Align deoxynucleoside transporter, permease component 1 (characterized)
to candidate SM_b20487 SM_b20487 sugar ABC transporter permease
Query= reanno::Burk376:H281DRAFT_01115 (357 letters) >FitnessBrowser__Smeli:SM_b20487 Length = 332 Score = 170 bits (431), Expect = 4e-47 Identities = 98/292 (33%), Positives = 162/292 (55%), Gaps = 4/292 (1%) Query: 25 LVVLVATWLSRGQFVDIDNLQSMGGQLPELGLLALGIMLSMVSGNGGIDLSGVGLANLSG 84 + V++ ++ QF+ S+ QLPELGLL L ++L +++G G++L+ ANL+G Sbjct: 24 VAVVLVFGIASPQFLSAATFGSVAFQLPELGLLTLAMLLPILTG--GLNLAITFTANLAG 81 Query: 85 MVAAMLVPRLVNGDDSPVLYTSLFCAIVLMMGLLGGLLNGVVIARLRLTPILCTLGTQLL 144 + A ++ + G D+ + + +M+G G++ G+VIA R PIL +L + Sbjct: 82 LTLAWVL-KANGGADAGFGIFLVGSLLAVMVGAASGVVMGLVIAFTRAHPILVSLSMMIF 140 Query: 145 FTGFAVVISNGASVHVDYVEPLSDIGNGTVLQVPIAFCIFLAAVIVLGWLLKRSPFGLRL 204 G ++ G + + + IG+G+V +P+ +F+ V+ LL R+ G Sbjct: 141 LRGLGEFLTRGGDIS-GFPPFVGVIGHGSVAGIPVPLIVFVVCVLAWHLLLGRTKLGFNT 199 Query: 205 YLMGTNPKAAFYAGIPRARMLITTYAMCGVLASLAGLISATHTSSAKWDYGNSYLLIAIL 264 Y++G+N +A Y+GI + ++ Y + GV+ S+AG+I +S + +G SYLLI +L Sbjct: 200 YMIGSNLEATRYSGINTRKAIVLVYTLSGVMCSIAGIIMLARFNSVRIGHGESYLLITVL 259 Query: 265 IAVMGGVNPAGGHGRIICVFFAATVLQFLSSLFNLLGVSQFFGDCAWGFLLL 316 +GGVNP GG GR+I VF A VLQ LSS NL+G +Q WG LL+ Sbjct: 260 ACFLGGVNPFGGFGRVIPVFVALVVLQLLSSGLNLIGANQHLATAVWGILLV 311 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: 343 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: 357 Length of database: 332 Length adjustment: 29 Effective length of query: 328 Effective length of database: 303 Effective search space: 99384 Effective search space used: 99384 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