Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate 6939439 Sama_3531 molybdenum ABC transporter, ATP-binding protein (RefSeq)
Query= uniprot:Q6MNM2 (347 letters) >FitnessBrowser__SB2B:6939439 Length = 370 Score = 145 bits (366), Expect = 2e-39 Identities = 88/220 (40%), Positives = 124/220 (56%), Gaps = 10/220 (4%) Query: 23 DLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGTISIDGKKI-------NDIEPQNR 75 D GEFL +VGPSG GK+TLLR +AGL ++G+I GK+I PQNR Sbjct: 22 DFSCRAGEFLAVVGPSGGGKTTLLRMIAGLAKPENGSIRC-GKRIWFDSDEGIHCSPQNR 80 Query: 76 DIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEISELLQIKHLLDRKPKELS 135 I V Q + L+P ++ N+ L +L + E R E + + L DR P +LS Sbjct: 81 HIGFVPQHFGLFPKLSALGNIMAALD--HLPSQERRPRALAALEKVNLHGLTDRLPSQLS 138 Query: 136 GGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKRLHHNSKSTMIYVTHDQM 195 GGQ+QRVAL RAL+R+ V+L DEP S +D R ++ LE+ RL +I VTHD Sbjct: 139 GGQKQRVALARALAREPRVLLLDEPFSAVDRETRERLYLELARLKAELNIPVIMVTHDLN 198 Query: 196 EATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIG 235 EA L D + ++ G + Q GTP +++ RP+N +A +G Sbjct: 199 EALLLADSMLLISQGHMLQHGTPQDVFSRPRNEAVARQMG 238 Lambda K H 0.318 0.136 0.383 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: 247 Number of extensions: 8 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: 347 Length of database: 370 Length adjustment: 29 Effective length of query: 318 Effective length of database: 341 Effective search space: 108438 Effective search space used: 108438 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 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