Align Xylose/arabinose import permease protein XacI (characterized, see rationale)
to candidate WP_086510783.1 BZY95_RS15420 carbohydrate ABC transporter permease
Query= uniprot:D4GP37 (309 letters) >NCBI__GCF_002151265.1:WP_086510783.1 Length = 292 Score = 151 bits (381), Expect = 2e-41 Identities = 94/293 (32%), Positives = 152/293 (51%), Gaps = 29/293 (9%) Query: 21 LRRVAQYALVVFFLGFFLVPLETGIMTAIKTNESVAR----SLPFAP---PVGEGFTLGN 73 L R YA+++ F+L+PL ++T++K + SLP P P G+ + Sbjct: 14 LGRAMLYAVLLLAALFYLLPLAVMLITSVKPLAEITPGTLLSLPREPTLAPWGKAWGEAC 73 Query: 74 IQFALEQLSGSFFNSLIMSIPATIGSVLFGSMAAYGLTMVNWRAQMGMLMLFVVGVFVPY 133 E + FFNS+ + +PA + S G++ Y LT ++ + L + G F+P+ Sbjct: 74 TGMRCEGIGVYFFNSIAIVVPAVLISTAIGALNGYALTKWRFKGSELLFALMLFGCFIPF 133 Query: 134 QAVLVPLARFWNNIFPLARMIEPMVASIPFFQGYHAELVPLVITHIAYGIPICTILFRSY 193 Q VL+P+A+ + G + L++ H+ +GI T+ FR++ Sbjct: 134 QVVLLPMAQTLG------------------WLGLSSSRAGLILVHVIFGIAFTTLFFRNF 175 Query: 194 YQSLPNSLVEAGKIDGASITKIYRRIILPISKPMFGVVFIYQFTQIYNEFLFAFTLVTGS 253 Y ++P LV A K+DGA +I+ RI+LP+S P+ V I+QFTQI+N+FLF V S Sbjct: 176 YVAVPTELVSAAKLDGAGFFRIFWRILLPVSAPIIVVSVIWQFTQIWNDFLFG---VAFS 232 Query: 254 DAPAAPVTLVL-PAIGASTSGINFGIRMSAAFLAAVPTLILYVAFAEQFAKGL 305 PVT+ L + ST + + M+AA +AA+PTLI+YV + F +GL Sbjct: 233 AHNTQPVTVALNNLVNTSTGAREYNVDMAAAMIAALPTLIVYVLAGKYFVRGL 285 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: 248 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: 309 Length of database: 292 Length adjustment: 27 Effective length of query: 282 Effective length of database: 265 Effective search space: 74730 Effective search space used: 74730 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 Apr 09 2024. 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