Align MalG, 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 SMc04137 SMc04137 ABC transporter permease
Query= TCDB::Q8DT26 (278 letters) >FitnessBrowser__Smeli:SMc04137 Length = 295 Score = 134 bits (338), Expect = 2e-36 Identities = 81/269 (30%), Positives = 138/269 (51%), Gaps = 4/269 (1%) Query: 12 IYALLILLSFIWLFPIIWVILTSFRGEGTAYVPYII-PKTWTLDNYIKLFTNSSFPFGRW 70 ++A LI S ++P++W+I S R E + + P + +Y++ + FGR+ Sbjct: 28 VHAALIAASIAMIYPLLWMISASVRPEDEIFASTSLWPSSVDFSSYVRGWFGLDVSFGRF 87 Query: 71 FLNTLIVSTATCVLSTSITVAMAYSLSRIKFKHRNGFLKLALVLNMFPGFMSMIAVYYIL 130 F N+L+++ T V + AY+ +R++F RN + + L M P +++I Y + Sbjct: 88 FWNSLVIAVLTVVGNVVACSLAAYAFARLRFAGRNFWFAIMLGTMMIPYHVTLIPQYVLF 147 Query: 131 KALNLTQTLTSLVLV-YSSGAALTFYIAKGFFDTIPYSLDESAMIDGATRKDIFLKITLP 189 L T LV+ + + A ++ FF IP LDE+AM+DG I+ KI LP Sbjct: 148 LDLGWVNTFLPLVVPKFLASDAFFIFLMVQFFRGIPRELDEAAMMDGCGAWRIYWKIMLP 207 Query: 190 LSKPIIVYTALLAFIAPWIDFIFAQVILGDATSKYTVAIGLFSMLQADTINNWFMAFAAG 249 LS P++ A+ +FI W DF + L D S YT+ +GL + + + + ++W FA Sbjct: 208 LSLPVLATAAIFSFIWTWDDFFGPLIYLNDMNS-YTIQLGLRTFVDSSSTSDWGGLFAM- 265 Query: 250 SVLIAIPITILFIFMQKYYVEGITGGSVK 278 S L +P+ F+F Q+ +EGI +K Sbjct: 266 STLSLVPVFFFFLFFQRLLIEGIATTGMK 294 Lambda K H 0.330 0.142 0.428 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: 227 Number of extensions: 15 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: 278 Length of database: 295 Length adjustment: 26 Effective length of query: 252 Effective length of database: 269 Effective search space: 67788 Effective search space used: 67788 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 47 (22.7 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