Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate WP_028489030.1 Q394_RS0109195 ABC transporter ATP-binding protein
Query= reanno::Smeli:SMc04256 (361 letters) >NCBI__GCF_000621325.1:WP_028489030.1 Length = 348 Score = 265 bits (677), Expect = 1e-75 Identities = 149/351 (42%), Positives = 213/351 (60%), Gaps = 32/351 (9%) Query: 1 MTSVSVRDLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQI 60 M + ++++ +G + + +++L+I GEF+V +G SGCGKSTLL IAGL ++ GQ+ Sbjct: 1 MAFLELKNVDKYYGKLHAIKQVSLEIQSGEFIVFVGPSGCGKSTLLRMIAGLEVINGGQL 60 Query: 61 FIKDRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEI 120 + R++T P R + MVFQSYALYP MTVE+N+SF L++AK+ PA I+++VK A++ Sbjct: 61 ILDGRDITEVPPSQRDLAMVFQSYALYPHMTVEENMSFALRLAKVDPAIIQEKVKMAADK 120 Query: 121 LQIQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLH 180 L + L+R P LSGGQRQRVAIGR++VR VFLFDEPLSNLDA LR RVEI LH Sbjct: 121 LNLTAYLQRTPKALSGGQRQRVAIGRSIVRSPKVFLFDEPLSNLDAALRGNTRVEIASLH 180 Query: 181 QSLKNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMN 240 + L T +YVTHDQ+EA+TLADR+ V++ G+I+Q+ P+ +Y+ P N FVA FIG P MN Sbjct: 181 RELGATTVYVTHDQVEAMTLADRVVVLRDGIIEQVGTPLELYDQPINRFVARFIGMPQMN 240 Query: 241 FFRGEVEPKDGRSFVRAGGIAFDVTAYPAHTRLQ-PGQKVVLGLRPEHVKVDEARDGEPT 299 PA Q P Q +G+RPEH+++ DG Sbjct: 241 -------------------------VAPASLFGQFPAQVAEVGIRPEHLQMVSPEDGLLA 275 Query: 300 HQAVVDIEEPMGADNLLWL----TFAGQSMSVRIAGQRRYPPGSTVRLSFD 346 + V + E +G + L+ + + + VR+ G+ G V L +D Sbjct: 276 GKVV--LVEALGNETLVHVRPDKVQLEEPLIVRLYGRTTVHVGDRVGLKWD 324 Lambda K H 0.320 0.137 0.392 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: 356 Number of extensions: 23 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 361 Length of database: 348 Length adjustment: 29 Effective length of query: 332 Effective length of database: 319 Effective search space: 105908 Effective search space used: 105908 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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