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 Ac3H11_2941 Various polyols ABC transporter, ATP-binding component
Query= TCDB::Q8DT25 (377 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2941 Length = 350 Score = 310 bits (793), Expect = 5e-89 Identities = 182/370 (49%), Positives = 235/370 (63%), Gaps = 32/370 (8%) Query: 1 MTTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEG 60 M L+L I K + +H +++ +L I EFIVFVGPSGCGKST LR+IAGLE I G Sbjct: 1 MAYLQLRGIEKFF--GEHRAIKGIDLTIQQGEFIVFVGPSGCGKSTLLRLIAGLEAIDGG 58 Query: 61 NLYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAA 120 +L +D + + D RD+AMVFQ+YALYPHMSVYENM+F LKL K K I+++V AA Sbjct: 59 SLMLDGRDITDQPSSKRDLAMVFQSYALYPHMSVYENMSFALKLAKVDKQVIDEKVQNAA 118 Query: 121 EILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAK 180 IL LT++L+R P +LSGGQRQRVA+GRAIVR KVFL DEPLSNLDA LR R EIAK Sbjct: 119 RILNLTQYLQRTPKELSGGQRQRVAIGRAIVRAPKVFLFDEPLSNLDAALRGQTRVEIAK 178 Query: 181 IHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANK 240 +HR +GATTIYVTHDQ EAMTLADR+V++ G IEQ+GTP ELY++PAN+ Sbjct: 179 LHRDLGATTIYVTHDQVEAMTLADRVVVLRD----------GIIEQVGTPLELYDKPANQ 228 Query: 241 FVAGFIGSPAMNFFEVTVEKERLVNQDGLSLALPQGQEKILEEKGYLGKKVTLGIRPEDI 300 FVA FIG+P MN V V+K LPQ ++ +G+RPE+I Sbjct: 229 FVAQFIGTPQMNV--VPVDK------------LPQPVQQQAPAAPAGAAVGAIGLRPENI 274 Query: 301 SSDQIVHETFPNASVTADILVSELLGSESMLYVKF-GSTEFTARVNARDSHSPGEKVQLT 359 + T V + + E LG+E+++YV G +F +R N R G+ V L Sbjct: 275 TV-----RTTGATPVGGQVDLIEALGAETLIYVTTPGGAQFVSRQNDRTDLRVGDAVSLD 329 Query: 360 FNIAKGHFFD 369 + ++ H+FD Sbjct: 330 IDASQAHWFD 339 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: 350 Number of extensions: 17 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: 350 Length adjustment: 29 Effective length of query: 348 Effective length of database: 321 Effective search space: 111708 Effective search space used: 111708 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