Align MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized)
to candidate SM_b20661 SM_b20661 sugar uptake ABC transporter ATP-binding protein
Query= TCDB::Q8DT25 (377 letters) >FitnessBrowser__Smeli:SM_b20661 Length = 355 Score = 328 bits (840), Expect = 2e-94 Identities = 184/359 (51%), Positives = 236/359 (65%), Gaps = 27/359 (7%) Query: 21 VENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEGNLYIDDKLMNDASPKDRDIA 80 ++ N++I D EF++ VGPSGCGKST LRM+AGLE+IT G + I ++++N PKDRDIA Sbjct: 19 IKGVNIEIEDGEFVILVGPSGCGKSTLLRMLAGLENITAGEIRIGNQVVNRLPPKDRDIA 78 Query: 81 MVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAAEILGLTEFLERKPADLSGGQ 140 MVFQNYALYPHM+V +NMAF L L K +I+KRV AAEILGL++ L+R P LSGGQ Sbjct: 79 MVFQNYALYPHMTVADNMAFSLMLAARPKSEIDKRVGVAAEILGLSKLLDRYPRQLSGGQ 138 Query: 141 RQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAKIHRRIGATTIYVTHDQTEAM 200 RQRVAMGRAIVRD +VFL DEPLSNLDAKLRVAMRAEI ++H+R+ TT+YVTHDQ EAM Sbjct: 139 RQRVAMGRAIVRDPQVFLFDEPLSNLDAKLRVAMRAEIKELHQRLKTTTVYVTHDQIEAM 198 Query: 201 TLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANKFVAGFIGSPAMNFFEVTV-- 258 T+AD+IV+M G +EQIG P ELY+ PAN FVAGFIGSPAMN + + Sbjct: 199 TMADKIVVMHD----------GIVEQIGAPLELYDNPANLFVAGFIGSPAMNMLKGRLDP 248 Query: 259 -EKERLVNQDGLSLALPQGQEKILEEKGYLGKKVTLGIRPEDISSDQIVHETFPNASVTA 317 + + DG ALP + + G+ + G+RPE ++ D PN + A Sbjct: 249 ADPSVFLTADG--TALPVARPAAAAQ----GRDLVYGLRPEYMALD-------PN-GLPA 294 Query: 318 DILVSELLGSESMLYVKFGSTEFTARVNARDSHSPGEKVQLTFNIAKGHFFDLETEKRI 376 +I V E G E+ L + G + T R + PGE + L + A H FD T +R+ Sbjct: 295 EIAVIEPTGYETQLIARLGGHDVTCVFRERVNAKPGETIHLAIDAAHVHLFDAGTGRRL 353 Lambda K H 0.318 0.135 0.379 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: 401 Number of extensions: 14 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: 355 Length adjustment: 30 Effective length of query: 347 Effective length of database: 325 Effective search space: 112775 Effective search space used: 112775 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