D-I-TASSER Q9H7M6

D-I-TASSER results for Q9H7M6

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

Summary of the Protein

Uniprot ID: Q9H7M6
Protein Name: Zinc finger SWIM domain-containing protein 4
Gene Name: ZSWIM4

Input Sequence in FASTA format

>Q9H7M6 (989 residues)
MEPPAAKRSRGCPAGPEERDAGAGAARGRGRPEALLDLSAKRVAESWAFEQVEERFSRVP
EPVQKRIVFWSFPRSEREICMYSSLGYPPPEGEHDARVPFTRGLHLLQSGAVDRVLQVGF
HLSGNIREPGSPGEPERLYHVSISFDRCKITSVSCGCDNRDLFYCAHVVALSLYRIRHAH
QVELRLPISETLSQMNRDQLQKFVQYLISAHHTEVLPTAQRLADEILLLGSEINLVNGAP
DPTAGAGIEDANCWHLDEEQIQEQVKQLLSNGGYYGASQQLRSMFSKVREMLRMRDSNGA
RMLILMTEQFLQDTRLALWRQQGAGMTDKCRQLWDELGALWVCVVLSPHCKPEERAGWLQ
LLSRWDKLDVCPLEEGNYSFDGPSLQPTMAPAPELLQKGSTCITNTEGWVGHPLDPIGCL
CRALLEACRLEEETLTLYPDSGPEKRKVAYQHVPVPGSPGESYLVLALEVALLGLGQQRA
LPEGLYAQDKVVRNEEQLLALLEEVELDERLVQVLRKQAGLLLEGGPFSGFGEVLFRESV
PMHTCARYLFTALLPHDPDLAYRLALRAMRLPILETAFPAGEPHPSPLDSIMSNRFPRWF
ILGHLETRQCELASTMLTAAKGDPKWLHTVLGSIQQNIHSPALLFKLAQDACKTATPVSA
PPDTTLLGIALELGLQVMRMTLNVMTWRRREMVRWLVSCATEIGPQALMNIMQNWYSLFT
PVEAATIVAVTGTTHATLLRLQLDTSRREELWACARTLALQCAMKDPQNCALPALTLCEK
NHSAFEAAYQIVLDAAAGGLGHAHLFTVARYMEHRGLPLRAYKLATLALAQLSIAFNQDS
HPAVNDVLWACSLSHSLGRHELSAIVPLIIRSIHCAPMLSDILRRWTLSAPGLGPLGARR
AAKPLGADRAPLCQLLDAAVTAYITTSHSRLTHISPRHYGDFIEFLGKARETFLLAPDGH
LQFSQFLENLKQTYKGKKKLMLLVRERFG

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

Contact Map

Distance Map

D-I-TASSER simulation is guided by the consensus contact map (left figure) and distance map (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.

Information of Domain

No. of Domain	Domain	Domain Boundary	Length of Domain	Models of Domain	Sequence
1	Q9H7M6-D1	1-186,369-539	357		MEPPAAKRSRGCPAGPEERDAGAGAARGRGRPEALLDLSAKRVAESWAFEQVEERFSRVPEPVQKRIVFWSFPRSEREICMYSSLGYPPPEGEHDARVPFTRGLHLLQSGAVDRVLQVGFHLSGNIREPGSPGEPERLYHVSISFDRCKITSVSCGCDNRDLFYCAHVVALSLYRIRHAHQVELRLDVCPLEEGNYSFDGPSLQPTMAPAPELLQKGSTCITNTEGWVGHPLDPIGCLCRALLEACRLEEETLTLYPDSGPEKRKVAYQHVPVPGSPGESYLVLALEVALLGLGQQRALPEGLYAQDKVVRNEEQLLALLEEVELDERLVQVLRKQAGLLLEGGPFSGFGEVLFRES
2	Q9H7M6-D2	187-368	182		PISETLSQMNRDQLQKFVQYLISAHHTEVLPTAQRLADEILLLGSEINLVNGAPDPTAGAGIEDANCWHLDEEQIQEQVKQLLSNGGYYGASQQLRSMFSKVREMLRMRDSNGARMLILMTEQFLQDTRLALWRQQGAGMTDKCRQLWDELGALWVCVVLSPHCKPEERAGWLQLLSRWDKL
3	Q9H7M6-D3	540-639	100		VPMHTCARYLFTALLPHDPDLAYRLALRAMRLPILETAFPAGEPHPSPLDSIMSNRFPRWFILGHLETRQCELASTMLTAAKGDPKWLHTVLGSIQQNIH
4	Q9H7M6-D4	640-767	128		SPALLFKLAQDACKTATPVSAPPDTTLLGIALELGLQVMRMTLNVMTWRRREMVRWLVSCATEIGPQALMNIMQNWYSLFTPVEAATIVAVTGTTHATLLRLQLDTSRREELWACARTLALQCAMKDP
5	Q9H7M6-D5	768-989	222		QNCALPALTLCEKNHSAFEAAYQIVLDAAAGGLGHAHLFTVARYMEHRGLPLRAYKLATLALAQLSIAFNQDSHPAVNDVLWACSLSHSLGRHELSAIVPLIIRSIHCAPMLSDILRRWTLSAPGLGPLGARRAAKPLGADRAPLCQLLDAAVTAYITTSHSRLTHISPRHYGDFIEFLGKARETFLLAPDGHLQFSQFLENLKQTYKGKKKLMLLVRERFG

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.46

(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	7dxjA	0.35	8.59	0.044	0.542	model1_7dxjA.pdb.gz
2	6yejA	0.34	9.07	0.050	0.538	model1_6yejA.pdb.gz
3	6sytA	0.34	8.47	0.043	0.518	model1_6sytA.pdb.gz
4	1qbkB	0.33	7.34	0.055	0.461	model1_1qbkB.pdb.gz
5	6reyc	0.33	7.69	0.061	0.467	model1_6reyc.pdb.gz
6	6w1sR	0.33	7.55	0.037	0.459	model1_6w1sR.pdb.gz
7	5t8vA	0.33	7.63	0.072	0.462	model1_5t8vA.pdb.gz
8	5mz61	0.32	8.09	0.053	0.473	model1_5mz61.pdb.gz
9	6af0A	0.32	8.17	0.054	0.472	model1_6af0A.pdb.gz
10	6bcuA	0.32	8.67	0.047	0.489	model1_6bcuA.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:0051879	1.00	Hsp90 protein binding
GO:0051787	1.00	misfolded protein binding
GO:0005102	1.00	receptor 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	0.79	cellular process
GO:0065007	0.75	biological regulation
GO:0050789	0.74	regulation of biological process
GO:0044699	0.74	single-organism process
GO:0050794	0.72	regulation of cellular process
GO:0016043	0.66	cellular component organization
GO:0051239	0.64	regulation of multicellular organismal process
GO:0032879	0.64	regulation of localization
GO:2000026	0.63	regulation of multicellular organismal development
GO:0051270	0.63	regulation of cellular component movement
GO:0045595	0.63	regulation of cell differentiation
GO:0040012	0.63	regulation of locomotion
GO:0050767	0.62	regulation of neurogenesis
GO:0044763	0.62	single-organism cellular process
GO:0048869	0.53	cellular developmental process
GO:0044767	0.53	single-organism developmental process
GO:0030334	0.51	regulation of cell migration
GO:0009653	0.51	anatomical structure morphogenesis
GO:2001222	0.50	regulation of neuron migration
GO:0048812	0.50	neuron projection morphogenesis

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	1.00	cell part
GO:0044421	0.90	extracellular region part
GO:0044424	0.89	intracellular part
GO:0005615	0.88	extracellular space
GO:0043226	0.79	organelle
GO:0043229	0.78	intracellular organelle
GO:0043227	0.75	membrane-bounded organelle
GO:0043231	0.74	intracellular membrane-bounded organelle
GO:0005634	0.70	nucleus
GO:0044446	0.62	intracellular organelle part
GO:0044428	0.58	nuclear part

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	2hpiA	0.253	9.29	0.042	0.406	2.7.7.7	104
2	0.060	1bglA	0.274	9.13	0.036	0.437	3.2.1.23	NA
3	0.060	3btaA	0.307	9.24	0.030	0.491	3.4.24.69	NA
4	0.060	2uv8G	0.259	9.08	0.028	0.409	2.3.1.86	NA
5	0.060	1jqoA	0.268	8.61	0.043	0.406	4.1.1.31	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	2h4m0	0.304	7.42	0.052	0.426	0.15	III	complex1.pdb.gz	99,100,103,106,107,109,110
2	0.01	3cmvB	0.282	9.29	0.027	0.455	0.24	ANP	complex2.pdb.gz	106,110,111,112,113
3	0.01	3cmvE	0.272	9.40	0.034	0.441	0.34	ANP	complex3.pdb.gz	100,101,102,103
4	0.01	3cmtA	0.284	9.05	0.041	0.449	0.11	QNA	complex4.pdb.gz	41,105,118
5	0.01	3cmvD	0.277	9.54	0.033	0.453	0.15	ANP	complex5.pdb.gz	100,101,102,103,106
6	0.01	2vu9A	0.152	7.31	0.039	0.210	0.19	UUU	complex6.pdb.gz	102,103,111,112
7	0.01	1i1eA	0.297	9.20	0.034	0.473	0.31	DM2	complex7.pdb.gz	105,110,112,113
8	0.01	1f31A	0.298	9.32	0.035	0.479	0.34	UUU	complex8.pdb.gz	104,105,110,112,113

	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, 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.