Align ABC transporter for D-Sorbitol, permease component 2 (characterized)
to candidate WP_086511130.1 BZY95_RS17255 sugar ABC transporter permease
Query= reanno::BFirm:BPHYT_RS16110 (311 letters) >NCBI__GCF_002151265.1:WP_086511130.1 Length = 296 Score = 375 bits (962), Expect = e-109 Identities = 175/277 (63%), Positives = 232/277 (83%) Query: 30 LATPSVAVLVLWMAIPLAMTIWFSFSRYNLLNPDLKGFAGFDNYKYLASDPSFGPSIGHT 89 L P+V +L+LWM +PL MT+WFS RYNLL P++ GFAG +NY++L +DP+ ++G+T Sbjct: 19 LQAPAVTLLLLWMLVPLGMTVWFSLQRYNLLMPEMVGFAGLENYEFLFTDPALWRAMGNT 78 Query: 90 LELIISVLVITVVGGVLMAILFDRKFYGQGIARLLAIAPFFVMPTVSALIWKNMILHPVY 149 L L+ SVL ITVVGGVL+A+LF ++F G+GIAR+LAI+PFFVMPTVSAL+WKNM++HP Sbjct: 79 LVLVGSVLTITVVGGVLLAVLFQQEFPGRGIARVLAISPFFVMPTVSALVWKNMMMHPSN 138 Query: 150 GLIAQGMRAMGMQPIDWFAEYPLTAVIMIVAWQWLPFAFLILFTAIQSLDQEQKEAARID 209 G++A G+ +DWF+ P+T++I+IVAWQWLPFA LIL TA+QSLD++Q EAAR+D Sbjct: 139 GVLAWLAGVFGLPAVDWFSALPMTSIIIIVAWQWLPFALLILLTAMQSLDEDQVEAARMD 198 Query: 210 GAGPFSMFFYITLPHLKRAIAVVVMMETIFLLSIFAEIYTTTGGGPGTATTNLSYLIYSL 269 GAGP ++FFYITLPHLKRAI+VV+M++ IFLL+IFAEIY TT GGPG ATTNL++LIY Sbjct: 199 GAGPIAVFFYITLPHLKRAISVVIMIQMIFLLTIFAEIYVTTSGGPGLATTNLAFLIYMQ 258 Query: 270 GLQQFDVGLASAGGILAVVLANIVSFFLVRMLAKNLK 306 L FDVGLASAGG++A++LANIV+ FLVR++A+NL+ Sbjct: 259 ALLDFDVGLASAGGVVAIILANIVAIFLVRLVARNLE 295 Lambda K H 0.328 0.141 0.431 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: 338 Number of extensions: 9 Number of successful extensions: 2 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: 311 Length of database: 296 Length adjustment: 27 Effective length of query: 284 Effective length of database: 269 Effective search space: 76396 Effective search space used: 76396 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: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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