Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate WP_043743902.1 AMB_RS08455 branched-chain amino acid ABC transporter permease
Query= reanno::azobra:AZOBR_RS08235 (301 letters) >NCBI__GCF_000009985.1:WP_043743902.1 Length = 291 Score = 163 bits (413), Expect = 4e-45 Identities = 109/304 (35%), Positives = 166/304 (54%), Gaps = 23/304 (7%) Query: 4 FLQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSLGIT 63 FLQ L +GL+ GAIY L +G+ ++Y +INFA GE MIG +A T +A G Sbjct: 5 FLQYLFSGLTSGAIYALAGLGFAIIYNASHVINFAQGEFIMIGG-MATATMVAAGVPIYL 63 Query: 64 WVPLALLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYVQILQG 123 +PLA+ ASML G +E+ A P R++ + +I IG SIF++ Q++ Sbjct: 64 AIPLAM----AASMLV----GVAMEKFAIEPARNADVVTIIIITIGASIFMRGAAQLIWD 115 Query: 124 ARSKPLQ------PILPGNLTLMDGAVSVSYVRLATIVITIALMYGFTQLITRTSLGRAQ 177 L PI TLM ++ V + + IAL++ F RT G+A Sbjct: 116 KEFHSLPAFSGETPIAVMGATLMPQSLWVFGIS----AVAIALLWYF---FNRTMFGKAM 168 Query: 178 RACEQDKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKAFT 237 ++ A L+GV V RV+ +F + A L AV G++V I ++ G + G+K F+ Sbjct: 169 LGTSHNRLAAQLVGVAVKRVLLASFALSALLGAVGGIVVTPIT-FTNYEAGIMLGLKGFS 227 Query: 238 AAVLGGIGSLPGAMLGGVVIGLIEAFWSGYMGSEWKDVATFTILVLVLIFRPTGLLGRPE 297 AAVLGG+G+ GA++GG+++G+ EA SGY+ S +KD F I++ VL F P+GL G+ Sbjct: 228 AAVLGGLGNGTGAIIGGLIVGIAEAMASGYLSSAYKDAIAFIIILFVLFFMPSGLFGKRG 287 Query: 298 IEKV 301 ++V Sbjct: 288 TDRV 291 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: 260 Number of extensions: 11 Number of successful extensions: 4 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: 291 Length adjustment: 26 Effective length of query: 275 Effective length of database: 265 Effective search space: 72875 Effective search space used: 72875 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