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Analysis of multi-domain proteins with putative hemerythrin-like domains

Our analysis showed a variety of large multi-domain proteins with a hemerythrin-like domain, usually at the C-terminus or N-terminus. Other domains present were generally identified by sequence comparison as being involved in signalling: mainly methyl-accepting chemotaxis proteins (MCPs), diguanylate cyclases (GGDEF domains), histidine kinase domains, CheY-like response receiver domains, and cAMP-binding domains, and in one case an apparent phosphatase domain. The most obvious interpretation is that the hemerythrin domains act as oxygen sensors, and the auxiliary domains function in signal transduction to alter the cell's state. Sequence comparisons allowed the majority of the putative multi-domain hemerythrins to be assigned to a few well defined families.

Multi-Domain Hemerythrins

Strain Locus Tag Length Code Group
Magnetococcus sp. MC-1 Mmc1_0194 1032 Magco1032 MCP-hem-2
Mmc1_0310 994 Magco994 MCP-hem-2
Mmc1_0400 320 Magco320 RR-hem
Mmc1_0606 779 Magco779 MCP-hem-2
Mmc1_1585 997 Magco997 MCP-hem-2
Mmc1_2454 871 Magco871 CNBP-hem
Mmc1_2834 249 Magco249 hem-X1
Mmc1_2935 941 magco941 MCP-hem-2
Mmc1_3109 253 Magco253 hem-X1
Mmc1_3168 926 Magco926 MCP-hem-2
Mmc1_3573 927 Magco927 MCP-hem-2
Magnetospirillum magneticum AMB-1 amb0220 807 Magam807 MCP-hem-1
amb0723 275 Magam275 hem-RR
amb0871 502 Magam502 hem-X2
amb1682 906 Magam906 CNBP-hem
amb2535 282 Magam282 hem-RR
amb3095 870 Magam870 CNBP-hem
amb3267 665 Magam665 MCP-hem-1
amb3610 499 Magam499 hem-X2
amb3793 810 Magam810 MCP-hem-1
amb4156 795 Magam795 MCP-hem-1
Magnetospirillum gryphiswaldense MSR1 mgI476, ORF12 524 or 525 Maggr524 RR-hem-X3
Magnetospirillum magnetotacticum MS-1 Magn03008576 272 Magms272 hem-RR
Magn03008774 274 Magms274 hem-RR
Magn03008962 870 Magms870 CNBP-hem
Magn03008983 500 Magms500 hem-X2
Magn03010318 889 Magms889 CNBP-hem
Magn03010618 808 Magms808 MCP-hem-1
Magn03010970 807 Magms807 MCP-hem-1
Magn03011185 699 Magms699 MCP-hem-1
Rhodospirillum rubrum ATCC 11170 Rru_A0632 736 Rhoru736 MCP-hem-1
Rru_A1523 262 Rhoru262 hem-hem
Rhodopseudomonas palustris BisA53 RPE_2062 507 RhopaA507 GGDEF-hem
Rhodopseudomonas palustris BisB18 RPC_2156 470 RhopaB470 hem-GGDEF
Rhodopseudomonas palustris CGA009 RPA1642 504 RhopaC504 GGDEF-hem
Dechloromonas aromatica RCB Daro_0965 681 Decar681 hem-HK
Daro_3954 667 Decar667 GGDEF-hem
Rhodoferax ferrireducens DSM 15236/T118 Rfer_1451 277 Rhofe277 X4-hem
Rfer_3626 840 Rhofe840 GGDEF-hem
Rfer_4030 498 Rhofe498 GGDEF-hem
Aeromonas hydrophila ATCC 7966 AHA_0130 678 Aerhy678 MCP-hem-3
AHA_2968 809 Aerhy809 GGDEF-hem
Colwellia psychrerythraea 34H CPS_1744 368 Colps368 hem-GGDEF
CPS_1939 1328 Colps1328 HK-RR-hem
CPS_3631 722 Colps722 hem-GGDEF
CPS_4695 519 Colps519 RR-hem
Idiomarina baltica OS145 OS145_02680 566 Idiba566 MCP-hem-3
Idiomarina lohoiensis L2TR IL0175 832 Idilo832 MCP-hem-3
Marinobacter aquaeoli VT8 MaquDRAFT_0582 662 Maraq662 hem-GGDEF
Shewanella amazonensis SB2B SamaDRAFT_0036 518 Sheam518 MCP-hem-3
Shewanella sp. ANA-3 Shewana3_0739 529 Shean529 MCP-hem-3
Shewanella baltica OS155 SbalDRAFT_2075 529 ShebaA529 MCP-hem-3
Shewanella baltica OS195 Sbal195DRAFT_1213 529 ShebaB529 MCP-hem-3
Shewanella sp. MR-4 Shewmr4_3223 529 Shemrf529 MCP-hem-3
Shewanella sp. MR-7 Shewmr7_0766 529 Shemrs529 MCP-hem-3
Shewanella oneidensis MR-1 SO3890 529 Sheon529 MCP-hem-3
Shewanella putrefaciens CN-32 Sputcn32DRAFT_3878 526 Shepu526 MCP-hem-3
Shewanella sp. PV-4 ShewDRAFT_3107 526 Shepv536 MCP-hem-3
Shewanella sp. W3-18-1 Sputw3181DRAFT_1600 526 Shewt526 MCP-hem-3
Vibrio cholerae O1 N16961 VC1216 372 Vibco372 hem-GGDEF
Vibrio cholerae V52 VchoV_01003238 372 Vibco372 hem-GGDEF
Vibrio cholerae O395 VchoO_01000773 372 Vibco372 hem-GGDEF
Vibrio cholerae MO10 VchoM_02002571 372 Vibco372 hem-GGDEF
Vibrio parahaemolyticus RIMD 2210633 VP1289 381 Vibpa381 hem-GGDEF
Vibrio splendidus 12B01 V12B01_04093 383 Vibsp383 hem-GGDEF
Vibrio vulnificus CMCP6 VV1_2369 371 VibvuC371 hem-GGDEF
Vibrio vulnificus YJ016 VV1972 371 VibvuY371 hem-GGDEF
Desulfotalea psychrophila LSv54 DP0972 370 Desps370 hem-GGDEF
DP2039 374 Desps374 hem-GGDEF
Desulfovibrio vulgaris DP4 DvulDRAFT_2548 963 DesvuD963 MCP-hem-4
DvulDRAFT_2859 689 DesvuD689 MCP-hem-4
DvulDRAFT_3043 659 DesvuD659 GGDEF-hem
Desulfovibrio vulgaris Hildenborough DVU0170 689 DesvuH689 MCP-hem-4
DVU3106 655 DesvuH655 GGDEF-hem
DVU3155, DcrH 963 or 959 DesvuH963 MCP-hem-4
Desulfuromonas acetoxidans DSM 684 Dace_0378 1174 Desac1174 GGDEF-hem
Dace_0592 368 Desac368 hem-GGDEF
Dace_0947 591 Desac591 hem-HK-RR
Dace_1299 371 Desac371 hem-GGDEF
Delta proteobacterium MLMS-1 MldDRAFT_3301, MldDRAFT_2276 457 Mlmso457 phos-hem?
Pelobacter propionicus DSM 2379 PproDRAFT_0329 518 Pelpr518 MCP-hem-4
Campylobacter fetus 82-40 CFF8240_0606 385 Camfe385 hem-GGDEF
Thiomicrospira denitrificans ATCC 33889 Tmden_0967 1004 Thide1004 hem-GGDEF-EAL
Mariprofundus ferrooxydans PV-1 SPV1_05088 373 Marfe373 hem-GGDEF
Kuenenia stuttgartensis kustc1183 872 Kuest872 CNBP-hem
Haloarcula marismortui ATCC 43049 pNG7265 617 Halma617 hem-CoA-ligase?

MCP = methyl-accepting chemotaxis receptor CNBP = cyclic nucleotide binding protein GGDEF = cyclic di-GMP synthase HK = histidine kinase RR = CheY-like receiver domain phos = phosphatase X = unknown

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