D-I-TASSER P09874-D1

D-I-TASSER results for P09874-D1

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

Input Sequence in FASTA format

>P09874 (242 residues)
MAESSDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFDGKVPHWYHFSCFWKV
GHSIRHPDVEVDGFSELRWDDQQKVKKTAEAGGVTKKSKKEKDKDSKLEKALKAQNDLIW
NIKDELKKVCSTNDLKELLIFNKQQVPSGESAILDRVADGMVFGALLPCEECSGQLVFKS
DAYYCTGDVTAWTKCMVKTQTPNRKEWVTPKEFREISYLKKLKVKKQDRIFPPETSASVA
AT

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| MAESSDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFDGKVPHWYHFSCFWKVGHSIRHPDVEVDGFSELRWDDQQKVKKTAEAGGVTKKSKKEKDKDSKLEKALKAQNDLIWNIKDELKKVCSTNDLKELLIFNKQQVPSGESAILDRVADGMVFGALLPCEECSGQLVFKSDAYYCTGDVTAWTKCMVKTQTPNRKEWVTPKEFREISYLKKLKVKKQDRIFPPETSASVAAT
Prediction	CCCCCCCCSSSSSSCCCCCCCCCCCCSCCCCCSSSSSSSCCCCCCCCCCSSSCHHHHHHCCCCCCCCHHHCCCHHHCCHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCSSSSSCCSSSSCCCCCCCCSCCCSCCCCCCCCCSCCHHHHHCHHHHHCCCCCCCCCCCCCCCCCCCCC
Confidence	99878987699992799853668898067895799999626777876443447066541111248863327995672889999999874303565322566542023431025788999999999985289899999999819999999999999999888728999999889889996885898451776215422647876445428978850837876476777640379888887889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| MAESSDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFDGKVPHWYHFSCFWKVGHSIRHPDVEVDGFSELRWDDQQKVKKTAEAGGVTKKSKKEKDKDSKLEKALKAQNDLIWNIKDELKKVCSTNDLKELLIFNKQQVPSGESAILDRVADGMVFGALLPCEECSGQLVFKSDAYYCTGDVTAWTKCMVKTQTPNRKEWVTPKEFREISYLKKLKVKKQDRIFPPETSASVAAT
Prediction	84657634010110444414443165405441010022144444534142021140145346536244540632740546125304623644636655446554554455445534530351253047315473034005306463554453003100100011216515616140304553030312122113052417616234140274057262056144346520032636554668
	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

CCCCCCCCSSSSSSCCCCCCCCCCCCSCCCCCSSSSSSSCCCCCCCCCCSSSCHHHHHHCCCCCCCCHHHCCCHHHCCHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCSSSSSCCSSSSCCCCCCCCSCCCSCCCCCCCCCSCCHHHHHCHHHHHCCCCCCCCCCCCCCCCCCCCC
MAESSDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFDGKVPHWYHFSCFWKVGHSIRHPDVEVDGFSELRWDDQQKVKKTAEAGGVTKKSKKEKDKDSKLEKALKAQNDLIWNIKDELKKVCSTNDLKELLIFNKQQVPSGESAILDRVADGMVFGALLPCEECSGQLVFKSDAYYCTGDVTAWTKCMVKTQTPNRKEWVTPKEFREISYLKKLKVKKQDRIFPPETSASVAAT

4opxA

0.93

0.71

20.07

1.00

DEthreader

----L-Y-RVEYA-------------------LRMA------------YHFSCF--WK--GHSIRHPDVEVDGFSELRWDDQQKVKKTAEA------SKKEKDKDSKLEKALKAQNDLIWNIKDELKKVCSTNDLKELLIFNKQQVPSGESAILDRVADGMVFGALLPCEECSGQLVFKSDAYYCTGDVTAWTKCMVKTQTPNRKEWVTPKEFREISYLKKLKVKKQDRIFPP---------

4opxA

1.00

0.92

25.69

4.09

SPARKS-K

-----DKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFDGKVPHWYHFSCFWKVGHSIRHPDVEVDGFSELRWDDQQKVKKTAEA------SKKEKDKDSKLEKALKAQNDLIWNIKDELKKVCSTNDLKELLIFNKQQVPSGESAILDRVADGMVFGALLPCEECSGQLVFKSDAYYCTGDVTAWTKCMVKTQTPNRKEWVTPKEFREISYLKKLKVKKQDRIFPP---------

4opxA

1.00

0.91

25.57

1.58

MapAlign

-----DKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFDGKVPHWYHFSCFWKVGHSIRHPDVEVDGFSELRWDDQQKVKKTAE------ASKKEKDKDSKLEKALKAQNDLIWNIKDELKKVCSTNDLKELLIFNKQQVPSGESAILDRVADGMVFGALLPCEECSGQLVFKSDAYYCTGDVTAWTKCMVKTQTPNRKEWVTPKEFREISYLKKLKVKKQDRIFPP---------

4opxA

0.99

0.91

25.46

1.70

CEthreader

-----DKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFDGKVPHWYHFSCFWKVGHSIRHPDVEVDGFSELRWDDQQKVKKTAEASK------KEKDKDSKLEKALKAQNDLIWNIKDELKKVCSTNDLKELLIFNKQQVPSGESAILDRVADGMVFGALLPCEECSGQLVFKSDAYYCTGDVTAWTKCMVKTQTPNRKEWVTPKEFREISYLKKLKVKKQDRIFPP---------

4opxA

1.00

0.92

25.69

3.13

MUSTER

-----DKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFDGKVPHWYHFSCFWKVGHSIRHPDVEVDGFSELRWDDQQKVKKTAEA------SKKEKDKDSKLEKALKAQNDLIWNIKDELKKVCSTNDLKELLIFNKQQVPSGESAILDRVADGMVFGALLPCEECSGQLVFKSDAYYCTGDVTAWTKCMVKTQTPNRKEWVTPKEFREISYLKKLKVKKQDRIFPP---------

4opxA

1.00

0.91

25.57

6.40

HHsearch

-----DKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFDGKVPHWYHFSCFWKVGHSIRHPDVEVDGFSELRWDDQQKVKKTAEAS------KKEKDKDSKLEKALKAQNDLIWNIKDELKKVCSTNDLKELLIFNKQQVPSGESAILDRVADGMVFGALLPCEECSGQLVFKSDAYYCTGDVTAWTKCMVKTQTPNRKEWVTPKEFREISYLKKLKVKKQDRIFPP---------

4opxA

1.00

0.91

25.57

3.07

FFAS-3D

-----DKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFDGKVPHWYHFSCFWKVGHSIRHPDVEVDGFSELRWDDQQKVKKTAE------ASKKEKDKDSKLEKALKAQNDLIWNIKDELKKVCSTNDLKELLIFNKQQVPSGESAILDRVADGMVFGALLPCEECSGQLVFKSDAYYCTGDVTAWTKCMVKTQTPNRKEWVTPKEFREISYLKKLKVKKQDRIFPP---------

4opxA

0.77

0.68

19.18

1.30

EigenThreader

-----DKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFDGKVPHWYHSCFWKVGHSIRHPDVEVFSEL---RWDDQQKVKKTAEA------SKKEKDKDSKLEKALKAQNDLIWNIKDELKKVCSTNDLKELLIFNKQQVPSGESAILDRVADGMVFGALLPCEECSGQLVFKSDAYYCTGDVTAWTKCMVKTPNWVTPKEFREISYLKK----------LKVKKQDRIFPP----

4opxA

1.00

0.92

25.69

3.06

CNFpred

-----DKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFDGKVPHWYHFSCFWKVGHSIRHPDVEVDGFSELRWDDQQKVKKTAEA------SKKEKDKDSKLEKALKAQNDLIWNIKDELKKVCSTNDLKELLIFNKQQVPSGESAILDRVADGMVFGALLPCEECSGQLVFKSDAYYCTGDVTAWTKCMVKTQTPNRKEWVTPKEFREISYLKKLKVKKQDRIFPP---------

4opxA2

0.96

0.60

16.69

0.83

DEthreader

--------------------------------------------------------------------------SELRWDDQQKVKKTAEA------SKKEKDKDSKLEKALKAQNDLIWNIKDELKKVCSTNDLKELLIFNKQQVPSGESAILDRVADGMVFGALLPCEECSGQLVFKSDAYYCTGDVTAWTKCMVKTQTPNRKEWVTPKEF--RE-ISYKKVKKQDRIFPP---------

(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	0.7745

(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	4opxA	0.91	0.68	1.000	0.917	model1_4opxA.pdb.gz
2	2riqA	0.47	1.64	0.851	0.492	model1_2riqA.pdb.gz
3	1y7912	0.44	5.51	0.067	0.715	model1_1y7912.pdb.gz
4	4ka7A	0.44	5.47	0.050	0.719	model1_4ka7A.pdb.gz
5	1l5jA	0.44	6.33	0.060	0.793	model1_1l5jA.pdb.gz
6	3sksA	0.41	5.85	0.036	0.678	model1_3sksA.pdb.gz
7	2o36A	0.40	6.06	0.039	0.707	model1_2o36A.pdb.gz
8	1g5aA	0.39	6.37	0.027	0.715	model1_1g5aA.pdb.gz
9	2qo3B1	0.37	6.22	0.035	0.669	model1_2qo3B1.pdb.gz
10	1c96A	0.36	6.55	0.064	0.686	model1_1c96A.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	1.00	catalytic activity
GO:0003909	0.98	DNA ligase activity
GO:0003910	0.97	DNA ligase (ATP) activity
GO:0016740	0.62	transferase activity
GO:1901363	0.60	heterocyclic compound binding
GO:0097159	0.60	organic cyclic compound binding
GO:0003950	0.59	NAD+ ADP-ribosyltransferase activity
GO:0003676	0.59	nucleic acid binding
GO:0047485	0.57	protein N-terminus binding
GO:0044822	0.57	poly(A) RNA binding
GO:0042802	0.57	identical protein binding
GO:0019901	0.57	protein kinase binding
GO:0008134	0.57	transcription factor binding
GO:0003677	0.57	DNA binding
GO:0070412	0.55	R-SMAD binding
GO:0051287	0.55	NAD binding
GO:0042826	0.55	histone deacetylase binding
GO:0008270	0.54	zinc ion 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:0043170	1.00	macromolecule metabolic process
GO:0006139	1.00	nucleobase-containing compound metabolic process
GO:0006259	0.99	DNA metabolic process
GO:0051103	0.95	DNA ligation involved in DNA repair
GO:0006273	0.95	lagging strand elongation
GO:0044763	0.63	single-organism cellular process
GO:0044710	0.63	single-organism metabolic process
GO:0006281	0.63	DNA repair
GO:0065007	0.62	biological regulation
GO:0006471	0.62	protein ADP-ribosylation
GO:0006302	0.62	double-strand break repair
GO:0048583	0.61	regulation of response to stimulus
GO:0048518	0.61	positive regulation of biological process
GO:0070212	0.59	protein poly-ADP-ribosylation
GO:0065008	0.59	regulation of biological quality
GO:0060255	0.59	regulation of macromolecule metabolic process
GO:0019219	0.59	regulation of nucleobase-containing compound metabolic process
GO:0010613	0.59	positive regulation of cardiac muscle hypertrophy
GO:1903827	0.58	regulation of cellular protein localization
GO:1901700	0.58	response to oxygen-containing compound
GO:0051128	0.58	regulation of cellular component organization
GO:0051052	0.58	regulation of DNA metabolic process
GO:0009725	0.58	response to hormone
GO:1904357	0.57	negative regulation of telomere maintenance via telomere lengthening
GO:0051276	0.57	chromosome organization
GO:0048522	0.57	positive regulation of cellular process
GO:0043504	0.57	mitochondrial DNA repair
GO:0043254	0.57	regulation of protein complex assembly
GO:0034599	0.57	cellular response to oxidative stress
GO:0032869	0.57	cellular response to insulin stimulus
GO:0006357	0.57	regulation of transcription from RNA polymerase II promoter
GO:2000113	0.56	negative regulation of cellular macromolecule biosynthetic process
GO:1900182	0.56	positive regulation of protein localization to nucleus
GO:0048869	0.56	cellular developmental process
GO:0048584	0.56	positive regulation of response to stimulus
GO:0045935	0.56	positive regulation of nucleobase-containing compound metabolic process
GO:0031328	0.56	positive regulation of cellular biosynthetic process
GO:0010604	0.56	positive regulation of macromolecule metabolic process
GO:0006289	0.56	nucleotide-excision repair
GO:0000724	0.56	double-strand break repair via homologous recombination
GO:2000679	0.55	positive regulation of transcription regulatory region DNA binding
GO:0070911	0.55	global genome nucleotide-excision repair
GO:0060391	0.55	positive regulation of SMAD protein import into nucleus
GO:0045944	0.55	positive regulation of transcription from RNA polymerase II promoter
GO:0042769	0.55	DNA damage response, detection of DNA damage
GO:0030225	0.55	macrophage differentiation
GO:0023019	0.55	signal transduction involved in regulation of gene expression
GO:0016925	0.55	protein sumoylation
GO:0016540	0.55	protein autoprocessing
GO:0007179	0.55	transforming growth factor beta receptor signaling pathway
GO:0006296	0.55	nucleotide-excision repair, DNA incision, 5'-to lesion
GO:0006295	0.55	nucleotide-excision repair, DNA incision, 3'-to lesion
GO:0006294	0.55	nucleotide-excision repair, preincision complex assembly
GO:0006293	0.55	nucleotide-excision repair, preincision complex stabilization
GO:0000717	0.55	nucleotide-excision repair, DNA duplex unwinding
GO:0000715	0.55	nucleotide-excision repair, DNA damage recognition
GO:0000122	0.55	negative regulation of transcription from RNA polymerase II promoter

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:0005737	0.83	cytoplasm

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	2ckjA	0.333	6.19	0.021	0.587	1.17.1.4 1.17.3.2	NA
2	0.060	1uwkA	0.401	5.57	0.086	0.645	4.2.1.49	NA
3	0.060	1w07B	0.401	6.30	0.050	0.703	1.3.3.6	NA
4	0.060	2etfB	0.401	5.65	0.070	0.653	3.4.24.69	NA
5	0.060	3b9jJ	0.300	6.21	0.021	0.537	1.17.1.4 1.17.3.2	162

	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	0.57	2riqA	0.469	1.64	0.851	0.492	1.90	ZN	complex1.pdb.gz	169,172,185,195
2	0.01	3eubS	0.248	5.71	0.054	0.417	0.62	FES	complex2.pdb.gz	172,186,187,188,189,195
3	0.01	2ckjC	0.361	6.05	0.021	0.645	0.66	FES	complex3.pdb.gz	172,173,174,188,189,190
4	0.01	2ckjD	0.411	5.99	0.042	0.703	0.62	FES	complex4.pdb.gz	172,173,175,185,186

	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.