Align ABC transporter for D-Sorbitol, permease component 1 (characterized)
to candidate SMc01498 SMc01498 sorbitol/mannitol transport inner membrane protein
Query= reanno::Phaeo:GFF1303 (276 letters) >FitnessBrowser__Smeli:SMc01498 Length = 276 Score = 452 bits (1163), Expect = e-132 Identities = 220/276 (79%), Positives = 249/276 (90%) Query: 1 MARAVTPRRKAINTALAWAVGLLIFFPILWTILTSFKTEAQAISDPPVFLFFDWTLENYS 60 MAR V+ RK I T +AW +G+LIFFPILWT LTSFKTEAQAI+ PPVFLFFDWT ENYS Sbjct: 1 MARNVSTGRKLITTVVAWTIGILIFFPILWTFLTSFKTEAQAIASPPVFLFFDWTTENYS 60 Query: 61 VVQERSDYMRFLWNSVIIAGGSTILGIIIAVPAAWSMAFVPSKRTKDILLWMLSTKMLPA 120 VQ RSDY++ NSV+++ GST+LG++IA+P+AW+MAF P+KRTKD+L+WMLSTKM+P Sbjct: 61 EVQSRSDYLKHFMNSVVVSFGSTLLGLLIAIPSAWAMAFSPTKRTKDVLMWMLSTKMMPP 120 Query: 121 VGVLYPIYILFIKMGLLDNRFGLVVVLMLINLPIIVWMLYTYFKEIPGEILEAARMDGAT 180 VGVL P+Y++F GLLD R GLV+VL LINLPII+WMLYTYFKEIPGEILEAARMDGA+ Sbjct: 121 VGVLVPMYLIFRNWGLLDTRTGLVIVLTLINLPIIIWMLYTYFKEIPGEILEAARMDGAS 180 Query: 181 LKEEILYVLTPMAIPGIASTLLLNIILAWNEAFWTLNLTAAKAAPLTAFIASYSSPEGLF 240 L +EI+YVLTPMAIPGIASTLLLNIILAWNEAFWTLNL+AAKAAPLTAFIASYSSPEGLF Sbjct: 181 LTKEIIYVLTPMAIPGIASTLLLNIILAWNEAFWTLNLSAAKAAPLTAFIASYSSPEGLF 240 Query: 241 YAKLSAASTMAIAPILILGWFSQKQLVSGLTFGAVK 276 YAKLSAASTMAIAPILILGWFSQKQLV GLTFGAVK Sbjct: 241 YAKLSAASTMAIAPILILGWFSQKQLVRGLTFGAVK 276 Lambda K H 0.327 0.139 0.428 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: 446 Number of extensions: 12 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: 276 Length of database: 276 Length adjustment: 25 Effective length of query: 251 Effective length of database: 251 Effective search space: 63001 Effective search space used: 63001 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