I-TASSER results

I-TASSER results for job id Rv2998

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

Input Sequence in FASTA format

>protein (153 residues)
MDVIWSATIATTVATGMRKPRMHGMPPITSGSMVTRVTRMSIRLAGDSTLGRFSTSRLGL
SSAKSKPEGDFGTACGAVSGGDAGVVALAEGVDDGQSKPGAAGGARGVGGFRESRADCGE
QFGVASWTPQGEFEFGGQEAKGVRSSWPASLTN

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MDVIWSATIATTVATGMRKPRMHGMPPITSGSMVTRVTRMSIRLAGDSTLGRFSTSRLGLSSAKSKPEGDFGTACGAVSGGDAGVVALAEGVDDGQSKPGAAGGARGVGGFRESRADCGEQFGVASWTPQGEFEFGGQEAKGVRSSWPASLTN
Prediction	CCEEEEEHHHHHHHHCCCCCCCCCCCCCCCCCEEEEEEEEEEEHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHCCCCCCCCCEEEEEEHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCEEEHCCCCCCCCCCCCCCCCCC
Conf.Score	975554434445554556766558888877765666777788874776544444555567666788888655444445688755788765677788887766666666765545554554445555678765665665455555567765579
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MDVIWSATIATTVATGMRKPRMHGMPPITSGSMVTRVTRMSIRLAGDSTLGRFSTSRLGLSSAKSKPEGDFGTACGAVSGGDAGVVALAEGVDDGQSKPGAAGGARGVGGFRESRADCGEQFGVASWTPQGEFEFGGQEAKGVRSSWPASLTN
Prediction	652223232332124324424345233244342123024231412344312413344231541664453422311222443421010014225545744333333422222454335135414434134624152336505424652445358
	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

                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCEEEEEHHHHHHHHCCCCCCCCCCCCCCCCCEEEEEEEEEEEHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHCCCCCCCCCEEEEEEHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCEEEHCCCCCCCCCCCCCCCCCC
MDVIWSATIATTVATGMRKPRMHGMPPITSGSMVTRVTRMSIRLAGDSTLGRFSTSRLGLSSAKSKPEGDFGTACGAVSGGDAGVVALAEGVDDGQSKPGAAGGARGVGGFRESRADCGEQFGVASWTPQGEFEFGGQEAKGVRSSWPASLTN

4om9A5

0.14

0.13

0.94

0.67

MUSTER

AIVTLNSSLDRTALTIHKGANVTASSSLFTTSNIKSGGDLTLTGATESTSMFYAAGGYELTEDGAN--KNQASVTGDIKSEKAAKLSFGSADKDNSATRYSQFALAMLDGFDSIKAAQSSAMNNALWKVTGNSELKKLNSTG-------SMVL

2outA

0.17

0.14

0.82

0.63

dPPAS

MDKTFCVVVQNRIKEGYRRA---GFSFHLGDNSLAAVSESQLQLKADPRLVVQITETGSQEGGEGLSKEPAGS---DEQKQLRADPPSTDLNTFTVEQLKAQLTERGITFKQSAKAELIALFAPA----DGE----KSEA-------------

4dnuA2

0.31

0.23

0.75

0.54

wdPPAS

-------RI-KQIACG----DSHCL--VTEGE---------VQSWGRNQNG-----QLGLGDTEDSPEGIR-----KVAAGAEHTAAVTEGD--GWGRYGNLGGDRTVTSTGGEKS-CGWRHTIS--SYSGLYTYGGQLGHGDLED-PEALSN

4jdmA

0.28

0.25

0.90

0.60

wMUSTER

LDGIADTIVDSTVQDILDKPSLG----LLKAFNNFPITN-KIQCNGPSNIETLGGTEIGKFTVTPKSSGSFLVSADIIASRE-GGVVLAL-VREGDSKPCAIGYSSGVPNLCSLRTSITNT-GLTPTT---SLRVGGLES-GV---WVNALSN

5dudA1

0.33

0.24

0.73

0.52

wPPAS

MKIIRA--MYTTV--G-RHGFRQGISH--CGAL-----MPALRIAGNATLG-------QLT----EFETD--GW--ALTGAGCE--ARLDDMKAGQ---KRPHGMRSVGGI-----DVPPVMGSCS-TLKV---IGGLEKDGIGKSKAQGVKQ

2outA

0.18

0.14

0.82

0.59

dPPAS2

MDKTFCVVVQNRIKEGYRRA---GFS-FHLGNSLAAVSESQLQLKADPRLVVQITETGSQEGGEGLSKEPAGS---DEQKQLRADPPSTDLNTFTVEQLKAQLTERGITFKQSAKAELIALFAPA----DGE----KSEA-------------

1maeH1

0.23

0.18

0.76

0.63

PPAS

-----SSASAAAAAAAADGPTNDEAPGADGR----RSYINLP--AHHSAIIQQWVL-----------DAGSGSILGHVNGGFLPNPVAA---HSGSE--ALAS-SRIAKG---KRTDYVEVFDPVTFLPIADIEL--PDAGSGPQ---LSVMN

3fq6B

0.27

0.19

0.71

0.64

Env-PPAS

-----TAFVPALVASGLPNEKFEGFLPQKKG----RQTRLK-ALAEEHRTVFYSPHRL-LKTLT-----QFAEYF----GTER-QATVSREI----SKLHEE-----T--VRGSLAELIEHF--TATEPRGEIVI-------VLA--GID--D

3jb8A

0.15

0.14

0.97

0.64

MUSTER

ADQILEIPVCAGIDFPAGPPRYIGAAKAAQSQMWNTIVFNSVRITWETFTADTTSGYISMAFLSDY-MLSLPTGVEDVARIVPSATIALKNRGPSIVMPQNRTAFRCIQAGQGSAADKQMRFIVAIPKASATQAVG--SYRGAAILQPALVP-

3jbmA

0.23

0.20

0.89

0.61

dPPAS

---------------GTNDVHLSGMSRISQAVLPAG-TGTDGYVVVDATIVPDLLPRLGHAARIETLEFEIQPMCPANTGGGY-VAGFLPDPTDNDHTFDALQATRGVAKWWESRTYTRTLLWTSSGKEQRLTSPGGNNTDSVLCRWSVRLSV

(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=-4.48

Estimated TM-score = 0.25±0.07

Estimated RMSD = 15.6±3.3Å

Download Model 2

C-score=-5.00

Download Model 3

C-score=-5.00

Download Model 4

C-score=-4.96

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	2btoB	0.446	4.67	0.050	0.739
2	3hkeD	0.446	4.73	0.072	0.739
3	1tubA	0.440	4.64	0.029	0.739
4	4maeA	0.439	5.08	0.049	0.758
5	2d0vA	0.432	5.01	0.028	0.752
6	4b46A	0.425	4.91	0.058	0.732
7	3popA	0.425	5.18	0.044	0.758
8	3gyxK	0.425	5.27	0.077	0.784
9	1zr6A	0.424	5.16	0.055	0.739
10	2e0wB	0.424	5.20	0.066	0.765

(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	3rf4A	ZN	Rep, Mult	113,117
2	0.05	3	3hkeB	T13	Rep, Mult	15,16,19,20,72,74
3	0.04	2	1sa0B	CN2	Rep, Mult	54,57,60,74
4	0.04	2	1e7fA	DAO	Rep, Mult	112,116
5	0.04	2	2b0qA	MG	Rep, Mult	70,93
6	0.04	2	2a2qL	FUC	Rep, Mult	41,58
7	0.04	2	2qflA	EEE	Rep, Mult	8,10,123,124,125
8	0.02	1	3hkeD	T13	Rep, Mult	13,116,123,124,125
9	0.02	1	3du7D	HOS	Rep, Mult	59,65,66,67,68
10	0.02	1	1z2bC	VLB	Rep, Mult	8,11,12
11	0.02	1	1pg6A	CA	Rep, Mult	31,32,33
12	0.02	1	3mi1B	FE	Rep, Mult	49,51
13	0.02	1	2buyB	CAQ	Rep, Mult	53,54,57
14	0.02	1	5a08B	CA	Rep, Mult	117,120
15	0.02	1	1yvpA	MG	Rep, Mult	30,32,73
16	0.02	1	3a9gA	TRE	Rep, Mult	43,47
17	0.02	1	2daaA	DCS	Rep, Mult	21,23
18	0.02	1	7adhA	NTN	Rep, Mult	19,55

	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	1k6wA	0.377	5.44	0.040	0.680	3.5.4.1	NA
2	0.060	2nruB	0.396	4.91	0.017	0.680	2.7.11.1	10
3	0.060	1e7pA	0.384	5.41	0.056	0.706	1.3.99.1	NA
4	0.060	1lrwC	0.424	5.08	0.021	0.745	1.1.99.8	58,120
5	0.060	1chuA	0.378	5.56	0.055	0.719	1.4.3.16	52
6	0.060	2z8kD	0.298	4.44	0.035	0.477	2.3.2.2	3,11
7	0.060	2dq7X	0.391	5.00	0.069	0.680	2.7.10.2	36
8	0.060	1g72A	0.430	4.96	0.049	0.745	1.1.99.8	NA
9	0.060	1uwkA	0.402	4.57	0.070	0.667	4.2.1.49	4
10	0.060	1kv9A	0.417	5.01	0.055	0.726	1.1.99.-	NA
11	0.060	1w6sC	0.425	5.22	0.028	0.758	1.1.99.8	NA
12	0.060	2qi8A	0.394	4.90	0.051	0.680	2.7.10.2	10
13	0.060	2fknB	0.400	4.58	0.062	0.667	4.2.1.49	NA
14	0.060	2hb6B	0.401	5.81	0.095	0.797	3.4.11.1	NA
15	0.060	2e0wB	0.424	5.20	0.066	0.765	2.3.2.2	136
16	0.060	2qtcB	0.383	5.16	0.061	0.712	1.2.4.1	93,115
17	0.060	2ptkA	0.403	5.01	0.042	0.712	2.7.10.2,2.7.1.112	36
18	0.060	1yi6A	0.318	5.27	0.048	0.575	2.7.10.2	NA
19	0.060	1l8aA	0.383	5.14	0.053	0.712	1.2.4.1	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	0.07	0.327	5.68	0.05	0.61	2btqA	GO:0000166 GO:0003924 GO:0005200 GO:0005525 GO:0005874 GO:0007017
1	0.06	0.398	4.98	0.07	0.71	1flgA	GO:0005509 GO:0006069 GO:0016020 GO:0016491 GO:0016614 GO:0018468 GO:0030288 GO:0042597 GO:0046872 GO:0052934 GO:0052935 GO:0052936 GO:0055114
2	0.06	0.417	5.01	0.06	0.73	1kv9A	GO:0005509 GO:0009055 GO:0016020 GO:0016491 GO:0016614 GO:0020037 GO:0030288 GO:0042597 GO:0046872 GO:0055114 GO:0070968
3	0.06	0.369	5.30	0.08	0.67	3rd5A
4	0.06	0.452	4.68	0.04	0.75	4i4tA	GO:0000166 GO:0000226 GO:0003725 GO:0003924 GO:0005200 GO:0005525 GO:0005737 GO:0005856 GO:0005874 GO:0005881 GO:0007017 GO:0031625 GO:0043209 GO:0070062 GO:0071353
5	0.06	0.320	5.78	0.06	0.65	4n6kA	GO:0006810 GO:0030288
6	0.06	0.318	5.80	0.07	0.62	3nv8B	GO:0003849 GO:0005618 GO:0005829 GO:0005886 GO:0008652 GO:0009073 GO:0009423 GO:0016740 GO:0030145 GO:0040007 GO:0046872 GO:0051260
7	0.06	0.416	5.04	0.07	0.72	1kb0A	GO:0005509 GO:0009055 GO:0016020 GO:0016491 GO:0016614 GO:0020037 GO:0030288 GO:0042597 GO:0046872 GO:0055114
8	0.06	0.305	5.50	0.01	0.59	3tkkA	GO:0016811 GO:0046872
9	0.06	0.419	4.96	0.06	0.72	1yiqA	GO:0005509 GO:0009055 GO:0016020 GO:0016491 GO:0016614 GO:0020037 GO:0042597 GO:0046872 GO:0055114 GO:0070968
10	0.06	0.298	5.80	0.06	0.59	4hdjA	GO:0009279 GO:0016020 GO:0043165 GO:0051205
11	0.06	0.425	5.22	0.03	0.76	1w6sC	GO:0005509 GO:0005886 GO:0015945 GO:0016020 GO:0016491 GO:0016614 GO:0030288 GO:0046872 GO:0052930 GO:0052931 GO:0052932 GO:0052933 GO:0055114
12	0.06	0.319	5.38	0.04	0.61	5flzC	GO:0000166 GO:0000928 GO:0000930 GO:0003924 GO:0005200 GO:0005525 GO:0005634 GO:0005737 GO:0005816 GO:0005822 GO:0005824 GO:0005856 GO:0005874 GO:0007017 GO:0007020 GO:0030472 GO:0031122 GO:2000767
13	0.06	0.393	5.38	0.05	0.73	4cvbA	GO:0046872
14	0.06	0.323	5.80	0.06	0.63	4ffbA	GO:0000070 GO:0000166 GO:0003924 GO:0005200 GO:0005525 GO:0005737 GO:0005816 GO:0005827 GO:0005828 GO:0005856 GO:0005874 GO:0005880 GO:0005881 GO:0007017 GO:0030473 GO:0034399 GO:0045143 GO:0045298
15	0.06	0.428	5.13	0.04	0.76	1lrwA	GO:0005509 GO:0015945 GO:0016020 GO:0016491 GO:0016614 GO:0030288 GO:0042597 GO:0046872 GO:0052930 GO:0052931 GO:0052932 GO:0052933 GO:0055114
16	0.06	0.417	5.03	0.03	0.73	4aahA	GO:0005509 GO:0005886 GO:0015945 GO:0016020 GO:0016491 GO:0016614 GO:0030288 GO:0046872 GO:0052930 GO:0052931 GO:0052932 GO:0052933 GO:0055114
17	0.06	0.419	5.18	0.03	0.75	4tqoA	GO:0005509 GO:0015946 GO:0016020 GO:0016614 GO:0018468 GO:0030288 GO:0046872 GO:0055114
18	0.06	0.305	5.26	0.04	0.57	2ai6A	GO:0004721 GO:0005737 GO:0005829 GO:0006470 GO:0008969 GO:0016787 GO:0019855 GO:0035774 GO:0035971 GO:0044325 GO:0050860 GO:0051350 GO:0070062 GO:2000147 GO:2000249 GO:2000984

Consensus prediction of GO terms

Molecular Function	GO:0005200	GO:0005525	GO:0003924	GO:0005509	GO:0052935	GO:0070968	GO:0052936	GO:0009055	GO:0018468	GO:0020037	GO:0003725	GO:0031625
GO-Score	0.13	0.13	0.13	0.12	0.07	0.07	0.07	0.07	0.07	0.07	0.06	0.06
Biological Processes	GO:0006069	GO:0000226	GO:0071353
GO-Score	0.07	0.06	0.06
Cellular Component	GO:0030288	GO:0016020	GO:0070062	GO:0005881	GO:0043209
GO-Score	0.12	0.12	0.06	0.06	0.06

(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.