Remote homology searches identify bacterial homologues of eukaryotic lipid transfer proteins, including Chorein-N domains in TamB and AsmA and Mdm31p

Table 1 Numbers of proteins in TULIP families under study

	UPr¹⁰⁰	URef⁵⁰	Pfam	Rep-MSA	Seed Seq	Residues
YceB (DUF1439)	2536	261	333	104	P0AB26	1–186
DUF4403 (N & C) ^a	926	144	200	118	J3A9I6	42–489
DUF2140	1613	258	316	114	Q039F2	1–205
Rv871c (DUF2993) ^b	5783	749	956	124	I6WZH9	1–270
Takeout	4377	485	1258	113	Q9VBV3	1–249
P47	380	135	47	110	6EKT_A	11–437
OrfX2	18	4	“^c	105	Q6RI02	1–750
AsmA (N-term: 1–180)	12,029	2825	2069	184	P28249	1–180
Chorein_N (1–115)	6222	2160	2810	118	HH cons. ^d	1–115
TamB (N-term: 1–150)	12,677	3525	2410	102 ^e	P39321	1–150
Mdm31p (131–382)	1030	194	747	136	P38880	131–382

Columns are: “Upr”: Uniprot (all sequences); “Uref”: Uniref (clustered for proteins with > 50% identity); Pfam number of sequences in all representative proteomes; Rep-MSA: number of sequences in the “representative MSA” produced by HHpred after three iterations of PSI-BLAST. These MSAs were used for all pairwise comparisons
^a MSA made to whole proteins then split: N = 42–287 (n = 113) and 288–489 (n = 111); ^b MSA made to whole proteins then used either all or just section including residues 1–130 of Rv087c; ^c All OrfX2 sequences are included in the P47 family; ^d for Chorein_N the seed sequence was the Tuebingen Toolkit’s consensus: FESLIADFLTKTIGKYIEDLDVNSVSVSLWNGNVQLKNLQVKKDACSAFNLPVIISKGILKTLEVEVPWKSIKTDPFKIKIKGLHIISQPQTVFVFDAEQYDLKKKEHRKEIIDR; ^e an alternative TamB (N-term) MSA was created with one iteration (n = 104)

ISSN: 2661-8850