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 SMc03065 SMc03065 alpha-glucoside ABC transporter ATP-binding protein
Query= TCDB::Q00752 (377 letters) >FitnessBrowser__Smeli:SMc03065 Length = 362 Score = 319 bits (818), Expect = 7e-92 Identities = 193/380 (50%), Positives = 239/380 (62%), Gaps = 27/380 (7%) Query: 1 MVELNLNHIYKKYPNSSHYSVEDFDLDIKNKEFIVFVGPSGCGKSTTLRMVAGLEDITKG 60 M L L I K Y + + DLDIK EF+VFVGPSGCGKST LRM+AGLE+IT G Sbjct: 1 MTGLLLKDIRKSY--GAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGG 58 Query: 61 ELKIDGEVVNDKAPKDRDIAMVFQNYALYPHMSVYDNMAFGLKLRHYSKEAIDKRVKEAA 120 ++ IDGE VND P R IAMVFQ+YALYPHM+VYDNMAFG+++ SKE ID+RV+ AA Sbjct: 59 DMFIDGERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAA 118 Query: 121 QILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVSMRAEIAK 180 +L LT +L+R P LSGGQRQRVA+GRAI R+ KVFL DEPLSNLDA LRV+ R EIAK Sbjct: 119 DMLQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAK 178 Query: 181 IHRRIGATT-IYVTHDQTEAMTLADRIVIMSSTKNEDGSGTIGRVEQVGTPQELYNRPAN 239 + R+ TT IYVTHDQ EAMTLADRIV++S+ G +EQVG P ELY RPAN Sbjct: 179 LSERMSDTTMIYVTHDQVEAMTLADRIVVLSA----------GHIEQVGAPLELYERPAN 228 Query: 240 KFVAGFIGSPAMNFFDVTIKDGHLVSKDGLTIAVTEGQLKMLE---SKGFKNKNLIFGIR 296 FVA FIGSPAMN TI + +++ G+ L+ + K FG+R Sbjct: 229 LFVARFIGSPAMNVIPATI----TATGQQTAVSLAGGKSVTLDVPTNASENGKTASFGVR 284 Query: 297 PEDISSSLLVQETYPDATVDAEVVVSELLGSETMLYLK--LGQTEFAARVDARDFHEPGE 354 PED L V E D + V + E LG T+LY++ + A++ G+ Sbjct: 285 PED----LRVTEA-DDFLFEGTVSIVEALGEVTLLYIEGLVENEPIIAKMPGIARVGRGD 339 Query: 355 KVSLTFNVAKGHFFDAETEA 374 KV T + AK H FD ++ Sbjct: 340 KVRFTADKAKLHLFDTNGQS 359 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: 344 Number of extensions: 14 Number of successful extensions: 5 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: 362 Length adjustment: 30 Effective length of query: 347 Effective length of database: 332 Effective search space: 115204 Effective search space used: 115204 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