Align ABC transporter for D-Sorbitol, permease component 1 (characterized)
to candidate HSERO_RS02200 HSERO_RS02200 mannitol ABC transporter permease
Query= reanno::BFirm:BPHYT_RS16105 (291 letters) >FitnessBrowser__HerbieS:HSERO_RS02200 Length = 271 Score = 411 bits (1056), Expect = e-120 Identities = 197/277 (71%), Positives = 240/277 (86%), Gaps = 6/277 (2%) Query: 15 MTVPAKSPFAAIRRGIPGVIAWLVALLLFFPIFWMTITAFKTEQQAYASSLFFIPTLDSF 74 M+ P KSP V+ W A++LFFPIFW+ +TAFKTE QAY SL F+PTL++F Sbjct: 1 MSDPKKSPLWV------AVLGWACAIVLFFPIFWVAVTAFKTESQAYTPSLVFLPTLETF 54 Query: 75 REVFARSNYFSFAWNSILISAGVTILCLILAVPAAYAMAFFPTRRTQKVLLWMLSTKMMP 134 REVF+RS+Y + NS+++S G T+L L+LAVPAAY+MAFFPT RTQK+LLWMLSTKMMP Sbjct: 55 REVFSRSHYLGYVQNSLIVSLGSTLLSLLLAVPAAYSMAFFPTGRTQKLLLWMLSTKMMP 114 Query: 135 SVGVLVPIYLLWKNSGLLDSVSGLVIVYTLINLPIAVWMSFTYFAEIPRDILEAGRIDGA 194 +VGVL+PIYL+ KN+GLLD+V+GL I+YTLINLPIAVWM+FTYF ++P++ILEA RIDGA Sbjct: 115 AVGVLIPIYLMAKNTGLLDTVTGLTIIYTLINLPIAVWMAFTYFNDVPKEILEAARIDGA 174 Query: 195 ATWQEIVYLLMPMSLPGLASTALLLVILSWNEAFWSINLSSSNAAPLTVFIASYSSPEGL 254 WQE++YLL+P ++PGLASTALLLVILSWNEAFWS+NL+S NAAPLTVFIASYS+PEGL Sbjct: 175 NAWQEMIYLLLPTAMPGLASTALLLVILSWNEAFWSLNLTSVNAAPLTVFIASYSNPEGL 234 Query: 255 FWAKLSAASLLAVAPILIVGWLSQKQLVRGLTFGAVK 291 FWAKLSAASLLA+API+ +GWL+QKQLVRGLTFGAVK Sbjct: 235 FWAKLSAASLLAIAPIMALGWLAQKQLVRGLTFGAVK 271 Lambda K H 0.326 0.136 0.421 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 428 Number of extensions: 19 Number of successful extensions: 1 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 291 Length of database: 271 Length adjustment: 26 Effective length of query: 265 Effective length of database: 245 Effective search space: 64925 Effective search space used: 64925 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory