Align Xylose/arabinose import permease protein XacI (characterized, see rationale)
to candidate SMc04394 SMc04394 ABC transporter permease
Query= uniprot:D4GP37 (309 letters) >FitnessBrowser__Smeli:SMc04394 Length = 293 Score = 143 bits (361), Expect = 4e-39 Identities = 95/309 (30%), Positives = 158/309 (51%), Gaps = 39/309 (12%) Query: 14 SLVEDVNLRRVAQYALVVFFLGFFLVPLETGIMTAIKTNESVAR----SLP---FAPPVG 66 +++ L R Y+ ++ F + L+PL ++ ++K + + + +LP P Sbjct: 8 NVISHNRLTRALIYSALILFALYSLLPLYVMLVNSLKPLDEIRQGGMLNLPQTWTVEPWL 67 Query: 67 EGFTLGNIQFALEQLSGSFFNSLIMSIPATIGSVLFGSMAAYGLTMVNWRAQ-----MGM 121 ++ I L F NS++M +PA S + G++ Y LT WR GM Sbjct: 68 SAWSTAQIGVQPTGLRPFFINSILMVVPAVAISTIIGALNGYVLT--KWRFPGANIFFGM 125 Query: 122 LMLFVVGVFVPYQAVLVPLARFWNNIFPLARMIEPMVASIPFFQGYHAELVPLVITHIAY 181 L+L F+P+Q VL+P+AR + G + L++ H+ Y Sbjct: 126 LLL---SCFIPFQIVLIPMARILGIL------------------GIAGSIWGLILVHVVY 164 Query: 182 GIPICTILFRSYYQSLPNSLVEAGKIDGASITKIYRRIILPISKPMFGVVFIYQFTQIYN 241 GI T+ FR+YY++ P LV A +IDGAS +I+RRI+LP S P+ V I+QFT I+N Sbjct: 165 GIGFTTLYFRNYYEAFPTELVRAAQIDGASFFQIFRRILLPSSGPIIVVSVIWQFTNIWN 224 Query: 242 EFLFAFTLVTGSDAPAAPVTLVLPAIGASTSGI-NFGIRMSAAFLAAVPTLILYVAFAEQ 300 +FLF + S + P+T+ L + +S++G+ + + + A LAA+PTLI+Y+ Sbjct: 225 DFLFGASF---SGPYSTPMTVALNNLVSSSTGVKEYNVHFAGAILAALPTLIVYIVSGRY 281 Query: 301 FAKGLRTEA 309 F +GL + A Sbjct: 282 FVRGLMSGA 290 Lambda K H 0.328 0.141 0.413 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: 253 Number of extensions: 9 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: 309 Length of database: 293 Length adjustment: 27 Effective length of query: 282 Effective length of database: 266 Effective search space: 75012 Effective search space used: 75012 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 48 (23.1 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