I-TASSER results

I-TASSER results for job id Rv0487

[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)
MTSSLPTVQRVIQNALEVSQLKYSQHPRPGGAPPALIVELPGERKLKINTILSVGEHSVR
VEAFVCRKPDENREDVYRFLLRRNRRLYGVAYTLDNVGDIYLVGQMALSAVDADEVDRVL
GQVLEVVDSDFNALLELGFRSSIQREWQWRLSRGESLQNLQAFAHLRPTTMQSAQRDEKE
LGG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MTSSLPTVQRVIQNALEVSQLKYSQHPRPGGAPPALIVELPGERKLKINTILSVGEHSVRVEAFVCRKPDENREDVYRFLLRRNRRLYGVAYTLDNVGDIYLVGQMALSAVDADEVDRVLGQVLEVVDSDFNALLELGFRSSIQREWQWRLSRGESLQNLQAFAHLRPTTMQSAQRDEKELGG
Prediction	CCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEHCCCCEEEEEEEEEEHCCEEEEEEEEEHCCCCCHHHHHHHHHHHHHHCCCEEEEHCCCCCEEEEEHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCC
Conf.Score	998789999999999999898654467888888769999588656788999998575899999987587765799999999999765665799868997899987566669989999999999999655689999999999999999999975876678999998577877877555555789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MTSSLPTVQRVIQNALEVSQLKYSQHPRPGGAPPALIVELPGERKLKINTILSVGEHSVRVEAFVCRKPDENREDVYRFLLRRNRRLYGVAYTLDNVGDIYLVGQMALSAVDADEVDRVLGQVLEVVDSDFNALLELGFRSSIQREWQWRLSRGESLQNLQAFAHLRPTTMQSAQRDEKELGG
Prediction	845627403500451066470515445655544410002023534140202011353103020000332555363013100432362300000114331010003133641447302300310042126413300231134014422512364444352151054135755654655666458
	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

CCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEHCCCCEEEEEEEEEEHCCEEEEEEEEEHCCCCCHHHHHHHHHHHHHHCCCEEEEHCCCCCEEEEEHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCC
MTSSLPTVQRVIQNALEVSQLKYSQHPRPGGAPPALIVELPGERKLKINTILSVGEHSVRVEAFVCRKPDENREDVYRFLLRRNRRLYGVAYTLDNVGDIYLVGQMALSAVDADEVDRVLGQVLEVVDSDFNALLELGFRSSIQREWQWRLSRGESLQNLQAFAHLRPTTMQSAQRDEKELGG

2plgA

0.18

0.13

0.70

0.88

MUSTER

LDAPLENAVEIIETVISSLHQGLVGQTDSGKGSAEVFVQLSGHTE----------EDFLTIWSPVLPLPVADELALYRKLLTLNLTTFEAHFAIAE-EQVQVVASRTLGGITAGEISRLITIVATLADDYDDALRAEFK--------------------------------------------

2plgA

0.17

0.13

0.74

1.19

dPPAS

LDAPLENAVEIIETVISSLHQG--DAPLVGQTDSGKIWFRYGSAEVFVQLSGHTEEDFLTIWSPVLPLPVADELALYRKLLTLNLTTFEAHFAI-AEEQVQVVASRTLGGITAGEISRLITIVATLADDYDDALRAEFK--------------------------------------------

2plgA

0.15

0.11

0.74

1.53

wdPPAS

LDAPLENAVEIIETVISSLHQG-DAPLVGQTDSGKIWFRY-GSAEVFVQLSGHTEEDFLTIWSPVLPLPVADELALYRKLLTLNLTTFEAHFAIAE-EQVQVVASRTLGGITAGEISRLITIVATLADDYDDALRAEFK--------------------------------------------

2plgA

0.18

0.13

0.69

1.10

wMUSTER

LDAPLENAVEIIETVISSLHQGLVGQTDSG-GSAEVFVQLSGHTE----------EDFLTIWSPVLPLPVADELALYRKLLTLNLTTFEAHFAIAE-EQVQVVASRTLGGITAGEISRLITIVATLADDYDDALRAEFK--------------------------------------------

2plgA

0.19

0.13

0.69

1.07

wPPAS

LTAPLENAVEIIETVISSLHQGLVGQTDSG-GSAEVFVQLSGHTE----------EDFLTIWSPVLPLPVADELALYRKLLTLNLTTFEAHFAIAE-EQVQVVASRTLGGITAGEISRLITIVATLADDYDDALRAEFK--------------------------------------------

2plgA

0.18

0.13

0.69

1.76

dPPAS2

LDAPLENAVEIIETVISSLHQGLVGQTDSGKGSAEVFVQLSGHTE----------EDFLTIWSPVLPLPVADELALYRKLLTLNLTTFEAHFAI--AEEVQVVASRTLGGITAGEISRLITIVATLADDYDDALRAEFK--------------------------------------------

2plgA

0.18

0.13

0.69

0.91

PPAS

LDAPLENAVEIIETVISSLHQGLVGQTDSG-GSAEVFVQLSGHTE----------EDFLTIWSPVLPLPVADELALYRKLLTLNLTTFEAHFAI--AEEVQVVASRTLGGITAGEISRLITIVATLADDYDDALRAEFK--------------------------------------------

2plgA

0.18

0.13

0.69

0.85

Env-PPAS

LDAPLENAVEIIETVISSLHQGLVGQTDSGKGSAEVFVQLSGHTE----------EDFLTIWSPVLPLPVADELALYRKLLTLNLTTFEAHFAI--AEEVQVVASRTLGGITAGEISRLITIVATLADDYDDALRAEFK--------------------------------------------

4h5bA

0.19

0.15

0.77

0.72

MUSTER

ETALLT--LDTLAKYLQEKEVQLDIEENGG----QRFIRM-GWRDAAVLVSVNDGPNRLEITCVTQKTYADRRAEVAMMLNDRNRE-RAFARSIDQEGNVWLEYV-TLAEMPQETFDTLFGGVLMHFQDDYAALE------------------------------YVPQEGMQIQQPQA----

4g6tA

0.07

0.05

0.70

1.06

dPPAS

---PVDMSNLFYKTLLDDFSRSLEMQPLVFDDHGTCNMIIDNT--FALTLSCDYARERLLLIGLLEPHKDIPQQCLLAGALNPLLNAGPGLGLDEKSGLYHAYQSIPREKLSVPTLKREMAGLLEWMRGWREA--------------------------------------------------

(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=-2.28

Estimated TM-score = 0.45±0.14

Estimated RMSD = 10.3±4.6Å

Download Model 2

C-score=-2.78

Download Model 3

C-score=-3.50

Download Model 4

C-score=-3.73

Download Model 5

C-score=-4.57

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	2plgA	0.633	2.00	0.165	0.716
2	4h5bA	0.619	2.92	0.153	0.765
3	3epuA	0.568	3.29	0.135	0.721
4	1s28A	0.563	2.62	0.137	0.672
5	3kxyA	0.562	3.37	0.122	0.716
6	1jyoA	0.554	3.00	0.079	0.689
7	2fm8A	0.543	3.02	0.143	0.689
8	1ry9A	0.534	2.94	0.114	0.667
9	3cxjA	0.531	3.19	0.120	0.683
10	4ff1A4	0.523	3.95	0.051	0.760

(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	0.08	3	3kxyH	III	Rep, Mult	20,39,40,41,42,43,44,47,117,121,124,125,128
2	0.07	3	3cr3A	MG	Rep, Mult	95,99
3	0.07	3	3sn0A	MG	Rep, Mult	95,136,155
4	0.05	2	2plg0	III	Rep, Mult	58,60,62,73,74,77,78,80,81,84,85,88,89,91,92,93,94,95,101,103,105,109,110,115,118
5	0.02	1	2w3nC	ACT	Rep, Mult	64,92
6	0.02	1	2o7eA	PMI	Rep, Mult	105,120,123
7	0.02	1	2bsj0	III	Rep, Mult	53,58,60,62,93,94,101,103,105,106,107
8	0.02	1	2zxkB	NA	Rep, Mult	84,87,88,91
9	0.02	1	3vmmA	MG	Rep, Mult	146,155
10	0.02	1	3ci0K	CA	Rep, Mult	125,128,130,146,159
11	0.02	1	1ttwA	III	Rep, Mult	36,40,41,50,64,95,101,117,121
12	0.02	1	1sk6B	YB	Rep, Mult	95,99,165
13	0.02	1	1ttw0	III	Rep, Mult	54,55,59,80,81,91,92,93,94,98,103,105

	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	1zn3A	0.472	4.95	0.060	0.749	3.4.24.69	84
2	0.060	2zxlA	0.466	4.95	0.064	0.749	1.3.1.80	37,51,53,59
3	0.060	2fpqA	0.464	4.84	0.034	0.738	3.4.24.69	NA
4	0.060	1b8fA	0.475	5.31	0.069	0.798	4.3.1.3	NA
5	0.060	1ylaA	0.458	4.43	0.040	0.678	6.3.2.19	NA
6	0.060	1uwkA	0.480	4.67	0.077	0.760	4.2.1.49	NA
7	0.060	3cegB	0.472	4.50	0.062	0.721	6.3.2.19	NA
8	0.060	1u6rA	0.453	4.63	0.057	0.678	2.7.3.2	43
9	0.060	1y2mB	0.493	4.92	0.048	0.776	4.3.1.24	NA
10	0.060	2fknB	0.472	4.59	0.066	0.743	4.2.1.49	NA
11	0.060	2nsmA	0.482	5.26	0.053	0.803	3.4.17.3	NA
12	0.060	1h8lA	0.475	5.44	0.064	0.809	3.4.17.22	134
13	0.060	1w27A	0.476	4.78	0.058	0.749	4.3.1.24	NA
14	0.060	2ewnA	0.473	4.56	0.027	0.710	6.3.4.15	NA
15	0.060	3fieA	0.457	4.86	0.065	0.760	3.4.24.69	NA
16	0.060	1zb7A	0.471	4.90	0.052	0.738	3.4.24.69	43
17	0.060	1bibA	0.469	4.28	0.045	0.683	6.3.4.15	28,45
18	0.060	1m56A	0.463	4.67	0.052	0.732	1.9.3.1	NA
19	0.060	2z8yD	0.474	4.52	0.044	0.732	1.2.7.4,1.2.99.2	66

(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	0.28	0.543	3.02	0.14	0.69	2fm8A	GO:0009405
1	0.20	0.562	3.37	0.12	0.72	3kxyA	GO:0005737 GO:0005886 GO:0016020 GO:0016021 GO:0030254 GO:0045893 GO:0050708
2	0.19	0.484	2.69	0.12	0.58	1k3sA	GO:0005737 GO:0009405
3	0.19	0.516	2.65	0.14	0.61	1xkpC	GO:0005737 GO:0005886 GO:0016020 GO:0050708
4	0.17	0.554	3.00	0.08	0.69	1jyoA	GO:0005737 GO:0009405 GO:0050708
5	0.16	0.504	2.89	0.09	0.62	1xkpB	GO:0005737 GO:0005886 GO:0009306 GO:0016020
6	0.15	0.568	3.29	0.14	0.72	3epuA	GO:0005737 GO:0050708
7	0.14	0.619	2.92	0.15	0.77	4h5bA	GO:0016049
8	0.11	0.534	2.94	0.11	0.67	1ry9A	GO:0009405
9	0.11	0.505	3.58	0.10	0.64	1n5bA	GO:0005737 GO:0006351 GO:0006355 GO:0009405 GO:0050708
10	0.11	0.574	2.66	0.13	0.69	1s28A	GO:0005737 GO:0050708
11	0.11	0.487	3.36	0.11	0.64	4gf3A	GO:0005737 GO:0050708
12	0.09	0.520	3.29	0.09	0.66	4g6tA	GO:0005737 GO:0050708
13	0.07	0.478	3.30	0.09	0.60	4jmfB	GO:0005737 GO:0009405 GO:0050708
14	0.06	0.453	3.15	0.08	0.56	1k3eB	GO:0005737 GO:0009405 GO:0050708
15	0.06	0.381	5.06	0.03	0.60	1prhA	GO:0001516 GO:0004601 GO:0004666 GO:0005634 GO:0005737 GO:0005783 GO:0005789 GO:0006629 GO:0006631 GO:0006633 GO:0006693 GO:0006954 GO:0006979 GO:0008217 GO:0016020 GO:0016021 GO:0016491 GO:0019371 GO:0020037 GO:0031090 GO:0043231 GO:0046872 GO:0051213 GO:0055114 GO:0098869
16	0.06	0.397	4.97	0.07	0.63	2aaxA	GO:0003677 GO:0003700 GO:0003707 GO:0005496 GO:0005634 GO:0005654 GO:0005737 GO:0005783 GO:0005789 GO:0006351 GO:0006355 GO:0006367 GO:0007165 GO:0008270 GO:0008289 GO:0016020 GO:0043235 GO:0043401 GO:0043565 GO:0046872
17	0.06	0.439	5.38	0.06	0.74	3c46A	GO:0000166 GO:0003899 GO:0005524 GO:0005525 GO:0016740 GO:0016779 GO:0019012 GO:0032774 GO:0046872
18	0.06	0.372	5.50	0.07	0.65	1o9lB	GO:0005739 GO:0008152 GO:0008260 GO:0008410 GO:0016740 GO:0042803 GO:0046950 GO:0046952
19	0.06	0.365	5.59	0.04	0.65	5aedA	GO:0003824 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0030246
20	0.06	0.368	5.38	0.05	0.64	1opeA	GO:0005739 GO:0008152 GO:0008260 GO:0008410 GO:0016740 GO:0042803 GO:0046950 GO:0046952
21	0.06	0.356	5.75	0.06	0.64	1gyhA	GO:0004553 GO:0005576 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0031222 GO:0046558 GO:0046872
22	0.06	0.358	5.41	0.06	0.62	3ck6E	GO:0005886 GO:0016020 GO:0016021 GO:0030001 GO:0046873 GO:0055085
23	0.06	0.356	5.74	0.04	0.67	1m3eB	GO:0005739 GO:0008152 GO:0008260 GO:0008410 GO:0016740 GO:0042803 GO:0046950 GO:0046952
24	0.06	0.322	5.34	0.07	0.54	2x77A	GO:0000166 GO:0005525 GO:0005622 GO:0005802 GO:0006622 GO:0007264 GO:0030100

Consensus prediction of GO terms

Molecular Function
GO-Score
Biological Processes	GO:0009405	GO:0050708	GO:0006355	GO:0010628	GO:1903508	GO:0071806
GO-Score	0.51	0.46	0.40	0.40	0.40	0.40
Cellular Component	GO:0005737	GO:0005886	GO:0031224
GO-Score	0.56	0.35	0.32

(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.