D-I-TASSER results for Q96G01-D2

Input Sequence in FASTA format

>Q96G01 (261 residues)
EYKFREARLLQDYTELEEENITLQKLVSTLKQNQVEYEGLKHEIKRFEEETVLLNSQLED
AIRLKEIAEHQLEEALETLKNEREQKNNLRKELSQYISLNDNHISISVDGLKFAEDGSEP
NNDDKMNGHIHGPLVKLNGDYRTPTLRKGESLNPVSDLFSELNISEIQKLKQQLMQVERE
KAILLANLQESQTQLEHTKGALTEQHERVHRLTEHVNAMRGLQSSKELKAELDGEKGRDS
GEEAHDYEVDINGLEILECKY

Predicted Secondary Structure

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Sequence
EYKFREARLLQDYTELEEENITLQKLVSTLKQNQVEYEGLKHEIKRFEEETVLLNSQLEDAIRLKEIAEHQLEEALETLKNEREQKNNLRKELSQYISLNDNHISISVDGLKFAEDGSEPNNDDKMNGHIHGPLVKLNGDYRTPTLRKGESLNPVSDLFSELNISEIQKLKQQLMQVEREKAILLANLQESQTQLEHTKGALTEQHERVHRLTEHVNAMRGLQSSKELKAELDGEKGRDSGEEAHDYEVDINGLEILECKY
Prediction
CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCC
Confidence
757999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999702257888678999987664223226787666656788633465401101122111033589985589999999999999989999999999999999999999999999999999999999988776889999987888751334799986011277775049

H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

                  20                  40                  60                  80                 100                 120                 140                 160                 180                 200                 220                 240                 260
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Sequence
EYKFREARLLQDYTELEEENITLQKLVSTLKQNQVEYEGLKHEIKRFEEETVLLNSQLEDAIRLKEIAEHQLEEALETLKNEREQKNNLRKELSQYISLNDNHISISVDGLKFAEDGSEPNNDDKMNGHIHGPLVKLNGDYRTPTLRKGESLNPVSDLFSELNISEIQKLKQQLMQVEREKAILLANLQESQTQLEHTKGALTEQHERVHRLTEHVNAMRGLQSSKELKAELDGEKGRDSGEEAHDYEVDINGLEILECKY
Prediction
846432540365255056534514531551463334255244425414541541454154044146334541551165045235434423520563354634424343641444455455455543554554515435543545445557454424301421335315504520461554355146515522541453464155245425504640540454555553545355554555565244142427434224158

Values range from 0 (buried residue) to 8 (highly exposed residue)

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

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 AttentionPotential. 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                 260                    |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |
							SS	CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCC
							Seq	EYKFREARLLQDYTELEEENITLQKLVSTLKQNQVEYEGLKHEIKRFEEETVLLNSQLEDAIRLKEIAEHQLEEALETLKNEREQKNNLRKELSQYISLNDNHISISVDGLKFAEDGSEPNNDDKMNGHIHGPLVKLNGDYRTPTLRKGESLNPVSDLFSELNISEIQKLKQQLMQVEREKAILLANLQESQTQLEHTKGALTEQHERVHRLTEHVNAMRGLQSSKELKAELDGEKGRDSGEEAHDYEVDINGLEILECKY
1	2tmaA	0.12	0.09	3.28	1.06	FFAS-3D		DAQEKLELAEKKATDAEADVASLNRRIQLVEEEQERLATALQKLEEAEKAADESERGMKVIESRAQKDEEKMEIQEIQLKEAKHIAEDADRKYEEV----------------------------------ARKLVIIESDLERAEERAELSEGKCAELEEEIKTNNLKSLEAQAEKYSQKEDKYEEEIKVLSDKLKEAETRAEFAERSVTKLEKSIDDLEELYAQKLKYKAISEELDHALND-------------------
2	6yvuB	0.10	0.10	3.67	1.22	SPARKS-K		SSNKDLEDEKMKFQESLKKVDEIKAQRKEIKDRISSCSSKEKTLVLERRELEGTRVSLEERTKNLVSKMEKAEKTLKSTKHSISEAENMLEELRGQQTEEIKDLTQLLEKERSILDDIKLSLKDKT-----KNISAEIIRHEKELEPWDLQLQEKESQIQLAEEETQAKLKKNVETLEEKILAKKTHKQELQDLILDLKKKLNSLKDERSQGEKNFTSAHLKLKEMQKVLNAHRQRAMEARSSLSKAQNKSKVLTALSRLQ
3	5nnvA	0.10	0.08	3.15	1.19	MUSTER		EELAESSAISAKEAKIEDTRDKIQALDESVDELQQVLLVTSEELEKLEGRKEVLKERKKNAVQNQEQLEEAIVQFQQKETVLKEELSKQEAVFETL----QAEVKQLRAQVKEKQQLSNELTE------LKIAAAKKEQACKGEEDNLARLKKELTET-----ELALKEAKEDLSFLTSE-SSSTSGEEKLEEAAKHKLNDKTKTIELIALRRDQRIKLQHGLDTYERELKEKRLYKQKTTLL------------------
4	4rsiB	0.09	0.09	3.38	0.46	CEthreader		TLEEKILAKKTHKQELQDLILDLKKKLNSLKDERSQGEKNFTSAHLKLKEMQKVLNAHRQRAMEARSSLSKAQNKSKVLTALSRLQKRINGFHGRLGDLGVIISTPENVPRLFDTLVAQNLKQANNVAYGKKRFRVVTVDGKLIDISGTMSGGGNHVAKGLMKLKVDDYTPEEVDKIERELSERENNFRVASDTVHEMEEELKKLRDHEPDLESQISKAEMEADSLASELTLAEQQVKEAEMAYVKAVSDKAQLNVVMKNL
5	7ko4P	0.08	0.08	3.07	0.73	EigenThreader		ALDRAEQAEADKKAAEDRSKQLEDELVSLQKKLKGTEDELDKYSEALKDAQEKLELAEKKATDAEADVASLNRRIQLVEEELDRAQERLATALQKLEEAEKAADESERGMKVIESRAQKDEEKMEIQEIQLKEAKHIAEDADRKYEEVARKLVIIESDLERAEERAELSEGKCAELEEELKTVTNNLKSLEAQAEKYSQKEDRYEEEIKVLSDKLKEAETRAEFAERSVTKLEKSIDDLEDELYAQKLKYKAISEELDHAL
6	5xg2A	0.20	0.14	4.53	1.03	FFAS-3D		--KGAIVRWGKRKEKLIEEIRAREEERNALVVRLGEIDRTEARIKRAEEEKERLKAEILTGEARLPGLRERAENLRRLVEEKRAEISELERRLSSI----------------------------------TSQSFELRIK--------------LSDLEKELELKDLEKVLAEERAVREEIEVAKRRINELDTLIERERGELAKLRGRIERLERKRDKLKKALENPEARELTEK---------------------------
7	6yvuA	0.11	0.10	3.78	1.18	SPARKS-K		ERIVVSYEYYNIKHKHTSIRETLENGETRMKMLNEFVKKTSEEIDSLNEDVEEIKLQKEKKENGLLNEISRLKTSLSIKVENLNDTTEKSKALESEIASSSAKLIEKKSAYANTEKDYKMVQEQLSKQRDLYKRKEELVS----TLADGGYNAQLAKAKTELNSMKMELLKKELLTIEPKLKEATKDNELNVKHVKQCQETCDKLRARLVEYPSRIKDLKQREDKLKSHYYQTCKNSEYLKRRVTNLEFNYTKPYPNFEAS
8	2tmaA	0.14	0.13	4.32	0.85	CNFpred		RSKQLEDELVSLQKKLKGTEDELDKYSEALKDAQEKLELAEKKATDAEADVASLNRRIQLVEEELDRAQERLATALQKLEEAEKAADESERGMKVIESR-AQKDEEKMEIQEIQLKEAKHIAEDADRKYEARKLVIIESDLERAEERAELSEGKCAELEEEIVTNNLKSLEAQAEKYSQKEDKYEEEIKVLSDKLKEAETRAEFAERSVTKLEKSIDDLEDELYAQKL------------------------KYKAISEEL
9	1sjjA	0.05	0.03	1.43	0.67	DEthreader		------------------------------KMRVHKISNVNKALDFIASKVLAVNQENEQLMEDYEALEKMVSDINNAWGGLEQAEKGY----------------------------------------------------------TYHVNAGTNTITPINGKWEHVRQLVPRRDQALMEEHARQQQNERLRKQFGAQANVIGPWIQTKMEEIGRISIEMHGTLR-AKGISQQMNESTTDTADQ----------------
10	6qajA	0.06	0.06	2.66	0.74	MapAlign		AAKSELDKAIITKDEAEKLFNQDVDAAVRGILRRCALINMVFQMETGVTNSLRMLQWDEAAVNLIWYNQTPNRAKRVITTFRTDAYAAEALELLEHCGVCRERLRPEREPRLLPCLHSATVYCNVHKHEPLVLFCESCDTLTCRDCQLNAHKDHQYQFLEDAVRNQRKLLASLVKRLGDKHATLQKSTKEVRSSIRQVSDVQKRVQVDVKMAILQIMKELNKRGRVLVNDAQKVTEGQQERLERQHWTMTKIQKHQEHILR


(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

Rank^a	Estimated TM-score^b
1	0.3676


(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 AttentionPotential, 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.
1	6z9lA	0.67	3.64	0.069	0.808
2	5nnvA	0.65	4.35	0.079	0.824
3	5xg2A	0.64	4.51	0.126	0.816
4	6yvuB	0.62	4.68	0.081	0.824
5	1ciiA	0.61	3.87	0.071	0.782
6	6yvuA	0.58	4.62	0.100	0.812
7	2w6dA	0.58	4.32	0.057	0.793
8	4tkoB	0.57	3.64	0.096	0.705
9	6ewyA	0.56	3.87	0.080	0.701
10	6ek7A	0.55	3.91	0.061	0.705



(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:0017137	0.76	Rab GTPase binding
GO:0045502	0.62	dynein binding
GO:0031871	0.59	proteinase activated receptor binding
GO:1901363	0.53	heterocyclic compound binding
GO:0097159	0.53	organic cyclic compound binding






(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:

Biological Process (BP)


GO term	Cscore^GO	Name
GO:0009987	0.88	cellular process
GO:0044699	0.83	single-organism process
GO:0044763	0.81	single-organism cellular process
GO:0065007	0.79	biological regulation
GO:0051234	0.79	establishment of localization
GO:0016043	0.79	cellular component organization
GO:0050794	0.78	regulation of cellular process
GO:0006996	0.78	organelle organization
GO:0006810	0.78	transport
GO:1902589	0.77	single-organism organelle organization
GO:0051649	0.77	establishment of localization in cell
GO:0051640	0.77	organelle localization
GO:0007017	0.77	microtubule-based process
GO:0051656	0.76	establishment of organelle localization
GO:0000226	0.76	microtubule cytoskeleton organization
GO:0006928	0.70	movement of cell or subcellular component
GO:0046907	0.69	intracellular transport
GO:0044765	0.69	single-organism transport
GO:0007018	0.69	microtubule-based movement
GO:0072393	0.68	microtubule anchoring at microtubule organizing center
GO:0072385	0.68	minus-end-directed organelle transport along microtubule
GO:0023051	0.67	regulation of signaling
GO:0010646	0.67	regulation of cell communication
GO:0048523	0.61	negative regulation of cellular process
GO:1900737	0.59	negative regulation of phospholipase C-activating G-protein coupled receptor signaling pathway
GO:0051128	0.54	regulation of cellular component organization
GO:0048518	0.52	positive regulation of biological process
GO:0048522	0.51	positive regulation of cellular process
GO:0033036	0.51	macromolecule localization






(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:

Cellular Component (CC)


GO term	Cscore^GO	Name
GO:0044444	1.00	cytoplasmic part
GO:0016020	1.00	membrane
GO:0043229	0.92	intracellular organelle
GO:0043231	0.91	intracellular membrane-bounded organelle
GO:0031410	0.90	cytoplasmic vesicle
GO:0005794	0.90	Golgi apparatus
GO:0044446	0.78	intracellular organelle part
GO:0005829	0.66	cytosol
GO:0044430	0.64	cytoskeletal part
GO:0099513	0.60	polymeric cytoskeletal fiber
GO:0005874	0.59	microtubule
GO:0044431	0.54	Golgi apparatus part
GO:0048471	0.53	perinuclear region of cytoplasm
GO:0072517	0.52	host cell viral assembly compartment
GO:0005881	0.52	cytoplasmic microtubule
GO:0005802	0.52	trans-Golgi network
GO:0005737	0.51	cytoplasm






(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:

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	3ffzA	0.320	5.24	0.043	0.479	3.4.24.69	NA
2	0.060	3a1cB	0.192	5.37	0.082	0.295	3.6.3.-	NA
3	0.060	3b8eA	0.387	5.48	0.040	0.609	3.6.3.9	NA
4	0.060	1w27A	0.368	4.24	0.083	0.483	4.3.1.24	NA
5	0.060	1p49A	0.337	4.73	0.070	0.467	3.1.6.2	NA



(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	Predicted binding site residues
1	0.01	2hdi1	0.167	4.59	0.080	0.230	0.25	III	76,77,78,79,146,150,152,153,156
2	0.01	1h8bA	0.127	3.43	0.044	0.157	0.33	III	106,110,111,113,119,120,128,140



(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.

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.