I-TASSER results

I-TASSER results for job id Rv3735

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

Input Sequence in FASTA format

>protein (162 residues)
MSLAWDVVSVDKPDDVNVVIGQAHFIKAVEDLHEAMVGVSPSLRFGLAFCEASGPRLVRH
TGNDGDLVELATRTALAIAAGHSFVIFLREGFPINILNPVQAVPEVCTIYCATANPVDVV
VAVTPHGRGIVGVVDGQTPLGVETDRDIAQRRDLLRAIGYKL

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MSLAWDVVSVDKPDDVNVVIGQAHFIKAVEDLHEAMVGVSPSLRFGLAFCEASGPRLVRHTGNDGDLVELATRTALAIAAGHSFVIFLREGFPINILNPVQAVPEVCTIYCATANPVDVVVAVTPHGRGIVGVVDGQTPLGVETDRDIAQRRDLLRAIGYKL
Prediction	CCEEEEEEHCCCCCCCEEEEEHCCHHHHHHHHHHHHHHHCCCCEEEEEEHCCCCCEEEEHCCCCHHHHHHHHHHHHHHCCCEEEEEEHCCCCCEHHHHHHHHCCEEEEEEEHCCCCEEEEEEHCCCCCEEEEEHCCCCCCCCCCHHHHHHHHHHHHHHCCCC
Conf.Score	986899997689998569998655568899999999984999779998746789868985799599999999999998799589999878885436888876873568887558995999999489878999986998888999999999999999988889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MSLAWDVVSVDKPDDVNVVIGQAHFIKAVEDLHEAMVGVSPSLRFGLAFCEASGPRLVRHTGNDGDLVELATRTALAIAAGHSFVIFLREGFPINILNPVQAVPEVCTIYCATANPVDVVVAVTPHGRGIVGVVDGQTPLGVETDRDIAQRRDLLRAIGYKL
Prediction	671415315073375130000211113004301410242144140000004342530133534364026103510441002000001146122020043045143103010112231300003175330000001434254225672264036004524255
	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

                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCEEEEEEHCCCCCCCEEEEEHCCHHHHHHHHHHHHHHHCCCCEEEEEEHCCCCCEEEEHCCCCHHHHHHHHHHHHHHCCCEEEEEEHCCCCCEHHHHHHHHCCEEEEEEEHCCCCEEEEEEHCCCCCEEEEEHCCCCCCCCCCHHHHHHHHHHHHHHCCCC
MSLAWDVVSVDKPDDVNVVIGQAHFIKAVEDLHEAMVGVSPSLRFGLAFCEASGPRLVRHTGNDGDLVELATRTALAIAAGHSFVIFLREGFPINILNPVQAVPEVCTIYCATANPVDVVVAVTPHGRGIVGVVDGQTPLGVETDRDIAQRRDLLRAIGYKL

2ekmA

0.57

0.99

4.36

MUSTER

--VKIDVIRVEIPEGTNVIIGQSHFIKTVEDLYETLASSSPHLKFGIAFCEASGKRLIRWDGNDEELIKLAQQTALKIGAGHTFVIYIKNGFPINVLNRIKNVEEVVRIFAATANPLQVLVAETDQGRGVIGVVDGYTPLGIETEADIKERKELLRKFGYKR

2ekmA

0.57

0.99

6.46

dPPAS

--VKIDVIRVEIPEGTNVIIGQSHFIKTVEDLYETLASSSPHLKFGIAFCEASGKRLIRWDGNDEELIKLAQQTALKIGAGHTFVIYIKNGFPINVLNRIKNVEEVVRIFAATANPLQVLVAETDQGRGVIGVVDGYTPLGIETEADIKERKELLRKFGYKR

2ekmA

0.57

0.99

6.24

wdPPAS

--VKIDVIRVEIPEGTNVIIGQSHFIKTVEDLYETLASSSPHLKFGIAFCEASGKRLIRWDGNDEELIKLAQQTALKIGAGHTFVIYIKNGFPINVLNRIKNVEEVVRIFAATANPLQVLVAETDQGRGVIGVVDGYTPLGIETEADIKERKELLRKFGYKR

2ekmA

0.57

0.99

5.03

wMUSTER

--VKIDVIRVEIPEGTNVIIGQSHFIKTVEDLYETLASSSPHLKFGIAFCEASGKRLIRWDGNDEELIKLAQQTALKIGAGHTFVIYIKNGFPINVLNRIKNVEEVVRIFAATANPLQVLVAETDQGRGVIGVVDGYTPLGIETEADIKERKELLRKFGYKR

2ekmA

0.57

0.99

5.73

wPPAS

--VKIDVIRVEIPEGTNVIIGQSHFIKTVEDLYETLASSSPHLKFGIAFCEASGKRLIRWDGNDEELIKLAQQTALKIGAGHTFVIYIKNGFPINVLNRIKNVEEVVRIFAATANPLQVLVAETDQGRGVIGVVDGYTPLGIETEADIKERKELLRKFGYKR

2ekmA

0.57

0.99

9.84

dPPAS2

--VKIDVIRVEIPEGTNVIIGQSHFIKTVEDLYETLASSSPHLKFGIAFCEASGKRLIRWDGNDEELIKLAQQTALKIGAGHTFVIYIKNGFPINVLNRIKNVEEVVRIFAATANPLQVLVAETDQGRGVIGVVDGYTPLGIETEADIKERKELLRKFGYKR

2ekmA

0.57

0.99

5.59

PPAS

--VKIDVIRVEIPEGTNVIIGQSHFIKTVEDLYETLASSSPHLKFGIAFCEASGKRLIRWDGNDEELIKLAQQTALKIGAGHTFVIYIKNGFPINVLNRIKNVEEVVRIFAATANPLQVLVAETDQGRGVIGVVDGYTPLGIETEADIKERKELLRKFGYKR

2ekmA

0.57

0.99

6.75

Env-PPAS

--VKIDVIRVEIPEGTNVIIGQSHFIKTVEDLYETLASSSPHLKFGIAFCEASGKRLIRWDGNDEELIKLAQQTALKIGAGHTFVIYIKNGFPINVLNRIKNVEEVVRIFAATANPLQVLVAETDQGRGVIGVVDGYTPLGIETEADIKERKELLRKFGYKR

2jb7A

0.55

0.54

0.99

4.26

MUSTER

-SIKFELIDVPIPQGTNVIIGQAHFIKTVEDLYEALVTSVPGVKFGIAFCEASGKRLVRHEANDEELRNLAIDLCKKIAAGHVFVIYIRNAWPINVLNAIKNVPEVVRIFAATANPLKVIVAEVEERRGVVGVVDGHSPLGVETEKDREERKKFLREVKYKL

2d16A

0.44

0.43

0.99

6.16

dPPAS

-MVRIEVIDIEKPEGVEVIIGQGNSIFTVDDLARALLTAVPGIKFGIAMNEAK-PQLTRYTGNDPELEALAAKNAVKIGAGHVFVILMKNAYPINVLNTIKNHPAVAMIYGASENPFQVIVAETELGRAVIGVVDGKAANKIETDEQKKERRELVEKIGYKI

(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=2.00

Estimated TM-score = 0.99±0.04

Estimated RMSD = 1.2±1.2Å

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	2ekmA	0.952	1.20	0.575	0.982
2	2jb7A	0.949	1.42	0.528	0.994
3	2d16A	0.929	1.37	0.444	0.982
4	1vggA	0.926	1.36	0.563	0.969
5	1rlhA	0.794	1.61	0.371	0.864
6	4k0eA	0.545	4.39	0.043	0.809
7	4mt1A	0.535	4.82	0.043	0.846
8	3k07A	0.530	4.70	0.079	0.827
9	2vdcA1	0.517	3.85	0.037	0.753
10	1llwA1	0.509	4.11	0.074	0.765

(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	0.74	12	2gl0A	ADN	Rep, Mult	17,92,94,113,114,159
2	0.34	7	2gl0A	ADN	Rep, Mult	24,25,82
3	0.13	3	2gl0D	ADN	Rep, Mult	17,92,113,114,115
4	0.02	1	1lm1A	F3S	Rep, Mult	30,31,32,35,36,37,46,61,62

	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	2z86C	0.437	5.25	0.059	0.772	2.4.1.175,2.4.1.226	98
2	0.060	1eqrA	0.430	4.62	0.045	0.660	6.1.1.12	44
3	0.060	1ct9A	0.454	4.97	0.053	0.790	6.3.5.4	NA
4	0.060	3ikmD	0.437	3.70	0.059	0.624	2.7.7.7	NA
5	0.060	1x87A	0.435	4.74	0.058	0.704	4.2.1.49	NA
6	0.060	1htoA	0.441	3.95	0.030	0.617	6.3.1.2	NA
7	0.060	1moqA	0.355	4.77	0.048	0.586	2.6.1.16	51
8	0.060	1gehC	0.436	3.91	0.061	0.624	4.1.1.39	35
9	0.060	3l4gB	0.428	4.79	0.083	0.685	6.1.1.20	NA
10	0.060	2fknB	0.471	4.00	0.058	0.698	4.2.1.49	NA
11	0.060	2vdcF	0.508	4.14	0.051	0.772	1.4.1.13	NA
12	0.060	1ea0A	0.507	4.13	0.051	0.765	1.4.1.13	37
13	0.060	2zxqA	0.439	4.46	0.025	0.704	3.2.1.97	23
14	0.060	1t3tA	0.456	4.72	0.051	0.747	6.3.5.3	21
15	0.060	2jguA	0.423	3.77	0.055	0.562	2.7.7.7	NA
16	0.060	3hmjA	0.429	4.99	0.043	0.765	2.3.1.86	64
17	0.060	1jxaA	0.431	5.29	0.096	0.778	2.6.1.16	NA
18	0.060	3gueA	0.430	4.83	0.087	0.722	2.7.7.9	153,161
19	0.060	1qk1A	0.425	4.88	0.056	0.710	2.7.3.2	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	0.69	0.948	1.45	0.53	0.99	2gl0A	GO:0000166
1	0.11	0.368	3.28	0.06	0.49	2bj3C	GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0010045 GO:0016151 GO:0046872
2	0.06	0.388	5.20	0.08	0.69	4kxwA	GO:0003824 GO:0004802 GO:0005634 GO:0005654 GO:0005777 GO:0005829 GO:0005999 GO:0006098 GO:0008152 GO:0009052 GO:0016740 GO:0031982 GO:0040008 GO:0042803 GO:0043209 GO:0046166 GO:0046872 GO:0048037 GO:0070062
3	0.06	0.309	5.54	0.08	0.56	3qvfA	GO:0000166 GO:0005524 GO:0016301 GO:0016310 GO:0016740
4	0.06	0.410	5.12	0.06	0.68	3hlfA	GO:0016740 GO:0016746 GO:0016787 GO:0017000 GO:0030639 GO:0050832
5	0.06	0.356	5.10	0.10	0.61	4fo4A	GO:0000166 GO:0003824 GO:0003938 GO:0006164 GO:0006177 GO:0009152 GO:0016491 GO:0046872 GO:0055114
6	0.06	0.372	5.08	0.05	0.66	5bxpA	GO:0004553 GO:0004563 GO:0005975 GO:0008152 GO:0016020 GO:0016021 GO:0016787 GO:0016798 GO:0047403
7	0.06	0.345	5.53	0.06	0.61	2jg1A	GO:0000166 GO:0005524 GO:0005975 GO:0005988 GO:0009024 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0019512 GO:2001059
8	0.06	0.392	5.60	0.03	0.72	4c20B	GO:0005737 GO:0005975 GO:0005996 GO:0006004 GO:0008736 GO:0016853 GO:0016861 GO:0019317 GO:0030145 GO:0042355 GO:0046872
9	0.06	0.365	5.05	0.10	0.60	1r1zA	GO:0000139 GO:0005509 GO:0005537 GO:0005783 GO:0005789 GO:0005793 GO:0005794 GO:0006810 GO:0006888 GO:0015031 GO:0016020 GO:0016021 GO:0016192 GO:0030246 GO:0033116 GO:0042802 GO:0043231 GO:0046872
10	0.06	0.377	3.64	0.14	0.53	4hacA	GO:0000166 GO:0000287 GO:0004496 GO:0005524 GO:0005737 GO:0006629 GO:0008152 GO:0008299 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0019287
11	0.06	0.325	5.28	0.08	0.59	3ofvB	GO:0004045 GO:0005737 GO:0006412 GO:0016787
12	0.06	0.312	4.40	0.05	0.48	1j6oA	GO:0004536 GO:0006308 GO:0016788
13	0.06	0.344	4.91	0.05	0.58	3gh4A	GO:0004553 GO:0004563 GO:0005975
14	0.06	0.329	5.63	0.06	0.62	3cesA	GO:0002098 GO:0005737 GO:0005829 GO:0008033 GO:0016491 GO:0030488 GO:0050660 GO:0055114
15	0.06	0.373	5.09	0.08	0.64	3w6zA	GO:0000166 GO:0004616 GO:0016491 GO:0051287 GO:0055114
16	0.06	0.311	5.81	0.09	0.59	1x19A	GO:0008168 GO:0008171 GO:0016740 GO:0032259 GO:0046872 GO:0051536 GO:0051539
17	0.06	0.389	5.27	0.03	0.66	4z38B	GO:0003824 GO:0004314 GO:0008152 GO:0016740
18	0.06	0.373	4.05	0.12	0.56	4mksA	GO:0000015 GO:0000287 GO:0004634 GO:0005576 GO:0005737 GO:0006096 GO:0009986 GO:0016829 GO:0046872

Consensus prediction of GO terms

Molecular Function	GO:0000166	GO:0043169
GO-Score	0.71	0.33
Biological Processes	GO:0010045	GO:0006355	GO:0040008	GO:0009052	GO:0046166	GO:0005999	GO:0016310	GO:0050832	GO:0017000	GO:0030639
GO-Score	0.11	0.11	0.07	0.07	0.07	0.07	0.06	0.06	0.06	0.06
Cellular Component	GO:0070062	GO:0005829	GO:0005654	GO:0005777	GO:0043209
GO-Score	0.07	0.07	0.07	0.07	0.07

(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.