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 SMc03065 SMc03065 alpha-glucoside ABC transporter ATP-binding protein
Query= TCDB::Q8DT25 (377 letters) >FitnessBrowser__Smeli:SMc03065 Length = 362 Score = 311 bits (796), Expect = 2e-89 Identities = 186/378 (49%), Positives = 240/378 (63%), Gaps = 33/378 (8%) Query: 1 MTTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEG 60 MT L L +I K Y + +LDI + EF+VFVGPSGCGKST LRMIAGLE+IT G Sbjct: 1 MTGLLLKDIRKSYGAVD--VIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGG 58 Query: 61 NLYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAA 120 +++ID + +ND P R IAMVFQ+YALYPHM+VY+NMAFG+++ + K++I++RV AA Sbjct: 59 DMFIDGERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAA 118 Query: 121 EILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAK 180 ++L LT +L+R P LSGGQRQRVA+GRAI R+ KVFL DEPLSNLDA LRVA R EIAK Sbjct: 119 DMLQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAK 178 Query: 181 IHRRIGATT-IYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPAN 239 + R+ TT IYVTHDQ EAMTLADRIV++SA G IEQ+G P ELY PAN Sbjct: 179 LSERMSDTTMIYVTHDQVEAMTLADRIVVLSA----------GHIEQVGAPLELYERPAN 228 Query: 240 KFVAGFIGSPAMNFFEVTVEKERLVNQDGLSLALPQGQEKILE---EKGYLGKKVTLGIR 296 FVA FIGSPAMN T+ Q +SLA G+ L+ GK + G+R Sbjct: 229 LFVARFIGSPAMNVIPATITATG--QQTAVSLA--GGKSVTLDVPTNASENGKTASFGVR 284 Query: 297 PEDI---SSDQIVHETFPNASVTADILVSELLGSESMLYVK--FGSTEFTARVNARDSHS 351 PED+ +D + E + + E LG ++LY++ + A++ Sbjct: 285 PEDLRVTEADDFLFE--------GTVSIVEALGEVTLLYIEGLVENEPIIAKMPGIARVG 336 Query: 352 PGEKVQLTFNIAKGHFFD 369 G+KV+ T + AK H FD Sbjct: 337 RGDKVRFTADKAKLHLFD 354 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: 357 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