Align Inner-membrane translocator (characterized, see rationale)
to candidate BPHYT_RS23880 BPHYT_RS23880 sugar ABC transporter permease
Query= uniprot:A0KWY6 (405 letters) >FitnessBrowser__BFirm:BPHYT_RS23880 Length = 343 Score = 290 bits (741), Expect = 6e-83 Identities = 156/326 (47%), Positives = 222/326 (68%), Gaps = 4/326 (1%) Query: 63 LWPLLALSILLLANLFIDSSFFNISYQDDRLYGSLIDILNRSAPVALLSIGMSLVIATGG 122 +WP + L +L NL+++ F ++ D L+G+ ID+LNR+AP+ L++ GM+LVIAT G Sbjct: 17 IWPCVTLVLLCGLNLWVNPHFLSLRMLDGHLFGAPIDVLNRAAPLVLVATGMTLVIATRG 76 Query: 123 IDLSVGAVMAIAGAVCANLLLV---PDISLVT-VIAAGLIVGLLAGCINGGLVSFLGIQP 178 ID+SVGAV+AIAGA A +L P +L+ + A LIVG+L+G NG LVSF+G+QP Sbjct: 77 IDISVGAVVAIAGAAAATILAAQPEPSSALIAQALIAALIVGVLSGMWNGVLVSFVGMQP 136 Query: 179 IVATLLLMVAGRGVAQLINQGQIITFQHPGFAAIGVGQFLGLPMPVWIVIGMLTFSQLLL 238 I+ATL+LMVAGRG+AQL+ GQII PG+ +G G LG+P VWI + + L+ Sbjct: 137 IIATLILMVAGRGIAQLLTAGQIIPIGAPGYLFVGGGYLLGVPSSVWIATVAVLATAALV 196 Query: 239 RKTALGLFIEAVGCNAKASRYLGINDKSIKLFAYGIAGLCAALAGMISTADIQGSDANNA 298 TALGLFI A+G N A+R +G+ K++ YG +GL AA+AG++ +++++ +D NNA Sbjct: 197 EGTALGLFIRAIGVNPVATRLVGLRSKALVFAVYGFSGLTAAMAGILISSNVRSADGNNA 256 Query: 299 GLWLELDAVLAVVIGGAALTGGRFSLILSVVGALIIQTLATTIIVSGLPAKFNLLIKAIV 358 GL LELDA+LAV +GG +L GGRFSL +V+GALIIQTL T G+P + L++KA V Sbjct: 257 GLLLELDAILAVTLGGTSLLGGRFSLAGTVLGALIIQTLTYTTYSIGVPPEATLVVKAAV 316 Query: 359 ILTVLLLQSAKFRRQLSALFKSKRHA 384 +L V ++QS R +L +R A Sbjct: 317 VLAVSVIQSPSARALGMSLVTHRRVA 342 Lambda K H 0.323 0.136 0.379 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: 342 Number of extensions: 18 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: 405 Length of database: 343 Length adjustment: 30 Effective length of query: 375 Effective length of database: 313 Effective search space: 117375 Effective search space used: 117375 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 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