Align Xylose/arabinose import permease protein XacI (characterized, see rationale)
to candidate BPHYT_RS05035 BPHYT_RS05035 sugar ABC transporter permease
Query= uniprot:D4GP37 (309 letters) >FitnessBrowser__BFirm:BPHYT_RS05035 Length = 285 Score = 152 bits (384), Expect = 9e-42 Identities = 96/304 (31%), Positives = 154/304 (50%), Gaps = 39/304 (12%) Query: 19 VNLRRVAQYALVVFFLGFFLVPLETGIMTAIKTNESVARSLPFAPPVGEGFTLGNIQFAL 78 + + R YA + F +FL PL + T+ K + + PP T I + Sbjct: 5 MTISRAVIYAALFLFALYFLFPLYVMLSTSFKDIDQLRTGNLLTPP-----THWTIDPWI 59 Query: 79 EQLSGS------------FFNSLIMSIPATIGSVLFGSMAAYGLTMVNWRAQMGMLMLFV 126 + SG+ F NS+ M IPA + S + G+ Y LT +R + + + Sbjct: 60 KAWSGACTGVRCDGMQPFFMNSVRMVIPAVLISSIIGAFNGYVLTHWRFRGADPIFTMIL 119 Query: 127 VGVFVPYQAVLVPLARFWNNIFPLARMIEPMVASIPFFQGYHAELVPLVITHIAYGIPIC 186 VG F+P+QA+L+P+ARF F G LV+ H+ YGI Sbjct: 120 VGCFIPFQAILLPMARFEG------------------FLGLSNTTTGLVVVHVIYGIAFT 161 Query: 187 TILFRSYYQSLPNSLVEAGKIDGASITKIYRRIILPISKPMFGVVFIYQFTQIYNEFLFA 246 T+ FR++Y S+P LV+A +IDGA I+ +I+LP+S P+F V I+QFTQI+N+FLF Sbjct: 162 TMFFRNFYVSIPAELVKAARIDGAGFFTIFTKILLPVSLPIFMVCLIWQFTQIWNDFLFG 221 Query: 247 FTLVTGSDAPAAPVTLVLPAIGASTSGI-NFGIRMSAAFLAAVPTLILYVAFAEQFAKGL 305 + S + P+T+ L + +++G+ + + M+ A +AA+PTL++Y+ F +GL Sbjct: 222 ---IVFSGVDSMPITVALNNLVNTSTGVKEYNVDMAGAIIAALPTLLVYIIAGRYFVRGL 278 Query: 306 RTEA 309 A Sbjct: 279 TAGA 282 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: 258 Number of extensions: 14 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: 285 Length adjustment: 26 Effective length of query: 283 Effective length of database: 259 Effective search space: 73297 Effective search space used: 73297 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