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 GFF1646 PGA1_c16690 binding protein-dependent transport system, inner membrane component
Query= TCDB::Q8DT26 (278 letters) >FitnessBrowser__Phaeo:GFF1646 Length = 283 Score = 131 bits (330), Expect = 1e-35 Identities = 83/279 (29%), Positives = 140/279 (50%), Gaps = 9/279 (3%) Query: 3 RKKQLQIGSIYALLILLSFIWLFPIIWVILTSFRGEGTAYVP--YIIPKTWTLDNYIKLF 60 R L G A+ L F LFP+ W++ + + + ++P T +N+ + Sbjct: 10 RHPALAFGKYAAIAFYLGFA-LFPLYWLMKIAITPDALIFSEGTRMLPSAVTFENFATVL 68 Query: 61 TNSSFPFGRWFLNTLIVSTATCVLSTSITVAMAYSLSRIKFKHRNGFLKLALVLNMFPGF 120 + F +F N+L VS T +T I Y+ SR F + + + L+ MFP Sbjct: 69 FETEFL--AYFRNSLTVSLGTAFFTTLIAAGAGYAFSRFVFAGKRIIIAVMLITQMFPLL 126 Query: 121 MSMIAVYYILKALNLTQTLTSLVLVYSS-GAALTFYIAKGFFDTIPYSLDESAMIDGATR 179 M + +Y I+ L L +LTSL++VY++ ++ + FFD IP L+E+AM+DG +R Sbjct: 127 MIIAPIYKIVADLGLLNSLTSLIVVYTAFNIPFATFLMQSFFDGIPKDLEEAAMMDGCSR 186 Query: 180 KDIFLKITLPLSKPIIVYTALLAFIAPWIDFIFAQVILGDATSKYTVAIGLFSMLQADTI 239 + PL+ P + T F A W + +FA +++ T +GL + + ++ Sbjct: 187 FQALRTVVFPLTLPGLGATLGFVFTAAWSELLFALMLI-SKNDAMTFPVGLLTFVSKFSV 245 Query: 240 NNWFMAFAAGSVLIAIPITILFIFMQKYYVEGITGGSVK 278 +W AAG VL +P + FIF+Q+Y V+G+T G+VK Sbjct: 246 -DWGQMMAAG-VLALVPSCLFFIFIQRYLVQGLTSGAVK 282 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: 223 Number of extensions: 17 Number of successful extensions: 3 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: 283 Length adjustment: 26 Effective length of query: 252 Effective length of database: 257 Effective search space: 64764 Effective search space used: 64764 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