Align Xylose/arabinose import permease protein XylH (characterized, see rationale)
to candidate BPHYT_RS30860 BPHYT_RS30860 sugar ABC transporter permease
Query= uniprot:Q4J711 (356 letters) >FitnessBrowser__BFirm:BPHYT_RS30860 Length = 329 Score = 201 bits (510), Expect = 3e-56 Identities = 115/317 (36%), Positives = 185/317 (58%), Gaps = 15/317 (4%) Query: 8 RRFEFQLFLVNVIIALFFYFENSAYFSSN-NITTIFQYLAEIGIIAIGEAMLMLCGEIDL 66 R E ++F V +I+ ++F N + + ++ + Q++A + IIA GE MLM+ GEIDL Sbjct: 20 RSSEIRIFAVALILCVYFETVNHDFLLTGASLQNLSQFIAPVAIIAFGEIMLMIGGEIDL 79 Query: 67 SPPALANFVPLITLTIYNSIYQAISPTPAIVVSILLSLGLASLIGLMNGLITTKAKVNSL 126 S + F P I +Y +I + P ++ ++ A ++GL+NG +T ++ S Sbjct: 80 SAGMVFAFAPFI---MYFAIEAGLPPWLGMLAGVVA----AGIVGLINGAVTVYLRIPSF 132 Query: 127 ITTVGTLFLFNGIALIYSGGYPESFP----YFRFLGGTVSILPVPFIWSLGALVFLILLL 182 +TT+GTLF NG+ L S G P S P + F+GG IW+L F+ +LL Sbjct: 133 VTTLGTLFFVNGLTLTISRGTPVSPPENSAFAAFMGGWGYS---EIIWTLALAAFMHVLL 189 Query: 183 HYTKIGVWTIAAGSNPTGASEVGVPVDRVKIINFIIMANIGALVGIIQGSRVLTIGATNF 242 +T+ G+ TIA+G+NP GASE G+ V R+K+ NFI+ A + L GI++G R+ +I Sbjct: 190 RHTRWGLHTIASGANPLGASEAGIQVRRLKLGNFILAALLAGLTGILEGFRITSIDPQAG 249 Query: 243 TADVVLEGIAAAVIGGTSLVGGKGSLVGAFLGSVFISELLNGFNILGINAYEFDAILGGA 302 ++ +AAAVIGGT L GG G+++G +G+ + L +GF ++GINA+ F+ ILG A Sbjct: 250 GNQIMFLAVAAAVIGGTPLAGGSGTIIGGLIGAAVLGILNDGFTLIGINAFTFNMILGAA 309 Query: 303 IVVVMVLSYYAKRASYK 319 I+ M+ + + R + K Sbjct: 310 ILGAMIFNIHVVRLARK 326 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: 372 Number of extensions: 31 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: 356 Length of database: 329 Length adjustment: 29 Effective length of query: 327 Effective length of database: 300 Effective search space: 98100 Effective search space used: 98100 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