Align Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate WP_078429421.1 BK574_RS17060 ABC transporter ATP-binding protein
Query= SwissProt::Q9YGA6 (372 letters) >NCBI__GCF_002019605.1:WP_078429421.1 Length = 351 Score = 234 bits (596), Expect = 4e-66 Identities = 120/243 (49%), Positives = 168/243 (69%), Gaps = 6/243 (2%) Query: 1 MAGVRLVDVWKVFGEVT--AVREMSLEVKDGEFMILLGPSGCGKTTTLRMIAGLEEPSRG 58 M+ ++ +V K + AV +++LE+ +GE + LLGPSGCGKTTTLRM+AG E+P+ G Sbjct: 1 MSFIQFDNVTKYYNRAATPAVDQLNLEILEGEIITLLGPSGCGKTTTLRMLAGFEQPTTG 60 Query: 59 QIYIGDKLVADPEKGIFVPPKDRDIAMVFQSYALYPHMTVYDNIAFPLKLRKVPRQEIDQ 118 +I IGD++V D + + PP+ R I MVFQ YAL+PH+T+ N+ F L K ++ + Sbjct: 61 KIRIGDEVVYDDRRAL--PPEKRGIGMVFQDYALFPHLTIEKNVTFGLNRWK--NRDKKK 116 Query: 119 RVREVAELLGLTELLNRKPRELSGGQRQRVALGRAIVRKPQVFLMDEPLSNLDAKLRVRM 178 R +EV EL+GL E +R P ELSGGQ+QRVAL RA+ +P+V LMDEP SNLDA LR +M Sbjct: 117 RAQEVLELVGLGEFGHRLPSELSGGQQQRVALARALAPRPKVILMDEPFSNLDAGLREKM 176 Query: 179 RAELKKLQRQLGVTTIYVTHDQVEAMTMGDRIAVMNRGVLQQVGSPDEVYDKPANTFVAG 238 R ++ + R+ T I VTHDQ +A + DR+ VMN G++QQ+ +P E+Y PAN FVA Sbjct: 177 RYDVTNILRKANATAIIVTHDQKDAFAVSDRVVVMNEGIIQQIAAPKEMYRCPANCFVAQ 236 Query: 239 FIG 241 F+G Sbjct: 237 FVG 239 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: 355 Number of extensions: 11 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: 351 Length adjustment: 29 Effective length of query: 343 Effective length of database: 322 Effective search space: 110446 Effective search space used: 110446 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: 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