D-I-TASSER Q8N9Z2-D1

D-I-TASSER results for Q8N9Z2-D1

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

Input Sequence in FASTA format

>Q8N9Z2 (235 residues)
MRRSMKRRRRRRPVAPATAARGGDFRAEDGAGLEAREEKVVYSRSQLSLADSTKALGDAF
KLFMPRSTEFMSSDAELWSFLCSLKHQFSPHILRSKDVYGYSSCRALVPDPPGPPTARGQ
ARRPVPRAAARRRRRGARAAAARRRKPRPPPPPPPPPEESCPAKPVAPGPCFGGRTLEEI
WRAATPTLTTFPTIRVGSDVWGERSLAAARRRARQVLRVNLEPMVRLRRFPVPRA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MRRSMKRRRRRRPVAPATAARGGDFRAEDGAGLEAREEKVVYSRSQLSLADSTKALGDAFKLFMPRSTEFMSSDAELWSFLCSLKHQFSPHILRSKDVYGYSSCRALVPDPPGPPTARGQARRPVPRAAARRRRRGARAAAARRRKPRPPPPPPPPPEESCPAKPVAPGPCFGGRTLEEIWRAATPTLTTFPTIRVGSDVWGERSLAAARRRARQVLRVNLEPMVRLRRFPVPRA
Prediction	CCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHCCCSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCCCCC
Confidence	9403455412688886421257875457776542035555444654201322479999999848454334312899999999988627853752365233222346889999998888888899999887787887765557789999999999886567888889888787897601022335777566742664133321334799999974443678477543323799999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MRRSMKRRRRRRPVAPATAARGGDFRAEDGAGLEAREEKVVYSRSQLSLADSTKALGDAFKLFMPRSTEFMSSDAELWSFLCSLKHQFSPHILRSKDVYGYSSCRALVPDPPGPPTARGQARRPVPRAAARRRRRGARAAAARRRKPRPPPPPPPPPEESCPAKPVAPGPCFGGRTLEEIWRAATPTLTTFPTIRVGSDVWGERSLAAARRRARQVLRVNLEPMVRLRRFPVPRA
Prediction	7555355447444434243343341436634415345441223234034354451024004102433551453443013103403752423114343122143044435744537655445654555455465544444454544445445454466565466544354134462435433434435144221130234124534144035304521504162034047253668
	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

CCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHCCCSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCCCCC
MRRSMKRRRRRRPVAPATAARGGDFRAEDGAGLEAREEKVVYSRSQLSLADSTKALGDAFKLFMPRSTEFMSSDAELWSFLCSLKHQFSPHILRSKDVYGYSSCRALVPDPPGPPTARGQARRPVPRAAARRRRRGARAAAARRRKPRPPPPPPPPPEESCPAKPVAPGPCFGGRTLEEIWRAATPTLTTFPTIRVGSDVWGERSLAAARRRARQVLRVNLEPMVRLRRFPVPRA

4hdjA

0.07

2.84

0.48

CEthreader

DVLWKKDLERPVSGGVGVGYGLVLVGVLSAPATNGDVVVVQTQDDKLIGLDAASGDQRWIYESTVPVLTLRGTGAPLIAGNMALAGLASGKVVAVDVQRGLPIWEQRVAIPQGRSELDRVVDIDGGLLLSGDTLYVVSYQGRAAALDVNSGRLLWQREASSYVGVAEGFGNIYVSQASGSVEGLDSRGASSLWNNDALARRQLSAPAVFSSNVVVGDLEGYVHLLSQVDGRFVGR

1ryxA

0.10

0.09

3.51

0.50

EigenThreader

TYLDCIKAIANNEADLDGGQAFEAGLAPYKLKPIAAEVYKTSCHTGLGRSAGWNIPIGTLLHRGAIEWEGIESGSVEQAVAK-----FFSASCVPGATIEQKLCRQKDEYELLCLDGSRQPVDNYKTCNWDIWSFLSKAQSDFGENRIQWCAVGKDEKSKCDRWSTAVGRTAGWVIPMGLIHNRTGTCDEYFSEGCAPGSEKYFGYTGALRCLVEKGDVALQMDDFELLCTDGRR

5x6oG

0.10

0.09

3.46

0.43

FFAS-3D

-RFTQIPPSSAATQIPTTLEVTTTTLNNKQSKNDNQVNQLNKAQGEASMLRDNIEREKEKNIQAVKVNELVKHLQELAKLKQELQKKFLQRGKSKREVITNVKPPSTTLNTITPDSSSVAIEAKPQSPQSKKRKISDNLLKKNMVPLNPNRIIPDETSLFLESILLHQIIGADLSTIEILNRLKLDYITKFKNFVIAKGAPIGKSIVSLLLRCKKTLTLD---------------

7abir

0.11

3.98

0.71

SPARKS-K

RLWISVARYHIEVNRVPALIEGVDQPIVKTATITEPRTSVIKIAVEPVNPSELPKMLDGLRKVNKSYPSLTTKVEELDCVMHDLRKMYSPVVAETPNKKNKITMIAE-PLEKGLENEVVQITWNRKKLGEFFQTKYDWDLLAARSIWAFGPDATGPNIDTLPSEVDKALLGSVKDSIVQGFQWGTRELCDELIRNVKFKILDIPTARRVVYSAFLMATRLMEPYYFVEVQAPADC

6wvsA

0.19

0.09

2.74

0.58

CNFpred

---------------------------------------IAVVSD------DWRILQEALDILIVNAT----DVDEMLKQVEILRRLGKQIAVVSDDWRILQ-GDILIVNA---------------------------------------------------------------TDVDEMLKQVE-ILRGAKQIAVVSD--DWRILQEALKKGGDILIVN---------------

2w6dA

0.09

0.06

2.45

0.67

DEthreader

----------------------VAT-RF----------LIGENL-LPSTAFKYKYTVVEYPLLLIEIV-ELGYVNNCHAI-LFVMRFLVNAW--------L--RLKNQADLD--G--KFMDSNTLTRERAIALR-VR-ARCNRVAIPLEQEKRIVEEFNKLGIEFKEINT-DTQARTISESFRSVLGIAV-ILGPFALGLGVGFLQADQARREL-VK---K------LQVAEQQV

4hdjA

0.09

3.23

0.79

MapAlign

-----LEPAVDGSTIYAASAEGRVMAIQRETGDVLWKKDLERPVSGGVGVGYGLVLVGTDVIALDEATGKKKWTKRVNSEVVVVVQTQDDKLIGLDAASGDQRWIYESTVPVLTLRGTGAPLIAGNMALAGLASGKVVAVDVQRGLPIWEQRVAIPQGRSELDRVVDIDGGLLLSGDTLYLARRQLSAPAVFSSNVVVGDLEGYVHLLPLMYVFGNGGKLVAYTI----------

6etxG

0.11

3.86

0.56

MUSTER

ISKFIYRHGQIRVFNHSRDRWLRVLSPFALFHRKGINEESCFSFLRFIDISPAEMANLMLQGLLARWLALFL-SLKASYRLHQLRSWGAPEYLRNKDFLLGVNFPLSFPNLCSCPKSLVFSSHCKAVSGYSDQVVHQRRSATSSLRRCLLTELPSFLCVASPRVTAVPLDSYCNDRSAEYERRVLKEGGSLAAKQCLLNG-APELAADWLNRRSQFFPEPAGGLWSIRPQNGWSF

2pffA1

0.16

0.13

4.26

0.90

HHsearch

IGAEVLQGLLQGKVVVTTSRFSKQVTDYYQSIYAKGSTLIVVPFNQGSKQD----VEALIEFIYDTIIPFADSKSELRMMGCV-KKQKSARGIETRP------AQVILPMSPNHGTFGGDG-MYSESKLSLETLF-------NRW----------------HSESWANQLTVCGAIIGWTR--GT-GLMSANNIIAEMGVRTFSQMAFN------LLGLLTPEVVELCQKSPVMA

3p1lA

0.06

2.61

0.44

CEthreader

AEKDGWFSKEPALLSGGVTVSGGHVYIGSEKAVAGEALSRPVVSDGLVLIHTSNGQLQALNEADGAVKWTVNLDMPSLSLRGESAPTTAFGAAVVGGDNGRVSAVLMEQGQMIWQQRISQATGSTEIDRLSDVDTTPVVVNGVDLRSGQIMWKRELGSVNDFIVDGNRIYLVDQNDRVMALTIDGGVTLWTQSDLLHRLLTSYNGNLVVGDSEGYLHWINVEDGRFVAQQKVDSS

(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	0.4303

(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	2wj2A	0.42	5.66	0.048	0.706	model1_2wj2A.pdb.gz
2	2q1fA2	0.42	6.14	0.049	0.749	model1_2q1fA2.pdb.gz
3	1wygA	0.42	6.42	0.031	0.774	model1_1wygA.pdb.gz
4	1jroB	0.41	6.50	0.049	0.774	model1_1jroB.pdb.gz
5	2qf7A	0.41	5.93	0.027	0.715	model1_2qf7A.pdb.gz
6	4eziA	0.41	5.30	0.058	0.664	model1_4eziA.pdb.gz
7	3fahA2	0.41	6.19	0.057	0.753	model1_3fahA2.pdb.gz
8	2veoA	0.41	6.27	0.035	0.745	model1_2veoA.pdb.gz
9	3a1iA	0.39	5.96	0.079	0.685	model1_3a1iA.pdb.gz
10	1t3qB	0.39	6.14	0.039	0.694	model1_1t3qB.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	0.70	catalytic activity
GO:0016879	0.52	ligase activity, forming carbon-nitrogen bonds

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:0065007	0.69	biological regulation
GO:0050789	0.69	regulation of biological process
GO:0050794	0.68	regulation of cellular process
GO:0009987	0.67	cellular process
GO:0007165	0.64	signal transduction
GO:0044699	0.59	single-organism process
GO:0030518	0.59	intracellular steroid hormone receptor signaling pathway
GO:0044763	0.50	single-organism 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:0044464	0.99	cell part
GO:0044424	0.98	intracellular part
GO:0044446	0.76	intracellular organelle part
GO:0016020	0.63	membrane
GO:0032991	0.62	macromolecular complex
GO:0044444	0.61	cytoplasmic part
GO:0044428	0.61	nuclear part
GO:0044451	0.60	nucleoplasm part
GO:0043234	0.60	protein complex
GO:0070847	0.59	core mediator complex
GO:0043226	0.59	organelle
GO:0016592	0.59	mediator complex
GO:0043227	0.58	membrane-bounded organelle
GO:0044425	0.52	membrane 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	1ogyI	0.371	6.07	0.023	0.660	1.7.99.4	NA
2	0.060	1kqfA	0.381	6.06	0.063	0.681	1.2.1.2	NA
3	0.060	2e7zA	0.398	5.88	0.048	0.681	4.2.1.71	NA
4	0.060	2frvD	0.391	6.22	0.066	0.698	1.12.2.1	82
5	0.060	1jroB	0.415	6.50	0.049	0.774	1.1.1.204	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	0.01	3lj7A	0.414	6.07	0.070	0.715	0.66	OHO	complex1.pdb.gz	56,57,98,99,100,101
2	0.01	2ckjD	0.315	6.53	0.034	0.596	0.56	FES	complex2.pdb.gz	48,49,50,53,54,55
3	0.01	1fiqA	0.232	5.53	0.082	0.374	0.68	FES	complex3.pdb.gz	47,48,49,56,57,59,100,103
4	0.01	1v97A	0.350	6.27	0.054	0.643	0.57	CA	complex4.pdb.gz	95,96,97,104
5	0.01	3eubS	0.231	5.58	0.108	0.374	0.68	FES	complex5.pdb.gz	57,58,61,63,101

	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, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. In preparation, 2020.