D-I-TASSER Q6ZNR0-D1

D-I-TASSER results for Q6ZNR0-D1

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

Input Sequence in FASTA format

>Q6ZNR0 (172 residues)
MDSPSLRELQQPLLEGTECETPAQKPGRHELGSPLREIAFAESLRGLQFLSPPLPSVSAG
LGEPRPPDVEDMSSSDSDSDWDGGSRLSPFLPHDHLGLAVFSMLCCFWPVGIAAFCLAQK
TNKAWAKGDIQGAGAASRRAFLLGVLAVGLGVCTYAAALVTLAAYLASRDPP

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MDSPSLRELQQPLLEGTECETPAQKPGRHELGSPLREIAFAESLRGLQFLSPPLPSVSAGLGEPRPPDVEDMSSSDSDSDWDGGSRLSPFLPHDHLGLAVFSMLCCFWPVGIAAFCLAQKTNKAWAKGDIQGAGAASRRAFLLGVLAVGLGVCTYAAALVTLAAYLASRDPP
Prediction	CCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
Confidence	9852221123676678999999999999888999888888778887778999988878888999999988887777788877888878899986028999999997748899999999998888980789999999999999999999999999999999999996267989
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MDSPSLRELQQPLLEGTECETPAQKPGRHELGSPLREIAFAESLRGLQFLSPPLPSVSAGLGEPRPPDVEDMSSSDSDSDWDGGSRLSPFLPHDHLGLAVFSMLCCFWPVGIAAFCLAQKTNKAWAKGDIQGAGAASRRAFLLGVLAVGLGVCTYAAALVTLAAYLASRDPP
Prediction	8657537434522454555744445466364544445434464264354444434434444445444545434444454435456444433142000001200221132202000120340352244322620450043022101201331333333322320001145548
	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

CCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
MDSPSLRELQQPLLEGTECETPAQKPGRHELGSPLREIAFAESLRGLQFLSPPLPSVSAGLGEPRPPDVEDMSSSDSDSDWDGGSRLSPFLPHDHLGLAVFSMLCCFWPVGIAAFCLAQKTNKAWAKGDIQGAGAASRRAFLLGVLAVGLGVCTYAAALVTLAAYLASRDPP

2uuiA

0.12

0.10

3.52

0.39

CEthreader

--------------------MHHHHHHKDEVALLAAVTLLGVLLQAYFSLQVISARRAFRVSPPLTTGPPEFERVYRAQVNCSEY------FPLFLATLWVAGIFFHEGAAALCGLVYLFARLRYFQGLRLAPLYASARALWLLVALAALGLLAHFLPAALRAALLGRLRTL

5oqlH

0.10

0.09

3.49

0.58

EigenThreader

SSLRHA----IQRRAHKERAQPLERQRLGILEKKKDYRLRARDYKKKQAVLKSLRQKAAERNEDEFYFGMMSRKGPGSALTRGKGFTGTLSVETVRLLKTQDLGYVRTMRNIAAKELKELEERYVLAGVLEKLARKVKAARKKLKALADAEYELELQQAKMATSGGFTKSGR

5unfA3

0.12

0.05

1.85

0.61

FFAS-3D

-------------------------------------------------------------------------------------------PPESAGIALMKNILGFIPLIFIATCYFGIRKHLLKTNSYGKNRITRDQVLKMAAAVVLAFIICWLPFHVLTFLDA------

6djyA

0.15

0.14

4.72

0.82

SPARKS-K

MTLKQMIQEQENELTHYVFTTPLSMPGKPMLGY-VPLNEVATSKFFSNVNDFDRDQLAMAHFP-------DTTITQAYNLTNSIKPGDTSLPAEVAALKWFWKFFTSPPMDNVMYWACQFLSSGTSKGSHICMFSNLRLSPILCPYYDLITSLLTYLCLCTIVGLCDTFTET

5oqtA

0.16

0.07

2.33

0.74

CNFpred

---------------------------------------------------------------------------------------------LVLSFILSGLACVFAALCYAEFASTVPVSGSAY--TYSYATFGELIAWILGWDLILEYGVASSAVAVGWSGYFQGLLSG

4a01A

0.07

0.06

2.41

0.83

DEthreader

ALPDLGTEILIPVCAVIGIALFQWLSKVK----------------ASGILVIGVVSFVALPTSFTIKDTF-A----ITTV---LTPKVIGLVGMLPYWFSAMTMKSVGSAALKMVEEVRRQFNTI-PGLTA-KPD-YATCVKISTDASIKEMIPPGALVMLTPLVVGGVAFA

6yvuB

0.03

1.94

0.55

MapAlign

CSVAVHFQYVIDESSGTSRIDEEKPGLIITRKAFKNNSSKYYINEKESSYTEVTKLLKNEGIDLDHKRFLILQGEVENIAQMKPKAEKESDDGLLEYLEDIIQQTEHETEIKDLTQLLEKERSILDDIMQNSKVESVCQKLDILVAKLKKVKSASKKSGGDVVKFQKLLQNS

5ztyA

0.12

4.13

0.61

MUSTER

TKSPSLNAAKSELDKAIGRNTNGVIT--KDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYARMRLDVELAKTLGLVLAVLLICWFPVLALMAHSLATTLSDQ

6rz6A2

0.05

0.02

1.13

0.81

HHsearch

--------------------------------------------------------------------------------------LNLYKIAKLQTMNYIALVVGCLPFFTLSICYLLIIRVLLKVEALAYLVSHRKALTTIIITLIIFFLCFLPYHTLRTVHLTTWKVGL

6xkwn

0.12

4.07

0.38

CEthreader

RTDPVIRMMVVSIGFYGMSTFEGPMMSIKAVNSLSHYTDWTIGHVHSGALGWNGMITFGML------------YFLTPRLWGRSGLYSLKLVSWHFWLATIGIVLYASSMWVSGIMEGLMWREVDAQGFLVNGFADTVGAKFPMNVVRGVGGVLYLTGGLIMAYNLWATVAK

(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	0.4416

(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	5tsiA	0.54	5.21	0.075	0.889	model1_5tsiA.pdb.gz
2	5twvB	0.53	5.15	0.068	0.872	model1_5twvB.pdb.gz
3	5u71A	0.53	5.32	0.050	0.889	model1_5u71A.pdb.gz
4	5uj9A3	0.52	5.36	0.063	0.872	model1_5uj9A3.pdb.gz
5	1st6A	0.49	4.98	0.060	0.849	model1_1st6A.pdb.gz
6	6hraA	0.49	5.04	0.075	0.814	model1_6hraA.pdb.gz
7	4xydA	0.49	5.17	0.053	0.779	model1_4xydA.pdb.gz
8	4qo5A	0.48	4.71	0.062	0.762	model1_4qo5A.pdb.gz
9	4a01A	0.48	5.16	0.053	0.779	model1_4a01A.pdb.gz
10	3ayfA2	0.48	5.01	0.045	0.785	model1_3ayfA2.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:0042803	0.70	protein homodimerization activity
GO:0035254	0.68	glutamate receptor binding
GO:1901363	0.55	heterocyclic compound binding
GO:0097159	0.55	organic cyclic compound binding

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:0009987	0.68	cellular process
GO:0065007	0.67	biological regulation
GO:0051179	0.66	localization
GO:0050794	0.64	regulation of cellular process
GO:0006810	0.63	transport
GO:0051641	0.59	cellular localization
GO:0051649	0.57	establishment of localization in cell
GO:0071702	0.56	organic substance transport
GO:0046907	0.55	intracellular transport
GO:0008104	0.54	protein localization
GO:0048522	0.53	positive regulation of cellular process
GO:0051128	0.52	regulation of cellular component organization
GO:0051240	0.51	positive regulation of multicellular organismal process
GO:0015031	0.51	protein transport
GO:0097091	0.50	synaptic vesicle clustering
GO:0051965	0.50	positive regulation of synapse assembly
GO:0006886	0.50	intracellular protein transport

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	0.98	cell part
GO:0044424	0.93	intracellular part
GO:0016020	0.92	membrane
GO:0043226	0.88	organelle
GO:0044425	0.87	membrane part
GO:0043229	0.85	intracellular organelle
GO:0044444	0.77	cytoplasmic part
GO:0044422	0.76	organelle part
GO:0044446	0.74	intracellular organelle part
GO:0043232	0.72	intracellular non-membrane-bounded organelle
GO:0044459	0.71	plasma membrane part
GO:0016021	0.69	integral component of membrane
GO:0042995	0.66	cell projection
GO:0043227	0.63	membrane-bounded organelle
GO:0097458	0.60	neuron part
GO:0043005	0.59	neuron projection
GO:0005886	0.58	plasma membrane
GO:0005887	0.57	integral component of plasma membrane
GO:0045202	0.56	synapse
GO:0044463	0.55	cell projection part
GO:0044456	0.54	synapse part
GO:0031090	0.54	organelle membrane
GO:0044297	0.53	cell body
GO:0014069	0.53	postsynaptic density
GO:0060076	0.52	excitatory synapse
GO:0043198	0.52	dendritic shaft
GO:0043197	0.52	dendritic spine
GO:0031901	0.52	early endosome membrane

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	2fonB	0.454	5.18	0.030	0.727	1.3.3.6	NA
2	0.060	1qi9B	0.463	5.34	0.104	0.796	1.11.1.10	NA
3	0.060	1is2A	0.461	4.89	0.031	0.715	1.3.3.6	111
4	0.060	1kraC	0.429	5.79	0.043	0.808	3.5.1.5	104,152
5	0.060	1vdkA	0.439	5.32	0.066	0.727	4.2.1.2	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	2ibfA	0.363	5.25	0.074	0.593	0.61	III	complex1.pdb.gz	100,101,103,104,107,108,111,114,115,140,147,151
2	0.01	2gdcA	0.361	5.10	0.068	0.564	0.42	III	complex2.pdb.gz	107,134,141,145,148,149,152
3	0.01	3o8lB	0.349	6.03	0.072	0.669	0.91	PO4	complex3.pdb.gz	110,114,144,145,148
4	0.01	1t01A	0.374	4.37	0.043	0.546	0.41	III	complex4.pdb.gz	102,103,106,109,110,113,116,117,150
5	0.01	1is2B	0.459	5.01	0.025	0.721	0.45	FAD	complex5.pdb.gz	104,106,107,110,147,149
6	0.01	3o8nA	0.433	5.37	0.083	0.744	0.41	ADP	complex6.pdb.gz	104,109,145,146,147,151
7	0.01	1zw2A	0.372	4.37	0.043	0.541	0.43	III	complex7.pdb.gz	114,133,137,140,144,147,151
8	0.01	2gwwA	0.370	4.91	0.044	0.570	0.47	III	complex8.pdb.gz	137,140,148,151

	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.