I-TASSER results

I-TASSER results for job id Rv2842c

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

Input Sequence in FASTA format

>protein (183 residues)
MTTGLPSQRQVIELLGADFACAGYEIEDVVIDARARPPRIAVIADGDAPLDLDTIAALSR
RASALLDGLDGANKIRGRYLLEVSSPGVERPLTSEKHFRRARGRKVELVLSDGSRLTGRV
GEMRAGTVALVIREDRGWAVREIPLAEIVKAVVQVEFSPPAPAELELAQSSEMGLARGTE
AGA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MTTGLPSQRQVIELLGADFACAGYEIEDVVIDARARPPRIAVIADGDAPLDLDTIAALSRRASALLDGLDGANKIRGRYLLEVSSPGVERPLTSEKHFRRARGRKVELVLSDGSRLTGRVGEMRAGTVALVIREDRGWAVREIPLAEIVKAVVQVEFSPPAPAELELAQSSEMGLARGTEAGA
Prediction	CCCCCCHHHHHHHHHHHHHHHHCCEEEEEEEEHCCCCCEEEEEEHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEHCCCCCCCCCCHHHHHHHCCEEEEEEHCCCEEEEEEEEEEHCCEEEEEEHCCCCCEEEEEEHHHCCEEEEEEHCCCCCHHHHHHHCCCCCCCCCCCCCCC
Conf.Score	998886699999999999999899899999996799859999997799999899999999999987665678888888799997799998899999999887968999987995999999999899899999589885899997654857899998589998999986777654445544589
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MTTGLPSQRQVIELLGADFACAGYEIEDVVIDARARPPRIAVIADGDAPLDLDTIAALSRRASALLDGLDGANKIRGRYLLEVSSPGVERPLTSEKHFRRARGRKVELVLSDGSRLTGRVGEMRAGTVALVIREDRGWAVREIPLAEIVKAVVQVEFSPPAPAELELAQSSEMGLARGTEAGA
Prediction	775635435203500451067360301102134566421000101377304062014005402520454455541654030000013263414446304413444040315765503030361565402020457665442503163055020203045446523621645775456465678
	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

                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCHHHHHHHHHHHHHHHHCCEEEEEEEEHCCCCCEEEEEEHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEHCCCCCCCCCCHHHHHHHCCEEEEEEHCCCEEEEEEEEEEHCCEEEEEEHCCCCCEEEEEEHHHCCEEEEEEHCCCCCHHHHHHHCCCCCCCCCCCCCCC
MTTGLPSQRQVIELLGADFACAGYEIEDVVIDARARPPRIAVIADGDAPLDLDTIAALSRRASALLDGLDGANKIRGRYLLEVSSPGVERPLTSEKHFRRARGRKVELVLSDGSRLTGRVGEMRAGTVALVIREDRGWAVREIPLAEIVKAVVQVEFSPPAPAELELAQSSEMGLARGTEAGA

1ib8A

0.21

0.17

0.84

3.07

MUSTER

IAT---IVELVREVVEPVIE-APFELVDIEYGKIGSDMILSIFVDKPEGITLNDTADLTEMISPVLDTIKP-DPFPEQYFLEITSPGLERPLKTKDAVAGAVGKYIHVGLYKQKVFEGTLLAFEEDELTMEYMDKTRKKTVQIPYSLVSKARLAVKLLE------------------------

1ib8A

0.20

0.17

0.86

7.20

dPPAS

VDAIATIVELVREVVEPVIE-APFELVDIEYGKIGSDMILSIFVDKPEGITLNDTADLTEMISPVLDT-IKPDPFPEQYFLEITSPGLERPLKTKDAVAGAVGKYIHVGLYKQKVFEGTLLAFEEDELTMEYMDKTRKKTVQIPYSLVSKARLAVKLLE------------------------

1ib8A

0.20

0.17

0.86

6.22

wdPPAS

VDAIATIVELVREVVEPVIE-APFELVDIEYGKIGSDMILSIFVDKPEGITLNDTADLTEMISPVLDTIKP-DPFPEQYFLEITSPGLERPLKTKDAVAGAVGKYIHVGLYKQKVFEGTLLAFEEDELTMEYMDKTRKKTVQIPYSLVSKARLAVKLLE------------------------

1ib8A

0.21

0.17

0.84

3.87

wMUSTER

IAT---IVELVREVVEPVIE-APFELVDIEYGKIGSDMILSIFVDKPEGITLNDTADLTEMISPVLDTIKP-DPFPEQYFLEITSPGLERPLKTKDAVAGAVGKYIHVGLYKQKVFEGTLLAFEEDELTMEYMDKTRKKTVQIPYSLVSKARLAVKLLE------------------------

1ib8A

0.21

0.17

0.84

4.89

wPPAS

IAT---IVELVREVVEPVIE-APFELVDIEYGKIGSDMILSIFVDKPEGITLNDTADLTEMISPVLDTIKP-DPFPEQYFLEITSPGLERPLKTKDAVAGAVGKYIHVGLYKQKVFEGTLLAFEEDELTMEYMDKTRKKTVQIPYSLVSKARLAVKLLE------------------------

1ib8A

0.21

0.17

0.84

12.62

dPPAS2

IAT---IVELVREVVEPVIE-APFELVDIEYGKIGSDMILSIFVDKPEGITLNDTADLTEMISPVLDTIKP-DPFPEQYFLEITSPGLERPLKTKDAVAGAVGKYIHVGLYKQKVFEGTLLAFEEDELTMEYMDKTRKKTVQIPYSLVSKARLAVKLLE------------------------

1ib8A

0.21

0.17

0.84

4.20

PPAS

IAT---IVELVREVVEPVIE-APFELVDIEYGKIGSDMILSIFVDKPEGITLNDTADLTEMISPVLDTIKP-DPFPEQYFLEITSPGLERPLKTKDAVAGAVGKYIHVGLYKQKVFEGTLLAFEEDELTMEYMDKTRKKTVQIPYSLVSKARLAVKLLE------------------------

1ib8A

0.21

0.17

0.84

4.67

Env-PPAS

IAT---IVELVREVVEPVIE-APFELVDIEYGKIGSDMILSIFVDKPEGITLNDTADLTEMISPVLDTIKP-DPFPEQYFLEITSPGLERPLKTKDAVAGAVGKYIHVGLYKQKVFEGTLLAFEEDELTMEYMDKTRKKTVQIPYSLVSKARLAVKLLE------------------------

1ib8A1

0.24

0.11

0.46

1.59

MUSTER

IAT---IVELVREVVEPVIE-APFELVDIEYGKIGSDMILSIFVDKPEGITLNDTADLTEMISPVLDTIKP-DPFPEQYFLEITSPGLE----------------------------------------------------------------------------------------------

1ib8A1

0.22

0.10

0.48

4.22

dPPAS

VDAIATIVELVREVVEPVIE-APFELVDIEYGKIGSDMILSIFVDKPEGITLNDTADLTEMISPVLDTIKP-DPFPEQYFLEITSPGLE----------------------------------------------------------------------------------------------

(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=0.04

Estimated TM-score = 0.72±0.11

Estimated RMSD = 5.1±3.3Å

Download Model 2

C-score=-0.11

Download Model 3

C-score=-0.46

Download Model 4

C-score=-3.07

Download Model 5

C-score=-3.95

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	1ib8A	0.831	1.05	0.197	0.858
2	5hx2D	0.517	4.83	0.087	0.809
3	1ez0A	0.514	5.27	0.072	0.847
4	2jg7A	0.505	5.10	0.063	0.798
5	1bxsA	0.503	4.93	0.069	0.781
6	3iwjA	0.500	5.13	0.034	0.798
7	1a4zA	0.498	5.06	0.057	0.792
8	4lihA	0.498	4.95	0.064	0.787
9	4yweA	0.498	5.06	0.045	0.798
10	2o2rA	0.497	5.17	0.035	0.798

(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	0.07	4	1qb8A	MG	Rep, Mult	45,54
2	0.05	3	4l6vf	CLA	Rep, Mult	55,58
3	0.05	3	1rvkA	MG	Rep, Mult	45,82,89
4	0.04	2	1nzwA	NA	Rep, Mult	105,106,151
5	0.04	2	3d7oA	NO2	Rep, Mult	15,27,29,62
6	0.04	2	2g42B	CA	Rep, Mult	51,54
7	0.04	2	1m8vG	NUC	Rep, Mult	89,90
8	0.04	2	3glnA	XE	Rep, Mult	26,29,58,82
9	0.02	1	4zmmB	C2E	Rep, Mult	17,18,19,20,21,61
10	0.02	1	1s61A	NBN	Rep, Mult	11,30,31,62,81
11	0.02	1	3iwkD	NAD	Rep, Mult	16,17,58,61,62
12	0.02	1	4w50B	BU2	Rep, Mult	43,45
13	0.02	1	3ajoA	MG	Rep, Mult	10,13
14	0.02	1	3quiC	ANP	Rep, Mult	110,116,141
15	0.02	1	2zyqB	TAR	Rep, Mult	86,87
16	0.02	1	2onmK	ADP	Rep, Mult	11,12,15,59,63

	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	1bxsA	0.503	4.93	0.069	0.781	1.2.1.36	NA
2	0.060	2j6lB	0.508	5.18	0.069	0.809	1.2.1.31,1.2.1.3	NA
3	0.060	1hbmA	0.491	4.87	0.072	0.770	2.8.4.1	NA
4	0.060	1bi9D	0.452	5.55	0.024	0.770	1.2.1.36,1.2.1.-	NA
5	0.060	1o9jA	0.503	4.96	0.076	0.787	1.2.1.3	147
6	0.060	2vroB	0.481	5.31	0.058	0.798	1.2.1.3	NA
7	0.060	3b4wA	0.470	5.46	0.098	0.792	1.2.1.-	NA
8	0.060	3ifh6	0.342	5.80	0.049	0.628	1.2.1.16	46
9	0.060	2esdA	0.487	5.22	0.059	0.781	1.2.1.9	NA
10	0.060	1wndA	0.495	5.21	0.055	0.792	1.2.1.19	14,28,48,82
11	0.060	1o01C	0.497	4.72	0.047	0.765	1.2.1.3	NA
12	0.060	2o2pA	0.467	5.49	0.047	0.798	1.5.1.6	89
13	0.060	1t90A	0.470	5.28	0.047	0.781	1.2.1.18,1.2.1.27	NA
14	0.060	2opxA	0.495	5.17	0.063	0.798	1.2.1.21,1.2.1.22	NA
15	0.060	3ju8A	0.487	5.29	0.086	0.803	1.2.1.71	NA
16	0.060	2d4eC	0.489	5.12	0.093	0.787	1.2.1.60	NA
17	0.060	2ve5A	0.491	4.98	0.057	0.787	1.2.1.8	NA
18	0.060	1cqxB	0.460	5.17	0.070	0.754	1.14.12.17	159
19	0.060	1uxvA	0.475	5.35	0.064	0.787	1.2.1.9	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	0.41	0.831	1.05	0.20	0.86	1ib8A	GO:0005737 GO:0042254 GO:0042274
1	0.07	0.474	5.35	0.07	0.79	4pz2B	GO:0004029 GO:0008152 GO:0016491 GO:0016620 GO:0055114
2	0.07	0.530	5.11	0.07	0.87	5iv5A	GO:0019012 GO:0019076 GO:0098025
3	0.07	0.488	5.33	0.08	0.81	3ju8A	GO:0004029 GO:0006525 GO:0006527 GO:0008152 GO:0016491 GO:0016620 GO:0019544 GO:0019545 GO:0043824 GO:0055114
4	0.07	0.497	5.35	0.05	0.83	3pqaB	GO:0008152 GO:0008911 GO:0016491 GO:0016620 GO:0055114
5	0.07	0.491	5.54	0.06	0.84	3v4cA	GO:0008152 GO:0016491 GO:0016620 GO:0033721 GO:0055114
6	0.07	0.500	5.13	0.03	0.80	3iwjA	GO:0000166 GO:0008152 GO:0016491 GO:0016620 GO:0055114
7	0.07	0.513	5.26	0.08	0.85	1eyyA	GO:0008152 GO:0016491 GO:0016620 GO:0033721 GO:0055114
8	0.07	0.448	5.75	0.06	0.80	4iymC	GO:0000166 GO:0004491 GO:0008152 GO:0016491 GO:0016620 GO:0055114
9	0.07	0.489	5.12	0.09	0.79	2d4eC	GO:0000166 GO:0008152 GO:0016491 GO:0016620 GO:0018480 GO:0055114 GO:1901023
10	0.07	0.487	5.22	0.06	0.78	2esdA	GO:0008152 GO:0008886 GO:0016491 GO:0016620 GO:0047100 GO:0055114
11	0.07	0.470	5.46	0.10	0.79	3b4wA	GO:0000166 GO:0005524 GO:0005886 GO:0008152 GO:0016208 GO:0016491 GO:0016620 GO:0043531 GO:0051287 GO:0055114 GO:0070404 GO:0071949
12	0.07	0.496	5.17	0.06	0.80	4dalB	GO:0000166 GO:0008152 GO:0016491 GO:0016620 GO:0055114
13	0.07	0.477	5.29	0.06	0.78	1ky8A	GO:0000166 GO:0003824 GO:0008152 GO:0008886 GO:0016491 GO:0016620 GO:0050661 GO:0051287 GO:0055114
14	0.07	0.466	5.08	0.04	0.75	3rosA	GO:0008152 GO:0009013 GO:0016491 GO:0016620 GO:0055114
15	0.07	0.476	5.50	0.05	0.81	4pxlB	GO:0008152 GO:0016491 GO:0016620 GO:0055114
16	0.07	0.502	5.11	0.07	0.79	5abmA	GO:0001758 GO:0004029 GO:0005737 GO:0008152 GO:0016491 GO:0016620 GO:0042572 GO:0055114 GO:0070062
17	0.07	0.497	4.99	0.03	0.79	4v37A	GO:0004030 GO:0006081 GO:0008152 GO:0008802 GO:0009507 GO:0009536 GO:0016491 GO:0016620 GO:0019285 GO:0055114
18	0.07	0.453	5.35	0.08	0.76	3r64A	GO:0008152 GO:0016491 GO:0016620 GO:0018479 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0016903
GO-Score	0.37
Biological Processes	GO:0042274	GO:0044710
GO-Score	0.41	0.37
Cellular Component	GO:0005737
GO-Score	0.41

(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.