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 Echvi_1022 Echvi_1022 ABC-type spermidine/putrescine transport systems, ATPase components
Query= TCDB::Q00752 (377 letters) >FitnessBrowser__Cola:Echvi_1022 Length = 345 Score = 152 bits (385), Expect = 1e-41 Identities = 84/248 (33%), Positives = 137/248 (55%), Gaps = 17/248 (6%) Query: 4 LNLNHIYKKYPNSSHYSVEDFDLDIKNKEFIVFVGPSGCGKSTTLRMVAGLEDITKGELK 63 L L+ I KK+P + ++V+D ++I+ VG +G GK+T L+++AGLE KGE+ Sbjct: 4 LQLHGISKKFPQTKQFAVKDIHMEIEEGSVQAIVGENGSGKTTLLKLIAGLEHPDKGEIV 63 Query: 64 IDGE-VVNDKAP---KDRDIAMVFQNYALYPHMSVYDNMAFGLKLRHYSKEAIDKRVKEA 119 G+ +VN K+ R++ ++FQ YAL+P M++ +N+ L H + ++ Sbjct: 64 FSGQTIVNGKSALPANQREVGVIFQEYALFPQMTLLENVREAL---HQESRNARQIAMDS 120 Query: 120 AQILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVSMRAEIA 179 + GL + P LS GQRQR A+ RA+ K+ L+D+P +LD + + + +I Sbjct: 121 LALAGLEDSFSAYPHQLSSGQRQRAALARALASRPKLLLLDDPFRSLDTRFKNEISEDIR 180 Query: 180 KIHRRIGATTIYVTHDQTEAMTLADRIVIMSSTKNEDGSGTIGRVEQVGTPQELYNRPAN 239 I + G T I +H +A++LAD I I+ G ++QVGTP E+Y +PAN Sbjct: 181 DIVKATGITAIVASHHAKDALSLADSIAILHK----------GILQQVGTPVEIYKKPAN 230 Query: 240 KFVAGFIG 247 +VA F G Sbjct: 231 AYVANFFG 238 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: 274 Number of extensions: 11 Number of successful extensions: 4 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: 345 Length adjustment: 29 Effective length of query: 348 Effective length of database: 316 Effective search space: 109968 Effective search space used: 109968 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: 49 (23.5 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