Align ABC-type Maltose/ Maltodextrin permease (characterized, see rationale)
to candidate BPHYT_RS35660 BPHYT_RS35660 membrane protein
Query= uniprot:Q6MNM1 (272 letters) >FitnessBrowser__BFirm:BPHYT_RS35660 Length = 283 Score = 174 bits (441), Expect = 2e-48 Identities = 85/277 (30%), Positives = 163/277 (58%), Gaps = 6/277 (2%) Query: 1 MLKKTFSWISILLFSLFSIYPILYVLSVSLRPDNAFQTQSLEIIGPNASFKNFVDLFATT 60 M + + W+++ + ++P +L +L+P + + + + NF D++ Sbjct: 7 MKRSLWCWLALSPLVVVVLFPFAVMLFTALKPASEIFVYPARWLPVHWQWSNFSDMWVAA 66 Query: 61 DFLIWMRNSLVVSAATTLLGVALASTSAYALARYRFRGRNMMLFSLLMTQMFPATMLMLP 120 +F + +RNS V+S +T L +A++ +AYALAR+ FRGR + LL+TQM +L++ Sbjct: 67 NFGVALRNSTVISLLSTALALAVSLPAAYALARFPFRGRGLYRQFLLVTQMLSPILLVVG 126 Query: 121 FYIILSKL-----RLIDSFWGLFLIYSSTALPFCIWQMKAYYDTIPRELEEAALLDGCSK 175 + + + + L+DS G+ + Y++ + F +W + +Y+ T+PR+LEE+A L+GC + Sbjct: 127 LFRLAAMIPYGDGNLVDSKIGVIVSYAAFNIAFAVWMLSSYFQTVPRDLEESAWLEGCGR 186 Query: 176 WMIFYKIILPVSSPALVITALFSFMSSWSEYVIAAVVLQDPQLYTLPLGLRSFQA-SLAT 234 +K+ LP++ PA+V+TA+F+F+++W+E+ + +++ P+ TL + + A Sbjct: 187 TKAVFKVFLPLAVPAIVVTAIFTFINAWNEFAVVYTLIRSPENKTLTVQVTDMVAGKYVV 246 Query: 235 QWGLYAAGALIVSVPVLILFISISRYLVSGLTMGSVK 271 QW L A L ++PV ++F + RYLV GL +G+VK Sbjct: 247 QWHLVMAATLCATLPVSVVFAWLQRYLVKGLALGAVK 283 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: 257 Number of extensions: 15 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: 283 Length adjustment: 25 Effective length of query: 247 Effective length of database: 258 Effective search space: 63726 Effective search space used: 63726 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