I-TASSER results

I-TASSER results for job id Rv1419

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

Input Sequence in FASTA format

>protein (157 residues)
MGELRLVGGVLRVLVVVGAVFDVAVLNAGAASADGPVQLKSRLGDVCLDAPSGSWFSPLV
INPCNGTDFQRWNLTDDRQVESVAFPGECVNIGNALWARLQPCVNWISQHWTVQPDGLVK
SDLDACLTVLGGPDPGTWVSTRWCDPNAPDQQWDSVP

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MGELRLVGGVLRVLVVVGAVFDVAVLNAGAASADGPVQLKSRLGDVCLDAPSGSWFSPLVINPCNGTDFQRWNLTDDRQVESVAFPGECVNIGNALWARLQPCVNWISQHWTVQPDGLVKSDLDACLTVLGGPDPGTWVSTRWCDPNAPDQQWDSVP
Prediction	CCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEHCCCEEEHCCCCCCCCCEEEHCCCCCCCEEEEEHCCCEEEEEHCCCEEEHCCCCCEEEEEHCCCCCCCEEEHCCCCEEHCCCCCEEHCCCCCCCCCEEEEEEHCCCCCCCCEHCCC
Conf.Score	9988778864555666655444455677778888767999746885897799898876899869999765799959986999865886787799987999958999764689859966885778867778999999769999857999876466699
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MGELRLVGGVLRVLVVVGAVFDVAVLNAGAASADGPVQLKSRLGDVCLDAPSGSWFSPLVINPCNGTDFQRWNLTDDRQVESVAFPGECVNIGNALWARLQPCVNWISQHWTVQPDGLVKSDLDACLTVLGGPDPGTWVSTRWCDPNAPDQQWDSVP
Prediction	7563444440431110011233234244444445443424443442001045444423120131445432303336644044343544104246434020111654541403344614143434400223335454130020102463444426638
	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

CCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEHCCCEEEHCCCCCCCCCEEEHCCCCCCCEEEEEHCCCEEEEEHCCCEEEHCCCCCEEEEEHCCCCCCCEEEHCCCCEEHCCCCCEEHCCCCCCCCCEEEEEEHCCCCCCCCEHCCC
MGELRLVGGVLRVLVVVGAVFDVAVLNAGAASADGPVQLKSRLGDVCLDAPSGSWFSPLVINPCNGTDFQRWNLTDDRQVESVAFPGECVNIGNALWARLQPCVNWISQHWTVQPDGLVKSDLDACLTVLGGPDPGTWVSTRWCDPNAPDQQWDSVP

1isyA

0.21

0.98

1.86

MUSTER

GDTPLLFNGDGSKKAAYTAVLNALNGGSSTPPPSGGGQIKGVGSGRCLDVPNASDGTQVQLYDCHSATNQQWTYTDAGELRVY--GDKCLDAGNGTKVQIYSCWGGDNQKWRLNSDGIVGVQSGLCLDAVGGGTANGTLIQLYSCSNGSNQRWTRT-

1isyA2

0.20

0.17

0.81

2.69

dPPAS

---------------------------SSTPPPSGGGQIKGVGSGRCLDVPSTTDGTQVQLYDCHSATNQQWTYTDAGELRVY--GDKCLDAAGGTKVQIYSCWGGDNQKWRLNSDGSIVGQSGLCLDAVGGGTANGTLIQLYSCSNGSNQRWTRT-

1isyA2

0.21

0.17

0.81

3.13

wdPPAS

---------------------------SSTPPPSGGGQIKGVGSGRCLDVPNTTDGTQVQLYDCHSATNQQWTYTDAGELRVY--GDKCLDAGNGTKVQIYSCWGGDNQKWRLNSDGSIVGQSGLCLDAVGGGTANGTLIQLYSCSNGSNQRWTRT-

1isyA

0.21

0.98

2.27

wMUSTER

GDTPLLFNGDGSKKAAYTAVLNALNGGSSTPPPSGGGQIKGVGSGRCLDVPNASDGTQVQLYDCHSATNQQWTYTDAGELRVY--GDKCLDAGNGTKVQIYSCWGGDNQKWRLNSDGIVGVQSGLCLDAVGGGTANGTLIQLYSCSNGSNQRWTRT-

1isyA2

0.21

0.17

0.81

3.25

wPPAS

---------------------------SSTPPPSGGGQIKGVGSGRCLDVPNTTDGTQVQLYDCHSATNQQWTYTDAGELRVY--GDKCLDAGNGTKVQIYSCWGGDNQKWRLNSDGSIVGQSGLCLDAVGGGTANGTLIQLYSCSNGSNQRWTRT-

1isyA2

0.20

0.17

0.81

4.37

dPPAS2

---------------------------SSTPPPSGGGQIKGVGSGRCLDVPSTTDGTQVQLYDCHSATNQQWTYTDAGELRVY--GDKCLDAAGGTKVQIYSCWGGDNQKWRLNSDGSIVGQSGLCLDAVGGGTANGTLIQLYSCSNGSNQRWTRT-

1isyA2

0.20

0.17

0.81

3.06

PPAS

---------------------------SSTPPPSGGGQIKGVGSGRCLDVPSTTDGTQVQLYDCHSATNQQWTYTDAGELRVY--GDKCLDAAGGTKVQIYSCWGGDNQKWRLNSDGSIVGQSGLCLDAVGGGTANGTLIQLYSCSNGSNQRWTRT-

4z8sB2

0.19

0.15

0.77

3.24

Env-PPAS

----------------------------------PIVTTIIGLRHMCLEATD--NDTNVWLESCKNKTKQYWALYSDDTIRVNNNRNLCVSSSTSKLIVIRRCDGSINQRWVFTPQGTISNGYEAVMDVAQNDVYLKKIVLSSATDKGNGQQWTVFY

1isyA2

0.23

0.18

0.81

1.71

MUSTER

---------------------------SSTPPPSGGGQIKGVGSGRCLDVPSTTDGTQVQLYDCHSATNQQWTYTDAGELRVY--GDKCLDAGNGTKVQIYSCWGGDNQKWRLNSDGIVGVQSGLCLDAVGGGTANGTLIQLYSCSNGSNQRWTRT-

3a07B

0.18

0.13

0.75

2.45

dPPAS

------------------------------SAQFASVTIRNAQTGRLLDSNY---NGNVYTLPANGGNYQRWTGPGDGTVRNA-QTGRCLDSNYDGAVYTLPCNGGSYQKWLFYSNGYIQNETGRVLDSNYNGN-----VYTLPANGGNYQKWYTG-

(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=0.30

Estimated TM-score = 0.75±0.10

Estimated RMSD = 4.2±2.8Å

Download Model 2

C-score=-3.07

Download Model 3

C-score=-3.40

Download Model 4

C-score=-3.41

Download Model 5

C-score=-3.57

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	1isyA	0.939	1.07	0.201	0.981
2	2ehiB	0.759	3.10	0.103	0.904
3	1hwpB	0.754	2.69	0.182	0.885
4	2vseA	0.748	2.56	0.128	0.854
5	2x2sA	0.747	1.57	0.134	0.809
6	2vlcA	0.747	1.88	0.159	0.815
7	4z8sB	0.746	2.72	0.154	0.885
8	1ybiA	0.743	2.55	0.086	0.854
9	1rzoB	0.739	2.72	0.142	0.873
10	3vsfA2	0.738	1.61	0.185	0.790

(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	0.28	44	1knmA	LAT	Rep, Mult	49,50,51,60,62,65,69
2	0.27	41	1iswA	XYP	Rep, Mult	128,129,130,131,132,141,143,146,150
3	0.03	6	1pumB	NAG	Rep, Mult	36,37,71,157
4	0.03	7	3ef2A	UUU	Rep, Mult	91,92,93,94,101,102,106,108
5	0.02	5	2r9kB	SGI	Rep, Mult	35,37,74,155,157
6	0.01	3	2vlcB	UUU	Rep, Mult	36,37,67,71,73
7	0.01	2	3d7wB	ZEA	Rep, Mult	35,74,75,76,155
8	0.01	2	1hwmB	GAL	Rep, Mult	49,50,51,60,62,137
9	0.01	2	1pumB	GOL	Rep, Mult	41,43,44,45,149,152
10	0.01	2	1vclA	MG	Rep, Mult	1,59
11	0.00	1	1djsB	SO4	Rep, Mult	31,37,155,156,157
12	0.00	1	1pumB	GOL	Rep, Mult	68,71,73,81,82,86
13	0.00	1	2zqnA	IMD	Rep, Mult	77,78,113,123
14	0.00	1	2x2t0	III	Rep, Mult	36,53,73,75,76,77,79,81,82,87,88,89,102,104,105,110
15	0.00	1	1puuB	GOL	Rep, Mult	40,157
16	0.00	1	2zqnA	IMD	Rep, Mult	84,85
17	0.00	1	1q1uA	SO4	Rep, Mult	44,148,149,150
18	0.00	1	1vclA	MG	Rep, Mult	97,98,139,140
19	0.00	1	1onkB	AZI	Rep, Mult	113,153,154,155
20	0.00	1	1pumB	GOL	Rep, Mult	14,19,20

	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	0.224	1knnA	0.736	1.11	0.233	0.764	3.2.1.8	NA
2	0.112	1abrB	0.742	2.68	0.199	0.873	3.2.2.22	141,153
3	0.104	3d7wB	0.736	2.83	0.170	0.873	3.2.2.22	132,137,141
4	0.094	2q3nB	0.728	2.81	0.163	0.873	3.2.2.22	NA
5	0.067	1rzoB	0.739	2.72	0.142	0.873	3.2.2.22	NA
6	0.060	1ry7A	0.643	2.23	0.068	0.745	2.7.10.1	NA
7	0.060	3btaA	0.665	2.88	0.052	0.822	3.4.24.69	NA
8	0.060	1f1hA	0.387	4.85	0.074	0.650	6.3.1.2	NA
9	0.060	3fwmA	0.330	5.83	0.054	0.669	2.4.1.129,	NA
10	0.060	1st8A	0.407	5.56	0.050	0.758	3.2.1.80	77,88
11	0.060	3fwlA	0.389	4.98	0.052	0.669	2.4.1.129	NA
12	0.060	1z0hB	0.652	2.72	0.039	0.802	3.4.24.69	88
13	0.060	2bixA	0.388	5.26	0.040	0.694	1.14.99.-	NA
14	0.060	1kblA	0.345	5.36	0.008	0.624	2.7.9.1	NA
15	0.060	1nunA	0.644	2.44	0.050	0.758	2.7.10.1	NA
16	0.060	2d7iA	0.683	2.52	0.145	0.790	2.4.1.41	77
17	0.060	1hwpB	0.754	2.69	0.182	0.885	3.2.2.22	95,108
18	0.060	1kc7A	0.390	5.36	0.040	0.720	2.7.9.1	60,81
19	0.060	1lgrA	0.382	5.23	0.061	0.675	6.3.1.2	NA
20	0.060	1v6yA	0.292	5.42	0.015	0.560	3.2.1.8	88
21	0.060	2aeyA	0.405	5.59	0.050	0.758	3.2.1.80	NA
22	0.060	1f1hL	0.387	4.85	0.074	0.650	6.3.1.2	115
23	0.060	2np0A	0.645	2.76	0.032	0.809	3.4.24.69	NA
24	0.060	1htoA	0.389	5.04	0.051	0.662	6.3.1.2	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	0.38	0.935	1.12	0.20	0.98	1isvA	GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0031176
1	0.34	0.747	1.88	0.16	0.82	2vlcA	GO:0006952 GO:0016787 GO:0017148 GO:0030598
2	0.28	0.651	2.09	0.18	0.74	1dqgA	GO:0004872 GO:0004888 GO:0005537 GO:0005768 GO:0005886 GO:0006897 GO:0006898 GO:0007165 GO:0009986 GO:0010008 GO:0016020 GO:0016021 GO:0030246 GO:0071222 GO:0071346 GO:0071353
3	0.27	0.700	1.88	0.13	0.78	4ionA	GO:0030246 GO:0042802
4	0.27	0.759	3.10	0.10	0.90	3ah1B	GO:0030246
5	0.24	0.740	1.26	0.23	0.77	1knmA	GO:0000272 GO:0004553 GO:0005576 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0030246 GO:0031176 GO:0045493
6	0.24	0.757	2.64	0.19	0.89	3c9zA	GO:0006952 GO:0016787 GO:0017148 GO:0030246 GO:0030598
7	0.24	0.685	1.69	0.19	0.75	3a07B	GO:0030246 GO:0050688
8	0.24	0.736	2.88	0.18	0.87	4eb2B	GO:0006952 GO:0016787 GO:0017148 GO:0030246 GO:0030598
9	0.23	0.673	2.03	0.15	0.76	1sr4A	GO:0009279 GO:0009405 GO:0016020 GO:0030246
10	0.21	0.735	1.61	0.13	0.78	3a21A	GO:0003824 GO:0004553 GO:0004557 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0052692
11	0.21	0.746	2.72	0.15	0.89	4z8sB	GO:0006952 GO:0016787 GO:0017148 GO:0030598
12	0.21	0.731	2.77	0.15	0.87	2zr1B	GO:0005829 GO:0006952 GO:0007157 GO:0016787 GO:0017148 GO:0030246 GO:0030598 GO:0044533
13	0.19	0.720	1.76	0.13	0.79	4g9mB	GO:0030246
14	0.18	0.730	2.82	0.15	0.87	1onkB	GO:0006952 GO:0016787 GO:0017148 GO:0030246 GO:0030598
15	0.18	0.679	2.17	0.19	0.76	4owlD	GO:0005576 GO:0019835 GO:0030246 GO:0044179 GO:0051715
16	0.15	0.748	2.78	0.18	0.89	1hwmB	GO:0006952 GO:0008152 GO:0016787 GO:0016798 GO:0017148 GO:0030598
17	0.14	0.733	2.62	0.16	0.87	2aaiB	GO:0000166 GO:0005783 GO:0006952 GO:0016787 GO:0017148 GO:0030246 GO:0030598 GO:0031640
18	0.14	0.739	2.72	0.14	0.87	1rzoB	GO:0000166 GO:0005783 GO:0006952 GO:0016787 GO:0017148 GO:0030246 GO:0030598
19	0.14	0.742	2.68	0.20	0.87	1abrB	GO:0005534 GO:0006952 GO:0016787 GO:0017148 GO:0030246 GO:0030598 GO:0045807
20	0.13	0.756	1.65	0.17	0.82	3vsfC	GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0030246
21	0.10	0.670	2.13	0.11	0.76	1xhbA	GO:0004653 GO:0005576 GO:0005794 GO:0006486 GO:0006493 GO:0016020 GO:0016021 GO:0016740 GO:0016757 GO:0018242 GO:0018243 GO:0030145 GO:0030246 GO:0032580 GO:0046872 GO:0048471

Consensus prediction of GO terms

Molecular Function	GO:0048029	GO:0038023	GO:0099600	GO:0005515	GO:0031176	GO:0030598
GO-Score	0.57	0.57	0.57	0.55	0.38	0.34
Biological Processes	GO:0071219	GO:1901701	GO:0032496	GO:0007154	GO:0071396	GO:0034341	GO:0006897	GO:0071345	GO:0070670	GO:0044700	GO:0000272	GO:0017148
GO-Score	0.57	0.57	0.57	0.57	0.57	0.57	0.57	0.57	0.57	0.57	0.38	0.34
Cellular Component	GO:0071944	GO:0044440	GO:0005774	GO:0031224
GO-Score	0.57	0.57	0.57	0.45

(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.