Supplementary Table 1: Non-redundant list of predicted interactions between membrane proteins of H. pylori and human. For each heteromeric template in iPfam, the table lists the frequency of occurrence, the annotation of representative proteins in the host and pathogen and the annotation of the template. Each field is seperated by tab and the description of fields is given below. #Field 1 - Representative H.pylori protein having one of the template Pfam domains #Field 2 - Representative Human protein having one of the template Pfam domains #Field 3 - H.pylori protein annotation #Field 4 - Human protein annotation #Field 5 - First Pfam domain present in the iPfam template #Field 6 - Second Pfam domain present in the iPfam template #Field 7 - frequency of occurrence of the iPfam domain combination in predicted list HP1207 NP_000695.2 hypothetical protein[H.pylori] ATPase, H+/K+ exchanging, alpha polypeptide [Homo sapiens] (PF00122) E1-E2 ATPase (PF00702) haloacid dehalogenase-like hydrolase 406 HP1207 NP_056415.1 hypothetical protein[H.pylori] abhydrolase domain containing 12 isoform b [Homo sapiens] (PF00561) alpha/beta hydrolase fold (PF00702) haloacid dehalogenase-like hydrolase 357 HP1207 NP_000695.2 hypothetical protein[H.pylori] ATPase, H+/K+ exchanging, alpha polypeptide [Homo sapiens] (PF00689) Cation transporting ATPase, C-terminus (PF00702) haloacid dehalogenase-like hydrolase 231 HP1538 XP_001722157.1 ubiquinol cytochrome c oxidoreductase, cytochrome c1 subunit[H.pylori] PREDICTED: hypothetical protein isoform 1 [Homo sapiens] (PF07654) Immunoglobulin C1-set domain (PF00034) Cytochrome c 219 HP0814 XP_001725719.1 thiamin biosynthesis protein[H.pylori] PREDICTED: similar to ubiquitin [Homo sapiens] (PF00240) Ubiquitin family (PF00899) ThiF family 108 HP1072 NP_000695.2 copper-transporting ATPase, P-type[H.pylori] ATPase, H+/K+ exchanging, alpha polypeptide [Homo sapiens] (PF00690) Cation transporter/ATPase, N-terminus (PF00122) E1-E2 ATPase 102 HP1072 NP_000695.2 copper-transporting ATPase, P-type[H.pylori] ATPase, H+/K+ exchanging, alpha polypeptide [Homo sapiens] (PF00689) Cation transporting ATPase, C-terminus (PF00122) E1-E2 ATPase 99 HP0889 NP_004290.2 iron(III) dicitrate ABC transporter, permease protein[H.pylori] ATP-binding cassette, sub-family B, member 7 [Homo sapiens] (PF00005) ABC transporter (PF01032) FecCD transport family 80 HP1082 NP_004290.2 multidrug resistance protein[H.pylori] ATP-binding cassette, sub-family B, member 7 [Homo sapiens] (PF00005) ABC transporter (PF00664) ABC transporter transmembrane region 80 HP1538 XP_001723466.1 ubiquinol cytochrome c oxidoreductase, cytochrome c1 subunit[H.pylori] PREDICTED: major histocompatibility complex, class II, DR beta 4 isoform 1 [Homo sapiens] (PF00969) Class II histocompatibility antigen, beta domain (PF00034) Cytochrome c 75 HP1069 NP_003110.1 cell division protein[H.pylori] spastic paraplegia 7 isoform 1 [Homo sapiens] (PF00004) ATPase family associated with various cellular activities (AAA) (PF01434) Peptidase family M41 74 HP1069 NP_003110.1 cell division protein[H.pylori] spastic paraplegia 7 isoform 1 [Homo sapiens] (PF00004) ATPase family associated with various cellular activities (AAA) (PF06480) FtsH Extracellular 74 HP1026 NP_852136.1 conserved hypothetical helicase-like protein[H.pylori] replication factor C 2 isoform 1 [Homo sapiens] (PF08542) Replication factor C (PF00004) ATPase family associated with various cellular activities (AAA) 54 HP1538 XP_001722157.1 ubiquinol cytochrome c oxidoreductase, cytochrome c1 subunit[H.pylori] PREDICTED: hypothetical protein isoform 1 [Homo sapiens] (PF00993) Class II histocompatibility antigen, alpha domain (PF00034) Cytochrome c 36 HP1429 NP_006868.3 polysialic acid capsule expression protein[H.pylori] guanosine monophosphate reductase [Homo sapiens] (PF00478) IMP dehydrogenase / GMP reductase domain (PF00571) CBS domain pair 27 HP1026 NP_009057.1 conserved hypothetical helicase-like protein[H.pylori] valosin-containing protein [Homo sapiens] (PF02359) Cell division protein 48 (CDC48), N-terminal domain (PF00004) ATPase family associated with various cellular activities (AAA) 27 HP0828 NP_620575.1 ATP synthase F0, subunit a[H.pylori] hemochromatosis protein isoform 6 precursor [Homo sapiens] (PF00129) Class I Histocompatibility antigen, domains alpha 1 and 2 (PF00119) ATP synthase A chain 26 HP0394 NP_008819.1 hypothetical protein[H.pylori] calmodulin 1 [Homo sapiens] (PF00036) EF hand (PF00149) Calcineurin-like phosphoesterase 21 HP1567 NP_056481.1 conserved hypothetical GTP-binding protein[H.pylori] GTP binding protein 5 [Homo sapiens] (PF01018) GTP1/OBG (PF01926) GTPase of unknown function 20 HP1088 NP_000047.1 transketolase A[H.pylori] branched chain keto acid dehydrogenase E1, beta polypeptide precursor [Homo sapiens] (PF02779) Transketolase, pyrimidine binding domain (PF02780) Transketolase, C-terminal domain 18 HP0394 NP_006230.2 hypothetical protein[H.pylori] serine/threonine protein phosphatase with EF-hand motifs 2 [Homo sapiens] (PF08321) PPP5 (PF00149) Calcineurin-like phosphoesterase 15 HP0814 NP_003325.2 thiamin biosynthesis protein[H.pylori] ubiquitin-activating enzyme E1 [Homo sapiens] (PF02134) Repeat in ubiquitin-activating (UBA) protein (PF00899) ThiF family 14 HP0814 NP_003325.2 thiamin biosynthesis protein[H.pylori] ubiquitin-activating enzyme E1 [Homo sapiens] (PF00899) ThiF family (PF05237) MoeZ/MoeB domain 14 HP1088 NP_000700.1 transketolase A[H.pylori] branched chain keto acid dehydrogenase E1, alpha polypeptide [Homo sapiens] (PF00676) Dehydrogenase E1 component (PF02779) Transketolase, pyrimidine binding domain 14 HP1088 NP_000700.1 transketolase A[H.pylori] branched chain keto acid dehydrogenase E1, alpha polypeptide [Homo sapiens] (PF00676) Dehydrogenase E1 component (PF02780) Transketolase, C-terminal domain 14 HP0623 NP_004948.4 UDP-N-acetylmuramate-alanine ligase[H.pylori] folylpolyglutamate synthase isoform a precursor [Homo sapiens] (PF02875) Mur ligase family, glutamate ligase domain (PF08245) Mur ligase middle domain 8 HP1088 NP_036385.2 transketolase A[H.pylori] transketolase-like 1 [Homo sapiens] (PF00456) Transketolase, thiamine diphosphate binding domain (PF02779) Transketolase, pyrimidine binding domain 6 HP1088 NP_036385.2 transketolase A[H.pylori] transketolase-like 1 [Homo sapiens] (PF00456) Transketolase, thiamine diphosphate binding domain (PF02780) Transketolase, C-terminal domain 6 HP1072 NP_003093.2 copper-transporting ATPase, P-type[H.pylori] superoxide dismutase 3, extracellular precursor [Homo sapiens] (PF00080) Copper/zinc superoxide dismutase (SODC) (PF00403) Heavy-metal-associated domain 6 HP1538 XP_001714183.1 ubiquinol cytochrome c oxidoreductase, cytochrome c1 subunit[H.pylori] PREDICTED: similar to ubiquinol-cytochrome c reductase complex [Homo sapiens] (PF05365) Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like (PF02167) Cytochrome C1 family 5 HP1538 XP_001714599.1 ubiquinol cytochrome c oxidoreductase, cytochrome c1 subunit[H.pylori] PREDICTED: similar to Ubiquinol-cytochrome c reductase, complex III subunit VII, 9.5kDa [Homo sapiens] (PF02939) UcrQ family (PF02167) Cytochrome C1 family 4 HP1539 XP_001714599.1 ubiquinol cytochrome c oxidoreductase, cytochrome b subunit[H.pylori] PREDICTED: similar to Ubiquinol-cytochrome c reductase, complex III subunit VII, 9.5kDa [Homo sapiens] (PF02939) UcrQ family (PF00033) Cytochrome b(N-terminal)/b6/petB 4 HP1539 XP_001714599.1 ubiquinol cytochrome c oxidoreductase, cytochrome b subunit[H.pylori] PREDICTED: similar to Ubiquinol-cytochrome c reductase, complex III subunit VII, 9.5kDa [Homo sapiens] (PF02939) UcrQ family (PF00032) Cytochrome b(C-terminal)/b6/petD 4 HP1538 NP_001083060.1 ubiquinol cytochrome c oxidoreductase, cytochrome c1 subunit[H.pylori] hypothetical protein LOC440567 [Homo sapiens] (PF02320) Ubiquinol-cytochrome C reductase hinge protein (PF02167) Cytochrome C1 family 4 HP1538 XP_001133753.1 ubiquinol cytochrome c oxidoreductase, cytochrome c1 subunit[H.pylori] PREDICTED: hypothetical protein [Homo sapiens] (PF02271) Ubiquinol-cytochrome C reductase complex 14kD subunit (PF02167) Cytochrome C1 family 4 HP1539 XP_001133753.1 ubiquinol cytochrome c oxidoreductase, cytochrome b subunit[H.pylori] PREDICTED: hypothetical protein [Homo sapiens] (PF02271) Ubiquinol-cytochrome C reductase complex 14kD subunit (PF00033) Cytochrome b(N-terminal)/b6/petB 4 HP1539 XP_001133753.1 ubiquinol cytochrome c oxidoreductase, cytochrome b subunit[H.pylori] PREDICTED: hypothetical protein [Homo sapiens] (PF02271) Ubiquinol-cytochrome C reductase complex 14kD subunit (PF00032) Cytochrome b(C-terminal)/b6/petD 4 HP1088 NP_001922.2 transketolase A[H.pylori] dihydrolipoamide S-acetyltransferase [Homo sapiens] (PF02817) e3 binding domain (PF02780) Transketolase, C-terminal domain 4 HP0144 NP_004365.1 cytochrome c oxidase, heme b and copper-binding subunit, membrane-bound[H.pylori] cytochrome c oxidase subunit VIc proprotein [Homo sapiens] (PF02937) Cytochrome c oxidase subunit VIc (PF00115) Cytochrome C and Quinol oxidase polypeptide I 4 HP1538 XP_001716694.1 ubiquinol cytochrome c oxidoreductase, cytochrome c1 subunit[H.pylori] PREDICTED: similar to hCG1641472 [Homo sapiens] (PF02921) Ubiquinol cytochrome reductase transmembrane region (PF02167) Cytochrome C1 family 3 HP1539 XP_001716694.1 ubiquinol cytochrome c oxidoreductase, cytochrome b subunit[H.pylori] PREDICTED: similar to hCG1641472 [Homo sapiens] (PF02921) Ubiquinol cytochrome reductase transmembrane region (PF00033) Cytochrome b(N-terminal)/b6/petB 3 HP0144 NP_001855.1 cytochrome c oxidase, heme b and copper-binding subunit, membrane-bound[H.pylori] cytochrome c oxidase subunit VIIa polypeptide 1 (muscle) precursor [Homo sapiens] (PF02238) Cytochrome c oxidase subunit VIIa (PF00115) Cytochrome C and Quinol oxidase polypeptide I 3 HP0144 NP_004065.1 cytochrome c oxidase, heme b and copper-binding subunit, membrane-bound[H.pylori] cytochrome c oxidase subunit 8A [Homo sapiens] (PF02285) Cytochrome oxidase c subunit VIII (PF00115) Cytochrome C and Quinol oxidase polypeptide I 2 HP0144 NP_570972.2 cytochrome c oxidase, heme b and copper-binding subunit, membrane-bound[H.pylori] cytochrome c oxidase subunit VIIb2 [Homo sapiens] (PF05392) Cytochrome C oxidase chain VIIB (PF00115) Cytochrome C and Quinol oxidase polypeptide I 2 HP0144 NP_001854.1 cytochrome c oxidase, heme b and copper-binding subunit, membrane-bound[H.pylori] cytochrome c oxidase subunit VIb [Homo sapiens] (PF02297) Cytochrome oxidase c subunit VIb (PF00115) Cytochrome C and Quinol oxidase polypeptide I 2 HP0144 NP_005196.1 cytochrome c oxidase, heme b and copper-binding subunit, membrane-bound[H.pylori] cytochrome c oxidase subunit VIa polypeptide 2 precursor [Homo sapiens] (PF02046) Cytochrome c oxidase subunit VIa (PF00115) Cytochrome C and Quinol oxidase polypeptide I 2 HP0144 NP_115998.2 cytochrome c oxidase, heme b and copper-binding subunit, membrane-bound[H.pylori] cytochrome c oxidase subunit IV isoform 2 [Homo sapiens] (PF02936) Cytochrome c oxidase subunit IV (PF00115) Cytochrome C and Quinol oxidase polypeptide I 2 HP0814 NP_789776.1 thiamin biosynthesis protein[H.pylori] molybdopterin synthase small subunit MOCS2A [Homo sapiens] (PF02597) ThiS family (PF05237) MoeZ/MoeB domain 1 HP1538 NP_061820.1 ubiquinol cytochrome c oxidoreductase, cytochrome c1 subunit[H.pylori] cytochrome c [Homo sapiens] (PF00034) Cytochrome c (PF02167) Cytochrome C1 family 1 HP1540 NP_536855.1 ubiquinol cytochrome c oxidoreductase, Rieske 2Fe-2S subunit[H.pylori] cytochrome b [Homo sapiens] (PF00033) Cytochrome b(N-terminal)/b6/petB (PF00355) Rieske [2Fe-2S] domain 1 HP1538 NP_536855.1 ubiquinol cytochrome c oxidoreductase, cytochrome c1 subunit[H.pylori] cytochrome b [Homo sapiens] (PF00033) Cytochrome b(N-terminal)/b6/petB (PF02167) Cytochrome C1 family 1 HP1540 NP_536855.1 ubiquinol cytochrome c oxidoreductase, Rieske 2Fe-2S subunit[H.pylori] cytochrome b [Homo sapiens] (PF00032) Cytochrome b(C-terminal)/b6/petD (PF00355) Rieske [2Fe-2S] domain 1 HP1538 NP_536855.1 ubiquinol cytochrome c oxidoreductase, cytochrome c1 subunit[H.pylori] cytochrome b [Homo sapiens] (PF00032) Cytochrome b(C-terminal)/b6/petD (PF02167) Cytochrome C1 family 1 HP1539 NP_536855.1 ubiquinol cytochrome c oxidoreductase, cytochrome b subunit[H.pylori] cytochrome b [Homo sapiens] (PF00032) Cytochrome b(C-terminal)/b6/petD (PF00033) Cytochrome b(N-terminal)/b6/petB 1 HP0144 NP_001858.1 cytochrome c oxidase, heme b and copper-binding subunit, membrane-bound[H.pylori] cytochrome c oxidase subunit VIIc precursor [Homo sapiens] (PF02935) Cytochrome c oxidase subunit VIIc (PF00115) Cytochrome C and Quinol oxidase polypeptide I 1 HP0144 NP_001853.2 cytochrome c oxidase, heme b and copper-binding subunit, membrane-bound[H.pylori] cytochrome c oxidase subunit Vb precursor [Homo sapiens] (PF01215) Cytochrome c oxidase subunit Vb (PF00115) Cytochrome C and Quinol oxidase polypeptide I 1 HP0144 NP_536849.1 cytochrome c oxidase, heme b and copper-binding subunit, membrane-bound[H.pylori] cytochrome c oxidase subunit III [Homo sapiens] (PF00510) Cytochrome c oxidase subunit III (PF00115) Cytochrome C and Quinol oxidase polypeptide I 1 HP0144 NP_536846.1 cytochrome c oxidase, heme b and copper-binding subunit, membrane-bound[H.pylori] cytochrome c oxidase subunit II [Homo sapiens] (PF02790) Cytochrome C oxidase subunit II, transmembrane domain (PF00115) Cytochrome C and Quinol oxidase polypeptide I 1 HP0144 NP_536846.1 cytochrome c oxidase, heme b and copper-binding subunit, membrane-bound[H.pylori] cytochrome c oxidase subunit II [Homo sapiens] (PF00116) Cytochrome C oxidase subunit II, periplasmic domain (PF00115) Cytochrome C and Quinol oxidase polypeptide I 1