{"id":"https://openalex.org/W2079790271","doi":"https://doi.org/10.1074/jbc.l109.075721","title":"Identifying Divergent HAMP Domains and Poly-HAMP Chains","display_name":"Identifying Divergent HAMP Domains and Poly-HAMP Chains","publication_year":2010,"publication_date":"2010-05-28","ids":{"openalex":"https://openalex.org/W2079790271","doi":"https://doi.org/10.1074/jbc.l109.075721","mag":"2079790271","pmid":"https://pubmed.ncbi.nlm.nih.gov/20511236","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/2878581"},"language":"en","primary_location":{"id":"doi:10.1074/jbc.l109.075721","doi":"https://doi.org/10.1074/jbc.l109.075721","is_oa":true,"landing_page_url":"https://doi.org/10.1074/jbc.l109.075721","pdf_url":"http://www.jbc.org/article/S0021925819355590/pdf","source":{"id":"https://openalex.org/S140251998","display_name":"Journal of Biological Chemistry","issn_l":"0021-9258","issn":["0021-9258","1067-8816","1083-351X"],"is_oa":false,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-b","doyens","jufo-2","ki-jl-2","medline","norway-2","poland-100","vabb-shw"],"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biological Chemistry","raw_type":"journal-article"},"volume":null,"type":"letter","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"http://www.jbc.org/article/S0021925819355590/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5089779126","display_name":"Michael V. Airola","orcid":"https://orcid.org/0000-0003-4981-1253","observed_orcids":["https://orcid.org/0000-0003-4981-1253"]},"institutions":[{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael V. Airola","raw_affiliation_strings":["Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853","institution_ids":["https://openalex.org/I205783295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090139271","display_name":"Kylie J. Watts","orcid":"https://orcid.org/0000-0002-8072-2745","observed_orcids":["https://orcid.org/0000-0002-8072-2745"]},"institutions":[{"id":"https://openalex.org/I26347476","display_name":"Loma Linda University","ror":"https://ror.org/04bj28v14","country_code":"US","type":"education","lineage":["https://openalex.org/I26347476"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kylie J. Watts","raw_affiliation_strings":["Division of Microbiology and Molecular Genetics, Loma Linda University, Loma Linda, California 92350"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Microbiology and Molecular Genetics, Loma Linda University, Loma Linda, California 92350","institution_ids":["https://openalex.org/I26347476"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5071526287","display_name":"Brian R. Crane","orcid":"https://orcid.org/0000-0001-8234-9991","observed_orcids":["https://orcid.org/0000-0001-8234-9991"]},"institutions":[{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Brian R. Crane","raw_affiliation_strings":["Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853","institution_ids":["https://openalex.org/I205783295"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5071526287"],"corresponding_institution_ids":["https://openalex.org/I205783295"],"apc_list":{"value":3430,"currency":"USD","value_usd":3430},"apc_paid":{"value":3430,"currency":"USD","value_usd":3430},"fwci":null,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":"285","issue":"23","first_page":"le7","last_page":"le7"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.8140000104904175,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.8140000104904175,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10497","display_name":"Fungal and yeast genetics research","score":0.035999998450279236,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.028999999165534973,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/hamp-domain","display_name":"HAMP domain","score":0.9160000085830688},{"id":"https://openalex.org/keywords/debaryomyces-hansenii","display_name":"Debaryomyces hansenii","score":0.8230000138282776},{"id":"https://openalex.org/keywords/hybrid-histidine-kinase","display_name":"hybrid histidine kinase","score":0.9120000004768372},{"id":"https://openalex.org/keywords/protein-domain-identification","display_name":"protein domain identification","score":0.31700000166893005},{"id":"https://openalex.org/keywords/methyl-accepting-chemotaxis-proteins","display_name":"methyl-accepting chemotaxis proteins","score":0.7310000061988831}],"concepts":[{"id":"https://openalex.org/C2777588556","wikidata":"https://www.wikidata.org/wiki/Q14882371","display_name":"HAMP","level":4,"score":0.964738130569458},{"id":"https://openalex.org/C10522644","wikidata":"https://www.wikidata.org/wiki/Q24775216","display_name":"HAMP domain","level":4,"score":0.6061524152755737},{"id":"https://openalex.org/C202264299","wikidata":"https://www.wikidata.org/wiki/Q905695","display_name":"UniProt","level":3,"score":0.4732024371623993},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3737093210220337},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.31489554047584534},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.2733767628669739},{"id":"https://openalex.org/C25166345","wikidata":"https://www.wikidata.org/wiki/Q4914012","display_name":"Binding domain","level":3,"score":0.19885075092315674},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.16698694229125977},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.10099613666534424},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08530619740486145},{"id":"https://openalex.org/C2776768029","wikidata":"https://www.wikidata.org/wiki/Q14882371","display_name":"Hepcidin","level":3,"score":0.0},{"id":"https://openalex.org/C2776914184","wikidata":"https://www.wikidata.org/wiki/Q101991","display_name":"Inflammation","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005800","descriptor_name":"Genes, Fungal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020798","descriptor_name":"Two-Hybrid System Techniques","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055165","descriptor_name":"Debaryomyces","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1074/jbc.l109.075721","doi":"https://doi.org/10.1074/jbc.l109.075721","is_oa":true,"landing_page_url":"https://doi.org/10.1074/jbc.l109.075721","pdf_url":"http://www.jbc.org/article/S0021925819355590/pdf","source":{"id":"https://openalex.org/S140251998","display_name":"Journal of Biological Chemistry","issn_l":"0021-9258","issn":["0021-9258","1067-8816","1083-351X"],"is_oa":false,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-b","doyens","jufo-2","ki-jl-2","medline","norway-2","poland-100","vabb-shw"],"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biological Chemistry","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2878581","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2878581","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"J Biol Chem","raw_type":"Text"},{"id":"pmid:20511236","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20511236","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The Journal of biological chemistry","raw_type":"Letter"}],"best_oa_location":{"id":"doi:10.1074/jbc.l109.075721","doi":"https://doi.org/10.1074/jbc.l109.075721","is_oa":true,"landing_page_url":"https://doi.org/10.1074/jbc.l109.075721","pdf_url":"http://www.jbc.org/article/S0021925819355590/pdf","source":{"id":"https://openalex.org/S140251998","display_name":"Journal of Biological Chemistry","issn_l":"0021-9258","issn":["0021-9258","1067-8816","1083-351X"],"is_oa":false,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-b","doyens","jufo-2","ki-jl-2","medline","norway-2","poland-100","vabb-shw"],"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biological Chemistry","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G692747634","display_name":"The Structure and Function of the Bacterial Chemosome","funder_award_id":"R01GM066775","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2079790271.pdf","grobid_xml":"https://content.openalex.org/works/W2079790271.grobid-xml"},"referenced_works_count":4,"referenced_works":["https://openalex.org/W2008800209","https://openalex.org/W2012241820","https://openalex.org/W2138243191","https://openalex.org/W2145261099"],"related_works":["https://openalex.org/W1973072243","https://openalex.org/W2070520962","https://openalex.org/W2890204844","https://openalex.org/W4242373229","https://openalex.org/W3173984291","https://openalex.org/W4389069163","https://openalex.org/W1920130006","https://openalex.org/W1995053766","https://openalex.org/W2044258872","https://openalex.org/W2188542605"],"abstract_inverted_index":{"Meena":[0,139],"et":[1,140,451,470],"al.":[2,141,471],"(1Meena":[3,142],"N.":[4,143],"Kaur":[5,144],"H.":[6,145],"Mondal":[7,146],"A.K.":[8,147],"J.":[9,148,206,239],"Biol.":[10,149,208,241],"Chem.":[11,150],"2010;":[12,151,209,242,297,411],"285:":[13,152],"12121-12132Abstract":[14,153],"Full":[15,17,154,156,300,302,414,416],"Text":[16,18,155,157,301,303,415,417],"PDF":[19,158,304,418,474],"PubMed":[20,159,212,245,305,419],"Scopus":[21,160,213,246,306,420],"(51)":[22,161],"Google":[23,162,215,248,308,422],"Scholar)":[24,163,216,423],"report":[25],"the":[26,74,101,111,130,169,181,251,259,264,283,322,325,335,375,378,385,392],"mechanistic":[27],"investigation":[28],"of":[29,90,103,121,127,171,184,198,253,269,285,327,339,352,365,377,384,395,457],"poly-HAMP":[30,220,256,274,400],"domains":[31,95,191,201,225,272,338,368,397,443],"from":[32,258],"Debaryomyces":[33],"hansenii":[34],"Nik1":[35],"(DhNik1),":[36],"a":[37,67,81,97,105,194,254,279,349,359,399,429,455,463,466],"soluble":[38,260],"hybrid":[39],"histidine":[40],"kinase.":[41],"A":[42,362],"standard":[43],"SMART":[44,82],"search":[45,85],"(http://smart.embl-heidelberg.de/)":[46],"predicts":[47],"hNik1":[48],"to":[49,72,193,321,357,439,449,465],"contain":[50,358],"5":[51,122],"successive":[52,117,270],"HAMP":[53,94,118,190,200,224,271,337,360,367,442],"(histidine":[54],"kinase,":[55],"adenylyl":[56],"cyclase,":[57],"methyl-accepting":[58],"chemotaxis":[59],"protein,":[60],"and":[61,76,133,266,276,317,382,424],"phosphatase)":[62],"domains,":[63,119],"each":[64],"separated":[65],"by":[66,138,444,468],"40-residue":[68],"linker.":[69],"We":[70],"wish":[71],"make":[73],"authors":[75,323],"general":[77],"community":[78],"aware":[79],"that":[80,110,217,334],"or":[83,454],"BLAST":[84],"(http://blast.ncbi.nlm.nih.gov/)":[86],"is":[87,314,331,369,462],"usually":[88],"incapable":[89],"correctly":[91],"identifying":[92],"all":[93],"in":[96,175,398,431],"protein":[98,354],"sequence.":[99],"In":[100,125,167],"case":[102],"DhNik1,":[104],"more":[106],"detailed":[107],"analysis":[108],"reveals":[109,263],"N-terminal":[112,379],"region":[113],"actually":[114],"contains":[115],"9":[116],"instead":[120],"(Fig.":[123,437],"1).":[124],"light":[126],"this":[128,311],"information,":[129],"domain":[131,173],"deletion":[132],"yeast":[134],"2-hybrid":[135],"results":[136],"reported":[137],"should":[164],"be":[165,426],"reassessed.":[166],"particular,":[168],"choice":[170],"inappropriate":[172],"boundaries":[174],"these":[176],"experiments":[177],"calls":[178],"into":[179],"question":[180],"proposed":[182],"model":[183],"side-on":[185],"HAMP-HAMP":[186],"interactions.":[187],"The":[188],"DhNik1":[189,340],"belong":[192],"recently":[195],"identified":[196,228],"subset":[197],"divergent":[199,223,336,366,441],"(2Dunin-Horkawicz":[202,235],"S.":[203,236],"Lupas":[204,237],"A.N.":[205,238],"Mol.":[207,240],"397:":[210,243],"1156-1174Crossref":[211,244],"(70)":[214,247],"form":[218],"repeating":[219],"units.":[221],"Most":[222],"have":[226],"been":[227],"using":[229],"sensitive":[230],"HMM-HMM":[231],"sequence":[232,286,355,446],"alignment":[233],"methods":[234],"Scholar).":[249,309],"However,":[250],"structure":[252],"3-unit":[255],"chain":[257,401],"receptor":[261],"Aer2":[262],"interwoven":[265],"linear":[267],"arrangement":[268],"within":[273],"chains":[275],"thereby":[277],"provides":[278],"useful":[280],"template":[281],"for":[282],"interpretation":[284],"alignments":[287],"(3Airola":[288,402],"M.V.":[289,403],"Watts":[290,404],"K.J.":[291,405],"Bilwes":[292,406],"A.M.":[293,407],"Crane":[294,408],"B.R.":[295,409],"Structure.":[296,410],"18:":[298,412],"436-448Abstract":[299,413],"(103)":[307,421],"As":[310],"new":[312],"knowledge":[313],"very":[315],"recent":[316],"was":[318],"not":[319,332],"available":[320],"at":[324,374],"time":[326],"their":[328],"study,":[329],"it":[330],"surprising":[333],"were":[341],"misassigned.":[342],"To":[343],"avoid":[344],"future":[345],"discrepancies":[346],"we":[347],"urge":[348],"careful":[350],"inspection":[351],"any":[353],"predicted":[356],"domain.":[361],"defining":[363],"feature":[364],"2":[370],"glycine":[371],"residues":[372,390],"located":[373],"end":[376],"helix":[380,387],"AS1":[381],"start":[383],"C-terminal":[386],"AS2.":[388],"These":[389],"allow":[391],"close":[393],"association":[394],"neighboring":[396],"can":[425],"used":[427],"as":[428],"marker,":[430],"conjunction":[432],"with":[433],"other":[434],"conserved":[435],"motifs":[436],"1),":[438],"identify":[440],"manual":[445],"inspection.":[447],"Reply":[448],"Airola":[450,469],"al.:":[452],"Linker":[453],"HAMP?Journal":[456],"Biological":[458],"ChemistryVol.":[459],"285Issue":[460],"23PreviewThis":[461],"response":[464],"letter":[467],"(1)":[472],"Full-Text":[473],"Open":[475],"Access":[476]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2013,"cited_by_count":2}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2016-06-24T00:00:00"}
