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_017177065.1 A1QA_RS0100960 ATP-binding cassette domain-containing protein
Query= TCDB::Q8DT25 (377 letters) >NCBI__GCF_000295095.1:WP_017177065.1 Length = 299 Score = 138 bits (347), Expect = 2e-37 Identities = 89/258 (34%), Positives = 134/258 (51%), Gaps = 23/258 (8%) Query: 4 LKLDNIYKRYP-----------NAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIA 52 ++ D++ KRYP A +V+ F+ I V +G SG GK+T +RM+ Sbjct: 5 IEFDSVTKRYPVPRRAKRQGTGTAAGPAVDAFSATIAPGTTTVLLGSSGSGKTTLMRMVN 64 Query: 53 GLEDITEGNLYID--DKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKD 110 + + + G + ID D D R I V QN L PH V +N+ +L + Sbjct: 65 RMVEPSSGRVLIDGEDVAGRDPVALRRSIGYVMQNGGLLPHRRVIDNITLVPRLNGTGRA 124 Query: 111 DINKRVHEAAEILGLTEFL-ERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAK 169 R HE +ILGL L ER P +LSGGQ QRV + RA+ D + LMDEP +D Sbjct: 125 QAAHRAHELMDILGLDPALAERYPHELSGGQAQRVGVARALAADPAILLMDEPFGAVDPL 184 Query: 170 LRVAMRAEIAKIHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGT 229 +R ++AE A++ R +G T ++VTHD EA+ L D I+++ + G+ RI Q G+ Sbjct: 185 VRRELQAETARLQRELGKTILFVTHDVDEALALGDEIIVL-------REGA--RIAQRGS 235 Query: 230 PQELYNEPANKFVAGFIG 247 ++ + PA+ FV F+G Sbjct: 236 GPQILHHPADAFVERFLG 253 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: 235 Number of extensions: 13 Number of successful extensions: 4 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: 299 Length adjustment: 28 Effective length of query: 349 Effective length of database: 271 Effective search space: 94579 Effective search space used: 94579 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: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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