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 RR42_RS18605 RR42_RS18605 sugar ABC transporter permease
Query= TCDB::Q8DT26 (278 letters) >FitnessBrowser__Cup4G11:RR42_RS18605 Length = 295 Score = 139 bits (350), Expect = 7e-38 Identities = 84/267 (31%), Positives = 143/267 (53%), Gaps = 6/267 (2%) Query: 11 SIYALLILLSFIWLFPIIWVILTSFRGEGTAYVPYIIPKTWTLDNYIKLFTNSSF--PFG 68 +IY L + F+ LFP W+ +T+F+ +G + P W + F F P+ Sbjct: 28 TIYIPLGIFVFVLLFPFYWMAITAFKPDGELLMRSANP-FWVMAPTFAHFKKLLFDTPYP 86 Query: 69 RWFLNTLIVSTATCVLSTSITVAMAYSLSRIKFKHRNGFLKLALVLNMFPGFMSMIAVYY 128 W LNT+IVST + S + +V AY++ R++F+ + + P + I + Sbjct: 87 EWLLNTVIVSTISTFASLAASVLAAYAIERLRFQGAKQVGLAVFLAYLIPPSILFIPLAS 146 Query: 129 ILKALNLTQTLTSLVLVYSSGAA-LTFYIAKGFFDTIPYSLDESAMIDGATRKDIFLKIT 187 I+ L L T +L+L Y + ++ G+F +IPY L+E A+IDGATR +I +KI Sbjct: 147 IVFQLGLFDTRWALILTYPTFLIPFCTWLLMGYFRSIPYELEECALIDGATRWEILVKII 206 Query: 188 LPLSKPIIVYTALLAFIAPWIDFIFAQVILGDATSKYTVAIGLFSMLQADTINNWFMAFA 247 LPL+ P ++ + AF W +FI+A + + K TV +G+ + L + +W A Sbjct: 207 LPLAVPGLISAGIFAFTLSWNEFIYALTFISSSEVK-TVPVGIVTELIEGDVYHW-GALM 264 Query: 248 AGSVLIAIPITILFIFMQKYYVEGITG 274 AG++L ++P+ +++ F +YYV G+TG Sbjct: 265 AGALLGSLPVALVYSFFVEYYVSGMTG 291 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: 276 Number of extensions: 17 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: 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