Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate WP_028321170.1 H567_RS0109125 branched-chain amino acid ABC transporter permease
Query= reanno::azobra:AZOBR_RS08235 (301 letters) >NCBI__GCF_000422285.1:WP_028321170.1 Length = 308 Score = 270 bits (689), Expect = 4e-77 Identities = 152/297 (51%), Positives = 204/297 (68%), Gaps = 3/297 (1%) Query: 7 QLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSLGITWV- 65 QLINGL++G IY LIA+GYT+VYGI+ MINFAHGEI+M G+F + G T Sbjct: 13 QLINGLTIGGIYALIALGYTLVYGILFMINFAHGEIFMFGSFAGYAALTFLLQYGFTEQR 72 Query: 66 PLA-LLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYVQILQGA 124 PLA +L +A+M+ +A+ G +ERIAYRPLR + RLAPLISAIG SIFLQN + I+ Sbjct: 73 PLASILAAFLAAMVVSALLGTILERIAYRPLRRASRLAPLISAIGASIFLQNVMLIIIKG 132 Query: 125 RSKPLQPILPGNLTLMDGAVSVSYVRLATIVITIALMYGFTQLITRTSLGRAQRACEQDK 184 R + + P L G ++S ++ I+ + LM G I RT GRA RA +D+ Sbjct: 133 RMQ-VYPDLLHETFFEIGWFNISNFQIMIILGSFFLMAGLYIFIQRTRTGRAMRAVAEDR 191 Query: 185 KMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKAFTAAVLGGI 244 A L+G++V+R+I +TFV+G+ALAA AG+MV + Y I+ +GF+ G+KAFTAAVLGGI Sbjct: 192 SAAALMGIDVNRIIMITFVIGSALAAAAGVMVGMYYTQINHMMGFIPGIKAFTAAVLGGI 251 Query: 245 GSLPGAMLGGVVIGLIEAFWSGYMGSEWKDVATFTILVLVLIFRPTGLLGRPEIEKV 301 G++PGAMLGG+ +GL EAF +M +++KDV F +LVLVLIFRP G+LG EKV Sbjct: 252 GNVPGAMLGGLFLGLAEAFGVLFMPAQYKDVIAFALLVLVLIFRPRGILGEVVSEKV 308 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: 338 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: 308 Length adjustment: 27 Effective length of query: 274 Effective length of database: 281 Effective search space: 76994 Effective search space used: 76994 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 Apr 09 2024. 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