I-TASSER results

I-TASSER results for job id Rv2367c

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

Input Sequence in FASTA format

>protein (182 residues)
MREHLMSIEVANESGIDVSEAELVSVARFVIAKMDVNPCAELSMLLLDTAAMADLHMRWM
DLPGPTDVMSFPMDELEPGGRPDAPEPGPSMLGDIVLCPEFAAEQAAAAGHSLGHELALL
TIHGVLHLLGYDHAEPDEEKEMFALQDRLLEEWVADQVEAYQHDRQDEKDRRLLDKSRYF
DL

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MREHLMSIEVANESGIDVSEAELVSVARFVIAKMDVNPCAELSMLLLDTAAMADLHMRWMDLPGPTDVMSFPMDELEPGGRPDAPEPGPSMLGDIVLCPEFAAEQAAAAGHSLGHELALLTIHGVLHLLGYDHAEPDEEKEMFALQDRLLEEWVADQVEAYQHDRQDEKDRRLLDKSRYFDL
Prediction	CCCCCCEEEEHCCCCCCCCHHHHHHHHHHHHHHHCCCHHHCEEEEEHCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEHCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC
Conf.Score	99888658875678999999999999999999979995655588887778999998998689999876677776789999999999998866748868999999999989999999999998757766588889979999999999999999999777766666665899999856577779
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MREHLMSIEVANESGIDVSEAELVSVARFVIAKMDVNPCAELSMLLLDTAAMADLHMRWMDLPGPTDVMSFPMDELEPGGRPDAPEPGPSMLGDIVLCPEFAAEQAAAAGHSLGHELALLTIHGVLHLLGYDHAEPDEEKEMFALQDRLLEEWVADQVEAYQHDRQDEKDRRLLDKSRYFDL
Prediction	87533020102223635143620140033006406123302000101246204601341174732120111202014246565666433110000000141046206624242430020011010000011224337445402510450044025644655656444641452045342465
	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

CCCCCCEEEEHCCCCCCCCHHHHHHHHHHHHHHHCCCHHHCEEEEEHCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEHCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC
MREHLMSIEVANESGIDVSEAELVSVARFVIAKMDVNPCAELSMLLLDTAAMADLHMRWMDLPGPTDVMSFPMDELEPGGRPDAPEPGPSMLGDIVLCPEFAAEQAAAAGHSLGHELALLTIHGVLHLLGYDHAEPDEEKEMFALQDRLLEEWVADQVEAYQHDRQDEKDRRLLDKSRYFDL

1xm5A

0.31

0.26

0.82

2.47

MUSTER

MSQVILDLQLACEDNSGLEESQFQTWLNAVIPQF--QEESEVTIRVVDTAESHSLNLTYRGKDKPTNVLSFPFE--------VPPGMEMSLLGDLVICRQVVEKEAQEQGKPLEAHWAHMVVHGSLHLLGYDHIEDDEAEEMEALETEIMLALYEDPYIA----------------------

1xm5A

0.31

0.25

0.80

5.08

dPPAS

MSQVILDLQLACEDNSGLEESQFQTWLNAVIPQFQ--EESEVTIRVVDTAESHSLNLTYRGKDKPTNVLSFPFE--------VPPGMEMSLLGDLVICRQVVEKEAQEQGKPLEAHWAHMVVHGSLHLLGYDHIEDDEAEEMEALETEIMLALYIA--------------------------

1xm5A

0.31

0.26

0.82

4.77

wdPPAS

MSQVILDLQLACEDNSGLEESQFQTWLNAVIPQFQEE--SEVTIRVVDTAESHSLNLTYRGKDKPTNVLSFPFEV--------PPGMEMSLLGDLVICRQVVEKEAQEQGKPLEAHWAHMVVHGSLHLLGYDHIEDDEAEEMEALETEIMLALYEDPYIA----------------------

1xm5A

0.31

0.25

0.82

2.63

wMUSTER

-SQVILDLQLACEDNSGLEESQFQTWLNAVIPQF--QEESEVTIRVVDTAESHSLNLTYRGKDKPTNVLSFPFE--------VPPGMEMSLLGDLVICRQVVEKEAQEQGKPLEAHWAHMVVHGSLHLLGYDHIEDDEAEEMEALETEIMLALYEDPYIA----------------------

1xaxA

0.30

0.23

0.76

3.05

wPPAS

V----VDLQIATENIEGLTEEQIVQWATGAVQPEGNE--VEMTVRIVDEAESHELNLTYRGKDRPTNVLSFPFEC------PD--EVELPLLGDLVICRQVVEREASEQEKPLMAHWAHMVVHGSLHLLGYDHIEDDEAEEMESLETQIMQGF-----------------------------

1xm5A

0.31

0.25

0.80

9.14

dPPAS2

MSQVILDLQLACEDNSGLEESQFQTWLNAVIPQFQ--EESEVTIRVVDTAESHSLNLTYRGKDKPTNVLSFPFE--------VPPGMEMSLLGDLVICRQVVEKEAQEQGKPLEAHWAHMVVHGSLHLLGYDHIEDDEAEEMEALETEIMLALYIA--------------------------

1xaxA

0.30

0.23

0.77

2.83

PPAS

VL---VDLQIATENIEGLTEEQIVQWATGAVQPEGNE--VEMTVRIVDEAESHELNLTYRGKDRPTNVLSFPFEC------PD--EVELPLLGDLVICRQVVEREASEQEKPLMAHWAHMVVHGSLHLLGYDHIEDDEAEEMESLETQIMQGF-----------------------------

1xm5A

0.31

0.26

0.82

3.62

Env-PPAS

MSQVILDLQLACEDNSGLEESQFQTWLNAVIPQF--QEESEVTIRVVDTAESHSLNLTYRGKDKPTNVLSFPFEV--------PPGMEMSLLGDLVICRQVVEKEAQEQGKPLEAHWAHMVVHGSLHLLGYDHIEDDEAEEMEALETEIMLALYEDPYIA----------------------

1oz9A

0.33

0.25

0.76

2.33

MUSTER

------KNRVLVKKKRKVRKDKIEKWAELALSALGLNN-VELSVYITDDQEIRELNKTYRKKDKPTDVLSFPMGE---------EFGGYKILGDVVISQDTAERQARELGHSLEEEVKRLIVHGIVHLLGYDHEKGEEEKKFRELENYVLSKLSK---------------------------

1oz9A

0.33

0.25

0.76

4.95

dPPAS

------KNRVLVKKKRKVRKDKIEKWAELALSALGLNN-VELSVYITDDQEIRELNKTYRKKDKPTDVLSFPMGE---------EFGGYKILGDVVISQDTAERQARELGHSLEEEVKRLIVHGIVHLLGYDHEKGEEEKKFRELENYVLSKLSK---------------------------

(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=-0.52

Estimated TM-score = 0.65±0.13

Estimated RMSD = 6.2±3.8Å

Download Model 2

C-score=-1.02

Download Model 3

C-score=-0.68

Download Model 4

C-score=-2.76

Download Model 5

C-score=-3.42

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	1xm5A	0.772	1.42	0.298	0.808
2	1oz9A	0.694	2.05	0.314	0.769
3	1tviA	0.582	3.57	0.238	0.786
4	3ffzA1	0.567	4.73	0.076	0.857
5	3fieA	0.565	4.79	0.087	0.863
6	1z7hA	0.565	4.82	0.099	0.863
7	1zb7A	0.560	4.65	0.122	0.846
8	3cmnA	0.557	3.73	0.050	0.764
9	2xdtA	0.552	3.71	0.067	0.753
10	4kx7A	0.545	3.97	0.107	0.769

(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	0.77	18	1slmA	ZN	Rep, Mult	123,127,133
2	0.02	1	4khoA	CA	Rep, Mult	138,141
3	0.02	1	3ftwA	ACT	Rep, Mult	68,70,123,124,127

	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	3ffzA	0.567	4.73	0.076	0.857	3.4.24.69	NA
2	0.060	2etfB	0.526	4.76	0.081	0.830	3.4.24.69	NA
3	0.060	3ewjB	0.487	4.80	0.085	0.747	3.4.24.86	116,123,127,133
4	0.060	1y791	0.504	4.26	0.069	0.742	3.4.15.5	NA
5	0.060	1omjA	0.500	4.47	0.046	0.747	3.4.24.40	NA
6	0.060	1aklA	0.501	4.35	0.059	0.742	3.4.24.40	116,135
7	0.060	1lmlA	0.529	4.09	0.099	0.753	3.4.24.36	NA
8	0.060	1eakD	0.473	4.35	0.105	0.681	3.4.24.24	71,127,133
9	0.060	8tlnE	0.501	4.30	0.070	0.731	3.4.24.27	116
10	0.060	2imcB	0.529	4.56	0.077	0.797	3.4.24.69	NA
11	0.060	1j7mA	0.142	3.69	0.023	0.192	3.4.24.24	68
12	0.060	1bqbA	0.511	3.87	0.075	0.709	3.4.21.19,3.4.24.29	123
13	0.060	1e1hD	0.236	5.86	0.043	0.429	3.4.24.69	NA
14	0.060	1h19A	0.532	3.67	0.113	0.742	3.3.2.6	NA
15	0.060	1e1hC	0.408	4.59	0.081	0.610	3.4.24.69	23,99,118
16	0.060	1zkxB	0.569	4.70	0.082	0.857	3.4.24.69	NA
17	0.060	1t3cA	0.566	4.78	0.082	0.863	3.4.24.69	NA
18	0.060	3ebgA	0.539	4.13	0.081	0.775	3.4.11.-	NA
19	0.060	1gw6A	0.533	3.80	0.114	0.731	3.3.2.6	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	0.55	0.772	1.42	0.30	0.81	1xm5A	GO:0000478 GO:0004222 GO:0004518 GO:0004519 GO:0004521 GO:0005737 GO:0006364 GO:0006412 GO:0006508 GO:0008270 GO:0009408 GO:0016151 GO:0016787 GO:0016892 GO:0030490 GO:0031564 GO:0042254 GO:0042274 GO:0046872
1	0.44	0.694	2.05	0.31	0.77	1oz9A	GO:0004222 GO:0004518 GO:0004519 GO:0004521 GO:0005737 GO:0006364 GO:0006508 GO:0008270 GO:0016787 GO:0042254 GO:0046872 GO:0090305 GO:0090502
2	0.39	0.566	4.80	0.11	0.86	1yvgA	GO:0004222 GO:0005576 GO:0005829 GO:0005886 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0008320 GO:0009405 GO:0016787 GO:0030666 GO:0030669 GO:0046872 GO:0046929 GO:0050827 GO:0051609 GO:0071806
3	0.34	0.560	4.65	0.12	0.85	1zb7A	GO:0004222 GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0008320 GO:0009405 GO:0016787 GO:0046872 GO:0050827 GO:0051609 GO:0071806
4	0.33	0.521	4.65	0.06	0.79	3debA	GO:0004222 GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0009405 GO:0016020 GO:0016021 GO:0016787 GO:0020002 GO:0030430 GO:0033619 GO:0033644 GO:0044156 GO:0044164 GO:0044221 GO:0044231 GO:0045955 GO:0046872 GO:0050827 GO:0051609
5	0.25	0.582	3.57	0.24	0.79	1tviA	GO:0004222 GO:0004518 GO:0004519 GO:0004521 GO:0005737 GO:0006364 GO:0006508 GO:0008270 GO:0016787 GO:0042254 GO:0046872 GO:0090305 GO:0090502
6	0.24	0.516	4.85	0.08	0.82	2np0A	GO:0004222 GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0008320 GO:0009405 GO:0016020 GO:0016021 GO:0016787 GO:0020002 GO:0030430 GO:0033644 GO:0044156 GO:0044164 GO:0044221 GO:0044231 GO:0046872 GO:0050827 GO:0051609 GO:0071806
7	0.10	0.487	3.98	0.21	0.68	1xaxA	GO:0004222 GO:0004518 GO:0004519 GO:0004521 GO:0005737 GO:0006364 GO:0006508 GO:0008270 GO:0016787 GO:0042254 GO:0046872 GO:0090305 GO:0090502
8	0.07	0.337	6.00	0.04	0.65	3r4sA	GO:0004222 GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0009405 GO:0016020 GO:0016021 GO:0016787 GO:0020002 GO:0030430 GO:0033619 GO:0033644 GO:0044156 GO:0044164 GO:0044221 GO:0044231 GO:0045955 GO:0046872 GO:0050827 GO:0051609
9	0.07	0.569	4.70	0.08	0.86	1zkxB	GO:0004222 GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0008320 GO:0009405 GO:0016020 GO:0016021 GO:0016787 GO:0020002 GO:0030430 GO:0033644 GO:0044156 GO:0044164 GO:0044221 GO:0044231 GO:0046872 GO:0050827 GO:0051609 GO:0071806
10	0.07	0.529	4.56	0.08	0.80	2imcB	GO:0004222 GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0008320 GO:0009405 GO:0016020 GO:0016021 GO:0016787 GO:0020002 GO:0030430 GO:0033644 GO:0044156 GO:0044164 GO:0044221 GO:0044231 GO:0046872 GO:0050827 GO:0051609 GO:0071806
11	0.07	0.507	4.67	0.07	0.78	3v0aB	GO:0004222 GO:0005576 GO:0006508 GO:0009405 GO:0050827 GO:0051609
12	0.07	0.516	4.86	0.07	0.82	3v0aA	GO:0004222 GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0008320 GO:0009405 GO:0016020 GO:0016021 GO:0016787 GO:0020002 GO:0030430 GO:0033644 GO:0044156 GO:0044164 GO:0044221 GO:0044231 GO:0046872 GO:0050827 GO:0051609 GO:0071806
13	0.07	0.515	4.45	0.06	0.76	3vuoA	GO:0004222 GO:0005576 GO:0006508 GO:0009405 GO:0050827 GO:0051609
14	0.06	0.567	4.73	0.08	0.86	3ffzA	GO:0004222 GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0008320 GO:0009405 GO:0016020 GO:0016021 GO:0016787 GO:0020002 GO:0030430 GO:0033644 GO:0044156 GO:0044164 GO:0044221 GO:0044231 GO:0046872 GO:0050827 GO:0051609 GO:0071806
15	0.06	0.417	5.28	0.05	0.71	5bqnA	GO:0004222 GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0008320 GO:0009405 GO:0016020 GO:0016021 GO:0016787 GO:0020002 GO:0030430 GO:0033644 GO:0044156 GO:0044164 GO:0044221 GO:0044231 GO:0046872 GO:0050827 GO:0051609 GO:0071806
16	0.06	0.352	5.45	0.04	0.63	4bjpA	GO:0008658 GO:0008955 GO:0016020 GO:0016021 GO:0016740 GO:0016757
17	0.06	0.341	5.63	0.06	0.62	5dfaA	GO:0004565 GO:0005975 GO:0006012 GO:0008152 GO:0009341 GO:0016787 GO:0016798 GO:0046872
18	0.06	0.346	5.83	0.07	0.64	1mjfA	GO:0003824 GO:0004766 GO:0005737 GO:0006596 GO:0008295 GO:0010487 GO:0016740 GO:0043918 GO:0043919 GO:0050314

Consensus prediction of GO terms

Molecular Function	GO:0008270	GO:0004222	GO:0050827	GO:0008320	GO:0016892	GO:0016151
GO-Score	0.93	0.93	0.73	0.60	0.55	0.55
Biological Processes	GO:0051609	GO:0009405	GO:0071806	GO:0000478	GO:0031564	GO:0006412	GO:0030490	GO:0009408	GO:0046929	GO:0033619	GO:0045955
GO-Score	0.73	0.73	0.60	0.55	0.55	0.55	0.55	0.55	0.39	0.33	0.33
Cellular Component	GO:0005576	GO:0005829	GO:0005886	GO:0030669	GO:0044164	GO:0044231	GO:0044156	GO:0016021
GO-Score	0.73	0.39	0.39	0.39	0.33	0.33	0.33	0.33

(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.