Align Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate WP_024852149.1 N745_RS0110835 ABC transporter ATP-binding protein
Query= SwissProt::Q9YGA6 (372 letters) >NCBI__GCF_000526715.1:WP_024852149.1 Length = 263 Score = 144 bits (362), Expect = 4e-39 Identities = 83/219 (37%), Positives = 127/219 (57%), Gaps = 10/219 (4%) Query: 22 MSLEVKDGEFMILLGPSGCGKTTTLRMIAGLEEPSRGQIYIGDKLVADPEKGIFVPPKDR 81 ++L + G+ ++G SGCGK+T L+MIAGL PS G + I K V P Sbjct: 28 INLNIPKGQLTAMIGRSGCGKSTLLQMIAGLLLPSDGVVRINGKTVVKPSA--------- 78 Query: 82 DIAMVFQSYALYPHMTVYDNIAFPLKLRKVPRQEIDQRVREVAELLGLTELLNRKPRELS 141 M+FQ +LYP M+V +N A L +Q+ D RV E+ +++GL+E ++ +ELS Sbjct: 79 KWNMMFQKPSLYPWMSVRENAALGLVFAGTYKQKQD-RVEELLDMVGLSEHKDKNVQELS 137 Query: 142 GGQRQRVALGRAIVRKPQVFLMDEPLSNLDAKLRVRMRAELKKLQRQLGVTTIYVTHDQV 201 GGQ+QRVAL R++ +P++ L+DEP S LDA R ++ E+ ++ + G+T I VTHD Sbjct: 138 GGQQQRVALARSLATEPEILLLDEPFSALDAFTRTALQTEVAQICHEQGITMIMVTHDIE 197 Query: 202 EAMTMGDRIAVMNRGVLQQVGSPDEVYDKPANTFVAGFI 240 EA+ M D++ +M+ + VG D P + A FI Sbjct: 198 EAIAMADKVVIMSHNPGEIVGDLDVPLTYPRDRSAADFI 236 Lambda K H 0.323 0.142 0.406 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: 216 Number of extensions: 8 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: 372 Length of database: 263 Length adjustment: 27 Effective length of query: 345 Effective length of database: 236 Effective search space: 81420 Effective search space used: 81420 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 48 (23.1 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