Align deoxynucleoside transporter, permease component 1 (characterized)
to candidate BWI76_RS00280 BWI76_RS00280 ribose ABC transporter permease
Query= reanno::Burk376:H281DRAFT_01115 (357 letters) >FitnessBrowser__Koxy:BWI76_RS00280 Length = 321 Score = 135 bits (339), Expect = 2e-36 Identities = 97/304 (31%), Positives = 155/304 (50%), Gaps = 15/304 (4%) Query: 19 LLIVNVLVVLVATWLSRGQFVDIDNLQSMGGQLPELGLLALGIMLSMVSGNGGIDLSGVG 78 L+ + VL+ +V+T F ++NL ++ Q ++A+G+ L +++ GIDLS Sbjct: 23 LIALLVLIAIVSTMSPN--FFTVNNLFNILQQTSVNAIMAVGMTLVILTS--GIDLSVGS 78 Query: 79 LANLSGMVAAMLVPRLVNGDDSPVLYTSLFCAIVLMMGLLGGLLNGVVIARLRLTPILCT 138 L L+G VAA +V VN + A L +G G + GV++A+ R+ + T Sbjct: 79 LLALTGAVAASIVGIEVNA--------LVAVAAALALGAAIGAVTGVIVAKGRVQAFIAT 130 Query: 139 LGTQLLFTGFAVVISNGASVHV---DYVEPLSDIGNGTVLQVPIAFCIFLAAVIVLGWLL 195 L LL G +V +NG+ V+ D + G G L +P I + ++L Sbjct: 131 LVMMLLLRGVTMVYTNGSPVNTGFTDNADLFGWFGIGRPLGIPTPVWIMAIVFLAAWYML 190 Query: 196 KRSPFGLRLYLMGTNPKAAFYAGIPRARMLITTYAMCGVLASLAGLISATHTSSAKWDYG 255 + G +Y +G N A +GI ++ I Y++CG+LASLAG+I SSA+ G Sbjct: 191 HHTRLGRYIYALGGNEAATRLSGISVNKVKIIVYSLCGMLASLAGIIEVARLSSAQPTAG 250 Query: 256 NSYLLIAILIAVMGGVNPAGGHGRIICVFFAATVLQFLSSLFNLLGVSQFFGDCAWGFLL 315 Y L AI V+GG + AGG GRI+ A +L FL++ NLLGVS ++ ++ Sbjct: 251 TGYELDAIAAVVLGGTSLAGGKGRIVGTLIGALILGFLNNGLNLLGVSSYYQMIVKAVVI 310 Query: 316 LLSL 319 LL++ Sbjct: 311 LLAV 314 Lambda K H 0.327 0.143 0.429 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: 277 Number of extensions: 18 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: 357 Length of database: 321 Length adjustment: 28 Effective length of query: 329 Effective length of database: 293 Effective search space: 96397 Effective search space used: 96397 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