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 SMc04140 SMc04140 ABC transporter ATP-binding protein
Query= TCDB::Q00752 (377 letters) >FitnessBrowser__Smeli:SMc04140 Length = 360 Score = 315 bits (808), Expect = 1e-90 Identities = 175/357 (49%), Positives = 238/357 (66%), Gaps = 21/357 (5%) Query: 21 VEDFDLDIKNKEFIVFVGPSGCGKSTTLRMVAGLEDITKGELKIDGEVVNDKAPKDRDIA 80 + DL I EF VFVGPSGCGKST LRM+AGLE+I+ G L +D + +N+ AP R IA Sbjct: 20 IHGIDLTIDPGEFAVFVGPSGCGKSTLLRMIAGLEEISGGTLMLDSDRMNEVAPARRGIA 79 Query: 81 MVFQNYALYPHMSVYDNMAFGLKLRHYSKEAIDKRVKEAAQILGLTEFLERKPADLSGGQ 140 MVFQ+YALYPHMSVY N+AFGL+ + K I+ +V+ AA+IL + + L+RKP LSGGQ Sbjct: 80 MVFQSYALYPHMSVYKNLAFGLETAGFKKAEIEPKVRRAAEILQIEKLLDRKPKALSGGQ 139 Query: 141 RQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVSMRAEIAKIHRRIGATTIYVTHDQTEAM 200 RQRVA+GRAIVR+ ++FL DEPLSNLDA+LRV MR EI+++HR +G T IYVTHDQ EAM Sbjct: 140 RQRVAIGRAIVREPRIFLFDEPLSNLDAELRVQMRVEISRLHRDLGNTMIYVTHDQVEAM 199 Query: 201 TLADRIVIMSSTKNEDGSGTIGRVEQVGTPQELYNRPANKFVAGFIGSPAMNFFDVTIKD 260 T+AD+IV+++S GR+EQVG P +LYN P N+FVAGFIGSP MNF I D Sbjct: 200 TMADKIVVLNS----------GRIEQVGAPLDLYNNPVNRFVAGFIGSPKMNFLKARIAD 249 Query: 261 GHLVSKDGLTIAVTEGQLKMLE--SKGFKNKNLIFGIRPEDISSSLLVQETYPDATVDAE 318 V+ I V G +++ + + +++ FGIRPE +S+ + ATV+ E Sbjct: 250 ---VTGSETAIEVCGGTIRLPRRLNGATQGQDVTFGIRPEHLSAR---EGGIELATVNVE 303 Query: 319 VVVSELLGSETMLY-LKLGQTEFAARVDARDFHEPGEKVSLTFNVAKGHFFDAETEA 374 +V E LG ETMLY + + + ++ + E G +++ F+ ++ H F A+ A Sbjct: 304 IV--ENLGGETMLYGITPDRQQLTVALEGQQKVERGSNLAVHFDPSRCHVFGADGRA 358 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: 358 Number of extensions: 17 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: 360 Length adjustment: 30 Effective length of query: 347 Effective length of database: 330 Effective search space: 114510 Effective search space used: 114510 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