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 8502259 DvMF_2969 ABC transporter related (RefSeq)
Query= TCDB::Q00752 (377 letters) >FitnessBrowser__Miya:8502259 Length = 418 Score = 198 bits (503), Expect = 3e-55 Identities = 100/245 (40%), Positives = 153/245 (62%), Gaps = 12/245 (4%) Query: 3 ELNLNHIYKKYPNSSHYSVEDFDLDIKNKEFIVFVGPSGCGKSTTLRMVAGLEDITKGEL 62 +L++ + K++ + +V D +++ F +GPSGCGK+T LRM+AG E G + Sbjct: 28 DLSVTRLVKRFEKFT--AVNDVSFEVEQGRFFSILGPSGCGKTTLLRMIAGFESPDSGVI 85 Query: 63 KIDGEVVNDKAPKDRDIAMVFQNYALYPHMSVYDNMAFGLKLRHYSKEAIDKRVKEAAQI 122 I G + AP R + ++FQ+ AL+P MSV +N+AFGLK R + I +RV++ + Sbjct: 86 AIRGRDMAGIAPNRRPVNLIFQHLALFPMMSVAENVAFGLKRRGMAGGEISRRVQDVLER 145 Query: 123 LGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVSMRAEIAKIH 182 +GL + + PA LSGGQ+QRVA+ R +V + V L+DEPL LD KLR M+ E+ + Sbjct: 146 VGLPGYGVKMPAQLSGGQKQRVAIARCLVLEPAVLLLDEPLGALDLKLREQMKVELKTLQ 205 Query: 183 RRIGATTIYVTHDQTEAMTLADRIVIMSSTKNEDGSGTIGRVEQVGTPQELYNRPANKFV 242 +G T +Y+THDQ+EA+ ++D + +M++ GR EQV TP+ LY RPA+ FV Sbjct: 206 AEVGTTFVYITHDQSEALVMSDHVAVMNA----------GRFEQVDTPRNLYRRPASAFV 255 Query: 243 AGFIG 247 AGF+G Sbjct: 256 AGFVG 260 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: 354 Number of extensions: 13 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: 418 Length adjustment: 31 Effective length of query: 346 Effective length of database: 387 Effective search space: 133902 Effective search space used: 133902 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