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 AZOBR_RS25590 AZOBR_RS25590 sugar ABC transporter permease
Query= TCDB::Q8DT26 (278 letters) >FitnessBrowser__azobra:AZOBR_RS25590 Length = 277 Score = 136 bits (342), Expect = 6e-37 Identities = 94/274 (34%), Positives = 141/274 (51%), Gaps = 8/274 (2%) Query: 9 IGSI-YALLILLSFIW-LFPIIWVILTSFRGEGTAYVPYIIPKTWTLDNYIKLFTNSSFP 66 IG I + LL+L W +FP W I+TS + + P +L NY +F P Sbjct: 7 IGRIAFGLLVLGIVAWAVFPFAWAIVTSLKAGSALFTVEAWPSQPSLANYAAIFKEQ--P 64 Query: 67 FGRWFLNTLIVSTATCVLSTSITVAMAYSLSRIKFKHRNGFLKLALVLNMFPGFMSMIAV 126 FGR LN+L+ ++A LS + V AY+L R++F+ R L + L ++MFP + + Sbjct: 65 FGRNILNSLLAASAVVALSLGLAVLAAYALGRVRFRGRGLLLFVVLGVSMFPQVAVLSGL 124 Query: 127 YYILKALNLTQTLTSLVLVY-SSGAALTFYIAKGFFDTIPYSLDESAMIDGATRKDIFLK 185 + +++ L L + SLVL Y T ++ F +P L+E+AM+DGA I + Sbjct: 125 FELVRWLGLYNRIGSLVLSYLIFTLPFTVWVLTTFMRELPKELEEAAMVDGAGPFVIVTR 184 Query: 186 ITLPLSKPIIVYTALLAFIAPWIDFIFAQVI-LGDATSKYTVAIGLFSMLQADTINNWFM 244 + LPL P + T LLAFIA W +F+FA L D VAI L S + W Sbjct: 185 VFLPLMGPALAATGLLAFIAAWNEFLFALTFTLTDDARTVPVAIALMSGASQYEL-PWGQ 243 Query: 245 AFAAGSVLIAIPITILFIFMQKYYVEGITGGSVK 278 AA SV++ +P+ L + Q+ V G+T G+VK Sbjct: 244 IMAA-SVVVTVPLIGLVLLFQRRIVSGLTAGAVK 276 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: 207 Number of extensions: 11 Number of successful extensions: 4 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: 277 Length adjustment: 25 Effective length of query: 253 Effective length of database: 252 Effective search space: 63756 Effective search space used: 63756 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