Align ABC-type Maltose/ Maltodextrin permease (characterized, see rationale)
to candidate Pf1N1B4_5114 Maltose/maltodextrin ABC transporter, permease protein MalG
Query= uniprot:Q6MNM1 (272 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5114 Length = 280 Score = 174 bits (442), Expect = 1e-48 Identities = 91/267 (34%), Positives = 150/267 (56%), Gaps = 4/267 (1%) Query: 8 WISILLFSLFSIYPILYVLSVSLRPDNAFQTQSLEIIGPNASFKNFVDLFATTDFLIWMR 67 W I + L++++P Y + SL+P +A S I P+ F N+ + FL + Sbjct: 16 WCLIGVLLLYAVFPFYYAIVTSLKPSSALFEVSYWIENPD--FSNYAAVLNQASFLRAIG 73 Query: 68 NSLVVSAATTLLGVALASTSAYALARYRFRGRNMMLFSLLMTQMFPATMLMLPFYIILSK 127 NSLVV+ L + L+ T+AYAL R +FRGR +L +L MFP ++ + ++ Sbjct: 74 NSLVVALCVVTLALFLSLTAAYALGRVKFRGRGTVLMMVLGVSMFPQVAVLSGLFEVIRA 133 Query: 128 LRLIDSFWGLFLIYSSTALPFCIWQMKAYYDTIPRELEEAALLDGCSKWMIFYKIILPVS 187 L L ++ W L L Y+ LPF +W + + +P ELEEAA++DG S W+ +++LP+ Sbjct: 134 LGLYNTSWALILSYTIFTLPFTVWVLTTFMGQLPHELEEAAIMDGASPWVTLTRVLLPLL 193 Query: 188 SPALVITALFSFMSSWSEYVIAAVVLQDPQLYTLPLGLRSFQASLATQ--WGLYAAGALI 245 PALV T L +F+++W+E++ A T+P+ + + WGL A +++ Sbjct: 194 WPALVTTGLLAFIAAWNEFLFALTFTLTDTQRTVPVAIALISGGSPHELPWGLLMAASVV 253 Query: 246 VSVPVLILFISISRYLVSGLTMGSVKG 272 V+VP++IL + R +VSGLT G++KG Sbjct: 254 VTVPLVILVLIFQRRIVSGLTAGALKG 280 Lambda K H 0.329 0.139 0.421 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: 250 Number of extensions: 15 Number of successful extensions: 2 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 ( 7.1 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