Align Xylose/arabinose import permease protein XylH (characterized, see rationale)
to candidate SMc02019 SMc02019 ABC transporter permease
Query= uniprot:Q4J711 (356 letters) >FitnessBrowser__Smeli:SMc02019 Length = 334 Score = 147 bits (371), Expect = 4e-40 Identities = 96/312 (30%), Positives = 162/312 (51%), Gaps = 16/312 (5%) Query: 11 EFQLFLVNVIIALFFYFENSAYFSSNNITTIFQYLAEIGIIAIGEAMLMLCGEIDLSPPA 70 E + L + + + +F+ N+ + + ++ IGI+A+G + + GEIDLS A Sbjct: 30 ELSVILAALAMFVALSLSTDTFFTELNLLNLLRQISVIGILAVGSTFIFISGEIDLSVGA 89 Query: 71 LANFVPLITLTIYNSIYQAISPTPAIVVSILLSLGLASLIGLMNGLITTKAKVNSLITTV 130 L + +I + AI I + L+ + L +++ +NG+ITTK ++ S ITT+ Sbjct: 90 LLGLLAMICAAL------AIKMEGNIYGAALVVVALGAILSGINGVITTKLRIPSFITTL 143 Query: 131 GTLFLFNGIALIYSGGYPESF---PYFRFL--GGTVSILPVPFIWSLGALVFLILLLHYT 185 G L +++G L+ S G P S FR L G ++P IW + A +F LL +T Sbjct: 144 GMLSIYSGATLVLSKGMPISGLQNDLFRSLVAGRLFGVVPAQVIWMVAAGIFGTYLLLFT 203 Query: 186 KIGVWTIAAGSNPTGASEVGVPVDRVKIINFIIMANIGALVGIIQGSRVLTI-GATNFTA 244 + G A G N A VG+ DRVKI+ F++ G +VG+ V G T Sbjct: 204 RFGYNVFATGGNKNAAKAVGINTDRVKILAFVVS---GIMVGVTSFILVGWFRGVDPQTG 260 Query: 245 D-VVLEGIAAAVIGGTSLVGGKGSLVGAFLGSVFISELLNGFNILGINAYEFDAILGGAI 303 + + L IAA +IGGT L GG+GS++G +G++ I + NG +LG+++Y G I Sbjct: 261 NGLELSVIAAVIIGGTGLFGGQGSVLGTLVGALIIGMISNGTVLLGVDSYYEPVAHGTVI 320 Query: 304 VVVMVLSYYAKR 315 ++ +++ + +R Sbjct: 321 LLAVIIDIWVRR 332 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: 337 Number of extensions: 37 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: 356 Length of database: 334 Length adjustment: 29 Effective length of query: 327 Effective length of database: 305 Effective search space: 99735 Effective search space used: 99735 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