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_RS25825 BPHYT_RS25825 ABC transporter permease
Query= uniprot:A0A1N7UKA9 (325 letters) >FitnessBrowser__BFirm:BPHYT_RS25825 Length = 333 Score = 233 bits (595), Expect = 4e-66 Identities = 140/323 (43%), Positives = 211/323 (65%), Gaps = 15/323 (4%) Query: 6 ITAPVTAAP--RNRLR------LSLDR-FGLPLVFILLCVVMAFSSEYFMTWRNWMDILR 56 +TA A+P ++R+R L DR + L F +L VV +F+S +F++ N+++I R Sbjct: 8 LTAERQASPLQKSRMRRIAQALLQGDRPYALYAAFAILLVVFSFASPWFLSIDNFLNIGR 67 Query: 57 QTSINGILAVGMTYVILTKGIDLSVGSILAFAGLCSAM-VATQGYGLLAAVSAGMFAGAM 115 QT++ I+A+GMT+VI+ + IDLSVGS LA +G+ +A+ +A G + AG+ GA+ Sbjct: 68 QTALVSIIAIGMTFVIIARQIDLSVGSTLALSGMSAALAMAYVGNNWVIGAIAGIGTGAI 127 Query: 116 LGVVNGFMVANLSIPPFVATLGMLSIARGMTFILNDGSPITDLPDAYLAL-GIGKIGPIG 174 +G +NG + ++IP F+ TLG LS ARG+ ++ P+ D+++++ G G I + Sbjct: 128 VGAINGIVTTRVNIPSFLVTLGTLSAARGLALMVTTTKPVIIDNDSFISIFGEGDIFGVP 187 Query: 175 VPII--IFAVVALIFWMVLRYTTYGRYVYAVGGNEKSARTSGIGVRKVMFSVYVVSGLLA 232 VPII + AV+A I ++L Y+ +GR +YA GGN +A SGI R+V ++++G+LA Sbjct: 188 VPIIWTLLAVIAGI--LLLHYSVFGRQIYAAGGNPTAALYSGINTRRVTTLAFILTGMLA 245 Query: 233 GLAGVVLSARTTSALPQAGVSYELDAIAAVVIGGTSLSGGTGSIVGTLFGALLIGVINNG 292 GLA +VLSAR+ +A P ELD IA+V +GG SL GG G ++GTL G+L+IG +NNG Sbjct: 246 GLAALVLSARSHAARPDVVQGMELDVIASVTLGGCSLFGGRGFVLGTLLGSLIIGTLNNG 305 Query: 293 LNLLGVSSYYQQVAKGLIIVFAV 315 L LLGVSS Q V KG+IIV AV Sbjct: 306 LVLLGVSSSLQLVIKGVIIVAAV 328 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: 236 Number of extensions: 22 Number of successful extensions: 4 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: 333 Length adjustment: 28 Effective length of query: 297 Effective length of database: 305 Effective search space: 90585 Effective search space used: 90585 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