Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate BWI76_RS00280 BWI76_RS00280 ribose ABC transporter permease
Query= uniprot:D8J112 (347 letters) >FitnessBrowser__Koxy:BWI76_RS00280 Length = 321 Score = 238 bits (606), Expect = 2e-67 Identities = 136/313 (43%), Positives = 200/313 (63%), Gaps = 5/313 (1%) Query: 27 RLFNPAARQKLLAFASLLLMILFFSFASPNFMEVDNLVSILQSTAVNGVLAIACTYVIIT 86 R F A + + +LL++I S SPNF V+NL +ILQ T+VN ++A+ T VI+T Sbjct: 10 RYFTKAWLMEQKSLIALLVLIAIVSTMSPNFFTVNNLFNILQQTSVNAIMAVGMTLVILT 69 Query: 87 SGIDLSVGTMMTFCAVMAGVVLTNWGMPLPLGIAAAIFFGALSGWISGMVIAKLKVPPFI 146 SGIDLSVG+++ +A ++ L + +AAA+ GA G ++G+++AK +V FI Sbjct: 70 SGIDLSVGSLLALTGAVAASIVGIEVNAL-VAVAAALALGAAIGAVTGVIVAKGRVQAFI 128 Query: 147 ATLGMMMLLKGLSLVISGTRPIYFNDTEGFSAIAQDSLIGDLIPSLPIPNAVLILFLVAI 206 ATL MM+LL+G+++V + P+ GF+ A + L IP V I+ +V + Sbjct: 129 ATLVMMLLLRGVTMVYTNGSPV----NTGFTDNADLFGWFGIGRPLGIPTPVWIMAIVFL 184 Query: 207 GASIILNKTVFGRYTFALGSNEEALRLSGVKVDFWKVAVYTFSGAICGIAGLIIASRLNS 266 A +L+ T GRY +ALG NE A RLSG+ V+ K+ VY+ G + +AG+I +RL+S Sbjct: 185 AAWYMLHHTRLGRYIYALGGNEAATRLSGISVNKVKIIVYSLCGMLASLAGIIEVARLSS 244 Query: 267 AQPALGQGYELDAIAAVVIGGTSLSGGTGTILGTIIGAFIMSVLVNGLRIMSVAQEWQTV 326 AQP G GYELDAIAAVV+GGTSL+GG G I+GT+IGA I+ L NGL ++ V+ +Q + Sbjct: 245 AQPTAGTGYELDAIAAVVLGGTSLAGGKGRIVGTLIGALILGFLNNGLNLLGVSSYYQMI 304 Query: 327 VTGVIIILAVYLD 339 V V+I+LAV +D Sbjct: 305 VKAVVILLAVLVD 317 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: 256 Number of extensions: 13 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: 347 Length of database: 321 Length adjustment: 28 Effective length of query: 319 Effective length of database: 293 Effective search space: 93467 Effective search space used: 93467 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