Align ABC-type Maltose/ Maltodextrin permease (characterized, see rationale)
to candidate WP_007665545.1 BN137_RS16135 carbohydrate ABC transporter permease
Query= uniprot:Q6MNM1 (272 letters) >NCBI__GCF_000319285.1:WP_007665545.1 Length = 281 Score = 158 bits (400), Expect = 1e-43 Identities = 87/271 (32%), Positives = 151/271 (55%), Gaps = 4/271 (1%) Query: 4 KTFSWISILLFSLFSIYPILYVLSVSLRPDNAFQTQSLEIIGPNASFKNFVDLFATTDFL 63 K +I L+ LF ++P Y + SLR T + G + + N+V Sbjct: 13 KAVIFIGALMACLFCVFPFYYAIISSLREGQELFTPAYFPTGWH--WDNYVVALVDNGIA 70 Query: 64 IWMRNSLVVSAATTLLGVALASTSAYALARYRFRGRNMMLFSLLMTQMFPATMLMLPFYI 123 + NS++V+A T L + ++ T+A+ALAR FRGR ++LF++L MFP ++ + Sbjct: 71 RSLLNSVLVAAVTVGLCLFVSVTAAFALARVPFRGRRVLLFTILCVSMFPQVAVLTGMFE 130 Query: 124 ILSKLRLIDSFWGLFLIYSSTALPFCIWQMKAYYDTIPRELEEAALLDGCSKWMIFYKII 183 ++ L L DS L + Y++ +LPF +W + + +IP ELEEAA++DG I +I Sbjct: 131 LVRFLGLYDSLGALVISYTTFSLPFTVWVLTTFMKSIPVELEEAAIVDGAKTGTIIRRIF 190 Query: 184 LPVSSPALVITALFSFMSSWSEYVIAAVVLQDPQLYTLPLGLRSFQ--ASLATQWGLYAA 241 PV +PA+V T L +F+ +W+E++ A + T+P+ + F +S WG A Sbjct: 191 APVLAPAMVTTGLLAFIGAWNEFMFALTFIISGDKRTVPVAISLFSGASSYELPWGSIMA 250 Query: 242 GALIVSVPVLILFISISRYLVSGLTMGSVKG 272 +++V++P+++L + + +VSGLT G++KG Sbjct: 251 ASVVVTLPIIVLVLIFQKRIVSGLTSGAIKG 281 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: 233 Number of extensions: 13 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: 281 Length adjustment: 25 Effective length of query: 247 Effective length of database: 256 Effective search space: 63232 Effective search space used: 63232 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 24 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