The Inner Membrane Proteins of E. coli K-12 have been broken into categories in EcoGene:

1) IMemProt(N)_Ei = Experimentally determined C-terminus in cytoplasm(inside)

2) IMemProt(N)_Eo = Experimentally determined C-terminus in periplasm(outside)

3) IMemProt(N)_Pi = Predicted inside topology based on paralogs

4) IMemProt(N)_Po = Predicted outside topology based on paralogs

5) IMemProt_Pred = Predicted membrane proteins >100 aa, no experimental result, no verified paralog

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The Global Topology Analysis of:

Daley DO, Rapp M, Granseth E, Melen K, Drew D, von Heijne G, Global topology analysis of the Escherichia coli inner membrane proteome, Science (2005) 308:1321-3

as summarized in their Supplementary Table S1

was used to initially identify the Verified and Predicted Inner Membrane Proteins in EcoGene.

Verification comes from Daley et al. having
Experimentally (E) determining the periplasmic (o) or
cytoplasmic (i) location of these membrane protein C-terminal tails.
The predictions (P) include proteins whose topology is predicted
using the experimentally-constrained topology of a verfied paralog.
The number of transmembrane helices predicted
using TMHMM are listed in parentheses ().

Some proteins predicted by TMHMM, but without paralogs or experimental data,
were also listed by Daley et al., if they were >100 amino acids long.
Daley et al. did not predict the number of TM helices for this third group

The Daley et al. IMemProt assignments include
514 IMemProt_E class, 99 IMemProt_P class and 125 IMemProt_Pred class
for a total of 738 IMemProt integral membrane protein assignments.
Using this dataset as a starting point, more information about additional verification studies, the unverified (prediction-only) IMemProts, the small <100 aa) inner membrane proteins, and inner-membrane associated proteins will be included.

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76 proteins have been identified in inner membrane preparations by 2D-gel
fractionation and MS identification of many protein isoform spots:
Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ, Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth, Mol Cell Proteomics (2005) 4:1205-9

The 76 proteins localized to the inner membrane, as identified in Supplementary Table 3 of Lopez-Campistrous et al., are labeled as IMem_Loc_2DMS on the GenePage links to this page. Unlike the IMemProt, the IMem_Loc proteins are not all predicted to have membrane spanning regions or to be integral membrane proteins.

Many of these IM-localized proteins bind to integral membrane proteins or have single membrane spanning domains predicted. In fact, only 7/738 IMemProts were identified among the 76 IMem_Loc proteins: cld, msbA, mtlA, pntB, sohB, tsr and yqiK.
The 2D gel step may have enriched for membrane-associated proteins with soluble domains, including some lipoproteins (LipoProt) excluded from the IMemProt classification. Some proteins with known or suspected cytoplasmic, periplasmic and outer membrane locations were assigned an inner membrane location in this study. This may result from some proteins sticking to inner membranes during sample preparation or from cross-contamination of cell fractions. However, it is likely that most, if not all, of these proteins do associate with the inner membrane, or inner membrane complexes, in vivo, in physiologiocally relevant interactions.

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In another study using 2D_MS to identify membrane proteins, Lai et al. examined total membrane preparations from minicells and rods to look for proteins with polar and septal localization. OmpW was identified as an outer membrane protein localized to the cell poles and the inner membrane protein YiaF was identified as having a polar and septal location bias:
Lai EM, Nair U, Phadke ND, Maddock JR, Proteomic screening and identification of differentially distributed membrane proteins in Escherichia coli, Mol Microbiol (2004) 52:1029-44.9

The five inner membrane proteins identified by Lai et al. include AtpA, YiaF and AcrA, all also localized to the IM by Lopez-Campistrous et al., IMemProt_E protein AtpB, and FtsZ, an inner membrane associated protein bound to the cytoplasmic side that was identified by Lopez-Campistrous et al. as a periplasmic protein, perhaps artifactually. The IMem_Loc button has been added to ftsZ and atpB basd on the Lai et al. results.