Align Phenylacetyl-CoA:acceptor oxidoreductase-like protein subunit C, PadD; EC 1.8.5.3 (characterized, see rationale)
to candidate WP_037375642.1 A3GO_RS24140 hypothetical protein
Query= uniprot:A0A2R4BLZ0 (293 letters) >NCBI__GCF_000428045.1:WP_037375642.1 Length = 294 Score = 216 bits (550), Expect = 5e-61 Identities = 134/293 (45%), Positives = 165/293 (56%), Gaps = 12/293 (4%) Query: 6 PELQPFWDARAAGNFIGGGTGTGLLLWAVL--AATAHDTALLPPLLLALACIGGGLFCVW 63 P LQ WD RAAGNFI GGTG+GLL+ A L A H T LLA A + GL VW Sbjct: 4 PTLQKRWDWRAAGNFICGGTGSGLLVVAALLSALGLHTTGYA---LLASAFVATGLGLVW 60 Query: 64 LEIGKPWRALNVFFHARTSWMTREAIVAMPLFAAGALAVLTGALAAAWLAALVGLGFLYC 123 LEIG+P R++NVF + TSWMTRE +VAM L G L TG+ + L+A+ FLY Sbjct: 61 LEIGRPLRSMNVFRNPATSWMTREGMVAMLLLPLGILTFFTGSTSLLILSAIPAALFLYA 120 Query: 124 QARILQAARGIPAWREAALLPLVITTGLAEGAGLFALVAALLPQGPGTAFA----LPMLI 179 QARIL A+GIPAWR A+ PL++TTGL EG G+ + A L+ F + L Sbjct: 121 QARILHMAKGIPAWRTNAINPLIVTTGLTEGMGVLLIFAGLVEGNVAALFVGYGWIIALS 180 Query: 180 LVVLRGWLWRRYRARLAAPDSAPLKAVRALDAEGRLFVPLGHYLPAVLLALALVLQGGAA 239 LV LRG W YR LA ++AP + ++ L+ + LG P VLL L Sbjct: 181 LVFLRGAAWLNYRYSLA--NNAPEQTLQVLERANIVITLLGIATPLVLLFLG-KSYAAYQ 237 Query: 240 TALMALAGVAMAAAGWHFKLALITRIAYTQGFALTHVPARTPGHARPGVKPGW 292 L A+AG M GW K +I AY QGFA+TH PAR G PG+KPGW Sbjct: 238 LPLAAVAGFFMVLCGWFCKYQIIIYAAYYQGFAITHTPARGGGKPGPGLKPGW 290 Lambda K H 0.328 0.140 0.457 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: 198 Number of extensions: 6 Number of successful extensions: 2 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: 293 Length of database: 294 Length adjustment: 26 Effective length of query: 267 Effective length of database: 268 Effective search space: 71556 Effective search space used: 71556 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