I-TASSER results

I-TASSER results for job id Rv1824

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

Input Sequence in FASTA format

>protein (121 residues)
MGSDTAWSPARMIGIAALAVGIVLGLVFHPGVPEVIQPYLPIAVVAALDAVFGGLRAYLE
RIFDPKVFVVSFVFNVLVAALIVYVGDQLGVGTQLSTAIIVVLGIRIFGNTAALRRRLFG
A

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MGSDTAWSPARMIGIAALAVGIVLGLVFHPGVPEVIQPYLPIAVVAALDAVFGGLRAYLERIFDPKVFVVSFVFNVLVAALIVYVGDQLGVGTQLSTAIIVVLGIRIFGNTAALRRRLFGA
Prediction	CCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEHHHHHHHHHHHHHHHHHHCCCCCCEEEEHHHHHHHHHHHHHHHHHHHHCC
Conf.Score	9877778876599999999999987533887898887755899999999999999999875468958987557899999999999887578886345556777889988999999999879
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MGSDTAWSPARMIGIAALAVGIVLGLVFHPGVPEVIQPYLPIAVVAALDAVFGGLRAYLERIFDPKVFVVSFVFNVLVAALIVYVGDQLGVGTQLSTAIIVVLGIRIFGNTAALRRRLFGA
Prediction	8455464433200012113312321331315124403431210200131132212223047405540001023322331131033023141444131000312223114211202332368
	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

                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEHHHHHHHHHHHHHHHHHHCCCCCCEEEEHHHHHHHHHHHHHHHHHHHHCC
MGSDTAWSPARMIGIAALAVGIVLGLVFHPGVPEVIQPYLPIAVVAALDAVFGGLRAYLERIFDPKVFVVSFVFNVLVAALIVYVGDQLGVGTQLSTAIIVVLGIRIFGNTAALRRRLFGA

5ezmA3

0.14

0.11

0.74

1.36

dPPAS2

--SPRSWIGMAIVAACGLLASPVVATLNANHIPRAYAVWVAVAFVVMLLGIAVARLLLRRGVLPS---VAVYAMGMYLGFTVALLGHET-VGRPAS-------------------------

3zgyA2

0.12

0.98

1.34

dPPAS2

-GLASLYDAAGLVMMWSILNGFLQGAALTAGVDATTFAPFITQGIGTVADWLPGYARQIDGAYPADD--AAIDTHLATMEHLIHESEFLGVNAELPRFIKALADRAVADGYPALIEQFRTH

3wajA

0.14

0.13

0.94

0.81

MUSTER

RWKGHDLTARQ--MAYPVIAGITIGLYV-----LSWGAGFIIAPIILAFMFFAFVLAGFVNADRKNLSLVAVVTFAVSALIYLPFANYPGFSTIFYFQLLVLLGSAVIAAAFYQIEKWNDV

3zgyA2

0.12

0.98

0.88

dPPAS

-GLASLYDAAGLVMMWSILNGFLQGAALTAGVDATTFAPFITQGIGTVADWLPGYARQIDGAYPADD--AAIDTHLATMEHLIHESEFLGVNAELPRFIKALADRAVADGYPALIEQFRTH

5ezmA3

0.14

0.10

0.70

0.83

wdPPAS

--SPRSWG--AIVAACGLLASPVVATLNANHIPRAYAVWVAVAFVVMLLGIAVARLLLRRGVLPS---VAVYAMGMYLGFTVALLGHET-VGS----------------------------

5d92D3

0.21

0.20

0.93

0.87

wMUSTER

WGAD---SYLDRVGDSSVFTGIVIWFFLGGA-NPTIAILALICLVLSSLVSYSKARAEGLG-LTANVGIAERLVVVLVATGLVGLGIPSWV---LLVVLAIASVVTIFQRVLTVREQAKAW

5ezmA3

0.14

0.10

0.70

0.81

wPPAS

--SPRSWG--AIVAACGLLASPVVATLNANHIPRAYAVWVAVAFVVMLLGIAVARLLLRRGVLPS---VAVYAMGMYLGFTVALLGHET-VGS----------------------------

4pgrA

0.12

0.99

1.16

dPPAS2

WMRRRKAVGYAFVYTFAFVSGITLFPIVSHYASIAGAYVVLEAFGSTFVIFAVLGTIGAKMKKDLS-FLWSFLLVAVLALAVVGIFNIFSPLNSAAMMAYSVIGTIVFSLYILYDLNQIKH

3zgyA2

0.12

0.11

0.93

0.83

PPAS

-GL----ASLYDAAGLVMMWSILNGFL-TAGVDATTFAPFITQGIGTVADWLPGYARQIDGAYPADDA--AIDTHLATMEHLIHESEFLGVNAELPRFIKALADRAVADGYPALIEQFRTH

2caiB2

0.14

0.13

0.98

0.70

Env-PPAS

MG-GTEEEYYNVEKLIGQAEDLEHEYYKTLMKPEEKQKIIKEILNGKVPVLLDIICESLKASTGK--LAVGTLADLVLIAVIDHVTDLDKEFLTGKYPEIHKHRENLLASSPRLAKYLSDR

(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=-2.32

Estimated TM-score = 0.44±0.14

Estimated RMSD = 9.4±4.6Å

Download Model 2

C-score=-2.79

Download Model 3

C-score=-3.05

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	0.686	3.46	0.108	0.992
2	1yfeA	0.679	3.68	0.099	1.000
3	3o0rB	0.676	3.48	0.059	0.984
4	1jswB	0.675	3.63	0.099	0.992
5	1xmeA	0.675	3.32	0.050	0.967
6	1r2jA	0.675	2.90	0.076	0.909
7	4irnA	0.673	2.97	0.076	0.917
8	1j3uA	0.672	3.61	0.074	1.000
9	1vdkA	0.669	3.58	0.083	0.992
10	3oceA	0.669	3.61	0.083	0.984

(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	0.19	14	3pfdA	FDA	Rep, Mult	29,32,35,36,84,85,89,90
2	0.07	5	2z1qA	FAD	Rep, Mult	25,42,44,78,79,80
3	0.03	2	1m9nA	AMZ	Rep, Mult	72,106,108
4	0.03	2	1egcC	FAD	Rep, Mult	29,34,36,37,81,82
5	0.03	2	1rx0A	FAD	Rep, Mult	37,40,80,81,83,96,98
6	0.01	1	1qwjC	NCC	Rep, Mult	72,115,116
7	0.01	1	2w0fC	HX0	Rep, Mult	79,80,104,108
8	0.01	1	4zzcA	XE	Rep, Mult	18,48,51
9	0.01	1	5c65A	37X	Rep, Mult	42,77
10	0.01	1	3mpjD	FAD	Rep, Mult	36,39,81,82,84
11	0.01	1	2jk5C	L2C	Rep, Mult	91,106
12	0.01	1	3rrpA	LMR	Rep, Mult	54,57,58,62,63,66
13	0.01	1	3qnqA	CBS	Rep, Mult	32,33,35
14	0.01	1	3r6vG	ASP	Rep, Mult	54,55,57,71
15	0.01	1	3s8gA	OLC	Rep, Mult	44,48,78,79,80
16	0.01	1	2a5vA	SCN	Rep, Mult	68,84
17	0.01	1	2bhwA	CLA	Rep, Mult	16,18

	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	1jqiA	0.658	3.00	0.076	0.909	1.3.99.2	NA
2	0.060	1k7wD	0.652	3.66	0.092	0.992	4.3.2.1	NA
3	0.060	1vdkA	0.669	3.58	0.083	0.992	4.2.1.2	NA
4	0.060	1h2rL	0.625	3.83	0.092	0.950	1.12.2.1	NA
5	0.060	1f1oA	0.466	3.79	0.034	0.711	4.3.2.2	NA
6	0.060	2ix6E	0.654	3.17	0.092	0.926	1.3.3.6	104
7	0.060	2pg0A	0.646	3.22	0.093	0.909	1.3.99.3	NA
8	0.060	1k62B	0.640	3.72	0.067	0.992	4.3.2.1	NA
9	0.060	1t9gC	0.654	2.99	0.068	0.909	1.3.99.3	NA
10	0.060	2pfmA	0.654	3.52	0.100	0.992	4.3.2.2	NA
11	0.060	2ohyB	0.648	3.58	0.085	0.975	5.4.3.6	NA
12	0.060	1h2aL	0.624	3.77	0.084	0.942	1.12.2.1	NA
13	0.060	1udyA	0.659	3.03	0.067	0.917	1.3.99.3	NA
14	0.060	1bucA	0.664	3.11	0.085	0.917	1.3.99.2	21
15	0.060	1siqA	0.646	3.11	0.059	0.909	1.3.99.7	NA
16	0.060	2wbiB	0.666	3.04	0.124	0.926	1.3.99.-	NA
17	0.060	1u8vA	0.635	3.44	0.099	0.934	5.3.3.3	NA
18	0.060	1i0aA	0.640	3.80	0.075	0.992	4.3.2.1	NA
19	0.060	1bucB	0.669	3.20	0.109	0.926	1.3.99.2	94

(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	0.24	0.667	3.64	0.07	1.00	3r6qF	GO:0003824 GO:0006099 GO:0006531 GO:0008797 GO:0016829
1	0.10	0.675	3.63	0.10	0.99	1jswB	GO:0003824 GO:0005829 GO:0006099 GO:0006106 GO:0006108 GO:0006531 GO:0008652 GO:0008797 GO:0016020 GO:0016829 GO:0051262
2	0.09	0.686	3.46	0.11	0.99	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
3	0.08	0.620	4.02	0.05	0.99	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
4	0.07	0.647	3.75	0.08	0.99	3ayfA	GO:0004129 GO:0005506 GO:0009055 GO:0009060 GO:0016020 GO:0016021 GO:0020037 GO:0046872 GO:0055114 GO:1902600
5	0.07	0.640	3.80	0.07	0.99	1i0aA	GO:0003824 GO:0005212 GO:0042450
6	0.07	0.605	3.97	0.11	0.99	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
7	0.07	0.676	3.48	0.06	0.98	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
8	0.07	0.664	3.60	0.13	1.00	4apbD	GO:0003824 GO:0004333 GO:0005576 GO:0005618 GO:0005737 GO:0005829 GO:0005886 GO:0006099 GO:0006106 GO:0006108 GO:0016829 GO:0040007 GO:0045239 GO:0051262
9	0.07	0.589	3.65	0.11	0.92	4flcB	GO:0003824 GO:0004018 GO:0005829 GO:0006164 GO:0006167 GO:0006189 GO:0009152 GO:0009168 GO:0016829 GO:0044208 GO:0051262 GO:0070626
10	0.07	0.619	3.88	0.07	0.99	3bhgA	GO:0003824 GO:0004018 GO:0006164 GO:0006188 GO:0006189 GO:0009152 GO:0016829 GO:0044208 GO:0070626
11	0.07	0.666	3.70	0.07	1.00	3c8tA	GO:0003824 GO:0016853 GO:0047472
12	0.06	0.654	3.52	0.10	0.99	2pfmA	GO:0003824 GO:0004018 GO:0006164 GO:0006189 GO:0009152 GO:0016829 GO:0044208 GO:0070626
13	0.06	0.632	3.82	0.12	0.98	2e9fB	GO:0003824 GO:0004056 GO:0005737 GO:0006526 GO:0008652 GO:0016829 GO:0042450
14	0.06	0.679	3.68	0.10	1.00	1yfeA	GO:0003824 GO:0004333 GO:0005737 GO:0005829 GO:0006099 GO:0006106 GO:0006108 GO:0006979 GO:0008152 GO:0016829 GO:0045239 GO:0051262
15	0.06	0.598	4.01	0.09	0.98	1tj7A	GO:0003824 GO:0004056 GO:0005737 GO:0005829 GO:0006526 GO:0008652 GO:0016829 GO:0042450 GO:0051262
16	0.06	0.608	3.69	0.06	0.95	1q5nA	GO:0003824 GO:0016853 GO:0019439 GO:0019619 GO:0042952 GO:0047472
17	0.06	0.681	3.70	0.10	1.00	3tv2A	GO:0003824 GO:0004333 GO:0005737 GO:0006099 GO:0006106 GO:0016829 GO:0045239
18	0.06	0.466	3.79	0.03	0.71	1f1oA	GO:0003824 GO:0004018 GO:0006164 GO:0006167 GO:0006189 GO:0009152 GO:0016829 GO:0044208 GO:0051262 GO:0070626

Consensus prediction of GO terms

Molecular Function	GO:0046906	GO:0046914	GO:0016676	GO:0015078	GO:0015002	GO:0008797
GO-Score	0.44	0.44	0.44	0.44	0.44	0.32
Biological Processes	GO:0098662	GO:0015992	GO:0006531	GO:0006099
GO-Score	0.44	0.44	0.32	0.32
Cellular Component	GO:0031224
GO-Score	0.35

(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.