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 N515DRAFT_1821 N515DRAFT_1821 putative ABC transport system ATP-binding protein
Query= TCDB::Q00752 (377 letters) >FitnessBrowser__Dyella79:N515DRAFT_1821 Length = 238 Score = 131 bits (329), Expect = 2e-35 Identities = 80/212 (37%), Positives = 117/212 (55%), Gaps = 10/212 (4%) Query: 4 LNLNHIYKKYPNS--SHYSVEDFDLDIKNKEFIVFVGPSGCGKSTTLRMVAGLEDITKGE 61 L + H+ K Y Y++ DF++D+K EF+ GPSG GK+T L + LE T GE Sbjct: 2 LKMTHLSKVYRTEVVETYALRDFNIDVKEGEFVAVTGPSGSGKTTFLTIAGLLETFTGGE 61 Query: 62 LKIDGEVV---NDKAP---KDRDIAMVFQNYALYPHMSVYDNMAFGLKLRHYSKEAIDKR 115 +DG V ND A ++ I +FQ + L P ++VYDN+ L+ R +R Sbjct: 62 YHLDGVEVSNLNDNARSKIRNEKIGFIFQAFNLIPDLNVYDNVEVPLRYRGMKALERKQR 121 Query: 116 VKEAAQILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVSMR 175 + +A + +GL + PA+LSGGQ+QRVA+ RA+ ++ L DEP NLD ++ + Sbjct: 122 IMDALERVGLASRAKHYPAELSGGQQQRVAIARALAGSPRLLLADEPTGNLDTQMARGVM 181 Query: 176 AEIAKIHRRIGATTIYVTHDQTEAMTLADRIV 207 + +IHR GAT + VTHD E T A R V Sbjct: 182 ELLEEIHRE-GATIVMVTHD-PELATRAQRNV 211 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: 211 Number of extensions: 10 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: 238 Length adjustment: 27 Effective length of query: 350 Effective length of database: 211 Effective search space: 73850 Effective search space used: 73850 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 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