This page was produced as an assignment for Genetics 677, an undergraduate course at UW-Madison.

Protein Homology

To elucidate the evolutionary history of the human GRM7 gene, candidate orthologous and paralogous proteins were identified. To identify candidate orthologs, "GRM7" was queried on the homologene website. Additionally, candidate orthologous proteins were found using a BLAST search on Wormbase and FlyBase for proteins similar to the human GRM7 isoform a protein. Candidate orthologs of the human GRM7 protein were found in animals ranging from nematodes to fruit flies to mice. No candidate orthologs of the GRM7 protein were found in plants or bacteria, perhaps because, unlike animals, these organisms do not have a nervous system, and therefore, would not need a neurotransmitter receptor like the GRM7 protein.

Candidate paralogs of the human GRM7 protein were identified by querying the GRM7 isoform a protein sequence against RefSeq protein on the
BLAST human sequences website. Not suprisingly, candidate paralogs of the GRM7 protein include the entire family of GRM protein (GRM1-GRM8). Two other proteins, CASR and TAS1R2, also show high similarity to the GRM7 protein and were identified as candidate paralogs
. Whether these proteins truly represent paralogs remains uncertain; however, they will be included in all analyses involving homologs of GRM7 conducted for this project.

Orthologs of Protein

Table
1. Orthologs of the GRM7 protein. For each orthologous protein, the table gives the organism in which it is found, the name of the protein, the accession number (with a link to the GenPept entry for that protein), the GI number, the size of the protein, the percent and fraction of the amino acids that are identical to the human isoform a GRM7 amino acid sequence (as determined by a BLAST align analysis), and the percent and fraction of the amino acids that are either identical with, or a conserved change to, the the human isoform a GRM7 amino acid sequence (as determined by a BLAST analysis) (Entrez Protein, 2008 and 2009). A conserved change represents a change that preserve the physico-chemical properties of the original residue (Altschul, et al., 2005).

Organism

 

Organism

Protein Name

Protein Accession Number

GI Number

Protein Size

% Identity

Similarity

Homo sapiens (human)

glutamate receptor, metabotropic 7 isoform a precursor

NP_000835.1

4504147

915 aa

n/a

n/a

Pan troglodytes (chimpanzee)

PREDICTED: glutamate receptor, metabotropic 7 isoform 3

XP_516252.2

114585243

915 aa

912/915 (99%)

914/915 (99%)

Mus musculus (mouse)

glutamate receptor, metabotropic 7

NP_796302.2

60460877

915 aa

910/915 (99%)

912/915 (99%)

Rattus norvegicus (rat)

glutamate receptor, metabotropic 7

NP_112302.1

13591963

915 aa

909/915 (99%)

913/915 (99%)

Canis lupus familiaris (dog)

PREDICTED: similar to glutamate receptor, metabotropic 7 isoform b precursor

XP_541789.2

73985040

922 aa

898/907 (99%)

901/907 (99%)

Gallus gallus (chicken)

PREDICTED: similar to glutamate receptor, metabotropic 7

XP_414442.2 

118097083

919 aa

814/884 (92%)

854/884 (96%)

Danio rerio (zebrafish)

hypothetical protein LOC565450

NP_001073489.1

121583804

905 aa

629/852 (73%)

742/852 (87%)

Caenorhabditis elegans (nematode)

Metabotropic GLutamate receptor family member (mgl-1)

NP_509674.1

17569063

999 aa

350/911 (38%)

501/911 (54%)

Drosophila melanogaster (fruit fly)

metabotropic glutamate receptor

NP_524639.2

24638732

976 aa

423/895 (47%)

554/895 (61%)

 

Paralogs of Protein

Table 2. Paralogs of the GRM7 protein. For each paralogous protein, the table gives the name of the protein, the accession number (with a link to the FASTA-formatted sequence for that protein), the GI number, the size of the protein, the percent and fraction of the amino acids that are identical to the human isoform a GRM7 amino acid sequence (as determined by a BLAST align analysis), and the percent and fraction of the amino acids that are either identical with, or a conserved change to, the the human isoform a GRM7 amino acid sequence (as determined by a BLAST analysis) (Entrez Protein, 2008 and 2009). A conserved change represents a change that preserve the physico-chemical properties of the original residue (Altschul, et al., 2005).

Protein Name

 

Protein Name

Protein Accession Number

GI Number

Protein Size

% Identity

Similarity

glutamate receptor, metabotropic 7 isoform a precursor

NP_000835.1

4504147

915 aa

n/a

n/a

glutamate receptor, metabotropic 1 isoform alpha precursor

NP_000829.2

166999098

1194 aa

367/868 (42%)

515/868 (59%)

glutamate receptor, metabotropic 2 isoform a precursor

NP_000830.2

66529100

872 aa

380/833 (45%)

513/833 (61%)

glutamate receptor, metabotropic 3 precursor

NP_000831.2

46358417

879 aa

387/849 (45%)

528/849 (62%)

glutamate receptor, metabotropic 4

NP_000832.1

4504141

912 aa

629/884 (71%)

753/884 (85%)

glutamate receptor, metabotropic 5 isoform a precursor

NP_001137303.1

219842343

1212 aa

346/826 (41%)

503/826 (60%)

glutamate receptor, metabotropic 6 precursor

NP_000834.2

110611176

877 aa

575/839 (68%)

703/839 (83%)

glutamate receptor, metabotropic 8 isoform a precursor

NP_000836.2

187960067

908 aa

668/885 (75%)

769/885 (86%)

calcium-sensing receptor

NP_000379.2

37577159

1078 aa

288/928 (31%)

438/928 (47%)

taste receptor, type 1, member 2

NP_689418.2

112789566

839 aa

244/904 (26%)

401/904 (44%)

 

References

References

 

Altschul, S.F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D. J. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research, 25:3389-3402.

Altschul, S. F., Wootton, J. C., Gertz, E. M., Agarwala, R., Morgulis, A., Schäffer, A. A., and Yu, Y. K. (2005). Protein database searches using compositionally adjusted substitution matrices. FEBS J., 272:5101-5109.

Entrez Protein. (2005). PREDICTED: similar to glutamate receptor, metabotropic 7 isoform b precursor [Canis familiaris]. Retrieved February 27, 2009, from, http://www.ncbi.nlm.nih.gov/protein/73985040.

Entrez Protein. (2006). PREDICTED: similar to glutamate receptor, metabotropic 7 [Gallus gallus]. Retrieved February 27, 2009, from, http://www.ncbi.nlm.nih.gov/protein/118097083.

Entrez Protein. (2006). PREDICTED: glutamate receptor, metabotropic 7 isoform 3 [Pan troglodytes]. Retrieved February 27, 2009, from, http://www.ncbi.nlm.nih.gov/protein/114585243.

Entrez Protein. (2007). hypothetical protein LOC565450 [Danio rerio]. Retrieved February 27, 2009, from, http://www.ncbi.nlm.nih.gov/protein/121583804.

Entrez Protein. (2008). glutamate receptor, metabotropic 7 [Rattus norvegicus]. Retrieved February 27, 2009, from, http://www.ncbi.nlm.nih.gov/protein/13591963.

Entrez Protein. (2008). Metabotropic GLutamate receptor family member (mgl-1) [Caenorhabditis elegans]. Retrieved February 27, 2009, from, http://www.ncbi.nlm.nih.gov/protein/17569063.

Entrez Protein. (2009). calcium-sensing receptor [Homo sapiens]. Retrieved February 27, 2009, from, http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=protein&dopt=GenPept&RID=UKA0ZMG6016&log%24=prottop&blast_rank=14&list_uids=37577159.

Entrez Protein. (2009). glutamate receptor, metabotropic 7 isoform a precursor [Homo sapiens]. Retrieved February 27, 2009, from, http://www.ncbi.nlm.nih.gov/protein/4504147.

Entrez Protein. (2009). glutamate receptor, metabotropic 1 isoform alpha precursor [Homo sapiens]. Retrieved February 27, 2009, from, http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=protein&dopt=GenPept&RID=UKA0ZMG6016&log%24=prottop&blast_rank=13&list_uids=166999098.

Entrez Protein. (2009). glutamate receptor, metabotropic 2 isoform a precursor [Homo sapiens]. Retrieved February 27, 2009, from, http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=protein&dopt=GenPept&RID=UKA0ZMG6016&log%24=prottop&blast_rank=8&list_uids=66529100.
Entrez Protein. (2009). glutamate receptor, metabotropic 3 precursor [Homo sapiens]. Retrieved February 27, 2009, from, http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=protein&dopt=GenPept&RID=UKA0ZMG6016&log%24=prottop&blast_rank=7&list_uids=46358417.
Entrez Protein. (2009). glutamate receptor, metabotropic 4 [Homo sapiens]. Retrieved February 27, 2009, from, http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=protein&dopt=GenPept&RID=UKA0ZMG6016&log%24=prottop&blast_rank=5&list_uids=4504141.
Entrez Protein. (2009). glutamate receptor, metabotropic 5 isoform a precursor [Homo sapiens]. Retrieved February 27, 2009, from, http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=protein&dopt=GenPept&RID=UKA0ZMG6016&log%24=prottop&blast_rank=11&list_uids=219842343.
Entrez Protein. (2009). glutamate receptor, metabotropic 6 precursor [Homo sapiens]. Retrieved February 27, 2009, from, http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=protein&dopt=GenPept&RID=UKA0ZMG6016&log%24=prottop&blast_rank=6&list_uids=110611176.

Entrez Protein. (2009). glutamate receptor, metabotropic 7 [Mus musculus]. Retrieved February 27, 2009, from, http://www.ncbi.nlm.nih.gov/protein/60460877.

Entrez Protein. (2009). glutamate receptor, metabotropic 8 isoform a precursor [Homo sapiens]. Retrieved February 27, 2009, from, http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=protein&dopt=GenPept&RID=UKA0ZMG6016&log%24=prottop&blast_rank=3&list_uids=187960067.

Entrez Protein. (2009). metabotropic glutamate receptor [Drosophila melanogaster]. Retrieved February 27, 2009, from, http://www.ncbi.nlm.nih.gov/protein/24638732.

Entrez Protein. (2009). taste receptor, type 1, member 2 [Homo sapiens]. Retrieved February 27, 2009, from, http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=protein&dopt=GenPept&RID=UKA0ZMG6016&log%24=prottop&blast_rank=15&list_uids=112789566.

 

 

Jennifer Wagner
wagner4@wisc.edu
Updated February 28, 2009
http://www.gen677.weebly.com