Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate 6938761 Sama_2864 ABC transporter related (RefSeq)
Query= TCDB::Q9HT70 (335 letters) >FitnessBrowser__SB2B:6938761 Length = 230 Score = 152 bits (385), Expect = 6e-42 Identities = 86/218 (39%), Positives = 129/218 (59%), Gaps = 3/218 (1%) Query: 1 MIEFHDVHKTYRVAGREIPALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGG 60 M+ +++K +R E AL+ L + G+ + G SG+GK+T L + LE SGG Sbjct: 1 MLTMKNINKLFRTDLVETHALRDFNLEVAEGEFVAVTGPSGSGKTTFLNIAGLLENASGG 60 Query: 61 RILVEGEDVTALDAEGLRRFR-QRVGMIFQHFNLLSSKTVADNIAMPLRLAGGFSRAEVD 119 ++GE+V L R R Q++G IFQ FNL+ +A+N+ +PLR G F +E Sbjct: 61 EYWLDGENVANLSDSAAARVRNQKIGFIFQGFNLIPDLNLAENVELPLRYRG-FGSSERK 119 Query: 120 ARVSELLARVGLSDHARKYPAQLSGGQKQRVGIARALACRPSILLCDEATSALDPQTTAS 179 RV + L++VGL+ + P+QLSGGQ+QRV IARALA P LL DE T LD Sbjct: 120 RRVEQALSQVGLAARQKHLPSQLSGGQQQRVAIARALAGEPRFLLADEPTGNLDSLMARQ 179 Query: 180 VLQLLAEINRELKLTIVLITHEMDVIRRVCDQVAVMDG 217 V++LL +INR+ TI+++TH+ ++ RR + ++DG Sbjct: 180 VMELLEDINRQ-GTTIIMVTHDGELARRAERNIQIVDG 216 Lambda K H 0.322 0.138 0.393 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: 197 Number of extensions: 10 Number of successful extensions: 4 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: 335 Length of database: 230 Length adjustment: 25 Effective length of query: 310 Effective length of database: 205 Effective search space: 63550 Effective search space used: 63550 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (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