Align MsmK aka SMU.882, component of The raffinose/stachyose transporter, MsmEFGK (MalK (3.A.1.1.27) can probably substitute for MsmK; Webb et al., 2008). This system may also transport melibiose, isomaltotriose and sucrose as well as isomaltosaccharides (characterized)
to candidate WP_035136158.1 Q763_RS16555 ABC transporter ATP-binding protein
Query= TCDB::Q00752 (377 letters) >NCBI__GCF_000769915.1:WP_035136158.1 Length = 234 Score = 120 bits (302), Expect = 3e-32 Identities = 67/186 (36%), Positives = 104/186 (55%), Gaps = 7/186 (3%) Query: 20 SVEDFDLDIKNKEFIVFVGPSGCGKSTTLRMVAGLEDITKGELKIDGEVVNDKAPKDR-- 77 ++ D +++K EF+ +G SGCGKST L +V L+ + G K+ +N + ++ Sbjct: 20 ALNDISIEVKKGEFVTIMGASGCGKSTLLNIVGLLDSASGGSYKLLDREINGLSESEKAK 79 Query: 78 ----DIAMVFQNYALYPHMSVYDNMAFGLKLRHYSKEAIDKRVKEAAQILGLTEFLERKP 133 +I VFQN+ L +SVYDN+ L + KRV+E A+ LG++ L+ P Sbjct: 80 VRKENIGFVFQNFNLIDELSVYDNIELPLIYNNVPSGERKKRVEEIAERLGISHRLKHYP 139 Query: 134 ADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVSMRAEIAKIHRRIGATTIYVT 193 LSGGQ+QR A+ RA+V + K+ L DEP NLD+K + + +H GAT + VT Sbjct: 140 QQLSGGQQQRAAVARALVNNPKIILADEPTGNLDSKNGNEVMELLTDLHAN-GATILMVT 198 Query: 194 HDQTEA 199 H + +A Sbjct: 199 HSEYDA 204 Lambda K H 0.318 0.135 0.375 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: 201 Number of extensions: 18 Number of successful extensions: 2 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: 234 Length adjustment: 26 Effective length of query: 351 Effective length of database: 208 Effective search space: 73008 Effective search space used: 73008 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: 48 (23.1 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