I-TASSER results

I-TASSER results for job id Rv1171

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

Input Sequence in FASTA format

>protein (146 residues)
MGHRVDTLSDRQRANLTTGATDRAIRLVVLALLTVDGVVSALAGALLMPWYIGSAPFPIS
ALISGLVNAALVWAAARWTTSSRVAALPLWAWLLTVAAMSFGGPGDDVILGGQGLLVYGA
LVFVVAGAVPPAWVLWRRRVQADGSG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MGHRVDTLSDRQRANLTTGATDRAIRLVVLALLTVDGVVSALAGALLMPWYIGSAPFPISALISGLVNAALVWAAARWTTSSRVAALPLWAWLLTVAAMSFGGPGDDVILGGQGLLVYGALVFVVAGAVPPAWVLWRRRVQADGSG
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCCCEEEHCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
Conf.Score	99888887777888888888766456789999999999999999999756548867658999999999999999998679856777689999999999967889997887577644799999999997677777765544688999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MGHRVDTLSDRQRANLTTGATDRAIRLVVLALLTVDGVVSALAGALLMPWYIGSAPFPISALISGLVNAALVWAAARWTTSSRVAALPLWAWLLTVAAMSFGGPGDDVILGGQGLLVYGALVFVVAGAVPPAWVLWRRRVQADGSG
Prediction	74542563645544546564444323220013023203211110233233332433233002313332120021033226432110222322331332112333432101324434313112113123321121012331556688
	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

CCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCCCEEEHCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
MGHRVDTLSDRQRANLTTGATDRAIRLVVLALLTVDGVVSALAGALLMPWYIGSAPFPISALISGLVNAALVWAAARWTTSSRVAALPLWAWLLTVAAMSFGGPGDDVILGGQGLLVYGALVFVVAGAVPPAWVLWRRRVQADGSG

4xydA1

0.17

0.14

0.87

1.07

wMUSTER

--------------KYQSQSIALVYFAVALGLFAIQVSGGLLLGWIYVPNFLSEI-LPFNIVRMLHTNSLIVWLLLGF-HSPLLAYLQLAIMVLGTLGVVVNLFEGNWLLGKEG-QPVWVKMGIVVAALIFMYNISMTVLQGRK--

4xydA1

0.18

0.15

0.84

1.31

wPPAS

M--KYQS-------------IALVYFAVALGLFAIQVSGGLLLGWIYVPNFLSEI-LPFNIVRMLHTNSLIVWLLLGF--SPLLAYLQLAIMVLGTLGVVVTNLFGNWLLGKEG---VWVKMGIVVAALIFMYNISMTVLQGRK--

4xydA1

0.16

0.14

0.89

1.23

dPPAS2

-------------MKYQSQSIALVYFAVALGLFAIQVSGGLLLGWIYVPNFLSEI-LPFNIVRMLHTNSLIVWLLLGFMHSPLLAYLQLAIMVLGTLGVVVNLFEGNWLLGKEGRQPVWVKMGIVVAALIFMYNISMTVLQGRK--

4xydA1

0.16

0.14

0.88

1.14

PPAS

-------------MKYQSQSIALVYFAVALGLFAIQVSGGLLLGWIYVPNFLSEI-LPFNIVRMLHTNSLIVWLLLGF-HSPLLAYLQLAIMVLGTLGVVVNLFEGNWLLGKEG-QPVWVKMGIVVAALIFMYNISMTVLQGRK--

4xydA1

0.16

0.14

0.88

0.93

MUSTER

-------------MKYQSQSIALVYFAVALGLFAIQVSGGLLLGWIYVPNFLSEI-LPFNIVRMLHTNSLIVWLLLGFMHSPLLAYLQLAIMVLGTLGVVVTYLFNNWLLGKEG-QPVWVKMGIVVAALIFMYNISMTVLQGRK--

4xydA1

0.16

0.14

0.90

0.71

dPPAS

-------------MKYQSQSIALVYFAVALGLFAIQVSGGLLLGWIYVSPNFLSEILPFNIVRMLHTNSLIVWLLLGFMHSPLLAYLQLAIMVLGTLGVVVNLFEGNWLLGKEGRQPVWVKMGIVVAALIFMYNISMTVLQGRK--

4xydA1

0.16

0.14

0.88

1.03

wdPPAS

-------------MKYQSQSIALVYFAVALGLFAIQVSGGLLLGWIYVPNFLSEI-LPFNIVRMLHTNSLIVWLLLGF-HSPLLAYLQLAIMVLGTLGVVVNLFEGNWLLGKEG-QPVWVKMGIVVAALIFMYNISMTVLQGRK--

4hzuS

0.15

0.14

0.92

wMUSTER

ILVVIP-------IPATKGIVTLCEVGIYTSAILYMGLLVGGASGFLIDILTGPVWCLFSLVIHGTQGLVVGWLLPRHHKGRSMLLPLLVGSLVMVIGYCL----ATTLLFGAGLASIFGNVVQVGFGAGVTLSIVGPLTRLKPD-

2mgyA

0.17

0.14

0.80

0.93

wPPAS

MPESW----------------------VPAVGLTLVPSLGGFMGAYFVRGEGLRHPLPIWGTLYSAMGYGSYIVWKELGGFTEDAMVPLGLYTGQLALNWAWPP---IFFGAQMGWALADLLLVSGVATATTLAWHR----SPPAA

3wdoA2

0.11

0.10

0.87

0.95

dPPAS2

-----------RESGMVKGSFSAEPRLLKLNFGIMCLHMLLMSTFVALPGQLADAGFLATMLIAFGSVVPFIIYAEVKRKMKQVFVFCVGLIVVAEIVLWNAQT--------QFWQLVVGVQLFFVAFNLMEALLPSLISKESPAG

(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=-1.01

Estimated TM-score = 0.59±0.14

Estimated RMSD = 6.8±4.1Å

Download Model 2

C-score=-2.16

Download Model 3

C-score=-1.26

Download Model 4

C-score=-5.00

Download Model 5

C-score=-5.00

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	4xydA	0.836	1.54	0.150	0.911
2	3o0rB	0.789	2.20	0.107	0.897
3	3ayfA	0.783	2.52	0.171	0.931
4	3mk7A	0.747	2.39	0.138	0.877
5	1fftA1	0.681	3.19	0.078	0.870
6	2yevA3	0.679	3.59	0.043	0.938
7	1m56A	0.659	2.99	0.093	0.870
8	1xmeA	0.657	3.69	0.086	0.911
9	1ocrN	0.644	3.27	0.088	0.843
10	3dwwA	0.626	3.35	0.066	0.822

(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	0.16	5	3fyeA	DMU	Rep, Mult	88,90,122,123,126,127,130
2	0.06	2	5jqhB	CLR	Rep, Mult	43,66,67
3	0.05	2	3mk7D	CA	Rep, Mult	81,86,131
4	0.05	2	1fipA	III	Rep, Mult	88,89
5	0.03	1	3dtuC	DMU	Rep, Mult	39,42,43,46
6	0.03	1	3d1lA	MPR	Rep, Mult	89,104
7	0.03	1	3h5xA	MN	Rep, Mult	106,107
8	0.03	1	2wscJ	CLA	Rep, Mult	56,60
9	0.03	1	2axtB	MGE	Rep, Mult	50,51
10	0.03	1	2gsmA	DMU	Rep, Mult	65,68,73
11	0.03	1	2wse1	CLA	Rep, Mult	134,138
12	0.03	1	2oi2A	MG	Rep, Mult	64,107

	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	0.183	2pnoL	0.596	3.21	0.122	0.788	4.4.1.20	93
2	0.147	3dwwA	0.626	3.35	0.066	0.822	5.3.99.3	37
3	0.142	2h8aA	0.574	2.65	0.056	0.712	2.5.1.18	30,116
4	0.060	2bl2A	0.538	3.67	0.062	0.760	3.6.3.14	71
5	0.060	2frvD	0.535	3.41	0.050	0.753	1.12.2.1	126
6	0.060	1tj7A	0.510	3.20	0.035	0.651	4.3.2.1	40
7	0.060	1rqiA	0.521	4.02	0.064	0.794	2.5.1.10	NA
8	0.060	2nyfA	0.530	3.54	0.109	0.747	4.3.1.5	NA
9	0.060	1m56A	0.659	2.99	0.093	0.870	1.9.3.1	NA
10	0.060	3czoB	0.467	3.80	0.034	0.671	4.3.1.3	NA
11	0.060	1rx0A	0.514	4.11	0.038	0.774	1.3.99.-	NA
12	0.060	1iduA	0.505	4.74	0.072	0.829	1.11.1.10	NA
13	0.060	1jswB	0.500	3.81	0.036	0.753	4.3.1.1	60
14	0.060	3iam4	0.511	3.76	0.066	0.719	1.6.99.5	NA
15	0.060	2r7oA	0.518	4.12	0.068	0.801	2.7.7.48	NA
16	0.060	3cf4A	0.518	3.54	0.043	0.733	1.2.99.2	4,6
17	0.060	1fftA	0.549	4.02	0.059	0.767	1.10.3.-	NA
18	0.060	1frvB	0.536	3.48	0.058	0.760	1.12.2.1	NA
19	0.060	1hxgA	0.528	3.98	0.036	0.767	4.2.3.9,4.1.99.7	34
20	0.060	1n1zA	0.505	4.52	0.065	0.794	5.5.1.8	NA
21	0.060	1b8fA	0.511	5.09	0.105	0.925	4.3.1.3	NA
22	0.060	1xmeA	0.657	3.69	0.086	0.911	1.9.3.1	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	0.19	0.836	1.54	0.15	0.91	4xydA	GO:0004129 GO:0005506 GO:0009055 GO:0009060 GO:0016020 GO:0016021 GO:0016491 GO:0016966 GO:0020037 GO:0055114 GO:0070469 GO:1902600
1	0.19	0.789	2.20	0.11	0.90	3o0rB	GO:0004129 GO:0005506 GO:0005886 GO:0009055 GO:0009060 GO:0016020 GO:0016021 GO:0016491 GO:0016966 GO:0019333 GO:0020037 GO:0046872 GO:0055114 GO:0070469 GO:1902600
2	0.15	0.748	2.39	0.14	0.88	5djqA	GO:0004129 GO:0005506 GO:0005507 GO:0005886 GO:0005887 GO:0006119 GO:0009055 GO:0009060 GO:0015078 GO:0015990 GO:0015992 GO:0016020 GO:0016021 GO:0016491 GO:0016705 GO:0019411 GO:0019646 GO:0019825 GO:0020037 GO:0045154 GO:0045278 GO:0046872 GO:0055114 GO:0070069 GO:0070469 GO:0070470 GO:1902600
3	0.12	0.626	3.55	0.10	0.88	2yevA	GO:0004129 GO:0005506 GO:0005507 GO:0005886 GO:0006119 GO:0006810 GO:0006811 GO:0009055 GO:0009060 GO:0015002 GO:0015992 GO:0016020 GO:0016021 GO:0016491 GO:0020037 GO:0022900 GO:0022904 GO:0046872 GO:0055114 GO:0070469 GO:1902600
4	0.07	0.783	2.52	0.17	0.93	3ayfA	GO:0004129 GO:0005506 GO:0009055 GO:0009060 GO:0016020 GO:0016021 GO:0020037 GO:0046872 GO:0055114 GO:1902600
5	0.06	0.359	5.22	0.05	0.64	5cuvA	GO:0000287 GO:0004427 GO:0005737 GO:0006796
6	0.06	0.340	5.76	0.05	0.69	4aq4A	GO:0001407 GO:0005215 GO:0006810 GO:0015794 GO:0030288 GO:0042597
7	0.06	0.351	5.35	0.05	0.65	2gp4B	GO:0003824 GO:0004456 GO:0005829 GO:0008152 GO:0009082 GO:0009255 GO:0016829
8	0.06	0.286	5.85	0.02	0.59	2uxyA	GO:0004040 GO:0006807 GO:0015976 GO:0016787 GO:0016810 GO:0043605
9	0.06	0.366	5.25	0.09	0.66	2vcvA	GO:0004364 GO:0005737 GO:0005829 GO:0006749 GO:0008152 GO:0016740 GO:0070062 GO:1901687
10	0.06	0.336	4.86	0.07	0.54	1kgsA	GO:0000160 GO:0003677 GO:0005622 GO:0006351 GO:0006355 GO:0046872
11	0.06	0.358	5.20	0.08	0.64	4q5rA	GO:0004364 GO:0016740
12	0.06	0.337	3.84	0.02	0.47	2ohfA	GO:0000166 GO:0005524 GO:0005525 GO:0005634 GO:0005730 GO:0005737 GO:0005813 GO:0005913 GO:0016020 GO:0016787 GO:0016887 GO:0043022 GO:0043023 GO:0046034 GO:0046872 GO:0070062 GO:0098609 GO:0098641
13	0.06	0.395	5.50	0.04	0.75	5chcA	GO:0016491 GO:0030151 GO:0046872 GO:0051536 GO:0051539 GO:0055114
14	0.06	0.315	4.78	0.01	0.55	3ieyA	GO:0000213 GO:0003676 GO:0004518 GO:0006388 GO:0008033 GO:0016829 GO:0090305 GO:0090501 GO:0090502
15	0.06	0.286	4.81	0.09	0.49	3pu6A	GO:0006508 GO:0008047 GO:0008233 GO:0043085
16	0.06	0.340	5.55	0.05	0.64	3e49A	GO:0003824 GO:0016740 GO:0019475 GO:0046872
17	0.06	0.274	5.28	0.07	0.48	4em8A	GO:0004751 GO:0005975 GO:0006098 GO:0016853
18	0.06	0.351	5.32	0.02	0.64	4ekzA	GO:0000302 GO:0003756 GO:0004656 GO:0005178 GO:0005576 GO:0005783 GO:0005788 GO:0005793 GO:0005886 GO:0005925 GO:0006457 GO:0009897 GO:0016020 GO:0016222 GO:0016853 GO:0018401 GO:0019899 GO:0031012 GO:0034663 GO:0034976 GO:0042158 GO:0042470 GO:0044822 GO:0045454 GO:0046598 GO:0046982 GO:0070062 GO:0071456 GO:1902175

Consensus prediction of GO terms

Molecular Function	GO:0020037	GO:0005506	GO:0004129	GO:0016966
GO-Score	0.54	0.54	0.54	0.34
Biological Processes	GO:0009060	GO:1902600	GO:0046034	GO:0016310	GO:0071941
GO-Score	0.54	0.54	0.49	0.49	0.37
Cellular Component	GO:0016021	GO:0070469	GO:0005886
GO-Score	0.54	0.50	0.39

(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.