RegulonDB

RegulonDB RegulonDB 10.9: Gene Form

bamA gene in Escherichia coli K-12 genome

Gene local context to scale (view description)

Gene
Name:	bamA
Synonym(s):	ECK0176, G6093, b0177, ecfK, yaeT, yzzN, yzzY
Genome position(nucleotides):	197928 --> 200360 Genome Browser
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	50.68
External database links:

ASAP:	ABE-0000605
ECHOBASE:	EB2541
ECOLIHUB:	bamA
OU-MICROARRAY:	b0177
STRING:	511145.b0177
COLOMBOS:	bamA

Product

Name:

outer membrane protein assembly factor BamA

Synonym(s):

BamA, EcfK, YaeT, YzzN, YzzY

Sequence:

Get amino acid sequence Fasta Format

Cellular location:

outer membrane

Molecular weight:

90.553

Isoelectric point:

4.711

Motif(s):

Type	Positions	Sequence
	494 -> 494	F
	661 -> 661	R
	771 -> 771	G
	366 -> 366	R
	430 -> 430	I

Type	Positions	Sequence
	494 -> 494	F
	661 -> 661	R
	771 -> 771	G
	366 -> 366	R
	430 -> 430	I
	470 -> 470	E
	484 -> 495	SLGGRLFYNDFQ
	505 -> 506	TN
	523 -> 535	NSLRAGLGYVHNS
	740 -> 740	D
	24 -> 91	FVVKDIHFEGLQRVAVGAALLSMPVRTGDTVNDEDISNTIRALFATGNFEDVRVLRDGDTLLVQVKER
	175 -> 263	AEIQQINIVGNHAFTTDELISHFQLRDEVPWWNVVGDRKYQKQKLAGDLETLRSYYLDRGYARFNIDSTQVSLTPDKKGIYVTVNITEG
	266 -> 344	YKLSGVEVSGNLAGHSAEIEQLTKIEPGELYNGTKVTKMEDDIKKLLGRYGYAYPRVQSMPEINDADKTVKLRVNVDAG
	347 -> 421	FYVRKIRFEGNDTSKDAVLRREMRQMEGAWLGSDLVDQGKERLNRLGFFETVDTDTQRVPGSPDQVDVVYKVKER
	361 -> 361	K
	373 -> 373	E
	448 -> 810	NWLGTGYAVGINGTKNDYQTYAELSVTNPYFTVDGVSLGGRLFYNDFQADDADLSDYTNKSYGTDVTLGFPINEYNSLRAGLGYVHNSLSNMQPQVAMWRYLYSMGEHPSTSDQDNSFKTDDFTFNYGWTYNKLDRGYFPTDGSRVNLTGKVTIPGSDNEYYKVTLDTATYVPIDDDHKWVVLGRTRWGYGDGLGGKEMPFYENFYAGGSSTVRGFQSNTIGPKAVYFPHQASNYDPDYDYECATQDGAKDLCKSDDAVGGNAMAVASLEFITPTPFISDKYANSVRTSFFWDMGTVWDTNWDSSQYSGYPDYSDPSNIRMSAGIALQWMSPLGPLVFSYAQPFKKYDGDKAEQFQFNIGKTW
	455 -> 462	AVGINGTK
	629 -> 639	VLGRTRWGYGD
	348 -> 421	YVRKIRFEGNDTSKDAVLRREMRQMEGAWLGSDLVDQGKERLNRLGFFETVDTDTQRVPGSPDQVDVVYKVKER
	464 -> 464	D
	466 -> 475	QTYAELSVTN
	547 -> 547	R
	564 -> 577	SFKTDDFTFNYGWT
	712 -> 712	A
	804 -> 808	FNIGK
	1 -> 20	MAMKKLLIASLLFSSATVYG
	92 -> 172	PTIASITFSGNKSVKDDMLKQNLEASGVRVGESLDRTTIADIEKGLEDFYYSVGKYSASVKAVVTPLPRNRVDLKLVFQEG
	115 -> 115	E
	181 -> 181	N
	251 -> 251	K
	632 -> 632	R
	675 -> 701	FPHQASNYDPDYDYECATQDGAKDLCK
	754 -> 755	YS
	768 -> 777	MSAGIALQWM
	769 -> 776	SAGIALQW
	808 -> 808	K
	176 -> 263	EIQQINIVGNHAFTTDELISHFQLRDEVPWWNVVGDRKYQKQKLAGDLETLRSYYLDRGYARFNIDSTQVSLTPDKKGIYVTVNITEG
	255 -> 255	Y
	415 -> 419	VYKVK
	417 -> 419	KVK
	435 -> 435	E
	591 -> 600	SRVNLTGKVT
	660 -> 663	VRGF
	425 -> 433	SFNFGIGYG
	429 -> 429	G
	556 -> 563	PSTSDQDN
	584 -> 584	G
	609 -> 619	YKVTLDTATYV
	658 -> 658	S
	673 -> 702	VYFPHQASNYDPDYDYECATQDGAKDLCKS
	677 -> 685	HQASNYDPD
	738 -> 738	F
	779 -> 789	PLGPLVFSYAQ
	807 -> 807	G
	21 -> 810	AEGFVVKDIHFEGLQRVAVGAALLSMPVRTGDTVNDEDISNTIRALFATGNFEDVRVLRDGDTLLVQVKERPTIASITFSGNKSVKDDMLKQNLEASGVRVGESLDRTTIADIEKGLEDFYYSVGKYSASVKAVVTPLPRNRVDLKLVFQEGVSAEIQQINIVGNHAFTTDELISHFQLRDEVPWWNVVGDRKYQKQKLAGDLETLRSYYLDRGYARFNIDSTQVSLTPDKKGIYVTVNITEGDQYKLSGVEVSGNLAGHSAEIEQLTKIEPGELYNGTKVTKMEDDIKKLLGRYGYAYPRVQSMPEINDADKTVKLRVNVDAGNRFYVRKIRFEGNDTSKDAVLRREMRQMEGAWLGSDLVDQGKERLNRLGFFETVDTDTQRVPGSPDQVDVVYKVKERNTGSFNFGIGYGTESGVSFQAGVQQDNWLGTGYAVGINGTKNDYQTYAELSVTNPYFTVDGVSLGGRLFYNDFQADDADLSDYTNKSYGTDVTLGFPINEYNSLRAGLGYVHNSLSNMQPQVAMWRYLYSMGEHPSTSDQDNSFKTDDFTFNYGWTYNKLDRGYFPTDGSRVNLTGKVTIPGSDNEYYKVTLDTATYVPIDDDHKWVVLGRTRWGYGDGLGGKEMPFYENFYAGGSSTVRGFQSNTIGPKAVYFPHQASNYDPDYDYECATQDGAKDLCKSDDAVGGNAMAVASLEFITPTPFISDKYANSVRTSFFWDMGTVWDTNWDSSQYSGYPDYSDPSNIRMSAGIALQWMSPLGPLVFSYAQPFKKYDGDKAEQFQFNIGKTW
	228 -> 228	S
	259 -> 259	N
	351 -> 353	KIR
	393 -> 393	G
	436 -> 446	SGVSFQAGVQQ
	500 -> 500	D
	554 -> 562	EHPSTSDQD
	665 -> 665	S
	709 -> 718	NAMAVASLEF
	733 -> 745	VRTSFFWDMGTVW
	800 -> 800	E

Classification:

Multifun Terms (GenProtEC)
Multifun Terms (GenProtEC)		6 - cell structure --> 6.1 - membrane
Gene Ontology Terms (GO)
	cellular_component	GO:0009279 - cell outer membrane GO:0019867 - outer membrane GO:0016020 - membrane GO:0016021 - integral component of membrane GO:1990063 - Bam protein complex
	molecular_function	GO:0005515 - protein binding GO:0051082 - unfolded protein binding
	biological_process	GO:0007155 - cell adhesion GO:0043165 - Gram-negative-bacterium-type cell outer membrane assembly GO:0051205 - protein insertion into membrane GO:0071709 - membrane assembly

Note(s):

Note(s): ...[more].

Evidence:

[APPH] Assay of protein purified to homogeneity
[APPHINH] Assay of protein purified to homogeneity from its native host
[IMP] Inferred from mutant phenotype

Reference(s):

[1] Bayan N., et al., 2006
[2] Bredemeier R., et al., 2007
[3] Browning DF., et al., 2015
[4] Browning DF., et al., 2013
[5] Collin S., et al., 2007
[6] Doerner PA., et al., 2017
[7] Fleming PJ., et al., 2016
[8] Hagan CL., et al., 2010
[9] Han L., et al., 2016
[10] Lee J., et al., 2019
[11] Leonard-Rivera M., et al., 2012
[12] Morgado L., et al., 2015
[13] Ni D., et al., 2014
[14] Pinto C., et al., 2018
[15] Plummer AM., et al., 2015
[16] Ricci DP., et al., 2012
[17] Rigel NW., et al., 2012
[18] Sinnige T., et al., 2015
[19] Sklar JG., et al., 2007
[20] Stegmeier JF., et al., 2007
[21] Tellez R., et al., 2012
[22] Thoma J., et al., 2018
[23] Ward R., et al., 2009
[24] Workman P., et al., 2012
[25] Wu T., et al., 2005

External database links:

DIP:

ECOCYC:

ECOLIWIKI:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

PANTHER:

PANTHER:

PDB:

PDB:

PDB:

PDB:

PDB:

PDB:

PDB:

PDB:

PDB:

PDB:

PDB:

PDB:

PDB:

PDB:

PDB:

PDB:

PFAM:

PFAM:

PRIDE:

PROSITE:

REFSEQ:

SMR:

UNIPROT:

Operon

Name:

bamA-skp-lpxD-fabZ-lpxAB-rnhB-dnaE

Operon arrangement:

Transcription unit	Promoter
bamA-hlpA-lpxD-fabZ-lpxAB-rnhB-dnaE	bamAp2
bamA	bamAp
hlpA-lpxD-fabZ-lpxA	hlpAp
lpxD	lpxDp
fabZ

Elements in the selected gene context region unrelated to any object in RegulonDB

Type	Name	Post Left	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
promoter	TSS_339	196978	forward	nd	[RS-EPT-CBR]	[26]
promoter	TSS_341 (cluster)	197487	forward	For this promoter, there is a cluster of 11 transcription start sites,in the interval 197487 to 197497, where the highest frequency is at position 197495. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[26]
promoter	TSS_342	197586	forward	nd	[RS-EPT-CBR]	[26]
promoter	TSS_343	197588	reverse	nd	[RS-EPT-CBR]	[26]
promoter	TSS_344	197883	forward	nd	[RS-EPT-CBR]	[26]
promoter	TSS_345	198507	forward	nd	[RS-EPT-CBR]	[26]
promoter	TSS_346	198777	forward	nd	[RS-EPT-CBR]	[26]
promoter	TSS_347	198782	forward	nd	[RS-EPT-CBR]	[26]
promoter	TSS_348 (cluster)	198858	forward	For this promoter, there is a cluster of 2 transcription start sites,in the interval 198858 to 198859, where the highest frequency is at position 198858. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[26]
promoter	TSS_349	198875	forward	nd	[RS-EPT-CBR]	[26]
promoter	TSS_350 (cluster)	198877	forward	For this promoter, there is a cluster of 2 transcription start sites,in the interval 198877 to 198878, where the highest frequency is at position 198878. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[26]
promoter	TSS_351 (cluster)	198881	forward	For this promoter, there is a cluster of 4 transcription start sites,in the interval 198881 to 198884, where the highest frequency is at position 198883. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[26]
promoter	TSS_352	198887	forward	nd	[RS-EPT-CBR]	[26]
promoter	TSS_353	198889	forward	nd	[RS-EPT-CBR]	[26]
promoter	TSS_354	198893	forward	nd	[RS-EPT-CBR]	[26]
promoter	TSS_355 (cluster)	198908	forward	For this promoter, there is a cluster of 2 transcription start sites,in the interval 198908 to 198909, where the highest frequency is at position 198909. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[26]
promoter	TSS_356	199004	forward	nd	[RS-EPT-CBR]	[26]
promoter	TSS_357	199007	forward	nd	[RS-EPT-CBR]	[26]
promoter	TSS_358	199009	forward	nd	[RS-EPT-CBR]	[26]
promoter	TSS_359	199012	forward	nd	[RS-EPT-CBR]	[26]
promoter	TSS_360	199980	forward	nd	[RS-EPT-CBR]	[26]
promoter	TSS_361	200131	forward	nd	[RS-EPT-CBR]	[26]
promoter	TSS_362 (cluster)	200135	forward	For this promoter, there is a cluster of 2 transcription start sites,in the interval 200135 to 200136, where the highest frequency is at position 200135. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[26]
promoter	TSS_363 (cluster)	200138	forward	For this promoter, there is a cluster of 2 transcription start sites,in the interval 200138 to 200139, where the highest frequency is at position 200138. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[26]
promoter	TSS_364	200212	forward	nd	[RS-EPT-CBR]	[26]
promoter	TSS_365	200317	forward	nd	[RS-EPT-CBR]	[26]
promoter	TSS_366	200399	forward	nd	[RS-EPT-CBR]	[26]

Evidence
[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

Reference(s)
[1] Bayan N., Guilvout I., Pugsley AP., 2006, Secretins take shape., Mol Microbiol 60(1):1-4
[2] Bredemeier R., Schlegel T., Ertel F., Vojta A., Borissenko L., Bohnsack MT., Groll M., von Haeseler A., Schleiff E., 2007, Functional and phylogenetic properties of the pore-forming beta-barrel transporters of the Omp85 family., J Biol Chem 282(3):1882-90
[3] Browning DF., Bavro VN., Mason JL., Sevastsyanovich YR., Rossiter AE., Jeeves M., Wells TJ., Knowles TJ., Cunningham AF., Donald JW., Palmer T., Overduin M., Henderson IR., 2015, Cross-species chimeras reveal BamA POTRA and β-barrel domains must be fine-tuned for efficient OMP insertion., Mol Microbiol
[4] Browning DF., Matthews SA., Rossiter AE., Sevastsyanovich YR., Jeeves M., Mason JL., Wells TJ., Wardius CA., Knowles TJ., Cunningham AF., Bavro VN., Overduin M., Henderson IR., 2013, Mutational and topological analysis of the Escherichia coli BamA protein., PLoS One 8(12):e84512
[5] Collin S., Guilvout I., Chami M., Pugsley AP., 2007, YaeT-independent multimerization and outer membrane association of secretin PulD., Mol Microbiol 64(5):1350-7
[6] Doerner PA., Sousa MC., 2017, Extreme Dynamics in the BamA β-Barrel Seam., Biochemistry 56(24):3142-3149
[7] Fleming PJ., Patel DS., Wu EL., Qi Y., Yeom MS., Sousa MC., Fleming KG., Im W., 2016, BamA POTRA Domain Interacts with a Native Lipid Membrane Surface., Biophys J 110(12):2698-2709
[8] Hagan CL., Kim S., Kahne D., 2010, Reconstitution of outer membrane protein assembly from purified components., Science 328(5980):890-2
[9] Han L., Zheng J., Wang Y., Yang X., Liu Y., Sun C., Cao B., Zhou H., Ni D., Lou J., Zhao Y., Huang Y., 2016, Structure of the BAM complex and its implications for biogenesis of outer-membrane proteins., Nat Struct Mol Biol 23(3):192-6
[10] Lee J., Tomasek D., Santos TM., May MD., Meuskens I., Kahne D., 2019, Formation of a β-barrel membrane protein is catalyzed by the interior surface of the assembly machine protein BamA., Elife 8
[11] Leonard-Rivera M., Misra R., 2012, Conserved residues of the putative L6 loop of Escherichia coli BamA play a critical role in the assembly of β-barrel outer membrane proteins, including BamA itself., J Bacteriol
[12] Morgado L., Zeth K., Burmann BM., Maier T., Hiller S., 2015, Characterization of the insertase BamA in three different membrane mimetics by solution NMR spectroscopy., J Biomol NMR 61(3-4):333-45
[13] Ni D., Yang K., Huang Y., 2014, Refolding, crystallization and preliminary X-ray crystallographic studies of the β-barrel domain of BamA, a membrane protein essential for outer membrane protein biogenesis., Acta Crystallogr F Struct Biol Commun 70(Pt 3):362-5
[14] Pinto C., Mance D., Sinnige T., Daniels M., Weingarth M., Baldus M., 2018, Formation of the β-barrel assembly machinery complex in lipid bilayers as seen by solid-state NMR., Nat Commun 9(1):4135
[15] Plummer AM., Fleming KG., 2015, BamA Alone Accelerates Outer Membrane Protein Folding In Vitro through a Catalytic Mechanism., Biochemistry 54(39):6009-11
[16] Ricci DP., Hagan CL., Kahne D., Silhavy TJ., 2012, Activation of the Escherichia coli β-barrel assembly machine (Bam) is required for essential components to interact properly with substrate., Proc Natl Acad Sci U S A 109(9):3487-91
[17] Rigel NW., Schwalm J., Ricci DP., Silhavy TJ., 2012, BamE modulates the Escherichia coli beta-barrel assembly machine component BamA., J Bacteriol 194(5):1002-8
[18] Sinnige T., Houben K., Pritisanac I., Renault M., Boelens R., Baldus M., 2015, Insight into the conformational stability of membrane-embedded BamA using a combined solution and solid-state NMR approach., J Biomol NMR 61(3-4):321-32
[19] Sklar JG., Wu T., Gronenberg LS., Malinverni JC., Kahne D., Silhavy TJ., 2007, Lipoprotein SmpA is a component of the YaeT complex that assembles outer membrane proteins in Escherichia coli., Proc Natl Acad Sci U S A 104(15):6400-5
[20] Stegmeier JF., Gluck A., Sukumaran S., Mantele W., Andersen C., 2007, Characterisation of YtfM, a second member of the Omp85 family in Escherichia coli., Biol Chem 388(1):37-46
[21] Tellez R., Misra R., 2012, Substitutions in the BamA β-barrel domain overcome the conditional lethal phenotype of a ΔbamB ΔbamE strain of Escherichia coli., J Bacteriol 194(2):317-24
[22] Thoma J., Manioglu S., Kalbermatter D., Bosshart PD., Fotiadis D., Muller DJ., 2018, Protein-enriched outer membrane vesicles as a native platform for outer membrane protein studies., Commun Biol 1:23
[23] Ward R., Zoltner M., Beer L., El Mkami H., Henderson IR., Palmer T., Norman DG., 2009, The orientation of a tandem POTRA domain pair, of the beta-barrel assembly protein BamA, determined by PELDOR spectroscopy., Structure 17(9):1187-94
[24] Workman P., Heide K., Giuliano N., Lee N., Mar J., Vuong P., Bennion D., Misra R., 2012, Genetic, biochemical, and molecular characterization of the polypeptide transport-associated domain of Escherichia coli BamA., J Bacteriol 194(13):3512-21
[25] Wu T., Malinverni J., Ruiz N., Kim S., Silhavy TJ., Kahne D., 2005, Identification of a multicomponent complex required for outer membrane biogenesis in Escherichia coli., Cell 121(2):235-45
[26] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

RegulonDB