I-TASSER results

I-TASSER results for job id Rv2466c

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

Input Sequence in FASTA format

>protein (207 residues)
MLEKAPQKSVADFWFDPLCPWCWITSRWILEVAKVRDIEVNFHVMSLAILNENRDDLPEQ
YREGMARAWGPVRVAIAAEQAHGAKVLDPLYTAMGNRIHNQGNHELDEVITQSLADAGLP
AELAKAATSDAYDNALRKSHHAGMDAVGEDVGTPTIHVNGVAFFGPVLSKIPRGEEAGKL
WDASVTFASYPHFFELKRTRTEPPQFD

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MLEKAPQKSVADFWFDPLCPWCWITSRWILEVAKVRDIEVNFHVMSLAILNENRDDLPEQYREGMARAWGPVRVAIAAEQAHGAKVLDPLYTAMGNRIHNQGNHELDEVITQSLADAGLPAELAKAATSDAYDNALRKSHHAGMDAVGEDVGTPTIHVNGVAFFGPVLSKIPRGEEAGKLWDASVTFASYPHFFELKRTRTEPPQFD
Prediction	CCCCCCCCCEEEEEEHCCCHHHHHHHHHHHHHHHHCCCEEEEEEEHCEHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCEEEEEHCCEEEEHCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEHCCCCCCCCCC
Conf.Score	998889987799998578877899999999999985987999998644446888899999999999987899999999999697899999999999998668888789999999998999999998689779999999999999997887775699999999986555789885899999999999985987577755788999999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MLEKAPQKSVADFWFDPLCPWCWITSRWILEVAKVRDIEVNFHVMSLAILNENRDDLPEQYREGMARAWGPVRVAIAAEQAHGAKVLDPLYTAMGNRIHNQGNHELDEVITQSLADAGLPAELAKAATSDAYDNALRKSHHAGMDAVGEDVGTPTIHVNGVAFFGPVLSKIPRGEEAGKLWDASVTFASYPHFFELKRTRTEPPQFD
Prediction	646648643301000012000011024103401762715040121102201446762376135215501210000000245346610440130003111556564245002500551503550152164761254035205502543374110000104430011110242253640240030013006332112022247662638
	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                 160                 180                 200

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCEEEEEEHCCCHHHHHHHHHHHHHHHHCCCEEEEEEEHCEHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCEEEEEHCCEEEEHCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEHCCCCCCCCCC
MLEKAPQKSVADFWFDPLCPWCWITSRWILEVAKVRDIEVNFHVMSLAILNENRDDLPEQYREGMARAWGPVRVAIAAEQAHGAKVLDPLYTAMGNRIHNQGNHELDEVITQSLADAGLPAELAKAATSDAYDNALRKSHHAGMDAVGEDVGTPTIHVNGVAFFGPVLSKIPRGEEAGKLWDASVTFASYPHFFELKRTRTEPPQFD

4nxiA

0.98

0.92

0.93

3.09

MUSTER

------QKSVADFWFDPLCPWCWITSRWILEVAKVRDIEVNFHVMSLAILNENRREG-------MARAWGPVRVAIAAEQAHGAKVLDPLYTAMGNRIHNQGNHELDEVITQSLADAGLPAELAKAATSDAYDNALRKSHHAGMDAVGEDVGTPTIHVNGVAFFGPVLSKIPRGEEAGKLWDASVTFASYPHFFELKRTRTEPPQF-

4nxiA

0.98

0.92

0.93

4.38

dPPAS

------QKSVADFWFDPLCPWCWITSRWILEVAKVRDIEVNFHVMSLAILNENRREG-------MARAWGPVRVAIAAEQAHGAKVLDPLYTAMGNRIHNQGNHELDEVITQSLADAGLPAELAKAATSDAYDNALRKSHHAGMDAVGEDVGTPTIHVNGVAFFGPVLSKIPRGEEAGKLWDASVTFASYPHFFELKRTRTEPPQF-

4nxiA

0.97

0.91

0.93

5.21

wdPPAS

------QKSVADFWFDPLCPWCWITSRWILEVAKVRDIEVNFHVMSLAILNENRREGMA-------RAWGPVRVAIAAEQAHGAKVLDPLYTAMGNRIHNQGNHELDEVITQSLADAGLPAELAKAATSDAYDNALRKSHHAGMDAVGEDVGTPTIHVNGVAFFGPVLSKIPRGEEAGKLWDASVTFASYPHFFELKRTRTEPPQF-

4nxiA

0.98

0.91

0.93

3.75

wMUSTER

-------KSVADFWFDPLCPWCWITSRWILEVAKVRDIEVNFHVMSLAILNENRREG-------MARAWGPVRVAIAAEQAHGAKVLDPLYTAMGNRIHNQGNHELDEVITQSLADAGLPAELAKAATSDAYDNALRKSHHAGMDAVGEDVGTPTIHVNGVAFFGPVLSKIPRGEEAGKLWDASVTFASYPHFFELKRTRTEPPQF-

4nxiA

0.98

0.92

0.93

5.04

wPPAS

------QKSVADFWFDPLCPWCWITSRWILEVAKVRDIEVNFHVMSLAILNENRREG-------MARAWGPVRVAIAAEQAHGAKVLDPLYTAMGNRIHNQGNHELDEVITQSLADAGLPAELAKAATSDAYDNALRKSHHAGMDAVGEDVGTPTIHVNGVAFFGPVLSKIPRGEEAGKLWDASVTFASYPHFFELKRTRTEPPQF-

4nxiA

0.98

0.92

0.93

9.61

dPPAS2

------QKSVADFWFDPLCPWCWITSRWILEVAKVRDIEVNFHVMSLAILNENRREG-------MARAWGPVRVAIAAEQAHGAKVLDPLYTAMGNRIHNQGNHELDEVITQSLADAGLPAELAKAATSDAYDNALRKSHHAGMDAVGEDVGTPTIHVNGVAFFGPVLSKIPRGEEAGKLWDASVTFASYPHFFELKRTRTEPPQF-

4nxiA

0.98

0.92

0.93

4.21

PPAS

------QKSVADFWFDPLCPWCWITSRWILEVAKVRDIEVNFHVMSLAILNENRREG-------MARAWGPVRVAIAAEQAHGAKVLDPLYTAMGNRIHNQGNHELDEVITQSLADAGLPAELAKAATSDAYDNALRKSHHAGMDAVGEDVGTPTIHVNGVAFFGPVLSKIPRGEEAGKLWDASVTFASYPHFFELKRTRTEPPQF-

4nxiA

0.98

0.92

0.93

5.47

Env-PPAS

------QKSVADFWFDPLCPWCWITSRWILEVAKVRDIEVNFHVMSLAILNENRREG-------MARAWGPVRVAIAAEQAHGAKVLDPLYTAMGNRIHNQGNHELDEVITQSLADAGLPAELAKAATSDAYDNALRKSHHAGMDAVGEDVGTPTIHVNGVAFFGPVLSKIPRGEEAGKLWDASVTFASYPHFFELKRTRTEPPQF-

2imfA

0.15

0.13

0.86

1.84

MUSTER

--------MIVDFYFDFLSPFSYLANQRLSKLAQDYGLTIRYNAIDLARVKIAIGNVGPSNRDLKVKLDYLKVDLQRWAQLYGEAQAAAYVNVVFNAVWGEGIAPDLSLPALVSEKLGWDSAFEHFLSSNAATERYDEQTHAAIER---VFGVPTMFLGDEMWWG--------NDRLFMLESAMGRLC---------RQNADLSS--

2imfA

0.13

0.12

0.86

2.39

dPPAS

--------MIVDFYFDFLSPFSYLANQRLSKLAQDYGLTIRYNAIDLARVKIAIGNVGPSNRDLKVKLDYLKVDLQRWAQLYGEAQAAAYVNVVFNAVWGEGIAPDLSLPALVSEKLGWDSAFEHFLSSNAATERYDEQTHAAIERK--VFGVPTMFLGDEMWWG----NDRLFMLESAMGRLCRQNADLSS---------------

(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=1.05

Estimated TM-score = 0.86±0.07

Estimated RMSD = 3.3±2.3Å

Download Model 2

C-score=-1.94

Download Model 3

C-score=-4.89

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	4nxiA	0.904	1.18	0.974	0.932
2	1yzxA	0.668	2.86	0.108	0.807
3	1r4wA	0.662	3.22	0.127	0.826
4	2imfA	0.642	3.29	0.115	0.797
5	3gl5A	0.634	3.15	0.165	0.783
6	5cnwA	0.622	3.42	0.124	0.787
7	4pwoA	0.619	2.98	0.168	0.763
8	3ghaA	0.617	3.22	0.086	0.778
9	3fz5C	0.611	3.01	0.135	0.749
10	4n30A	0.598	3.28	0.129	0.768

(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	0.32	11	5hfiA	GSH	Rep, Mult	19,20,21,47,151,152,153
2	0.12	4	3fz5B	GSH	Rep, Mult	19,20,21,152,153,154,164,165,175,176
3	0.03	1	3fz5A	CA	Rep, Mult	27,96
4	0.03	1	3dksC	III	Rep, Mult	19,20,21,46,47
5	0.03	1	3puiA	NA	Rep, Mult	94,107,109,110,113

	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	0.203	1r4wC	0.664	3.18	0.138	0.826	2.5.1.18	18,48,142,164
2	0.060	1bwkA	0.409	5.71	0.049	0.701	1.6.99.1	136
3	0.060	1fsuA	0.413	5.46	0.051	0.701	3.1.6.12	NA
4	0.060	1xdmB	0.366	5.81	0.030	0.623	4.1.2.13	NA
5	0.060	1b26A	0.415	4.81	0.053	0.647	1.4.1.3	NA
6	0.060	1ehiB	0.429	4.53	0.068	0.623	6.3.2.4	NA
7	0.060	1lf6A	0.344	6.45	0.053	0.667	3.2.1.3	105
8	0.060	1yzxB	0.666	2.73	0.102	0.802	2.5.1.18	18,73,142
9	0.060	1xdmY	0.363	5.56	0.036	0.604	4.1.2.13	44
10	0.060	1n2lA	0.423	5.23	0.065	0.696	3.1.6.8	165
11	0.060	1fbaC	0.392	5.68	0.045	0.696	4.1.2.13	NA
12	0.060	2zc1A	0.407	4.83	0.048	0.614	3.1.8.1	NA
13	0.060	1fdjA	0.350	6.29	0.074	0.667	4.1.2.13	NA
14	0.060	1jqnA	0.456	5.43	0.048	0.763	4.1.1.31	NA
15	0.060	2ff2B	0.413	5.46	0.033	0.696	3.2.2.1	NA
16	0.060	1hrdA	0.427	4.88	0.069	0.686	1.4.1.2	NA
17	0.060	1gr0A	0.416	4.86	0.053	0.633	5.5.1.4	48,78,127
18	0.060	2bmaA	0.451	5.08	0.062	0.701	1.4.1.4	NA
19	0.060	1ehiA	0.427	4.48	0.073	0.618	6.3.2.4	NA
20	0.060	1xmeA	0.418	4.57	0.046	0.618	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	0.66	0.873	2.25	0.96	0.95	4zilA	GO:0005618 GO:0005737 GO:0015035 GO:0016491 GO:0055114
1	0.63	0.840	2.55	0.74	0.94	4wkwA	GO:0015035 GO:0055114
2	0.23	0.662	3.22	0.13	0.83	1r4wA	GO:0004364 GO:0004602 GO:0005102 GO:0005622 GO:0005739 GO:0005743 GO:0005759 GO:0005777 GO:0006749 GO:0015035 GO:0016020 GO:0016740 GO:0030855 GO:0043231 GO:0055114 GO:0070062 GO:0098869
3	0.21	0.619	2.98	0.17	0.76	4pwoA	GO:0016020 GO:0016021
4	0.21	0.642	3.36	0.12	0.80	2imdA	GO:0015035 GO:0016853 GO:0018845 GO:0019439 GO:0055114 GO:1901170
5	0.21	0.552	3.54	0.13	0.74	4p3yB	GO:0015035 GO:0016853 GO:0042597 GO:0055114
6	0.20	0.623	3.13	0.13	0.77	3fz5C	GO:0015035 GO:0016853 GO:0046872 GO:0055114
7	0.19	0.590	3.12	0.11	0.75	3f4tA	GO:0003756 GO:0019153 GO:0055114
8	0.18	0.563	2.94	0.10	0.70	4xvwL	GO:0005623 GO:0045454
9	0.17	0.555	3.61	0.11	0.73	3bciA	GO:0016853
10	0.17	0.580	2.99	0.15	0.72	3gykA
11	0.17	0.637	3.34	0.16	0.80	3gl5A	GO:0015035 GO:0055114
12	0.17	0.592	3.00	0.14	0.74	4gxzA	GO:0005623 GO:0015035 GO:0045454 GO:0055114
13	0.17	0.588	3.07	0.10	0.74	4xvwA	GO:0005623 GO:0045454
14	0.15	0.500	3.57	0.10	0.64	2h0hB	GO:0003756 GO:0015035 GO:0042597 GO:0055114
15	0.14	0.598	3.28	0.13	0.77	4n30A	GO:0016853
16	0.14	0.544	4.12	0.16	0.80	4k2dA	GO:0015035 GO:0042597 GO:0045454 GO:0055114
17	0.09	0.672	2.92	0.12	0.82	3rpnA	GO:0004364 GO:0004602 GO:0005102 GO:0005622 GO:0005739 GO:0005743 GO:0005759 GO:0005777 GO:0006749 GO:0015035 GO:0016020 GO:0016740 GO:0030855 GO:0043231 GO:0055114 GO:0070062 GO:0098869 GO:1901687
18	0.07	0.617	3.21	0.09	0.78	3eu3A	GO:0016491 GO:0030420 GO:0055114
19	0.07	0.566	3.55	0.13	0.75	3gmfA	GO:0016020 GO:0016021 GO:0016853
20	0.07	0.483	2.93	0.15	0.59	3gv1A

Consensus prediction of GO terms

Molecular Function	GO:0015035	GO:0016765	GO:0004601	GO:0005515	GO:0016860
GO-Score	0.92	0.45	0.45	0.45	0.41
Biological Processes	GO:0055114	GO:0006790	GO:0006575	GO:0006518	GO:0060429	GO:0030154	GO:1990748	GO:1901361	GO:0044248	GO:0018931
GO-Score	0.92	0.45	0.45	0.45	0.45	0.45	0.45	0.41	0.41	0.41
Cellular Component	GO:0005618	GO:0019866	GO:1903561	GO:0031966	GO:0031988	GO:0042579	GO:0070013	GO:0031224
GO-Score	0.66	0.45	0.45	0.45	0.45	0.45	0.45	0.34

(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.