Align Xylose/arabinose import permease protein XylH (characterized, see rationale)
to candidate H281DRAFT_02714 H281DRAFT_02714 monosaccharide ABC transporter membrane protein, CUT2 family
Query= uniprot:Q4J711 (356 letters) >FitnessBrowser__Burk376:H281DRAFT_02714 Length = 331 Score = 130 bits (327), Expect = 5e-35 Identities = 97/321 (30%), Positives = 166/321 (51%), Gaps = 27/321 (8%) Query: 1 MNILNVVRRFEFQLFLVNVIIALFFYFENSAYF-SSNNITTIFQYLAEIGIIAIGEAMLM 59 +N+L+V L LV ++I++F S YF ++NN+ +F+ + I +++IG +++ Sbjct: 28 LNVLSV-------LLLVGLLISVF-----SPYFLTTNNLMGVFRSFSLIALMSIGMMLVI 75 Query: 60 LCGEIDLSPPALANFVPLITLTIYNSIYQAISPTPAIVVSILLSLGLASLIGLMNGLITT 119 + G IDLS ++ L+T ++ Y A PA + L++G+A +G NG + T Sbjct: 76 ITGGIDLSVGSVMGLSSLVTALVFQHGYNA----PA-AIGAGLAVGIA--VGAFNGFMIT 128 Query: 120 KAKVNSLITTVGTLFLFNGIALIYSGGYPESFPY---FRFLG-GTVSILPVPFIWSLGAL 175 ++ I T+GTL + G+ I + G P + F F+G G + +P P + L Sbjct: 129 WIQLPPFIATLGTLSIGRGLMYIITKGVPVTPDVPDSFTFIGQGYIGFVPFPVVILLAMT 188 Query: 176 VFLILLLHYTKIGVWTIAAGSNPTGASEVGVPVDRVKIINFIIMANIGALVGIIQGSRVL 235 +++ T+ G + A G N A GV RVK +++ I ++ G+I SR + Sbjct: 189 AVFSVVMRQTRFGRYVYATGGNEVAARLSGVRTARVKFTVYVLSGLIASMAGVIAFSRFV 248 Query: 236 TIG-ATNFTADVVLEGIAAAVIGGTSLVGGKGSLVGAFLGSVFISELLNGFNILGINAYE 294 + A+ F A+ L+ IAAA IGG SL GG GS+ GA +G+ + NG +L I+ Y Sbjct: 249 SAEPASGFGAE--LDVIAAAAIGGASLSGGAGSVEGAIIGAALAGIITNGVVLLNIDTYA 306 Query: 295 FDAILGGAIVVVMVLSYYAKR 315 AI G I++ + + + R Sbjct: 307 QQAITGCVILIAVSIDIWRVR 327 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: 319 Number of extensions: 27 Number of successful extensions: 4 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: 331 Length adjustment: 29 Effective length of query: 327 Effective length of database: 302 Effective search space: 98754 Effective search space used: 98754 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