D-I-TASSER P78352-D2

D-I-TASSER results for P78352-D2

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

Input Sequence in FASTA format

>P78352 (246 residues)
AEKVMEIKLIKGPKGLGFSIAGGVGNQHIPGDNSIYVTKIIEGGAAHKDGRLQIGDKILA
VNSVGLEDVMHEDAVAALKNTYDVVYLKVAKPSNAYLSDSYAPPDITTSYSQHLDNEISH
SSYLGTDYPTAMTPTSPRRYGTASLRSNPKRGFYIRALFDYDKTKDCGFLSQALSFRFGD
VLHVIDASDEEWWQARRVHSDSETDDIGFIPSKRRVERREWSRLKAKDWGSSSGSQGRED
SVLSYE

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| AEKVMEIKLIKGPKGLGFSIAGGVGNQHIPGDNSIYVTKIIEGGAAHKDGRLQIGDKILAVNSVGLEDVMHEDAVAALKNTYDVVYLKVAKPSNAYLSDSYAPPDITTSYSQHLDNEISHSSYLGTDYPTAMTPTSPRRYGTASLRSNPKRGFYIRALFDYDKTKDCGFLSQALSFRFGDVLHVIDASDEEWWQARRVHSDSETDDIGFIPSKRRVERREWSRLKAKDWGSSSGSQGREDSVLSYE
Prediction	CCCSSSSSSSSCCCCCCSSSSCCCCCCCCCCCCCSSSSSSCCCCHHHHCCCCCCCCSSSSSCCSSCCCCCHHHHHHHHHHCCCSSSSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSCCCCCHHHHHHHHCCCCCCCCCCSSCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCC
Confidence	994699999988997638997477887777887589999789995786199889929999999867999999999999857992999999567887776678766677767655543345666888898766677876433222346667654311134424567887611048975264899944888014553010678875522041578899999999875136678877555654342269
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| AEKVMEIKLIKGPKGLGFSIAGGVGNQHIPGDNSIYVTKIIEGGAAHKDGRLQIGDKILAVNSVGLEDVMHEDAVAALKNTYDVVYLKVAKPSNAYLSDSYAPPDITTSYSQHLDNEISHSSYLGTDYPTAMTPTSPRRYGTASLRSNPKRGFYIRALFDYDKTKDCGFLSQALSFRFGDVLHVIDASDEEWWQARRVHSDSETDDIGFIPSKRRVERREWSRLKAKDWGSSSGSQGREDSVLSYE
Prediction	874324030324761000002003435446542000013025612034433043302004016330461316301510472753020102243533365434344244424441444233443444433443343443323323343444343333324423436433222451514321102022553541120243367456442110115432533532445446475574554466233638
	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                 240

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCSSSSSSSSCCCCCCSSSSCCCCCCCCCCCCCSSSSSSCCCCHHHHCCCCCCCCSSSSSCCSSCCCCCHHHHHHHHHHCCCSSSSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSCCCCCHHHHHHHHCCCCCCCCCCSSCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCC
AEKVMEIKLIKGPKGLGFSIAGGVGNQHIPGDNSIYVTKIIEGGAAHKDGRLQIGDKILAVNSVGLEDVMHEDAVAALKNTYDVVYLKVAKPSNAYLSDSYAPPDITTSYSQHLDNEISHSSYLGTDYPTAMTPTSPRRYGTASLRSNPKRGFYIRALFDYDKTKDCGFLSQALSFRFGDVLHVIDASDEEWWQARRVHSDSETDDIGFIPSKRRVERREWSRLKAKDWGSSSGSQGREDSVLSYE

1wygA

0.06

0.04

1.94

0.67

DEthreader

----ADPETTLVRLCGEGG-------------------SVNACLAPICSLHHV-------GRVTDAKL--TEIGIEMKFKNM-LFPLIVCPAWIPE-LNSSCPLVEGVLNPVASGLCFSALAEELQLADAPGGM--DMLGGRHPIMERFHGFG----------PAEEVRRMPWDECSS---IPTKFG-----SYGVVMSLLRDCP---FLSSIFFAIKDAIRAAR-AQHGDNA---FIRNAC----

4wsiA

0.26

0.20

6.15

1.95

SPARKS-K

GETVKIVRIEKARDPLGATVRNEMD--------SVIISRIVKGGAAEKSGLLHEGDEVLEINGIEIRGKDVNEVFDLLSDMHGTLTFVLIPSQQIKPPPA------------------------------------------------KETVIHVKAHFDYDPSDDPYVPCRGLSFQKGDILHVISQEDPNWWQAYREGDEDNQPLAGLVPGKECGQNELRQRLMNKEKDRDQEVAGRDYHFVSRQ

2xkxA

0.53

0.52

14.91

1.26

MapAlign

EMEYEEITLERGNSGLGFSIAGGTDNPHIGDDPSIFITKIIPGGAAAQDGRLRVNDSILFVNEVDVREVTHSAAVEALKEAGSIVRLYVMRRKPPQAAIALKNAGQTVTIIAQYKPEEYSRFEAKIHDLREQLMNSSLGSGTASLRSNPKRGFYIRALFDYDKTKDCGFLSQALSFRFGDVLHVIDAGDEEWWQARRVHSDSETDDIGFIPSKRRVEKDRANDDLEAGQYNSHLYGTSV-------

2xkxA

1.00

27.89

0.75

CEthreader

AEKVMEIKLIKGPKGLGFSIAGGVGNQHIPGDNSIYVTKIIEGGAAHKDGRLQIGDKILAVNSVGLEDVMHEDAVAALKNTYDVVYLKVAKPSNAYLSDSYAPPDITTSYSQHLDNEISHSSYLGTDYPTAMTPTSPRRYGTASLRSNPKRGFYIRALFDYDKTKDCGFLSQALSFRFGDVLHVIDAGDEEWWQARRVHSDSETDDIGFIPSKRRVERREWSRLKAKDWGSSSGSQGREDSVLSYE

3tswB

0.30

0.22

6.52

1.24

MUSTER

-PSMKLVKFRKG-DSVGLRLAGGNDV-------GIFVAGVLEDSPAAKEG-LEEGDQILRVNNVDFTNIIREEAVLFLLDLGEEVTILAQKKKDVYRRIVESDVGDS---------------------------------------------FYIRTHFEYEKESPYGL-----SFNKGEVFRVVDTGKLGSWLAIRIGKNHKEVERGIIPNKNRAEQLAS------------VQYTLPKTFPAYE

2xkxA

0.98

27.56

2.64

HHsearch

AEKVMEIKLIKGPKGLGFSIAGGVGNQHIPGDNSIYVTKIIEGGAAHKDGRLQIGDKILAVNSVGLEDVMHEDAVAALKNTYDVVYLKVAKPSNAYLSDSYAPPDITTSYSQHLDNEISHSSYLGTDYPTAMTPTKPEEYGTASLRSNPKRGFYIRALFDYDKTKDCGFLSQALSFRFGDVLHVIDAGDEEWWQARRVHSDSETDDIGFIPSKRRVERREWSRLKAKDWGSSSGSQGREDSVLSYE

3tswB

0.32

0.22

6.74

1.61

FFAS-3D

--SMKLVKFRKG-DSVGLRLAGG-------NDVGIFVAGVLEDSPAAKEG-LEEGDQILRVNNVDFTNIIREEAVLFLLDLGEEVTILAQKKKDVY---------------------------------------------RRIVESDVGDSFYIRTHFEYEKESPY-----GLSFNKGEVFRVVDTGKLGSWLAIRIGKNHKEVERGIIPNKNRAEQLASVQ------------YTLPKTFPAYE

2xkxA

0.82

0.81

22.83

1.37

EigenThreader

AEKVMEIKLIKGPKGLGFSIAGGVGNQHIPGDNSIYVTKIIEGGAAHKDGRLQIGDKILAVNSVGLEDVMHEDAVAALKNTYDVVYLKVAKPSNAYLSDSYAPPDITTSYSQHLDNEISHSSYLGTDYPTAMTPTSSLGSGTASLRSNPKRGFYIRALFDYDKTKDCGFLSQALSFRFGDVLHVIDAGDEEWWQARRVHDSETDDIGFIPSKRRVERREWS----RLKAKDWGSSSGSQGREMEVH

2xkxA

0.65

0.57

16.25

3.18

CNFpred

PREPRRIVIHRGSTGLGFNIVGGED------GEGIFISFILAGGPADLSGELRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVTIIAQYKPEEYSRFEAKIHDLRE-----------------------QLMNSSLGSGTASLRSNPKRGFYIRALFDYDKTKDCGFLSQALSFRFGDVLHVIDAGDEEWWQARRVHSDSETDDIGFIPSKRRVERREWSRLKAKDWGSSSGSQGREDSVLSYE

3zyvA

0.05

0.03

1.59

0.67

DEthreader

----LADPEVNFKYCGGGD-------------------SATACLVPICSLHGA-------GRTTSAPL--NTYLGLHMKDVS--PIIISPARILELFV-GGLQVKLLLQLISAAGMLYSCGICEEVSLLAPGGM--RMLGGRHPVIEYLKGFF----------PPEKVRNMYLWECNS---IPMKFS-----VFGAMDLLTPTPN---FLCSVFFAIAAAVAAAREER---------IRMAC----

(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	0.6755

(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	2xkxA	0.92	2.25	0.951	1.000	model1_2xkxA.pdb.gz
2	6pcvA	0.43	4.63	0.111	0.602	model1_6pcvA.pdb.gz
3	2zkmX	0.42	5.82	0.033	0.691	model1_2zkmX.pdb.gz
4	3qr0A	0.41	5.85	0.061	0.691	model1_3qr0A.pdb.gz
5	5medA	0.41	5.37	0.035	0.646	model1_5medA.pdb.gz
6	6lknA	0.41	6.16	0.036	0.703	model1_6lknA.pdb.gz
7	4nreA2	0.41	5.22	0.057	0.638	model1_4nreA2.pdb.gz
8	4gwmA	0.41	6.30	0.076	0.736	model1_4gwmA.pdb.gz
9	2qt5A	0.41	3.44	0.193	0.480	model1_2qt5A.pdb.gz
10	3dy5A3	0.40	5.20	0.042	0.626	model1_3dy5A3.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:0005102	0.69	receptor binding
GO:0003824	0.68	catalytic activity
GO:0016740	0.67	transferase activity
GO:0016301	0.66	kinase activity
GO:0004385	0.65	guanylate kinase activity
GO:0035254	0.62	glutamate receptor binding
GO:0035255	0.61	ionotropic glutamate receptor binding
GO:0008022	0.51	protein C-terminus 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:0044699	0.91	single-organism process
GO:0009987	0.89	cellular process
GO:0044763	0.86	single-organism cellular process
GO:0016043	0.84	cellular component organization
GO:0051179	0.76	localization
GO:0008104	0.72	protein localization
GO:0065007	0.70	biological regulation
GO:0051641	0.70	cellular localization
GO:0007163	0.70	establishment or maintenance of cell polarity
GO:1902578	0.67	single-organism localization
GO:0045197	0.67	establishment or maintenance of epithelial cell apical/basal polarity
GO:1902580	0.66	single-organism cellular localization
GO:0034613	0.66	cellular protein localization
GO:0032502	0.66	developmental process
GO:0072657	0.65	protein localization to membrane
GO:0050789	0.62	regulation of biological process
GO:0050794	0.61	regulation of cellular process
GO:0048856	0.61	anatomical structure development
GO:0043113	0.58	receptor clustering
GO:0035418	0.58	protein localization to synapse
GO:0097120	0.57	receptor localization to synapse

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:0044424	1.00	intracellular part
GO:0016020	0.89	membrane
GO:0043226	0.88	organelle
GO:0044425	0.78	membrane part
GO:0043229	0.76	intracellular organelle
GO:0044459	0.75	plasma membrane part
GO:0005737	0.74	cytoplasm
GO:0097458	0.71	neuron part
GO:0044456	0.71	synapse part
GO:0030054	0.70	cell junction
GO:0098590	0.69	plasma membrane region
GO:0005886	0.64	plasma membrane
GO:0044444	0.63	cytoplasmic part
GO:0043232	0.63	intracellular non-membrane-bounded organelle
GO:0032991	0.62	macromolecular complex
GO:0043234	0.60	protein complex
GO:0043227	0.58	membrane-bounded organelle
GO:0014069	0.58	postsynaptic density
GO:0045211	0.56	postsynaptic membrane
GO:0016323	0.54	basolateral plasma membrane
GO:0045202	0.50	synapse

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	2cqsA	0.402	6.01	0.037	0.687	2.4.1.20	72
2	0.060	1sllA	0.366	6.27	0.030	0.667	4.2.2.15	57
3	0.060	1t3qB	0.378	5.80	0.035	0.626	1.3.99.17	NA
4	0.060	2zkmX	0.416	5.82	0.033	0.691	3.1.4.11	71
5	0.060	2pa6A	0.378	5.92	0.078	0.634	4.2.1.11	48

	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	0.78	2g2lA	0.354	1.08	0.878	0.366	1.81	III	complex1.pdb.gz	15,16,17,18,19,20,38,71,75,78
2	0.38	2g2lB	0.354	1.11	0.878	0.366	1.76	III	complex2.pdb.gz	16,17,18,20,79
3	0.11	2x7z0	0.367	1.25	0.840	0.382	1.68	III	complex3.pdb.gz	2,3,4,5,6,7,8,49,51
4	0.06	2i0iA	0.315	1.40	0.407	0.329	1.59	III	complex4.pdb.gz	12,13,43,44,45,48
5	0.05	1pdr2	0.335	1.82	0.347	0.358	1.56	III	complex5.pdb.gz	9,10,43,45,48
6	0.05	1pdr0	0.335	1.82	0.347	0.358	1.33	III	complex6.pdb.gz	19,20,21,24,38,39,41,42,71,75

	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.