D-I-TASSER Q9H4H8

D-I-TASSER results for Q9H4H8

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

Summary of the Protein

Uniprot ID: Q9H4H8
Protein Name: Protein FAM83D
Gene Name: FAM83D

Input Sequence in FASTA format

>Q9H4H8 (585 residues)
MALLSEGLDEVPAACLSPCGPPNPTELFSESRRLALEELVAGGPEAFAAFLRRERLARFL
NPDEVHAILRAAERPGEEGAAAAAAAEDSFGSSHDCSSGTYFPEQSDLEPPLLELGWPAF
YQGAYRGATRVETHFQPRGAGEGGPYGCKDALRQQLRSAREVIAVVMDVFTDIDIFRDLQ
EICRKQGVAVYILLDQALLSQFLDMCMDLKVHPEQEKLMTVRTITGNIYYARSGTKIIGK
VHEKFTLIDGIRVATGSYSFTWTDGKLNSSNLVILSGQVVEHFDLEFRILYAQSKPISPK
LLSHFQSSNKFDHLTNRKPQSKELTLGNLLRMRLARLSSTPRKADLDPEMPAEGKAERKP
HDCESSTVSEEDYFSSHRDELQSRKAIDAATQTEPGEEMPGLSVSEVGTQTSITTACAGT
QTAVITRIASSQTTIWSRSTTTQTDMDENILFPRGTQSTEGSPVSKMSVSRSSSLKSSSS
VSSQGSVASSTGSPASIRTTDFHNPGYPKYLGTPHLELYLSDSLRNLNKERQFHFAGIRS
RLNHMLAMLSRRTLFTENHLGLHSGNFSRVNLLAVRDVALYPSYQ

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	Q9H4H8-D1	1-585	585		MALLSEGLDEVPAACLSPCGPPNPTELFSESRRLALEELVAGGPEAFAAFLRRERLARFLNPDEVHAILRAAERPGEEGAAAAAAAEDSFGSSHDCSSGTYFPEQSDLEPPLLELGWPAFYQGAYRGATRVETHFQPRGAGEGGPYGCKDALRQQLRSAREVIAVVMDVFTDIDIFRDLQEICRKQGVAVYILLDQALLSQFLDMCMDLKVHPEQEKLMTVRTITGNIYYARSGTKIIGKVHEKFTLIDGIRVATGSYSFTWTDGKLNSSNLVILSGQVVEHFDLEFRILYAQSKPISPKLLSHFQSSNKFDHLTNRKPQSKELTLGNLLRMRLARLSSTPRKADLDPEMPAEGKAERKPHDCESSTVSEEDYFSSHRDELQSRKAIDAATQTEPGEEMPGLSVSEVGTQTSITTACAGTQTAVITRIASSQTTIWSRSTTTQTDMDENILFPRGTQSTEGSPVSKMSVSRSSSLKSSSSVSSQGSVASSTGSPASIRTTDFHNPGYPKYLGTPHLELYLSDSLRNLNKERQFHFAGIRSRLNHMLAMLSRRTLFTENHLGLHSGNFSRVNLLAVRDVALYPSYQ

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.562

(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	7v53A1	0.34	6.00	0.105	0.443	model1_7v53A1.pdb.gz
2	6kz8A2	0.32	5.23	0.080	0.388	model1_6kz8A2.pdb.gz
3	6ohmA	0.31	5.16	0.063	0.392	model1_6ohmA.pdb.gz
4	7mftG	0.31	6.98	0.037	0.456	model1_7mftG.pdb.gz
5	3ecqB	0.30	7.60	0.047	0.487	model1_3ecqB.pdb.gz
6	6ohrA	0.30	4.96	0.068	0.371	model1_6ohrA.pdb.gz
7	7tuiB	0.30	7.49	0.037	0.472	model1_7tuiB.pdb.gz
8	7z12A	0.30	7.36	0.038	0.456	model1_7z12A.pdb.gz
9	5y81A	0.29	6.64	0.046	0.422	model1_5y81A.pdb.gz
10	2vdcA	0.29	6.83	0.043	0.434	model1_2vdcA.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:0019899	0.77	enzyme binding
GO:0019901	0.75	protein kinase binding
GO:0008092	0.55	cytoskeletal protein binding
GO:0008017	0.54	microtubule 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:0044699	0.96	single-organism process
GO:0050794	0.93	regulation of cellular process
GO:0009987	0.81	cellular process
GO:0008283	0.78	cell proliferation
GO:0080090	0.70	regulation of primary metabolic process
GO:0060255	0.70	regulation of macromolecule metabolic process
GO:0051179	0.70	localization
GO:0031323	0.70	regulation of cellular metabolic process
GO:0051641	0.68	cellular localization
GO:0016043	0.68	cellular component organization
GO:0044763	0.66	single-organism cellular process
GO:0051234	0.64	establishment of localization
GO:0048583	0.64	regulation of response to stimulus
GO:0023051	0.64	regulation of signaling
GO:0031399	0.63	regulation of protein modification process
GO:0009966	0.63	regulation of signal transduction
GO:0070372	0.62	regulation of ERK1 and ERK2 cascade
GO:0051310	0.62	metaphase plate congression
GO:0048518	0.53	positive regulation of biological process
GO:0048522	0.52	positive regulation of cellular process

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:0044424	1.00	intracellular part
GO:0044446	0.92	intracellular organelle part
GO:0044430	0.85	cytoskeletal part
GO:0005737	0.76	cytoplasm
GO:0097431	0.69	mitotic spindle pole

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	1itwB	0.250	7.56	0.054	0.393	1.1.1.42	151,157
2	0.060	2vdcF	0.295	6.96	0.041	0.441	1.4.1.13	NA
3	0.060	2pffD	0.281	7.74	0.032	0.451	2.3.1.86	182
4	0.060	3bicA	0.259	7.18	0.035	0.398	5.4.99.2	NA
5	0.060	1llwA	0.288	7.17	0.045	0.436	1.4.7.1	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	1iwbL	0.264	6.94	0.036	0.390	0.15	B12	complex1.pdb.gz	156,287,288
2	0.01	1lm1A	0.292	6.74	0.045	0.427	0.14	FMN	complex2.pdb.gz	157,255,256
3	0.01	2vdcB	0.295	6.96	0.041	0.441	0.17	OMT	complex3.pdb.gz	201,224,225
4	0.01	2uvbA	0.282	7.46	0.039	0.441	0.12	NAP	complex4.pdb.gz	158,276,280
5	0.01	2x2iA	0.264	7.86	0.032	0.434	0.28	QPS	complex5.pdb.gz	153,251,252
6	0.01	1ea0A	0.292	6.91	0.043	0.432	0.19	FMN	complex6.pdb.gz	166,225,226,239
7	0.01	1dioA	0.264	6.96	0.036	0.390	0.17	PGO	complex7.pdb.gz	254,278,283
8	0.01	2uvaI	0.294	7.47	0.033	0.458	0.12	FMN	complex8.pdb.gz	134,152,249,250
9	0.01	1eexA	0.264	6.91	0.039	0.388	0.27	PGO	complex9.pdb.gz	165,169,196,197,223
10	0.01	1ofdB	0.253	7.59	0.031	0.398	0.32	F3S	complex10.pdb.gz	163,164,179,219

	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.