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 AZOBR_RS25595 AZOBR_RS25595 sugar ABC transporter ATP-binding protein
Query= TCDB::Q00752 (377 letters) >FitnessBrowser__azobra:AZOBR_RS25595 Length = 358 Score = 297 bits (760), Expect = 3e-85 Identities = 175/362 (48%), Positives = 224/362 (61%), Gaps = 43/362 (11%) Query: 21 VEDFDLDIKNKEFIVFVGPSGCGKSTTLRMVAGLEDITKGELKIDGEVVNDKAPKDRDIA 80 + DL++ + EF+ FVGPSGCGKST LR++AGLE+ + G+L I G+ VND+ P R IA Sbjct: 19 IHGVDLEVADGEFVAFVGPSGCGKSTLLRLIAGLEEPSGGDLSIGGQRVNDRPPAARGIA 78 Query: 81 MVFQNYALYPHMSVYDNMAFGLKLRHYSKEAIDKRVKEAAQILGLTEFLERKPADLSGGQ 140 MVFQ+YALYPHM+ YDNMAFGL L K I +RV+ AA++L + + L+RKP DLSGGQ Sbjct: 79 MVFQSYALYPHMTAYDNMAFGLTLSRTDKGTIAERVRAAARLLQIEDLLDRKPRDLSGGQ 138 Query: 141 RQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVSMRAEIAKIHRRIGATTIYVTHDQTEAM 200 RQRVA+GRAIVR+ +VFL DEPLSNLDA LRV MR EIAK+ + AT IYVTHDQ EAM Sbjct: 139 RQRVAIGRAIVREPQVFLFDEPLSNLDAGLRVQMRLEIAKLKADLRATMIYVTHDQVEAM 198 Query: 201 TLADRIVIMSSTKNEDGSGTIGRVEQVGTPQELYNRPANKFVAGFIGSPAMNFFDVTIKD 260 TLADRIV++++ GRVEQ GTP ELY+RP N+FVAGFIGSPAMNF DV + + Sbjct: 199 TLADRIVVLNA----------GRVEQAGTPLELYHRPRNRFVAGFIGSPAMNFLDV-VSE 247 Query: 261 GHLVSKDGLTIAVTEGQLKMLESKGF------------KNKNLIFGIRPEDISSSLLVQE 308 G +T+G +++ G L G+RPE + + Sbjct: 248 G-----------LTDGSVRVWLPGGVPLDIAVDGAAPAAGTPLTLGVRPEHVGLA----- 291 Query: 309 TYPDATVDAEVVVSELLGSETMLYLKL--GQTEFAARVDARDFHEPGEKVSLTFNVAKGH 366 A + A ++ E LG ET + L GQ R+D GE++ L H Sbjct: 292 -DGGAGLLATILAVERLGGETHCHAALEDGQ-RLLVRLDGDRPVAAGERLRLNLRGETAH 349 Query: 367 FF 368 F Sbjct: 350 LF 351 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: 397 Number of extensions: 13 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: 358 Length adjustment: 30 Effective length of query: 347 Effective length of database: 328 Effective search space: 113816 Effective search space used: 113816 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