Align Oligosaccharide:H+ symporter family protein (characterized, see rationale)
to candidate BWI76_RS09125 BWI76_RS09125 MFS transporter
Query= uniprot:Q4KBP0 (429 letters) >FitnessBrowser__Koxy:BWI76_RS09125 Length = 414 Score = 322 bits (825), Expect = 1e-92 Identities = 171/409 (41%), Positives = 254/409 (62%), Gaps = 7/409 (1%) Query: 6 KREYWLISGLLFFFFFSWSSSYSLFSIWLHRVIGLNGTETGFIFAANAIAALLVQPFYGA 65 KR Y L+S F + F+WSS+ + F IW + +G++ T+TG +++ NA ALL+QPF+G Sbjct: 6 KRNYILLSLFDFLYLFAWSSTMAFFVIWTTQHLGISATKTGLLYSVNAFIALLMQPFFGF 65 Query: 66 LQDRLGLSKKLLVWIGILLCAAAPFAIYVYAGLLAQNVMLGALVGAAFLALAMLAGVGVI 125 + D+ GL K+L+ + +L PF IY+YA LL + LGAL+G +L + +G GVI Sbjct: 66 ISDKFGLKKRLIWILVAMLLPVGPFFIYLYAPLLVHSFWLGALLGGVYLGIIFNSGCGVI 125 Query: 126 ESYTERLSRHAGFEFGTTRMWGSLGWASATGVVGVVFNIDPDIAFYMSSLAGIVFLLILF 185 +SY +++SR FE+G RMWGSLGWA+A +VG + +P++AF+++S+A IV I F Sbjct: 126 DSYIDKISRRYQFEYGRVRMWGSLGWAAAAWIVGKYIDSNPNLAFWLASVA-IVIAAICF 184 Query: 186 RLDLDRLAQPAVQAGAVVHPVRLNDLWKLLALPRFWAFSLYLTGVCGIYMIYEQQFPVYF 245 L L + +Q + ++++ +L +FW ++ V IY Y+QQF YF Sbjct: 185 MLTKIELTEAEMQKSSA---LKVSHALELAKNGQFWMLLVFTLFVTQIYDTYDQQFAQYF 241 Query: 246 SSFFPTPEEGTRAYGYLNSSQVLVEAVLMLLAPWVVSRTGAKYGLILAGSIMFVRILGSG 305 S F TPEEG R YG L S QV E + + L PW V+RTGAK+ LI+AG IM VRI+GS Sbjct: 242 SLQFSTPEEGNRWYGILASIQVCGETLFLCLMPWFVNRTGAKWALIIAGLIMSVRIVGSA 301 Query: 306 LVTQAWAIAACKMLHALEVPILLVSIFKYISLNFDSRLSASIYLVGFQFAQQLTAMLLSP 365 + I A KM+HALE P++LVS+FK+I+ NFD++LS+++YL+ F + + SP Sbjct: 302 IPLGPVWIGAVKMMHALEKPLILVSVFKFIAANFDNKLSSTVYLL-VLFVASIATAIYSP 360 Query: 366 LVGYGYDHFGFSSVYVLMAGLVGACLLLSWTLLR--KDPVRDASQVGAG 412 L GY YD GF+ Y ++ G+ G L+S LR ++P + GAG Sbjct: 361 LAGYLYDTIGFAHTYYILGGIAGLFTLISVFTLRDNREPTAPGAAPGAG 409 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: 509 Number of extensions: 30 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: 429 Length of database: 414 Length adjustment: 32 Effective length of query: 397 Effective length of database: 382 Effective search space: 151654 Effective search space used: 151654 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