Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate BWI76_RS01820 BWI76_RS01820 maltose transporter permease
Query= uniprot:A8LLL4 (385 letters) >FitnessBrowser__Koxy:BWI76_RS01820 Length = 296 Score = 89.4 bits (220), Expect = 1e-22 Identities = 66/213 (30%), Positives = 105/213 (49%), Gaps = 9/213 (4%) Query: 179 FNTLTVTIPATIIPILVAAFAAYALAWMEFPGRALLIALIVGLLVVPLQLALIPLLTLHN 238 +N++ V I + ++ AYA A M FPG+A L+ ++ + P L+L+ L L + Sbjct: 86 WNSIKVAGITAIGIVALSTTCAYAFARMRFPGKATLLKGMLIFQMFPAVLSLVALYALFD 145 Query: 239 AIGIGKGYLG------TWLAHTGFGMPLAIYLLRNYMVGLPRDIIENAKVDGATDFQIFT 292 +G ++G A+ G G+ L ++ ++ Y + + E A +DGAT +Q F Sbjct: 146 RLGQYVPFVGLNTHGGVIFAYMG-GIALHVWTIKGYFETIDGSLEEAAALDGATPWQAFR 204 Query: 293 KIVLPLSFPALASFAIFQFLWTWNDLLVAKVFLIDATGQTTVMTNQIVELLGTRGGNWEI 352 ++LPLS P LA I F+ ++ VA + L D T + Q + L + W Sbjct: 205 LVLLPLSVPILAVVFILSFIAAITEVPVASLLLRDVNSYTLAVGMQ--QYLNPQNYLWGD 262 Query: 353 LATAAFVSIAVPLLVFFSMQRFLVRGLLAGSVK 385 A AA +S +VF QR+LV GL AG VK Sbjct: 263 FAAAAVLSAIPITVVFLLAQRWLVNGLTAGGVK 295 Lambda K H 0.323 0.138 0.419 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: 266 Number of extensions: 13 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 385 Length of database: 296 Length adjustment: 28 Effective length of query: 357 Effective length of database: 268 Effective search space: 95676 Effective search space used: 95676 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 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