Align Oligosaccharide:H+ symporter family protein (characterized, see rationale)
to candidate BWI76_RS02760 BWI76_RS02760 MFS transporter
Query= uniprot:Q4KBP0 (429 letters) >FitnessBrowser__Koxy:BWI76_RS02760 Length = 410 Score = 311 bits (798), Expect = 2e-89 Identities = 150/396 (37%), Positives = 242/396 (61%), Gaps = 1/396 (0%) Query: 5 AKREYWLISGLLFFFFFSWSSSYSLFSIWLHRVIGLNGTETGFIFAANAIAALLVQPFYG 64 + + Y++ FFF W Y S+WL IG+N T+ G +++ A+ A+ VQP +G Sbjct: 4 SNKNYYISCLFFLFFFIGWGCCYPYLSLWLTETIGINYTDVGLVYSFTAVIAVCVQPLFG 63 Query: 65 ALQDRLGLSKKLLVWIGILLCAAAPFAIYVYAGLLAQNVMLGALVGAAFLALAMLAGVGV 124 + DRL K L+ + I++ AP+ IYV+A LL NV LGAL G ++ +A AG G+ Sbjct: 64 FISDRLVYRKNLMWMLAIIITLFAPYWIYVFAPLLKVNVFLGALAGGIYIGMAYGAGCGI 123 Query: 125 IESYTERLSRHAGFEFGTTRMWGSLGWASATGVVGVVFNIDPDIAFYMSSLAGIVFLLIL 184 E+Y +++SR +GFEFG RM+G +G A T G ++ ID ++ F+++S AG+ L+I+ Sbjct: 124 CEAYIDKVSRASGFEFGRARMFGGIGAAIGTFAAGKLYGIDQNMIFWLASCAGVCLLVIV 183 Query: 185 FRLDLDRLAQPAVQAGAVVHPVRLNDLWKLLALPRFWAFSLYLTGVCGIYMIYEQQFPVY 244 +++ + Q A+Q+ PV L+D LL + +FW F++Y GV +Y Y+QQF +Y Sbjct: 184 WKMQISAHKQDAMQSRKA-SPVTLSDAASLLKMKKFWFFAIYTIGVGAVYETYDQQFAIY 242 Query: 245 FSSFFPTPEEGTRAYGYLNSSQVLVEAVLMLLAPWVVSRTGAKYGLILAGSIMFVRILGS 304 +S FF + G +GYL + Q+ ++AV+M APW V++ G K L+ G IM +RI+GS Sbjct: 243 YSHFFESKARGAEVFGYLTTGQIFLDAVVMFFAPWFVNKIGPKNALLYCGMIMSLRIIGS 302 Query: 305 GLVTQAWAIAACKMLHALEVPILLVSIFKYISLNFDSRLSASIYLVGFQFAQQLTAMLLS 364 +I+ K+LH E +LLV+ KYI+ NF+ LSA++YL+GFQF++ +++ LS Sbjct: 303 AWAMGPVSISLIKLLHGFESSVLLVAALKYITANFNPLLSATVYLIGFQFSKSFSSIFLS 362 Query: 365 PLVGYGYDHFGFSSVYVLMAGLVGACLLLSWTLLRK 400 +G+ Y GF+S Y+++ G+ L+S+ L K Sbjct: 363 TGIGHMYQSMGFTSSYIVLGGIALCFTLISFITLDK 398 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: 454 Number of extensions: 24 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: 410 Length adjustment: 32 Effective length of query: 397 Effective length of database: 378 Effective search space: 150066 Effective search space used: 150066 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: 50 (23.9 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