PMC:3746430 / 4026-6501 JSONTXT

{"target":"http://pubannotation.org/docs/sourcedb/PMC/sourceid/3746430","sourcedb":"PMC","sourceid":"3746430","source_url":"http://www.ncbi.nlm.nih.gov/pmc/3746430","text":"Classification and features\nH. halophila belongs to the Gammaproteobacteria [3] (Table 1). The 16S rRNA gene sequence of H. halophila SL1 reveals closer relationships with H. halochloris and Alkalilimnicola ehrlichii, the other representatives of the Ectothiorhodospiraceae (Figure 1), than with A. vinosum, a purple sulfur bacterium in the Chromatiaceae family, and the haloalkaliphilic chemolithoautotrophic Thioalkalivibrio strains.\nTable 1 Classification and general features of H. halophila SL1 according to the MIGS recommendations [25]. aEvidence codes - IDA: Inferred from Direct Assay; TAS: Traceable Author Statement (i.e., a direct report exists in the literature); NAS: Non-traceable Author Statement (i.e., not directly observed for the living, isolated sample, but based on a generally accepted property for the species, or anecdotal evidence). These evidence codes are from the Gene Ontology project [36]. If the evidence code is IDA, then the property should have been directly observed, for the purpose of this specific publication, for a live isolate by one of the authors, or an expert or reputable institution mentioned in the acknowledgements.\nFigure 1 Phylogram representation of a phylogenetic tree highlighting the position of Halorhodospira halophila strain SL1 relative to other organisms of interest, including members of the Ectothiorhodospiraceae, as well as additional strains that were included for comparison purposes, based on environmental and functional considerations. The strains (type=T) and their corresponding GenBank accession numbers (and coordinates) for 16S rRNA genes are: H. halophila strain SL1T, CP00544:380025-381562; Alkalilimnicola ehrlichii strain MLHE-1, CP00453:369818-369894; Thioalkalivibrio sp. HL-EbGR7, CP001339:2548250-2549775; Thioalkalivibrio sp. K90mix, CP001905:423231-424758; Allochromatium vinosum DSM 180T, CP001896:112452-113967; Ectothiorhodospira halochloris M59152; Burkholderia phytofirmans PsJN, CP001052:1541578-1543101; Desulfovibrio vulgaris subsp. vulgaris strain Hildenborough, AE017285:105921-107426; Rhodobacter sphaeroides 2.4.1, CP000143:1-1464; Rhodospirillum rubrum ATCC 11170, CP000230: 192528-194004; Escherichia coli B strain REL606, CP000819: 226609-228150. The 16S rRNA sequences were aligned by MUSCLE [37]. The tree was determined by the maximum likelihood model of PhyML [38] and rendered with TreeDyn [39], using the “one click” pipeline of the Phylogeny.fr web resource [40].\n\nG","divisions":[{"label":"Title","span":{"begin":0,"end":27}},{"label":"Table caption","span":{"begin":436,"end":1167}},{"label":"Title","span":{"begin":445,"end":544}},{"label":"Figure caption","span":{"begin":1167,"end":2474}}],"tracks":[{"project":"2_test","denotations":[{"id":"23991253-8593098-140435758","span":{"begin":77,"end":78},"obj":"8593098"},{"id":"23991253-18464787-140435759","span":{"begin":540,"end":542},"obj":"18464787"},{"id":"23991253-10802651-140435773","span":{"begin":918,"end":920},"obj":"10802651"},{"id":"23991253-15034147-140435774","span":{"begin":2296,"end":2298},"obj":"15034147"},{"id":"23991253-14530136-140435775","span":{"begin":2367,"end":2369},"obj":"14530136"},{"id":"23991253-17032440-140435776","span":{"begin":2398,"end":2400},"obj":"17032440"}],"attributes":[{"subj":"23991253-8593098-140435758","pred":"source","obj":"2_test"},{"subj":"23991253-18464787-140435759","pred":"source","obj":"2_test"},{"subj":"23991253-10802651-140435773","pred":"source","obj":"2_test"},{"subj":"23991253-15034147-140435774","pred":"source","obj":"2_test"},{"subj":"23991253-14530136-140435775","pred":"source","obj":"2_test"},{"subj":"23991253-17032440-140435776","pred":"source","obj":"2_test"}]},{"project":"MicrobeTaxon","denotations":[{"id":"T47","span":{"begin":28,"end":40},"obj":"1053"},{"id":"T48","span":{"begin":410,"end":426},"obj":"106633"},{"id":"T49","span":{"begin":56,"end":75},"obj":"1236"},{"id":"T50","span":{"begin":121,"end":137},"obj":"349124"},{"id":"T51","span":{"begin":172,"end":186},"obj":"1052"},{"id":"T52","span":{"begin":191,"end":216},"obj":"351052"},{"id":"T53","span":{"begin":251,"end":273},"obj":"72276"},{"id":"T54","span":{"begin":296,"end":306},"obj":"1049"},{"id":"T55","span":{"begin":310,"end":333},"obj":"1046"},{"id":"T56","span":{"begin":341,"end":354},"obj":"1046"},{"id":"T67","span":{"begin":1791,"end":1818},"obj":"396595"},{"id":"T68","span":{"begin":1844,"end":1875},"obj":"572477"},{"id":"T69","span":{"begin":1901,"end":1931},"obj":"1052"},{"id":"T70","span":{"begin":1940,"end":1970},"obj":"398527"},{"id":"T71","span":{"begin":1998,"end":2057},"obj":"882"},{"id":"T72","span":{"begin":2083,"end":2112},"obj":"272943"},{"id":"T73","span":{"begin":2131,"end":2163},"obj":"269796"},{"id":"T74","span":{"begin":2190,"end":2222},"obj":"413997"},{"id":"T75","span":{"begin":484,"end":500},"obj":"349124"},{"id":"T62","span":{"begin":1254,"end":1289},"obj":"349124"},{"id":"T63","span":{"begin":1356,"end":1378},"obj":"72276"},{"id":"T64","span":{"begin":1621,"end":1645},"obj":"349124"},{"id":"T65","span":{"begin":1670,"end":1709},"obj":"187272"},{"id":"T66","span":{"begin":1734,"end":1763},"obj":"396588"}],"namespaces":[{"prefix":"_base","uri":"http://purl.bioontology.org/ontology/NCBITAXON/"}],"attributes":[{"subj":"T47","pred":"source","obj":"MicrobeTaxon"},{"subj":"T48","pred":"source","obj":"MicrobeTaxon"},{"subj":"T49","pred":"source","obj":"MicrobeTaxon"},{"subj":"T50","pred":"source","obj":"MicrobeTaxon"},{"subj":"T51","pred":"source","obj":"MicrobeTaxon"},{"subj":"T52","pred":"source","obj":"MicrobeTaxon"},{"subj":"T53","pred":"source","obj":"MicrobeTaxon"},{"subj":"T54","pred":"source","obj":"MicrobeTaxon"},{"subj":"T55","pred":"source","obj":"MicrobeTaxon"},{"subj":"T56","pred":"source","obj":"MicrobeTaxon"},{"subj":"T67","pred":"source","obj":"MicrobeTaxon"},{"subj":"T68","pred":"source","obj":"MicrobeTaxon"},{"subj":"T69","pred":"source","obj":"MicrobeTaxon"},{"subj":"T70","pred":"source","obj":"MicrobeTaxon"},{"subj":"T71","pred":"source","obj":"MicrobeTaxon"},{"subj":"T72","pred":"source","obj":"MicrobeTaxon"},{"subj":"T73","pred":"source","obj":"MicrobeTaxon"},{"subj":"T74","pred":"source","obj":"MicrobeTaxon"},{"subj":"T75","pred":"source","obj":"MicrobeTaxon"},{"subj":"T62","pred":"source","obj":"MicrobeTaxon"},{"subj":"T63","pred":"source","obj":"MicrobeTaxon"},{"subj":"T64","pred":"source","obj":"MicrobeTaxon"},{"subj":"T65","pred":"source","obj":"MicrobeTaxon"},{"subj":"T66","pred":"source","obj":"MicrobeTaxon"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#a893ec","default":true},{"id":"MicrobeTaxon","color":"#98ec93"}]}]}}