Align MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized)
to candidate CA265_RS15880 CA265_RS15880 sugar ABC transporter ATP-binding protein
Query= TCDB::Q8DT25 (377 letters) >FitnessBrowser__Pedo557:CA265_RS15880 Length = 330 Score = 134 bits (338), Expect = 3e-36 Identities = 86/282 (30%), Positives = 147/282 (52%), Gaps = 19/282 (6%) Query: 2 TTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEGN 61 T + + N+ K+Y + ++N + +I + + +G SG GKST L+ I GL EG Sbjct: 4 TIISVKNLTKQYQAEQAGGIKNVSFEIKQGDVVAIIGESGSGKSTLLKSIYGLLKTDEGE 63 Query: 62 LYIDDKLMNDAS----PKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYK-KDDINKRV 116 ++ +DK + P + + MV Q+++L + VY+N+A L K K + ++ Sbjct: 64 IFFEDKRVKGPDEQLIPGHKQMKMVTQDFSLNIYAKVYDNIASQLSNTDLKTKAEKTLQI 123 Query: 117 HEAAEILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRA 176 E IL L +K +LSGG++QRVA+ +A+V D +V L+DEP S +DA L+ +RA Sbjct: 124 MEHLRILPLQN---KKIIELSGGEQQRVAIAKAMVADTQVLLLDEPFSQVDALLKNQLRA 180 Query: 177 EIAKIHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNE 236 +I ++ G T I V+HD + + LAD+++I+ G + Q G P E+Y Sbjct: 181 DIKRVASETGVTVILVSHDPADGLFLADQLLILKN----------GELLQTGKPSEIYQH 230 Query: 237 PANKFVAGFIGSPAMNFFEVTVEKERLVNQDGLSLALPQGQE 278 P + + A +G+ A+ + EK L + + P+ E Sbjct: 231 PKHIYTAQILGN-AVVLSQADAEKIGLKTERNSVVFYPEWAE 271 Lambda K H 0.318 0.135 0.379 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: 243 Number of extensions: 14 Number of successful extensions: 4 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: 377 Length of database: 330 Length adjustment: 29 Effective length of query: 348 Effective length of database: 301 Effective search space: 104748 Effective search space used: 104748 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (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