Align Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate WP_028489030.1 Q394_RS0109195 ABC transporter ATP-binding protein
Query= SwissProt::P19566 (369 letters) >NCBI__GCF_000621325.1:WP_028489030.1 Length = 348 Score = 313 bits (802), Expect = 4e-90 Identities = 165/317 (52%), Positives = 210/317 (66%), Gaps = 24/317 (7%) Query: 1 MASVQLRNVTKAWGDVVVSKDINLDIHDGEFVVFVGPSGCGKSTLLRMIAGLETITSGDL 60 MA ++L+NV K +G + K ++L+I GEF+VFVGPSGCGKSTLLRMIAGLE I G L Sbjct: 1 MAFLELKNVDKYYGKLHAIKQVSLEIQSGEFIVFVGPSGCGKSTLLRMIAGLEVINGGQL 60 Query: 61 FIGETRMNDIPPAERGVGMVFQSYALYPHLSVAENMSFGLKLAGAKKEVMNQRVNQVAEV 120 + + ++PP++R + MVFQSYALYPH++V ENMSF L+LA ++ ++V A+ Sbjct: 61 ILDGRDITEVPPSQRDLAMVFQSYALYPHMTVEENMSFALRLAKVDPAIIQEKVKMAADK 120 Query: 121 LQLAHLLERKPKALSGGQRQRVAIGRTLVAEPRVFLLDEPLSNLDAALRVQMRIEISRLH 180 L L L+R PKALSGGQRQRVAIGR++V P+VFL DEPLSNLDAALR R+EI+ LH Sbjct: 121 LNLTAYLQRTPKALSGGQRQRVAIGRSIVRSPKVFLFDEPLSNLDAALRGNTRVEIASLH 180 Query: 181 KRLGRTMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGFIGSPKMN 240 + LG T +YVTHDQVEAMTLAD++VVL G + QVG PLELY P +RFVA FIG P+MN Sbjct: 181 RELGATTVYVTHDQVEAMTLADRVVVLRDGIIEQVGTPLELYDQPINRFVARFIGMPQMN 240 Query: 241 FLPVKVTATAIEQVQVELPNRQQIWLPVESRGVQVGANMSLGIRPEHLLPSDIADVTLEG 300 P + QV +GIRPEHL D L G Sbjct: 241 VAPASLFGQFPAQV------------------------AEVGIRPEHLQMVSPEDGLLAG 276 Query: 301 EVQVVEQLGHETQIHIQ 317 +V +VE LG+ET +H++ Sbjct: 277 KVVLVEALGNETLVHVR 293 Lambda K H 0.321 0.138 0.396 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: 384 Number of extensions: 15 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: 369 Length of database: 348 Length adjustment: 29 Effective length of query: 340 Effective length of database: 319 Effective search space: 108460 Effective search space used: 108460 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