D-I-TASSER Q06787

D-I-TASSER results for Q06787

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

Summary of the Protein

Uniprot ID: Q06787
Protein Name: Synaptic functional regulator FMR1
Gene Name: FMR1

Input Sequence in FASTA format

>Q06787 (632 residues)
MEELVVEVRGSNGAFYKAFVKDVHEDSITVAFENNWQPDRQIPFHDVRFPPPVGYNKDIN
ESDEVEVYSRANEKEPCCWWLAKVRMIKGEFYVIEYAACDATYNEIVTIERLRSVNPNKP
ATKDTFHKIKLDVPEDLRQMCAKEAAHKDFKKAVGAFSVTYDPENYQLVILSINEVTSKR
AHMLIDMHFRSLRTKLSLIMRNEEASKQLESSRQLASRFHEQFIVREDLMGLAIGTHGAN
IQQARKVPGVTAIDLDEDTCTFHIYGEDQDAVKKARSFLEFAEDVIQVPRNLVGKVIGKN
GKLIQEIVDKSGVVRVRIEAENEKNVPQEEEIMPPNSLPSNNSRVGPNAPEEKKHLDIKE
NSTHFSQPNSTKVQRVLVASSVVAGESQKPELKAWQGMVPFVFVGTKDSIANATVLLDYH
LNYLKEVDQLRLERLQIDEQLRQIGASSRPPPNRTDKEKSYVTDDGQGMGRGSRPYRNRG
HGRRGPGYTSGTNSEASNASETESDHRDELSDWSLAPTEEERESFLRRGDGRRRGGGGRG
QGGRGRGGGFKGNDDHSRTDNRPRNPREAKGRTTDGSLQIRVDCNNERSVHTKTLQNTSS
EGSRLRTGKDRNQKKEKPDSVDGQQPLVNGVP

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	Q06787-D1	1-126	126		MEELVVEVRGSNGAFYKAFVKDVHEDSITVAFENNWQPDRQIPFHDVRFPPPVGYNKDINESDEVEVYSRANEKEPCCWWLAKVRMIKGEFYVIEYAACDATYNEIVTIERLRSVNPNKPATKDTF
2	Q06787-D2	127-216	90		HKIKLDVPEDLRQMCAKEAAHKDFKKAVGAFSVTYDPENYQLVILSINEVTSKRAHMLIDMHFRSLRTKLSLIMRNEEASKQLESSRQLA
3	Q06787-D3	217-283	67		SRFHEQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDEDTCTFHIYGEDQDAVKKARSFLEFAE
4	Q06787-D4	284-420	137		DVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNVPQEEEIMPPNSLPSNNSRVGPNAPEEKKHLDIKENSTHFSQPNSTKVQRVLVASSVVAGESQKPELKAWQGMVPFVFVGTKDSIANATVLLDYH
5	Q06787-D5	421-499	79		LNYLKEVDQLRLERLQIDEQLRQIGASSRPPPNRTDKEKSYVTDDGQGMGRGSRPYRNRGHGRRGPGYTSGTNSEASNA
6	Q06787-D6	500-564	65		SETESDHRDELSDWSLAPTEEERESFLRRGDGRRRGGGGRGQGGRGRGGGFKGNDDHSRTDNRPR
7	Q06787-D7	565-632	68		NPREAKGRTTDGSLQIRVDCNNERSVHTKTLQNTSSEGSRLRTGKDRNQKKEKPDSVDGQQPLVNGVP

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.514

(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	4qvzA	0.30	0.80	1.000	0.307	model1_4qvzA.pdb.gz
2	6l7eA	0.30	8.47	0.028	0.516	model1_6l7eA.pdb.gz
3	7w0aA	0.29	8.06	0.033	0.476	model1_7w0aA.pdb.gz
4	6zymA	0.29	7.99	0.030	0.467	model1_6zymA.pdb.gz
5	7tdtA	0.29	8.09	0.030	0.471	model1_7tdtA.pdb.gz
6	3qmzA	0.29	8.20	0.020	0.478	model1_3qmzA.pdb.gz
7	7lkpA	0.29	8.04	0.041	0.465	model1_7lkpA.pdb.gz
8	8dfvA	0.29	7.75	0.036	0.453	model1_8dfvA.pdb.gz
9	8iqhA	0.29	7.74	0.042	0.449	model1_8iqhA.pdb.gz
10	7wb4E	0.29	7.11	0.041	0.422	model1_7wb4E.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:0003723	1.00	RNA binding
GO:0003729	0.96	mRNA 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:0065007	0.94	biological regulation
GO:0050794	0.93	regulation of cellular process
GO:2000112	0.91	regulation of cellular macromolecule biosynthetic process
GO:0051171	0.91	regulation of nitrogen compound metabolic process
GO:0032268	0.91	regulation of cellular protein metabolic process
GO:0010468	0.91	regulation of gene expression
GO:0006417	0.90	regulation of translation
GO:0048523	0.88	negative regulation of cellular process
GO:0017148	0.87	negative regulation of translation
GO:0009987	0.60	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:0044464	0.99	cell part
GO:0044424	0.98	intracellular part
GO:0005737	0.89	cytoplasm
GO:0043229	0.88	intracellular organelle
GO:0043231	0.86	intracellular membrane-bounded organelle
GO:0005634	0.85	nucleus
GO:0032991	0.82	macromolecular complex
GO:0030529	0.79	intracellular ribonucleoprotein complex
GO:0005844	0.78	polysome

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	3btaA	0.235	8.06	0.039	0.385	3.4.24.69	NA
2	0.060	3gtgB	0.234	7.51	0.040	0.364	2.7.7.6	236,246,277
3	0.060	1ea0A	0.241	8.01	0.043	0.394	1.4.1.13	154
4	0.060	2jfdA	0.117	7.08	0.048	0.174	2.3.1.85	NA
5	0.060	2qf7B	0.242	8.29	0.025	0.407	6.4.1.1	22

	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	1d0xA	0.200	7.86	0.039	0.317	0.29	MNQ	complex1.pdb.gz	237,238,239,240,241,242,243
2	0.01	2xelA	0.195	7.72	0.035	0.312	0.29	IA2	complex2.pdb.gz	229,233,277
3	0.01	3cmvH	0.239	8.19	0.055	0.394	0.30	ANP	complex3.pdb.gz	233,234,235,239,240,241,242
4	0.01	2xo8A	0.179	7.94	0.024	0.290	0.39	H70	complex4.pdb.gz	232,233,243,275
5	0.01	1jwyA	0.204	7.94	0.043	0.328	0.18	BGC	complex5.pdb.gz	231,276,406
6	0.01	2aka0	0.190	7.91	0.032	0.305	0.25	III	complex6.pdb.gz	241,242,243,244,245
7	0.01	1mmaA	0.201	7.59	0.037	0.312	0.18	ADP	complex7.pdb.gz	268,274,275
8	0.01	3cmvB	0.235	8.24	0.036	0.386	0.24	ANP	complex8.pdb.gz	229,231,232,233,234
9	0.01	1n03A	0.121	7.14	0.030	0.182	0.27	ADP	complex9.pdb.gz	227,229,230,231
10	0.01	1yv3A	0.193	7.78	0.045	0.310	0.22	BIT	complex10.pdb.gz	229,230,236,240,405

	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.