Align Polar amino acid ABC transporter, inner membrane subunit (characterized, see rationale)
to candidate H281DRAFT_00222 H281DRAFT_00222 amino acid ABC transporter membrane protein 2, PAAT family
Query= uniprot:B2TBJ8 (250 letters) >FitnessBrowser__Burk376:H281DRAFT_00222 Length = 237 Score = 132 bits (332), Expect = 6e-36 Identities = 78/208 (37%), Positives = 113/208 (54%), Gaps = 1/208 (0%) Query: 22 TLGLFFCSLILGGLLSLVIVTMRVSPHWLPNRFARAYILVFRGSPLLIQMFLVYYGMGQF 81 TL L S+ LG LS+ + RVS + Y +FRG+PL +Q+ L Y G+ Sbjct: 26 TLWLLVVSIGLGFCLSIPLAVARVSKKKWLSTLVWLYTYIFRGTPLYVQLLLCYTGLYSL 85 Query: 82 GVIRESFLWPVL-REPYMCAVLSLALCTAGYTAEIIRGGLMAVPVGQIEAGYSIGLSGFA 140 ++R L RE C +L+ L T YT EI G + A P G+IEA + G+S F Sbjct: 86 EIVRNHELTNAFFREGMNCTLLAFTLNTCAYTTEIFAGAIKATPYGEIEAARAYGMSSFT 145 Query: 141 LLRRVIGPIALRQCLPAYSTEAVLLVKSTALASLVTVWEVTGVAQQIIQQTYRTTEVFIC 200 L RRVI P ALR+ LP YS E +L++ +T +A TV ++ +A+ + TY++ F Sbjct: 146 LYRRVILPSALRRALPYYSNEVILMLHATTVAFTATVPDILKIARDVNSATYQSFNAFGI 205 Query: 201 AALIYLFLNFVIVRLLGMLETRLSRHLR 228 AAL+YL ++F +V L E R +LR Sbjct: 206 AALLYLCISFALVWLFRRAERRWLAYLR 233 Lambda K H 0.331 0.143 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: 162 Number of extensions: 6 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: 250 Length of database: 237 Length adjustment: 23 Effective length of query: 227 Effective length of database: 214 Effective search space: 48578 Effective search space used: 48578 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 46 (22.3 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