Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate BWI76_RS00280 BWI76_RS00280 ribose ABC transporter permease
Query= uniprot:D8IZC8 (344 letters) >FitnessBrowser__Koxy:BWI76_RS00280 Length = 321 Score = 239 bits (609), Expect = 9e-68 Identities = 133/322 (41%), Positives = 198/322 (61%), Gaps = 21/322 (6%) Query: 24 TAQWLLHRLGMLPVLVVLYLLFYGLTLYLSGDGTSNFASAENTMNILRQVAINLVLAAGM 83 T WL+ + ++ +LV++ ++ + NF + N NIL+Q ++N ++A GM Sbjct: 13 TKAWLMEQKSLIALLVLIAIV---------STMSPNFFTVNNLFNILQQTSVNAIMAVGM 63 Query: 84 TFVILTAGIDLSVGSVLAVS-----AVLGMQVSLGAAPGWAIPMFIFSGLVMGMVNGAMV 138 T VILT+GIDLSVGS+LA++ +++G++V+ A A+ + G +G V G +V Sbjct: 64 TLVILTSGIDLSVGSLLALTGAVAASIVGIEVNALVAVAAALAL----GAAIGAVTGVIV 119 Query: 139 ALLNINAFVVTLGTMTAFRGAAYLLADGTTV---LNNDIPSFEWIGNGDFLHVPWLIWVA 195 A + AF+ TL M RG + +G+ V ++ F W G G L +P +W+ Sbjct: 120 AKGRVQAFIATLVMMLLLRGVTMVYTNGSPVNTGFTDNADLFGWFGIGRPLGIPTPVWIM 179 Query: 196 VAVVLLSWVILRKTVLGMHIYAIGGNLQAARLTGIRVGLVLLFVYSISGLFSGLAGAMSA 255 V L +W +L T LG +IYA+GGN A RL+GI V V + VYS+ G+ + LAG + Sbjct: 180 AIVFLAAWYMLHHTRLGRYIYALGGNEAATRLSGISVNKVKIIVYSLCGMLASLAGIIEV 239 Query: 256 SRLYGANGNWGSGYELDAIAAVVLGGTSLMGGVGSIWGTVVGALIIGVMNNGLTILGLSS 315 +RL A G+GYELDAIAAVVLGGTSL GG G I GT++GALI+G +NNGL +LG+SS Sbjct: 240 ARLSSAQPTAGTGYELDAIAAVVLGGTSLAGGKGRIVGTLIGALILGFLNNGLNLLGVSS 299 Query: 316 FWQYVAKGAVIVLAVILDKWRQ 337 ++Q + K VI+LAV++D +Q Sbjct: 300 YYQMIVKAVVILLAVLVDNKKQ 321 Lambda K H 0.324 0.138 0.417 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: 297 Number of extensions: 16 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: 344 Length of database: 321 Length adjustment: 28 Effective length of query: 316 Effective length of database: 293 Effective search space: 92588 Effective search space used: 92588 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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