Align ABC transporter permease (characterized, see rationale)
to candidate BWI76_RS01825 BWI76_RS01825 maltose ABC transporter permease MalF
Query= uniprot:A0A166QFV1 (320 letters) >FitnessBrowser__Koxy:BWI76_RS01825 Length = 514 Score = 114 bits (285), Expect = 5e-30 Identities = 72/233 (30%), Positives = 128/233 (54%), Gaps = 16/233 (6%) Query: 99 TLYFTVVSVGLEVVLGLLVALLLNIK-FTGRALVRALILIPWAIPTIVSAKIWSWMLNDQ 157 T+ F+V++V L V +G+++A L+ + G+A+ R L+++P+A+P+ +S I+ + N Sbjct: 284 TVVFSVLTVILTVAVGMVLACLVQWEALKGKAIYRVLLILPYAVPSFISILIFKGLFNQS 343 Query: 158 FGIINHLMLSLGLIDAPLAWTADADLSMWAVIIVDVWKTVPFVTLLMLAALQMLPSDCYE 217 FG IN +MLS L AW +D + +IIV+ W P++ +L + L+ +P D YE Sbjct: 344 FGEIN-MMLS-ALFGIKPAWFSDPTTARTMIIIVNTWLGYPYMMILCMGLLKAIPDDLYE 401 Query: 218 AARVDGIHPLKVFWRVTLPLLMPALLVAAIFRILDSLRVFDVIYVLTSNSSSTMSMSVYA 277 A+ +DG P + F+++TLPLL+ L I + F +I +LT+ + + A Sbjct: 402 ASAMDGATPFQNFFKITLPLLIKPLTPLMIASFAFNFNNFVLIQLLTNGGPDRLGTTTPA 461 Query: 278 --RQHLVEF-----------QDVGYGSAASTLLFLVVAVIALLYLYLGRRQLE 317 LV + QD G +A +TL+FL+V ++A++ L R + + Sbjct: 462 GYTDLLVSYTYRIAFEGGGGQDFGLAAAIATLIFLLVGLLAIVNLKATRMKFD 514 Lambda K H 0.329 0.140 0.443 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: 368 Number of extensions: 23 Number of successful extensions: 3 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: 320 Length of database: 514 Length adjustment: 31 Effective length of query: 289 Effective length of database: 483 Effective search space: 139587 Effective search space used: 139587 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 (21.8 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