D-I-TASSER P28328-D1

D-I-TASSER results for P28328-D1

[Click result.zip to download all results on this page]

Input Sequence in FASTA format

>P28328 (229 residues)
MASRKENAKSANRVLRISQLDALELNKALEQLVWSQFTQCFHGFKPGLLARFEPEVKACL
WVFLWRFTIYSKNATVGQSVLNIKYKNDFSPNLRYQPPSKNQKIWYAVCTIGGRWLEERC
YDLFRNHHLASFGKVKQCVNFVIGLLKLGGLINFLIFLQRGKFATLTERLLGIHSVFCKP
QNICEVGFEYMNRELLWHGFAEFLIFLLPLINVQKLKAKLSSWCIPLTG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MASRKENAKSANRVLRISQLDALELNKALEQLVWSQFTQCFHGFKPGLLARFEPEVKACLWVFLWRFTIYSKNATVGQSVLNIKYKNDFSPNLRYQPPSKNQKIWYAVCTIGGRWLEERCYDLFRNHHLASFGKVKQCVNFVIGLLKLGGLINFLIFLQRGKFATLTERLLGIHSVFCKPQNICEVGFEYMNRELLWHGFAEFLIFLLPLINVQKLKAKLSSWCIPLTG
Prediction	CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHCCSSSCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHCCSSSCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCCCCC
Confidence	9988899998776554378759999999999999999999997085025555599999999999996506999983378729375426566555676416899999999999999999999999737841578999999999999999999999999971988889999766655327888766355113668999999999999999862499999999998523479
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MASRKENAKSANRVLRISQLDALELNKALEQLVWSQFTQCFHGFKPGLLARFEPEVKACLWVFLWRFTIYSKNATVGQSVLNIKYKNDFSPNLRYQPPSKNQKIWYAVCTIGGRWLEERCYDLFRNHHLASFGKVKQCVNFVIGLLKLGGLINFLIFLQRGKFATLTERLLGIHSVFCKPQNICEVGFEYMNRELLWHGFAEFLIFLLPLINVQKLKAKLSSWCIPLTG
Prediction	8264666354433021001100430262025103530350053045423540330020003100010023453322032024031325345444444343211000001200142014204420464635434303300420330130011300120034041320020002023233444343413143121111110122321330031224301420441144368
	Values range from 0 (buried residue) to 8 (highly exposed residue)

Predicted Contact, Hydrogen and Distance Map Used in D-I-TASSER simulation

Contact Map

Distance Map

Hydrogen bond networks

D-I-TASSER simulation is guided by the consensus contact map (left figure), distance map (middle figure) and Hydrogen bond network (right figure) derived based on confidence scores of DeepPotential. In the contact, distance map and hydrogen bond networks, the axes mark the residue index along the sequence. For the contact map, each dot represents a residue pair with predicted contact, while for the distance map and hydrogen bond network, a color scale represents a distance of 1-20+ angstroms or a angle of 0-180 degree.

Top 10 threading templates used by D-I-TASSER

Rank

PDB
hit

ID1

ID2

Cov

Norm.
Zscore

Download
alignment

                  20                  40                  60                  80                 100                 120                 140                 160                 180                 200                 220

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHCCSSSCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHCCSSSCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCCCCC
MASRKENAKSANRVLRISQLDALELNKALEQLVWSQFTQCFHGFKPGLLARFEPEVKACLWVFLWRFTIYSKNATVGQSVLNIKYKNDFSPNLRYQPPSKNQKIWYAVCTIGGRWLEERCYDLFRNHHLASFGKVKQCVNFVIGLLKLGGLINFLIFLQRGKFATLTERLLGIHSVFCKPQNICEVGFEYMNRELLWHGFAEFLIFLLPLINVQKLKAKLSSWCIPLTG

3wjkA

0.04

1.93

0.49

CEthreader

HDDVVDESDMRRGKATANAAFGNAASVLVGDFIYTRAFQMMTSLGSLKVLEVMSEAVNVIAEGEVLQ-----------------------------LMITEENYMRVIYSKTARLFEAAAQCSGILCTPEEEKGLQDYGRYLGTAFQLIDDLLDYNANVGDDLNEGKPTLPLLHAMHHGTPEQAQMIRTAIEQGNGRHLLEPVLEAMNACGSLEWTRQRAEEEADKAIA

2axtA

0.06

0.05

2.12

0.65

EigenThreader

------------SANLWERFCNWVT---------------STDNRLYVGWFGVIMIPTLLAATICFVIAFIAAPPVDIDGIEPVSGSLLNNIITGAVVPSEWLYNGGPYQLIIFHFLLGASCYMGRQWELSYRLCVAYSAPLASAFAVFLIYPIGQG----SFSDG------MPLG----ISGTFNFMIVFQAEHNFHQLGVAGVFGGALFCAMHGSLVTSSLIRETTE

5v6pA2

0.08

0.06

2.42

0.74

FFAS-3D

---------------ELRLIEHEHIFERLPFTIINTLF-MSSLFHERYFFTVAFFGLLLLYLKVFHWILK-------DRLEALLQSINDSTTMKTLIFSRFSFNLVLLAVVDYQIITRCISSIYTNQKSDIESTSLYLIQVMEFTMLLIDLLNLFL-----------QTCLNF--------------WEFYRSKFMYEKAIDVFTRFLKTADILALYQSGTSLWK----

6w2rA

0.09

0.07

2.86

0.74

SPARKS-K

------------GTTEDERRELEKVARKAIEAAREQLQRALEIARESTKTAVKLALDVALRVAQEAAKRGNKDAIAAEVVVRIAEESNN------------SDALEQALRVLEEIAKAVLKSEKTEDAKKAVKLVQEAYKAAQRAIEAAKRTKLAIKLAKLAARAALEVIKR-----PKSE---EVNEALKKIVKAIQEAVESLREAEESEKREKARERVREAVERAEE

3w3tA

0.09

0.07

2.83

0.78

CNFpred

---------------FAAMMALSSAAEGCADVLIGEIPKILDMVIPLINDP-HPRVQYGCCNVLGQISTDFSQRTAHDRILPALISKL----------ECTSRVQTHAAAALVNFSEFASKDILEPYLDSLLTNLLVLLQSLYVQEQALTTIAFIAEAAKNKFIKYYDTLMPLL-------------LNVLK-SVLKGKCMECATLIGFAVGKEKFHEHSQELISILVA

6z16A

0.04

1.94

0.83

DEthreader

-----LH-GWLYSIYLLFYYLLLFMAMTSSTMFGGLLMLGGVA-PLFIPALVILFGAFTKSAPFYIWLP----DAM-EAPTPS---LASK--QTDLKA---ILAYSTVSQLGLITSLLGIGGLSFHYDGMGENVFM-VAVLAAIFHLFNHATFKGSLVITIAGSSMAFTFYSLLVT---VLKKAHEAP-FGM-LIAPIVLASLVVFIVPNVLS-VHISHWHG-FTPEFM

4f4cA5

0.04

0.03

1.81

0.74

MapAlign

-----------KVSIPQLYRYTTTLEKLLL-FIGTLVAVITGAVGMWAA----GQITVTCYLYVAEQMNN-RLRREFVKSILRQEISWFNHSGTLATKLFDNLERVKEGTGDKIGQFITGFIVAFTHSNFGDMLTTFSSVMMGSMALGLAGPQLAVLG-------TAQGAAVIDSSSIENVRTVQALAREDTFYENFCEKLDIPHKEAIK--EAFIQGLSYGCAS----

5cwqA

0.10

3.53

0.51

MUSTER

LERESEEAERRLQEARKRSEEARERLKELAEALIEEARAVQELARVACERGNSEEAERASEKAQRVLEEARK---VSEEAR------------EQGDDEVLALALIAIALAVLALAEVACCRGNSEEAERASEKAQRVLEEARKVSEEAREQDEVLALALIAIALAVLALAEVACCRGNKEEAERAYVEEEARKVKESAEEQSEVKRLAEEAEQLAREARRHVQECRGG

2pffB

0.12

4.14

0.97

HHsearch

MAKRPFDKKSNSALFRAVGEGNAQLVAIFTDDYFEELRDLYQTYH--VLV--GDLIKFSAETLSELIRTLDAEKVFTQGL-NILEWLENNTPDKDYLLSIPISCPLIGVIQLAHYVVTKLLGFLSYLKSGLVVAIASWESFFVSVRKAITVLFFIGVRCYEPNTSLPPSILEDSLENNEPSSISNLTQEQ--VQ----DYVNKTNSHLPAGKPQSLYLTLRKAKAPSGL

2o98B

0.08

0.07

2.77

0.48

CEthreader

SLGSEELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRGNEEHVNSIREYRSKIENELSKICDGILKLLDAKL---------------------IPSAASGDSKVFYLKMKGDYHRYLAEFKTGAERKEAAESTLTAYKAAQDIATTELAP------THPIRLGLALNFSVFYYEILNSPDRACNLAKQAFDEAIAELDTLGEESYKDSTLIMQLLRDNLTLWT

(a)	ID1 is the number of template residues identical to query divided by number of aligned residues.
(b)	ID2 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 and is highlighted in bold.
(e)	Download alignment lists the threading program used to identify the template, and provide the 3D structure of aligned regions of threading templates (threading[1-10].pdb.gz).
(f)	Template residues identical to query sequence are highlighted in color.

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.6885

(a)

D-I-TASSER simulations generate a large ensemble of structural conformations, i.e. decoys. These decoys are clustered by SPICKER based on pairwise structure similarity to report up to five final models from the five largest clusters. Models are ranked in descending order of cluster size. If the simulations converge well, it is possible to have less than 5 models generated, which is usually an indication of good model quality.

(b)

The model confidence is quantitatified by estimated TM-score (eTM-score), calculated based on significance of threading template alignments, contact map satisfaction rate, mean absolute error between distance of model and distance of DeepPotential, and convergence of D-I-TASSER simulations. eTM-score is typically in the range of [0, 1], with higher eTM-score signifies higher model confidence.

Proteins with similar structure

Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	6z16A	0.52	5.38	0.090	0.847	model1_6z16A.pdb.gz
2	6s1yA	0.50	5.00	0.056	0.751	model1_6s1yA.pdb.gz
3	4a01A	0.49	5.45	0.033	0.769	model1_4a01A.pdb.gz
4	6cfwH	0.48	5.48	0.064	0.799	model1_6cfwH.pdb.gz
5	2qr4A	0.48	4.69	0.061	0.703	model1_2qr4A.pdb.gz
6	1b25A	0.48	5.68	0.050	0.817	model1_1b25A.pdb.gz
7	6e8jA	0.48	5.63	0.061	0.799	model1_6e8jA.pdb.gz
8	7d3uD	0.48	5.13	0.049	0.725	model1_7d3uD.pdb.gz
9	1j36A	0.48	5.47	0.046	0.764	model1_1j36A.pdb.gz
10	3vuoA	0.48	5.68	0.059	0.790	model1_3vuoA.pdb.gz

(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 Gene Ontology (GO) Terms

Molecular Function (MF)

GO term	Cscore^GO	Name
GO:0003824	0.63	catalytic activity
GO:0016740	0.60	transferase activity
GO:0004842	0.59	ubiquitin-protein transferase activity
GO:0043169	0.53	cation binding

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Molecular Function. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Biological Process (BP)

GO term	Cscore^GO	Name
GO:0009987	1.00	cellular process
GO:0007031	0.95	peroxisome organization
GO:0044699	0.83	single-organism process
GO:0008152	0.82	metabolic process
GO:0071704	0.81	organic substance metabolic process
GO:0044763	0.81	single-organism cellular process
GO:0044238	0.81	primary metabolic process
GO:0044237	0.81	cellular metabolic process
GO:0006810	0.74	transport
GO:1902578	0.73	single-organism localization
GO:0071702	0.73	organic substance transport
GO:0051641	0.73	cellular localization
GO:0008104	0.73	protein localization
GO:1902580	0.72	single-organism cellular localization
GO:0055085	0.72	transmembrane transport
GO:0006886	0.72	intracellular protein transport
GO:1902589	0.71	single-organism organelle organization
GO:0044743	0.71	intracellular protein transmembrane import
GO:0006625	0.71	protein targeting to peroxisome
GO:0016558	0.70	protein import into peroxisome matrix
GO:0044710	0.64	single-organism metabolic process
GO:0006629	0.63	lipid metabolic process
GO:0044281	0.62	small molecule metabolic process
GO:0044255	0.62	cellular lipid metabolic process
GO:0019752	0.61	carboxylic acid metabolic process
GO:0006631	0.60	fatty acid metabolic process
GO:0065007	0.53	biological regulation
GO:0050794	0.52	regulation of cellular process

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Biological Process. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Cellular Component (CC)

GO term	Cscore^GO	Name
GO:0044444	1.00	cytoplasmic part
GO:0044446	0.92	intracellular organelle part
GO:0044439	0.87	peroxisomal part
GO:0043229	0.87	intracellular organelle
GO:0043227	0.87	membrane-bounded organelle
GO:0043231	0.86	intracellular membrane-bounded organelle
GO:0042579	0.80	microbody
GO:0016020	0.68	membrane
GO:0005778	0.66	peroxisomal membrane
GO:0044425	0.58	membrane part
GO:0031224	0.57	intrinsic component of membrane
GO:0005779	0.56	integral component of peroxisomal membrane
GO:0044428	0.53	nuclear part

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Cellular Component. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Predicted Enzyme Commission (EC) Numbers

Top 5 enzyme homologs in PDB

Rank	Cscore^EC	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	EC Number	Predicted Active Site Residues
1	0.060	2e9eA	0.391	5.90	0.063	0.672	1.11.1.7	NA
2	0.060	2iukA	0.352	5.40	0.054	0.546	1.13.11.12	153
3	0.060	1fziA	0.400	5.46	0.025	0.651	1.14.13.25	NA
4	0.060	3lmdA	0.427	4.70	0.028	0.638	2.5.1.30	110,117
5	0.060	1jqnA	0.434	5.74	0.055	0.716	4.1.1.31	NA

	Click on the radio buttons to visualize predicted active site residues.
(a)	Cscore^EC is the confidence score for the Enzyme Commission (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.

Predicted Ligand Binding Sites

Template proteins with similar binding site:

Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
1	0.09	2x93A	0.492	5.02	0.047	0.747	0.17	X93	complex1.pdb.gz	18,19,22,78
2	0.01	1uzeA	0.444	5.31	0.043	0.707	0.24	EAL	complex2.pdb.gz	22,23,26,162,163,164
3	0.01	1azs3	0.235	3.90	0.013	0.310	0.22	III	complex3.pdb.gz	143,145,148,150,152,153,154,156,157,160,161
4	0.01	1su6A	0.456	5.76	0.056	0.755	0.32	SF4	complex4.pdb.gz	162,163,165,172,173,174
5	0.01	1hu9A	0.380	5.36	0.029	0.611	0.25	4HM	complex5.pdb.gz	152,156,157,161
6	0.01	3rkoC	0.381	5.51	0.050	0.633	0.25	LFA	complex6.pdb.gz	152,155,159
7	0.01	3zqzA	0.477	5.50	0.046	0.764	0.12	SLC	complex7.pdb.gz	77,162,188
8	0.01	2x97A	0.490	5.01	0.042	0.747	0.13	RX4	complex8.pdb.gz	77,78,110,115
9	0.01	3rkoM	0.440	5.10	0.078	0.664	0.19	LFA	complex9.pdb.gz	149,156,160
10	0.01	2xhmA	0.489	5.19	0.047	0.751	0.20	K26	complex10.pdb.gz	18,19,22,26,77,78,161

	Click on the radio buttons to visualize predicted binding site and residues.
(a)	Cscore^LB is the confidence score of predicted binding site. Cscore^LB values range in between [0-1]; where a higher score indicates a more reliable ligand-binding site prediction.
(b)	BS-score is a measure of local similarity (sequence & structure) between template binding site and predicted binding site in the query structure. Based on large scale benchmarking analysis, we have observed that a BS-score >1 reflects a significant local match between the predicted and template binding site.
(c)	TM-score is a measure of global structural similarity between query and template protein.
(d)	RMSD^a the RMSD between residues that are structurally aligned by TM-align.
(e)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(f)	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.

[Click result.zip to download all results on this page]

References:
1.	Wei Zheng, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.