smpB:Gene Product(s): Difference between revisions

Standard name	SmpB
Synonyms	trans-translation protein^[1], B2620^[2]^[1], SmqB^[2]^[1], SmpB^[2]^[1] , ECK2616, JW2601, smqB, b2620
Product description	small protein B^[2]^[3] tmRNA RNA-binding protein; required for peptide-tagging trans-translation and association of tmRNA(SsrA) with ribosomes^[4]
EC number (for enzymes)
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Notes

Function

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Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier	GO ID	GO term name	Reference	Evidence Code	with/from	Aspect	Notes	Status
	GO:0003723	RNA binding	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00023	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003723	RNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000037	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003723	RNA binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0694	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00023	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0963	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-0086	C	Seeded from EcoCyc (v14.0)	complete
	GO:0006412	translation	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000037	P	Seeded from EcoCyc (v14.0)	complete
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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type	Partner	References	Evidence
Protein	aidB	PMID:15690043^[5]	Experiment(s):EBI-882920
Protein	clpA	PMID:15690043^[5]	Experiment(s):EBI-882920
Protein	infB	PMID:15690043^[5]	Experiment(s):EBI-882920
Protein	malP	PMID:15690043^[5]	Experiment(s):EBI-882920
Protein	parC	PMID:15690043^[5]	Experiment(s):EBI-882920
Protein	rplF	PMID:15690043^[5]	Experiment(s):EBI-882920, EBI-890426
Protein	rpsA	PMID:15690043^[5]	Experiment(s):EBI-882920, EBI-890426
Protein	rpsB	PMID:15690043^[5]	Experiment(s):EBI-882920, EBI-890426
Protein	rpsC	PMID:15690043^[5]	Experiment(s):EBI-882920
Protein	secA	PMID:15690043^[5]	Experiment(s):EBI-882920
Protein	selB	PMID:15690043^[5]	Experiment(s):EBI-882920
Protein	ycbB	PMID:15690043^[5]	Experiment(s):EBI-882920
Protein	yfiF	PMID:15690043^[5]	Experiment(s):EBI-882920
Protein	gyrA	PMID:15690043^[5]	Experiment(s):EBI-890426
Protein	gyrB	PMID:15690043^[5]	Experiment(s):EBI-890426
Protein	skp	PMID:15690043^[5]	Experiment(s):EBI-890426
Protein	hupA	PMID:15690043^[5]	Experiment(s):EBI-890426
Protein	hupB	PMID:15690043^[5]	Experiment(s):EBI-890426
Protein	rplM	PMID:15690043^[5]	Experiment(s):EBI-890426
Protein	rplX	PMID:15690043^[5]	Experiment(s):EBI-890426
Protein	rpmB	PMID:15690043^[5]	Experiment(s):EBI-890426
Protein	rpsE	PMID:15690043^[5]	Experiment(s):EBI-890426
Protein	rpsN	PMID:15690043^[5]	Experiment(s):EBI-890426
Protein	yeeX	PMID:15690043^[5]	Experiment(s):EBI-890426
Protein	vsr	PMID:16606699^[6]	Experiment(s):EBI-1143521
Protein	yibK	PMID:16606699^[6]	Experiment(s):EBI-1143521
Protein	rplA	PMID:16606699^[6]	Experiment(s):EBI-1143521
Protein	ycgE	PMID:16606699^[6]	Experiment(s):EBI-1143521
Protein	ycfJ	PMID:16606699^[6]	Experiment(s):EBI-1143521
Protein	secA	PMID:19402753^[7]	MALDI(Z-score):18.851547
Protein	aidB	PMID:19402753^[7]	LCMS(ID Probability):98.3 MALDI(Z-score):27.388524
Protein	rplF	PMID:19402753^[7]	LCMS(ID Probability):99.6 MALDI(Z-score):35.816231
Protein	skp	PMID:19402753^[7]	LCMS(ID Probability):99.6
Protein	rpsA	PMID:19402753^[7]	LCMS(ID Probability):99.6 MALDI(Z-score):26.098127
Protein	gyrA	PMID:19402753^[7]	LCMS(ID Probability):99.6
Protein	parC	PMID:19402753^[7]	MALDI(Z-score):37.105392
Protein	malP	PMID:19402753^[7]	MALDI(Z-score):28.886498
Protein	clpA	PMID:19402753^[7]	MALDI(Z-score):25.712309
Protein	hupB	PMID:19402753^[7]	LCMS(ID Probability):99.6
Protein	rpsN	PMID:19402753^[7]	LCMS(ID Probability):99.6
Protein	rpmB	PMID:19402753^[7]	LCMS(ID Probability):99.6
Protein	gyrB	PMID:19402753^[7]	LCMS(ID Probability):99.6
Protein	hupA	PMID:19402753^[7]	LCMS(ID Probability):99.6
Protein	yfiF	PMID:19402753^[7]	MALDI(Z-score):36.128347
Protein	rplM	PMID:19402753^[7]	LCMS(ID Probability):99.6
Protein	yeeX	PMID:19402753^[7]	LCMS(ID Probability):99.6
Protein	ycbB	PMID:19402753^[7]	MALDI(Z-score):24.925478
RNA	SsrA RNA
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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment	Description	Evidence	Reference/Source	Notes
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Notes

Structure and Physical Properties

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Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence	at EcoCyc MTKKKAHKPG SATIALNKRA RHEYFIEEEF EAGLALQGWE VKSLRAGKAN ISDSYVLLRD GEAFLFGANI TPMAVASTHV VCDPTRTRKL LLNQRELDSL YGRVNREGYT VVALSLYWKN AWCKVKIGVA KGKKQHDKRS DIKEREWQVD KARIMKNAHR
Length	160
Mol. Wt	18.269 kDa
pI	10.4 (calculated)
Extinction coefficient	29,450 - 29,700 (calc based on 5 Y, 4 W, and 2 C residues)
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Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type	Residues	Description	Notes	References
Initiator Methionine	1	Removed	UniProt:P0A832
Domain	12..80	PF01668 SmpB protein		PMID:19920124^[8]
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<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=smpB taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

Notes

Gene Product Resources

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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type	Source	Notes/Reference
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
NCBI (Protein) (EcoliWiki Page)	GI:16130539	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947296	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008622	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0A832	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11782	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11782	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947296	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001716	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1730	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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References

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See Help:References for how to manage references in EcoliWiki.

↑ ^1.0 ^1.1 ^1.2 ^1.3 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.0 ^2.1 ^2.2 ^2.3 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^5.00 ^5.01 ^5.02 ^5.03 ^5.04 ^5.05 ^5.06 ^5.07 ^5.08 ^5.09 ^5.10 ^5.11 ^5.12 ^5.13 ^5.14 ^5.15 ^5.16 ^5.17 ^5.18 ^5.19 ^5.20 ^5.21 ^5.22 ^5.23 Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
↑ ^6.0 ^6.1 ^6.2 ^6.3 ^6.4 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
↑ ^7.00 ^7.01 ^7.02 ^7.03 ^7.04 ^7.05 ^7.06 ^7.07 ^7.08 ^7.09 ^7.10 ^7.11 ^7.12 ^7.13 ^7.14 ^7.15 ^7.16 ^7.17 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

smpB:Gene Product(s): Difference between revisions

Latest revision as of 20:53, 17 February 2015

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

References

Categories

Navigation menu

@@ Line 44: / Line 44: @@
 !align=left {{table heading style}} |Synonyms
 ||
-trans-translation protein<ref name='LIB:Riley_2006'/>, B2620<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, SmqB<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, SmpB<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>
+''trans-translation protein<ref name='LIB:Riley_2006'/>, B2620<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, SmqB<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, SmpB<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK2616, JW2601, smqB, b2620''
 |-
 !align=left {{table heading style}} |Product description
@@ Line 75: / Line 75: @@
 *
 ****************************************************************************************** -->{{Product_GO_help}}
-{|   id="G46aab3a2e07b0"  class=" tableEdit GO_table_product dataTable"
+{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="G46aab3a2e07b0"  class=" tableEdit GO_table_product dataTable"
 |- {{table_heading_style}}
-!|Qualifier!!GO ID!!GO term name!!Reference(s)!!Evidence Code!!with/from!!Aspect!!Notes!!Status
+!|Qualifier!!GO ID!!GO term name!!Reference!!Evidence Code!!with/from!!Aspect!!Notes!!Status
 |-
 |
@@ Line 225: / Line 225: @@
 *
 ****************************************************************************************** -->{{Product_interactions_help}}
-{| {{Prettytable}}  id="I46aab3a977eab"  class=" tableEdit Product_interactions_table dataTable"
+{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="I46aab3a977eab"  class=" tableEdit Product_interactions_table dataTable"
 |- {{table heading style}}
 !|Partner Type!!Partner!!Notes!!References!!Evidence
@@ Line 551: / Line 551: @@
 Protein
 |
-[[secA:Gene_Product(s)|secA]]
+secA
 |
@@ Line 557: / Line 557: @@
 PMID:19402753
 |
- MALDI(Z-score):18.851547
+MALDI(Z-score):18.851547
 |-
 |
 Protein
 |
-[[aidB:Gene_Product(s)|aidB]]
+aidB
 |
@@ Line 573: / Line 573: @@
 Protein
 |
-[[rplF:Gene_Product(s)|rplF]]
+rplF
 |
@@ Line 584: / Line 584: @@
 Protein
 |
-[[skp:Gene_Product(s)|skp]]
+skp
 |
@@ Line 593: / Line 593: @@
 |-
 |
-RNA
+Protein
+|
+rpsA
+|
+|
+PMID:19402753
+|
+LCMS(ID Probability):99.6 MALDI(Z-score):26.098127
+|-
+|
+Protein
+|
+gyrA
+|
+|
+PMID:19402753
+|
+LCMS(ID Probability):99.6
+|-
+|
+Protein
+|
+parC
+|
+|
+PMID:19402753
+|
+MALDI(Z-score):37.105392
+|-
+|
+Protein
+|
+malP
+|
+|
+PMID:19402753
+|
+MALDI(Z-score):28.886498
+|-
+|
+Protein
+|
+clpA
+|
+|
+PMID:19402753
+|
+MALDI(Z-score):25.712309
+|-
+|
+Protein
+|
+hupB
+|
+|
+PMID:19402753
+|
+LCMS(ID Probability):99.6
+|-
+|
+Protein
+|
+rpsN
+|
+|
+PMID:19402753
+|
+LCMS(ID Probability):99.6
+|-
+|
+Protein
+|
+rpmB
+|
+|
+PMID:19402753
+|
+LCMS(ID Probability):99.6
+|-
+|
+Protein
+|
+gyrB
+|
+|
+PMID:19402753
+|
+LCMS(ID Probability):99.6
+|-
+|
+Protein
+|
+hupA
+|
+|
+PMID:19402753
+|
+LCMS(ID Probability):99.6
+|-
+|
+Protein
+|
+yfiF
+|
+|
+PMID:19402753
+|
+MALDI(Z-score):36.128347
+|-
+|
+Protein
 |
-SsrA RNA
+rplM
 |
+|
+PMID:19402753
+|
+LCMS(ID Probability):99.6
+|-
+|
+Protein
+|
+yeeX
 |
 |
+PMID:19402753
+|
+LCMS(ID Probability):99.6
 |-
 |
 Protein
 |
-[[rpsA:Gene_Product(s)|rpsA]]
+ycbB
 |
@@ Line 612: / Line 744: @@
 PMID:19402753
 |
-LCMS(ID Probability):99.6 MALDI(Z-score):26.098127
+MALDI(Z-score):24.925478
+|-
+|
+RNA
+|
+SsrA RNA
+|
+|
+|
 |- class="tableEdit_footer"
@@ Line 631: / Line 774: @@
 *
 ****************************************************************************************** -->{{Product_localization_help}}
-{|   id="S46a84b7176e26"  class=" tableEdit Product_localization_table"
+{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="S46a84b7176e26"  class=" tableEdit Product_localization_table"
 |- {{table heading style}}
-!|Compartment!!Description!!Evidence!!Source!!Notes
+!|Compartment!!Description!!Evidence!!Reference/Source!!Notes
 |- class="tableEdit_footer"
@@ Line 657: / Line 800: @@
 ****************************************************************************************** -->{{Product_physical_properties_help}}
 {|   id="G46aab3ab62efa"  class=" tableEdit Product_phys_prop_table"
+|-
+!align=left {{table heading style}} |Name
+||
 |-
@@ Line 697: / Line 844: @@
 *
 ****************************************************************************************** -->{{Product_domains_motifs_help}}
-{|   id="V46aab3abd226b"  class=" tableEdit Product_motif_table dataTable"
+{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="V46aab3abd226b"  class=" tableEdit Product_motif_table dataTable"
 |- {{table heading style}}
 !|Type!!Residues!!Description!!Notes!!References
@@ Line 757: / Line 904: @@
 ||
 View models at:
-* [http://dragon.bio.purdue.edu/ecolpredict2/localsearch/cgi-bin/search3.cgi?q=recA EcoliPredict]
+* [http://www.proteinmodelportal.org/query/uniprot/P0A832 Protein Model Portal]
-* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=recA&organism=562&organismtext= ModBase]
+* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P0A832 PSI-PRED (P0A832)]
-* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
+* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P0A832 Genomes TO Protein (P0A832)] (GTOP)
-* [http://www.ebi.ac.uk/msd-srv/pqs/ Protein Quaternary Structure] (PQS)
-* [http://spock.genes.nig.ac.jp/~genome/search.html Genomes TO Protein] (GTOP)
 |- class="tableEdit_footer"
@@ Line 802: / Line 947: @@
 *
 ****************************************************************************************** -->{{Product_resources_help}}
-{|   id="B46aab3ac9b648"  class=" tableEdit Product_resource_table"
+{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="B46aab3ac9b648"  class=" tableEdit Product_resource_table"
 |- {{table_heading_style}}
 !|Resource type!!Source!!Notes/Reference
@@ Line 824: / Line 969: @@
 *
 ****************************************************************************************** -->{{Gene_accessions_help}}
-{|   id="Y46aab3ad05694"  class=" tableEdit Gene_accessions_table"
+{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Y46aab3ad05694"  class=" tableEdit Gene_accessions_table"
 |- {{table_heading_style}}
 !|Database!!Accession!!Notes
 |-
 |
-[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
+[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
 |
-[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11782-MONOMER EcoCyc:EG11782-MONOMER]
+[http://www.ncbi.nlm.nih.gov/protein/16130539 GI:16130539]
 |
+Escherichia coli str. K-12 substr. MG1655
+|-
+|
+[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
+|
+[http://www.ncbi.nlm.nih.gov/protein/NP_417110.1 GeneID:947296]
+|
+Escherichia coli str. K-12 substr. MG1655
+|-
+|
+[[ASAP]]
+|
+ASAP:ABE-0008622
+|
+''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
+|-
+|
+[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
+|
+[http://www.uniprot.org/uniprot/P0A832 UniProtKB/Swiss-Prot:P0A832]
+|
+Escherichia coli str. K-12 substr. MG1655
+|-
+|
+[[EcoCyc]]
+|
+EcoCyc:EG11782
+|
+''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
 |-
 |
-[http://swissmodel.expasy.org/repository/ SwissModel] ([[SwissModel|EcoliWiki Page]])
+[[EcoGene]]
 |
-[http://swissmodel.expasy.org/repository/smr.php?job=2&sptr_ac=P0A832 SwissModel:P0A832]
+EcoGene:EG11782
 |
+''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
 |-
 |
-[http://uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
+[http://www.ncbi.nlm.nih.gov/gene NCBI (Gene)] ([[NCBI (Gene)|EcoliWiki Page]])
 |
-[http://www.uniprot.org/uniprot/P0A832 UniProt:P0A832]
+[http://www.ncbi.nlm.nih.gov/gene?term=947296 GeneID:947296]
 |
+Escherichia coli str. K-12 substr. MG1655
 |-
 |
-[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])
+[[RegulonDB]]
 |
-[http://pfam.janelia.org/protein/P0A832 Pfam:P0A832]
+RegulonDB:ECK120001716
 |
+''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
 |-
 |
-[http://www.ncbi.nlm.nih.gov/RefSeq/ RefSeq] ([[RefSeq|EcoliWiki Page]])
+[[EchoBASE]]
 |
-[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=NP_417110 RefSeq:NP_417110]
+EchoBASE:EB1730
 |
+''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
 |- class="tableEdit_footer"
@@ Line 881: / Line 1,054: @@
 *
 ****************************************************************************************** -->
-{|   id="A46a84b76a5031"  class=" tableEdit Links_table"
+{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="A46a84b76a5031"  class=" tableEdit Links_table"
 |- {{table_heading_style}}
 !|Name!!URL!!Comments

smpB:Gene Product(s): Difference between revisions

Latest revision as of 20:53, 17 February 2015

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

References

Categories

Navigation menu

Search