Align Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate WP_028488909.1 Q394_RS0108480 spermidine/putrescine ABC transporter ATP-binding protein PotA
Query= SwissProt::P19566 (369 letters) >NCBI__GCF_000621325.1:WP_028488909.1 Length = 369 Score = 218 bits (554), Expect = 3e-61 Identities = 109/230 (47%), Positives = 153/230 (66%) Query: 6 LRNVTKAWGDVVVSKDINLDIHDGEFVVFVGPSGCGKSTLLRMIAGLETITSGDLFIGET 65 L N++K + V D NL I DGEF +GPSGCGK+T+LR+IAG E G + + Sbjct: 9 LSNISKRFASQEVLSDFNLTIQDGEFFTILGPSGCGKTTVLRLIAGFEQPNEGQILLNGD 68 Query: 66 RMNDIPPAERGVGMVFQSYALYPHLSVAENMSFGLKLAGAKKEVMNQRVNQVAEVLQLAH 125 + IP +R VFQSYAL+PHL+V +N++FGLK+AG + + RV +++L+ Sbjct: 69 DIARIPAEKRPFNTVFQSYALFPHLTVFDNVAFGLKMAGVDVQDIAVRVADALAIVRLSE 128 Query: 126 LLERKPKALSGGQRQRVAIGRTLVAEPRVFLLDEPLSNLDAALRVQMRIEISRLHKRLGR 185 RKP LSGGQ+QRVAI R +V P++ LLDE LS LD LR QM++E+ +L ++LG Sbjct: 129 FATRKPHQLSGGQKQRVAIARAVVNRPKILLLDESLSALDYKLRQQMQLELKQLQRQLGI 188 Query: 186 TMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGFIG 235 T +YVTHDQ EA++++D+I+V+ G+ QVG P E+Y P + FVA FIG Sbjct: 189 TFVYVTHDQEEALSMSDRILVMHNGQAQQVGTPREIYESPRNLFVAQFIG 238 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: 303 Number of extensions: 7 Number of successful extensions: 1 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: 369 Length adjustment: 30 Effective length of query: 339 Effective length of database: 339 Effective search space: 114921 Effective search space used: 114921 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