Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate 3607448 Dshi_0861 inner-membrane translocator (RefSeq)
Query= reanno::azobra:AZOBR_RS08235 (301 letters) >FitnessBrowser__Dino:3607448 Length = 305 Score = 143 bits (361), Expect = 4e-39 Identities = 100/309 (32%), Positives = 161/309 (52%), Gaps = 29/309 (9%) Query: 5 LQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSLGITW 64 ++Q++NGL G + L+A G T+V+G++G+IN AHG +YM+GAF A A GS Sbjct: 7 IEQVLNGLQFGVMLFLMAAGLTLVFGVMGLINLAHGSLYMVGAFAAAAVAGATGS----- 61 Query: 65 VPLALLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYVQILQGA 124 ++ L A++ A G +E R L + L +++ + + + + G+ Sbjct: 62 ----FVLGLAAALAAAAAAGALIEVTIIRRLYARDHLDQVLATFALILIFSEGTRWIFGS 117 Query: 125 RSKPLQ--PILPGNLTLMDGAVSVSYVRLATIVITIALMYGFTQLITRTSLGRAQRACEQ 182 L+ L G +TL G +Y RLA I I +A+ LI +T +G RA E Sbjct: 118 FPLFLEVPAALSGPVTLPFGIEYPAY-RLAIIGIGLAIAAALFWLIAKTRIGVQIRAGEA 176 Query: 183 DKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKAFTAAVLG 242 D++M LGV++DR+ +L F +GAALA +AG +V + V +G + AF V+G Sbjct: 177 DREMIAALGVDIDRLYTLVFALGAALAGLAGALVGALQSV-QVGMGEPVLILAFVVIVIG 235 Query: 243 GIGSLPGAMLGGVVIGL----------------IEAFWSGYMGSEWKDVATFTILVLVLI 286 GIGS+ GA +G +++GL +E + +GS +A + ++ VLI Sbjct: 236 GIGSIKGAFVGALLLGLTDTLGRTLLPVAFGTVLEPSMATAVGSALASMAIYILMAGVLI 295 Query: 287 FRPTGLLGR 295 FRP+GL G+ Sbjct: 296 FRPSGLFGQ 304 Lambda K H 0.329 0.144 0.425 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: 301 Number of extensions: 24 Number of successful extensions: 5 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: 301 Length of database: 305 Length adjustment: 27 Effective length of query: 274 Effective length of database: 278 Effective search space: 76172 Effective search space used: 76172 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: 48 (23.1 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