D-I-TASSER A6NHM9-D3

D-I-TASSER results for A6NHM9-D3

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

Input Sequence in FASTA format

>A6NHM9 (162 residues)
DVLQLGFFTFPIHFIPPGAESFMSYGLCRTEKFEEMNGAPMPDIQVYGYLLHTHLAGRAL
QAVQYRNGTQLRKICKDDSYDFNLQETRDLPSRVEIKPGDELLVECHYQTLDRDSMTFGG
PSTINEMCLIFLFYYPQNNISSCMGYPDIIYVAHELGEEASE

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| DVLQLGFFTFPIHFIPPGAESFMSYGLCRTEKFEEMNGAPMPDIQVYGYLLHTHLAGRALQAVQYRNGTQLRKICKDDSYDFNLQETRDLPSRVEIKPGDELLVECHYQTLDRDSMTFGGPSTINEMCLIFLFYYPQNNISSCMGYPDIIYVAHELGEEASE
Prediction	CSSSSSSCCCCCSSCCCCCCCSSSSSSSCHHHHHHHHCCCCCCSSSSSSSHHHCCCCSSSSSSSSSCCCSSSSSSSCCCCCCCCCCSSSCCCCSSSCCCCSSSSSSSSCCCCCCCSSSCCCCCCCHHHHCCSSSSCCCCCCCSSCCCCHHHHHHHHCCCCCC
Confidence	948963104774432978973468667552775455327888728998641104253399999992994658875169999765315864996563999389999997389998516546988762563012352588744111689989999870865369
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| DVLQLGFFTFPIHFIPPGAESFMSYGLCRTEKFEEMNGAPMPDIQVYGYLLHTHLAGRALQAVQYRNGTQLRKICKDDSYDFNLQETRDLPSRVEIKPGDELLVECHYQTLDRDSMTFGGPSTINEMCLIFLFYYPQNNISSCMGYPDIIYVAHELGEEASE
Prediction	821411333334120115376143413134512542453445403222133313330330203213667414401644413242013241665150444330303031305546432322432411003001321154415304122424310431445458
	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

                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CSSSSSSCCCCCSSCCCCCCCSSSSSSSCHHHHHHHHCCCCCCSSSSSSSHHHCCCCSSSSSSSSSCCCSSSSSSSCCCCCCCCCCSSSCCCCSSSCCCCSSSSSSSSCCCCCCCSSSCCCCCCCHHHHCCSSSSCCCCCCCSSCCCCHHHHHHHHCCCCCC
DVLQLGFFTFPIHFIPPGAESFMSYGLCRTEKFEEMNGAPMPDIQVYGYLLHTHLAGRALQAVQYRNGTQLRKICKDDSYDFNLQETRDLPSRVEIKPGDELLVECHYQTLDRDSMTFGGPSTINEMCLIFLFYYPQNNISSCMGYPDIIYVAHELGEEASE

4zelA3

0.30

0.29

8.80

1.33

DEthreader

GIMELGLVYTPVMAIPPRETAFILTGYCTDKCTQLA---LPPGIHIFASQLHTHLTGRKVVTVLVRDGREWEIVNQDNHYSPHFQEIRMLKKVVSVHPGDVLITSCTYNTEDRELATVGGFGILEEMCVNYVHYYP-QTQLELCKSAVDAGFLQK-YFHVSQ

4zelA

0.31

0.30

9.15

3.12

SPARKS-K

GIMELGLVYTPVMAIPPRETAFILTGYCTDKCTQLAL--PPSGIHIFASQLHTHLTGRKVVTVLVRDGREWEIVNQDNHYSPHFQEIRMLKKVVSVHPGDVLITSCTYNTEDRELATVGGFGILEEMCVNYVHYYPQTQLELCKSAVDAGFLQKYFHLINRF

4zelA3

0.31

0.30

9.14

2.45

MapAlign

GIMELGLVYTPVMAIPPRETAFILTGYCTDKCTQLA--LPPSGIHIFASQLHTHLTGRKVVTVLVRDGREWEIVNQDNHYSPHFQEIRMLKKVVSVHPGDVLITSCTYNTEDRELATVGGFGILEEMCVNYVHYYPQTQLELCKSAVDAGFLQKYFHLIN--

4zelA3

0.31

0.30

9.15

1.51

CEthreader

GIMELGLVYTPVMAIPPRETAFILTGYCTDKCTQLA--LPPSGIHIFASQLHTHLTGRKVVTVLVRDGREWEIVNQDNHYSPHFQEIRMLKKVVSVHPGDVLITSCTYNTEDRELATVGGFGILEEMCVNYVHYYPQTQLELCKSAVDAGFLQKYFHLINRF

4zelA

0.31

0.30

9.15

2.15

MUSTER

GIMELGLVYTPVMAIPPRETAFILTGYCTDKCTQLA--LPPSGIHIFASQLHTHLTGRKVVTVLVRDGREWEIVNQDNHYSPHFQEIRMLKKVVSVHPGDVLITSCTYNTEDRELATVGGFGILEEMCVNYVHYYPQTQLELCKSAVDAGFLQKYFHLINRF

4zelA

0.31

0.30

9.15

4.30

HHsearch

GIMELGLVYTPVMAIPPRETAFILTGYCTDKCTQLA--LPPSGIHIFASQLHTHLTGRKVVTVLVRDGREWEIVNQDNHYSPHFQEIRMLKKVVSVHPGDVLITSCTYNTEDRELATVGGFGILEEMCVNYVHYYPQTQLELCKSAVDAGFLQKYFHLINRF

4zelA3

0.31

0.30

9.14

2.15

FFAS-3D

GIMELGLVYTPVMAIPPRETAFILTGYCTDKCTQLA--LPPSGIHIFASQLHTHLTGRKVVTVLVRDGREWEIVNQDNHYSPHFQEIRMLKKVVSVHPGDVLITSCTYNTEDRELATVGGFGILEEMCVNYVHYYPQTQLELCKSAVDAGFLQKYFHLIN--

4zelA3

0.31

0.30

9.15

1.25

EigenThreader

GIMELGLVYTPVMAIPPRETAFILTGYCTDKCTQLALPP--SGIHIFASQLHTHLTGRKVVTVLVRDGREWEIVNQDNHYSPHFQEIRMLKKVVSVHPGDVLITSCTYNTEDRELATVGGFGILEEMCVNYVHYYPQTQLELCKSAGFLQKYFHLINRFNNE

4zelA

0.31

0.30

9.15

4.26

CNFpred

GIMELGLVYTPVMAIPPRETAFILTGYCTDKCTQLA--LPPSGIHIFASQLHTHLTGRKVVTVLVRDGREWEIVNQDNHYSPHFQEIRMLKKVVSVHPGDVLITSCTYNTEDRELATVGGFGILEEMCVNYVHYYPQTQLELCKSAVDAGFLQKYFHLINRF

4zelA

0.30

0.29

8.80

1.33

DEthreader

GIMELGLVYTPVMAIPPRETAFILTGYCTDKCTQLA---LPPGIHIFASQLHTHLTGRKVVTVLVRDGREWEIVNQDNHYSPHFQEIRMLKKVVSVHPGDVLITSCTYNTEDRELATVGGFGILEEMCVNYVHYYP-QTQLELCKSAVDAGFLQK-YFHVSQ

(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	0.8931

(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	4zelA3	0.95	1.07	0.306	0.988	model1_4zelA3.pdb.gz
2	1sdwA	0.75	1.75	0.204	0.815	model1_1sdwA.pdb.gz
3	2ztnA	0.56	4.28	0.073	0.858	model1_2ztnA.pdb.gz
4	1c8nC	0.49	3.93	0.069	0.735	model1_1c8nC.pdb.gz
5	1h6fB	0.40	5.00	0.050	0.679	model1_1h6fB.pdb.gz
6	4h3wA2	0.40	3.69	0.095	0.574	model1_4h3wA2.pdb.gz
7	2yz1A	0.34	4.58	0.047	0.537	model1_2yz1A.pdb.gz
8	1k1yA	0.34	5.73	0.041	0.660	model1_1k1yA.pdb.gz
9	2p62A	0.28	5.67	0.030	0.512	model1_2p62A.pdb.gz
10	1jweA	0.23	5.05	0.038	0.389	model1_1jweA.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	0.93	catalytic activity
GO:0016491	0.92	oxidoreductase activity
GO:0016705	0.87	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
GO:0004497	0.87	monooxygenase activity
GO:0016715	0.85	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen
GO:0046872	0.84	metal ion binding
GO:0046914	0.80	transition metal ion binding
GO:0005507	0.73	copper ion binding
GO:0004500	0.57	dopamine beta-monooxygenase activity

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:1901564	0.98	organonitrogen compound metabolic process
GO:0044237	0.98	cellular metabolic process
GO:0044249	0.90	cellular biosynthetic process
GO:1901566	0.88	organonitrogen compound biosynthetic process
GO:0046189	0.88	phenol-containing compound biosynthetic process
GO:0065007	0.86	biological regulation
GO:0044699	0.79	single-organism process
GO:0042424	0.76	catecholamine catabolic process
GO:0042423	0.76	catecholamine biosynthetic process
GO:0042417	0.76	dopamine metabolic process
GO:0042415	0.76	norepinephrine metabolic process
GO:0065008	0.74	regulation of biological quality
GO:0044763	0.73	single-organism cellular process
GO:0050789	0.70	regulation of biological process
GO:0032501	0.70	multicellular organismal process
GO:0044707	0.67	single-multicellular organism process
GO:0003008	0.65	system process
GO:0050794	0.63	regulation of cellular process
GO:0050877	0.62	neurological system process
GO:0042421	0.62	norepinephrine biosynthetic process
GO:0042420	0.62	dopamine catabolic process
GO:0007610	0.62	behavior
GO:0050896	0.61	response to stimulus
GO:0034641	0.59	cellular nitrogen compound metabolic process
GO:0007611	0.56	learning or memory
GO:0044710	0.55	single-organism metabolic process
GO:0010033	0.55	response to organic substance
GO:0007612	0.54	learning
GO:0051239	0.52	regulation of multicellular organismal process
GO:0048609	0.52	multicellular organismal reproductive process
GO:0009719	0.52	response to endogenous stimulus
GO:0007165	0.52	signal transduction
GO:0006950	0.52	response to stress
GO:0044281	0.51	small molecule metabolic process
GO:0009628	0.51	response to abiotic stimulus
GO:0090066	0.50	regulation of anatomical structure size
GO:0040011	0.50	locomotion
GO:0033500	0.50	carbohydrate homeostasis
GO:0030534	0.50	adult behavior
GO:0019098	0.50	reproductive behavior
GO:0010243	0.50	response to organonitrogen compound

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	0.93	intracellular part
GO:0044444	0.86	cytoplasmic part
GO:0016020	0.85	membrane
GO:0044446	0.79	intracellular organelle part
GO:0043227	0.78	membrane-bounded organelle
GO:0044421	0.77	extracellular region part
GO:0005615	0.63	extracellular space
GO:0043231	0.59	intracellular membrane-bounded organelle
GO:0044433	0.58	cytoplasmic vesicle part
GO:0044425	0.56	membrane part
GO:0030667	0.54	secretory granule membrane
GO:0034774	0.51	secretory granule lumen

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	1oopA	0.493	4.30	0.034	0.747	2.7.7.48	94,102,134
2	0.060	1yjlA	0.641	1.88	0.192	0.710	1.14.17.3 4.3.2.5	NA
3	0.060	1jew1	0.432	4.63	0.047	0.698	3.4.22.28	94,103
4	0.060	3lxuX	0.487	3.44	0.055	0.667	3.4.14.10	NA
5	0.060	1euuA	0.479	3.96	0.071	0.691	3.2.1.18	58,60

	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:

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
	1	0.15	3mihA	0.746	1.92	0.197	0.821	1.37	AZI	complex1.pdb.gz	65,66,67,68,99,101
	2	0.04	1opmA	0.744	1.96	0.197	0.821	0.51	IYG	complex2.pdb.gz	4,6,49,129,131

	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.