Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate BWI76_RS07245 BWI76_RS07245 ABC transporter
Query= uniprot:D8J112 (347 letters) >FitnessBrowser__Koxy:BWI76_RS07245 Length = 343 Score = 199 bits (506), Expect = 9e-56 Identities = 116/324 (35%), Positives = 186/324 (57%), Gaps = 30/324 (9%) Query: 40 FASLLLMILFFSFAS------PNFMEVDNLVSILQSTAVNGVLAIACTYVIITSGIDLSV 93 F +L++ L F A + + L+ I+ A+ G++A+ T VIIT+GIDLS Sbjct: 32 FIVMLVIALTFEIAGWYVRDQSFLLNTNRLILIVLQVAIIGIIAVGVTQVIITTGIDLSS 91 Query: 94 GTMMTFCAVMAGVVLTNW-----------GMPLPLGIAAAIFFGALSGWISGMVIAKLKV 142 G+++ AV+A + MP + I A I G L G +G ++ + + Sbjct: 92 GSVIALAAVVAASLAQTSDSLSPMFPSLVNMPAIIPIGAGIGVGLLCGLTNGFLVTRTGI 151 Query: 143 PPFIATLGMMMLLKGLSLVISGTRPIYFNDTEGFSAIAQDSLIGDLIPSLPIPNAVLILF 202 PPFIATLGMM+ +GL+ + PI F ++ F+AI Q ++ V+I F Sbjct: 152 PPFIATLGMMVSARGLAQYYTQGNPISFL-SDSFTAIGQGAM------------PVIIFF 198 Query: 203 LVAIGASIILNKTVFGRYTFALGSNEEALRLSGVKVDFWKVAVYTFSGAICGIAGLIIAS 262 +VA I L T +G+Y +A+G N + ++SG+ V+ + V VY +GA+ G+AG+++A+ Sbjct: 199 VVAAVFHIALKHTRYGKYVYAIGGNMTSAKVSGINVNKYLVIVYAIAGALSGLAGVVLAA 258 Query: 263 RLNSAQPALGQGYELDAIAAVVIGGTSLSGGTGTILGTIIGAFIMSVLVNGLRIMSVAQE 322 R++S Q ++G YELDAIAA VIGG+SL GG G I GT+IGA I+ ++ +G + V Sbjct: 259 RVSSGQSSMGMSYELDAIAAAVIGGSSLMGGVGRITGTLIGAMILGLIKSGFTFVGVDAY 318 Query: 323 WQTVVTGVIIILAVYLDILRRRRR 346 Q ++ G+II+ AV +D+ R R++ Sbjct: 319 VQDIIKGIIIVAAVTIDMRRNRKK 342 Lambda K H 0.326 0.139 0.398 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: 274 Number of extensions: 12 Number of successful extensions: 4 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: 347 Length of database: 343 Length adjustment: 29 Effective length of query: 318 Effective length of database: 314 Effective search space: 99852 Effective search space used: 99852 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 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