I-TASSER results

I-TASSER results for job id Rv2023c

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

Input Sequence in FASTA format

>protein (119 residues)
MAARHARAGRWAAQPRPMLGSGAVRYEVGANIDATGFGGIAAVHRLVTRLGLVTRLGLVE
RVDAHSRFSSSNLPKSSRRISGRVSLSGMSNSAAKVVASTSSSPWGQPLSVGLRRRWRS

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MAARHARAGRWAAQPRPMLGSGAVRYEVGANIDATGFGGIAAVHRLVTRLGLVTRLGLVERVDAHSRFSSSNLPKSSRRISGRVSLSGMSNSAAKVVASTSSSPWGQPLSVGLRRRWRS
Prediction	CCCHHHHHHHCCCCCCCCCCCCCEEEEHCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCEEHCCCCCCCCCCCCCCCCCEEEEEEEHCCCCCCCEEEEEHCCCCCCCCCCEEEEEHHHCC
Conf.Score	97555555444567887777875688764555556665468999999988777765453434554445667899765556666776568876535665468898888654444334459
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MAARHARAGRWAAQPRPMLGSGAVRYEVGANIDATGFGGIAAVHRLVTRLGLVTRLGLVERVDAHSRFSSSNLPKSSRRISGRVSLSGMSNSAAKVVASTSSSPWGQPLSVGLRRRWRS
Prediction	74454453442344444324433232423341434222111102300432221333221541434441466514544541434141432454214223435643244313311354268
	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

CCCHHHHHHHCCCCCCCCCCCCCEEEEHCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCEEHCCCCCCCCCCCCCCCCCEEEEEEEHCCCCCCCEEEEEHCCCCCCCCCCEEEEEHHHCC
MAARHARAGRWAAQPRPMLGSGAVRYEVGANIDATGFGGIAAVHRLVTRLGLVTRLGLVERVDAHSRFSSSNLPKSSRRISGRVSLSGMSNSAAKVVASTSSSPWGQPLSVGLRRRWRS

4hznA2

0.25

0.24

0.97

0.69

MUSTER

REARTAHTFRALDEPGFRLLPDEVEHPVDIVRDVNGVGLDKAALALWRRLGRSDRAFLRRVVDQQCYLGNADLD-SVLTLGARVRVSTETPGEELVDVVISDRDSGRVIAVSTLH--Q-

4hznA2

0.25

0.24

0.97

0.74

dPPAS

REARTAHTFRALDEPGFRLLPDEVEHPVDIVRDVNGVGLDKAALALWRRLGRSDRAFLRRVVDQQCYLGNADL-DSVLTLGARVRVSTETPGEELVDVVISDRDSGRVIAVSTLHTQ--

4hznA2

0.23

0.22

0.93

0.56

wdPPAS

VYREARTAHTFRALDEPLPDTVEVEHPVDIVRDVNGVG-DKAALALWRRLG--SDRAFLRRVVVDQQCYLGNADLDS-GARVRVSTETPGEELVDVVISDRDS--GRVIAVSTLHT-Q-

4hznA2

0.26

0.24

0.93

0.63

wMUSTER

VYREARTAHTFRAEPGFRLLPDEVEHPVDIVRDVNGVG-DKAALALWRRLGRSDRAFLRRVVDQQCYLGNADL--SVLTLGARVRVSTETPGEVDVVISDRDS--GRVIAVSTLH--Q-

2dxcA

0.17

0.13

0.76

0.53

wPPAS

VWDRTHHAKMATGIPKGM--AGKSKFNVGKDLPDLF-------Y---TRTTYT-ATGTIVRL--VYES----AAEDE----------GNEENVFYSIVFAQKDLWPEALETEIPERYKA

4hznA2

0.25

0.24

0.97

0.70

dPPAS2

REARTAHTFRALDEPGFRLLPDEVEHPVDIVRDVNGVGLDKAALALWRRLGRSDRAFLRRVVDQQCYLGNADL-DSVLTLGARVRVSTETPGEELVDVVISDRDSGRVIAVSTLHQ---

4hznA2

0.27

0.25

0.92

0.69

PPAS

REARTAHTFRALDEPGFRLLPDEVEHPVDIVRDVNGVG-DKAALALWRRLG--SDRAFLRRVDQQCYLGNADL-DSVLTLGARVRVSTETPGEVDVVISDRDS--GRVIAVSTLH--Q-

3l9fA1

0.18

0.13

0.76

0.79

Env-PPAS

MQGKDIILGILSKKER----SG---YEINDILQNQLSYFYDGTYMIYPTLRKLEKDGKITKEVVI----QDGRP---NKNIYAITESGK-----KELASYLQSDVNDEI----------

2zbiB2

0.23

0.18

0.82

0.64

MUSTER

RTTSTIDATDLTKYDTAAAGDLTINVDVG-KIDAAST----AQERAAQLTEAINRVS-----------SQTNVGASYDKTTGQVTLT--SNAAIAVAGAANDATWANNATTGTAT----

2x0fB3

0.11

0.10

0.89

0.66

dPPAS

-FIETSIPEITPFNARTSSIKGKRLNLLVPSINEHMFGGISTALKLFEQF---DNAAFAKRIILTD---ATPNPKDLQSFKSFKYVMPEEDKDFALQIVPFNDRYNRTIPV------AK

(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=-1.79

Estimated TM-score = 0.50±0.15

Estimated RMSD = 8.1±4.4Å

Download Model 2

C-score=-3.04

Download Model 3

C-score=-3.52

Download Model 4

C-score=-4.96

Download Model 5

C-score=-4.54

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	4hznA	0.818	2.25	0.233	0.975
2	4ncpA	0.607	2.94	0.082	0.807
3	3b7kA	0.605	2.82	0.063	0.807
4	4mtuA	0.604	2.75	0.052	0.798
5	1yliB	0.603	3.18	0.088	0.840
6	3hrqB2	0.602	3.12	0.054	0.840
7	4ienA	0.602	2.89	0.052	0.790
8	3kg8A	0.600	3.44	0.078	0.849
9	2qq2C	0.597	2.84	0.101	0.798
10	4zv3A	0.596	2.85	0.091	0.798

(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	0.08	4	3f5oC	UUU	Rep, Mult	61,62,63,114,115,117
2	0.06	3	3f5oE	UUU	Rep, Mult	40,43,44,62,63,114,115
3	0.06	3	2gf6A	COA	Rep, Mult	39,40,43,64,65,66,67
4	0.06	3	1hgdA	UUU	Rep, Mult	102,104,105
5	0.04	2	1yliB	COA	Rep, Mult	34,35,67,68,69,71,72,110
6	0.04	2	2f3xB	MLC	Rep, Mult	43,47,56,58
7	0.02	1	2zmyA	CU	Rep, Mult	5,44
8	0.02	1	1vpmB	COA	Rep, Mult	66,67,69,70,110
9	0.02	1	3lsmA	SO3	Rep, Mult	83,88
10	0.02	1	2wsc1	CLA	Rep, Mult	10,91
11	0.02	1	2xvaB	ZN	Rep, Mult	5,6
12	0.02	1	2q78B	MLC	Rep, Mult	67,108
13	0.02	1	3f5oA	UUU	Rep, Mult	82,84,95,96,97,99

	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	1tbuB	0.544	3.02	0.083	0.731	3.1.2.2	38,46,50
2	0.066	3ir3A	0.586	2.70	0.113	0.781	4.2.1.-	NA
3	0.066	1iq6B	0.590	2.86	0.090	0.790	4.2.1.17	NA
4	0.060	3i4zA	0.518	3.71	0.039	0.807	2.5.1.34	NA
5	0.060	1y7uA	0.575	2.97	0.074	0.773	3.1.2.20	36
6	0.060	3l24A	0.490	4.46	0.037	0.857	3.1.8.2,3.4.13.9,3.1.8.1	NA
7	0.060	1z6bA	0.587	3.22	0.061	0.807	4.2.1.-	NA
8	0.060	1pn4C	0.591	2.81	0.070	0.773	4.2.1.-	NA
9	0.060	3khpC	0.590	3.04	0.094	0.815	1.-.-.-	NA
10	0.060	3ggrC	0.492	4.18	0.030	0.807	3.1.11.2	NA
11	0.060	2vz8A	0.530	3.06	0.120	0.748	2.3.1.85	NA
12	0.060	2jfdA	0.329	5.05	0.061	0.664	2.3.1.85	NA
13	0.060	2hx5A	0.555	3.43	0.074	0.790	3.1.2.-	113,115
14	0.060	1u1zB	0.583	3.21	0.096	0.807	4.2.1.-	NA
15	0.060	1lo8A	0.592	2.92	0.095	0.798	3.1.2.23	68,99,101
16	0.060	2oknA	0.494	4.46	0.061	0.866	3.4.13.9	106
17	0.060	2ownB	0.586	3.43	0.130	0.840	3.1.2.14	NA
18	0.060	2cf2C	0.576	3.31	0.101	0.815	2.3.1.85	59
19	0.060	2vkzG	0.572	3.18	0.090	0.815	2.3.1.38,3.1.2.14	NA
20	0.060	3b7kC	0.572	2.85	0.064	0.790	3.1.2.1	NA
21	0.060	2iw2A	0.493	4.47	0.070	0.866	3.4.13.9	NA
22	0.060	3d6xB	0.561	3.09	0.028	0.756	4.2.1.-	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	0.26	0.598	2.94	0.09	0.80	3spsA	GO:0016787
1	0.20	0.603	3.18	0.09	0.84	1yliB	GO:0016787
2	0.18	0.831	2.22	0.22	0.99	4hzoA	GO:0016417
3	0.16	0.561	2.93	0.06	0.76	2fs2B	GO:0010124 GO:0016289 GO:0016787 GO:0016790
4	0.15	0.577	2.99	0.07	0.80	5dm5B	GO:0016787
5	0.14	0.604	2.75	0.05	0.80	4mtuA	GO:0016829 GO:0046872
6	0.14	0.578	2.81	0.06	0.77	2gvhB	GO:0016787
7	0.10	0.559	3.37	0.10	0.82	1q6wC
8	0.09	0.558	3.12	0.12	0.77	3d6lA	GO:0016787
9	0.09	0.613	3.55	0.05	0.87	4mobA	GO:0003986 GO:0005524 GO:0005737 GO:0005829 GO:0006084 GO:0006090 GO:0006629 GO:0006631 GO:0006637 GO:0008289 GO:0016787 GO:0035338 GO:0047617 GO:0052689
10	0.09	0.589	3.14	0.12	0.81	4k00A	GO:0004778 GO:0016290 GO:0016787 GO:0016790 GO:0042372 GO:0047617
11	0.08	0.604	2.92	0.08	0.81	1y7uA	GO:0016787 GO:0046872 GO:0047617
12	0.07	0.593	3.03	0.07	0.82	4mocA	GO:0003986 GO:0005524 GO:0005737 GO:0005829 GO:0006084 GO:0006090 GO:0006629 GO:0006631 GO:0006637 GO:0008289 GO:0016787 GO:0035338 GO:0047617 GO:0052689
13	0.07	0.584	3.12	0.02	0.80	4zw0C	GO:0005737 GO:0006629 GO:0006633 GO:0009245 GO:0016829 GO:0016836 GO:0019171 GO:0047451
14	0.07	0.596	2.87	0.09	0.80	4zv3B	GO:0000062 GO:0005654 GO:0005737 GO:0005829 GO:0009062 GO:0015937 GO:0016290 GO:0016787 GO:0036042 GO:0036114 GO:0036116 GO:0042803 GO:0043005 GO:0044297 GO:0051792 GO:0052689 GO:0070062 GO:1900535
15	0.07	0.527	3.51	0.09	0.81	4ffuI	GO:0016491 GO:0055114
16	0.07	0.602	2.89	0.05	0.79	4ienA	GO:0016787
17	0.06	0.388	4.69	0.02	0.75	1yycA	GO:0005829 GO:0005886 GO:0009269 GO:0048046
18	0.06	0.312	5.35	0.04	0.65	1up6E	GO:0003824 GO:0004553 GO:0005975 GO:0008152 GO:0008706 GO:0016616 GO:0016787 GO:0016798 GO:0046872 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0016747	GO:0016788
GO-Score	0.35	0.31
Biological Processes	GO:0072329	GO:0042178
GO-Score	0.31	0.31
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.