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 GFF5028 PS417_25760 spermidine/putrescine ABC transporter ATP-binding protein
Query= TCDB::Q8DT25 (377 letters) >FitnessBrowser__WCS417:GFF5028 Length = 370 Score = 228 bits (580), Expect = 3e-64 Identities = 127/294 (43%), Positives = 181/294 (61%), Gaps = 16/294 (5%) Query: 9 IYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEGNLYIDDKL 68 + K Y + ++ V++ NL+I EF+ +GPSG GK+T+L M+AG E T G + + + Sbjct: 16 VQKSY-DGENLIVKDLNLEIRKGEFLTLLGPSGSGKTTSLMMLAGFETPTAGEIQLAGRS 74 Query: 69 MNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAAEILGLTEF 128 +N+ P RDI MVFQNYAL+PHM+V EN+AF L +R K DI++RV ++ L F Sbjct: 75 INNVPPHKRDIGMVFQNYALFPHMTVAENLAFPLSVRALSKTDISERVKRVLSMVQLDAF 134 Query: 129 LERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAKIHRRIGAT 188 +R PA LSGGQ+QRVA+ RA+V + ++ LMDEPL LD +LR M+ EI +H+R+G T Sbjct: 135 AQRYPAQLSGGQQQRVALARALVFEPQLVLMDEPLGALDKQLREHMQMEIKHLHQRLGVT 194 Query: 189 TIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANKFVAGFIG- 247 +YVTHDQ EA+T++DR+ + G I+QI P+ LY EP N FVA FIG Sbjct: 195 VVYVTHDQGEALTMSDRVAVFHQ----------GEIQQIAAPRTLYEEPKNTFVANFIGE 244 Query: 248 SPAMNFFEVTVEKERLVNQDGLSLALPQGQEKILEEKGYLGKKVTLGIRPEDIS 301 + +N + ER V + LA + E + G +G VTL +RPE +S Sbjct: 245 NNRLNGRLHSHSGERCV----VELARGEKVEALAVNVGQVGGPVTLSVRPERVS 294 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: 293 Number of extensions: 13 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: 377 Length of database: 370 Length adjustment: 30 Effective length of query: 347 Effective length of database: 340 Effective search space: 117980 Effective search space used: 117980 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: 50 (23.9 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