D-I-TASSER Q6ZSZ5

D-I-TASSER results for Q6ZSZ5

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

Summary of the Protein

Uniprot ID: Q6ZSZ5
Protein Name: Rho guanine nucleotide exchange factor 18
Gene Name: ARHGEF18

Input Sequence in FASTA format

>Q6ZSZ5 (1361 residues)
MGDDQEDDFPRRLSESMEDLSLDLGALQGSEYLQDLGLGAPSHSQPGETPDSRPTGEEPG
RDSLFSSLAGSQDLSRRRSWERSRSCSESWRRLSLDASAVDEEPCLPRTLASLALNLPGG
GLKTWTQGCLSGGGTPAESPGKECDSPKKRGRSRSVPVSFYEIRSPEISPGLEVPTPPVQ
GLEPPVLECMEKDHVEPDHVLIVQQVLQELRQYHGARQRACMSASPGGAHSNLTWFEFLS
ESEDGAGKNEKSDKSTSVKRRLSCLRSRVTRQKEKGKSPAHLKDKGQDARERRECVNGHQ
LLQGTFSGPSSCPLCGKPFLSSASLKEHPRGTLLSDGSPALSRNVGMTVSQKGGPQPTPS
PAGPGTQLGPITGEMDEADSAFLKFKQTADDSLSLTSPNTESIFVEDPYTASLRSEIESD
GHEFEAESWSLAVDAAYAKKQKREVVKRQDVLYELMQTEVHHVRTLKIMLKVYSRALQEE
LQFSSKAIGRLFPCADDLLETHSHFLARLKERRQESLEEGSDRNYVIQKIGDLLVQQFSG
ENGERMKEKYGVFCSGHNEAVSHYKLLLQQNKKFQNLIKKIGNFSIVRRLGVQECILLVT
QRITKYPVLVERIIQNTEAGTEDYEDLTQALNLIKDIISQVDAKVSECEKGQRLREIAGK
MDLKSSSKLKNGLTFRKEDMLQRQLHLEGMLCWKTTSGRLKDILAILLTDVLLLLQEKDQ
KYVFASVDSKPPVISLQKLIVREVANEEKAMFLISASLQGPEMYEIYTSSKEDRNAWMAH
IQRAVESCPDEEEGPFSLPEEERKVVEARATRLRDFQERLSMKDQLIAQSLLEKQQIYLE
MAEMGGLEDLPQPRGLFRGGDPSETLQGELILKSAMSEIEGIQSLICRQLGSANGQAEDG
GSSTGPPRRAETFAGYDCTNSPTKNGSFKKKVSSTDPRPRDWRGPPNSPDLKLSDSDIPG
SSEESPQVVEAPGTESDPRLPTVLESELVQRIQTLSQLLLNLQAVIAHQDSYVETQRAAI
QEREKQFRLQSTRGNLLLEQERQRNFEKQREERAALEKLQSQLRHEQQRWERERQWQHQE
LERAGARLQEREGEARQLRERLEQERAELERQRQAYQHDLERLREAQRAVERERERLELL
RRLKKQNTAPGALPPDTLAEAQPPSHPPSFNGEGLEGPRVSMLPSGVGPEYAERPEVARR
DSAPTENRLAKSDVPIQLLSATNQFQRQAAVQQQIPTKLAASTKGGKDKGGKSRGSQRWE
SSASFDLKQQLLLNKLMGKDESTSRNRRSLSPILPGRHSPAPPPDPGFPAPSPPPADSPS
EGFSLKAGGTALLPGPPAPSPLPATPLSAKEDASKEDVIFF

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	Q6ZSZ5-D1	1-1361	1361		MGDDQEDDFPRRLSESMEDLSLDLGALQGSEYLQDLGLGAPSHSQPGETPDSRPTGEEPGRDSLFSSLAGSQDLSRRRSWERSRSCSESWRRLSLDASAVDEEPCLPRTLASLALNLPGGGLKTWTQGCLSGGGTPAESPGKECDSPKKRGRSRSVPVSFYEIRSPEISPGLEVPTPPVQGLEPPVLECMEKDHVEPDHVLIVQQVLQELRQYHGARQRACMSASPGGAHSNLTWFEFLSESEDGAGKNEKSDKSTSVKRRLSCLRSRVTRQKEKGKSPAHLKDKGQDARERRECVNGHQLLQGTFSGPSSCPLCGKPFLSSASLKEHPRGTLLSDGSPALSRNVGMTVSQKGGPQPTPSPAGPGTQLGPITGEMDEADSAFLKFKQTADDSLSLTSPNTESIFVEDPYTASLRSEIESDGHEFEAESWSLAVDAAYAKKQKREVVKRQDVLYELMQTEVHHVRTLKIMLKVYSRALQEELQFSSKAIGRLFPCADDLLETHSHFLARLKERRQESLEEGSDRNYVIQKIGDLLVQQFSGENGERMKEKYGVFCSGHNEAVSHYKLLLQQNKKFQNLIKKIGNFSIVRRLGVQECILLVTQRITKYPVLVERIIQNTEAGTEDYEDLTQALNLIKDIISQVDAKVSECEKGQRLREIAGKMDLKSSSKLKNGLTFRKEDMLQRQLHLEGMLCWKTTSGRLKDILAILLTDVLLLLQEKDQKYVFASVDSKPPVISLQKLIVREVANEEKAMFLISASLQGPEMYEIYTSSKEDRNAWMAHIQRAVESCPDEEEGPFSLPEEERKVVEARATRLRDFQERLSMKDQLIAQSLLEKQQIYLEMAEMGGLEDLPQPRGLFRGGDPSETLQGELILKSAMSEIEGIQSLICRQLGSANGQAEDGGSSTGPPRRAETFAGYDCTNSPTKNGSFKKKVSSTDPRPRDWRGPPNSPDLKLSDSDIPGSSEESPQVVEAPGTESDPRLPTVLESELVQRIQTLSQLLLNLQAVIAHQDSYVETQRAAIQEREKQFRLQSTRGNLLLEQERQRNFEKQREERAALEKLQSQLRHEQQRWERERQWQHQELERAGARLQEREGEARQLRERLEQERAELERQRQAYQHDLERLREAQRAVERERERLELLRRLKKQNTAPGALPPDTLAEAQPPSHPPSFNGEGLEGPRVSMLPSGVGPEYAERPEVARRDSAPTENRLAKSDVPIQLLSATNQFQRQAAVQQQIPTKLAASTKGGKDKGGKSRGSQRWESSASFDLKQQLLLNKLMGKDESTSRNRRSLSPILPGRHSPAPPPDPGFPAPSPPPADSPSEGFSLKAGGTALLPGPPAPSPLPATPLSAKEDASKEDVIFF

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.3848

(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	6jxaA	0.27	9.75	0.024	0.409	model1_6jxaA.pdb.gz
2	4d0nB	0.27	1.63	0.527	0.270	model1_4d0nB.pdb.gz
3	4bedB	0.26	9.67	0.049	0.390	model1_4bedB.pdb.gz
4	3hmjG	0.25	10.32	0.039	0.403	model1_3hmjG.pdb.gz
5	6um1A	0.25	10.32	0.037	0.402	model1_6um1A.pdb.gz
6	2pffB	0.25	9.79	0.039	0.383	model1_2pffB.pdb.gz
7	2uvcG	0.25	10.07	0.028	0.393	model1_2uvcG.pdb.gz
8	6u5vB	0.25	10.43	0.040	0.402	model1_6u5vB.pdb.gz
9	6z2wE	0.25	9.94	0.030	0.386	model1_6z2wE.pdb.gz
10	3odoA	0.25	2.96	0.294	0.262	model1_3odoA.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:0098772	0.77	molecular function regulator
GO:0005085	0.75	guanyl-nucleotide exchange factor activity
GO:0005088	0.63	Ras guanyl-nucleotide exchange factor activity
GO:0005089	0.55	Rho guanyl-nucleotide exchange factor 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:0065007	0.83	biological regulation
GO:0050794	0.81	regulation of cellular process
GO:0044699	0.71	single-organism process
GO:0009987	0.70	cellular process
GO:0044763	0.66	single-organism cellular process
GO:0048518	0.59	positive regulation of biological process
GO:0048522	0.58	positive regulation of cellular process
GO:0048583	0.57	regulation of response to stimulus
GO:0023051	0.56	regulation of signaling
GO:0010646	0.56	regulation of cell communication
GO:0009966	0.55	regulation of signal transduction
GO:1902531	0.54	regulation of intracellular signal transduction
GO:0051056	0.50	regulation of small GTPase mediated signal transduction

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:0005737	0.76	cytoplasm
GO:0044444	0.72	cytoplasmic part
GO:0016020	0.67	membrane
GO:0043226	0.61	organelle
GO:0005829	0.60	cytosol

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	2fhcA	0.176	9.41	0.033	0.268	3.2.1.41	NA
2	0.060	2pffB	0.138	8.30	0.029	0.192	2.3.1.86	NA
3	0.060	2vkzG	0.254	10.38	0.037	0.407	2.3.1.38 3.1.2.14	519
4	0.060	3hmjA	0.213	10.07	0.039	0.332	2.3.1.86	NA
5	0.060	2r7oA	0.179	9.01	0.041	0.261	2.7.7.48	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:

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	0.11	1x860	0.241	3.72	0.270	0.262	0.78	III	complex1.pdb.gz	428,450,451,454,461,557,565,590,591,594,597,600,601,604,605,608,609

	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.