Align ABC-type branched-chain amino acid transport system, permease component protein (characterized, see rationale)
to candidate WP_023434296.1 N177_RS20205 branched-chain amino acid ABC transporter permease
Query= uniprot:D8IUY4 (309 letters) >NCBI__GCF_000496075.1:WP_023434296.1 Length = 312 Score = 243 bits (620), Expect = 4e-69 Identities = 140/324 (43%), Positives = 198/324 (61%), Gaps = 41/324 (12%) Query: 1 MDIFIQQIINGLVLGSMYALIALGYTMVYGVLNLINFAHGDILMVGAMVGLSLLKVVQQV 60 M+ F+QQ+INGL LGS+Y LIA+GYTMVYG++ +INFAHGDI MVG+ + L + + Sbjct: 1 MEYFVQQLINGLTLGSIYGLIAIGYTMVYGIIGMINFAHGDIFMVGSFIALIAI-----I 55 Query: 61 APGLPGIVQLVIAIVGAIPVCIVVSLL-------IERIAYRPLRNAPRLAPLITAIGVSI 113 A GL L + I+ I V ++ L +ER+AYRPLR + RLAPLITAIG+SI Sbjct: 56 AFGLTAGSSLAVLILALILVLLIAMALTSVYGWTVERLAYRPLRGSFRLAPLITAIGMSI 115 Query: 114 LLQTLAMMIWGRSPLPFPQVMPSDPVHIAG----ALISPT-----------QIMLLALAV 158 +LQ + G +V P P+ G L PT QI+++ V Sbjct: 116 VLQNFVQIAQGA------RVKPLQPLFSGGFTLMELEGPTGAVFRVNLSFAQILIIVTTV 169 Query: 159 LAMVGLVLIVEKTKMGRAMRATAENPRIAGLMGVDANKVIVVTFAIGAGLAAIAGVMWAA 218 + M LI+ KT +GR+ RA ++ ++A L+GV+ ++ I +TF +GA LAA+AG+M+ Sbjct: 170 VLMTVFTLIIAKTSLGRSQRACEQDRKMAALLGVNVDRTISLTFVMGAALAAVAGLMYLL 229 Query: 219 NYSTAQFAMGFVPGLKAFSAAVLGGIGNIYGAMLGGILLGLIESLGAGYIGDLTGNFLGS 278 Y F +GF+ G+KAF+AAVLGGIG++ GAMLGG+L+GLIE+ + Y Sbjct: 230 YYGVIDFYIGFIAGVKAFTAAVLGGIGSLPGAMLGGLLIGLIETFWSAY--------FSI 281 Query: 279 NYQDIFAFIVLIIVLTLRPSGIMG 302 Y+D+ AF +L IVL PSGI+G Sbjct: 282 EYKDVAAFSILAIVLIFLPSGILG 305 Lambda K H 0.328 0.144 0.416 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: 306 Number of extensions: 17 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: 309 Length of database: 312 Length adjustment: 27 Effective length of query: 282 Effective length of database: 285 Effective search space: 80370 Effective search space used: 80370 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 (21.7 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