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 8501226 DvMF_1960 putrescine/spermidine ABC transporter ATPase protein (RefSeq)
Query= TCDB::Q00752 (377 letters) >FitnessBrowser__Miya:8501226 Length = 399 Score = 230 bits (586), Expect = 6e-65 Identities = 109/228 (47%), Positives = 160/228 (70%), Gaps = 10/228 (4%) Query: 20 SVEDFDLDIKNKEFIVFVGPSGCGKSTTLRMVAGLEDITKGELKIDGEVVNDKAPKDRDI 79 +++ DL I+N EF+ +GPSGCGK+T LR+V+G E T GE++I+G+VVN P+ R + Sbjct: 22 ALDSIDLTIRNGEFLTLLGPSGCGKTTILRLVSGFEQPTSGEVRINGQVVNRVPPEQRQV 81 Query: 80 AMVFQNYALYPHMSVYDNMAFGLKLRHYSKEAIDKRVKEAAQILGLTEFLERKPADLSGG 139 VFQNYAL+PHM+V DN+AFGLK++ + + +RV +A +++ L F +RKP LSGG Sbjct: 82 NTVFQNYALFPHMTVRDNVAFGLKMQGVAADETARRVLDALRMVHLENFADRKPRQLSGG 141 Query: 140 QRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVSMRAEIAKIHRRIGATTIYVTHDQTEA 199 Q+QRVA+ RA++ + V L+DEP S LD KLR M+ EI + R++G T ++VTHDQ EA Sbjct: 142 QQQRVAIARAVINNPLVLLLDEPFSALDFKLRKQMQLEIKHLQRQLGITFVFVTHDQEEA 201 Query: 200 MTLADRIVIMSSTKNEDGSGTIGRVEQVGTPQELYNRPANKFVAGFIG 247 ++DR+V+M+ GR+EQ+G P+E+Y PAN +VA F+G Sbjct: 202 FAMSDRVVVMNE----------GRIEQIGAPKEIYEEPANMYVARFVG 239 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: 350 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: 399 Length adjustment: 30 Effective length of query: 347 Effective length of database: 369 Effective search space: 128043 Effective search space used: 128043 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