I-TASSER results

I-TASSER results for job id Rv1290A

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

Input Sequence in FASTA format

>protein (104 residues)
MLALHGLSEGVSGSGGSGGRWGAGEVLEGARIGVIADGVSCFPTKADCRRIRGVPVFDGY
TRMVARLMGSLAVLRSVSIPKGYRDFGFGSLRAVAPKNCPDVSG

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MLALHGLSEGVSGSGGSGGRWGAGEVLEGARIGVIADGVSCFPTKADCRRIRGVPVFDGYTRMVARLMGSLAVLRSVSIPKGYRDFGFGSLRAVAPKNCPDVSG
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCEHCCCEEEEEHCCCEHCCCCCCCCEEHCCEHCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEHCCCCCCCCC
Conf.Score	97555666777788888876554344456457887656544567544445547655565799999999888776435788764435887467765788999999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MLALHGLSEGVSGSGGSGGRWGAGEVLEGARIGVIADGVSCFPTKADCRRIRGVPVFDGYTRMVARLMGSLAVLRSVSIPKGYRDFGFGSLRAVAPKNCPDVSG
Prediction	52203223542536435433222242254131220143142234544054145132233234202413331231341423531453323303222376157378
	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

CCCCCCCCCCCCCCCCCCCCCCCCCEHCCCEEEEEHCCCEHCCCCCCCCEEHCCEHCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEHCCCCCCCCC
MLALHGLSEGVSGSGGSGGRWGAGEVLEGARIGVIADGVSCFPTKADCRRIRGVPVFDGYTRMVARLMGSLAVLRSVSIPKGYRDFGFGSLRAVAPKNCPDVSG

3lk7A1

0.20

0.17

0.87

0.69

MUSTER

ITTFENKKVLVLGLARSG---AAARLLLGAIVTVNDGK--PFDENPTAQSLLGIKVVCGSHP-LELLDEDFCYIKNPGIPYN------NPVKKALEKQIPVL--

3lk7A1

0.18

0.16

0.89

0.67

dPPAS

ITTFENKKVLVLGLARSGE--AAARLLLGAIVTVNDGKPFDENPTAQSLLEEGIKVVCGSHPLELLDEDFCYIK-NPGIPYNN------PVKKALEKQIPVL--

3lk7A1

0.20

0.16

0.84

0.58

wdPPAS

ITTFENKKVLVLGLARSG---AAARLLLGAIVTVNDGKPF--DENPTAQSLLGIKVVCG----LELLDEDFCYIKNPGIPYNN------PVKKALEKQIPVL--

3k7dA2

0.31

0.25

0.82

0.75

wMUSTER

MVARYGKPNHLNEREGRGGKLGGWELGYSSDLIFLHDC----PMDADGEREIDGRQF--YLRLAQRIMHLFST-RTSS-GILYEDAR---LR-------PS-AG

2d8yA

0.37

0.25

0.68

0.56

wPPAS

---------GSSGSSGMKFQAPARETCVQKTVRLLANQISCF--RSYCNNK-G--SLHGYKPHFNQLFK----------SKGNYDEGFGS----GPS-----SG

2d8yA

0.33

0.24

0.72

dPPAS2

---------GSSGSSGMKFQAPARETCVQKTVRLLANQISCF-RCSYCNNKGTYASLHGYKPHFNQLFK----------SKGNYDEGFGS----GPS-----SG

2d8yA

0.37

0.25

0.67

0.69

PPAS

---------GSSGSSGMKFQAPARETCVQKTVRLLANQISCF---SYCNNK-G--SLHGYKPHFNQLFK----------SKGNYDEGFGS----GPS-----SG

3lk7A1

0.21

0.18

0.88

0.85

Env-PPAS

ITTFENKKVLVLGLARSG--EAAARLLLGAIVTVNDGK--PFDENPTAQSLLGIKVVCGSHP-LELLDEDFCYIKNPGIP---YNNPV--KKALE-KQIPVL--

4ea7A2

0.27

0.23

0.87

0.67

MUSTER

-LVIHSVSPSVR---GEGVAVMAGVAIADSWIGIINTGAVVDHD-GAACHL-AS-ALAGGVSVA--FLGVGAVIPGVTIGADTI--GAG---GVVVRDLPDAIG

2d8yA

0.28

0.20

0.72

0.60

dPPAS

---------GSSGSSGMKFQAPARETCVQKTVRLLANQISCF-RCSYCNNKGTYASLHGRKPHFNQLFK----------SKGNYDEGFGSGPSSG---------

(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=-2.75

Estimated TM-score = 0.40±0.13

Estimated RMSD = 10.0±4.6Å

Download Model 2

C-score=-3.47

Download Model 3

C-score=-4.76

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	4fn4A	0.636	3.63	0.124	0.933
2	3r1iA	0.634	3.52	0.156	0.923
3	1cydA	0.628	3.33	0.170	0.894
4	3qljA	0.628	3.52	0.175	0.933
5	1iy8A	0.627	3.67	0.158	0.913
6	1yb1A	0.626	3.61	0.103	0.923
7	3gvcB	0.625	3.65	0.188	0.923
8	1spxA	0.625	3.49	0.146	0.913
9	1xkqA	0.625	3.54	0.156	0.913
10	4oaqA	0.624	3.33	0.118	0.894

(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	0.07	4	2z8yM	XE	Rep, Mult	10,63,75,92,93,94
2	0.05	3	3ch6E	311	Rep, Mult	31,32,67,71,94
3	0.03	2	3oq1A	3OQ	Rep, Mult	23,77,90
4	0.03	2	5j7iD	ADP	Rep, Mult	12,13,35,36,37,59,81,90
5	0.03	2	2b1mA	UUU	Rep, Mult	85,88,98
6	0.03	2	3lz6B	A0D	Rep, Mult	21,34,48
7	0.03	2	3b5zD	UUU	Rep, Mult	12,13,14,15,17
8	0.03	2	1rx6A	NAP	Rep, Mult	13,14,15,17,35,36,37,39,58,78,79,90
9	0.02	1	3m0jA	MN	Rep, Mult	13,47,58,97
10	0.02	1	2bo6B	MN	Rep, Mult	37,47
11	0.02	1	1muuC	SUC	Rep, Mult	7,68,69,70,71,96,97,99
12	0.02	1	2irwA	NN4	Rep, Mult	23,30,62,63,66,67,71
13	0.02	1	2p66A	PO4	Rep, Mult	14,17,18
14	0.02	1	1ko7B	PO4	Rep, Mult	5,12,16,52
15	0.02	1	3fcoB	IIG	Rep, Mult	66,67,70
16	0.02	1	3bzuC	A21	Rep, Mult	60,63,82,83,88
17	0.02	1	3ojyB	BMA	Rep, Mult	17,21,50
18	0.02	1	1gzmA	C8E	Rep, Mult	64,67

	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	0.066	1wo8A	0.547	3.79	0.033	0.865	4.2.3.3	NA
2	0.060	1iy8A	0.627	3.67	0.158	0.913	1.1.1.-	76
3	0.060	2a4kB	0.612	3.52	0.160	0.894	1.1.1.100	NA
4	0.060	2vhxE	0.618	3.37	0.117	0.894	1.4.1.1	26
5	0.060	3gvcB	0.625	3.65	0.188	0.923	1.-.-.-	76
6	0.060	2xaaA	0.621	3.21	0.143	0.875	1.1.1.1	13,16,79
7	0.060	2qq5A	0.615	3.46	0.146	0.913	1.1.-.-	NA
8	0.060	3lk7A	0.615	3.14	0.167	0.865	6.3.2.9	14,15
9	0.060	1pjbA	0.609	3.40	0.117	0.894	1.4.1.1	NA
10	0.060	2a4kA	0.618	3.50	0.188	0.904	1.1.1.100	45
11	0.060	3ch6B	0.619	3.55	0.237	0.923	1.1.1.146	76
12	0.060	1gz6B	0.621	3.57	0.196	0.923	1.1.1.62	76
13	0.060	1g6kA	0.619	3.61	0.141	0.942	1.1.1.47	76
14	0.060	1xhlA	0.624	3.48	0.137	0.904	1.1.1.236	76
15	0.060	2vhwE	0.616	3.46	0.116	0.904	1.4.1.1	NA
16	0.060	1npdB	0.613	3.36	0.151	0.885	1.1.1.282	NA
17	0.060	1rjwC	0.620	3.43	0.160	0.904	1.1.1.1	22
18	0.060	1uufA	0.615	3.22	0.174	0.885	1.-.-.-	NA
19	0.060	1zbqA	0.623	3.52	0.186	0.923	4.2.1.107,1.1.1.35	76
20	0.060	1ahiA	0.616	3.42	0.126	0.894	1.1.1.159	76

(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	0.11	0.614	3.64	0.21	0.91	5jy1A	GO:0004316 GO:0016491 GO:0055114 GO:0102132
1	0.11	0.606	3.75	0.14	0.92	1vl8B	GO:0000166 GO:0016491 GO:0055114
2	0.11	0.628	3.52	0.17	0.93	3qljA	GO:0016491 GO:0055114
3	0.11	0.625	3.65	0.19	0.92	3gvcB	GO:0016491 GO:0055114
4	0.11	0.618	3.59	0.20	0.91	2jahC	GO:0000166
5	0.10	0.622	3.59	0.18	0.92	4kzpC	GO:0004316 GO:0016491 GO:0055114 GO:0102132
6	0.10	0.617	3.74	0.16	0.92	4ya6A	GO:0016491 GO:0055114
7	0.10	0.611	3.75	0.20	0.93	4jroA	GO:0000166 GO:0004316 GO:0006633 GO:0016491 GO:0051287 GO:0055114
8	0.10	0.614	3.63	0.18	0.91	4bmnA	GO:0000166
9	0.10	0.608	3.69	0.21	0.93	4mowA	GO:0016491 GO:0047936 GO:0055114
10	0.10	0.616	3.41	0.13	0.90	3uf0A	GO:0000166 GO:0008678 GO:0016491 GO:0055114
11	0.10	0.612	3.66	0.18	0.91	4bmsF	GO:0000166
12	0.10	0.613	3.56	0.18	0.90	2ewmB	GO:0000166 GO:0010130 GO:0016491 GO:0016616 GO:0051289 GO:0055114
13	0.10	0.602	3.73	0.15	0.92	3sx2F	GO:0000166 GO:0016491 GO:0055114
14	0.10	0.619	3.56	0.24	0.92	4ijuB	GO:0003845 GO:0005783 GO:0005789 GO:0006629 GO:0006704 GO:0008202 GO:0016020 GO:0016021 GO:0016491 GO:0030324 GO:0055114 GO:0070524
15	0.09	0.597	3.71	0.14	0.92	2p68A	GO:0004316 GO:0006629 GO:0006631 GO:0006633 GO:0016491 GO:0030497 GO:0050661 GO:0051287 GO:0055114 GO:0102132
16	0.09	0.627	3.67	0.16	0.91	1iy8A	GO:0016491 GO:0055114
17	0.09	0.625	3.54	0.16	0.91	1xkqA	GO:0000166 GO:0016491 GO:0055114
18	0.09	0.606	3.69	0.13	0.92	1ja9A	GO:0000166 GO:0016491 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0036094	GO:1901265	GO:0016491
GO-Score	0.41	0.41	0.38
Biological Processes	GO:0055114
GO-Score	0.38
Cellular Component
GO-Score

(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.