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

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Nmar_1671 CENSYa_0516 39 1,530,045 1,531,619 1,575 f 451,910 453,436 509 r streptogramin lyase Nmar_1673 CENSYa_1238 53 1,532,270 1,533,415 1,146 r 1,263,583 1,264,740 386 f trypsin-like serine protease Nmar_1674 CENSYa_1788 30 1,533,567 1,534,310 744 f 1,768,797 1,769,285 163 r hypothetical protein Nmar_1676 CENSYa_1874 30 1,534,989 1,536,710 1,722 r 1,846,587 1,848,137 517 r secreted periplasmic Zn-dependent protease Nmar_1678 CENSYa_1796 40 1,537,367 1,538,377 1,011 r 1,775,021 1,776,016 332 f copper binding protein, plastocyanin/azurin family Nmar_1679 CENSYa_1905 57 1,539,601 1,540,227 627 f 1,872,493 1,873,206 238 f hypothetical protein Nmar_1684 CENSYa_1799 45 1,543,991 1,545,364 457 r 1,779,532 1,780,869 445 r hypothetical protein Nmar_1686 CENSYa_1440 73 1,546,135 1,547,064 309 r 1,454,784 1,455,713 309 r aspartate carbamoyltransferase Nmar_1687 CENSYa_1441 75 1,547,106 1,547,567 153 f 1,455,753 1,456,214 153 f aspartate carbamoyltransferase, regulatory subunit Nmar_1688 CENSYa_1442 69 1,547,603 1,547,911 102 r 1,456,242 1,456,541 99 r H+transporting two-sector ATPase C subunit Nmar_1689 CENSYa_1444 83 1,548,095 1,548,724 209 r 1,456,722 1,457,087 121 r V-type ATPase, D subunit Nmar_1690 CENSYa_1445 88 1,548,729 1,550,114 461 r 1,457,356 1,458,744 462 r sodium-transporting two-sector ATPase Nmar_1691 CENSYa_1446 86 1,550,111 1,551,889 592 r 1,458,741 1,460,519 592 r H+transporting two-sector ATPase alpha/beta subunit central region Nmar_1692 CENSYa_1447 50 1,551,891 1,552,487 198 r 1,460,521 1,461,117 198 r H+transporting two-sector ATPase E subunit Nmar_1693 CENSYa_1451 66 1,552,577 1,554,676 699 f 1,462,539 1,464,614 691 f V-type ATPase 116 kDa subunit Nmar_1697 CENSYa_1452 51 1,557,401 1,558,177 258 r 1,464,598 1,465,389 263 r rhodanese domain protein Nmar_1698 CENSYa_1453 81 1,558,251 1,559,816 521 r 1,465,453 1,467,018 521 r ammonium transporter Nmar_1699 CENSYa_1454 48 1,559,945 1,560,610 221 f 1,467,168 1,467,824 218 f hypothetical protein Nmar_1700 CENSYa_1456 59 1,560,670 1,561,704 344 f 1,468,122 1,469,162 346 f proton-transporting two-sector ATPase Nmar_1701 CENSYa_1458 61 1,561,983 1,562,630 215 f 1,469,415 1,470,062 215 f hypothetical protein Nmar_1703 CENSYa_1533 40 1,562,875 1,563,429 184 r 1,546,355 1,546,888 177 f hypothetical protein Nmar_1704 CENSYa_1532 60 1,563,501 1,563,851 116 f 1,545,916 1,546,263 115 r hypothetical protein Nmar_1705 CENSYa_1531 64 1,563,854 1,564,537 227 r 1,545,226 1,545,912 228 f uridylate kinase, putative Nmar_1706 CENSYa_1530 56 1,564,534 1,565,769 411 r 1,544,003 1,545,226 407 f metal dependent phosphohydrolase Nmar_1707 CENSYa_1529 40 1,565,766 1,566,347 193 r 1,543,420 1,543,980 186 f thymidylate kinase Nmar_1708 CENSYa_1510 52 1,566,629 1,567,009 126 f 1,522,043 1,522,426 127 r heat shock protein Hsp20 Nmar_1709 CENSYa_1509 64 1,567,013 1,568,557 514 r 1,520,453 1,521,997 514 f ABC-1 domain protein Nmar_1710 CENSYa_1508 39 1,568,561 1,568,944 127 r 1,519,903 1,520,436 177 f conserved hypothetical protein Nmar_1712 CENSYa_1507 56 1,569,640 1,570,932 430 r 1,518,604 1,519,875 423 f hypothetical protein Nmar_1713 CENSYa_1506 68 1,570,929 1,571,552 207 r 1,517,927 1,518,607 226 f ABC transporter related Nmar_1714 CENSYa_1505 77 1,571,629 1,572,816 395 r 1,516,768 1,517,925 385 f protein of unknown function DUF214 Nmar_1715 CENSYa_1504 56 1,572,933 1,573,835 300 f 1,515,644 1,516,588 314 r putative transcriptional regulator, AsnC family Nmar_1717 CENSYa_1503 53 1,574,377 1,575,357 326 r 1,514,679 1,515,656 325 f phosphate uptake regulator, PhoU Nmar_1718 CENSYa_1502 49 1,575,422 1,576,333 303 f 1,513,742 1,514,614 290 r GHMP kinase Nmar_1719 CENSYa_1501 52 1,576,344 1,577,108 254 f 1,512,977 1,513,735 252 r Ppotein of unknown function DUF137 Nmar_1720 CENSYa_1500 57 1,577,101 1,577,940 279 f 1,512,166 1,512,954 262 r 3-methyl-2-oxobutanoate hydroxymethyltransferase Nmar_1721 CENSYa_1499 57 1,577,930 1,579,174 414 f 1,510,896 1,512,083 395 r phosphopantothenoylcysteine decarboxylase/phosphopantothenate--cysteine ligase Nmar_1722 CENSYa_1498 43 1,579,343 1,580,185 280 f 1,510,052 1,510,873 273 r methyltransferase type 11 Nmar_1724 CENSYa_1497 63 1,580,685 1,581,749 354 r 1,508,989 1,510,050 353 f peptidase M24 Nmar_1725 CENSYa_1496 74 1,581,822 1,582,835 337 f 1,507,907 1,508,917 336 r tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase Nmar_1726 CENSYa_1495 75 1,582,909 1,583,187 92 f 1,507,570 1,507,869 99 r protein of unknown function DUF1621 Nmar_1727 CENSYa_1545 79 1,583,179 1,585,119 646 r 1,554,047 1,555,984 645 r beta-lactamase domain protein Nmar_1728 CENSYa_1546 82 1,585,127 1,585,759 210 r 1,555,992 1,556,579 195 r proteasome endopeptidase complex Nmar_1729 CENSYa_1547 64 1,585,837 1,586,901 354 f 1,556,693 1,557,757 354 f 3-dehydroquinate synthase Nmar_1730 CENSYa_1548 45 1,586,903 1,587,649 248 r 1,557,762 1,558,547 261 r peptidylprolyl isomerase FKBP-type Nmar_1731 CENSYa_1549 70 1,587,692 1,588,837 381 r 1,558,576 1,559,706 376 r serine--pyruvate transaminase Nmar_1732 CENSYa_1550 41 1,588,879 1,589,373 164 r 1,559,764 1,560,099 111 r cytidyltransferase-related domain Nmar_1733 CENSYa_1552 42 1,589,437 1,590,453 338 f 1,560,320 1,561,339 339 f RNA-3'-phosphate cyclase Nmar_1734 CENSYa_1553 58 1,590,433 1,590,930 165 r 1,561,319 1,561,828 169 r hypothetical protein Nmar_1735 CENSYa_1554 46 1,591,012 1,591,506 164 f 1,561,963 1,562,388 141 f hypothetical protein Nmar_1736 CENSYa_1556 66 1,591,671 1,592,381 236 f 1,562,476 1,563,285 269 f cob(II)yrinic acid a,c-diamide reductase Nmar_1737 CENSYa_1558 60 1,592,549 1,593,073 174 f 1,563,477 1,564,001 174 f NADPH-dependent FMN reductase Nmar_1738 CENSYa_1559 28 1,593,432 1,593,893 153 r 1,564,055 1,564,522 155 r hypothetical protein Nmar_1739 CENSYa_1439 61 1,593,978 1,594,208 76 r 1,454,255 1,454,566 103 f hypothetical protein Nmar_1740 CENSYa_1438 75 1,594,446 1,594,922 158 f 1,453,532 1,454,011 159 r peptidylprolyl isomerase Nmar_1741 CENSYa_1437 33 1,594,923 1,595,819 298 f 1,452,639 1,453,535 298 r hypothetical protein Nmar_1744 CENSYa_1435 50 1,596,801 1,597,250 149 f 1,451,646 1,452,200 184 r hypothetical protein Nmar_1745 CENSYa_1434 75 1,597,262 1,598,155 297 f 1,450,743 1,451,636 297 r PfkB domain protein Nmar_1746 CENSYa_1433 66 1,598,195 1,598,542 115 f 1,450,340 1,450,642 100 r dUTPase Nmar_1747 CENSYa_1432 43 1,598,547 1,599,014 155 r 1,449,921 1,450,346 141 f tetrahydromethanopterin S-methyltransferase 23 kD subunit Nmar_1748 CENSYa_1431 52 1,599,007 1,600,140 377 r 1,448,791 1,449,873 360 f glutamine--scyllo-inositol transaminase Nmar_1749 CENSYa_1430 63 1,600,176 1,600,748 190 f 1,448,141 1,448,704 187 r hypothetical protein Nmar_1751 CENSYa_1428 63 1,601,298 1,602,344 348 f 1,446,783 1,447,820 345 r tyrosyl-tRNA synthetase Nmar_1752 CENSYa_1427 75 1,602,341 1,603,135 264 r 1,446,017 1,446,802 261 f precorrin-3B C17-methyltransferase Nmar_1753 CENSYa_1424 47 1,603,180 1,604,646 488 r 1,442,671 1,444,221 516 f hypothetical protein Nmar_1754 CENSYa_1423 58 1,604,682 1,606,085 467 r 1,441,118 1,442,497 459 f aspartate kinase Nmar_1755 CENSYa_1422 77 1,606,121 1,606,867 248 r 1,440,313 1,441,059 248 f proliferating cell nuclear antigen PcnA Nmar_1756 CENSYa_1421 60 1,606,902 1,607,219 105 r 1,439,929 1,440,240 103 f transcription termination factor Tfs Nmar_1757 CENSYa_1420 54 1,607,221 1,607,499 92 r 1,439,648 1,439,932 94 f hypothetical protein Nmar_1758 CENSYa_1300 62 1,607,551 1,608,087 178 f 1,310,299 1,310,913 204 r hypothetical protein Nmar_1759 CENSYa_1298 50 1,608,281 1,608,427 48 f 1,309,959 1,310,108 49 r hypothetical protein Nmar_1760 CENSYa_1297 58 1,608,424 1,608,933 169 r 1,309,462 1,309,962 166 f dual specificity protein phosphatase Nmar_1761 CENSYa_0285 50 1,608,962 1,609,603 213 r 248,375 249,004 209 r cyclase family protein Nmar_1762 CENSYa_0286 64 1,609,679 1,609,936 85 f 249,085 249,345 86 f transcriptional regulator, AsnC family Nmar_1763 CENSYa_0287 50 1,609,931 1,611,076 381 r 249,340 250,464 374 r aminotransferase class V Nmar_1764 CENSYa_0288 24 1,611,103 1,611,699 198 f 250,539 251,102 187 f hypothetical protein Nmar_1765 CENSYa_0289 92 1,611,819 1,612,118 99 f 251,173 251,472 99 f 4Fe-4S ferredoxin iron-sulfur binding domain protein Nmar_1766 CENSYa_0926 44 1,612,286 1,614,061 591 f 978,506 980,158 550 f adenylate/guanylate cyclase with integral membrane sensor Nmar_1767 CENSYa_0925 55 1,614,058 1,615,212 384 r 977,223 978,425 400 f heat shock protein DnaJ domain protein Nmar_1768 CENSYa_0920 73 1,615,312 1,615,734 140 r 975,284 975,703 139 f UspA domain protein Nmar_1770 CENSYa_1873 64 1,617,135 1,617,791 218 r 1,845,999 1,846,613 204 f hypothetical protein Nmar_1771 CENSYa_1872 79 1,617,863 1,619,308 481 r 1,844,447 1,845,874 475 f glutamine synthetase, type I Nmar_1772 CENSYa_1871 70 1,619,396 1,620,742 448 r 1,843,004 1,844,374 456 f lysine 2,3-aminomutase related protein Nmar_1773 CENSYa_1870 65 1,620,969 1,622,612 547 f 1,841,072 1,842,844 590 r MscS Mechanosensitive ion channel Nmar_1774 CENSYa_1869 48 1,622,652 1,623,530 292 f 1,840,087 1,840,938 283 r ribose-phosphate pyrophosphokinase Nmar_1776 CENSYa_1867 59 1,624,474 1,625,373 299 f 1,838,172 1,839,068 298 r ribonuclease Z Nmar_1779 CENSYa_1865 38 1,626,908 1,627,312 134 r 1,837,467 1,837,871 134 f protein of unknown function DUF54 Nmar_1780 CENSYa_1864 57 1,627,309 1,627,902 197 r 1,836,923 1,837,453 176 f dephospho-CoA kinase, CoaE Nmar_1781 CENSYa_1863 38 1,627,930 1,628,472 180 f 1,836,293 1,836,820 175 r 2'-5' RNA ligase Nmar_1782 CENSYa_1862 45 1,628,469 1,629,800 443 f 1,834,968 1,836,296 442 r tRNA cytidylyltransferase
Nmar_1783 CENSYa_1861 52 1,629,775 1,630,536 253 f 1,834,247 1,834,936 229 r putative serine/threonine protein kinase Nmar_1784 CENSYa_1858 50 1,630,667 1,630,876 69 f 1,833,306 1,833,506 66 r hypothetical protein Nmar_1786 CENSYa_1857 77 1,632,027 1,632,767 246 r 1,832,578 1,833,309 243 f short-chain dehydrogenase/reductase SDR Nmar_1787 CENSYa_1856 75 1,632,871 1,633,092 73 f 1,832,252 1,832,497 81 r AN1-type Zinc finger protein Nmar_1788 CENSYa_1855 53 1,633,089 1,633,373 94 r 1,831,980 1,832,255 91 f hypothetical protein Nmar_1789 CENSYa_1854 45 1,633,406 1,633,963 185 r 1,831,380 1,831,976 198 f hypothetical protein Nmar_1790 CENSYa_1853 82 1,634,005 1,635,477 490 f 1,829,910 1,831,358 482 r glutamine synthetase, type I Nmar_1791 CENSYa_1852 57 1,635,474 1,635,752 92 r 1,829,653 1,829,907 84 f hypothetical protein Nmar_1792 CENSYa_1851 82 1,635,808 1,637,520 570 r 1,827,824 1,829,524 566 f thermosome Nmar_1793 CENSYa_1849 77 1,637,624 1,638,946 440 f 1,825,900 1,827,225 441 r glycine hydroxymethyltransferase Nmar_1794 CENSYa_1827 70 1,638,948 1,642,325 1125 r 1,804,970 1,808,308 1112 r DNA polymerase II, large subunit DP2 Nmar_1795 CENSYa_1828 68 1,642,337 1,643,089 250 r 1,808,313 1,809,098 261 r geranylgeranylglyceryl phosphate synthase Nmar_1796 CENSYa_1834 58 1,643,155 1,643,517 120 f 1,811,835 1,812,197 120 f hypothetical protein Nmar_1797 CENSYa_1835 40 1,643,644 1,644,246 200 f 1,812,229 1,812,876 215 f hypothetical protein Nmar_1798 CENSYa_1836 56 1,644,373 1,644,534 53 f 1,813,052 1,813,207 51 f transcriptional regulator, AbrB family Nmar_1799 CENSYa_1838 62 1,644,540 1,644,926 128 r 1,813,938 1,814,321 127 r hypothetical protein N. maritimus ORFs highlighted in blue and bold represent genes implicated in the proposed archaeal ammonia oxidation pathway.
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 and 14: Supplemental Table 2: Predicted coo
Page 15 and 16: Supplemental Table 3: Gene predicti
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 31: Nmar_1564 CENSYa_2017 44 1,432,780
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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