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 AZOBR_RS30410 AZOBR_RS30410 ABC transporter ATP-binding protein
Query= TCDB::Q00752 (377 letters) >FitnessBrowser__azobra:AZOBR_RS30410 Length = 371 Score = 241 bits (615), Expect = 2e-68 Identities = 128/260 (49%), Positives = 171/260 (65%), Gaps = 17/260 (6%) Query: 17 SHYSVEDFDLDIKNKEFIVFVGPSGCGKSTTLRMVAGLEDITKGELKIDGEVVNDKAPKD 76 SH ++D LDIK EF F+GPSGCGK+T LR++AG +G + I G ++ Sbjct: 30 SHRVLKDIHLDIKPGEFFAFLGPSGCGKTTLLRLIAGFNTAQRGAVTIGGRDISGLPAHK 89 Query: 77 RDIAMVFQNYALYPHMSVYDNMAFGLKLRHYSKEAIDKRVKEAAQILGLTEFLERKPADL 136 RD+ MVFQ+YAL+PHM+V N+AFGL+ R + I++RV A ++GL +R+P+ L Sbjct: 90 RDVGMVFQSYALWPHMTVRRNVAFGLEERRVPRAEIERRVDAALDLVGLKHLADRRPSQL 149 Query: 137 SGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVSMRAEIAKIHRRIGATTIYVTHDQ 196 SGGQ+QRVA+ R IV + KV L+DEPLSNLDAKLRV MR E+ + R++G TTI+VTHDQ Sbjct: 150 SGGQQQRVALARTIVIEPKVLLLDEPLSNLDAKLRVQMRQELLSLQRKLGLTTIFVTHDQ 209 Query: 197 TEAMTLADRIVIMSSTKNEDGSGTIGRVEQVGTPQELYNRPANKFVAGFIGSPAMNFFDV 256 EA T+ DRI +M EDG V+QVGTPQELY+ PAN FVAGF+G+ Sbjct: 210 EEANTICDRIAVM-----EDGI-----VQQVGTPQELYDHPANLFVAGFLGT-------A 252 Query: 257 TIKDGHLVSKDGLTIAVTEG 276 + +G + + DG T V G Sbjct: 253 NVLEGQVRAVDGGTAFVMGG 272 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: 333 Number of extensions: 14 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: 371 Length adjustment: 30 Effective length of query: 347 Effective length of database: 341 Effective search space: 118327 Effective search space used: 118327 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 Sep 17 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