Align ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale)
to candidate 7024902 Shewana3_2076 inner membrane ABC transporter permease protein YjfF (RefSeq)
Query= uniprot:A0A1N7UKA9 (325 letters) >FitnessBrowser__ANA3:7024902 Length = 320 Score = 175 bits (444), Expect = 1e-48 Identities = 104/295 (35%), Positives = 175/295 (59%), Gaps = 8/295 (2%) Query: 30 VFILLCVVMAFSSEYFMTWRNWMDILRQTSINGILAVGMTYVILTKGIDLSVGSILAFAG 89 + + + +V F + F + R ++LR + I A+GMT VI++ GIDLSVG+++A +G Sbjct: 15 LLLTMFLVGTFQFDGFASGRVVTNLLRDNAFLLITALGMTLVIISGGIDLSVGAVIALSG 74 Query: 90 LCSAMVAT--QGYGLLAAVSAGMFAGAMLGVVNGFMVANLSIPPFVATLGMLSIARGMTF 147 + ++++ T Q + LLA V + G + G + G ++ + PF+ TL + +ARG+ Sbjct: 75 VVTSLLITEYQWHPLLAFVVI-LPLGTLFGALMGTIIHVYKLQPFIVTLAGMFLARGLAT 133 Query: 148 ILNDGSPITDLPD----AYLALGIGKIGPIGVPIIIFAVVALIFWMVLRYTTYGRYVYAV 203 L++ S D P A +++ + G + + +IF + +I +V+ YT +G VYA+ Sbjct: 134 TLSEESIAIDHPFYDAVAEMSIALPGNGALDLSSLIFILFFVIIAVVMHYTRFGTNVYAI 193 Query: 204 GGNEKSARTSGIGVRKVMFSVYVVSGLLAGLAGVVLSARTTSALPQAGVSYELDAIAAVV 263 GGN+ SA GI + K S+Y +S LA LAG+V + T S + ELDAIAAVV Sbjct: 194 GGNQHSAELMGISIAKTTISIYAISSFLATLAGIVFTFYTFSGYALGAIGVELDAIAAVV 253 Query: 264 IGGTSLSGGTGSIVGTLFGALLIGVINNGLNLLG-VSSYYQQVAKGLIIVFAVLI 317 IGGT L+GG+G ++GT+ G +L+GVI + G +SS++ ++ GL++ F +L+ Sbjct: 254 IGGTLLTGGSGFVLGTVLGVILMGVIQTYITFDGSLSSWWTKIVIGLLLFFFILL 308 Lambda K H 0.326 0.141 0.412 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: 232 Number of extensions: 10 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: 325 Length of database: 320 Length adjustment: 28 Effective length of query: 297 Effective length of database: 292 Effective search space: 86724 Effective search space used: 86724 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 (21.6 bits) S2: 48 (23.1 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