I-TASSER results

I-TASSER results for job id Rv3108

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

Input Sequence in FASTA format

>protein (146 residues)
MTPNAASTGDSAKNTITGCCLITARALVARTRSISLPGMPFRMPADYHNASSDEPTNRHP
WPAPARCCRHEWRTMRRTNACDRRRFGLSLTIHEDACRIISVVPVVLEVRRAEPAHPATP
YPEPLARCSRSPGLNESSHMSGRIPP

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MTPNAASTGDSAKNTITGCCLITARALVARTRSISLPGMPFRMPADYHNASSDEPTNRHPWPAPARCCRHEWRTMRRTNACDRRRFGLSLTIHEDACRIISVVPVVLEVRRAEPAHPATPYPEPLARCSRSPGLNESSHMSGRIPP
Prediction	CCCCCCCCCCCCCCEEEEEEEEEHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCEEEEEEEEHCCCCEEEEEEEEEEEEEHCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCCCCCC
Conf.Score	98766677877655465556654555555434556899865687655578888998899999875455567776565456777577667887444434445677888887568899999997545654689898876666788999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MTPNAASTGDSAKNTITGCCLITARALVARTRSISLPGMPFRMPADYHNASSDEPTNRHPWPAPARCCRHEWRTMRRTNACDRRRFGLSLTIHEDACRIISVVPVVLEVRRAEPAHPATPYPEPLARCSRSPGLNESSHMSGRIPP
Prediction	74464454464344202000101041113424515145232423252452657634654414231400445144253453454431303031354003102001100203436464443434521340574442455543555348
	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

CCCCCCCCCCCCCCEEEEEEEEEHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCEEEEEEEEHCCCCEEEEEEEEEEEEEHCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCCCCCC
MTPNAASTGDSAKNTITGCCLITARALVARTRSISLPGMPFRMPADYHNASSDEPTNRHPWPAPARCCRHEWRTMRRTNACDRRRFGLSLTIHEDACRIISVVPVVLEVRRAEPAHPATPYPEPLARCSRSPGLNESSHMSGRIPP

2d38A

0.13

0.12

0.90

0.64

MUSTER

M---AEVIKSIMRKFPLGVAIVTTNW----------KGELVGMTVNTFNSLSLNPRMKGNDIPESYFVDNEELFNIFALKPVKERFEIKYKEGIGGCPILYDSYAYIEAKLYD-TIDVGDH-EVIDGYQIRDNFTPLVYMNRKLSS

4q6uA3

0.15

0.11

0.75

0.67

dPPAS

----GPLKWDLTRGVATD----TPESLTNS-------GKNPEVEITYGRAFAEDLPARELNPN-------ETQVLAAVKAKPGKTLCSIWDLTDWQGTPIRIGFVARSALEPGPNGRD----HLVARANWRAETK-----------

4dvkA

0.34

0.25

0.75

0.58

wdPPAS

--ENITNLQDNGTEGI-------QRAMFQRGVNRSLPGVPSHLATDTEDAS--EKTN-----TCCRLQRHEWNKHGWCNGQPLRECAVTCRYDRDS------LNVVTQARDS---------PTPLTGCKK--GKNFS--FAGIL-P

3j39N

0.25

0.22

0.87

0.65

wMUSTER

PRPTARRLGYRAKQ---GFVIYRIR--VRRGRKRPVPGCTYGKPK-SHGVNQLKPYRGLQSIAEERVGRR-------GGL----RVLNSYWIAQDASKYFEVILIDTHIRRCKHVHKELRGLTSAGKSSR--GIGKGYRYSQTIGG

4dvkA

0.45

0.32

0.72

0.55

wPPAS

IT-NLQDNG-----T-EG---I-QRAMFQRNRSL--PGVPSHLATDTHDAS--EKTN---YTC-CRLQRHEWNKHGWCN------YNINLT-RECACRYDSDLNVVTQAR--SP----TP----LTGCKK--GKNFS--FAGIL-P

1r5sA

0.24

0.18

0.77

0.57

dPPAS2

LGSPSKDCGSPKYAYFNGC------------SSPTAPLSPM-SPPGYRNNSSCRNYNKQAWAYSAEQNRMGQAGSTISNSHAQP-----FDFPDDNQ----------NAKKVAAGHELQPLAIVDQRSSRA-----SSRASSRPRP

1r5sA

0.24

0.18

0.77

0.66

PPAS

LGSPSKDCGSPKYAYFNGC------------SSPTAPLSPMS-PPGYKLVTGD-RNNSSCRNYNKQASEQNW-----ANSAEQNRMGQA-TIHAQP----FDFP---NAKKVAAGHELQPIVDQ--PSSRA-----SSRASSRPRP

1e4eA3

0.21

0.16

0.80

0.70

Env-PPAS

-------SGC----EVGCAVLGNSAALVVEVDQIRLQYGIFRIHQEVEPEKGSENA-VITVPADGRIQETVKKIYKTLGCRGLARVDMFLQ--DNG------RIVLNEVNT----LPGTSYP-RMMAAA---GISLPE-LIDRLIV

2yqyA

0.32

0.25

0.79

0.57

MUSTER

-------TWDEALKRLEA----SRKALLALLREAD--------PA-WLSA----PLREGAW-TPLMVAEHVALVEDSTARVLRRRLALSL---EEVLALLDRARAFLEVAKADPQNPATPHPNPLGWL-RA-AYHEAHHLKALQAS

1r5sA

0.18

0.15

0.83

0.61

dPPAS

LGSPSKDCGSPKYAYFNGC-----SSPTAPLSPMSPPG--YKLVTGDRNNSSCRNYNKQAWANYSAEQNRMGQAGSTISNSHAQPF----DFPDDNQ----------NAKKVAAGHELQPLAI----VDQRPSSRASSRASSRPRP

(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=-4.44

Estimated TM-score = 0.25±0.07

Estimated RMSD = 15.4±3.4Å

Download Model 2

C-score=-4.70

Download Model 3

C-score=-4.66

Download Model 4

C-score=-4.91

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	2v0gA	0.464	4.66	0.024	0.767
2	1no3A2	0.453	5.25	0.056	0.808
3	3ziuB	0.445	4.80	0.024	0.760
4	1qo8A	0.443	4.74	0.035	0.767
5	5hygA	0.442	5.02	0.038	0.753
6	3i6sA	0.439	5.17	0.037	0.808
7	4at0A	0.436	4.67	0.009	0.747
8	1fokA	0.436	3.93	0.048	0.664
9	1syyA	0.434	5.12	0.053	0.740
10	1q9iA	0.432	4.85	0.069	0.740

(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	0.10	5	1jrzA	HEM	Rep, Mult	11,12,17,19,20,73,74,75
2	0.10	5	3f1fW	MG	Rep, Mult	76,78
3	0.06	3	3ildA	MG	Rep, Mult	93,95
4	0.06	3	3q2wA	MAN	Rep, Mult	90,101
5	0.04	2	2jlrA	MN	Rep, Mult	8,94,95
6	0.04	2	1c3oB	GLN	Rep, Mult	73,76
7	0.02	1	1yp6A	PRZ	Rep, Mult	5,63,86,105,107,125
8	0.02	1	3zwuA	CA	Rep, Mult	95,113
9	0.02	1	2chhA	UNX	Rep, Mult	86,88,105
10	0.02	1	3t6cA	MG	Rep, Mult	95,108,123
11	0.02	1	1e39A	NA	Rep, Mult	1,2,4,15,16,17,18

	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	1qo8D	0.444	4.65	0.062	0.760	1.3.99.1	4,33
2	0.060	1lj1A	0.425	5.01	0.052	0.753	1.3.99.1	43
3	0.060	1qw6A	0.404	4.76	0.053	0.671	1.14.13.39	19
4	0.060	1g8mA	0.407	4.95	0.077	0.733	3.5.4.10,2.1.2.3	NA
5	0.060	1fokA	0.436	3.93	0.048	0.664	3.1.21.4	NA
6	0.060	1d0cA	0.406	4.77	0.053	0.671	1.14.13.39	NA
7	0.060	1rsrB	0.432	5.10	0.023	0.740	1.17.4.1	NA
8	0.060	3eqvA	0.415	4.96	0.109	0.712	3.4.16.4	NA
9	0.060	1h0nA	0.413	5.14	0.022	0.740	1.17.4.1	NA
10	0.060	1vs1D	0.405	4.86	0.063	0.712	2.5.1.54	NA
11	0.060	3etcB	0.412	5.29	0.077	0.747	6.2.1.-	NA
12	0.060	2iukA	0.455	5.22	0.035	0.808	1.13.11.12	NA
13	0.060	1p4rA	0.405	4.69	0.043	0.719	2.1.2.3,3.5.4.10	NA
14	0.060	1ei1A	0.416	4.75	0.036	0.726	5.99.1.3	9
15	0.060	2iukB	0.355	5.14	0.043	0.664	1.13.11.12	4,8
16	0.060	1yiqA	0.406	4.90	0.045	0.740	1.1.99.-	NA
17	0.060	1jk0A	0.413	4.85	0.023	0.706	1.17.4.1	NA
18	0.060	1uzrB	0.418	5.10	0.038	0.719	1.17.4.1	NA
19	0.060	1e39A	0.431	5.02	0.060	0.767	1.3.99.1	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	0.458	4.70	0.03	0.77	2bteA	GO:0000166 GO:0002161 GO:0004812 GO:0004823 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006429 GO:0006450 GO:0016874 GO:0046872
1	0.07	0.436	4.53	0.05	0.72	3zgzD	GO:0000166 GO:0002161 GO:0004812 GO:0004823 GO:0005524 GO:0005737 GO:0005829 GO:0006412 GO:0006418 GO:0006429 GO:0006450 GO:0016874
2	0.06	0.335	5.82	0.06	0.70	1gaxA	GO:0000166 GO:0002161 GO:0004812 GO:0004832 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006438 GO:0006450 GO:0016874 GO:0046872
3	0.06	0.443	4.79	0.02	0.76	3ziuA	GO:0000166 GO:0004812 GO:0004823 GO:0005524 GO:0006418 GO:0006429 GO:0016874
4	0.06	0.305	5.65	0.06	0.60	1obhA	GO:0000166 GO:0002161 GO:0004812 GO:0004823 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006429 GO:0006450 GO:0016874 GO:0046872
5	0.06	0.356	5.57	0.06	0.69	1a8hA	GO:0000049 GO:0000166 GO:0003723 GO:0004812 GO:0004825 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006431 GO:0016874 GO:0046872
6	0.06	0.369	5.37	0.03	0.69	5ah5A	GO:0000166 GO:0002161 GO:0004812 GO:0004823 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006429 GO:0006450 GO:0016874
7	0.06	0.360	5.92	0.07	0.77	1ileA	GO:0000166 GO:0002161 GO:0004812 GO:0004822 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006428 GO:0006450 GO:0008270 GO:0016874 GO:0046872
8	0.06	0.405	5.14	0.03	0.75	3kflA	GO:0000166 GO:0000287 GO:0004812 GO:0004825 GO:0005524 GO:0005737 GO:0005829 GO:0006412 GO:0006418 GO:0006431 GO:0016874
9	0.06	0.390	4.89	0.07	0.68	4dlpC	GO:0000166 GO:0004812 GO:0004825 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006431 GO:0016874
10	0.06	0.321	5.24	0.02	0.58	1irxB	GO:0000049 GO:0000166 GO:0004812 GO:0004824 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006430 GO:0016874 GO:0046872
11	0.06	0.363	5.11	0.06	0.64	1pg0A	GO:0000049 GO:0000166 GO:0003723 GO:0004812 GO:0004825 GO:0005524 GO:0005737 GO:0005829 GO:0006412 GO:0006418 GO:0006431 GO:0008270 GO:0016020 GO:0016874 GO:0046872
12	0.06	0.348	5.34	0.03	0.66	1rqgA	GO:0000049 GO:0000166 GO:0003723 GO:0004812 GO:0004825 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006431 GO:0016874 GO:0046872
13	0.06	0.350	5.06	0.06	0.63	1pfuA	GO:0000049 GO:0000166 GO:0003723 GO:0004812 GO:0004825 GO:0005524 GO:0005737 GO:0005829 GO:0006412 GO:0006418 GO:0006431 GO:0008270 GO:0016020 GO:0016874 GO:0046872
14	0.06	0.338	5.70	0.03	0.67	3tqoA	GO:0000166 GO:0004812 GO:0004817 GO:0005524 GO:0005737 GO:0005829 GO:0006412 GO:0006418 GO:0006423 GO:0008270 GO:0016874 GO:0046872
15	0.06	0.346	4.49	0.05	0.55	3o0aB	GO:0000166 GO:0002161 GO:0004812 GO:0004823 GO:0005524 GO:0005737 GO:0005829 GO:0006412 GO:0006418 GO:0006429 GO:0006450 GO:0016874
16	0.06	0.326	5.51	0.05	0.60	4xkzA	GO:0000166 GO:0002161 GO:0004812 GO:0004832 GO:0005524 GO:0005737 GO:0005829 GO:0006412 GO:0006418 GO:0006438 GO:0006450 GO:0016874
17	0.06	0.340	5.44	0.04	0.64	1wp9A	GO:0000166 GO:0003676 GO:0003677 GO:0004386 GO:0004518 GO:0005524 GO:0006259 GO:0006281 GO:0046872 GO:0090305
18	0.06	0.379	4.73	0.04	0.64	4k5rB	GO:0000166 GO:0016491 GO:0055114 GO:0071949

Consensus prediction of GO terms

Molecular Function	GO:0016876	GO:0035639	GO:0032550	GO:0032559	GO:0052689	GO:0043169
GO-Score	0.57	0.57	0.57	0.57	0.47	0.36
Biological Processes	GO:0043039	GO:0006448	GO:0065008
GO-Score	0.57	0.47	0.47
Cellular Component	GO:0044424
GO-Score	0.47

(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.