RegulonDB

Gene
Name:	yfhM
Synonym(s):	ECK2516, G7323, b2520
Genome position(nucleotides):	2647326 <-- 2652287 Genome Browser
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	52.96
External database links:

ASAP:	ABE-0008296
ECHOBASE:	EB3175
OU-MICROARRAY:	b2520
PortEco:	yfhM
STRING:	511145.b2520
COLOMBOS:	yfhM

Gene

Name:

yfhM

Synonym(s):

ECK2516, G7323, b2520

Genome position(nucleotides):

2647326 <-- 2652287 Genome Browser

Strand:

reverse

Sequence:

Get nucleotide sequence FastaFormat

GC content %:

52.96

External database links:

ASAP:

ECHOBASE:

OU-MICROARRAY:

PortEco:

STRING:

COLOMBOS:

Type

Positions

Sequence

57 -> 164

KLAQQSAGKVLTLLDLSEVQLDGAATLVLTFSIPLDPDQDFSRVIHVVDKKSGKVDGAWELSDNLKELRLRHLEPKRDLIVTIGKEVKALNNATFSKDYEKTITTRDI

165 -> 289

QPSVGFASRGSLLPGKVVEGLPVMALNVNNVDVNFFRVKPESLPAFISQWEYRNSLANWQSDKLLQMADLVYTGRFDLNPARNTREKLLLPLGDIKPLQQAGVYLAVMNQAGRYDYSNPATLFTL

388 -> 479

FFMFGPRDLYRPGETVILNGLLRDADGKALPNQPIKLDVIKPDGQVLRSVVSQPENGLYHFTWPLDSNAATGMWHIRANTGDNQYRMWDFHV

854 -> 934

DENRRLDLALETPAKMRPNQPLTVKIKASTKNGEKPKQVNVLVSAVDSGVLNITDYVTPDPWQAFFGQKRYGADIYDIYGQ

18 -> 1653

CDNNDNAPTAVKKDAPSEVTKAASSENASSAKLSVPERQKLAQQSAGKVLTLLDLSEVQLDGAATLVLTFSIPLDPDQDFSRVIHVVDKKSGKVDGAWELSDNLKELRLRHLEPKRDLIVTIGKEVKALNNATFSKDYEKTITTRDIQPSVGFASRGSLLPGKVVEGLPVMALNVNNVDVNFFRVKPESLPAFISQWEYRNSLANWQSDKLLQMADLVYTGRFDLNPARNTREKLLLPLGDIKPLQQAGVYLAVMNQAGRYDYSNPATLFTLSDIGVSAHRYHNRLDIFTQSLENGAAQQGIEVSLLNEKGQTLTQATSDAQGHVQLENDKNAALLLARKDGQTTLLDLKLPALDLAEFNIAGAPGYSKQFFMFGPRDLYRPGETVILNGLLRDADGKALPNQPIKLDVIKPDGQVLRSVVSQPENGLYHFTWPLDSNAATGMWHIRANTGDNQYRMWDFHVEDFMPERMALNLTGEKTPLTPKDEVKFSVVGYYLYGAPANGNTLQGQLFLRPLREAVSALPGFEFGDIAAENLSRTLDEVQLTLDDKGRGEVSTESQWKETHSPLQVIFQGSLLESGGRPVTRRAEQAIWPADALPGIRPQFASKSVYDYRTDSTVKQPIVDEGSNAAFDIVYSDAQGVKKAVSGLQVRLIRERRDYYWNWSEDEGWQSQFDQKDLIENEQTLDLKADETGKVSFPVEWGAYRLEVKAPNEAVSSVRFWAGYSWQDNSDGSGAVRPDRVTLKLDKASYRPGDTIKLHIAAPTAGKGYAMVESSEGPLWWQEIDVRAQGLDLTIPVDKTWNRHDLYLSTLVVRPGDKSRSATPKRAVGVLHLPLGDENRRLDLALETPAKMRPNQPLTVKIKASTKNGEKPKQVNVLVSAVDSGVLNITDYVTPDPWQAFFGQKRYGADIYDIYGQVIEGQGRLAALRFGGDGDELKRGGKPPVNHVNIVVQQALPVTLNEQGEGSVTLPIGDFNGELRVMAQAWTADDFGSNESKVIVAAPVIAELNMPRFMASGDTSRLTLDITNLTDKPQKLNVALTASGLLELVSDSPAAVELAPGVRTTLFIPVRALPGYGDGEIQATISGLALPGETVADQHKQWKIGVRPAFPAQTVNYGTALQPGETWAIPADGLQNFSPVTLEGQLLLSGKPPLNIARYIKELKAYPYGCLEQTASGLFPSLYTNAAQLQALGIKGDSDEKRRASVDIGISRLLQMQRDNGGFALWDKNGDEEYWLTAYVMDFLVRAGEQGYSVPTDAINRGNERLLRYLQDPGMMSIPYADNLKASKFAVQSYAALVLARQQKAPLGALREIWEHRADAASGLPLLQLGVALKTMGDATRGEEAIALALKTPRNSDERIWLGDYGSSLRDNALMLSLLEENKLLPDEQYTLLNTLSQQAFGERWLSTQESNALFLAARTIQDLPGKWQAQTSFSAEQLTGEKAQNSNLNSDQLVTLQVSNSGDQPLWLRMDASGYPQSAPLPANNVLQIERHILGTDGKSKSLDSLRSGDLVLVWLQVKASNSVPDALVVDLLPAGLELENQNLANGSASLEQSGGEVQNLLNQMQQASIKHIEFRDDRFVAAVAVDEYQPVTLVYLARAVTPGTYQVPQPMVESMYVPQWRATGAAEDLLIVRP

Type

Positions

Sequence

57 -> 164

KLAQQSAGKVLTLLDLSEVQLDGAATLVLTFSIPLDPDQDFSRVIHVVDKKSGKVDGAWELSDNLKELRLRHLEPKRDLIVTIGKEVKALNNATFSKDYEKTITTRDI

165 -> 289

QPSVGFASRGSLLPGKVVEGLPVMALNVNNVDVNFFRVKPESLPAFISQWEYRNSLANWQSDKLLQMADLVYTGRFDLNPARNTREKLLLPLGDIKPLQQAGVYLAVMNQAGRYDYSNPATLFTL

388 -> 479

FFMFGPRDLYRPGETVILNGLLRDADGKALPNQPIKLDVIKPDGQVLRSVVSQPENGLYHFTWPLDSNAATGMWHIRANTGDNQYRMWDFHV

854 -> 934

DENRRLDLALETPAKMRPNQPLTVKIKASTKNGEKPKQVNVLVSAVDSGVLNITDYVTPDPWQAFFGQKRYGADIYDIYGQ

18 -> 1653

485 -> 610

ERMALNLTGEKTPLTPKDEVKFSVVGYYLYGAPANGNTLQGQLFLRPLREAVSALPGFEFGDIAAENLSRTLDEVQLTLDDKGRGEVSTESQWKETHSPLQVIFQGSLLESGGRPVTRRAEQAIWP

755 -> 853

PDRVTLKLDKASYRPGDTIKLHIAAPTAGKGYAMVESSEGPLWWQEIDVRAQGLDLTIPVDKTWNRHDLYLSTLVVRPGDKSRSATPKRAVGVLHLPLG

901 -> 966

SGVLNITDYVTPDPWQAFFGQKRYGADIYDIYGQVIEGQGRLAALRFGGDGDELKRGGKPPVNHVN

59 -> 163

AQQSAGKVLTLLDLSEVQLDGAATLVLTFSIPLDPDQDFSRVIHVVDKKSGKVDGAWELSDNLKELRLRHLEPKRDLIVTIGKEVKALNNATFSKDYEKTITTRD

368 -> 385

LPALDLAEFNIAGAPGYS

616 -> 741

GIRPQFASKSVYDYRTDSTVKQPIVDEGSNAAFDIVYSDAQGVKKAVSGLQVRLIRERRDYYWNWSEDEGWQSQFDQKDLIENEQTLDLKADETGKVSFPVEWGAYRLEVKAPNEAVSSVRFWAGY

1176 -> 1285

YIKELKAYPYGCLEQTASGLFPSLYTNAAQLQALGIKGDSDEKRRASVDIGISRLLQMQRDNGGFALWDKNGDEEYWLTAYVMDFLVRAGEQGYSVPTDAINRGNERLLR

1505 -> 1638

LQIERHILGTDGKSKSLDSLRSGDLVLVWLQVKASNSVPDALVVDLLPAGLELENQNLANGSASLEQSGGEVQNLLNQMQQASIKHIEFRDDRFVAAVAVDEYQPVTLVYLARAVTPGTYQVPQPMVESMYVPQ

289 -> 381

LSDIGVSAHRYHNRLDIFTQSLENGAAQQGIEVSLLNEKGQTLTQATSDAQGHVQLENDKNAALLLARKDGQTTLLDLKLPALDLAEFNIAGA

290 -> 367

SDIGVSAHRYHNRLDIFTQSLENGAAQQGIEVSLLNEKGQTLTQATSDAQGHVQLENDKNAALLLARKDGQTTLLDLK

386 -> 483

KQFFMFGPRDLYRPGETVILNGLLRDADGKALPNQPIKLDVIKPDGQVLRSVVSQPENGLYHFTWPLDSNAATGMWHIRANTGDNQYRMWDFHVEDFM

484 -> 611

PERMALNLTGEKTPLTPKDEVKFSVVGYYLYGAPANGNTLQGQLFLRPLREAVSALPGFEFGDIAAENLSRTLDEVQLTLDDKGRGEVSTESQWKETHSPLQVIFQGSLLESGGRPVTRRAEQAIWPA

612 -> 754

DALPGIRPQFASKSVYDYRTDSTVKQPIVDEGSNAAFDIVYSDAQGVKKAVSGLQVRLIRERRDYYWNWSEDEGWQSQFDQKDLIENEQTLDLKADETGKVSFPVEWGAYRLEVKAPNEAVSSVRFWAGYSWQDNSDGSGAVR

977 -> 1056

LNEQGEGSVTLPIGDFNGELRVMAQAWTADDFGSNESKVIVAAPVIAELNMPRFMASGDTSRLTLDITNLTDKPQKLNVA

1127 -> 1187

FPAQTVNYGTALQPGETWAIPADGLQNFSPVTLEGQLLLSGKPPLNIARYIKELKAYPYGC

1169 -> 1441

PPLNIARYIKELKAYPYGCLEQTASGLFPSLYTNAAQLQALGIKGDSDEKRRASVDIGISRLLQMQRDNGGFALWDKNGDEEYWLTAYVMDFLVRAGEQGYSVPTDAINRGNERLLRYLQDPGMMSIPYADNLKASKFAVQSYAALVLARQQKAPLGALREIWEHRADAASGLPLLQLGVALKTMGDATRGEEAIALALKTPRNSDERIWLGDYGSSLRDNALMLSLLEENKLLPDEQYTLLNTLSQQAFGERWLSTQESNALFLAARTIQDL

1191 -> 1498

TASGLFPSLYTNAAQLQALGIKGDSDEKRRASVDIGISRLLQMQRDNGGFALWDKNGDEEYWLTAYVMDFLVRAGEQGYSVPTDAINRGNERLLRYLQDPGMMSIPYADNLKASKFAVQSYAALVLARQQKAPLGALREIWEHRADAASGLPLLQLGVALKTMGDATRGEEAIALALKTPRNSDERIWLGDYGSSLRDNALMLSLLEENKLLPDEQYTLLNTLSQQAFGERWLSTQESNALFLAARTIQDLPGKWQAQTSFSAEQLTGEKAQNSNLNSDQLVTLQVSNSGDQPLWLRMDASGYPQSAP

759 -> 906

TLKLDKASYRPGDTIKLHIAAPTAGKGYAMVESSEGPLWWQEIDVRAQGLDLTIPVDKTWNRHDLYLSTLVVRPGDKSRSATPKRAVGVLHLPLGDENRRLDLALETPAKMRPNQPLTVKIKASTKNGEKPKQVNVLVSAVDSGVLNI

1020 -> 1126

PVIAELNMPRFMASGDTSRLTLDITNLTDKPQKLNVALTASGLLELVSDSPAAVELAPGVRTTLFIPVRALPGYGDGEIQATISGLALPGETVADQHKQWKIGVRPA

1 -> 17

MKKLRVAACMLMLALAG

958 -> 1019

GKPPVNHVNIVVQQALPVTLNEQGEGSVTLPIGDFNGELRVMAQAWTADDFGSNESKVIVAA

1499 -> 1653

LPANNVLQIERHILGTDGKSKSLDSLRSGDLVLVWLQVKASNSVPDALVVDLLPAGLELENQNLANGSASLEQSGGEVQNLLNQMQQASIKHIEFRDDRFVAAVAVDEYQPVTLVYLARAVTPGTYQVPQPMVESMYVPQWRATGAAEDLLIVRP

Multifun Terms (GenProtEC)

5 - cell processes --> 5.6 - protection

Gene Ontology Terms (GO)

cellular_component

GO:0005615 - extracellular space
GO:0016020 - membrane
GO:0005886 - plasma membrane
GO:0031362 - anchored component of external side of plasma membrane

molecular_function

GO:0004866 - endopeptidase inhibitor activity
GO:0030414 - peptidase inhibitor activity
GO:0042803 - protein homodimerization activity

biological_process

GO:0010466 - negative regulation of peptidase activity
GO:0010951 - negative regulation of endopeptidase activity

Type	Name	Post Left	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
promoter	pbpCp2	2647368	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 4.525. P-value: 2.123e-5 Read more >	[ICWHO]	[4]
promoter	pbpCp1	2647493	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: poor homology. Score: 3.196. P-value: 8.872e-5 Read more >	[ICWHO]	[4]
promoter	TSS_2819	2647653	reverse	nd	[RS-EPT-CBR]	[5]
promoter	TSS_2820	2651918	reverse	nd	[RS-EPT-CBR]	[5]
promoter	TSS_2821 (cluster)	2651928	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 2651927 to 2651928, where the highest frequency is at position 2649949. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[5]
promoter	TSS_2822 (cluster)	2652468	forward	For this promoter, there is a cluster of 2 transcription start sites,in the interval 2652468 to 2652469, where the highest frequency is at position 2650491. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[5]

Type

Name

Post Left

Post Right

Strand

Notes

Evidence (Confirmed, Strong, Weak)

References

promoter

pbpCp2

2647368

reverse

Similarity to the consensus
Read more >

[ICWHO]

[4]

promoter

pbpCp1

2647493

reverse

Similarity to the consensus
Read more >

[ICWHO]

[4]

promoter

TSS_2819

2647653

reverse

[RS-EPT-CBR]

[5]

promoter

TSS_2820

2651918

reverse

[RS-EPT-CBR]

[5]

promoter

TSS_2821 (cluster)

2651928

reverse

For this promoter, there
Read more >

[RS-EPT-CBR]

[5]

promoter

TSS_2822 (cluster)

2652468

forward

For this promoter, there
Read more >

[RS-EPT-CBR]

[5]

Evidence
[ICWHO] Inferred computationally without human oversight
[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

Evidence

[ICWHO] Inferred computationally without human oversight

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

Reference(s)
[1] Budd A., Blandin S., Levashina EA., Gibson TJ., 2004, Bacterial alpha2-macroglobulins: colonization factors acquired by horizontal gene transfer from the metazoan genome?, Genome Biol 5(6):R38
[2] Doan N., Gettins PG., 2008, alpha-Macroglobulins are present in some gram-negative bacteria: characterization of the alpha2-macroglobulin from Escherichia coli., J Biol Chem 283(42):28747-56
[3] Garcia-Ferrer I., Arede P., Gomez-Blanco J., Luque D., Duquerroy S., Caston JR., Goulas T., Gomis-Ruth FX., 2015, Structural and functional insights into Escherichia coli α2-macroglobulin endopeptidase snap-trap inhibition., Proc Natl Acad Sci U S A 112(27):8290-5
[4] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78
[5] 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.

Reference(s)

[1] Budd A., Blandin S., Levashina EA., Gibson TJ., 2004, Bacterial alpha2-macroglobulins: colonization factors acquired by horizontal gene transfer from the metazoan genome?, Genome Biol 5(6):R38

[2] Doan N., Gettins PG., 2008, alpha-Macroglobulins are present in some gram-negative bacteria: characterization of the alpha2-macroglobulin from Escherichia coli., J Biol Chem 283(42):28747-56

[3] Garcia-Ferrer I., Arede P., Gomez-Blanco J., Luque D., Duquerroy S., Caston JR., Goulas T., Gomis-Ruth FX., 2015, Structural and functional insights into Escherichia coli α2-macroglobulin endopeptidase snap-trap inhibition., Proc Natl Acad Sci U S A 112(27):8290-5

[4] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

[5] 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.