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 18063 b4035 fused maltose transport subunit, ATP-binding component of ABC superfamily/regulatory protein (NCBI)
Query= TCDB::Q8DT25 (377 letters) >FitnessBrowser__Keio:18063 Length = 371 Score = 320 bits (819), Expect = 5e-92 Identities = 172/340 (50%), Positives = 232/340 (68%), Gaps = 21/340 (6%) Query: 1 MTTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEG 60 M +++L N+ K + ++ NLDIH+ EF+VFVGPSGCGKST LRMIAGLE IT G Sbjct: 1 MASVQLQNVTKAWGEV--VVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIAGLETITSG 58 Query: 61 NLYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAA 120 +L+I +K MND P +R + MVFQ+YALYPH+SV ENM+FGLKL KK+ IN+RV++ A Sbjct: 59 DLFIGEKRMNDTPPAERGVGMVFQSYALYPHLSVAENMSFGLKLAGAKKEVINQRVNQVA 118 Query: 121 EILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAK 180 E+L L L+RKP LSGGQRQRVA+GR +V + VFL+DEPLSNLDA LRV MR EI++ Sbjct: 119 EVLQLAHLLDRKPKALSGGQRQRVAIGRTLVAEPSVFLLDEPLSNLDAALRVQMRIEISR 178 Query: 181 IHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANK 240 +H+R+G T IYVTHDQ EAMTLAD+IV++ A GR+ Q+G P ELY+ PA++ Sbjct: 179 LHKRLGRTMIYVTHDQVEAMTLADKIVVLDA----------GRVAQVGKPLELYHYPADR 228 Query: 241 FVAGFIGSPAMNFFEVTVEKERLVNQDGLSLALPQGQEKILEEKG---YLGKKVTLGIRP 297 FVAGFIGSP MNF V V ++Q + L +P Q+ L + +G ++LGIRP Sbjct: 229 FVAGFIGSPKMNFLPVKV-TATAIDQVQVELPMPNRQQVWLPVESRDVQVGANMSLGIRP 287 Query: 298 EDISSDQIVHETFPNASVTADILVSELLGSESMLYVKFGS 337 E + I + + ++ V E LG+E+ ++++ S Sbjct: 288 EHLLPSDIA-----DVILEGEVQVVEQLGNETQIHIQIPS 322 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: 349 Number of extensions: 10 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: 371 Length adjustment: 30 Effective length of query: 347 Effective length of database: 341 Effective search space: 118327 Effective search space used: 118327 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: 50 (23.9 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