1.B.93. The MipA-interacting Protein (MipA) Family The MipA family is a large family of outer membrane proteins called OmpV. MltA is designated as a lytic transglycosylase, and MipA may be a scaffolding protein in E. coli (Vollmer et al., 1999). Synthesis of the E. coli MipA is suppressed by glucose (Yang et al., 2011). It is related to the DUF2141 family. One member, YiaT of E. coli, has been considered to be a porin (Vinson et al., 2010). It may have ~10 TM β-strands, and may be a member of the large OMPP Superfamily 1. Evidence for this is as follows: TC Blast searches with various members of the MipA family bring up members of the OMPP superfamily with low scores, but usually not proteins outside of this superfamily with similar scores. Also, one of the proteins (TC# 1.B.93.1.3) hits 1.B.39.1.9 (a known member of the OMPP superfamily (Reddy and Saier 2016) with a score of e^-6 (with filters, e^-5) for centrally located 120 aa length segments in corresponding portions of the two proteins (residues 78 and 39 to residues 245 and 216, respectively). These observations strengthen the possibility that MipA family proteins are porins of the OMPP superfamily.
References:
Li, H., D.F. Zhang, X.M. Lin, and X.X. Peng. (2015). Outer membrane proteomics of kanamycin-resistant Escherichia coli identified MipA as a novel antibiotic resistance-related protein. FEMS Microbiol. Lett. 362:.
Reddy, B.L. and M.H. Saier, Jr. (2016). Properties and Phylogeny of 76 Families of Bacterial and Eukaryotic Organellar Outer Membrane Pore-Forming Proteins. PLoS One 11: e0152733.
van Straaten, K.E., B.W. Dijkstra, W. Vollmer, and A.M. Thunnissen. (2005). Crystal structure of MltA from Escherichia coli reveals a unique lytic transglycosylase fold. J. Mol. Biol. 352: 1068-1080.
Vinson, H.M., A. Gautam, S. Olet, P.S. Gibbs, and R. Barigye. (2010). Molecular analysis of porin gene transcription in heterogenotypic multidrug-resistant Escherichia coli isolates from scouring calves. J Antimicrob Chemother 65: 1926-1935.
Vollmer, W., M. von Rechenberg, and J.V. Höltje. (1999). Demonstration of molecular interactions between the murein polymerase PBP1B, the lytic transglycosylase MltA, and the scaffolding protein MipA of Escherichia coli. J. Biol. Chem. 274: 6726-6734.
Yang, J.N., C. Wang, C. Guo, X.X. Peng, and H. Li. (2011). Outer membrane proteome and its regulation networks in response to glucose concentration changes in Escherichia coli. Mol Biosyst 7: 3087-3093.
Examples:
TC#	Name	Organismal Type	Example
1.B.93.1.1	*YiaT putative porin of 246 aas and 10 putative TM β-strands (Yang et al., 2011).*	Proteobacteria	*YiaT of E. coli* (P37681)**

1.B.93.1.10	MipA/OmpV family protein of 276 aas and 1 N-terminal TM		MipA of Cellvibrio mixtus

1.B.93.1.11	MipA/OmpV family protein of 286 aa		MipA of Fusobacterium nucleatum

1.B.93.1.12	MipA family protein of 429 aa		MipA of Ferrimonas kyonanensis

1.B.93.1.13	MipA/OmpV family protein of 275 aa		MipA of Niveispirillum cyanobacteriorum

1.B.93.1.14	Uncharacterized protein of 295 aas [Candidatus Muproteobacteria bacterium		UP of Candidatus Muproteobacteria bacterium

1.B.93.1.2	MipA (YeaF) (Vollmer et al., 1999). This outer membrane protein of 248 aas and 10 TM β-strands is involved in antibiotic resistance (Li et al. 2015). It is also an MltA (outer membrane lytic transglycosylase (P0A935))-interacting protein (van Straaten et al. 2005; Vollmer et al. 1999).	Proteobacteria	*MipA of E. coli* (P0A908)**

1.B.93.1.3	The putative outer membrane scaffolding protein for murein-synthesizing holoenzyme of 245 aas and 10 putative TM β-strands, MipA. Resembles several porins.	Proteobacteria	MipA of Pseudoalteromonas haloplanktis

1.B.93.1.4	N-terminal DUF2141 domain/C-terminal MipA domain protein. The N-terminal domain may be an artifactual fusion of a full length DUF2141 domain with a full length putative C-terminal porin domain, but this seems less likely since the same fusion has been observed in another family member (TC# 1.B.93.2.8).	Proteobacteria	*DUF2141 homologue of Desulfurivibrio alkaliphilus* (D6Z2E5)**

1.B.93.1.5	Outer membrane protein, OmpV	Proteobacteria	OmpV ofVibrio parahaemolyticus

1.B.93.1.6	Uncharacterized protein of 282 aas and 10 predicted β-strands.	Proteobacteria	UP of Geobacter lovleyi

1.B.93.1.7	MipA,OmpV family protein of 295 aas and one N-terminal TMS.		MipA of Thalassotalea euphylliae

1.B.93.1.8	MipA/OmpV family protein of 248 aas and 1 N-terminal TMS.		MipA of Thiofilum flexile

1.B.93.1.9	MipA/OmpV family protein of 253 aas and 1 N-terminal TMS.		MipA of unclassified Herbaspirillum

Examples:
TC#	Name	Organismal Type	Example
1.B.93.2.1	Uncharacterized DUF2141 protein of 153 aas. This protein is homologous only to the N-terminal domain in 9.B.99.1.4, but no other members of subfamily 9.B.99.1. It is therefore not homologous to other members of subfamily 9.B.99.1. The N-terminal domain of 9.B.99.1.4 may be artifactual.	Cyanobacteria	UP of Calothrix sp. PCC 6303

1.B.93.2.2	Uncharacterized DUF2141 protein of 157 aas. This protein is homologous to the N-terminal domain in 9.B.99.1.4, but not to other members of subfamily 9.B.99.1. The N-terminal domain of 9.B.99.1.4 may be a fusion of a DUF2141 domain with a putative C-terminal porin domain of the MipA type, distant from other proteins listed in subfamily 1.B.93.1.	Chlorobi	UP of Chlorobium tepidum

1.B.93.2.3	DUF2141 domain-containing protein of 249 aas and 1 central TMS.		*DUF2141 protein of Brevundimonas* sp.**

1.B.93.2.4	Uncharacterized DUF2141 protein of 138 aas and one N-terminal TMS.		UP of Psychroflexus sediminis

1.B.93.2.5	Uncharacterized conserved protein, DUF2141 family, 175 aas and 1 C-terminal TMS.		UP of Cribrihabitans marinus

1.B.93.2.6	DUF2141 domain-containing protein of 161 aas and 1 N-terminal TMS		DUF2141 domain protein of Henriciella algicola

1.B.93.2.7	Uncharacterized protein (DUF2141 family) of 264 aa		UP of Rhodothalassium salexigens

1.B.93.2.8	Uncharacterized fatty acid hydroxylase domain protein of 711 aas and 7 TMSs in a 6 + 1 TMS arrangement. This protein has three domains, first an integral membrane fatty acid hydroxylase domain, second, a DUF2141 domain, and third, a MipA domain with an N-terminal TMS. The protein with TC# 1.B.93.1.4 has the latter two domains fused together in the same order as for this protein.		UP of Diploscapter pachys

1.B.93.2.9	Uncharacteerized DUF2141 protein of 171 aas and 1 N-terminal TMS		UP of Sphingopyxis indica

Examples:
TC#	Name	Organismal Type	Example
1.B.93.3.1	Uncharacterized protein conserved in bacteria (DUF2141) of 708 aas.		UP of Prevotella denticola

1.B.93.3.2	DUF2141 domain-containing protein of 623 aas. Residues 513 - 583 in this protein align with residues 36 - 105 of TC# 1.B.93.2.2 with 31% identity. The latter protein has a 157 aa DUF2141 domain with an N-terminal TMS.		DUF2141 protein of Odoribacter splanchnicus

1.B.93.3.3	Uncharacterized DUF2141 protein of 609 aas and one N-terminal TMS.		UP of Elizabethkingia meningoseptica (Chryseobacterium meningosepticum)