Align Inner-membrane translocator (characterized, see rationale)
to candidate BPHYT_RS01815 BPHYT_RS01815 sugar ABC transporter permease
Query= uniprot:A0KWY6 (405 letters) >FitnessBrowser__BFirm:BPHYT_RS01815 Length = 336 Score = 194 bits (494), Expect = 2e-54 Identities = 119/338 (35%), Positives = 196/338 (57%), Gaps = 13/338 (3%) Query: 33 QPRMQESHKTMVQEKNARYQAGKSTSMGRYLWPLLALSILLLANLFIDSSFFNISYQDDR 92 +PR+ E+ Q+ A A +T++ ++ + +++L + + + F + + Sbjct: 4 EPRLGET----AQQITAAPPASAATTVRKWRHLAMQREVIVLLAMVLFNLIFTPHFWSLQ 59 Query: 93 LYGSLIDILNRSAPVALLSIGMSLVIATGGIDLSVGAVMAIAGAVCANLLLVPDISLVTV 152 + + + + ++ IGM+LV+ATGGIDLSVGA MAI+GA+ L L +I+ Sbjct: 60 TFNVN---MTQVVTIVIVGIGMTLVVATGGIDLSVGASMAISGALAPMLFL--NIAGPGG 114 Query: 153 IAAGLIVGLLA----GCINGGLVSFLGIQPIVATLLLMVAGRGVAQLINQGQIITFQHPG 208 IA ++ +LA G NG LV+ L +QPIVATL+L +AGRG+AQ++ G + F P Sbjct: 115 IALAFVLPVLAAALCGVFNGLLVTRLSVQPIVATLVLFIAGRGIAQVVTDGSLQAFNTPA 174 Query: 209 FAAIGVGQFLGLPMPVWIVIGMLTFSQLLLRKTALGLFIEAVGCNAKASRYLGINDKSIK 268 F I +G+ G+P V +++ ++ ++RKT G ++ G N KA+ G+ ++K Sbjct: 175 FQWIALGKVAGVPFQVLLMLALVGLFAWVVRKTLFGQYLLITGGNEKAAYLCGVPTATVK 234 Query: 269 LFAYGIAGLCAALAGMISTADIQGSDANNAGLWLELDAVLAVVIGGAALTGGRFSLILSV 328 L AY + A LAG+IS + SDAN GL +ELDA+ AV +GG ALTGG+ + ++ Sbjct: 235 LIAYTLCAALAGLAGLISISVNSSSDANVVGLGVELDAIAAVAVGGTALTGGKAYIGGTL 294 Query: 329 VGALIIQTLATTIIVSGLPAKFNLLIKAIVILTVLLLQ 366 +GALIIQ L T++ G+P L++KA +I+ + +Q Sbjct: 295 IGALIIQLLRYTLLAHGIPDAAALVVKAGIIVAAVYVQ 332 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: 329 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: 336 Length adjustment: 30 Effective length of query: 375 Effective length of database: 306 Effective search space: 114750 Effective search space used: 114750 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: 49 (23.5 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