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Table 1 A list of predicted selenoproteins encoded by UGA read-through

From: A computational method to predict genetically encoded rare amino acids in proteins

Accession ID

Organism

Computationally identified selenoproteins* annotated by their homologs

AE000657

Aquifex aeolicus

1. gi|12515210|gb|AAG56295.1|AE005358_3 formate dehydrogenase-N, nitrate-inducible, alpha subunit [Escherichia coli]

  

2. gi|51589698|emb|CAH21328.1| selenide, water dikinase [Yersinia pseudotuberculosis IP 32953]

AE017125

Helicobacter hepaticus

1.gi|27362035|gb|AAO10941.1|AE016805_198 formate dehydrogenase, alpha subunit [Vibrio vulnificus CMCP6]

  

2. gi|46914191|emb|CAG20971.1| putative selenophosphate synthase [Photobacterium profundum]

AE017143

Haemophilus ducreyi 35000HP

1. gi|26108424|gb|AAN80626.1|AE016761_201 selenide, water dikinase [Escherichia coli CFT073]

AE004439

Pasteurella multocida

1. gi|2983532|gb|AAC07107.1| formate dehydrogenase, alpha subunit [Aquifex aeolicus VF5]

  

2. gi|5103639|dbj|BAA79160.1| 194 amino acid long hypothetical protein [ Aeropyrum pernix K1]

AE005674

Shigella flexneri 2a

1. gi|12515215|gb|AAG56300.1|AE005358_8 orf; unknown function [ Escherichia coli O157:H7 EDL933]

  

2. gi|1788928|gb|AAC75627.1| quinolinate synthetase, B protein; quinolinate synthetase, B protein, catalytic and NAD/flavoprotein subunit [ Escherichia coli >K12]

  

3. gi|2983532|gb|AAC07107.1| formate dehydrogenase, alpha subunit [Aquifex aeolicus VF5]

  

4. gi|2983532|gb|AAC07107.1| formate dehydrogenase, alpha subunit [Aquifex aeolicus VF5]

  

5. gi|3868721|gb|AAD13462.1| selenopolypeptide subunit of formate dehydrogenase H; formate dehydrogenase H, selenopolypeptide subunit [Escherichia coli K12]

AE014073

Shigella flexneri 2a

1. gi|2983532|gb|AAC07107.1| formate dehydrogenase, alpha subunit [Aquifex aeolicus VF5]

  

2. gi|1788928|gb|AAC75627.1| quinolinate synthetase, B protein; quinolinate synthetase, B protein, catalytic and NAD/flavoprotein subunit [ Escherichia coli K12]

  

3. gi|2983532|gb|AAC07107.1| formate dehydrogenase, alpha subunit [Aquifex aeolicus VF5]

  

4. gi|3868721|gb|AAD13462.1| selenopolypeptide subunit of formate dehydrogenase H; formate dehydrogenase H, selenopolypeptide subunit [Escherichia coli K12]

AE006469

Sinorhizobium meliloti

1. gi|2983532|gb|AAC07107.1| formate dehydrogenase, alpha subunit [Aquifex aeolicus VF5]

AE008691

Thermoanaerobacter tengcongensis

1. gi|41816370|gb|AAS11237.1| glycine reductase complex selenoprotein GrdA [Treponema denticola ATCC 35405]

  

2. gi|51857693|dbj|BAD41851.1| glycine reductase complex selenoprotein B [Symbiobacterium thermophilum IAM 14863]

  

3. gi|46914191|emb|CAG20971.1| putative selenophosphate synthase [Photobacterium profundum]

AE014075

Escherichia coli CFT073

1. gi|2983532|gb|AAC07107.1| formate dehydrogenase, alpha subunit [Aquifex aeolicus VF5]

  

2. gi|56130341|gb|AAV79847.1| formate dehydrogenase H [Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150]

  

3. gi|2983532|gb|AAC07107.1| formate dehydrogenase, alpha subunit [Aquifex aeolicus VF5]

BA000007

Escherichia coli O157H7

1. gi|56130341|gb|AAV79847.1| formate dehydrogenase H [Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150]

  

2. gi|2983532|gb|AAC07107.1| formate dehydrogenase, alpha subunit [Aquifex aeolicus VF5]

  

3. gi|2983532|gb|AAC07107.1| formate dehydrogenase, alpha subunit [Aquifex aeolicus VF5]

U00096

Escherichia coli K12

1. gi|5105267|dbj|BAA80580.1| 114 amino acid long hypothetical protein [ Aeropyrum pernix K1]

  

2. gi|2983532|gb|AAC07107.1| formate dehydrogenase, alpha subunit [Aquifex aeolicus VF5]

  

3. gi|56130341|gb|AAV79847.1| formate dehydrogenase H [Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150]

  

4. gi|2983532|gb|AAC07107.1| formate dehydrogenase, alpha subunit [Aquifex aeolicus VF5]

AE014299

Shewanella oneidensis

1. gi|2983532|gb|AAC07107.1| formate dehydrogenase, alpha subunit [Aquifex aeolicus VF5]

AE015451

Pseudomonas putida KT2440

1. gi|2983532|gb|AAC07107.1| formate dehydrogenase, alpha subunit [Aquifex aeolicus VF5]

AE004091

Pseudomonas aeruginosa

1. gi|2983532|gb|AAC07107.1| formate dehydrogenase, alpha subunit [Aquifex aeolicus VF5]

AE016958

Mycobacterium avium paratuberculosis

1. gi|13880045|gb|AAK44759.1| hypothetical protein MT0536 [ Mycobacterium tuberculosis CDC1551]

  

2. gi|2983532|gb|AAC07107.1| formate dehydrogenase, alpha subunit [Aquifex aeolicus VF5]

AE017042

Yersinia pestis biovar Mediaevalis

1. gi|2983532|gb|AAC07107.1| formate dehydrogenase, alpha subunit [Aquifex aeolicus VF5]

AE009952

Yersinia pestis KIM

1. gi|2983532|gb|AAC07107.1| formate dehydrogenase, alpha subunit [Aquifex aeolicus VF5]

AL590842

Yersinia pestis CO92

1. gi|2983532|gb|AAC07107.1| formate dehydrogenase, alpha subunit [Aquifex aeolicus VF5]

AE017180

Geobacter sulfurreducens

1. gi|19918170|gb|AAM07420.1| 4-carboxymuconolactone decarboxylase [Methanosarcina acetivorans str. C2A]

  

2. gi|21956737|gb|AAM83670.1|AE013608_5 glutaredoxin 3 [Yersinia pestis KIM]

  

3. gi|37201109|dbj|BAC96933.1| thiol-disulfide isomerase and thioredoxins [Vibrio vulnificus YJ016]

  

4. gi|2983532|gb|AAC07107.1| formate dehydrogenase, alpha subunit [Aquifex aeolicus VF5]

  

5. gi|34105000|gb|AAQ61356.1| conserved hypothetical protein [Chromobacterium violaceum ATCC 12472]; gi|53758707|gb|AAU92998.1| HesB/YadR/YfhF family protein [Methylococcus capsulatus str. Bath];

  

6. gi|46914191|emb|CAG20971.1| Putative selenophosphate synthase [Photobacterium profundum]

  

7. gi|32448022|emb|CAD77542.1| peroxiredoxin [Pirellula sp.]

  

8. gi|29605647|dbj|BAC69712.1 hypothetical protein [Streptomyces avermitilis MA-4680] (SelW)

  

9. gi|34482757|emb|CAE09757.1| sulfur transferase precursor [Wolinella succinogenes]

AE017226

Treponema denticola ATCC 35405

1. gi|51857694|dbj|BAD41852.1| glycine reductase complex selenoprotein A [Symbiobacterium thermophilum IAM 14863]

  

2. gi|51857693|dbj|BAD41851.1| glycine reductase complex selenoprotein B [Symbiobacterium thermophilum IAM 14863]

  

3. gi|56380162|dbj|BAD76070.1| glutathione peroxidase [Geobacillus kaustophilus HTA426]

  

4. gi|51857693|dbj|BAD41851.1| glycine reductase complex selenoprotein B [Symbiobacterium thermophilum IAM 14863]

  

5. gi|26108424|gb|AAN80626.1|AE016761_201 selenide, water dikinase [Escherichia coli CFT073]

  

6. gi|52209545|emb|CAH35498.1| thioredoxin 1 [Burkholderia pseudomallei K96243]

AL111168

Campylobacter jejuni

1. gi|27362035|gb|AAO10941.1|AE016805_198 formate dehydrogenase, alpha subunit [Vibrio vulnificus CMCP6]

  

2. gi|54018125|dbj|BAD59495.1| hypothetical protein [Nocardia farcinica IFM 10152]; (SelW)

AL513382

Salmonella typhi

1. gi|3868721|gb|AAD13462.1| selenopolypeptide subunit of formate dehydrogenase H; formate dehydrogenase H, selenopolypeptide subunit [Escherichia coli K12]

  

2. gi|2983532|gb|AAC07107.1| formate dehydrogenase, alpha subunit [Aquifex aeolicus VF5]

AE006468

Salmonella typhimurium LT2

1. gi|2983532|gb|AAC07107.1| formate dehydrogenase, alpha subunit [Aquifex aeolicus VF5]

  

2. gi|2983532|gb|AAC07107.1| formate dehydrogenase, alpha subunit [Aquifex aeolicus VF5]

  

3. gi|3868721|gb|AAD13462.1| selenopolypeptide subunit of formate dehydrogenase H; formate dehydrogenase H, selenopolypeptide subunit [Escherichia coli K12]

BA000016

Clostridium perfringens

1. gi|28202985|gb|AAO35429.1| conserved protein [Clostridium tetani E88]; gi|20906561|gb|AAM31712.1| HesB protein [Methanosarcina mazei Goe1]

  

2. gi|46914191|emb|CAG20971.1| putative selenophosphate synthase [Photobacterium profundum]

BX470251

Photorhabdus luminescens

1. gi|2983532|gb|AAC07107.1| formate dehydrogenase alpha subunit [Aquifex aeolicus VF5]

BX571656

Wolinella succinogenes

1. gi|27362035|gb|AAO10941.1|AE016805_198 formate dehydrogenase, alpha subunit [Vibrio vulnificus CMCP6]

L42023

Haemophilus influenzae

1. gi|2983532|gb|AAC07107.1| formate dehydrogenase, alpha subunit [Aquifex aeolicus VF5]

  

2. gi|26108424|gb|AAN80626.1|AE016761_201 selenide, water dikinase [Escherichia coli CFT073]

CR354531

Photobacterium profundum

1. gi|58428447|gb|AAW77484.1| conserved hypothetical protein [ Xanthomonas oryzae pv. oryzae KACC10331]

CR354532

Photobacterium profundum

1. gi|41816370|gb|AAS11237.1| glycine reductase complex selenoprotein GrdA [Treponema denticola ATCC 35405]

  

2. gi|51589698|emb|CAH21328.1| selenide, water dikinase [Yersinia pseudotuberculosis IP 32953]

  

3. gi|41816370|gb|AAS11237.1| glycine reductase complex selenoprotein GrdA [Treponema denticola ATCC 35405]

  

4. gi|41818450|gb|AAS12639.1| glycine reductase complex selenoprotein GrdB2 [Treponema denticola ATCC 35405]

AE009439

Methanopyrus kandleri (archaea)

1. gi|2622673|gb|AAB86026.1| formate dehydrogenase, alpha subunit homolog [Methanothermobacter thermautotrophicus]; gi|2622681|gb|AAB86033.1| tungsten formylmethanofuran dehydrogenase, subunit B [Methanothermobacter thermautotrophicus]

  

2. gi|57160335|dbj|BAD86265.1| probable formate dehydrogenase, alpha subunit [Thermococcus kodakaraensis KOD1]

  

3. gi|33566318|emb|CAE37231.1| putative iron-sulfur binding protein [Bordetella parapertussis]

  

4. gi|44921146|emb|CAF30381.1| heterodisulfide reductase, subunit A [Methanococcus maripaludis]

  

5. gi|44921142|emb|CAF30377.1| coenzyme F420-non-reducing hydrogenase, subunit delta [Methanococcus maripaludis]; gi|2622243|gb|AAB85627.1| methyl viologen-reducing hydrogenase, delta subunit homolog FlpD [Methanothermobacter thermautotrophicus]; gi|20904385|gb|AAM29752.1| heterodisulfate reductase, subunit A [Methanosarcina mazei Goe1]

  

6. gi|45047811|emb|CAF30938.1| coenzyme F420-reducing hydrogenase subunit alpha [Methanococcus maripaludis]

  

7. gi|39576202|emb|CAE80367.1| selenide, water dikinase [Bdellovibrio bacteriovorus HD100]

L77117

Methanococcus jannaschii (archaea)

1. gi|44921146|emb|CAF30381.1| heterodisulfide reductase subunit A [Methanococcus maripaludis]

  

2. gi|45047811|emb|CAF30938.1| coenzyme F420-reducing hydrogenase subunit alpha [Methanococcus maripaludis]

  

3. gi|50875900|emb|CAG35740.2| methyl-viologen-reducing hydrogenase, delta subunit [Desulfotalea psychrophila LSv54]

  

4. gi|2622240|gb|AAB85625.1| methyl viologen-reducing hydrogenase, delta subunit [Methanothermobacter thermautotrophicus]; gi|44921142|emb|CAF30377.1| coenzyme F420-non-reducing hydrogenase subunit delta [Methanococcus maripaludis]

  

5. gi|2622673|gb|AAB86026.1| formate dehydrogenase, alpha subunit homolog [Methanothermobacter thermautotrophicus]; gi|45048129|emb|CAF31247.1| tungsten containing formylmethanofuran dehydrogenase, subunit B [Methanococcus maripaludis] (overlaps with #4)

  

6. gi|26108424|gb|AAN80626.1|AE016761_201 selenide, water dikinase [Escherichia coli CFT073]

  

7. gi|53758707|gb|AAU92998.1| HesB/YadR/YfhF family protein [Methylococcus capsulatus str. Bath]

  

8. gi|45047727|emb|CAF30854.1| formate dehydrogenase, alpha subunit [Methanococcus maripaludis]

BX950229

Methanococcus maripaludis (archaea)

1. gi|2622673|gb|AAB86026.1| formate dehydrogenase, alpha subunit homolog [Methanothermobacter thermautotrophicus]; gi|19886584|gb|AAM01476.1| Formylmethanofuran dehydrogenase subunit B [Methanopyrus kandleri AV19]

  

2. gi|2622673|gb|AAB86026.1| formate dehydrogenase, alpha subunit homolog [Methanothermobacter thermautotrophicus]

  

3. gi|2622240|gb|AAB85625.1| methyl viologen-reducing hydrogenase, delta subunit [Methanothermobacter thermautotrophicus]; gi|39981962|gb|AAR33424.1| heterodisulfide reductase subunit [Geobacter sulfurreducens PCA]

  

4. gi|2622673|gb|AAB86026.1| formate dehydrogenase, alpha subunit homolog [Methanothermobacter thermautotrophicus]

  

5. gi|2622673|gb|AAB86026.1| formate dehydrogenase, alpha subunit homolog [Methanothermobacter thermautotrophicus]; gi|19918286|gb|AAM07526.1| formylmethanofuran dehydrogenase, subunit B [Methanosarcina acetivorans str. C2A]

  

6. gi|19886593|gb|AAM01482.1| Heterodisulfide reductase, subunit A, polyferredoxin [Methanopyrus kandleri AV19]

  1. Organism names, National Center for Biotechnology Information accession numbers for the genomes and the top PSI-BLAST hit(s) from our database are shown. Seven novel candidate selenoproteins are shown in bold type. *Each entry corresponds to a computationally identified read-through protein in the organism indicated to the left. FASTA files for these recoded protein sequences are provided in the Additional file 2. For each recoded protein, the GI number and the functional annotation for a homologous protein are given.
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