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 RR42_RS22875 RR42_RS22875 ABC transporter
Query= TCDB::Q8DT25 (377 letters) >FitnessBrowser__Cup4G11:RR42_RS22875 Length = 351 Score = 241 bits (615), Expect = 2e-68 Identities = 133/310 (42%), Positives = 199/310 (64%), Gaps = 25/310 (8%) Query: 1 MTTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEG 60 M T++ ++ KR+ +V+ +L +H+ EF+V +GPSG GK+T LR+IAGLE T G Sbjct: 1 MATVETRSLTKRFDGTN--AVDGIDLAVHEAEFLVLLGPSGSGKTTLLRLIAGLEAPTSG 58 Query: 61 NLYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAA 120 ++ + +++ P+ ++AMVFQ+YALYPH+SV N+AF L+ ++ ++ I ++V AA Sbjct: 59 DILVGGRVVTGLPPRAHNMAMVFQSYALYPHLSVAGNIAFPLEAQRMPREAIARKVSWAA 118 Query: 121 EILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAK 180 + G+ L RKP LSGG+RQRVA+ RA+VR+ FL+DEPLSNLDAKLR + R E+ + Sbjct: 119 ALFGIGHLLSRKPRQLSGGERQRVALARAVVREPVAFLLDEPLSNLDAKLRTSAREELQQ 178 Query: 181 IHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANK 240 + RR+ TTIYVTHDQ EA+ L DR+ I+ GR+ Q+GTPQ++Y +PA+ Sbjct: 179 LQRRLATTTIYVTHDQIEALALGDRVAILDH----------GRVHQLGTPQQVYEQPADT 228 Query: 241 FVAGFIGSPAMNFFEVTVEKERLVNQDGLSLALPQ---GQEKILEEKGYLGKKVTLGIRP 297 FVA FIGSP MN V+ + LV LP+ G ++ LE + +T R Sbjct: 229 FVATFIGSPPMNL----VDTDALVTGFRPEHFLPREVYGSDEALEPFPF---HIT---RI 278 Query: 298 EDISSDQIVH 307 E++ SD++V+ Sbjct: 279 ENLGSDRLVY 288 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: 309 Number of extensions: 10 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: 351 Length adjustment: 29 Effective length of query: 348 Effective length of database: 322 Effective search space: 112056 Effective search space used: 112056 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