Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate WP_029133958.1 A3GO_RS0114215 branched-chain amino acid ABC transporter permease
Query= reanno::azobra:AZOBR_RS08235 (301 letters) >NCBI__GCF_000428045.1:WP_029133958.1 Length = 304 Score = 461 bits (1185), Expect = e-134 Identities = 226/304 (74%), Positives = 268/304 (88%), Gaps = 3/304 (0%) Query: 1 MEYFLQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSL 60 MEYF+QQLING++LG+IYGLIAIGYTMVYGIIGMINFAHG+++MIGAF++LI FL +G + Sbjct: 1 MEYFIQQLINGVTLGSIYGLIAIGYTMVYGIIGMINFAHGDVFMIGAFLSLIAFLVLGII 60 Query: 61 GITWVPLALLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYVQI 120 GITW+PLALLV+L+ SML +VYGWTVER+AYRPLR S RLAPLISAIGMSIFLQNYVQ+ Sbjct: 61 GITWIPLALLVVLLVSMLIASVYGWTVERLAYRPLRGSFRLAPLISAIGMSIFLQNYVQL 120 Query: 121 LQGARSKPLQPILPGNLTLMDGA---VSVSYVRLATIVITIALMYGFTQLITRTSLGRAQ 177 LQGAR +P+ P++ G T ++G+ ++VSY+++ +++TIALM GF LI RTSLGRAQ Sbjct: 121 LQGARVRPMPPVISGGFTFLEGSDFPITVSYLQIVIVLLTIALMTGFALLIARTSLGRAQ 180 Query: 178 RACEQDKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKAFT 237 R CEQD+ M+ LLG+NVDR ISLTFVMGAALAAVAGMM +L YGVIDFYIGFLAG+KAFT Sbjct: 181 RGCEQDRTMSALLGINVDRTISLTFVMGAALAAVAGMMFVLYYGVIDFYIGFLAGIKAFT 240 Query: 238 AAVLGGIGSLPGAMLGGVVIGLIEAFWSGYMGSEWKDVATFTILVLVLIFRPTGLLGRPE 297 AAVLGGIGSLPGAMLGG++IGLIE +WS Y E+KDVA F ILVLVLIFRPTGLLG+PE Sbjct: 241 AAVLGGIGSLPGAMLGGLLIGLIETYWSAYFSIEYKDVAAFAILVLVLIFRPTGLLGKPE 300 Query: 298 IEKV 301 IEKV Sbjct: 301 IEKV 304 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: 470 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: 304 Length adjustment: 27 Effective length of query: 274 Effective length of database: 277 Effective search space: 75898 Effective search space used: 75898 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