Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
0  structures 1824  species 0  interactions 2312  sequences 13  architectures

Family: MVIN (PF03023)

Summary: MviN-like protein

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "MOP flippase ". More...

MOP flippase Edit Wikipedia article

The multidrug/oligosaccharidyl-lipid/polysaccharide (MOP) flippase superfamily (TC# 2.A.66) is a group of integral membrane protein families. The MOP flippase superfamily includes twelve distantly related families, six for which functional data are available:

  1. One ubiquitous family (MATE) specific for drugs - (TC# 2.A.66.1) The Multi Antimicrobial Extrusion (MATE) Family
  2. One (PST) specific for polysaccharides and/or their lipid-linked precursors in prokaryotes - (TC# 2.A.66.2) The Polysaccharide Transport (PST) Family
  3. One (OLF) specific for lipid-linked oligosaccharide precursors of glycoproteins in eukaryotes - (TC# 2.A.66.3) The Oligosaccharidyl-lipid Flippase (OLF) Family
  4. One (MVF) lipid-peptidoglycan precursor flippase involved in cell wall biosynthesis - (TC# 2.A.66.4) The Mouse Virulence Factor (MVF) Family
  5. One (AgnG) which includes a single functionally characterized member that extrudes the antibiotic, Agrocin 84 - (TC# 2.A.66.5) The Agrocin 84 Antibiotic Exporter (AgnG) Family
  6. And finally, one (Ank) that shuttles inorganic pyrophosphate (PPi) - (TC# 2.A.66.9) The Progressive Ankylosis (Ank) Family

All functionally characterized members of the MOP superfamily catalyze efflux of their substrates, presumably by cation antiport.[1][2]

Functionally characterized families

2.A.66.1 The Multi Antimicrobial Extrusion (MATE) Family

Multi-antimicrobial extrusion protein
Identifiers
Symbol MatE
Pfam PF01554
Pfam clan CL0222
InterPro IPR002528
TCDB 2.A.66
OPM superfamily 249
OPM protein 3mkt

The MATE family is made up of several members and includes a functionally characterized multidrug efflux system from Vibrio parahaemolyticus NorM (TC# 2.A.66.1.1), and several homologues from other closely related bacteria that function by a drug:Na+ antiport mechanism, a putative ethionine resistance protein of Saccharomyces cerevisiae (ERC1 (YHR032w); TC# 2.A.66.1.5), a cationic drug efflux pump in A. thaliana (i.e., AtDTX1 aka AT2G04040; TC# 2.A.66.1.8) and the functionally uncharacterized DNA damage-inducible protein F (DinF; TC# 2.A.66.1.4) of E. coli.[3]

The family includes hundreds of functionally uncharacterized but sequenced homologues from bacteria, archaea, and all eukaryotic kingdoms.[4] A representative list of proteins belonging to the MATE family can be found in the Transporter Classification Database.

Structure

The bacterial proteins are of about 450 amino acyl residues in length and exhibit 12 putative transmembrane segments (TMSs). They arose by an internal gene duplication event from a primordial 6 TMS encoding genetic element. The yeast proteins are larger (up to about 700 residues) and exhibit about 12 TMSs.

hMATE1

Human MATE1 (hMATE1) is an electroneutral H+/organic cation (OC) exchanger responsible for the final excretion step of structurally unrelated toxic organic cations in kidney and liver. Glu273, Glu278, Glu300 and Glu389 are conserved in the transmembrane regions. Substitution with alanine or aspartate reduced export of tetraethylammonium (TEA) and cimetidine, and several had altered substrate affinities.[5] Thus, all of these glutamate residues are involved in binding and/or transport of TEA and cimetidine, but their roles are different.

MATE (NorM) Transport Reaction

The probable transport reaction catalyzed by NorM, and possibly by other proteins of the MATE family is:

Antimicrobial (in) + nNa+ (out) → Antimicrobial (out) + nNa+ (in).

2.A.66.2 The Polysaccharide Transport (PST) Family

Analyses conducted in 1997 showed that members of the PST family formed two major clusters.[6] One is concerned with lipopolysaccharide O-antigen (undecaprenol pyrophosphate-linked O-antigen repeat unit) export (flipping from the cytoplasmic side to the periplasmic side of the inner membranes) in Gram-negative bacteria. On the periplasmic side, polymerization occurs catalyzed by Wzy.[7] The other is concerned with exopolysaccharide or capsular polysaccharide export in both Gram-negative and Gram-positive bacteria. However, arachaeal and eukaryotic homologues are now recognized. The mechanism of energy coupling is not established, but homology with the MATE family suggests that they are secondary carriers. These transporters may function together with auxiliary proteins that allow passage across just the cytoplasmic membrane or both membranes of the Gram-negative bacterial envelope. They may also regulate transport. Thus, each Gram-negative bacterial PST system specific for an exo- or capsular polysaccharide functions in conjunction with a cytoplasmic membrane-periplasmic auxiliary (MPA) protein with a cytoplasmic ATP-binding domain (MPA1-C; TC# 3.C.3) as well as an outer membrane auxiliary protein (OMA; TC #3.C.5). Each Gram-positive bacterial PST system functions in conjunction with a homologous MPA1 + C pair of proteins equivalent to an MPA1-C proteins of Gram-negative bacteria. The C-domain has been shown to possess tyrosine protein kinase activity, so it may function in a regulatory capacity. The lipopolysaccharide exporters may function specifically in the translocation of the lipid-linked O-antigen side chain precursor from the inner leaflet of the cytoplasmic membrane to the outer leaflet.[8] In this respect, they correlate in function with the flippase activities of members of the oligosaccharidyl-lipid flippase (OLF) family of the MVF families.

Structure

The protein members of the PST family are generally of 400-500 amino acyl residues in length and traverse the membrane as putative α-helical spanners twelve times.

PST Transport Reaction

The generalized transport reaction catalyzed by PST family proteins is:

Lipid-linked polysaccharide precursor (in) + energy → Lipid-linked polysaccharide precursor (out).

2.A.66.3 The Oligosaccharidyl-lipid Flippase (OLF) Family

The OLF family is found in the endoplasmic reticular membranes of eukaryotes. N-linked glycosylation in eukaryotic cells follows a conserved pathway in which a tetradecasaccharide substrate (Glc3Man9GlcNAc2) is initially assembled in the ER membrane as a dolichylpyrophosphate (Dol-PP)-linked intermediate before being transferred to an asparaginyl residue in a lumenal protein. An intermediate, Man5GlcNAc2-PP-Dol is made on the cytoplasmic side of the membrane and translocated across the membrane so that the oligosaccharide chain faces the ER lumen where biosynthesis continues to completion. The flippase that catalyzes the translocation step is dependent on the Rft1 protein (TC# 2.A.66.3.1) of S. cerevisiae.[9]

Homologues

Homologues are found in plants, animals and fungi including C. elegans, D. melanogaster, H. sapiens, A. thaliana, S. cerevisiae and S. pombe. These proteins are distantly related to MATE and PST family members and therefore are believed to be secondary carriers.

Structure

The yeast protein, called the nuclear division Rft1 protein (TC# 2.A.66.3.1), is 574 aas with 12 putative TMSs. The homologue in A. thaliana is 401 aas in length with 8 or 9 putative TMSs while that in C. elegans is 522 aas long with 11 putative TMSs.

2.A.66.4 The Mouse Virulence Factor (MVF) Family

One member of the MVF family, MviN (TC# 2.A.66.4.1) of Salmonella typhimurium, has been shown to be an important virulence factor for this organism when infecting the mouse.[10] In several bacteria, mviN genes occur in operons including glnD genes that encode the uridyl transferase that participates in the regulation of nitrogen metabolism.[11] It is thought that MviN may flip the Lipid II peptidoglycan (PG) precursor from the cytoplasmic side of the inner membrane to the periplasmic surface acting as a putative lipid flippase in Salmonella typhimurium.[12][13] In E. coli, MviN is an essential protein which when defective results in the accumulation of polyprenyl diphosphate-N-acetylmuramic acid-(pentapeptide)-N-acetyl-glucosamine, thought to be the peptidoglycan intermediated exported via MviN.[14] In Mycobacterium tuberculosis, MviN is thought to play an essential role in peptidoglycan biosynthesis.[15]

Another MVF protein, MurJ, functions as a peptidoglycan biosynthesis protein.[16] A 3-d structureal model shows that MurJ contains a solvent-exposed cavity within the plane of the membrane.[17] MurJ has 14 TMSs, and specific charged residues localized in the central cavity are essential for function. This structural homology model suggests that MurJ functions as an essential transporter in PG biosynthesis.[17] Based on an in vivo assay, MurJ acts as a flippase for the lipid-linked cell wall precursor, polyisoprenoid-linked disaccharide-peptapeptide.[18] There is controversy about the role of this porter and FtsW/RodA which on the basis of an in vitro assay, were thought to be flippases for the same intermediate.[19]

2.A.66.5 The Agrocin 84 Antibiotic Exporter (AgnG) Family

Agrocin 84 is a disubstituted adenine nucleotide antibiotic made by and specific for Agrobacteria. It is encoded by the pAgK84 plasmid of A. tumefaciens [20] and targets a tRNA synthetase.[21] The agnG gene encodes a protein of 496 aas with 12-13 putative TMSs and a short hydrophilic N-terminal domain of 80 residues. A TCDB Blast search with 2 iterations shows that members of the AgnG family are related to the U-MOP12 family (TC# 2.A.66.12) and the PST family (TC# 2.A.66.2) and more distantly related to the OLF (TC# 2.A.66.3), MVF (TC# 2.A.66.4), and LPS-F (TC# 2.A.66.10) families.

Transport Reaction

The reaction catalyzed by AgnG is:

agrocin (in) → agrocin (out)

AgnG homologue 2 of Lyngbya sp. (TC# 2.A.66.5.3) is thought to be a polysaccharide exporter.[22]

2.A.66.9 The Progressive Ankylosis (Ank) Family

Craniometaphyseal dysplasia (CMD) is a bone dysplasia characterized by overgrowth and sclerosis of the craniofacial bones and abnormal modeling of the metaphyses of the tubular bones. Hyperostosis and sclerosis of the skull may lead to cranial nerve compressions resulting in hearing loss and facial palsy. An autosomal dominant form of the disorder has been linked to chromosome 5p15.2-p14.1 within a region harboring the human homolog (ANKH; TC# 2.A.66.9.1) of the mouse progressive ankylosis (ank) gene. The ANK protein spans the cell membrane and shuttles inorganic pyrophosphate (PPi), a major inhibitor of physiologic and pathologic calcification, bone mineralization and bone resorption.[23]

Structure

The ANK protein has 12 membrane-spanning helices with a central channel permitting the passage of PPi. Mutations occur at highly conserved amino acid residues presumed to be located in the cytosolic portion of the protein. The PPi carrier ANK is concerned with bone formation and remodeling.[23]

Other Families

  • 2.A.66.6 - The Putative Exopolysaccharide Exporter (EPS-E) Family
  • 2.A.66.7 - Putative O-Unit Flippase (OUF) Family
  • 2.A.66.8 - Unknown MOP-1 (U-MOP1) Family
  • 2.A.66.10 - LPS Precursor Flippase (LPS-F) Family
  • 2.A.66.11 - Uncharacterized MOP-11 (U-MOP11) Family
  • 2.A.66.12 - Uncharacterized MOP-12 (U-MOP12) Family

See also

References

  1. ^ Hvorup, Rikki N.; Winnen, Brit; Chang, Abraham B.; Jiang, Yong; Zhou, Xiao-Feng; Saier, Milton H. (2003-03-01). "The multidrug/oligosaccharidyl-lipid/polysaccharide (MOP) exporter superfamily". European journal of biochemistry / FEBS. 270 (5): 799–813. doi:10.1046/j.1432-1033.2003.03418.x. ISSN 0014-2956. PMID 12603313. 
  2. ^ Yen, Ming Ren; Chen, Jonathan S.; Marquez, Jose L.; Sun, Eric I.; Saier, Milton H. (2010-01-01). "Multidrug resistance: phylogenetic characterization of superfamilies of secondary carriers that include drug exporters". Methods in Molecular Biology (Clifton, N.J.). 637: 47–64. doi:10.1007/978-1-60761-700-6_3. ISSN 1940-6029. PMID 20419429. 
  3. ^ Saier, MH Jr. "2.A.66.1 The Multi Antimicrobial Extrusion (MATE) Family". Transporter Classification Database. Saier Lab Bioinformatics Group / SDSC. 
  4. ^ Kuroda, Teruo; Tsuchiya, Tomofusa (2009-05-01). "Multidrug efflux transporters in the MATE family". Biochimica et Biophysica Acta. 1794 (5): 763–768. doi:10.1016/j.bbapap.2008.11.012. ISSN 0006-3002. PMID 19100867. 
  5. ^ Matsumoto, Takuya; Kanamoto, Takuji; Otsuka, Masato; Omote, Hiroshi; Moriyama, Yoshinori (2008-04-01). "Role of glutamate residues in substrate recognition by human MATE1 polyspecific H+/organic cation exporter". American Journal of Physiology. Cell Physiology. 294 (4): C1074–1078. doi:10.1152/ajpcell.00504.2007. ISSN 0363-6143. PMID 18305230. 
  6. ^ Paulsen, I. T.; Beness, A. M.; Saier, M. H. (1997-08-01). "Computer-based analyses of the protein constituents of transport systems catalysing export of complex carbohydrates in bacteria". Microbiology (Reading, England). 143 ( Pt 8): 2685–2699. doi:10.1099/00221287-143-8-2685. ISSN 1350-0872. PMID 9274022. 
  7. ^ Marolda, Cristina L.; Tatar, Laura D.; Alaimo, Cristina; Aebi, Markus; Valvano, Miguel A. (2006-07-01). "Interplay of the Wzx translocase and the corresponding polymerase and chain length regulator proteins in the translocation and periplasmic assembly of lipopolysaccharide o antigen". Journal of Bacteriology. 188 (14): 5124–5135. doi:10.1128/JB.00461-06. ISSN 0021-9193. PMC 1539953Freely accessible. PMID 16816184. 
  8. ^ Islam, Salim T.; Lam, Joseph S. (2013-04-01). "Wzx flippase-mediated membrane translocation of sugar polymer precursors in bacteria". Environmental Microbiology. 15 (4): 1001–1015. doi:10.1111/j.1462-2920.2012.02890.x. ISSN 1462-2920. PMID 23016929. 
  9. ^ Helenius, Jonne; Ng, Davis T. W.; Marolda, Cristina L.; Walter, Peter; Valvano, Miguel A.; Aebi, Markus (2002-01-24). "Translocation of lipid-linked oligosaccharides across the ER membrane requires Rft1 protein". Nature. 415 (6870): 447–450. doi:10.1038/415447a. ISSN 0028-0836. PMID 11807558. 
  10. ^ Kutsukake, K.; Okada, T.; Yokoseki, T.; Iino, T. (1994-05-27). "Sequence analysis of the flgA gene and its adjacent region in Salmonella typhimurium, and identification of another flagellar gene, flgN". Gene. 143 (1): 49–54. ISSN 0378-1119. PMID 8200538. 
  11. ^ Rudnick, P. A.; Arcondéguy, T.; Kennedy, C. K.; Kahn, D. (2001-04-01). "glnD and mviN are genes of an essential operon in Sinorhizobium meliloti". Journal of Bacteriology. 183 (8): 2682–2685. doi:10.1128/JB.183.8.2682-2685.2001. ISSN 0021-9193. PMC 95188Freely accessible. PMID 11274131. 
  12. ^ Vasudevan, Pradeep; McElligott, Jessica; Attkisson, Christa; Betteken, Michael; Popham, David L. (2009-10-01). "Homologues of the Bacillus subtilis SpoVB protein are involved in cell wall metabolism". Journal of Bacteriology. 191 (19): 6012–6019. doi:10.1128/JB.00604-09. ISSN 1098-5530. PMC 2747891Freely accessible. PMID 19648239. 
  13. ^ Fay, Allison; Dworkin, Jonathan (2009-10-01). "Bacillus subtilis homologs of MviN (MurJ), the putative Escherichia coli lipid II flippase, are not essential for growth". Journal of Bacteriology. 191 (19): 6020–6028. doi:10.1128/JB.00605-09. ISSN 1098-5530. PMC 2747889Freely accessible. PMID 19666716. 
  14. ^ Inoue, Azusa; Murata, Yoshimitsu; Takahashi, Hiroshi; Tsuji, Naoko; Fujisaki, Shingo; Kato, Jun-ichi (2008-11-01). "Involvement of an essential gene, mviN, in murein synthesis in Escherichia coli". Journal of Bacteriology. 190 (21): 7298–7301. doi:10.1128/JB.00551-08. ISSN 1098-5530. PMC 2580715Freely accessible. PMID 18708495. 
  15. ^ Gee, Christine L.; Papavinasasundaram, Kadamba G.; Blair, Sloane R.; Baer, Christina E.; Falick, Arnold M.; King, David S.; Griffin, Jennifer E.; Venghatakrishnan, Harene; Zukauskas, Andrew (2012-01-24). "A phosphorylated pseudokinase complex controls cell wall synthesis in mycobacteria". Science Signaling. 5 (208): ra7. doi:10.1126/scisignal.2002525. ISSN 1937-9145. PMC 3664666Freely accessible. PMID 22275220. 
  16. ^ Ruiz, Natividad (2008-10-07). "Bioinformatics identification of MurJ (MviN) as the peptidoglycan lipid II flippase in Escherichia coli". Proceedings of the National Academy of Sciences of the United States of America. 105 (40): 15553–15557. doi:10.1073/pnas.0808352105. ISSN 1091-6490. PMC 2563115Freely accessible. PMID 18832143. 
  17. ^ a b Butler, Emily K.; Davis, Rebecca M.; Bari, Vase; Nicholson, Paul A.; Ruiz, Natividad (2013-10-01). "Structure-function analysis of MurJ reveals a solvent-exposed cavity containing residues essential for peptidoglycan biogenesis in Escherichia coli". Journal of Bacteriology. 195 (20): 4639–4649. doi:10.1128/JB.00731-13. ISSN 1098-5530. PMC 3807429Freely accessible. PMID 23935042. 
  18. ^ Sham, Lok-To; Butler, Emily K.; Lebar, Matthew D.; Kahne, Daniel; Bernhardt, Thomas G.; Ruiz, Natividad (2014-07-11). "Bacterial cell wall. MurJ is the flippase of lipid-linked precursors for peptidoglycan biogenesis". Science (New York, N.Y.). 345 (6193): 220–222. doi:10.1126/science.1254522. ISSN 1095-9203. PMC 4163187Freely accessible. PMID 25013077. 
  19. ^ Young, Kevin D. (2014-07-11). "Microbiology. A flipping cell wall ferry". Science (New York, N.Y.). 345 (6193): 139–140. doi:10.1126/science.1256585. ISSN 1095-9203. PMID 25013047. 
  20. ^ Kim, Jung-Gun; Park, Byoung Keun; Kim, Sung-Uk; Choi, Doil; Nahm, Baek Hie; Moon, Jae Sun; Reader, John S.; Farrand, Stephen K.; Hwang, Ingyu (2006-06-06). "Bases of biocontrol: sequence predicts synthesis and mode of action of agrocin 84, the Trojan horse antibiotic that controls crown gall". Proceedings of the National Academy of Sciences of the United States of America. 103 (23): 8846–8851. doi:10.1073/pnas.0602965103. ISSN 0027-8424. PMC 1482666Freely accessible. PMID 16731618. 
  21. ^ Reader, John S.; Ordoukhanian, Phillip T.; Kim, Jung-Gun; de Crécy-Lagard, Valerie; Hwang, Ingyu; Farrand, Stephen; Schimmel, Paul (2005-09-02). "Major biocontrol of plant tumors targets tRNA synthetase". Science (New York, N.Y.). 309 (5740): 1533. doi:10.1126/science.1116841. ISSN 1095-9203. PMID 16141066. 
  22. ^ "2.A.66.5: The Agrocin 84 Antibiotic Exporter (AgnG) Family". Transporter Classification Database. Retrieved 2016-03-08. 
  23. ^ a b Nürnberg, P.; Thiele, H.; Chandler, D.; Höhne, W.; Cunningham, M. L.; Ritter, H.; Leschik, G.; Uhlmann, K.; Mischung, C. (2001-05-01). "Heterozygous mutations in ANKH, the human ortholog of the mouse progressive ankylosis gene, result in craniometaphyseal dysplasia". Nature Genetics. 28 (1): 37–41. doi:10.1038/88236. ISSN 1061-4036. PMID 11326272. 

As of 19:37, 24 February 2016 (UTC), this article is derived in whole or in part from Transporter Classification Database. The copyright holder has licensed the content in a manner that permits reuse under CC BY-SA 3.0 and GFDL. All relevant terms must be followed. The original text was at "2.A.66 The Multidrug/Oligosaccharidyl-lipid/Polysaccharide (MOP) Flippase Superfamily".

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

MviN-like protein Provide feedback

Deletion of the mviN virulence gene in Salmonella enterica serovar. Typhimurium greatly reduces virulence in a mouse model of typhoid-like disease [1]. Open reading frames encoding homologues of MviN have since been identified in a variety of bacteria [2] including pathogens and non-pathogens and plant-symbionts. In the nitrogen-fixing symbiont Rhizobium tropici, mviN is required for motility. The MviM protein is predicted to be membrane-associated.

Literature references

  1. Carsiotis M, Stocker BA, Weinstein DL, O'Brien AD; , Infect Immun 1989;57:3276-3280.: A Salmonella typhimurium virulence gene linked to flg. PUBMED:2680969 EPMC:2680969

  2. Rudnick PA, Arcondeguy T, Kennedy CK, Kahn D; , J Bacteriol 2001;183:2682-2685.: glnD and mviN are genes of an essential operon in Sinorhizobium meliloti. PUBMED:11274131 EPMC:11274131

  3. O'Connell KP, Raffel SJ, Saville BJ, Handelsman J; , Microbiology 1998;144:2607-2617.: Mutants of Rhizobium tropici strain CIAT899 that do not induce chlorosis in plants. PUBMED:9782510 EPMC:9782510


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004268

Peptidoglycan synthesis (PG) biosynthesis involves the formation of peptidoglycan precursor lipid II (undecaprenyl-pyrophosphate-linked N-acetyl glucosamine-N-acetyl muramic acid-pentapeptide) on the cytosolic face of the cell membrane. Lipid II is then translocated across the membrane and its glycopeptide moiety becomes incorporated into the growing cell wall mesh.

MviN, renamed as MurJ, is a lipid II flippase essential for cell wall peptidoglycan synthesis [PUBMED:18832143, PUBMED:24688094].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

Loading domain graphics...

Pfam Clan

This family is a member of clan MviN_MATE (CL0222), which has the following description:

This superfamily consists of a variety of integral membrane protein families. The MATE family are known to be transporters. Other proteins have been implicated in virulence and polysaccharide biosynthesis.

The clan contains the following 7 members:

ANKH MatE MVIN Polysacc_synt Polysacc_synt_3 Polysacc_synt_C Rft-1

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(13)
Full
(2312)
Representative proteomes UniProt
(9328)
NCBI
(24541)
Meta
(3955)
RP15
(746)
RP35
(1886)
RP55
(3177)
RP75
(4906)
Jalview View  View  View  View  View  View  View  View  View 
HTML View  View               
PP/heatmap 1 View               

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(13)
Full
(2312)
Representative proteomes UniProt
(9328)
NCBI
(24541)
Meta
(3955)
RP15
(746)
RP35
(1886)
RP55
(3177)
RP75
(4906)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(13)
Full
(2312)
Representative proteomes UniProt
(9328)
NCBI
(24541)
Meta
(3955)
RP15
(746)
RP35
(1886)
RP55
(3177)
RP75
(4906)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Pfam-B_1348 (release 6.4)
Previous IDs: none
Type: Family
Author: Griffiths-Jones SR, Studholme DJ
Number in seed: 13
Number in full: 2312
Average length of the domain: 438.50 aa
Average identity of full alignment: 24 %
Average coverage of the sequence by the domain: 79.49 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 17690987 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.4 27.4
Trusted cut-off 27.4 27.4
Noise cut-off 27.3 27.3
Model length: 452
Family (HMM) version: 12
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.