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

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Nmar_1356 ABX13252 R 1,243,134 1,242,610 IsiB, flavodoxin/nitric oxide synthase [cl00438] flavodoxin/nitric oxide synthase Nmar_1357 ABX13253 F 1,243,214 1,243,858 nitroreductase [Nitro_FMN_reductase] Nitro_FMN_reductase Nmar_0650 ABX12546 R 588,034 587,297 Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase Nmar_1650 ABX13546 R periplasmic membrane BCP (1 TMS [C], complete upstream CxxxxxC domain, 1,508,803 1,509,615 complete CxxHxxM domain [M]) plastocyanin monoheme cytochrome c Nmar_1651 ABX13547 R 1,510,321 1,509,629 hypothetical protein Nmar_1652 ABX13548 F periplasmic Cu resistance membrane hybrid protein: CopC - [8 TMS] - CopD - [1 1,510,361 1,513,144 TMS] CENSYa_1798 copC-copD 3' of amoCAB(E)D Nmar_1653 ABX13549 R 1,513,952 1,513,134 ABC-3 protein; ABC-ATPase subunit interface [CDD:119348] Nmar_1654 ABX13550 R 1,514,677 1,513,955 ABC-type Mn/Zn transport systems, ATPase component [COG1121] Nmar_1655 ABX13551 R periplasmic solute binding protein [ABC transport of ferric siderophores and metal 1,515,591 1,514,671 cation BP ions such as Mn 2+ , Fe 3+ , Cu 2+ and/or Zn 2+ ] NikR; transcriptional regulator with C-terminal nickel binding domain Nmar_1656 ABX13552 R 1,516,066 1,515,683 [pfam08753] Nmar_1657 ABX13553 F 1,516,198 1,516,479 hypothetical protein protease inhibitor, cytoplasmic membrane BCP (1 TMS [N], complete upstream Nmar_1250 ABX13146 R 1,148,436 1,147,717 cytoplasmic protease inhibitor CxxxxxC domain, complete CxxHxxM domain [C]) Red labelling indicates presence in C. symbiosum genome. Green shading indicates gene cluster encoding a 2dMCO (Nmar_1663) and a 3dMCO-NirK (Nmar_1667) preceeded by a NsrR binding site. Both genes flank a gene encoding a soluble periplasmic blue copper redox protein. This resembles AOB and nitrite-oxidizing bacteria in which the MCO-encoded genes flank genes encoding cytochrome c proteins. Blue shading indicates gene cluster that may have arisen by incomplete gene duplication of the cluster shaded in green (loss of BCP gene), followed by modification of the 3dMCO gene (loss of nirK-specific domains) and acquisition of genes Nmar_1134 and Nmar_1135). Orange shading indicates gene cluster containing a unique combination of gene homologues implicated in nitrogen oxide processing. Gene cluster Nmar_1650-7 may encode inventory responsible for copper uptake and homeostatis. Nmar_1652 encodes a fusion protein of the CopC and CopD proteins, whose encoding genes are found in tandem immediately downstream of amo genes.
Supplemental Table 3: Gene prediction coordinates for stable RNAs and TFBs/TBPs Gene Name Start End Product Note STABLE RNAs Nmar_rR16S 896,240 897,711 Nmar_rR23S 893,105 896,109 Nmar_rR5S 262,500 262,619 Nmar_SRP 95,541 95,248 Nmar_RNaseP 569,667 569,388 Nmar_sR1 100,802 100,856 Nmar_sR2 537,407 537,466 Nmar_sR3 256,057 256,113 Nmar_sR4 1,131,193 1,131,136 Nmar_sR5 471,299 471,354 Nmar_sR6 1,376,278 1,376,344 16S ribosomal RNA 23S ribosomal RNA 5S ribosomal RNA SRP RNA RNase P RNA C/D box guide sRNA C/D box guide sRNA C/D box guide sRNA C/D box guide sRNA C/D box guide sRNA C/D box guide sRNA Nmar_tR01 88,221 88,305 LeuCAG Nmar_tR02 171,008 171,081 LysCTT Nmar_tR03 177,670 177,744 ValTAC Small subunit ribosomal RNA Large subunit ribosomal RNA 5S ribosomal RNA; detected by Rfam model Signal recognition particle RNA; detected by Rfam model Detected by Rfam model Predicted to modify tRNA tR12-LeuCAA at Cm36 (anticodon) by snoscan; conserved region in C. symbiosum Predicted to modify 23S rRNA at Cm2014 by snoscan Predicted to modify tRNA tR06-AlaGGC at Am60 by snoscan; conserved sRNA in C. symbiosum Predicted to modify tRNA tR35-TyrGTA at Am83 by snoscan; conserved sRNA in C. symbiosum No predicted target, but conserved with sRNA in C. symbiosum No predicted target, but conserved with sRNA in C. symbiosum No introns; tRNAscan-SE v1.23 Score 53.62 No introns; tRNAscan-SE v1.23 Score 71.92 No introns; tRNAscan-SE v1.23 Score 74.7 Nmar_tR04 188,725 188,796 AlaCGC No introns; tRNAscan-SE v1.23 Score 70.62 Nmar_tR05 210,730 210,813 SerTGA No introns; tRNAscan-SE
Page 1 and 2: Nitrosopumilus maritimus genome rev
Page 3 and 4: ammonia oxidation. There are two hy
Page 5 and 6: Fig. 3. Comparison of N. maritimus
Page 7 and 8: Supporting Information Walker et al
Page 9 and 10: Fig. S2. Archaeal ammonia monooxyge
Page 11 and 12: A. 0.1 B. 100 90 52 Other Supportin
Page 13: Supplemental Table 2: Predicted coo
Page 17 and 18: Nmar_tR26 1,630,610 1,630,537 ProGG
Page 19 and 20: Supplemental Table 4: Gene predicti
Page 21 and 22: Nmar_0258 CENSYa_1705 82 227,624 22
Page 29 and 30: Nmar_1303 CENSYa_0131 86 1,193,261
Page 35 and 36: Molybdopterin-guanine dinucleotide
Page 37 and 38: Nmar0935 DeepAntEC39 f 815,847 816,
Page 39 and 40: Nmar0101 EQ085329 r 91,543 93,711 A
Page 41 and 42: Nmar0436 EQ085799 f 386,930 387,319
Page 43 and 44: Nmar0982 EP710054 r 859,116 859,526
Page 45 and 46: Nmar1297 EQ086682 f 1,187,165 1,188

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

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