Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate Dsui_2060 Dsui_2060 branched-chain amino acid ABC-type transport system, permease component
Query= reanno::azobra:AZOBR_RS08235 (301 letters) >FitnessBrowser__PS:Dsui_2060 Length = 293 Score = 178 bits (452), Expect = 1e-49 Identities = 99/293 (33%), Positives = 167/293 (56%), Gaps = 12/293 (4%) Query: 6 QQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSLGITWV 65 QQL+N L+LG++Y L A+G+T+V+G++ +IN +HG ++M+G++ AL ++ + Sbjct: 4 QQLLNALTLGSVYALFALGFTLVFGVLAVINLSHGAVFMVGSYAALAM--------VSHL 55 Query: 66 PLALLVMLVASMLFTAVYGWTVERIAYRPLRS--SPRLAPLISAIGMSIFLQNYVQILQG 123 L V ++ +M+ + G V+ + +PLR+ +P L P+I+ IG+ I L + Q L G Sbjct: 56 NAPLWVAMLGAMVVSGTIGLLVDVLVLKPLRARNAPHLIPMIATIGVGIMLTSAAQGLFG 115 Query: 124 ARSKPL-QPILPGNLTLMDGAVSVSYVRLATIVITIALMYGFTQLITRTSLGRAQRACEQ 182 A + ++P M G V V + +A + I LM ++ RT LGRA RA + Sbjct: 116 AEVLRFPEDVMPAG-EFMVGDVHVRALEIAIVAIAFLLMAVLFTILKRTQLGRALRAIAE 174 Query: 183 DKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKAFTAAVLG 242 K A LLG+NV+ + +T + AAL +AG+++ L + I ++G K +LG Sbjct: 175 SPKAAYLLGINVEGLFHITSFVAAALGGIAGVLIGLNFNAITPFMGQPMLHKGIAVIILG 234 Query: 243 GIGSLPGAMLGGVVIGLIEAFWSGYMGSEWKDVATFTILVLVLIFRPTGLLGR 295 G+G + GA++GG+ +G E Y+ S+ D F +L L+L+ RP+GL GR Sbjct: 235 GMGDIRGALIGGLFLGFAEVISKAYLSSQMGDAVAFGLLFLILLVRPSGLFGR 287 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: 277 Number of extensions: 18 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: 301 Length of database: 293 Length adjustment: 26 Effective length of query: 275 Effective length of database: 267 Effective search space: 73425 Effective search space used: 73425 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