Align Xylose/arabinose import permease protein XylH (characterized, see rationale)
to candidate BPHYT_RS25825 BPHYT_RS25825 ABC transporter permease
Query= uniprot:Q4J711 (356 letters) >FitnessBrowser__BFirm:BPHYT_RS25825 Length = 333 Score = 139 bits (349), Expect = 1e-37 Identities = 96/310 (30%), Positives = 157/310 (50%), Gaps = 30/310 (9%) Query: 12 FQLFLVNVIIALFFYFENSAYFSSNNITTIFQYLAEIGIIAIGEAMLMLCGEIDLSPP-- 69 + L+ I+ + F F + + S +N I + A + IIAIG +++ +IDLS Sbjct: 36 YALYAAFAILLVVFSFASPWFLSIDNFLNIGRQTALVSIIAIGMTFVIIARQIDLSVGST 95 Query: 70 -ALANFVPLITLTIYNSIYQAISPTPAIVVSILLSLGLASLIGLMNGLITTKAKVNSLIT 128 AL+ + + + + V+ + +G +++G +NG++TT+ + S + Sbjct: 96 LALSGMSAALAMAYVGNNW---------VIGAIAGIGTGAIVGAINGIVTTRVNIPSFLV 146 Query: 129 TVGTLFLFNGIALIYSGGYPESFPYFRFLG----GTVSILPVPFIWSLGALVFLILLLHY 184 T+GTL G+AL+ + P F+ G + +PVP IW+L A++ ILLLHY Sbjct: 147 TLGTLSAARGLALMVTTTKPVIIDNDSFISIFGEGDIFGVPVPIIWTLLAVIAGILLLHY 206 Query: 185 TKIGVWTIAAGSNPTGASEVGVPVDRVKIINFIIMANIGALVGIIQGSRVLTIGATNFTA 244 + G AAG NPT A G+ RV + FI L G++ G L + A + A Sbjct: 207 SVFGRQIYAAGGNPTAALYSGINTRRVTTLAFI-------LTGMLAGLAALVLSARSHAA 259 Query: 245 --DVV----LEGIAAAVIGGTSLVGGKGSLVGAFLGSVFISELLNGFNILGINAYEFDAI 298 DVV L+ IA+ +GG SL GG+G ++G LGS+ I L NG +LG+++ + Sbjct: 260 RPDVVQGMELDVIASVTLGGCSLFGGRGFVLGTLLGSLIIGTLNNGLVLLGVSS-SLQLV 318 Query: 299 LGGAIVVVMV 308 + G I+V V Sbjct: 319 IKGVIIVAAV 328 Lambda K H 0.325 0.143 0.404 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: 305 Number of extensions: 29 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: 356 Length of database: 333 Length adjustment: 29 Effective length of query: 327 Effective length of database: 304 Effective search space: 99408 Effective search space used: 99408 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 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