Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate PP_0618 PP_0618 Branched-chain amino acid ABC transporter, permease protein
Query= reanno::azobra:AZOBR_RS08235 (301 letters) >FitnessBrowser__Putida:PP_0618 Length = 286 Score = 157 bits (398), Expect = 2e-43 Identities = 97/300 (32%), Positives = 161/300 (53%), Gaps = 21/300 (7%) Query: 1 MEYFLQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSL 60 ++ +L QL+NGL LG IY LIA+G T+++G++ +NFAHG +++GA+ + + A+ Sbjct: 2 LDLYLFQLLNGLGLGMIYFLIAVGLTIIFGLLNFVNFAHGAFFLLGAY---LCYTAVAVT 58 Query: 61 GITWVPLALLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYVQI 120 G W+ L + ++VA++ W VER+ + + P ++ +G+++ +Q + Sbjct: 59 GNFWLALLIAPLVVAAL------AWAVERLLIKRIYHLPHTFQILVTLGIALIIQEASVL 112 Query: 121 LQGARSK--PLQPILPGNLTLMDGAVSVSYVRLATIVITIALMYGFTQLITRTSLGRAQR 178 + G K + P L G L L G Y RL I + G L+ RT G R Sbjct: 113 IWGPVGKNIAVPPELRGVLIL--GDFIYPYYRLFLIGFAALIGIGLWLLLERTRFGALVR 170 Query: 179 ACEQDKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKAFTA 238 A + + LLG N+ R+ SLTF +G LA VAG++ + G F + G+ AF Sbjct: 171 AGSESTETVSLLGTNIFRLFSLTFALGVGLAGVAGVLFAPLRGAQPFVGPEILGI-AFVV 229 Query: 239 AVLGGIGSLPGAMLGGVVIGLIEAFWSGYMGSEWKDVATFTI---LVLVLIFRPTGLLGR 295 V+GG+GS GA++GG+++G++++ M S W A+ I + V++ RP GL GR Sbjct: 230 VVIGGMGSFGGALVGGLLVGVVQSM----MTSLWPQGASLMIYGAMAAVILVRPYGLFGR 285 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: 325 Number of extensions: 26 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: 286 Length adjustment: 26 Effective length of query: 275 Effective length of database: 260 Effective search space: 71500 Effective search space used: 71500 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