I-TASSER results

I-TASSER results for job id Rv0692

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

Input Sequence in FASTA format

>protein (109 residues)
MWGLLTVPAPAQARRADSSEFDPDRGWRLHPQVAVRPEPFGALLYHFGTRKLSFLKNRTI
LAVVQTLADYPDIRSACRGAGVDDCDQDPYLHALSVLAGSNMLVPRQTT

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MWGLLTVPAPAQARRADSSEFDPDRGWRLHPQVAVRPEPFGALLYHFGTRKLSFLKNRTILAVVQTLADYPDIRSACRGAGVDDCDQDPYLHALSVLAGSNMLVPRQTT
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEHCCCCCCEEEEEHCCCEEEHCCCCHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCEEHCCCC
Conf.Score	9887678888888888888899655766686566555678657787488747764785699999986558999999999899988869999999999987987766889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MWGLLTVPAPAQARRADSSEFDPDRGWRLHPQVAVRPEPFGALLYHFGTRKLSFLKNRTILAVVQTLADYPDIRSACRGAGVDDCDQDPYLHALSVLAGSNMLVPRQTT
Prediction	7443243334454664544414373315134414243442110023344430311454401400440472651530144341567634303400330374522444688
	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

                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEHCCCCCCEEEEEHCCCEEEHCCCCHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCEEHCCCC
MWGLLTVPAPAQARRADSSEFDPDRGWRLHPQVAVRPEPFGALLYHFGTRKLSFLKNRTILAVVQTLADYPDIRSACRGAGVDDCDQDPYLHALSVLAGSNMLVPRQTT

1xs5A

0.16

0.96

0.98

wMUSTER

MRG--DILMNFFQHVPHMQQFNQEHNGDLVSVGNVHVEPL--ALYSRTYRHVSDFPAGAVIAIPNDSSNEARALRLLEAAGFIRMRAGSGLFAVEDVQQNVRLQEVESA

4bs9A1

0.13

0.09

0.72

1.15

dPPAS2

-----------------------------PTALQIKPH-FPKQVYLLGEQGNHALTGQLYCQILPFLNGEYTREQIVEKLD-GQVPEEYIDFVLSRLVEKGYLTEVAPE

4bs9A1

0.13

0.09

0.72

1.00

PPAS

-----------------------------PTALQIKPEIIPKQVYLLGEQGNHALTGQLYCQILPFLNGEYTREQIVEKLD-GQVPEEYIDFVLSRLVEKGYLTEVAPE

3ir1B

0.12

0.96

0.97

wMUSTER

AEG--ELDINVFQHKPYLDDFKKEHNLDITEVFQVPTAPL--GLYPGKLKSLEEVKDGSTVSAPNDPSNFARVLVMLDELGWIKLKDGIPLTAKADIAENLKIVELEAA

1xs5A

0.16

0.96

0.98

MUSTER

MRG--DILMNFFQHVPHMQQFNQEHNGDLVSVGNVHVEPL--ALYSRTYRHVSDFPAGAVIAIPNDSSNEARALRLLEAAGFIRMRAGSGLFAVEDVQQNVRLQEVESA

4bs9A1

0.11

0.08

0.72

0.90

dPPAS

-----------------------------PTALQIKPHFHPKQVYLLGEQGNHALTGQLYCQILPFLNGEYTREQIVEKLD-GQVPEEYIDFVLSRLVEKGYLTEVAPE

4bs9A1

0.14

0.10

0.71

0.89

wdPPAS

------------------------------PTLQIKPH-FPKQVYLLGEQGNHALTGQLYCQILPFLNGEYTREQIVEKLD-GQVPEEYIDFVLSRLVEKGYLTEVAPE

3k2dA

0.13

0.96

0.90

wMUSTER

DDG--SIDMNAFQHKPYLDRQVEDRDYKLTIAGNTFVYPI--AGYSKQVKSVAALADGVRIAVPNDPTNLGRSLLLLEQQGLIKLRPEVGLLAVRDIVENNIIMELDAA

4bs9A1

0.14

0.10

0.71

0.80

wPPAS

------------------------------PTLQIKPH-FPKQVYLLGEQGNHALTGQLYCQILPFLNGEYTREQIVEKLD-GQVPEEYIDFVLSRLVEKGYLTEVAPE

3g2bA

0.15

0.11

0.75

0.74

dPPAS2

-------------------TISRDSCPALRAGVRLQHDRADVLLAPERVVEL----DDIALVVAQRYDGTQSAQTLAAEFDADSEIETDVIELTTTLHQKRLLRL----

(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 4 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=-1.93

Estimated TM-score = 0.48±0.15

Estimated RMSD = 8.2±4.5Å

Download Model 2

C-score=-2.00

Download Model 3

C-score=-3.52

Download Model 4

C-score=-2.28

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	4q5tA	0.510	4.29	0.084	0.890
2	2c6xA	0.497	4.49	0.060	0.872
3	4yahX	0.496	4.22	0.118	0.844
4	3up9A	0.496	4.23	0.097	0.862
5	4qhqA	0.493	4.08	0.089	0.835
6	4ib2A	0.489	4.14	0.118	0.844
7	3k2dA	0.484	4.37	0.109	0.844
8	4k3fA	0.483	4.36	0.127	0.844
9	3vs8A	0.482	4.38	0.080	0.844
10	1p99A	0.481	4.31	0.059	0.835

(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	0.10	5	3ak1B	EDO	Rep, Mult	93,94,97
2	0.06	3	2axtH	CLA	Rep, Mult	90,91,94
3	0.04	2	1qpiA	IMD	Rep, Mult	46,47,49,50
4	0.04	2	3kllA	MAL	Rep, Mult	31,32,33,34,98,108
5	0.04	2	2bf0X	CA	Rep, Mult	97,100
6	0.04	2	3pfvA	NA	Rep, Mult	64,66,68,70,73,76
7	0.02	1	3u5zC	08T	Rep, Mult	38,50
8	0.02	1	3iilA	MG	Rep, Mult	37,38
9	0.02	1	2dwlA	NUC	Rep, Mult	21,22,27,47,48,55,56
10	0.02	1	2hn2A	CA	Rep, Mult	84,88
11	0.02	1	4ej7B	CA	Rep, Mult	24,33
12	0.02	1	3eyxB	ACT	Rep, Mult	40,54
13	0.02	1	2cixA	MAN	Rep, Mult	59,67
14	0.02	1	3msuB	OAA	Rep, Mult	73,74,77,94,97
15	0.02	1	3gc9B	ZN	Rep, Mult	16,69,71

	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	2ib7D	0.460	4.89	0.072	0.862	2.3.1.9	NA
2	0.060	2q85A	0.453	4.19	0.034	0.771	1.1.1.158	NA
3	0.060	3k92A	0.447	4.56	0.104	0.844	1.4.1.2	95
4	0.060	3il7A	0.444	4.47	0.085	0.807	2.3.1.180	NA
5	0.060	3gpyA	0.451	4.62	0.101	0.807	3.2.2.23	47,79
6	0.060	3cf4A	0.453	3.89	0.059	0.716	1.2.99.2	NA
7	0.060	1wogA	0.461	4.84	0.088	0.881	3.5.3.11	72
8	0.060	2i7vA	0.453	4.84	0.046	0.881	3.1.27.-	NA
9	0.060	1bw9A	0.426	4.75	0.057	0.817	1.4.1.20	72
10	0.060	1z1eA	0.459	4.52	0.079	0.853	2.3.1.95	NA
11	0.060	1u0uA	0.444	4.68	0.078	0.862	2.3.1.-	NA
12	0.060	3ffzA	0.450	4.93	0.069	0.881	3.4.24.69	NA
13	0.060	1e9iD	0.448	4.74	0.050	0.835	4.2.1.11	NA
14	0.060	1k3pA	0.461	4.19	0.112	0.817	2.3.3.1	NA
15	0.060	2irpA	0.457	4.22	0.060	0.752	4.2.1.109	NA
16	0.060	1gq7E	0.435	4.36	0.078	0.789	3.5.3.22	NA
17	0.060	2p0uA	0.456	4.75	0.078	0.853	2.3.1.74	NA
18	0.060	1iomA	0.453	4.78	0.071	0.862	4.1.3.7	NA
19	0.060	1vgmA	0.442	4.72	0.051	0.826	4.1.3.7	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	0.07	0.496	4.22	0.12	0.84	4yahX	GO:0005886 GO:0006810 GO:0006865 GO:0016020 GO:0048473
1	0.07	0.479	4.21	0.08	0.84	1xs5A	GO:0005886 GO:0016020
2	0.07	0.477	4.37	0.10	0.84	4gotA	GO:0005886 GO:0006810 GO:0006865 GO:0016020
3	0.07	0.467	4.20	0.11	0.83	4oteB	GO:0046872
4	0.07	0.442	4.72	0.05	0.83	1vgmA	GO:0005737 GO:0006099 GO:0016020 GO:0016021 GO:0016740 GO:0016746 GO:0046912
5	0.07	0.456	4.32	0.04	0.82	1o7xC	GO:0003824 GO:0005737 GO:0006099 GO:0008152 GO:0016740 GO:0046912
6	0.06	0.417	4.54	0.06	0.75	1x0aA	GO:0000166 GO:0008152 GO:0016491 GO:0055114
7	0.06	0.422	4.49	0.07	0.74	4ntlA	GO:0046872
8	0.06	0.301	4.72	0.06	0.53	4ryeA	GO:0004175 GO:0004180 GO:0005887 GO:0006508 GO:0009002 GO:0009252 GO:0016787
9	0.06	0.461	4.19	0.11	0.82	4g6bA	GO:0003824 GO:0004108 GO:0005737 GO:0005829 GO:0006099 GO:0008152 GO:0016740 GO:0042802 GO:0046912
10	0.06	0.447	4.24	0.02	0.81	1vgpA	GO:0005737 GO:0006099 GO:0016740 GO:0016746 GO:0046912
11	0.06	0.442	4.82	0.05	0.83	1aj8A	GO:0003824 GO:0005737 GO:0006099 GO:0008152 GO:0016740 GO:0046912
12	0.06	0.364	5.22	0.01	0.78	2ibpA	GO:0005737 GO:0006099 GO:0016740 GO:0046912
13	0.06	0.451	4.73	0.07	0.83	4xghA	GO:0004108 GO:0005737 GO:0006099 GO:0016740 GO:0016746 GO:0046912
14	0.06	0.335	4.70	0.01	0.59	2l2cA	GO:0005549
15	0.06	0.456	4.24	0.11	0.82	4e6yA	GO:0004108 GO:0005737 GO:0006099 GO:0016020 GO:0016021 GO:0016740 GO:0016746 GO:0046912
16	0.06	0.453	4.78	0.07	0.86	1iomA	GO:0005737 GO:0016740 GO:0046912
17	0.06	0.421	4.91	0.08	0.85	2h12B	GO:0003824 GO:0004108 GO:0005737 GO:0006099 GO:0008152 GO:0016740 GO:0046912
18	0.06	0.339	4.67	0.02	0.61	1t72A	GO:0005315 GO:0005436 GO:0005737 GO:0005886 GO:0006810 GO:0006817 GO:0010629 GO:0015321 GO:0030643 GO:0035435 GO:0035725 GO:0042803 GO:0044341 GO:0045936 GO:0055085 GO:2000186

Consensus prediction of GO terms

Molecular Function	GO:0046872	GO:0046912
GO-Score	0.07	0.07
Biological Processes	GO:0048473	GO:0006099
GO-Score	0.07	0.07
Cellular Component	GO:0071944
GO-Score	0.37

(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.