D-I-TASSER results for A6NCK2-D1

Input Sequence in FASTA format

>A6NCK2 (100 residues)
MDSDFSHAFQKELTCVICLNYLVDPVTICCGHSFCRPCLCLSWEEAQSPANCPACREPSP
KMDFKTNILLKNLVTIARKASLWQFLSSEKQICGTHRQTK

Predicted Secondary Structure

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Sequence
MDSDFSHAFQKELTCVICLNYLVDPVTICCGHSFCRPCLCLSWEEAQSPANCPACREPSPKMDFKTNILLKNLVTIARKASLWQFLSSEKQICGTHRQTK
Prediction
CCCHHHHHHHHHCSCHHHHHHCCCCCSCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCSCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCHHHHHCCCC
Confidence
9631788969813175353452697224899713599998999823886359988637257679834699999999999654434553222125237779

H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

                  20                  40                  60                  80                 100
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Sequence
MDSDFSHAFQKELTCVICLNYLVDPVTICCGHSFCRPCLCLSWEEAQSPANCPACREPSPKMDFKTNILLKNLVTIARKASLWQFLSSEKQICGTHRQTK
Prediction
7556436404730331003130432132432231035104413675754241330354154771430320240043037354564576656337546658

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                    |                   |                   |                   |                   |
							SS	CCCHHHHHHHHHCSCHHHHHHCCCCCSCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCSCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCHHHHHCCCC
							Seq	MDSDFSHAFQKELTCVICLNYLVDPVTICCGHSFCRPCLCLSWEEAQSPANCPACREPSPKMDFKTNILLKNLVTIARKASLWQFLSSEKQICGTHRQTK
1	4wz3B	0.20	0.18	5.78	1.33	DEthreader		--ANLSHPTTPTLTCPIDSGFLKDPVITPEGFVYNKSSILKWLE-T--KKEDPQSRKPLTAKDLQPFPELLIIVNRFVETQTNYEKLKNRLVQARVA---
2	7jzvA1	0.24	0.22	6.86	2.05	SPARKS-K		-ALRVEEVQNKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQESTRFSQLVEELLKIICAFQLDTGLEYA-------
3	5vo0D	0.19	0.19	6.11	0.89	MapAlign		GYDVEFDPPLSKYECPICLMGLRSAVQTPCGHRFCDSCIRKSIRDT--GQKCPVDNEVLLEEQLFPDNFAKREILSLMELRQLEKHLSATAPCPQCQESV
4	7bbdB	0.32	0.26	7.83	0.61	CEthreader		ASAARLTMMWEEVTCPICLDPFVEPVSIECGHSFCQECISQVG--KGGGSVCPVCRQRFLLKNLRPNRQLANMVNNLKEISQE-----------------
5	5olmA	0.31	0.28	8.47	1.60	MUSTER		ASAARLTMMWEEVTCPICLDPFVEPVSIECGHSFCQECISQVGKS-----VCPVCRQRFLLKNLRPNRQLANMVNNLKEISQEAR----GERCAVHGERL
6	2c2lA	0.13	0.11	3.82	1.30	HHsearch		DEKRKKRDIPDYLCGKISFELMREPCITPSGITYDRKDIEEHLQRV--GHFNPVTRSPLTQEQLIPNLAMKEVIDAFISENGWVEDY-------------
7	6yxeA	0.26	0.21	6.47	1.52	FFAS-3D		-SKVVIQDITMELHCPLCNDWFRDPLMLSCGHNFCEACIQDFWRLQAKETFCPECKMLCQYNNCTFNPVLDKLVEKIKKLP-------------------
8	7l3lA	0.18	0.18	5.85	1.17	EigenThreader		IEYQFVERLEERYKCAFCHSVLHNPHQTGCGHRFCQHCILSLREL-NTVPICPVDKEVIKSQEVFKDNCCKREVLNLYVYCSNAPGCREPVLRKDLKEHL
9	5olmA	0.31	0.28	8.47	1.74	CNFpred		ASAARLTMMWEEVTCPICLDPFVEPVSIECGHSFCQECISQVGK-----SVCPVCRQRFLLKNLRPNRQLANMVNNLKEISQEAR----GERCAVHGERL
10	1jm7A	0.27	0.24	7.38	1.33	DEthreader		EVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQESTRFSQLVEELLKIICAFQLDTG-L---------


(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	0.8187


(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	1jm7A	0.81	1.77	0.255	0.940
2	7jzvA	0.80	2.25	0.250	0.960
3	5olmA	0.77	2.12	0.289	0.890
4	2y43A	0.75	1.75	0.238	0.840
5	7bbdB	0.74	1.39	0.333	0.810
6	4epoG	0.71	1.91	0.247	0.810
7	4wz3B	0.71	2.54	0.165	0.850
8	6yxeA	0.71	1.88	0.262	0.830
9	2c2lA	0.71	1.90	0.122	0.820
10	3lrqA	0.70	1.63	0.190	0.790



(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	0.93	catalytic activity
GO:0004842	0.86	ubiquitin-protein transferase activity
GO:0043167	0.71	ion binding
GO:0046872	0.70	metal ion binding
GO:0008270	0.69	zinc ion binding
GO:1901363	0.57	heterocyclic compound binding
GO:0097159	0.57	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	0.96	cellular process
GO:0008152	0.91	metabolic process
GO:0071704	0.90	organic substance metabolic process
GO:0044238	0.90	primary metabolic process
GO:0044237	0.90	cellular metabolic process
GO:0043170	0.89	macromolecule metabolic process
GO:0044260	0.88	cellular macromolecule metabolic process
GO:0065007	0.86	biological regulation
GO:0050789	0.86	regulation of biological process
GO:0019538	0.85	protein metabolic process
GO:0050794	0.84	regulation of cellular process
GO:0006464	0.80	cellular protein modification process
GO:0070647	0.78	protein modification by small protein conjugation or removal
GO:0016567	0.77	protein ubiquitination
GO:0019222	0.74	regulation of metabolic process
GO:0060255	0.73	regulation of macromolecule metabolic process
GO:0031323	0.72	regulation of cellular metabolic process
GO:0080090	0.71	regulation of primary metabolic process
GO:0044699	0.69	single-organism process
GO:0048518	0.68	positive regulation of biological process
GO:0010468	0.68	regulation of gene expression
GO:0019219	0.66	regulation of nucleobase-containing compound metabolic process
GO:2001141	0.65	regulation of RNA biosynthetic process
GO:0006355	0.64	regulation of transcription, DNA-templated
GO:0048522	0.62	positive regulation of cellular process
GO:0000209	0.61	protein polyubiquitination
GO:0044763	0.59	single-organism cellular process
GO:0048519	0.58	negative regulation of biological process
GO:0048523	0.57	negative regulation of cellular process
GO:0016043	0.57	cellular component organization
GO:0031325	0.56	positive regulation of cellular metabolic process
GO:0010604	0.56	positive regulation of macromolecule metabolic process
GO:0065009	0.55	regulation of molecular function
GO:0051246	0.54	regulation of protein metabolic process
GO:0050896	0.54	response to stimulus
GO:0051091	0.53	positive regulation of sequence-specific DNA binding transcription factor activity
GO:0032268	0.53	regulation of cellular protein metabolic process
GO:0070534	0.52	protein K63-linked ubiquitination
GO:0051247	0.52	positive regulation of protein metabolic process
GO:0051092	0.51	positive regulation of NF-kappaB transcription factor activity
GO:0043933	0.51	macromolecular complex subunit organization
GO:0032502	0.51	developmental process
GO:0032270	0.51	positive regulation of cellular protein metabolic process
GO:0006950	0.51	response to stress
GO:0051865	0.50	protein autoubiquitination
GO:0048583	0.50	regulation of response to stimulus






(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	1.00	intracellular part
GO:0043226	0.91	organelle
GO:0043229	0.90	intracellular organelle
GO:0043227	0.87	membrane-bounded organelle
GO:0043231	0.85	intracellular membrane-bounded organelle
GO:0044446	0.82	intracellular organelle part
GO:0005634	0.81	nucleus
GO:0032991	0.77	macromolecular complex
GO:0005737	0.68	cytoplasm
GO:0044428	0.66	nuclear part
GO:0044444	0.65	cytoplasmic part
GO:0043234	0.56	protein complex






(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	0.067	3eb6A	0.495	1.91	0.250	0.590	6.3.2.19	NA
2	0.060	2iz1B	0.505	3.57	0.036	0.810	1.1.1.44	NA
3	0.060	1knpA	0.488	4.59	0.043	0.930	1.4.3.16	NA
4	0.060	1x1nA	0.495	3.75	0.049	0.770	2.4.1.25	NA
5	0.060	1xl7A	0.505	3.73	0.048	0.810	2.3.1.137	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	0.35	2ecwA	0.571	2.04	0.375	0.680	0.90	ZN	28,31,52,55
2	0.05	2ckl0	0.677	1.98	0.262	0.780	0.86	III	6,7,8,9,10,12,14,18,20,21,23,26,27,29,31,32,35,36,37,42,63,64,65,66,68,72,75,76,77,78



(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.