Align ABC transporter for Xylitol, permease component 2 (characterized)
to candidate Pf1N1B4_5114 Maltose/maltodextrin ABC transporter, permease protein MalG
Query= reanno::Dino:3607127 (272 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5114 Length = 280 Score = 175 bits (443), Expect = 1e-48 Identities = 90/263 (34%), Positives = 149/263 (56%), Gaps = 4/263 (1%) Query: 13 LLVLIITVCVFPFYWMVTTSLKTQIVALEAPPVWIFEPTLSNYREALFEDGVLRTLINSL 72 L+ +++ VFPFY+ + TSLK E WI P SNY L + LR + NSL Sbjct: 18 LIGVLLLYAVFPFYYAIVTSLKPSSALFEVS-YWIENPDFSNYAAVLNQASFLRAIGNSL 76 Query: 73 IIAISTTFLALVLGVPAAFALARFEFRGKKDLWFWFITNRMISPIVLALPFFLIARNLGL 132 ++A+ LAL L + AA+AL R +FRG+ + + M + + F + R LGL Sbjct: 77 VVALCVVTLALFLSLTAAYALGRVKFRGRGTVLMMVLGVSMFPQVAVLSGLFEVIRALGL 136 Query: 133 LDKHITLILIYLTFNLPIVIWIVTDQFRGIPYDLDEAARLEGASQFTIMRKICLPLAMPG 192 + LIL Y F LP +W++T +P++L+EAA ++GAS + + ++ LPL P Sbjct: 137 YNTSWALILSYTIFTLPFTVWVLTTFMGQLPHELEEAAIMDGASPWVTLTRVLLPLLWPA 196 Query: 193 VAVSAIFSFIFSWNELMFGLILTRSEAKTAPAMAVSFMEG---YNLPYGKIMATSTLIVI 249 + + + +FI +WNE +F L T ++ + +A++ + G + LP+G +MA S ++ + Sbjct: 197 LVTTGLLAFIAAWNEFLFALTFTLTDTQRTVPVAIALISGGSPHELPWGLLMAASVVVTV 256 Query: 250 PVLIFALIASKQLVRGLTMGAVK 272 P++I LI +++V GLT GA+K Sbjct: 257 PLVILVLIFQRRIVSGLTAGALK 279 Lambda K H 0.331 0.143 0.431 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: 243 Number of extensions: 14 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: 272 Length of database: 280 Length adjustment: 25 Effective length of query: 247 Effective length of database: 255 Effective search space: 62985 Effective search space used: 62985 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 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