Align Glycine betaine/proline betaine transport system permease protein ProW (characterized)
to candidate BWI76_RS15035 BWI76_RS15035 metal ABC transporter permease
Query= SwissProt::P14176 (354 letters) >FitnessBrowser__Koxy:BWI76_RS15035 Length = 223 Score = 76.6 bits (187), Expect = 5e-19 Identities = 63/207 (30%), Positives = 105/207 (50%), Gaps = 20/207 (9%) Query: 148 TLALVLTALLFCIVIGLPLGIWLARSPRAAKIIRPLLDAM--------QTTPAFVYLVPI 199 T+ +V A LF +++GLP G+ L S R P L+A+ ++ P V L+ + Sbjct: 21 TVYIVGLAALFTVLLGLPTGVLLFVSRRNGLAPMPKLNAVLGAIINFGRSLPFIVLLIAL 80 Query: 200 V----MLFG--IGNVPGVVVTIIFALPPIIRLTILGINQVPADLIEASRSFGASPRQMLF 253 + ++ G +G+ VV I A P RLT +++V IEA S G + ++F Sbjct: 81 IPFTRLIIGTTLGSTAAVVPVTIGAFPFFARLTENALDEVDYGRIEAILSMGGNIWHVIF 140 Query: 254 KVQLPLAMPTIMAGVNQTLMLALSMVVIASMIAVGGLGQMVLR-GIGRLDMGLATVGGVG 312 K LP A+PT++AG+ T+++ + +A +I GGLG + +R G R + + VG Sbjct: 141 KSLLPEALPTLLAGITLTIVMLIGFSSMAGVIGGGGLGDLAIRYGYQRFNNEVM----VG 196 Query: 313 IVILAIILDRLTQAVG-RDSRSRGNRR 338 V++ + L + Q G R R +RR Sbjct: 197 TVLILVALVQGVQMAGDRLVRGLAHRR 223 Lambda K H 0.326 0.141 0.435 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: 181 Number of extensions: 14 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: 354 Length of database: 223 Length adjustment: 26 Effective length of query: 328 Effective length of database: 197 Effective search space: 64616 Effective search space used: 64616 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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