D-I-TASSER results for Q2M3A8-D1

Input Sequence in FASTA format

>Q2M3A8 (158 residues)
MDLASEITSATQTSSLCSSGRGHAGYPAPGIVAHGFETHGTARVAQGHLLPPCLLPPPQM
PVLAALRDLSRRGSTSSSRSPSRPVSTSASKPCLPASCLGETWSISINLVGSSGHLQSPG
AQRDAQRETGCLGPSWLPHHQGRDEELSLSHSAQGEEF

Predicted Secondary Structure

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Sequence
MDLASEITSATQTSSLCSSGRGHAGYPAPGIVAHGFETHGTARVAQGHLLPPCLLPPPQMPVLAALRDLSRRGSTSSSRSPSRPVSTSASKPCLPASCLGETWSISINLVGSSGHLQSPGAQRDAQRETGCLGPSWLPHHQGRDEELSLSHSAQGEEF
Prediction
CCHHHHCCSCCCHHHHHCCCCCCCCCCCCCSSSSSSSSCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCSCCCCCCCCC
Confidence
96233022001123321147544788876514666675152000267779988899998842778887753389987778999865788999987433586522575034577765682122121112334588789887886665112133434559

H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

                  20                  40                  60                  80                 100                 120                 140
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Sequence
MDLASEITSATQTSSLCSSGRGHAGYPAPGIVAHGFETHGTARVAQGHLLPPCLLPPPQMPVLAALRDLSRRGSTSSSRSPSRPVSTSASKPCLPASCLGETWSISINLVGSSGHLQSPGAQRDAQRETGCLGPSWLPHHQGRDEELSLSHSAQGEEF
Prediction
75225534422434412554514341524212233133433343544442354134446242131334146554454454454425436554433242334424132432455441444234453545330334512454553655231334463665

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                    |                   |                   |                   |                   |                   |                   |
							SS	CCHHHHCCSCCCHHHHHCCCCCCCCCCCCCSSSSSSSSCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCSCCCCCCCCC
							Seq	MDLASEITSATQTSSLCSSGRGHAGYPAPGIVAHGFETHGTARVAQGHLLPPCLLPPPQMPVLAALRDLSRRGSTSSSRSPSRPVSTSASKPCLPASCLGETWSISINLVGSSGHLQSPGAQRDAQRETGCLGPSWLPHHQGRDEELSLSHSAQGEEF
1	3bykA	0.06	0.06	2.71	0.62	CEthreader		FDANDSILKDQTQEWSGSATFTSDGKIRLFYTDFSGKHYGKQTLTTAQVNVSSLNINGVEDYKSIFDGDGKTYQNVQQFIDEGNYSSGDNHTLRAPHYVEDKLVFEANTGTEDGYQGEESLFNKAYYGKSTSFFLQSDKKRTAELANGALGMIELNDD
2	5lj3S	0.05	0.04	2.11	0.55	EigenThreader		WSDMEVAKLVNSFAHWEAAQ---QEYERSSALYQVAIEKNQLLKAGLLDFEKQFNSIEETISYKRKMDYETILSNYDTWWLYLDLISEFPKQIMQTFEKAIVDS----------KFSKIWLMYAKFLIRDVPKARKILGKAIGTFKGYIELEVKLEFD
3	4lj2A1	0.23	0.13	4.17	0.34	FFAS-3D		------------------------------VTTCG-ESHGVGLIVDG--VPPGL----ALTEEDLQKDLDRRKPGTSKFATQRKEPDQVISGVFEGKTTGTPIGLLIRNTDQKSKRDYRGGGRSSARET-----------------------------
4	6ahfC1	0.08	0.08	2.97	0.82	SPARKS-K		-----QFTERALTLAQKLASDHQHPQLQPIHILAAFTPEDGSVPYLQNLIEKGRYDYDLF--KKVVNRNLVRIPQQQPAPAEITPSYALGKVLKIQKQQKDS------FIAQDHILFALFNDSSIQQIFKEAQVDIEAIKQQALELRGNTRIDSRGAD
5	6vcwA	0.14	0.05	1.72	0.47	CNFpred		------------------------------GHMFGYATDET-----PELMPLTHVLA--TKLGAKLTEVRKNKTCAWLRP-------------------DGKTQVTVEYQND----------------------------------------------
6	4zohA1	0.05	0.04	1.79	0.83	DEthreader		TI-SDTLI--NQRV-IA-SPLETRTAFGSGHGRDKKLKF--------ANLGAYANDD-ESGNVKSTVLGYFIERIVNAQYGVSSYIEITPT------------------DVAQAIGGIVQGMAQALLEGFLTTYPIPTA-----IGEGAIATPTIINI
7	3bykA	0.06	0.05	2.22	0.76	MapAlign		WSGSATFTSDGKIRLFYTDFSGKHYGKQTLTTAQVNVSNINGVEDYKSIFDGDGKTYQNSFFRQESQKLLQSDKKKVMKPLIASNTVTDEIERANVFKMNGKWYLFTDSRGSKMTI-----------------------DGITSNDIYMLGYVSNSLT
8	1jvrA	0.12	0.11	3.77	0.52	MUSTER		-----------HMGQIHGLSPTPIPKAPRGL-----STHHWLNFLQAAYRLQPGPSDFDFQQLRRFLKLALK-TPIWLNPIDYSLLASLIPKGYP----GRVVEIINILVKNQVSPSAPAAPVPTPICPTTTPPPPPPPSPEAHVPPPYVEPTTTQCF
9	2pffB	0.19	0.18	5.74	0.54	HHsearch		DSWESFFVSVRKAITVRCYEAYPNTSLPPSILEDTQEQVQNGKQVEISLVNGAVSGPPQS--LYGLNTLRKAKAPSGLDQSRPVASPFHSHLLVPASDLINKNNVSFNAKDIQIPVYDTFDGSDLERIVDCII--RLPVKWETTTQFKATHI---LDF
10	2q4nA	0.07	0.06	2.40	0.56	CEthreader		PPVHPFVAPLSYTWRGQGEGEYPTIPSFRYGEEIRFSHSGKPVIAYTQKTWKLESGAPHAESGYFRP-------------------RPDGSIEVVIAQSTGLVEVQKGTYNVDEQSI---KLKSDLVGNASKVKEISREFELVDGKLSYVVRSTTTNP


(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	0.5277


(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	1ej6A	0.44	5.25	0.038	0.759
2	4pedA	0.44	5.59	0.084	0.791
3	2hc9A2	0.44	5.23	0.079	0.753
4	7d3uA	0.43	5.12	0.052	0.759
5	1ecgB1	0.43	5.12	0.045	0.753
6	1te5A	0.42	4.98	0.094	0.703
7	1gph12	0.40	5.38	0.067	0.734
8	2j6hA1	0.40	5.64	0.038	0.747
9	1gytL2	0.38	5.02	0.048	0.671
10	2ewbA	0.37	5.43	0.038	0.696



(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:0097493	0.76	structural molecule activity conferring elasticity
GO:0051371	0.76	muscle alpha-actinin binding
GO:0051015	0.76	actin filament binding
GO:0008307	0.76	structural constituent of muscle
GO:0046872	0.54	metal ion binding
GO:0003824	0.54	catalytic activity






(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:0055008	0.76	cardiac muscle tissue morphogenesis
GO:0055003	0.76	cardiac myofibril assembly
GO:0048739	0.76	cardiac muscle fiber development
GO:0045214	0.76	sarcomere organization
GO:0030241	0.76	skeletal muscle myosin thick filament assembly
GO:0030240	0.76	skeletal muscle thin filament assembly
GO:0006941	0.76	striated muscle contraction






(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:0044424	0.97	intracellular part
GO:0044444	0.81	cytoplasmic part
GO:0043234	0.78	protein complex
GO:0044446	0.77	intracellular organelle part
GO:0031430	0.76	M band
GO:0030018	0.76	Z disc
GO:0005865	0.76	striated muscle thin filament
GO:0005859	0.76	muscle myosin complex
GO:0005737	0.65	cytoplasm
GO:0005622	0.59	intracellular






(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	2nyfA	0.417	4.88	0.087	0.696	4.3.1.5	NA
2	0.060	2c6fA	0.418	5.02	0.051	0.715	3.4.15.1	NA
3	0.060	1e6yA	0.347	4.79	0.050	0.570	2.8.4.1	NA
4	0.060	2f6dA	0.413	5.12	0.056	0.709	3.2.1.3	64
5	0.060	1h8lA	0.412	5.21	0.047	0.741	3.4.17.22	135



(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	2ojvA	0.421	5.12	0.090	0.741	0.45	UUU	17,20,25



(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.