Align Phenylacetyl-CoA:acceptor oxidoreductase-like protein subunit C, PadD; EC 1.8.5.3 (characterized, see rationale)
to candidate WP_043744129.1 AMB_RS10180 hypothetical protein
Query= uniprot:A0A2R4BLZ0 (293 letters) >NCBI__GCF_000009985.1:WP_043744129.1 Length = 275 Score = 211 bits (536), Expect = 2e-59 Identities = 133/279 (47%), Positives = 161/279 (57%), Gaps = 16/279 (5%) Query: 4 VQPELQPFWDARAAGNFIGGGTGTGLLLWAVLAATAHDTALLPPLLLALACIGGGLFCVW 63 + LQ WD RAAGNFIGGG GTGL+L +VL D L L+ LA +G GL VW Sbjct: 5 ITARLQRSWDLRAAGNFIGGGAGTGLVLASVLLG---DGGL--SLVAGLALVGLGLAMVW 59 Query: 64 LEIGKPWRALNVFFHARTSWMTREAIVAMPLFAAGALAVLTGALAAAWLAALVGLGFLYC 123 LEIGKPWRALNVFFH +TSWMTRE IVA PL A G L G A ++ GFLYC Sbjct: 60 LEIGKPWRALNVFFHPQTSWMTREGIVAGPLMAVGGGYWLLGHPALLVPLVVLAAGFLYC 119 Query: 124 QARILQAARGIPAWREAALLPLVITTGLAEGAGLFALVAALLPQGPGTAFALPMLILVVL 183 Q+RIL+A+RGIPAW++A ++PL+IT+GLAEGAGL AL A P A L + Sbjct: 120 QSRILRASRGIPAWKQAEIVPLIITSGLAEGAGLLALFAE-----PAPAVLAWALAAGLA 174 Query: 184 RGWLWRRYRARLAAPDSAPLKAVRALDAEGRLFVPLGHYLPAVLLALALVLQGGAATALM 243 R W YR L A +A A+ G P A LALAL L A + Sbjct: 175 REGAWMLYRRGLVASGNA--SGALAIFGSG----PAQAARMAQGLALALWLLALAGLPVA 228 Query: 244 ALAGVAMAAAGWHFKLALITRIAYTQGFALTHVPARTPG 282 LAG+ A +GW K LITR A+T+G ++ + P R G Sbjct: 229 PLAGLLAAGSGWGIKALLITRAAFTRGASVPYAPVRGRG 267 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: 200 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: 275 Length adjustment: 26 Effective length of query: 267 Effective length of database: 249 Effective search space: 66483 Effective search space used: 66483 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: 47 (22.7 bits)
This GapMind analysis is from Sep 17 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