Align Oligosaccharide:H+ symporter family protein (characterized, see rationale)
to candidate BWI76_RS00610 BWI76_RS00610 MFS transporter
Query= uniprot:Q4KBP0 (429 letters) >FitnessBrowser__Koxy:BWI76_RS00610 Length = 421 Score = 327 bits (837), Expect = 6e-94 Identities = 160/388 (41%), Positives = 240/388 (61%), Gaps = 2/388 (0%) Query: 9 YWLISGLLFFFFFSWSSSYSLFSIWLHRVIGLNGTETGFIFAANAIAALLVQPFYGALQD 68 +W+ F +FF ++ + IWL VIGLN TETG +F++ ++ A+ QP G + D Sbjct: 14 FWIFGLFFFLYFFIMATCFPFLPIWLSDVIGLNKTETGIVFSSLSLFAICFQPILGVISD 73 Query: 69 RLGLSKKLLVWIGILLCAAAPFAIYVYAGLLAQNVMLGALVGAAFLALAMLAGVGVIESY 128 +LGL K L+ + +LL APF +YV+A LL N+ LGAL G A++ AG G +E+Y Sbjct: 74 KLGLKKHLMWIVTVLLVLIAPFFLYVFAPLLKTNIWLGALSGGAYIGFVFSAGAGAMEAY 133 Query: 129 TERLSRHAGFEFGTTRMWGSLGWASATGVVGVVFNIDPDIAFYMSSLAGIVFLLI--LFR 186 ER+SR++GFE+G R +G LGWA G++F+++P+ F+M S A +V +++ + + Sbjct: 134 IERVSRNSGFEYGKARTFGCLGWALCATTAGMLFSVNPEWVFWMGSAAALVLVVLVAIAK 193 Query: 187 LDLDRLAQPAVQAGAVVHPVRLNDLWKLLALPRFWAFSLYLTGVCGIYMIYEQQFPVYFS 246 + AQ GA V L ++ + W F LY+ GV +Y +++QQF +F Sbjct: 194 PQASQTAQVMDSLGANRSSVDLKTAVRMFRQRKMWMFILYVIGVACVYDVFDQQFATFFK 253 Query: 247 SFFPTPEEGTRAYGYLNSSQVLVEAVLMLLAPWVVSRTGAKYGLILAGSIMFVRILGSGL 306 SFF TPE GTRA+G+ ++ + A++M +PW+++R GAK L++AG +M R++GS Sbjct: 254 SFFATPESGTRAFGFATTAGEICNAIIMFSSPWIINRIGAKNTLLIAGMVMAARMIGSSF 313 Query: 307 VTQAWAIAACKMLHALEVPILLVSIFKYISLNFDSRLSASIYLVGFQFAQQLTAMLLSPL 366 T A + A KMLHALEVP LLV FKYI+ FD RLSA+IYLVGFQF++Q+ A+ LS Sbjct: 314 ATTAAEVVALKMLHALEVPFLLVGAFKYITGVFDVRLSATIYLVGFQFSKQVAAIFLSAF 373 Query: 367 VGYGYDHFGFSSVYVLMAGLVGACLLLS 394 G YD GF Y+++ G+ L+S Sbjct: 374 AGNMYDRIGFQDTYMILGGIALTVTLIS 401 Lambda K H 0.329 0.142 0.441 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: 468 Number of extensions: 18 Number of successful extensions: 2 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: 429 Length of database: 421 Length adjustment: 32 Effective length of query: 397 Effective length of database: 389 Effective search space: 154433 Effective search space used: 154433 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 (21.8 bits) S2: 51 (24.3 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