I-TASSER results

I-TASSER results for job id Rv1044

[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)
MCAKPYLIDTIAHMAIWDRLVEVAAEQHGYVTTRDARDIGVDPVQLRLLAGRGRLERVGR
GVYRVPVLPRGEHDDLAAAVSWTLGRGVISHESALALHALADVNPSRIHLTVPRNNHPRA
AGGELYRVHRRDLQAAHVTSVDGIPVTTVARTIKDCVKTGTDPYQLRAAIERAEAEGTLR
RGSAAELRAALDETTAGLRARPKRASA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MCAKPYLIDTIAHMAIWDRLVEVAAEQHGYVTTRDARDIGVDPVQLRLLAGRGRLERVGRGVYRVPVLPRGEHDDLAAAVSWTLGRGVISHESALALHALADVNPSRIHLTVPRNNHPRAAGGELYRVHRRDLQAAHVTSVDGIPVTTVARTIKDCVKTGTDPYQLRAAIERAEAEGTLRRGSAAELRAALDETTAGLRARPKRASA
Prediction	CCCCCCHCCCCCCCCHHHHHHHHHHHHCCCHCHHHHHHHCCCHHHHHHHHHHCCEEEEHCCEEHCCCCCCCHHHHHHHHHHHHCCCCEEHHHHHHHHHCCCCCCCCEEEEEHCCCCCCCCCCCCCEEEEHCCCCCCEEEEHCCEHCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCCHHHHHHHHC
Conf.Score	998765344466776899999999998995579999998999999999999898899759878858988876899999999988994655889999989998999758999858999887888858999767788779999878868999999999985998899999999999988898678999999999747764566666659
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MCAKPYLIDTIAHMAIWDRLVEVAAEQHGYVTTRDARDIGVDPVQLRLLAGRGRLERVGRGVYRVPVLPRGEHDDLAAAVSWTLGRGVISHESALALHALADVNPSRIHLTVPRNNHPRAAGGELYRVHRRDLQAAHVTSVDGIPVTTVARTIKDCVKTGTDPYQLRAAIERAEAEGTLRRGSAAELRAALDETTAGLRARPKRASA
Prediction	714442315204515335303500674401010420373503352024005533023034434123433332221000001213430200010001004134331440232134434344464420101214245431132430453310300010013344351023004201443434463154024105724532222134328
	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

CCCCCCHCCCCCCCCHHHHHHHHHHHHCCCHCHHHHHHHCCCHHHHHHHHHHCCEEEEHCCEEHCCCCCCCHHHHHHHHHHHHCCCCEEHHHHHHHHHCCCCCCCCEEEEEHCCCCCCCCCCCCCEEEEHCCCCCCEEEEHCCEHCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCCHHHHHHHHC
MCAKPYLIDTIAHMAIWDRLVEVAAEQHGYVTTRDARDIGVDPVQLRLLAGRGRLERVGRGVYRVPVLPRGEHDDLAAAVSWTLGRGVISHESALALHALADVNPSRIHLTVPRNNHPRAAGGELYRVHRRDLQAAHVTSVDGIPVTTVARTIKDCVKTGTDPYQLRAAIERAEAEGTLRRGSAAELRAALDETTAGLRARPKRASA

4zu9A2

0.12

0.05

0.42

1.72

dPPAS2

---------RKSDLEKNEDFQKLSILKGGIKEEREIILEGIPKEILTLSIKRKYAHRIGEYLIISDE----LLKKYINELKELGKT--FNVQQAKNKLGLT----------------------------------------------------------------------------------------------------------

4o6jA1

0.16

0.04

0.28

1.11

dPPAS2

--------RSVTEEDYLKIIQELVLYKGYATLADISRSLNVKRDEINHLISLSMAEKIERGKYRLT---------------------------------------------------------------------------------------------------------------------------------------------

5cwnA

0.15

0.14

0.91

0.76

MUSTER

-------------MDPEEILERAKESLE---RAREASERG-DEEEFRKAAEKA--LELAKRLVEQAKKEGDKVALRVAELAAKNGDKEVFKKAAESALEVAKRLVEVASEGDPELVLEAAKVALRVAELAAKNGDKEVFKKAAESALEVAKRLVEVASKEGDPELVEEAAKVAEEVRKLKKQGDEEVYEKARETAREVKEELKRVRE

4zu9A2

0.11

0.06

0.55

0.72

dPPAS

---------RKSDLEKNEDFQKLSILKGGIKEEREIILEGIPKEILTLSIKRKYAHRIGEYLII------SDELLKKYINELKELGKTFNVQQAKNKLGLTRKYLIPLLEYLDYLGLTVREGNERRWKR------------------------------------------------------------------------------

1zelB

0.16

0.15

0.97

0.88

wdPPAS

MVVSPAGADRRIPTWASRVVSGLARDRPVVVTTQRLTEAGCGDSAIRELRRIGWLVQLVKGTWAFIPPGEAAIYLPLRSWLARDQNAMLAGASAAWHLGYLDRQPDRIPIWLPPAKRLPDGLASYVSVVRIPWNAADTALLTGLPALGPEALLVQIATR-GPWADLVPHLDDLVAD-----CSDERLERLLSGRPTSAWQRASYLLD

1zelB

0.16

0.15

0.98

0.77

wMUSTER

MVVSPAGADRRIPTWASRVVSGLARDRPVVVTTQRLTEAGCPDSAIRELRRIGWLVQLVKGTWAFGEAAISDPYLPLRSWLARDQNAMLAGASAAWHLGYLDRQPDRIPIWLPPAKRLPDGLASYVSVVRIPWNAADTALLTGLPALGPEALLVQIATRPGPWADLVPHLDDLVAD-----CSDERLERLLSGRPTSAWQRASYLLD

1zelB

0.16

0.15

0.95

0.81

wPPAS

MVVSPAGADRRIPTWASRVVSGLARDRPVVVTTQRLTEAGCGDSAIRELRRIGWLVQL-KGTWA-PPGEADPYLPLRSWLAR-NAGFMLAGASAAWHLGYLDRQPDRIPIWLPPAKRLPDGLASYVSVVRIPWNAADTALLTGLPALGPEALLVQIATRPASADLVPHLDDLVAD-------SDERLERLLSGRPTSAWQRASYLLD

3hotA

0.09

0.92

1.01

dPPAS2

FDVDDKEHGKPPKRYEDAELQALLDEDDAQTQKQLAEQLEVSQQAVSNRLREMGKIQKVG---RWVPHELNERQMERRKNTCEI---LLSRYKRKSFLHIFFVNPKRKKSYVDPGQPATSTARPNLCVWWDQSGVIYYELLKPGETVN----------AARYQQQLINLNRALQRKRPEYQHRVIFLHDNAPSHTARAVRDTLETLN

5cwnA

0.13

0.95

0.87

PPAS

-------MDPEEILERAKESLERAREASERGDEEEFRKAAEKALELAKRLVEQAKKEGDPELVLEAA---KVALRVAELAAKNGDKEVFKKAAESALEVAKRLVEVASKEGDPELVLEAAKVALRVAELAAKNGDKEVFKKAAESALEVAKRLVEVASKEGDPELVEEAAKVAEEVRKLKKQGDEEVYEKARETAREVKEELKRVRE

1jq5A1

0.12

0.09

0.72

0.84

Env-PPAS

ISPAKYVQ----GKNVITKIANYLEGIGNVIADEIVWKIA--GHTIVNELKKGNIAAEE--VVFSGEASRNEVERIANIARKAEAAIVIGGGKTLDTAKAVADELDAYIVIVPTAASTDAPTSALSVIYSDDGVFESYRFYKKNPDL----VLVD-------TKIIANA--------------------------------------

(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=-1.16

Estimated TM-score = 0.57±0.15

Estimated RMSD = 7.9±4.4Å

Download Model 2

C-score=-1.15

Download Model 3

C-score=-4.42

Download Model 4

C-score=-5.00

Download Model 5

C-score=-4.96

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	1zelB	0.869	1.98	0.149	0.976
2	2gafD	0.489	4.95	0.075	0.754
3	5fg0A	0.486	5.58	0.049	0.816
4	5a2vA	0.485	5.33	0.038	0.807
5	1kq3A	0.480	5.92	0.081	0.889
6	4mcaA	0.480	5.75	0.077	0.870
7	1jq5A	0.473	5.84	0.106	0.860
8	3okfA	0.473	5.72	0.057	0.836
9	1kwgA	0.472	5.53	0.044	0.807
10	4kf7A	0.470	5.61	0.091	0.797

(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	5dnmG	RAX	Rep, Mult	171,174
2	0.08	4	4kjcT	MG	Rep, Mult	151,155
3	0.06	3	3uhjC	GOL	Rep, Mult	90,91,92,147,148,155
4	0.04	2	5j1pA	MN3	Rep, Mult	98,149
5	0.02	1	2iefB	NUC	Rep, Mult	59,60
6	0.02	1	1bjyA	CTC	Rep, Mult	187,191
7	0.02	1	3rbxA	CA	Rep, Mult	53,72
8	0.02	1	3b04D	MG	Rep, Mult	91,93
9	0.02	1	1vd5A	GLY	Rep, Mult	153,170
10	0.02	1	2xfhA	CL6	Rep, Mult	153,157,170,183,184,187
11	0.02	1	2h6bA	3C4	Rep, Mult	20,23
12	0.02	1	1y66A	DIO	Rep, Mult	16,20
13	0.02	1	2jfrA	MG	Rep, Mult	107,142
14	0.02	1	3lw5K	CLA	Rep, Mult	169,173
15	0.02	1	3dfmA	ZN	Rep, Mult	137,142
16	0.02	1	3ro8A	MG	Rep, Mult	104,105,106

	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	1ta9B	0.467	5.97	0.062	0.874	1.1.1.6	NA
2	0.060	1vhdA	0.439	5.93	0.056	0.787	1.1.1.-	NA
3	0.060	1bf2A	0.421	5.65	0.039	0.730	3.2.1.68	NA
4	0.060	1qd1B	0.317	6.40	0.071	0.623	2.1.2.5,4.3.1.4	NA
5	0.060	2v4jE	0.429	5.93	0.086	0.768	1.8.99.3	NA
6	0.060	2pfdB	0.434	5.20	0.088	0.705	2.1.2.5,4.3.1.4	187
7	0.060	1xahA	0.435	5.95	0.067	0.797	4.2.3.4	167
8	0.060	3bfjT	0.438	6.09	0.058	0.816	1.1.1.202	NA
9	0.060	1kv3A	0.356	5.77	0.088	0.623	2.3.2.13	NA
10	0.060	1xagA	0.441	6.04	0.072	0.821	4.2.3.4	NA
11	0.060	2q3zA	0.428	5.19	0.022	0.705	2.3.2.13	NA
12	0.060	1jqoA	0.453	5.27	0.065	0.744	4.1.1.31	NA
13	0.060	3afhA	0.421	5.59	0.082	0.730	6.1.1.17	133
14	0.060	2wk5A	0.424	5.51	0.052	0.710	2.4.2.4	NA
15	0.060	2qubA	0.423	5.71	0.073	0.739	3.1.1.3	NA
16	0.060	1l5jA	0.420	5.45	0.065	0.686	4.2.1.3	NA
17	0.060	2gruA	0.449	6.11	0.077	0.845	4.2.3.-	NA
18	0.060	1rmgA	0.422	6.03	0.027	0.768	3.2.1.-	132
19	0.060	3bfjA	0.452	5.85	0.072	0.807	1.1.1.202	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	0.07	0.480	5.92	0.08	0.89	1kq3A	GO:0006071 GO:0008888 GO:0016491 GO:0016616 GO:0019588 GO:0046872 GO:0055114
1	0.07	0.473	5.72	0.06	0.84	3okfA	GO:0003856 GO:0005737 GO:0008652 GO:0009073 GO:0009423 GO:0016829 GO:0016838
2	0.07	0.481	5.45	0.04	0.81	5a2vB	GO:0000287 GO:0002134 GO:0004652 GO:0005524 GO:0005739 GO:0006378 GO:0030145 GO:0042802 GO:0042803 GO:0043231 GO:0044822 GO:0071044
3	0.07	0.441	5.75	0.09	0.81	1nvbB	GO:0000166 GO:0003824 GO:0003855 GO:0003856 GO:0003866 GO:0004764 GO:0004765 GO:0005524 GO:0005737 GO:0008152 GO:0008652 GO:0009073 GO:0009423 GO:0016301 GO:0016310 GO:0016491 GO:0016740 GO:0016765 GO:0016829 GO:0046872 GO:0055114
4	0.07	0.460	5.97	0.10	0.86	3uhjA	GO:0008888 GO:0016491 GO:0046872 GO:0055114
5	0.07	0.475	5.68	0.05	0.85	3ce9A	GO:0046872
6	0.07	0.452	5.85	0.07	0.81	3bfjA	GO:0016491 GO:0046872 GO:0047516 GO:0055114
7	0.07	0.485	4.95	0.06	0.74	3owgA	GO:0000166 GO:0004652 GO:0005524 GO:0006351 GO:0006397 GO:0016740
8	0.07	0.447	5.75	0.06	0.78	1vhdA	GO:0000166 GO:0005829 GO:0008106 GO:0016491 GO:0018455 GO:0046872 GO:0055114 GO:1990002
9	0.07	0.436	5.88	0.07	0.80	4fr2A	GO:0016491 GO:0046872 GO:0055114
10	0.07	0.437	6.02	0.08	0.83	4rgqB	GO:0005737 GO:0006629 GO:0006650 GO:0008654 GO:0016491 GO:0016616 GO:0046872 GO:0050492 GO:0055114
11	0.06	0.409	5.77	0.05	0.74	5br4A	GO:0004022 GO:0005829 GO:0005975 GO:0006004 GO:0008198 GO:0008912 GO:0016491 GO:0019301 GO:0019317 GO:0042355 GO:0042846 GO:0046872 GO:0051143 GO:0055114
12	0.06	0.480	5.75	0.08	0.87	4mcaA	GO:0008888 GO:0016491 GO:0046872 GO:0055114
13	0.06	0.457	5.88	0.09	0.83	3zdrA	GO:0004022 GO:0006066 GO:0008152 GO:0008774 GO:0015976 GO:0016491 GO:0016620 GO:0046872 GO:0055114
14	0.06	0.381	5.35	0.05	0.62	3pq1A	GO:0000166 GO:0000287 GO:0002134 GO:0003723 GO:0004652 GO:0005524 GO:0005737 GO:0005739 GO:0006351 GO:0006378 GO:0006397 GO:0016740 GO:0016779 GO:0030145 GO:0042802 GO:0042803 GO:0043231 GO:0044822 GO:0046872 GO:0071044
15	0.06	0.380	5.76	0.07	0.68	3iv7A	GO:0016491 GO:0018506 GO:0046872 GO:0055114
16	0.06	0.450	5.89	0.07	0.81	3owoA	GO:0004022 GO:0016491 GO:0046872 GO:0055114
17	0.06	0.449	6.11	0.08	0.85	2gruA	GO:0009073 GO:0016829 GO:0016838 GO:0017000 GO:0046872
18	0.06	0.406	5.89	0.08	0.73	1oj7A	GO:0000302 GO:0005829 GO:0008106 GO:0008270 GO:0016491 GO:0018455 GO:0033721 GO:0046872 GO:0055114 GO:1990002

Consensus prediction of GO terms

Molecular Function	GO:0043169
GO-Score	0.37
Biological Processes	GO:0044710
GO-Score	0.37
Cellular Component	GO:0005739
GO-Score	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.