I-TASSER results

I-TASSER results for job id Rv3004

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

Input Sequence in FASTA format

>protein (112 residues)
MAHFAVGFLTLGLLVPVLTWPVSAPLLVIPVALSASIIRLRTLADERGVTVRTLVGSRAV
RWDDIDGLRFHRGSWARATLKDGTELRLPAVTFATLPHLTEASSGRVPNPYR

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MAHFAVGFLTLGLLVPVLTWPVSAPLLVIPVALSASIIRLRTLADERGVTVRTLVGSRAVRWDDIDGLRFHRGSWARATLKDGTELRLPAVTFATLPHLTEASSGRVPNPYR
Prediction	CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCEEHCCCEEEEEEHCCCCEHCHHHHCEEEHCCCEEEEEEHCCCCEEHCCCEHCCHHHHHHHHHCCCCCCCCC
Conf.Score	7558999999999999988899999999999999999863458849889999845787566777445565898689999589988985766646578999985799999999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MAHFAVGFLTLGLLVPVLTWPVSAPLLVIPVALSASIIRLRTLADERGVTVRTLVGSRAVRWDDIDGLRFHRGSWARATLKDGTELRLPAVTFATLPHLTEASSGRVPNPYR
Prediction	4233113333323333334333333333333332321221414045620302222465514164055141464130303055655140210334413402603634254448
	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

CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCEEHCCCEEEEEEHCCCCEHCHHHHCEEEHCCCEEEEEEHCCCCEEHCCCEHCCHHHHHHHHHCCCCCCCCC
MAHFAVGFLTLGLLVPVLTWPVSAPLLVIPVALSASIIRLRTLADERGVTVRTLVGSRAVRWDDIDGLRFHRGSWARATLKDGTELRLPAVTFATLPHLTEASSGRVPNPYR

3imoA

0.16

0.14

0.88

1.06

wdPPAS

VKDVNILSQYISGVMARADHHAGNVEEIALALAGAILWRK----DDTNIKVMA--DTKNVLWVTINGERY-NHSSEKIEMRKGNIQGNTIHEFDNLSKLVEIFKGL------

5da0A2

0.13

0.12

0.96

1.08

wMUSTER

KGETVVMLATVAVTVFTHDLSLGVLIGVVLSALFFARKVSQPVDEVDGTRTYRVRG--QLSTHDFLQFDFTHPARVVIDL---SDAHFWAVGADKVMLKFMRQGTSVAASAT

5e04A1

0.31

0.21

0.66

0.97

wPPAS

SA-KAIGAYILGFA-----------IPIILKALYMLSTRGRTVKDNKGTRIRF-------SFEEVNGIRKPKH------L----YVSMPTAQKAE-----EITPGR----FR

3j2wE

0.16

0.05

0.34

1.29

dPPAS2

IS--TTAMSWVQKITGGVGLIVAVAALILIVVLCVSFSRH------------------------------------------------------------------------

2ifoA

0.10

0.04

0.37

1.29

dPPAS2

VDVGDVVSAIQGAAGPIAAIGGAVLTVMVGIKVYKWVRRAM-----------------------------------------------------------------------

1iijA

0.17

0.05

0.31

1.27

dPPAS2

------EQRASPVTFIIATVVGVLLFLILVVVVGILIKRRR-----------------------------------------------------------------------

2mmuA

0.12

0.04

0.37

1.25

dPPAS2

IGLMLIGLIWLMVFQLLGPWNYAIAFAFMITGLLLTMRHLE-----------------------------------------------------------------------

2metA

0.14

0.04

0.33

1.18

dPPAS2

------EKTNLEIIILEGTAVIAMFFWLLLVIILRTVKRA-----NGG----------------------------------------------------------------

5da0A2

0.14

0.13

0.96

0.90

MUSTER

KGETVVMLATVAVTVFTHDLSLGVLIGVVLSALFFARKVSQPVDEVDGTRTYRVRGQ--VSTHDFLQFDFTHPARVVIDL---SDAHFWAVGADKVMLKFMRQGTSVAASAT

3imoA

0.14

0.12

0.91

0.87

dPPAS

VKDVNILSQYISGVMARADHHAGNVEEIALALAGAILWRK----DDTNIKVMAHGATKNVLWVTINGERYASSEKIEMRKGNIQGNTIHEFDNSTLSKLVEIFKGL------

(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=-2.21

Estimated TM-score = 0.45±0.15

Estimated RMSD = 8.9±4.6Å

Download Model 2

C-score=-4.83

Download Model 3

C-score=-4.93

Download Model 4

C-score=-4.91

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	3i8uX	0.558	3.29	0.074	0.804
2	2uvcG	0.525	4.10	0.050	0.839
3	1m4pA	0.515	3.39	0.033	0.777
4	3hmjG	0.514	4.31	0.029	0.839
5	1v7vA	0.508	4.71	0.084	0.893
6	1m56A	0.505	4.62	0.107	0.911
7	3ba6A	0.504	3.99	0.047	0.786
8	1iwpB	0.505	4.18	0.105	0.884
9	1dioB	0.497	4.27	0.095	0.884
10	1fbvA	0.497	3.90	0.058	0.804

(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	0.09	4	3wmm3	CRT	Rep, Mult	11,15,18
2	0.05	2	4pe1A	DCD	Rep, Mult	28,31
3	0.05	2	4ni1A	2JX	Rep, Mult	5,8,11,30
4	0.05	2	1otuA	CL	Rep, Mult	73,74,83,97
5	0.02	1	1j9lA	CA	Rep, Mult	62,64
6	0.02	1	1m4pA	III	Rep, Mult	62,65,70,71,86,108
7	0.02	1	3c2mA	MN	Rep, Mult	42,45
8	0.02	1	2o012	CLA	Rep, Mult	35,39
9	0.02	1	2vjlA	COA	Rep, Mult	67,69
10	0.02	1	1llrD	UUU	Rep, Mult	56,58
11	0.02	1	2wsc4	CLA	Rep, Mult	4,8
12	0.02	1	3v5uA	MYS	Rep, Mult	31,35,36
13	0.02	1	2wse1	CLA	Rep, Mult	37,41
14	0.02	1	2h6bA	3C4	Rep, Mult	11,14
15	0.02	1	4z9vB	III	Rep, Mult	19,23,26,27,30
16	0.02	1	3wmnA	CRT	Rep, Mult	26,29,33,37

	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	1ug9A	0.475	4.44	0.097	0.786	3.2.1.70	NA
2	0.060	3edrC	0.334	5.14	0.053	0.661	3.4.22.60	100
3	0.060	1iduA	0.495	4.25	0.071	0.839	1.11.1.10	NA
4	0.060	1qtnB	0.318	3.94	0.078	0.482	3.4.22.61,3.4.22.-	NA
5	0.060	1i4eB	0.486	4.73	0.095	0.848	3.4.22.61	NA
6	0.060	1qleA	0.464	4.25	0.057	0.812	1.9.3.1	NA
7	0.060	3ebgA	0.480	4.46	0.039	0.830	3.4.11.-	NA
8	0.060	2gepA	0.487	4.03	0.076	0.804	1.8.1.2	81
9	0.060	2d0gA	0.488	4.35	0.116	0.839	3.2.1.135	54,72
10	0.060	3edrA	0.337	5.07	0.054	0.652	3.4.22.60	100
11	0.060	1maaD	0.402	4.08	0.025	0.643	3.1.1.7	NA
12	0.060	1dioB	0.497	4.27	0.095	0.884	4.2.1.28	35,44,96
13	0.060	2uv8G	0.520	4.36	0.048	0.848	2.3.1.86	NA
14	0.060	2qljD	0.320	4.08	0.091	0.491	3.4.22.60	17,23,31,37,72
15	0.060	1izjA	0.488	4.32	0.116	0.839	3.2.1.135,3.2.1.1	NA
16	0.060	1mmfE	0.502	4.24	0.105	0.884	4.2.1.30	52,63
17	0.060	1bmqB	0.302	4.21	0.056	0.482	3.4.22.36	NA
18	0.060	2k7zA	0.434	4.80	0.067	0.804	3.4.22.61	NA
19	0.060	1vncA	0.492	4.30	0.082	0.839	1.11.1.10	33,61,79

(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	0.10	0.562	3.18	0.05	0.79	2g18D	GO:0010024 GO:0016491 GO:0016636 GO:0050620 GO:0050897 GO:0055114
1	0.07	0.566	3.29	0.06	0.81	2d1eA	GO:0010024 GO:0016491 GO:0016636 GO:0050620 GO:0050897 GO:0055114
2	0.07	0.454	3.89	0.11	0.71	3anlA	GO:0008299 GO:0016114 GO:0016491 GO:0019288 GO:0030145 GO:0030604 GO:0042802 GO:0046872 GO:0051484 GO:0055114 GO:0070402
3	0.07	0.422	3.69	0.04	0.65	4r2wD	GO:0003824 GO:0004850 GO:0005737 GO:0006139 GO:0009116 GO:0009166 GO:0016740 GO:0016757 GO:0016763 GO:0044206
4	0.07	0.431	4.64	0.05	0.77	4bmqA	GO:0004748 GO:0005971 GO:0006260 GO:0009186 GO:0009263 GO:0016020 GO:0016021 GO:0016491 GO:0046872 GO:0055114
5	0.07	0.422	3.55	0.03	0.64	2hn9A	GO:0003824 GO:0004850 GO:0005737 GO:0009116 GO:0009166 GO:0016740 GO:0016757 GO:0016763 GO:0044206
6	0.07	0.451	4.42	0.06	0.75	5jmfA	GO:0016829 GO:0042597
7	0.07	0.391	4.55	0.03	0.67	1t0uA	GO:0003824 GO:0004850 GO:0005737 GO:0005829 GO:0006974 GO:0009116 GO:0009166 GO:0016020 GO:0016740 GO:0016757 GO:0016763 GO:0042802 GO:0044206
8	0.07	0.399	4.90	0.02	0.79	1pn4D	GO:0003824 GO:0005777 GO:0006629 GO:0006631 GO:0006635 GO:0008152 GO:0016491 GO:0016616 GO:0016829 GO:0016853 GO:0055114
9	0.06	0.424	3.64	0.04	0.65	4g8jB	GO:0003824 GO:0004850 GO:0005737 GO:0009116 GO:0009166 GO:0016740 GO:0016757 GO:0016763 GO:0044206
10	0.06	0.395	4.90	0.08	0.79	3lacA	GO:0005737 GO:0005829 GO:0006508 GO:0008233 GO:0008234 GO:0016787 GO:0016920
11	0.06	0.493	3.31	0.05	0.71	2x9oA	GO:0010024 GO:0016491 GO:0016636 GO:0050617 GO:0050897 GO:0055114
12	0.06	0.399	4.90	0.03	0.77	2qo3B	GO:0003824 GO:0008152 GO:0016491 GO:0016740 GO:0016746 GO:0017000 GO:0031177 GO:0033068 GO:0047879 GO:0048037 GO:0055114
13	0.06	0.369	4.98	0.05	0.72	2c2nA	GO:0003824 GO:0004314 GO:0005739 GO:0006629 GO:0006631 GO:0006633 GO:0008152 GO:0016740 GO:0044822
14	0.06	0.373	5.38	0.08	0.78	2h1yB	GO:0003824 GO:0004314 GO:0008152 GO:0016740 GO:0016746
15	0.06	0.393	5.18	0.03	0.81	4bmsF	GO:0000166
16	0.06	0.378	4.75	0.09	0.68	3k89A	GO:0003824 GO:0004314 GO:0008152 GO:0016740 GO:0016746
17	0.06	0.352	5.32	0.14	0.75	3qatA	GO:0003824 GO:0004314 GO:0008152 GO:0016740 GO:0016746
18	0.06	0.373	5.16	0.06	0.78	4bmnA	GO:0000166

Consensus prediction of GO terms

Molecular Function	GO:0016627	GO:0046914
GO-Score	0.31	0.31
Biological Processes	GO:0044710	GO:0051188	GO:0051202	GO:0033014
GO-Score	0.53	0.31	0.31	0.31
Cellular Component	GO:0016021	GO:0005971
GO-Score	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.