Table 3. Unique regions in M. extorquens AM1 and DM4 chromosomes.
| Start CDS (META1_) | Start (nt) | End CDS (META1_) | End (nt) | Length (bp) | [Left border][Inside][Right border] a | IS | Features (proposed role) | Total CDS (%) | Unique CDS b (%) | AH CDS c (%) |
| Methylobacterium extorquens AM1 | ||||||||||
| 0035 | 37982 | 0046 | 51448 | 13467 | [none][GC][IS] | 1 | 14 | 11 (78.6) | 0 | |
| tRNA/0058 | 61782 | 0073 | 80559 | 18778 | [tRNA][int-AH][none] | 1 | 17 | 16 (94.1) | 5 (29.4) | |
| 0149 | 156863 | tRNA/0165 | 174721 | 17859 | [none][int-AH-mob][tRNA] | 0 | 16 | 13 (81.3) | 0 | |
| tRNA/0241 | 261958 | 0273 | 289656 | 27699 | [tRNA][GC][IS] | 4 (1) | 34 | 25 (73.5) | 0 | |
| 1078 | 1126013 | 1115 | 1164815 | 38802 | [IS][GC-mob-tRNA-tRNA][IS] | 8 | 45 | 19 (42.2) | 4 (8.9) | |
| 1226 | 1283284 | 1257 | 1308115 | 24832 | [none][GC][tRNA] | 0 | sulfur metabolism | 33 | 29 (87.9) | 0 |
| tRNA/1555 | 1629314 | 1614 | 1691767 | 62454 | [tRNA][none][IS] | 2 | 59 | 53 (89.8) | 0 | |
| tRNA/1825 | 1911338 | 1924 | 1995805 | 84467 | [tRNA][GC][int] | 6 (1) | copper resistance | 100 | 82 (82.0) | 0 |
| 2402 | 2475649 | 2415/tRNA | 2538027 | 62379 | [none][GC][tRNA] | 0 | giant META1_2412 gene | 13 | 13 (100) | 0 |
| 2573 | 2704934 | 2598 | 2734385 | 29452 | [none][GC][none] | 0 | sulfur metabolism | 25 | 14 (56.0) | 0 |
| 2622 | 2753794 | 2652 | 2781501 | 27708 | [none][GC][none] | 0 | metal transport | 31 | 31 (100) | 0 |
| 2657 | 2787350 | META1_2681 | 2808325 | 20976 | [none][GC][integrase] | 0 | 22 | 22 (100) | 0 | |
| 2687 | 2814961 | 2697 | 2823774 | 8814 | [none][GC][none] | 0 | 11 | 10 (90.9) | 0 | |
| 2755 | 2879429 | 2817 | 2939813 | 60385 | [IS][tRNA-AH][tRNA] | 2 d | included mau gene cluster | 63 | 50 (79.4) | 10 (15.9) |
| tRNA/3934 | 4056642 | 4086 | 4163355 | 106714 | [tRNA][AH][int] | 12 (3) | phage-related | 148 | 145 (98.0) | 25 (16.9) |
| 4747 | 4874344 | 4792/tRNA | 4901372 | 27028 | [integrase][GC][tRNA] | 5 | phage-related | 43 | 41 (95.3) | 6 (14.0) |
| Methylobacterium extorquens DM4 | ||||||||||
| 0036 | 37946 | 0052 | 51383 | 13438 | [Mite][int - GC][IS] | 2 d | 16 | 13 (81.3) | 11 (68.8) | |
| 0137 | 137916 | 0147/tRNA | 146122 | 8207 | [none][AH][tRNA] | 2 (1) | SOS repair (umuCD) | 8 | 0 | 4 (50.0) |
| tRNA/0225 | 232397 | 0336 | 321727 | 89331 | [tRNA][AH][none] | 4 | sensors/regulators, transport; carbon metabolism | 109 | 62 (56.9) | 27 (24.8) |
| 0345 | 328235 | 0426 | 390700 | 62466 | [none][GC][int] | 1 | Beta-lactamase-like domain repeat region | 78 | 57 (73.1) | 12 (15.4) |
| 0707 | 673123 | 0725 | 683063 | 9941 | [int][AH][none] | 1 | Beta-lactamase-like domain repeat region | 17 | 11 (64.7) | 11 (64.7) |
| 0736 | 689280 | 0748 | 702730 | 13451 | [none][AH][IS] | 2 (1) | efflux determinant | 14 | 13 (92.9) | 13 (92.9) |
| 0769 | 717385 | 0782 | 730568 | 13184 | [none][GC][none] | 0 | carbon metabolism | 13 | 10 (76.9) | 0 |
| 0786 | 733379 | 0825/tRNA | 759448 | 26070 | [none][AH][tRNA] | 1 d | gene decay region | 39 | 34 (87.2) | 28 (71.8) |
| tRNA/0840 | 774084 | 0935 | 848713 | 74630 | [tRNA][int-mob(3)-int-AH][none] | 8 d (3) | contains putative 5-formyl-H4F cyclo-ligase | 93 | 37 (39.8) | 30 (32.3) |
| 1157 | 1065633 | 1204 | 1108451 | 42819 | [int][int-int-AH][none] | 2 (1) | 45 | 25 (55.6) | 19 (42.2) | |
| 1209 | 1114522 | 1243 | 1136772 | 22251 | [none][GC][none] | 0 | 34 | 26 (76.5) | 10 (29.4) | |
| 1275 | 1161654 | 1336 | 1215594 | 53941 | [none][GC][none] | 5 (3) | 62 | 21 (33.9) | 19 (30.6) | |
| 1341 | 1219900 | 1375 | 1252518 | 32619 | [none][GC-AH][none] | 1 d | copper resistance | 36 | 5 (13.9) | 3 (8.3) |
| 1382 | 1257095 | 1424 | 1290282 | 33188 | [none][AH][IS] | 5 | metal resistance | 41 | 35 (85.4) | 16 (39.0) |
| 1586 | 1452662 | 1650 | 1512578 | 59917 | [none][GC][none] | 7 d (4) | 66 | 54 (81.8) | 45 (68.2) | |
| 1656 | 1520241 | 1683 | 1548181 | 27941 | [none][GC][none] | 0 | putative sulfur compound transport/amidase region | 28 | 26 (92.9) | 9 (32.1) |
| 1860 | 1741524 | 1886 | 1767524 | 26001 | [none][GC][none] | 0 | carbon utilisation, transport, molybdopterin-related | 25 | 25 (100) | 0 |
| 1917 | 1800884 | 1956 | 1830642 | 29759 | [none][GC][none] | 3 d | carbon utilisation, transport, amide-related | 36 | 27 (75.0) | 18 (50.0) |
| tRNA/2330 | 2227106 | 2333 | 2244311 | 17206 | [tRNA][none][IS] | 1 (1) | 4 | 4 (100) | 0 | |
| 2348 | 2263918 | 2380 | 2300422 | 36505 | [none][GC-AH][none] | 0 | 33 | 27 (81.8) | 6 (18.2) | |
| 2551 | 2460335 | 2682 | 2587253 | 126919 | [none][mob-tRNA-int-AH][none] | 6 (1) | dcm region | 129 | 127 (98.4) | 127 (98.4) |
| tRNA/3361 | 3293492 | 3383 | 3308142 | 14651 | [tRNA][tRNA-int-AH][int] | 0 | 23 | 19 (82.6) | 19 (82.6) | |
| 4329 | 4266669 | 4356 | 4283718 | 17050 | [none][AH][int] | 3 | 27 | 18 (66.7) | 10 (37.0) | |
| 4367 | 4291118 | 4487 | 4393993 | 102876 | [none][AH][none] | 5 d | nitrogen metabolism, urease-like operon | 122 | 108 (88.5) | 59 (48.4) |
| 4495 | 4400484 | 4514 | 4415275 | 14792 | [IS][AH][IS] | 2 | 20 | 16 (80.0) | 16 (80.0) | |
| tRNA/4746 | 4641080 | 4776 | 4668490 | 27411 | [tRNA][int-mob-tRNA-AH][none] | 0 | efflux determinant | 30 | 26 (86.7) | 14 (46.7) |
| tRNA/5356 | 5288636 | 5390 | 5336993 | 48358 | [tRNA][int][none] | 0 | virulence determinant | 35 | 32 (91.4) | 22 (62.9) |
| tRNA/5552 | 5522860 | 5566 | 5532024 | 9165 | [tRNA][int-AH][none] | 20 | 16 | 15 (93.8) | 15 (93.8) | |
a
int: integrase; mob: mobility determinant; GC: region with atypical GC content; AH: region rich in genes detected by Alien Hunter; IS: Insertion Sequence; MITE: Miniature Inverted Repeat Transposable Element.
b
no homolog with >80% identity/0.8 minLrap value in the chromosome of the compared strain.
c
as detected by Alien Hunter ([46], see Materials and Methods).
d
including one putative MITE.