Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate WP_029134157.1 A3GO_RS0115370 branched-chain amino acid ABC transporter permease
Query= reanno::azobra:AZOBR_RS08235 (301 letters) >NCBI__GCF_000428045.1:WP_029134157.1 Length = 293 Score = 175 bits (444), Expect = 1e-48 Identities = 105/300 (35%), Positives = 171/300 (57%), Gaps = 9/300 (3%) Query: 2 EYFLQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSLG 61 + LQ L+ G+++G+ Y L+ +G+ ++Y ++NF+ GE MIGA A+ L+ G G Sbjct: 3 DQILQFLLTGITVGSTYALVGLGFAIIYNASDVVNFSQGEFVMIGAMSAVA--LSAGDTG 60 Query: 62 ITWVPLALLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYVQIL 121 L L +A++L T + G ++R A P R + + +I IG SIFL+ ++ Sbjct: 61 -----LPLWAAALAAVLITTLVGMALQRFAIXPARGASVVTTIIITIGASIFLRGVALLV 115 Query: 122 QGARSKPLQPILPGNLTLMDGAVSVSYVRLATIVITIALMYGFTQLITRTSLGRAQRACE 181 G L P GN + G +V L + L++G T T+LG+A AC Sbjct: 116 WGKDLFALPPF-SGNEPIXIGNATVLPQSLWVMGGAAVLVFGAQYFFTHTTLGKAILACS 174 Query: 182 QDKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKAFTAAVL 241 +K A L+G+NV ++ + + + AAL A+AG++V I + G + G+K F+AA+L Sbjct: 175 CNKTAAHLVGINVGVMLLVAYGLSAALGAMAGILVAPIT-FASYDTGVMLGLKGFSAAIL 233 Query: 242 GGIGSLPGAMLGGVVIGLIEAFWSGYMGSEWKDVATFTILVLVLIFRPTGLLGRPEIEKV 301 GG+G+ GA+ GG+++GLIE+ +G + S +KD F IL+LVL FRP+GL G+ +E+V Sbjct: 234 GGMGNPMGAVAGGLLLGLIESLSAGLISSGYKDAIGFIILLLVLFFRPSGLFGKASVERV 293 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: 315 Number of extensions: 25 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: 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 24 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