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_028488909.1 Q394_RS0108480 spermidine/putrescine ABC transporter ATP-binding protein PotA
Query= TCDB::Q8DT25 (377 letters) >NCBI__GCF_000621325.1:WP_028488909.1 Length = 369 Score = 219 bits (557), Expect = 1e-61 Identities = 126/300 (42%), Positives = 183/300 (61%), Gaps = 15/300 (5%) Query: 4 LKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEGNLY 63 L L NI KR+ A + +FNL I D EF +GPSGCGK+T LR+IAG E EG + Sbjct: 7 LTLSNISKRF--ASQEVLSDFNLTIQDGEFFTILGPSGCGKTTVLRLIAGFEQPNEGQIL 64 Query: 64 IDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAAEIL 123 ++ + + R VFQ+YAL+PH++V++N+AFGLK+ DI RV +A I+ Sbjct: 65 LNGDDIARIPAEKRPFNTVFQSYALFPHLTVFDNVAFGLKMAGVDVQDIAVRVADALAIV 124 Query: 124 GLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAKIHR 183 L+EF RKP LSGGQ+QRVA+ RA+V K+ L+DE LS LD KLR M+ E+ ++ R Sbjct: 125 RLSEFATRKPHQLSGGQKQRVAIARAVVNRPKILLLDESLSALDYKLRQQMQLELKQLQR 184 Query: 184 RIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANKFVA 243 ++G T +YVTHDQ EA++++DRI++M G+ +Q+GTP+E+Y P N FVA Sbjct: 185 QLGITFVYVTHDQEEALSMSDRILVMHN----------GQAQQVGTPREIYESPRNLFVA 234 Query: 244 GFIGSPAMNFFEVTVEKERLVNQDGLSLALPQGQEKILEEKGYLGKKVTLGIRPEDISSD 303 FIG +N F+ + + Q S+ +E + + +G KV + +RPED+ D Sbjct: 235 QFIGE--INVFDGEIVQALGEYQYEASIN-GVVREIRCDHRFAVGDKVHVMLRPEDLRID 291 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: 319 Number of extensions: 15 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: 377 Length of database: 369 Length adjustment: 30 Effective length of query: 347 Effective length of database: 339 Effective search space: 117633 Effective search space used: 117633 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: 50 (23.9 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