D-I-TASSER Q2VPA4

D-I-TASSER results for Q2VPA4

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

Summary of the Protein

Uniprot ID: Q2VPA4
Protein Name: Complement component receptor 1-like protein
Gene Name: CR1L

Input Sequence in FASTA format

>Q2VPA4 (569 residues)
MAPPVRLERPFPSRRFPGLLLAALVLLLSSFSDQCNVPEWLPFARPTNLTDDFEFPIGTY
LNYECRPGYSGRPFSIICLKNSVWTSAKDKCKRKSCRNPPDPVNGMAHVIKDIQFRSQIK
YSCPKGYRLIGSSSATCIISGNTVIWDNKTPVCDRIICGLPPTIANGDFTSISREYFHYG
SVVTYHCNLGSRGKKVFELVGEPSIYCTSKDDQVGIWSGPAPQCIIPNKCTPPNVENGIL
VSDNRSLFSLNEVVEFRCQPGFGMKGPSHVKCQALNKWEPELPSCSRVCQPPPDVLHAER
TQRDKDNFSPGQEVFYSCEPGYDLRGSTYLHCTPQGDWSPAAPRCEVKSCDDFLGQLPNG
HVLFPLNLQLGAKVDFVCDEGFQLKGSSASYCVLAGMESLWNSSVPVCERKSCETPPVPV
NGMVHVITDIHVGSRINYSCTTGHRLIGHSSAECILSGNTAHWSMKPPICQQIFCPNPPA
ILNGRHTGTPLGDIPYGKEVSYTCDPHPDRGMTFNLIGESTIRRTSEPHGNGVWSSPAPR
CELPVGAGSHDALIVGKFYEVFAEEFCHL

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 AttentionPotential. 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	Q2VPA4-D1	1-227	227		MAPPVRLERPFPSRRFPGLLLAALVLLLSSFSDQCNVPEWLPFARPTNLTDDFEFPIGTYLNYECRPGYSGRPFSIICLKNSVWTSAKDKCKRKSCRNPPDPVNGMAHVIKDIQFRSQIKYSCPKGYRLIGSSSATCIISGNTVIWDNKTPVCDRIICGLPPTIANGDFTSISREYFHYGSVVTYHCNLGSRGKKVFELVGEPSIYCTSKDDQVGIWSGPAPQCIIP
2	Q2VPA4-D2	228-286	59		NKCTPPNVENGILVSDNRSLFSLNEVVEFRCQPGFGMKGPSHVKCQALNKWEPELPSCS
3	Q2VPA4-D3	287-347	61		RVCQPPPDVLHAERTQRDKDNFSPGQEVFYSCEPGYDLRGSTYLHCTPQGDWSPAAPRCEV
4	Q2VPA4-D4	348-411	64		KSCDDFLGQLPNGHVLFPLNLQLGAKVDFVCDEGFQLKGSSASYCVLAGMESLWNSSVPVCERK
5	Q2VPA4-D5	412-472	61		SCETPPVPVNGMVHVITDIHVGSRINYSCTTGHRLIGHSSAECILSGNTAHWSMKPPICQQ
6	Q2VPA4-D6	473-569	97		IFCPNPPAILNGRHTGTPLGDIPYGKEVSYTCDPHPDRGMTFNLIGESTIRRTSEPHGNGVWSSPAPRCELPVGAGSHDALIVGKFYEVFAEEFCHL

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.63

(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 AttentionPotential, 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	6fwvA	0.38	5.74	0.097	0.506	model1_6fwvA.pdb.gz
2	2gsxA	0.36	7.82	0.090	0.591	model1_2gsxA.pdb.gz
3	6vg4A	0.34	7.46	0.043	0.548	model1_6vg4A.pdb.gz
4	5sznA	0.34	6.75	0.041	0.504	model1_5sznA.pdb.gz
5	2wiiC	0.33	3.87	0.232	0.392	model1_2wiiC.pdb.gz
6	2v5yA	0.33	6.82	0.038	0.499	model1_2v5yA.pdb.gz
7	5t9tA	0.33	7.47	0.055	0.527	model1_5t9tA.pdb.gz
8	1ojyC	0.33	2.06	0.375	0.344	model1_1ojyC.pdb.gz
9	6m3yA	0.33	6.81	0.049	0.481	model1_6m3yA.pdb.gz
10	2zuoM	0.33	7.35	0.035	0.515	model1_2zuoM.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:0004872	0.51	receptor 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	0.89	biological regulation
GO:0050789	0.86	regulation of biological process
GO:0050896	0.74	response to stimulus
GO:0048518	0.74	positive regulation of biological process
GO:0048583	0.73	regulation of response to stimulus
GO:0002682	0.70	regulation of immune system process
GO:0050794	0.68	regulation of cellular process
GO:0008152	0.68	metabolic process
GO:0002376	0.67	immune system process
GO:0044699	0.66	single-organism process
GO:0050776	0.65	regulation of immune response
GO:0006955	0.65	immune response
GO:0009987	0.61	cellular process
GO:0002684	0.57	positive regulation of immune system process
GO:0071704	0.56	organic substance metabolic process
GO:0002252	0.56	immune effector process
GO:0019222	0.55	regulation of metabolic process
GO:0060255	0.54	regulation of macromolecule metabolic process
GO:0048584	0.54	positive regulation of response to stimulus
GO:0080090	0.53	regulation of primary metabolic process
GO:0044238	0.53	primary metabolic process
GO:0044763	0.52	single-organism cellular process
GO:0050778	0.51	positive regulation of immune response
GO:0051246	0.50	regulation of protein metabolic process
GO:0048522	0.50	positive regulation of cellular process
GO:0043170	0.50	macromolecule metabolic process
GO:0002253	0.50	activation of immune response

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	0.85	cell part
GO:0044425	0.61	membrane part
GO:0044459	0.53	plasma membrane part
GO:0044421	0.47	extracellular region part
GO:0032991	0.43	macromolecular complex
GO:0044424	0.42	intracellular part
GO:0043234	0.42	protein complex
GO:0043226	0.42	organelle
GO:0043227	0.40	membrane-bounded organelle
GO:0016020	0.40	membrane
GO:0005576	0.32	extracellular region
GO:0005579	0.30	membrane attack complex

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	2qy0C	0.201	2.90	0.163	0.221	3.4.21.41 3.4.21.42	130
2	0.060	2e1rA	0.195	6.93	0.041	0.293	3.6.5.3	NA
3	0.060	1g0dA	0.199	7.44	0.036	0.315	2.3.2.13	NA
4	0.060	1kv3A	0.183	7.86	0.041	0.304	2.3.2.13	NA
5	0.060	1mc0A	0.142	6.59	0.055	0.211	3.1.4.17	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	1w7jA	0.170	6.78	0.029	0.253	0.12	UUU	complex1.pdb.gz	124,125,126,127,128
2	0.01	1h8bA	0.058	4.27	0.066	0.070	0.23	III	complex2.pdb.gz	103,126,127,128,130
3	0.01	1utcA	0.113	6.38	0.078	0.163	0.11	III	complex3.pdb.gz	124,127,129
4	0.01	2omy1	0.088	4.87	0.067	0.113	0.11	III	complex4.pdb.gz	95,96,97,98,125
5	0.01	2qkiA	0.151	6.85	0.016	0.230	0.15	III	complex5.pdb.gz	106,120,122,123,124
6	0.01	1w7i0	0.166	7.79	0.027	0.271	0.22	III	complex6.pdb.gz	95,97,126
7	0.01	2b4h0	0.120	5.88	0.056	0.167	0.10	III	complex7.pdb.gz	106,133,134,135,136,137,138
8	0.01	1c9iA	0.115	6.74	0.043	0.172	0.26	III	complex8.pdb.gz	103,104,124,129,131
9	0.01	3rzfA	0.194	6.66	0.021	0.286	0.20	XNM	complex9.pdb.gz	123,131,132,151

	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, 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.