Align ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale)
to candidate BPHYT_RS16055 BPHYT_RS16055 sugar ABC transporter permease
Query= uniprot:A0A1N7UKA9 (325 letters) >FitnessBrowser__BFirm:BPHYT_RS16055 Length = 335 Score = 291 bits (745), Expect = 2e-83 Identities = 158/325 (48%), Positives = 213/325 (65%), Gaps = 6/325 (1%) Query: 1 MNAKTITAPV--TAAPRNRLRLSLDRFGLPLVFILLCVVMAFSSEYFMTWRNWMDILRQT 58 +N+ T APV T A R L GL +++C+VM F+S+ F++ N ++LRQ Sbjct: 15 VNSDTPGAPVRFTWAALKRSTLFYPFIGL----LVVCIVMVFASDSFLSGANIENVLRQV 70 Query: 59 SINGILAVGMTYVILTKGIDLSVGSILAFAGLCSAMVATQGYGLLAAVSAGMFAGAMLGV 118 SIN I+AVGMT VILT GIDLSVGS++A AG +A + G +AA++ G+ G G Sbjct: 71 SINAIIAVGMTCVILTGGIDLSVGSVMALAGTLAAGLMVAGMNAVAALAIGIAVGLGFGA 130 Query: 119 VNGFMVANLSIPPFVATLGMLSIARGMTFILNDGSPITDLPDAYLALGIGKIGPIGVPII 178 NGF VA +PP + TL + IARG+ I G PI LPD G GKI + P++ Sbjct: 131 ANGFFVAFAGMPPIIVTLATMGIARGLALIYTGGYPIDGLPDWVSFFGSGKILGVQAPVV 190 Query: 179 IFAVVALIFWMVLRYTTYGRYVYAVGGNEKSARTSGIGVRKVMFSVYVVSGLLAGLAGVV 238 I AV+ +I W++L +GRYVYA+GGNE++ R SG+ V +V VY ++GL + A +V Sbjct: 191 IMAVIYVIAWVLLERMPFGRYVYAIGGNEQATRLSGVRVARVKLIVYTIAGLTSAFAAIV 250 Query: 239 LSARTTSALPQAGVSYELDAIAAVVIGGTSLSGGTGSIVGTLFGALLIGVINNGLNLLGV 298 L+AR S P AGV +ELDAIAAVV+GGTS+SGG GSI+GTL GALL+GV+NNGLN++GV Sbjct: 251 LTARLMSGQPNAGVGFELDAIAAVVMGGTSISGGRGSIIGTLIGALLLGVLNNGLNMVGV 310 Query: 299 SSYYQQVAKGLIIVFAVLIDVWRKK 323 + Y Q V KG II+ A+ I R+K Sbjct: 311 NPYVQNVIKGGIILLAIYISRDRRK 335 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: 272 Number of extensions: 12 Number of successful extensions: 1 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: 335 Length adjustment: 28 Effective length of query: 297 Effective length of database: 307 Effective search space: 91179 Effective search space used: 91179 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: 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