Align Xylose/arabinose import permease protein XacI (characterized, see rationale)
to candidate Pf6N2E2_2890 Glucose ABC transport system, inner membrane component 2
Query= uniprot:D4GP37 (309 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2890 Length = 281 Score = 165 bits (418), Expect = 1e-45 Identities = 101/293 (34%), Positives = 165/293 (56%), Gaps = 26/293 (8%) Query: 19 VNLRRVAQYALVVFFLGFFLVPLETGIMTAIKTNESVAR-SLPFAPPVGEGFTLGNIQFA 77 ++L R+A YA+++ + +LVPL ++T+ KT E ++ +L P V G +G ++ A Sbjct: 10 ISLSRIAIYAVLILAVLLYLVPLVVMLLTSFKTPEDISTGNLLSWPTVVSG--IGWVK-A 66 Query: 78 LEQLSGSFFNSLIMSIPATIGSVLFGSMAAYGLTMVNWRAQMGMLMLFVVGVFVPYQAVL 137 + G F+NS+ +++PA + S G++ Y L+M +R L + G F+P+Q VL Sbjct: 67 WATVDGYFWNSIKITVPAVLISTAIGALNGYVLSMWRFRGSQLFFGLLLFGCFLPFQTVL 126 Query: 138 VPLARFWNNIFPLARMIEPMVASIPFFQGYHAELVPLVITHIAYGIPICTILFRSYYQSL 197 +P + F L +M G + LV H+ YG+ T+ FR+YY S+ Sbjct: 127 LPAS------FTLGKM------------GLASTTTGLVFVHVVYGLAFTTLFFRNYYVSI 168 Query: 198 PNSLVEAGKIDGASITKIYRRIILPISKPMFGVVFIYQFTQIYNEFLFAFTLVTGSDAPA 257 P++LV+A ++DGA I+RRIILP+S P+ V I+QFTQI+N+FLF V S + Sbjct: 169 PDALVKAARLDGAGFFTIFRRIILPMSTPIIMVCLIWQFTQIWNDFLFG---VVFSSGDS 225 Query: 258 APVTLVL-PAIGASTSGINFGIRMSAAFLAAVPTLILYVAFAEQFAKGLRTEA 309 P+T+ L + ST + + M+AA +A +PTL++YV + F +GL A Sbjct: 226 QPITVALNNLVNTSTGAKEYNVDMAAAMIAGLPTLLVYVVAGKYFVRGLTAGA 278 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: 247 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: 281 Length adjustment: 26 Effective length of query: 283 Effective length of database: 255 Effective search space: 72165 Effective search space used: 72165 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