Summary: Mitochondrial ribosomal protein L31
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Ribosomal protein Edit Wikipedia article
|This article needs additional citations for verification. (October 2011)|
|Mitochondrial ribosomal protein L31|
A ribosomal protein is any of the proteins that, in conjunction with rRNA, make up the ribosomal subunits involved in the cellular process of translation. A large part of the knowledge about these organic molecules has come from the study of E. coli ribosomes. Most ribosomal proteins have been isolated and specific antibodies have been produced. These, together with electronic microscopy and the use of certain reactives, have allowed for the determination of the topography of the proteins in the ribosome. E.coli, other bacteria and Archaea have a 30S small subunit and a 50S large subunit, whereas humans and yeasts have a 40S small subunit and a 60S large subunit. Equivalent subunits are frequently numbered differently between bacteria, Archaea, yeasts and humans.
- 1 Proteins in E. coli ribosomes
- 2 Disposition in the small ribosomal subunit
- 3 Table of E.coli small 30S ribosomal subunit proteins
- 4 Assembly of the ribosome in eukaryotes
- 5 Table of E.coli large 50S ribosomal subunit proteins
- 6 Table of Human small 40S ribosomal subunit proteins
- 7 Table of Human large 60S ribosomal subunit proteins
- 8 See also
- 9 References
- 10 Further reading
- 11 External links
Proteins in E. coli ribosomes
The ribosome of E. coli has about 22 proteins in the small subunit (labelled S1 to S22) and 34 proteins in the large subunit (L1 to L36). All of them are different with three exceptions: one protein is found in both subunits (S20 and L26), L7 and L12 are acetylated and methylated forms of the same protein, and L8 is a complex of L7/L12 and L10. In addition, L31 is known to exist in two forms, the full length at 7.9 kilodaltons (kDa) and fragmented at 7.0 kDa. This is why the number of proteins in a ribosome is of 56. Except for S1 (with a molecular weight of 61.2 kDa), the other proteins range in weight between 4.4 and 29.7 kDa.
Recent 'de novo' proteomics experiments where the authors characterized in vivo ribosome-assembly intermediates and associated assembly factors from wild-type Escherichia coli cells using a general quantitative mass spectrometry (qMS) approach have confirmed the presence of all the known small and large subunit components and have identified a total of 21 known and potentially new ribosome-assembly-factors that co-localise with various ribosomal particles.
Disposition in the small ribosomal subunit
In the small (30S) subunit of E. coli ribosomes, the proteins denoted S4, S7, S8, S15, S17, S20 bind independently to 16S rRNA. After assembly of these primary binding proteins, S5, S6, S9, S12, S13, S16, S18, and S19 bind to the growing ribosome. These proteins also potentiate the addition of S2, S3, S10, S11, S14, and S21. Protein binding to helical junctions is important for initiating the correct tertiary fold of RNA and to organize the overall structure. Nearly all the proteins contain one or more globular domains. Moreover, nearly all contain long extensions that can contact the RNA in far-reaching regions. Additional stabilization results from the proteins' basic residues, as these neutralize the charge repulsion of the RNA backbone. Protein-protein interactions also exist to hold structure together by electrostatic and hydrogen bonding interactions. Theoretical investigations pointed to correlated effects of protein-binding onto binding affinities during the assembly process 
Table of E.coli small 30S ribosomal subunit proteins
|Subunit No.||Subunit name||E.coli protein||Pfam family with E.coli protein|
|1||30S ribosomal protein S1||RS1_ECOLI||PF00575|
|2||30S ribosomal protein S2||RS2_ECOLI||PF00318|
|3||30S ribosomal protein S3||RS3_ECOLI||PF00189 ,PF07650|
|4||30S ribosomal protein S4||RS4_ECOLI||PF00163 ,PF01479|
|5||30S ribosomal protein S5||RS5_ECOLI||PF00333 ,PF03719|
|6||30S ribosomal protein S6||RS6_ECOLI||PF01250|
|7||30S ribosomal protein S7||RS7_ECOLI||PF00177|
|8||30S ribosomal protein S8||RS8_ECOLI||PF00410|
|9||30S ribosomal protein S9||RS9_ECOLI||PF00380|
|10||30S ribosomal protein S10||RS10_ECOLI||PF00338|
|11||30S ribosomal protein S11||RS11_ECOLI||PF00411|
|12||30S ribosomal protein S12||RS12_ECOLI||PF00164|
|13||30S ribosomal protein S13||RS13_ECOLI||PF00416|
|14||30S ribosomal protein S14||RS14_ECOLI||PF00253|
|15||30S ribosomal protein S15||RS15_ECOLI||PF00312|
|16||30S ribosomal protein S16||RS16_ECOLI||PF00886|
|27||30S ribosomal protein S17||RS17_ECOLI||PF00366|
|28||30S ribosomal protein S18||RS18_ECOLI||PF01084|
|29||30S ribosomal protein S19||RS19_ECOLI||PF00203|
|20||30S ribosomal protein S20||RS20_ECOLI||PF01649|
|21||30S ribosomal protein S21||RS21_ECOLI||PF01165|
Assembly of the ribosome in eukaryotes
Ribosomes, which synthesize the proteome of cells, are complex ribonucleoproteins that, in eukaryotes, contain 79–80 proteins and four ribosomal RNAs(rRNAs). General or specialized chaperones solubilize the ribosomal proteins and facilitate their import into the nucleus. Assembly of the eukaryotic ribosome appears to be driven by the ribosomal proteins in vivo when assembly is also aided by chaperones. Most ribosomal proteins assemble with rRNA co-transcriptionally, becoming associated more stably as assembly proceeds, and the active sites of both subunits are constructed last.
Table of E.coli large 50S ribosomal subunit proteins
|Subunit No.||Subunit name||E.coli protein||Pfam family with E.coli protein|
|1||50S ribosomal protein L1||RL1_ ECOLI||PF00687 Ribosomal protein L1p/L10e family|
|2||50S ribosomal protein L2||RL2_ ECOLI||PF03947 Ribosomal Proteins L2, C-terminal domain|
|2||50S ribosomal protein L2||RL2_ ECOLI||PF00181 Ribosomal Proteins L2, RNA binding domain|
|3||50S ribosomal protein L3||RL3_ ECOLI||PF00297 Ribosomal protein L3|
|4||50S ribosomal protein L4||RL4_ ECOLI||PF00573 Ribosomal protein L4/L1 family|
|5||50S ribosomal protein L5||RL5_ ECOLI||PF00281 Ribosomal protein L5|
|5||50S ribosomal protein L5||RL5_ ECOLI||PF00673 ribosomal L5P family C-terminus|
|6||50S ribosomal protein L6||RL6_ ECOLI||PF00347 Ribosomal protein L6|
|7/12||50S ribosomal protein L7/L12||RL7_ ECOLI||PF16320 Ribosomal protein L7/L12 dimerisation domain|
|8||50S ribosomal protein L7/L12||RL7_ ECOLI||PF00542 Ribosomal protein L7/L12 C-terminal domain|
|9||50S ribosomal protein L9||RL9_ ECOLI||PF03948 Ribosomal protein L9, C-terminal domain|
|9||50S ribosomal protein L9||RL9_ ECOLI||PF01281 Ribosomal protein L9, N-terminal domain|
|10||50S ribosomal protein L10||RL10_ ECOLI||PF00466 Ribosomal protein L10|
|11||50S ribosomal protein L11||RL11_ ECOLI||PF03946 Ribosomal protein L11, N-terminal domain|
|11||50S ribosomal protein L11||RL11_ ECOLI||PF00298 Ribosomal protein L11, RNA binding domain|
|13||50S ribosomal protein L13||RL13_ ECOLI||PF00572 Ribosomal protein L13|
|14||50S ribosomal protein L14||RL14_ ECOLI||PF00238 Ribosomal protein L14p/L23e|
|15||50S ribosomal protein L15||RL15_ ECOLI||PF00828 Ribosomal protein L18e/L15|
|16||50S ribosomal protein L16||RL16_ ECOLI||PF00252 Ribosomal protein L16p/L10e|
|17||50S ribosomal protein L17||RL17_ ECOLI||PF01196 Ribosomal protein L17|
|18||50S ribosomal protein L18||RL18_ ECOLI||PF00861 Ribosomal L18p/L5e family|
|19||50S ribosomal protein L19||RL19_ ECOLI||PF01245 Ribosomal protein L19|
|20||50S ribosomal protein L20||RL20_ ECOLI||PF00453 Ribosomal protein L20|
|21||50S ribosomal protein L21||RL21_ ECOLI||PF00829 Ribosomal prokaryotic L21 protein|
|22||50S ribosomal protein L22||RL22_ ECOLI||PF00237 Ribosomal protein L22p/L17e|
|23||50S ribosomal protein L23||RL23_ ECOLI||PF00276 Ribosomal protein L23|
|24||50S ribosomal protein L24||RL24_ ECOLI||PF00467 KOW motif|
|25||50S ribosomal protein L25||RL25_ ECOLI||PF01386 Ribosomal L25p family|
|27||50S ribosomal protein L27||RL27_ ECOLI||PF01016 Ribosomal L27 protein|
|28||50S ribosomal protein L28||RL28_ ECOLI||PF00830 Ribosomal L28 family|
|29||50S ribosomal protein L29||RL29_ ECOLI||PF00831 Ribosomal L29 protein|
|30||50S ribosomal protein L30||RL30_ ECOLI||PF00327 Ribosomal protein L30p/L7e|
|31||50S ribosomal protein L31||RL31_ ECOLI||PF01197 Ribosomal protein L31|
|31B||50S ribosomal protein L31 type B||RL31B_ ECOLI||PF01197 Ribosomal protein L31|
|32||50S ribosomal protein L32||RL32_ ECOLI||PF01783 Ribosomal L32p protein family|
|33||50S ribosomal protein L33||RL33_ ECOLI||PF00471 Ribosomal protein L33|
|34||50S ribosomal protein L34||RL34_ ECOLI||PF00468 Ribosomal protein L34|
|35||50S ribosomal protein L35||RL35_ ECOLI||PF01632 Ribosomal protein L35|
|36||50S ribosomal protein L36||RL36_ ECOLI||PF00444 Ribosomal protein L36|
Table of Human small 40S ribosomal subunit proteins
|Subunit No.||Subunit name||Human protein||Pfam family with Human protein|
|2||40S ribosomal protein S2||RS2_HUMAN||PF03719 Ribosomal protein S5, C-terminal domain|
|2||40S ribosomal protein S2||RS2_HUMAN||PF00333 Ribosomal protein S5, N-terminal domain|
|3||40S ribosomal protein S3||RS3_HUMAN||PF00189 Ribosomal protein S3, C-terminal domain|
|3A||40S ribosomal protein S3a||RS3A_HUMAN||PF01015 Ribosomal S3Ae family|
|4||40S ribosomal protein S4, X isoform||RS4X_HUMAN||PF08071 RS4NT (NUC023) domain|
|4||40S ribosomal protein S4, X isoform||RS4X_HUMAN||PF01479 S4 domain|
|4||40S ribosomal protein S4, X isoform||RS4X_HUMAN||PF00900 Ribosomal family S4e|
|4||40S ribosomal protein S4, X isoform||RS4X_HUMAN||PF16121 40S ribosomal protein S4 C-terminus|
|4||40S ribosomal protein S4, Y isoform 1||RS4Y1_HUMAN||PF08071 RS4NT (NUC023) domain|
|4||40S ribosomal protein S4, Y isoform 1||RS4Y1_HUMAN||PF00900 Ribosomal family S4e|
|4||40S ribosomal protein S4, Y isoform 1||RS4Y1_HUMAN||PF16121 40S ribosomal protein S4 C-terminus|
|4||40S ribosomal protein S4, Y isoform 2||RS4Y2_HUMAN||PF08071 RS4NT (NUC023) domain|
|4||40S ribosomal protein S4, Y isoform 2||RS4Y2_HUMAN||PF00900 Ribosomal family S4e|
|4||40S ribosomal protein S4, Y isoform 2||RS4Y2_HUMAN||PF16121 40S ribosomal protein S4 C-terminus|
|5||40S ribosomal protein S5||RS5_HUMAN||PF00177 Ribosomal protein S7p/S5e|
|6||40S ribosomal protein S6||RS6_HUMAN||PF01092 Ribosomal protein S6e|
|7||40S ribosomal protein S7||RS7_HUMAN||PF01251 Ribosomal protein S7e|
|8||40S ribosomal protein S8||RS8_HUMAN||PF01201 Ribosomal protein S8e|
|9||40S ribosomal protein S9||RS9_HUMAN||PF01479 S4 domain|
|9||40S ribosomal protein S9||RS9_HUMAN||PF00163 Ribosomal protein S4/S9 N-terminal domain|
|10||40S ribosomal protein S10||RS10_HUMAN||PF03501 Plectin/S10 domain|
|11||40S ribosomal protein S11||RS11_HUMAN||PF16205 Ribosomal_S17 N-terminal|
|11||40S ribosomal protein S11||RS11_HUMAN||PF00366 Ribosomal protein S17|
|12||40S ribosomal protein S12||RS12_HUMAN||PF01248 Ribosomal protein L7Ae/L30e/S12e/Gadd45 family|
|13||40S ribosomal protein S13||RS13_HUMAN||PF08069 Ribosomal S13/S15 N-terminal domain|
|13||40S ribosomal protein S13||RS13_HUMAN||PF00312 Ribosomal protein S15|
|14||40S ribosomal protein S14||RS14_HUMAN||PF00411 Ribosomal protein S11|
|15||40S ribosomal protein S15||RS15_HUMAN||PF00203 Ribosomal protein S19|
|15A||40S ribosomal protein S15a||RS15A_HUMAN||PF00410 Ribosomal protein S8|
|16||40S ribosomal protein S16||RS16_HUMAN||PF00380 Ribosomal protein S9/S16|
|17||40S ribosomal protein S17||RS17_HUMAN||PF00833 Ribosomal S17|
|18||40S ribosomal protein S18||RS18_HUMAN||PF00416 Ribosomal protein S13/S18|
|19||40S ribosomal protein S19||RS19_HUMAN||PF01090 Ribosomal protein S19e|
|20||40S ribosomal protein S20||RS20_HUMAN||PF00338 Ribosomal protein S10p/S20e|
|21||40S ribosomal protein S21||RS21_HUMAN||PF01249 Ribosomal protein S21e|
|23||40S ribosomal protein S23||RS23_HUMAN||PF00164 Ribosomal protein S12/S23|
|24||40S ribosomal protein S24||RS24_HUMAN||PF01282 Ribosomal protein S24e|
|25||40S ribosomal protein S25||RS25_HUMAN||PF03297 S25 ribosomal protein|
|26||40S ribosomal protein S26||RS26_HUMAN||PF01283 Ribosomal protein S26e|
|27||40S ribosomal protein S27||RS27_HUMAN||PF01667 Ribosomal protein S27|
|28||40S ribosomal protein S28||RS28_HUMAN||PF01200 Ribosomal protein S28e|
|29||40S ribosomal protein S29||RS29_HUMAN||PF00253 Ribosomal protein S14p/S29e|
|30||40S ribosomal protein S30||RS30_HUMAN||PF04758 Ribosomal protein S30|
|A||40S ribosomal protein SA||RSSA_HUMAN||PF16122 40S ribosomal protein SA C-terminus|
|A||40S ribosomal protein SA||RSSA_HUMAN||PF00318 Ribosomal protein S2|
Table of Human large 60S ribosomal subunit proteins
|Subunit No.||Subunit name||Human protein||Pfam family with Human protein|
|3||60S ribosomal protein L3||RL3_HUMAN||PF00297 Ribosomal protein L3|
|4||60S ribosomal protein L4||RL4_HUMAN||PF00573 Ribosomal protein L4/L1 family|
|4||60S ribosomal protein L4||RL4_HUMAN||PF14374 60S ribosomal protein L4|
|5||60S ribosomal protein L5||RL5_HUMAN||PF00861 Ribosomal L18p/L5e family|
|5||60S ribosomal protein L5||RL5_HUMAN||PF14204 Ribosomal L18 C-terminal region|
|6||60S ribosomal protein L6||RL6_HUMAN||PF01159 Ribosomal protein L6e|
|6||60S ribosomal protein L6||RL6_HUMAN||PF03868 Ribosomal protein L6, N-terminal|
|7A||60S ribosomal protein L7a||RL7A_HUMAN||PF01248 Ribosomal protein L7Ae/L30e/S12e/Gadd45 family|
|7||60S ribosomal protein L7||RL7_HUMAN||PF00327 Ribosomal protein L30p/L7e|
|7||60S ribosomal protein L7||RL7_HUMAN||PF08079 Ribosomal L30 N-terminal domain|
|8||60S ribosomal protein L8||RL8_HUMAN||PF00181 Ribosomal Proteins L2, RNA-binding domain|
|8||60S ribosomal protein L8||RL8_HUMAN||PF03947 Ribosomal Proteins L2, C-terminal|
|9||60S ribosomal protein L9||RL9_HUMAN||PF00347 Ribosomal protein L6|
|9||60S ribosomal protein L9||RL9_HUMAN||PF00347 Ribosomal protein L6|
|10A||60S ribosomal protein L10a||RL10A_HUMAN||PF00687 Ribosomal protein L1p/L10e family|
|10||60S ribosomal protein L10||RL10_HUMAN||PF00252 Ribosomal protein L16p/L10e|
|11||60S ribosomal protein L11||RL11_HUMAN||PF00281 Ribosomal protein L5|
|11||60S ribosomal protein L11||RL11_HUMAN||PF00673 ribosomal L5P family C-terminus|
|12||60S ribosomal protein L12||RL12_HUMAN||PF00298 Ribosomal protein L11, RNA-binding domain|
|12||60S ribosomal protein L12||RL12_HUMAN||PF03946 Ribosomal protein L11, N-terminal|
|13A||60S ribosomal protein L13a||RL13A_HUMAN||PF00572 Ribosomal protein L13|
|13||60S ribosomal protein L13||RL13_HUMAN||PF01294 Ribosomal protein L13e|
|14||60S ribosomal protein L14||RL14_HUMAN||PF01929 Ribosomal protein L14|
|15||60S ribosomal protein L15||RL15_HUMAN||PF00827 Ribosomal L15|
|17||60S ribosomal protein L17||RL17_HUMAN||PF00237 Ribosomal protein L22p/L17e|
|18A||60S ribosomal protein L18a||RL18A_HUMAN||PF01775 Ribosomal L18ae/LX protein domain|
|18||60S ribosomal protein L18||RL18_HUMAN||PF00828 Ribosomal_L18e|
|19||60S ribosomal protein L19||RL19_HUMAN||PF01280 Ribosomal protein L19e|
|21||60S ribosomal protein L21||RL21_HUMAN||PF01157 Ribosomal protein L21e|
|22||60S ribosomal protein L22||RL22_HUMAN||PF01776 Ribosomal L22e protein family|
|23A||60S ribosomal protein L23a||RL23A_HUMAN||PF00276 Ribosomal protein L23|
|23A||60S ribosomal protein L23a||RL23A_HUMAN||PF03939 Ribosomal protein L23, N-terminal|
|23||60S ribosomal protein L23||RL23_HUMAN||PF00238 Ribosomal protein L14p/L23e|
|24||60S ribosomal protein L24||RL24_HUMAN||PF01246 Ribosomal protein L24e|
|26||60S ribosomal protein L26||RL26_HUMAN||PF16906 Ribosomal proteins L26 eukaryotic, L24P archaeal|
|27A||60S ribosomal protein L27a||RL27A_HUMAN||PF00828 Ribosomal protein L18e/L15|
|27||60S ribosomal protein L27||RL27_HUMAN||PF01777 Ribosomal L27e protein family|
|28||60S ribosomal protein L28||RL28_HUMAN||PF01778 Ribosomal L28e protein family|
|29||60S ribosomal protein L29||RL29_HUMAN||PF01779 Ribosomal L29e protein family|
|30||60S ribosomal protein L30||RL30_HUMAN||PF01248 Ribosomal protein L7Ae/L30e/S12e/Gadd45 family|
|31||60S ribosomal protein L31||RL31_HUMAN||PF01198 Ribosomal protein L31e|
|32||60S ribosomal protein L32||RL32_HUMAN||PF01655 Ribosomal protein L32|
|34||60S ribosomal protein L34||RL34_HUMAN||PF01199 Ribosomal protein L34e|
|35A||60S ribosomal protein L35a||RL35A_HUMAN||PF01247 Ribosomal protein L35Ae|
|35||60S ribosomal protein L35||RL35_HUMAN||PF00831 Ribosomal L29 protein|
|36A||60S ribosomal protein L36a||RL36A_HUMAN||PF00935 Ribosomal protein L44|
|34||60S ribosomal protein L36||RL36_HUMAN||PF01158 Ribosomal protein L36e|
|37A||60S ribosomal protein L37a||RL37A_HUMAN||PF01780 Ribosomal L37ae protein family|
|37||60S ribosomal protein L37||RL37_HUMAN||PF01907 Ribosomal protein L37e|
|38||60S ribosomal protein L38||RL38_HUMAN||PF01781 Ribosomal L38e protein family|
|39||60S ribosomal protein L39||RL39_HUMAN||PF00832 Ribosomal L39 proteiin|
|40||Ubiquitin-60S ribosomal protein L40||RL40_HUMAN||PF01020 Ribosomal L40e family|
|41||60S ribosomal protein L41||RL41_HUMAN||PF05162 Ribosomal protein L41|
|P0||60S acidic ribosomal protein P0||RLA0_HUMAN||PF00466 Ribosomal protein L10|
|P0||60S acidic ribosomal protein P0||RLA0_HUMAN||PF00428 60s Acidic ribosomal protein|
|P1||60S acidic ribosomal protein P1||RLA1_HUMAN||PF00428 60s Acidic ribosomal protein|
|P1||60S acidic ribosomal protein P2||RLA2_HUMAN||PF00428 60s Acidic ribosomal protein|
- Rodnina MV, Wintermeyer W (Apr 2011). "The ribosome as a molecular machine: the mechanism of tRNA-mRNA movement in translocation". Biochemical Society Transactions 39 (2): 658–62. doi:10.1042/BST0390658. PMID 21428957.
- Ban N, Beckmann R, Cate JH, Dinman JD, Dragon F, Ellis SR, et al. (Feb 2014). "A new system for naming ribosomal proteins". Current Opinion in Structural Biology 24: 165–9. doi:10.1016/j.sbi.2014.01.002. PMID 24524803. Cite error: Invalid
<ref>tag; name "pmid24524803" defined multiple times with different content (see the help page).
- Arnold RJ, Reilly JP (Apr 1999). "Observation of Escherichia coli ribosomal proteins and their posttranslational modifications by mass spectrometry". Analytical Biochemistry 269 (1). doi:10.1006/abio.1998.3077. PMID 10094780.
- Chen SS, Williamson JR (Feb 2013). "Characterization of the ribosome biogenesis landscape in E. coli using quantitative mass spectrometry". Journal of Molecular Biology 425 (4): 767–79. doi:10.1016/j.jmb.2012.11.040. PMC 3568210. PMID 23228329.
- Hamacher K, Trylska J, McCammon JA (Feb 2006). "Dependency map of proteins in the small ribosomal subunit". PLoS Computational Biology 2 (2). doi:10.1371/journal.pcbi.0020010. PMID 16485038.
- Korobeinikova AV, Garber MB, Gongadze GM (Jun 2012). "Ribosomal proteins: structure, function, and evolution". Biochemistry (Moscow) 77 (6): 562–74. doi:10.1134/S0006297912060028. PMID 22817455.
- Ban N, Beckmann R, Cate JH, Dinman JD, Dragon F, Ellis SR, et al. (Feb 2014). "A new system for naming ribosomal proteins". Current Opinion in Structural Biology 24: 165–9. doi:10.1016/j.sbi.2014.01.002. PMID 24524803.
- 30S Ribosomal proteins at biochem.umd.edu
- Ribosomal Protein at the US National Library of Medicine Medical Subject Headings (MeSH)
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Mitochondrial ribosomal protein L31 Provide feedback
This is a family of mitochondrial ribosomal proteins. L31 is essential for mitochondrial function in yeast .
Grohmann L, Graack HR, Kitakawa M; , Eur J Biochem. 1989;183:155-160.: Molecular cloning of the nuclear gene for mitochondrial ribosomal protein YmL31 from Saccharomyces cerevisiae. PUBMED:2666132 EPMC:2666132
Graack HR, Grohmann L, Kitakawa M; , Biochimie. 1991;73:837-844.: The nuclear coded mitoribosomal proteins YmL27 and YmL31 are both essential for mitochondrial function in yeast. PUBMED:1764528 EPMC:1764528
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You can also change the order in which sequences are listed in the alignment, change how insertions are represented, alter the characters that are used to represent gaps in sequences and, finally, choose whether to download the alignment or to view it in your browser directly.
You may find that large alignments cause problems for the viewers and the reformatting tool, so we also provide all alignments in Stockholm format. You can download either the plain text alignment, or a gzipped version of it.
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.
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
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.
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
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...
If you find these logos useful in your own work, please consider citing the following article:
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.
|Seed source:||Pfam-B_24102 (release 21.0)|
|Author:||Mistry J, Wood V|
|Number in seed:||63|
|Number in full:||193|
|Average length of the domain:||98.90 aa|
|Average identity of full alignment:||49 %|
|Average coverage of the sequence by the domain:||87.89 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 11927849 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||6|
|Download:||download the raw HMM for this family|
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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the More....
This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.
How the sunburst is generated
The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:
Colouring and labels
Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.
As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.
Anomalies in the taxonomy tree
There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.
Missing taxonomic levels
Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.
Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".
Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
Too many species/sequences
For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.
The tree shows the occurrence of this domain across different species. More...
We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.
Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.
If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.
For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.
Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
You can use the tree controls to manipulate how the interactive tree is displayed:
- show/hide the summary boxes
- highlight species that are represented in the seed alignment
- expand/collapse the tree or expand it to a given depth
- select a sub-tree or a set of species within the tree and view them graphically or as an alignment
- save a plain text representation of the tree
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.
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the L31 domain has been found. There are 1 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
Loading structure mapping...