAGADIVQPLQDKPWGLRQYLVRDLEGHLWEFTRGAVAMT--------------

3itwB

0.30

0.25

0.83

9.66

dPPAS2

------SHMVVELAYTDPDRAVDWLVRVFGFRLLLRQPAI-GTIRHADLDTGGGIVMVRRTGEPYTVSCAG-----GHTCKQVIVWVSDVDEHFMRSTAAGADIVQPLQDKPWGLRQYLVRDLEGHLWEFTRGAVAMT--------------

3itwB

0.30

0.25

0.83

3.63

PPAS

------SHMVVELAYTDPDRAVDWLVRVFGFRLLLRQPAI-GTIRHADLDTGGGIVMVRRTGEPY-----TVSCAGGHTCKQVIVWVSDVDEHFMRSTAAGADIVQPLQDKPWGLRQYLVRDLEGHLWEFTRGAVAMT--------------

3itwB

0.30

0.25

0.83

3.69

Env-PPAS

------SHMVVELAYTDPDRAVDWLVRVFGFRLLLRQP-AIGTIRHADLDTGGGIVMVRRTGEPY-----TVSCAGGHTCKQVIVWVSDVDEHFMRSTAAGADIVQPLQDKPWGLRQYLVRDLEGHLWEFTRGAVAMT--------------

1xy7B

0.27

0.21

0.78

3.16

MUSTER

VFTEFK-----QLLVEAVGDAVTFYKSAFGAIESGHS----LHVLSSELNLAGSSFVVCDVSSLPGFS----TAKSEGSGVTFLLGTKDAEAAVAKAVDAGAVKVEVTEAEVELGFKGKVTDPFGVTWIFAE--------------------

1xy7B

0.27

0.21

0.78

6.67

dPPAS

-----VFTEFKQLLVEAVGDAVTFYKSAFGAIESGHS----LHVLSSELNLAGSSFVVCDVSSLPGFSTA----KSEGSGVTFLLGTKDAEAAVAKAVDAGAVKVEVTEAEVELGFKGKVTDPFGVTWIFAE--------------------

(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=-0.31

Estimated TM-score = 0.67±0.13

Estimated RMSD = 5.4±3.4Å

Download Model 2

C-score=-1.02

Download Model 3

C-score=-0.68

Download Model 4

C-score=-1.35

Download Model 5

C-score=-2.86

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	3itwB	0.754	1.71	0.288	0.809
2	1sp9B	0.663	3.36	0.073	0.888
3	1sp8D	0.660	3.78	0.107	0.914
4	3hpvA	0.655	3.54	0.109	0.842
5	3r4qA	0.654	3.35	0.152	0.855
6	3ecjA	0.651	3.36	0.110	0.829
7	3oxhA	0.650	3.32	0.180	0.829
8	4ro6A	0.645	3.16	0.163	0.803
9	1t47A	0.642	3.51	0.099	0.862
10	1mpyA	0.641	3.42	0.116	0.829

(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	0.12	5	4jd1A	FCN	Rep, Mult	10,12,48,55,57,59
2	0.09	3	1kllA	MC	Rep, Mult	10,46,60,64,68
3	0.08	3	3sy9A	C8E	Rep, Mult	118,130
4	0.05	2	2p1hA	ZN	Rep, Mult	89,91
5	0.05	2	2zw7A	BLM	Rep, Mult	37,46,57
6	0.03	1	2p7qD	GG6	Rep, Mult	84,86,131,133
7	0.03	1	2a4wA	BLM	Rep, Mult	112,113,114,117
8	0.02	1	1f9z0	III	Rep, Mult	10,11,12,13,14,51,57,82,83,84,85,86,88,126,129,131
9	0.02	1	2c21B	NI	Rep, Mult	82,129
10	0.02	1	2ei3A	BPY	Rep, Mult	20,24,28,122,123
11	0.02	1	4nb0A	CYS	Rep, Mult	12,13,14,59

	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	0.165	1f9zA	0.610	2.84	0.195	0.737	4.4.1.5	NA
2	0.147	1npbA	0.585	2.78	0.172	0.711	2.5.1.18	123,126,130
3	0.142	2c21A	0.599	3.34	0.160	0.757	4.1.1.-	NA
4	0.121	1lqkA	0.582	2.81	0.122	0.711	2.5.1.18	NA
5	0.060	1nqkA	0.465	4.81	0.083	0.770	1.14.14.5	53,85
6	0.060	2hpiA	0.439	4.69	0.056	0.691	2.7.7.7	92
7	0.060	2zi8A	0.508	4.31	0.047	0.770	1.13.11.39	NA
8	0.060	1mpyA	0.641	3.42	0.116	0.829	1.13.11.2	NA
9	0.060	3hx0A	0.418	4.82	0.033	0.671	2.7.7.7,	NA
10	0.060	3lm4D	0.621	3.36	0.090	0.809	1.13.11.2	NA
11	0.060	1jajA	0.425	4.42	0.067	0.671	2.7.7.7	NA
12	0.060	1sqiA	0.611	3.57	0.089	0.849	1.13.11.27	NA
13	0.060	1f1uA	0.500	4.86	0.100	0.809	1.13.11.15	NA
14	0.060	1jmsA	0.448	4.57	0.066	0.711	2.7.7.31	NA
15	0.060	1qipB	0.571	3.95	0.165	0.763	4.4.1.5	NA
16	0.060	1fa7B	0.586	2.98	0.187	0.724	4.4.1.5	13,83,85,123,125
17	0.060	3i4zA	0.451	4.71	0.062	0.750	2.5.1.34	NA
18	0.060	1nmtA	0.426	4.97	0.048	0.743	2.3.1.97	85
19	0.060	2p6eC	0.423	5.06	0.086	0.750	2.3.1.97	NA
20	0.060	1iykA	0.408	4.96	0.054	0.730	2.3.1.97	NA
21	0.060	1lqoB	0.581	2.82	0.122	0.711	2.5.1.18	123,125
22	0.060	2v4iH	0.285	4.93	0.051	0.507	2.3.1.35	26,51
23	0.060	2ihmB	0.426	4.34	0.103	0.658	2.7.7.7	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	0.582	2.81	0.12	0.71	1lqkA	GO:0004364 GO:0005737 GO:0016740 GO:0046677 GO:0046872
1	0.29	0.614	3.01	0.20	0.77	3vcxA	GO:0051213 GO:0055114
2	0.27	0.621	3.18	0.21	0.77	4hc5D	GO:0051213 GO:0055114
3	0.24	0.571	2.90	0.17	0.72	5cj3A	GO:0008144 GO:0046677
4	0.23	0.586	3.19	0.15	0.75	2p7pA	GO:0005737 GO:0046677 GO:0046872
5	0.22	0.571	3.95	0.17	0.76	1qipB	GO:0004462 GO:0005737 GO:0005829 GO:0005975 GO:0006090 GO:0006357 GO:0006749 GO:0008270 GO:0009438 GO:0016829 GO:0030316 GO:0043066 GO:0046872 GO:0070062
6	0.19	0.609	2.62	0.12	0.72	3kolA	GO:0004462 GO:0046872 GO:0051213 GO:0055114
7	0.19	0.592	2.81	0.17	0.73	4g6xA	GO:0051213 GO:0055114
8	0.18	0.564	2.82	0.16	0.70	1jieA	GO:0008144 GO:0046677
9	0.18	0.611	3.04	0.20	0.75	4mtsA	GO:0004462 GO:0016829 GO:0046872
10	0.16	0.570	3.80	0.14	0.82	4mymA	GO:0051213 GO:0055114
11	0.15	0.567	2.79	0.13	0.70	1bylA	GO:0008144 GO:0046677
12	0.10	0.642	3.51	0.10	0.86	1t47A	GO:0003868 GO:0006559 GO:0006572 GO:0009072 GO:0016491 GO:0016701 GO:0046872 GO:0051213 GO:0055114
13	0.09	0.663	3.36	0.07	0.89	1sp9B	GO:0003868 GO:0005737 GO:0006559 GO:0006572 GO:0009072 GO:0016491 GO:0016701 GO:0042802 GO:0046872 GO:0051213 GO:0055114
14	0.08	0.611	3.48	0.10	0.84	1sqiB	GO:0000139 GO:0003868 GO:0005737 GO:0005783 GO:0005789 GO:0005794 GO:0006559 GO:0006572 GO:0009072 GO:0016020 GO:0016491 GO:0016701 GO:0046872 GO:0051213 GO:0055114
15	0.08	0.625	3.58	0.12	0.86	3zgjB	GO:0003868 GO:0009072 GO:0016701 GO:0046872 GO:0051213 GO:0055114
16	0.07	0.622	3.56	0.09	0.86	5ec3A	GO:0003868 GO:0005829 GO:0006559 GO:0006572 GO:0009072 GO:0016491 GO:0016701 GO:0046872 GO:0051213 GO:0055114 GO:0070062
17	0.07	0.612	3.68	0.10	0.86	2r5vA	GO:0003868 GO:0005506 GO:0009072 GO:0016491 GO:0016701 GO:0017000 GO:0033072 GO:0046872 GO:0050585 GO:0055114
18	0.07	0.660	3.78	0.11	0.91	1sp8D
19	0.07	0.579	3.77	0.07	0.85	1cjxA	GO:0003868 GO:0006559 GO:0006572 GO:0009072 GO:0016491 GO:0016701 GO:0046872 GO:0051213 GO:0055114
20	0.06	0.352	5.67	0.02	0.68	2cxiA	GO:0000166 GO:0000287 GO:0003723 GO:0004812 GO:0004826 GO:0005524 GO:0005737 GO:0006412 GO:0006432 GO:0016874
21	0.06	0.369	5.21	0.06	0.63	1r3nA	GO:0003837 GO:0008152 GO:0016787 GO:0016813 GO:0046872
22	0.06	0.361	5.66	0.04	0.70	5firA	GO:0000738 GO:0003676 GO:0004518 GO:0004527 GO:0004534 GO:0005634 GO:0005730 GO:0006139 GO:0006351 GO:0006353 GO:0006355 GO:0006397 GO:0007275 GO:0008409 GO:0010587 GO:0016787 GO:0040028 GO:0040034 GO:0046872 GO:0060965 GO:0090503
23	0.06	0.355	4.84	0.06	0.59	5f3jA	GO:0004872 GO:0009405 GO:0016020 GO:0016021
24	0.06	0.340	3.52	0.15	0.45	3rmuA	GO:0004493 GO:0005739 GO:0005759 GO:0016853 GO:0019626 GO:0046491 GO:0046872
25	0.06	0.348	4.03	0.12	0.47	1jc5B	GO:0004493 GO:0016853
26	0.06	0.340	4.85	0.02	0.60	3d2jA	GO:0003824 GO:0009820 GO:0016023 GO:0016491 GO:0016614 GO:0031410 GO:0050468 GO:0050660 GO:0055114
27	0.06	0.323	5.16	0.05	0.58	4e0vB	GO:0001716 GO:0005576 GO:0006915 GO:0016491 GO:0019835 GO:0042742 GO:0044179 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0046872	GO:0051213	GO:0004364
GO-Score	0.53	0.48	0.39
Biological Processes	GO:0046677	GO:0055114
GO-Score	0.64	0.48
Cellular Component	GO:0005737
GO-Score	0.53

(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.