Align Glucose/galactose transporter (characterized, see rationale)
to candidate 6937233 Sama_1403 glucose/galactose transporter (RefSeq)
Query= uniprot:A0KXM0 (423 letters) >FitnessBrowser__SB2B:6937233 Length = 415 Score = 594 bits (1531), Expect = e-174 Identities = 305/413 (73%), Positives = 345/413 (83%), Gaps = 11/413 (2%) Query: 9 SHTSSVSEAGNGNYRFALVSLTSLFFMWGFITCLNDILIPHLKAVFSLNYTQAMLIQFCF 68 ++ + AG NYRFAL SLT+LFFMWGFITCLNDILIPHLKAVFSLNY QAMLIQFCF Sbjct: 7 ANANHAGAAGAENYRFALGSLTTLFFMWGFITCLNDILIPHLKAVFSLNYAQAMLIQFCF 66 Query: 69 FGAYFLVSIPAGQLVKRLGYQKGIVTGLVIASIGCGLFYPAASFATYGLFLGALFVLASG 128 FGAYFLVS+PAG LVKRLGYQKGIV GL+ A++GCGLFYPAA ATYG+FLGALFVLASG Sbjct: 67 FGAYFLVSVPAGVLVKRLGYQKGIVVGLLTAALGCGLFYPAAVSATYGVFLGALFVLASG 126 Query: 129 ITILQVAANPYVNALGSSETASSRLNLTQAFNALGTTVAPFFGSILILSVAASVSSELAQ 188 IT+LQVAANPYV ALG +TASSRL LTQAFN+LGTT+AP FGS+LILSVA S+E Sbjct: 127 ITVLQVAANPYVTALGPVQTASSRLTLTQAFNSLGTTIAPAFGSVLILSVAVGASAE--- 183 Query: 189 ANAEAEVVKLPYLLLAAALAVLAIIFAKLDLPVIREHSQAAAEEVQTHLGKTSALQSMHL 248 AEA+ VKLPYLLL L VLA++FA L LP I + A Q SAL HL Sbjct: 184 --AEADAVKLPYLLLCGMLIVLAVVFALLKLPHIHDQEDEVAATGQ------SALAHRHL 235 Query: 249 VLGAVGIFVYVGAEVSIGSFLVNFLGEAHIVGMPEEQAAHYIAYYWGGAMVGRFIGSAVM 308 VLGA+GIFVYVG EV+IGSFLVNFLGE+H+ GM E AAHYIA+YWGGAMVGRFIG+AVM Sbjct: 236 VLGAIGIFVYVGGEVAIGSFLVNFLGESHVAGMAEADAAHYIAFYWGGAMVGRFIGAAVM 295 Query: 309 QKIPAGTVLAFNAFMAALLVLVAMTTSGSVAMWAILGVGLFNSIMFPTIFSLALRDLGPH 368 QK+ AG VL FNA MAALLVLVAM +SG++AMWAIL VGLFNSIMFPTIFSLAL++LGP Sbjct: 296 QKVDAGKVLGFNATMAALLVLVAMNSSGALAMWAILAVGLFNSIMFPTIFSLALKNLGPA 355 Query: 369 TSQGSGILCLAIVGGAIVPLLQGVLADNLGIQLAFILPVVCYGFILFYGAKGS 421 T+QGSGILCLAIVGGA+VPLLQG+LAD++G+ +FILPV+CYG+ILFYG KGS Sbjct: 356 TAQGSGILCLAIVGGALVPLLQGLLADSVGLSASFILPVLCYGYILFYGLKGS 408 Lambda K H 0.326 0.138 0.402 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: 638 Number of extensions: 28 Number of successful extensions: 3 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: 423 Length of database: 415 Length adjustment: 32 Effective length of query: 391 Effective length of database: 383 Effective search space: 149753 Effective search space used: 149753 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: 50 (23.9 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