Align Xylose/arabinose import permease protein XylH (characterized, see rationale)
to candidate HSERO_RS05325 HSERO_RS05325 ribose ABC transporter permease
Query= uniprot:Q4J711 (356 letters) >FitnessBrowser__HerbieS:HSERO_RS05325 Length = 328 Score = 149 bits (376), Expect = 1e-40 Identities = 98/299 (32%), Positives = 160/299 (53%), Gaps = 13/299 (4%) Query: 19 VIIALFFYFENSAYFSSNNITTIFQYLAEIGIIAIGEAMLMLCGEIDLSPPALANFVPLI 78 V+++L + +F+ +N + + ++ +GI+A+G + ++L G IDLS A I Sbjct: 37 VVVSLLMGLASDNFFTLSNWFNVLRQVSIVGILAVGMSFVILTGGIDLSVGAAMALAGTI 96 Query: 79 TLTIYNSIYQAISPTPAIVVSILLSLGLASLIGLMNGLITTKAKVNSLITTVGTLFLFNG 138 + + I + P P +++L +GLA+ IGL+NG + ++ ++I T+ T+ + G Sbjct: 97 SAGL---IVNSGLPAP---LALLCGVGLATCIGLLNGALVAWGRMPAIIVTLATMGVARG 150 Query: 139 IALIYSGGYPES-FP-YFRFLG-GTVSILPVPFIWSLGALVFLILLLHYTKIGVWTIAAG 195 + LIYSGGYP S P + + G G + ++PVP I L LLL T G A G Sbjct: 151 VGLIYSGGYPISGLPGWISWFGVGRIGMVPVPVILMLIVYALAWLLLQRTAFGRHVYAIG 210 Query: 196 SNPTGASEVGVPVDRVKIINFIIMANIGALVGIIQGSRVLTIGATNFTADVVLEGIAAAV 255 N A GV R+K+ + I L II R+++ G N L+ IAA V Sbjct: 211 GNEMAARLSGVKTTRIKLAVYAISGFTSGLAAIILTGRLMS-GQPNAGVGFELDAIAAVV 269 Query: 256 IGGTSLVGGKGSLVGAFLGSVFISELLNGFNILGINAYEFDAILGGAIVVVMVLSYYAK 314 +GGT++ GG+G +VG +G+V + L NG N++GIN Y D I G V++++ Y A+ Sbjct: 270 LGGTAIAGGRGLVVGTLIGAVLLGILNNGLNLMGINPYLQDIIRG---VIILLAIYIAR 325 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: 303 Number of extensions: 19 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: 328 Length adjustment: 29 Effective length of query: 327 Effective length of database: 299 Effective search space: 97773 Effective search space used: 97773 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