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 WP_011384263.1 AMB_RS09395 ABC transporter ATP-binding protein
Query= TCDB::Q8DT25 (377 letters) >NCBI__GCF_000009985.1:WP_011384263.1 Length = 273 Score = 152 bits (383), Expect = 1e-41 Identities = 80/196 (40%), Positives = 118/196 (60%), Gaps = 3/196 (1%) Query: 18 HYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEGNLYIDDKLMNDASPKDR 77 H +VE+F+L+I EF+ +GPSGCGKST L +AG G + +D + P+ Sbjct: 29 HAAVEDFSLEIEPGEFVCLLGPSGCGKSTALNAVAGFLRPARGRVAVDGVEVTGPGPER- 87 Query: 78 DIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAAEILGLTEFLERKPADLS 137 MVFQ ++L+P +V EN+AFG +++ + + E +++GL +R PA LS Sbjct: 88 --GMVFQQHSLFPWKTVLENVAFGPRMQGKTRAEARDLAREYLDLVGLGGSAQRYPAALS 145 Query: 138 GGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAKIHRRIGATTIYVTHDQT 197 GG QRV + RA+V V LMDEP LDA+ R M+ + ++ +IG T ++VTHD Sbjct: 146 GGMAQRVGIARALVNHPSVLLMDEPFGALDAQTRSIMQESLLRLWGQIGNTVLFVTHDID 205 Query: 198 EAMTLADRIVIMSATP 213 EA+ LADR+V+MSA P Sbjct: 206 EALFLADRVVVMSAAP 221 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: 226 Number of extensions: 10 Number of successful extensions: 2 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: 273 Length adjustment: 28 Effective length of query: 349 Effective length of database: 245 Effective search space: 85505 Effective search space used: 85505 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: 48 (23.1 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