I-TASSER results

I-TASSER results for job id Rv0459

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

Input Sequence in FASTA format

>protein (163 residues)
MNAPAGVLITAEAAALLAGLQDRHGPVMFHQSGGCCDGSAPMCYPRADFLVGDRDILLGV
LDVGEDGVPVWISGPQYQAWKHTQLIIDVVPGRGGGFSLEAPEGVRFLSRGRVFSDAEKA
MREAAPVITGAAYECGERPLVRGLVVDLDDPDATPGVCRASRR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MNAPAGVLITAEAAALLAGLQDRHGPVMFHQSGGCCDGSAPMCYPRADFLVGDRDILLGVLDVGEDGVPVWISGPQYQAWKHTQLIIDVVPGRGGGFSLEAPEGVRFLSRGRVFSDAEKAMREAAPVITGAAYECGERPLVRGLVVDLDDPDATPGVCRASRR
Prediction	CCCCCCEHCCHHHHHHHHHHHHHHCCEEEEHCCCCCCCCCCCCCCCCCCHCCCCCEEEEEEHCCCCCEEEEHCHHHHHHHHCCEEEEEEHCCCCCCEEHCCCCCEEEEEEEHCCCHHHHHHHHCCCCCCCHHHHHCCCCCCCCCEEHCCCCCCCCCCCCCCCC
Conf.Score	9987635548999999999999979769986689888888766677765568876789998768998579977889998865648999875888755656899858999875699999999856899986567766789988875655555568888887889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MNAPAGVLITAEAAALLAGLQDRHGPVMFHQSGGCCDGSAPMCYPRADFLVGDRDILLGVLDVGEDGVPVWISGPQYQAWKHTQLIIDVVPGRGGGFSLEAPEGVRFLSRGRVFSDAEKAMREAAPVITGAAYECGERPLVRGLVVDLDDPDATPGVCRASRR
Prediction	8742531401640350054037522300000012114322211125431422531010030436754130102561132153230001025263421214345433020313213562254167541443652644553446433132433531424364668
	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

                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCEHCCHHHHHHHHHHHHHHCCEEEEHCCCCCCCCCCCCCCCCCCHCCCCCEEEEEEHCCCCCEEEEHCHHHHHHHHCCEEEEEEHCCCCCCEEHCCCCCEEEEEEEHCCCHHHHHHHHCCCCCCCHHHHHCCCCCCCCCEEHCCCCCCCCCCCCCCCC
MNAPAGVLITAEAAALLAGLQDRHGPVMFHQSGGCCDGSAPMCYPRADFLVGDRDILLGVLDVGEDGVPVWISGPQYQAWKHTQLIIDVVPGRGGGFSLEAPEGVRFLSRGRVFSDAEKAMREAAPVITGAAYECGERPLVRGLVVDLDDPDATPGVCRASRR

1nwbA

0.26

0.14

0.55

1.41

dPPAS2

MQEQAQFKVTDKAVEEIKKVAQENNIPILRIRGGCSGFQYAM-----GFDVEEGD-----HVFEYDGVKVVIDPFSMPYVNGA--ELDYVVFMGGGFTIRNP-------------------------------------------------------------

2apnA

0.22

0.13

0.61

1.25

dPPAS2

MDMAVPLTFTDAAANKVKSLISEEENRVYITGGGCSGFQYGFTFDEK---VNDGDL---TIE--KSGVQLVIDPMSLQYLIGG--TVDYTEGLGSRFTVNNPNGSSFSI------------------------------------------------------

4kfrA

0.11

0.10

0.95

0.64

MUSTER

--NPDDIVVSYLIKHYFIPVLKAHKIYIIDDHNLGSEYSKFGYNATSLSDIVSKQYVVVYDRAKNDDFKLWASKLHSKKYGTTVLIIDFKYNRHAGLGL-RVYDLLIIM--YTREPNELRWISK---YISAEAAEKVKTLKQYHLIYDVNSQTIKIHKPILEH

1nwbA

0.22

0.12

0.56

0.85

dPPAS

QAQQFIFKVTDKAVEEIKKVAQENNIRIRVVPGGCSGFQYAMGFDDT---VEEGD-----HVFEYDGVKVVIDPFSMPYVNGA--ELDYVVFMGGGFTIRNP-------------------------------------------------------------

2apnA

0.27

0.15

0.56

0.99

wdPPAS

MDMAVPLTFTDAAANKVKSLISEEENLRV-TGGG-CSG---FQY---TF-VNDGDL---TIE--KSGVQLVIDPMSLQYLIGG--TVDYTEGLGSRFTVNNP-GSSFSI------------------------------------------------------

2apnA

0.27

0.15

0.57

0.70

wMUSTER

IDDMAVLTFTDAAANKVKSLISEEENLRV-TGGGCS-G---FQYG--TFKVNDGDL---TIEKS--GVQLVIDPMSLQYLIGG--TVDYTEGEGSRFTVNNP-GSSFI-------------------------------------------------------

2apnA

0.27

0.15

0.56

0.91

wPPAS

MDMAVPLTFTDAAANKVKSLISEEENLRV-TGGGCS-G---FQY---TF-VNDGDL---TIE--KSGVQLVIDPMSLQYLIGG--TVDYTEG-GSRFTVNNP-GSSFSI------------------------------------------------------

1r95A

0.26

0.13

0.49

1.14

dPPAS2

MS----ITLSDSAAARVNTFLANRGKRLGVRTSGCSDEPTP-----------------EDIVFEDKGVKVVVDGKSLQFLDGT--QLDFVKGLNEGFKFTNPD------------------------------------------------------------

2apnA

0.26

0.15

0.56

0.76

PPAS

MDMAVPLTFTDAAANKVKSLISEEENLRV-TGGGCS-G---FQY---TF-VNDGDL---TIE--KSGVQLVIDPMSLQYLIGG--TVDYTELEGSRFTVNNP-GSSFSI------------------------------------------------------

3fezA

0.13

0.12

0.89

0.95

Env-PPAS

YFQGKKVFITTGTEHYLRQLANYTGGLLYQESTGEKLFQEGAEYRSGSL-KGFGVVVFEYIHLRDEE------IPIFLQYQRASLHFSETPGLQS-TKLTKANN-KFLIISFWDSEVFFHDWKKTPLS--KEITNIKKNN------TQSGFSHEDIYHYPEF-

(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=-3.71

Estimated TM-score = 0.31±0.10

Estimated RMSD = 13.6±4.0Å

Download Model 2

C-score=-3.83

Download Model 3

C-score=-3.93

Download Model 4

C-score=-4.58

Download Model 5

C-score=-4.51

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	2apnA	0.460	2.70	0.143	0.558
2	1nwbA	0.449	2.70	0.172	0.546
3	4gbyA	0.445	4.93	0.019	0.724
4	3krtA	0.440	5.29	0.053	0.773
5	3o7pA	0.439	5.02	0.014	0.718
6	1sirA	0.431	5.02	0.040	0.730
7	5jscA	0.426	5.07	0.055	0.742
8	2d2aA	0.426	3.16	0.125	0.552
9	2k4zA	0.423	3.20	0.149	0.558
10	3ldkA	0.422	5.20	0.092	0.742

(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	3rgdE	FE	Rep, Mult	20,24
2	0.06	3	1bpyA	MG	Rep, Mult	53,55
3	0.04	2	2ppbM	STD	Rep, Mult	28,31,87
4	0.04	2	3lw5K	CLA	Rep, Mult	14,18
5	0.04	2	1xrmA	ALA	Rep, Mult	17,20
6	0.02	1	8icnA	ATP	Rep, Mult	33,53,55,114
7	0.02	1	1zyrM	STD	Rep, Mult	31,32,33,34,37
8	0.02	1	3jcuD	CLA	Rep, Mult	17,56
9	0.02	1	1rfuF	ZN	Rep, Mult	88,90
10	0.02	1	2iuwA	FE	Rep, Mult	30,37,82
11	0.02	1	1yklG	DHB	Rep, Mult	25,26
12	0.02	1	2ppbC	STD	Rep, Mult	74,78,81
13	0.02	1	1oauO	III	Rep, Mult	87,97
14	0.02	1	2a6hC	STD	Rep, Mult	47,52,72
15	0.02	1	2fvkB	ZN	Rep, Mult	30,82
16	0.02	1	2d2a1	III	Rep, Mult	43,44,49,95,96,97,98
17	0.02	1	3nl5A	TZE	Rep, Mult	41,42

	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	1ksdA	0.390	5.02	0.059	0.669	3.2.1.4	88
2	0.060	1vzvA	0.390	5.35	0.054	0.706	3.4.21.97	NA
3	0.060	1siqA	0.429	5.19	0.027	0.755	1.3.99.7	15
4	0.060	1ks8A	0.391	5.01	0.059	0.669	3.2.1.4	NA
5	0.060	1euuA	0.397	5.07	0.051	0.693	3.2.1.18	44,98
6	0.060	1cvmA	0.394	5.15	0.031	0.675	3.1.3.8	88
7	0.060	1w0eA	0.373	5.34	0.050	0.687	1.14.13.67,1.14.14.1	NA
8	0.060	1vcoA	0.391	4.72	0.015	0.632	6.3.4.2	NA
9	0.060	2q9fA	0.391	5.22	0.098	0.681	1.14.13.98	39,100
10	0.060	1ltuA	0.388	5.74	0.081	0.736	1.14.16.1	NA
11	0.060	2ix6A	0.431	4.99	0.007	0.736	1.3.3.6	NA
12	0.060	3hsiB	0.396	5.64	0.038	0.724	2.7.8.8	7
13	0.060	2ix6E	0.429	5.12	0.020	0.755	1.3.3.6	17,47
14	0.060	2yyjA	0.413	4.85	0.055	0.699	1.14.13.3	NA
15	0.060	1eusA	0.402	5.00	0.044	0.681	3.2.1.18	NA
16	0.060	3iydC	0.409	5.63	0.067	0.779	2.7.7.6	NA
17	0.060	2d1rA	0.397	5.03	0.035	0.693	1.13.12.7	NA
18	0.060	3ikmD	0.388	5.06	0.054	0.675	2.7.7.7	NA
19	0.060	3e2tA	0.391	5.02	0.040	0.675	1.14.16.4	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	0.09	0.449	2.70	0.17	0.55	1nwbA	GO:0005198 GO:0005759 GO:0006790 GO:0008198 GO:0016226 GO:0051536 GO:0051537 GO:0051539 GO:0097428
1	0.08	0.460	2.70	0.14	0.56	2apnA	GO:0005198 GO:0005506 GO:0005759 GO:0005829 GO:0006790 GO:0008198 GO:0016226 GO:0046872 GO:0051536 GO:0051537 GO:0051539 GO:0097428
2	0.07	0.421	3.13	0.17	0.53	1r94A	GO:0005198 GO:0005506 GO:0005759 GO:0005829 GO:0006790 GO:0008198 GO:0016226 GO:0034986 GO:0046872 GO:0051536 GO:0051537 GO:0051539 GO:0097428
3	0.07	0.413	5.48	0.03	0.76	4ybqB	GO:0003044 GO:0005215 GO:0005353 GO:0005355 GO:0005886 GO:0005887 GO:0006810 GO:0008643 GO:0015755 GO:0015758 GO:0016020 GO:0016021 GO:0016324 GO:0022857 GO:0022891 GO:0042383 GO:0055085 GO:0070061 GO:0071332 GO:1904659 GO:1990539
4	0.07	0.346	5.16	0.05	0.59	4zw9A	GO:0005215 GO:0005355 GO:0005536 GO:0005886 GO:0005887 GO:0005975 GO:0006810 GO:0008643 GO:0015758 GO:0016020 GO:0016021 GO:0019852 GO:0022857 GO:0022891 GO:0033300 GO:0055056 GO:0055085 GO:0070062 GO:0070837 GO:1904659
5	0.06	0.276	5.18	0.04	0.47	3gazA	GO:0008270 GO:0016491 GO:0055114
6	0.06	0.352	5.21	0.06	0.64	4cpdA	GO:0000166 GO:0004022 GO:0008270 GO:0016491 GO:0046872 GO:0055114
7	0.06	0.353	5.39	0.04	0.64	2ouiA	GO:0005737 GO:0008270 GO:0016491 GO:0046872 GO:0050009 GO:0055114
8	0.06	0.426	3.16	0.12	0.55	2d2aA	GO:0005198 GO:0005759 GO:0005829 GO:0006790 GO:0006979 GO:0008198 GO:0016226 GO:0051536 GO:0051537 GO:0051539 GO:0097428
9	0.06	0.403	2.79	0.18	0.52	1x0gC	GO:0005198 GO:0016226 GO:0046872 GO:0051536 GO:0051537
10	0.06	0.287	5.95	0.04	0.55	4dvjB	GO:0008270 GO:0016491 GO:0055114
11	0.06	0.345	5.83	0.06	0.69	2dphA	GO:0000166 GO:0008270 GO:0016491 GO:0046872 GO:0055114
12	0.06	0.350	5.59	0.07	0.66	1pl6A	GO:0003939 GO:0005615 GO:0005739 GO:0005829 GO:0005929 GO:0006006 GO:0006060 GO:0006062 GO:0006970 GO:0008270 GO:0009725 GO:0016020 GO:0016491 GO:0019640 GO:0030246 GO:0030317 GO:0031514 GO:0031667 GO:0031966 GO:0042493 GO:0042802 GO:0042995 GO:0046370 GO:0046526 GO:0046686 GO:0046688 GO:0046872 GO:0051160 GO:0051164 GO:0051287 GO:0055114 GO:0070062
13	0.06	0.316	5.84	0.01	0.63	4yb9D	GO:0003044 GO:0005215 GO:0005353 GO:0005886 GO:0005887 GO:0006810 GO:0008643 GO:0009750 GO:0015755 GO:0016020 GO:0016021 GO:0016324 GO:0022857 GO:0022891 GO:0042383 GO:0055085 GO:0070061 GO:0071332 GO:1990539
14	0.06	0.295	5.74	0.04	0.56	2eerB	GO:0004022 GO:0008270 GO:0016491 GO:0046872 GO:0055114
15	0.06	0.382	5.39	0.06	0.68	4ja4A	GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0008643 GO:0015293 GO:0015519 GO:0015753 GO:0016020 GO:0016021 GO:0022857 GO:0022891 GO:0055085
16	0.06	0.261	5.96	0.05	0.53	1piwA	GO:0006066 GO:0006081 GO:0008106 GO:0008270 GO:0016491 GO:0033833 GO:0033845 GO:0033859 GO:0046872 GO:0055114
17	0.06	0.378	4.94	0.07	0.64	1cdoA	GO:0004022 GO:0005737 GO:0008270 GO:0016491 GO:0046872 GO:0055114
18	0.06	0.363	5.19	0.08	0.64	3cosD	GO:0001523 GO:0003960 GO:0004022 GO:0004024 GO:0004032 GO:0004745 GO:0005503 GO:0005737 GO:0005829 GO:0006066 GO:0006067 GO:0006069 GO:0006081 GO:0008270 GO:0016491 GO:0016620 GO:0019115 GO:0019841 GO:0035276 GO:0042572 GO:0046164 GO:0046872 GO:0051287 GO:0055114 GO:1901661

Consensus prediction of GO terms

Molecular Function	GO:0051540	GO:0005506
GO-Score	0.44	0.44
Biological Processes	GO:0006790	GO:0031163	GO:0051188	GO:0051604
GO-Score	0.44	0.44	0.44	0.44
Cellular Component	GO:0044429	GO:0070013
GO-Score	0.44	0.44

(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.