Align D-methionine ABC transporter membrane protein, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate BPHYT_RS22450 BPHYT_RS22450 phosphonate ABC transporter permease
Query= TCDB::Q9HT69 (225 letters) >FitnessBrowser__BFirm:BPHYT_RS22450 Length = 280 Score = 45.1 bits (105), Expect = 1e-09 Identities = 40/131 (30%), Positives = 61/131 (46%), Gaps = 5/131 (3%) Query: 83 MIPLTVLITGTSLGVAGAIPPLVVGATPFFARLVETALREVDKGIIEATQAMGASTRQII 142 M+ + I LG + L V T A+L A+ +D E +A GA++ I Sbjct: 141 MVFAMLFIVAVGLGPFAGVLALWVHTTGVLAKLFAEAVEAIDPRPAEGVRATGATSLDEI 200 Query: 143 WNALLPEARPGIIAAITVTAITLVSYTAMAGVVGAGGLGDL---AIR-FGY-QRFQTDVM 197 +LP+ P I+ + V + G+VGAGG+G + AIR F Y Q +M Sbjct: 201 IYGVLPQVLPLWISYALYRFESNVRSAMVVGMVGAGGIGVVLYEAIRSFNYAQTAAVMIM 260 Query: 198 VVTVVMLLILV 208 V+ VV ++ LV Sbjct: 261 VIVVVTVIDLV 271 Lambda K H 0.329 0.143 0.419 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: 111 Number of extensions: 4 Number of successful extensions: 1 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: 225 Length of database: 280 Length adjustment: 24 Effective length of query: 201 Effective length of database: 256 Effective search space: 51456 Effective search space used: 51456 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: 46 (22.3 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