Nitrosopumilus maritimus genome reveals unique - de la Torre ...

Supplemental Table 2: Predicted coordinates for genes implicated in novel archaeal biochemistry for ammonia oxidation and respiratory chain.
NCBI locus
tag
Protein # Strand Left bp Right bp Annotation Best Hit Analog in Ammonia oxidizing Bacteria
Nmar_0588 ABX12484 F 523,890 525,197 ammonium transporter AmtB
Nmar_1698 ABX13594 R 1,559,816 1,558,251 ammonium transporter AmtB
Nmar_1500 ABX13396 R 1,367,890 1,367,240 putative ammonia monooxygenase, subunit A AMO (AmoA)
Nmar_1501 ABX13397 R 1,368,387 1,368,025 hypothetical protein
Nmar_1502 ABX13398 R 1,369,079 1,368,507 putative ammonia monooxygenase, subunit C AMO (AmoC)
Nmar_1503 ABX13399 F 1,369,326 1,369,895 putative ammonia monooxygenase, subunit B AMO (AmoB)
Nmar_0815 ABX12711 R 718,761 720,380
soluble periplasmic BCP (complete upstream CxxxxxC domain, complete
CxxHxxM domain [C])
PetE, plastocyanin cytochrome c552
Nmar_1102 ABX12998 F
soluble periplasmic BCP (complete upstream CxxxxxC domain, complete
1,004,439 1,005,395
CxxHxxM domain [C])
PetE, plastocyanin cytochrome c552
Nmar_1443 ABX13339 R
soluble periplasmic BCP (complete upstream CxxxxxC domain, complete
1,314,030 1,313,572
CxxHxxM domain [C])
PetE, plastocyanin cytochrome c552
Nmar_1637 ABX13533 R
soluble periplasmic BCP (complete upstream CxxxxxC domain, complete
1,494,547 1,492,676
CxxHxxM domain [C])
PetE, plastocyanin cytochrome c552
Nmar_0004 ABX11904 F 3,463 4,359
soluble periplasmic BCP (modified upstream CxxxxxC domain, modified
CxxHxxM domain [C])
Halocyanin, P39442 cytochrome c552
Nmar_1307 ABX13203 F
soluble periplasmic BCP (modified upstream CxxxxxC domain, modified
1,195,212 1,195,736
CxxHxxM domain [C])
Halocyanin, P39442 cytochrome c552
Nmar_0918 ABX12814 R 802,019 802,861
periplasmic membrane BCP (1 TMS [C], modified upstream CxxxxxC domain,
complete CxxHxxM domain [M])
plastocyanin anchored cytochrome c552
Nmar_1678 ABX13574 R
periplasmic membrane BCP (1 TMS [C], modified upstream CxxxxxC domain,
1,538,377 1,537,367
complete CxxHxxM domain [N])
plastocyanin anchored cytochrome c552
Nmar_1273 ABX13169 R
periplasmic membrane BCP (1 TMS [C], complete upstream CxxxxxC domain,
1,169,255 1,168,392
modified CxxHxxM domain [C])
plastocyanin anchored cytochrome c552
Nmar_1161 ABX13057 R 1063718 1062348
periplasmic membrane BCP (1 TMS [N], modified upstream CxxxxxC domain,
modified CxxHxxM domain [M])
plastocyanin anchored cytochrome c552
Nmar_1226 ABX13122 F
periplasmic membrane BCP (4 TMS [N], modified upstream CxxxxxC domain, 2
1,126,185 1,127,261
complete CxxHxxM domains [C])
plastocyanin cM552 Nmar_1142 ABX13038 F
cytoplasmic membrane BCP (1 TMS [N], modified upstream CxxxxxC domain,
1,045,689 1,046,150
complete CxxHxxM domain [C])
Nmar_1542 "cytoplasmic BCP"
Nmar_0276 ABX12172 F 243,850 244,182 CI, NADH-ubiquinone/plastoquinone oxidoreductase chain 3
Nmar_0277 ABX12173 F 244,223 244,747 CI, NADH-quinone oxidoreductase, B subunit
Nmar_0278 ABX12174 F 244,747 245,349 CI, NADH dehydrogenase (ubiquinone) 30 kDa subunit
Nmar_0279 ABX12175 F 245,352 246,488 CI, NADH dehydrogenase (quinone)
Nmar_0280 ABX12176 F 246,489 247,787 CI, NADH dehydrogenase (quinone)
Nmar_0281 ABX12177 F 247,787 248,284 CI, [4Fe-4S] ferredoxin iron-sulfur binding domain protein Complex I
Nmar_0282 ABX12178 F 248,277 248,789 CI, NADH-ubiquinone/plastoquinone oxidoreductase chain 6
Nmar_0283 ABX12179 F 248,770 249,075 CI, NADH-ubiquinone oxidoreductase chain 4L
Nmar_0284 ABX12180 F 249,075 250,628 CI, proton-translocating NADH-quinone oxidoreductase, chain M
Nmar_0285 ABX12181 F 250,630 252,708 CI, proton-translocating NADH-quinone oxidoreductase, chain L
Nmar_0286 ABX12182 F 252,721 254,205 CI, proton-translocating NADH-quinone oxidoreductase, chain N
Nmar_1542 ABX13438 R
CIII, cytoplasmic membrane BCP, 1 TMS (N), modified upstream CxxxxxC
1,404,537 1,404,073
domain, complete CxxHxxM domain (C)
Nmar_1142 membrane-bound cytochrome c1 Nmar_1543 ABX13439 R 1,406,185 1,404,590 CIII, Cytochrome b/b6 domain Complex III cyt. B
Nmar_1544 ABX13440 R 1,406,774 1,406,169 CIII, Rieske [2Fe-2S] domain protein Complex III [Fe-S]
Nmar_0182 ABX12078 F 166,066 166,326 CIV, hypothetical protein HCO subunit IV
Nmar_0183 ABX12079 F 166,329 166,760 CIV, heme-copper oxidase subunit II HCO subunit II
Nmar_0184 ABX12080 F 166,798 168,324 CIV, heme-copper oxidase subunit I HCO subunit I
Nmar_0185 ABX12081 F 168,337 169,284
CIV, periplasmic membrane BCP, 1 TMS (N), complete upstream CxxxxxC
domain, complete CxxHxxM domain (C)
Nmar_1354 cytochrome c subunit III
Nmar_1259 ABX13155 R 1,155,995 1,154,583 NirK, soluble periplasmic MCO (Cu-oxidase_1; Cu-oxidase_2; Cu-oxidase_3),
Nwi_2648;
Nham_3281; NE0924;
Neut_1403; Noc_0089
3dMCO, NirK
Nmar_1661 ABX13557 R 1,519,832 1,519,440 Transcriptional regulator, MarR family (winged helix-turn-helix HxlR type) HTH -regulator MarR
Nmar_1662 ABX13558 R 1,521,322 1,520,144 Metal cation transporter (ZIP Zinc transporter; cl00437) Zip
Nmar_1663 ABX13559 R
soluble periplasmic 2dMCO (Cu-oxidase_2; Cu-oxidase_3), similar to NcgA
1,522,373 1,521,312
(BCO)
Nwi_2651;
Nham_3284; NE0927;
Neut_1406
2dMCO, NcgA (BCO)
Nmar_1664 ABX13560 R 1,522,974 1,522,483 metal (Mn, Fe) dependent repressor protein, DtxR family Nmar_1132 HTH -regulator DtxR
Nmar_1665 ABX13561 R
soluble periplasmic BCP (modified upstream CxxxxxC domain, modified
1,523,638 1,523,135
CxxHxxM domain [C])
Halocyanin, P39442 monoheme cytochrome c
Nmar_1666 ABX13562 R
beta-propeller structure oxidase (Kelch repeat-containing protein
1,524,788 1,523,754
[CDD:121499])
Nmar_1133 beta propeller structure
Nmar_1667 ABX13563 R 1,526,542 1,525,130
Nmar_1136 ABX13032 R 1,041,807 1,040,200
NirK, soluble periplasmic 3d MCO (Cu-oxidase_1; Cu-oxidase_2; Cuoxidase_3),
NsrR motif in upstream region.
soluble periplasmic 3dMCO (Cu-oxidase_1; Cu-oxidase_2; Cu-oxidase_3),
similar to NcgA
Nwi_2648;
Nham_3281; NE0924;
Neut_1403; Noc_0089
Nwi_2651;
Nham_3284; NE0927;
Neut_1406
3dMCO, Nirk
3dMCO- modified NcgA (BCO)
Nmar_1135 ABX13031 R 1,040,071 1,038,395 putative dehydrogenase with Rossmann-fold NAD(P) + -binding domain [cl09931] Rossmann-fold - DH
Nmar_1134 ABX13030 R 1,038,244 1,037,921 hypothetical protein
Nmar_1133 ABX13029 R
beta-propeller structure oxidase (Kelch repeat-containing protein
1,037,891 1,036,866
[CDD:121499])
Nmar_1666 beta propeller structure
Nmar_1132 ABX13028 R 1,036,419 1,035,937 metal (Mn, Fe) dependent repressor protein, DtxR family Nmar_1664 HTH -regulator DtxR
Nmar_1131 ABX13027 R
soluble periplasmic 2d MCO (Cu-oxidase_2; Cu-oxidase_3), similar to NcgA
1,035,788 1,034,733
(BCO)
Nwi_2651;
Nham_3284; NE0927;
Neut_1406
2dMCO NcgA (BCO)
Nmar_1130 ABX13026 R 1,034,743 1,033,565 Metal cation transporter (ZIP Zinc transporter; cl00437) Zip
Nmar_1129 ABX13025 R
cytoplasmic membrane BCP (3 TMS [1N, 2C], complete upstream CxxxxxC
1,031,846 1,033,210
domain, complete CxxHxxM domain [N)
"cytoplasmic BCP"
Nmar_1128 ABX13024 R
periplasmic binding protein (transport of ferric siderophores and metal ions such
1,031,477 1,030,587
as Mn2+, Fe3+, Cu2+ and/or Zn2+)
cation BP
Nmar_1352 ABX13248 R 1,238,660 1,237,860 Transcriptional regulator, ArsR family (winged helix-turn-helix type, COG4742) HTH -regulator
Nmar_1353 ABX13249 R 1,239,270 1,238,728 Uncharacterized conserved protein [COG3945; Function unknown]
Nmar_1354 ABX13250 R
Fusion Protein: soluble periplasmic 2d MCO (Cu-oxidase_2; Cu-oxidase_3) -
1,240,615 1,239,281
BCP (modified upstream CxxxxxC domain & CxxHxxM domain [C])
Nmar_1131;
Nmar_0185
2dMCO - BCP bi-functional MCO
Nmar_1355 ABX13251 R 1,242,507 1,241,821 hypothetical protein