Align Fructose import permease protein FruG (characterized)
to candidate BWI76_RS14865 BWI76_RS14865 ribose ABC transporter permease
Query= SwissProt::Q8G845 (340 letters) >FitnessBrowser__Koxy:BWI76_RS14865 Length = 339 Score = 176 bits (447), Expect = 6e-49 Identities = 107/300 (35%), Positives = 166/300 (55%), Gaps = 11/300 (3%) Query: 29 VVIFILMIIMGQALFGTYIRLGFISSLFIDHAYLIILAVAMTLPILTGGIDLSVGAIVAI 88 +V+ +L+I+M + R+ + ++ + ILA MT ILT GIDLSVG+IVA+ Sbjct: 29 IVLLVLLILMS-TFAPNFNRVDNLLNIARSISVNAILAAGMTFVILTSGIDLSVGSIVAV 87 Query: 89 TAVVGLKLANAGVPAFLVMIIMLLIGAVFGLLAGTLIEEFNMQPFIATLSTMFLARGLAS 148 + VV + A AG+PA L ++ + +GA+ GLL G L + PFI TL TM RG+A Sbjct: 88 SGVVSVVAAMAGIPAPLAILAGVGVGALCGLLNGVLTAYLALAPFIVTLGTMTFLRGMAY 147 Query: 149 IISTDSLTFPQGNDFSFISNVIKIIDNPKISNDLSFNVGVIIALVVVVFGYVFLHHTRTG 208 I+ F + N I + VII LVV + + L TR G Sbjct: 148 TITEGQPIVSSSLSFRELGNGYLI----------GIPIPVIIMLVVYLLAWFILERTRFG 197 Query: 209 RTIYAIGGSRSSAELMGLPVKRTQYIIYLTSATLAALASIVYTANIGSAKNTVGVGWELD 268 R IYA+GG+ +A L G+ VKR +Y+ + A LA I++ A + SA+ T G G+ELD Sbjct: 198 RHIYAVGGNAQAARLAGVRVKRVLAAVYMIAGVCAGLAGIIFAARVISAQPTAGTGYELD 257 Query: 269 AVASVVIGGTIITGGFGYVLGSVLGSLVRSILDPLTSDFGVPAEWTTIVIGLMILVFVVL 328 A+A+VV+GGT + GG G ++G+++GS++ +L VP ++ G++I++ V + Sbjct: 258 AIAAVVLGGTSLAGGRGRIIGTLIGSIILGVLSTGLILLSVPFFTQLLIKGIVIILAVAI 317 Lambda K H 0.327 0.142 0.400 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: 279 Number of extensions: 17 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 340 Length of database: 339 Length adjustment: 28 Effective length of query: 312 Effective length of database: 311 Effective search space: 97032 Effective search space used: 97032 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: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. 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