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_RS18180 AZOBR_RS18180 sugar ABC transporter
Query= TCDB::Q8DT26 (278 letters) >FitnessBrowser__azobra:AZOBR_RS18180 Length = 273 Score = 132 bits (332), Expect = 8e-36 Identities = 85/271 (31%), Positives = 143/271 (52%), Gaps = 15/271 (5%) Query: 14 ALLILLSFIWLFPIIWVILTSFRGEGTAYV--PYIIPKTWTLDNYIKLFTNSSFPFGRWF 71 A+L+LL + FP+ W+++TS + P ++P + Y FT +S +W Sbjct: 11 AVLVLLG-VAAFPLYWMLVTSLTPSERLFDDRPNLLPTLSQIGTYAAAFTETSLR--QWL 67 Query: 72 LNTLIVSTATCVLSTSITVAMAYSLSRIKFKHRNGFLKLALVL---NMFPGFMSMIAVYY 128 +N+LIV+ T VLS ++V AY+LSR+ F NG L L L M P M ++ +Y Sbjct: 68 INSLIVAVGTTVLSILLSVLPAYALSRLTF---NGKLLLGFALFMTQMLPEAMLVVPLYD 124 Query: 129 ILKALNLTQTLTSLVLVYSSGAA-LTFYIAKGFFDTIPYSLDESAMIDGATRKDIFLKIT 187 I L+L TL L+L ++ + +I KG D +P ++E+A +DG +R I L + Sbjct: 125 IFTKLSLLNTLLGLILANTAFTVPVVTWILKGAIDGVPSEIEEAARVDGCSRLGIVLAVV 184 Query: 188 LPLSKPIIVYTALLAFIAPWIDFIFAQVILGDATSKYTVAIGLFSMLQADTINNWFMAFA 247 +PL P + A++AF W +++FAQ + D + T ++GL S + ++ Sbjct: 185 VPLIAPTLAAAAVIAFFHGWNEYVFAQTFISDDALR-TASVGLASFV--GELSTPVHTVM 241 Query: 248 AGSVLIAIPITILFIFMQKYYVEGITGGSVK 278 A + +P + ++F+Q+Y V G+T G VK Sbjct: 242 AVGFIYTLPAVVFYLFVQRYVVAGMTTGGVK 272 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: 206 Number of extensions: 14 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: 273 Length adjustment: 25 Effective length of query: 253 Effective length of database: 248 Effective search space: 62744 Effective search space used: 62744 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