Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate WP_028584460.1 G494_RS0110180 branched-chain amino acid ABC transporter permease
Query= reanno::azobra:AZOBR_RS08235 (301 letters) >NCBI__GCF_000429965.1:WP_028584460.1 Length = 300 Score = 320 bits (821), Expect = 2e-92 Identities = 165/301 (54%), Positives = 223/301 (74%), Gaps = 1/301 (0%) Query: 1 MEYFLQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSL 60 MEYF++ L +GL+ G+IY LIA+GYTMVYGIIG+INFAHGEIYMIGAF AL+ A+ Sbjct: 1 MEYFIELLFSGLTRGSIYALIALGYTMVYGIIGLINFAHGEIYMIGAFTALVVSTALTIY 60 Query: 61 GITWVPLALLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYVQI 120 G + + +L L A++ + A YG+T+ER+AYRPLRS+PRL+PLISAIGMSIFLQNYV + Sbjct: 61 GFPLLAVVVLTALAAAV-WAASYGYTIERLAYRPLRSAPRLSPLISAIGMSIFLQNYVLL 119 Query: 121 LQGARSKPLQPILPGNLTLMDGAVSVSYVRLATIVITIALMYGFTQLITRTSLGRAQRAC 180 Q + P ++P + A V +A +V++ M T +I T G+A RA Sbjct: 120 AQTSDFVPFPALVPEFAFMEPYAHIVGSSDMAILVVSALAMIILTCMIKYTRTGKAMRAT 179 Query: 181 EQDKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKAFTAAV 240 QD+KMA L+G+NVD VIS+TF+ G+ALAA+ G+++ G I+FYIGF+AG+KAFTAAV Sbjct: 180 AQDQKMALLVGINVDNVISITFITGSALAAIGGLLIASHIGQINFYIGFIAGIKAFTAAV 239 Query: 241 LGGIGSLPGAMLGGVVIGLIEAFWSGYMGSEWKDVATFTILVLVLIFRPTGLLGRPEIEK 300 LGGIGS+PGA+LG ++GL EAF +GY+ S+++DV F++LVL+LIF+P GLLG+ IEK Sbjct: 240 LGGIGSIPGAVLGSFILGLTEAFATGYVSSDYEDVFAFSLLVLILIFKPAGLLGKATIEK 299 Query: 301 V 301 V Sbjct: 300 V 300 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: 370 Number of extensions: 16 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: 300 Length adjustment: 27 Effective length of query: 274 Effective length of database: 273 Effective search space: 74802 Effective search space used: 74802 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