Align Phenylacetyl-CoA:acceptor oxidoreductase-like protein subunit C, PadD; EC 1.8.5.3 (characterized, see rationale)
to candidate WP_051302224.1 A3GO_RS0111475 hypothetical protein
Query= uniprot:A0A2R4BLZ0 (293 letters) >NCBI__GCF_000428045.1:WP_051302224.1 Length = 291 Score = 221 bits (563), Expect = 2e-62 Identities = 133/287 (46%), Positives = 171/287 (59%), Gaps = 11/287 (3%) Query: 4 VQPELQPFWDARAAGNFIGGGTGTGLLLWA-VLAATAHDTALLPPLLLALACIGGGLFCV 62 + +Q WD RAAGNF+GGG+G+GL+LWA +L+ +D ++P L+ LA + GGLFCV Sbjct: 11 ISSRVQRNWDWRAAGNFVGGGSGSGLILWAALLSPLGYD--VIPLLVTGLALVAGGLFCV 68 Query: 63 WLEIGKPWRALNVFFHARTSWMTREAIVAMPLFAAGALAVLTGALAAAWLAALVGLGFLY 122 WLEIG+PWRALNV H +SWM+REA VA LF +G A L L W AL+ FLY Sbjct: 69 WLEIGRPWRALNVLKHVSSSWMSREAWVAPLLFLSGLAAWLFTPL-LLWPTALLAGAFLY 127 Query: 123 CQARILQAARGIPAWREAALLPLVITTGLAEGAGLFALVAALLPQGPGTAFALPMLILVV 182 Q+RIL+A +GIPAWR LV+ TGL EGAGL L+ L Q A+ +LIL+ Sbjct: 128 SQSRILRADKGIPAWRHPRAGLLVVVTGLTEGAGLLVLLLPLFDQPQPLAWG-ALLILLA 186 Query: 183 LRGWLWRRYRARLAAPDSAPLKAVRALDAEGRLFVPLGHYLPAVLLALALVLQGGAATAL 242 LR + WR YR LA APL + + L A F GH LP +LL LALV+ + Sbjct: 187 LRAFAWRHYRDGLAEA-KAPLASQKRLAAIDTGFFWGGHLLPGLLLGLALVV-----PVV 240 Query: 243 MALAGVAMAAAGWHFKLALITRIAYTQGFALTHVPARTPGHARPGVK 289 +AG + G K LITR A+TQGF + H+P R A V+ Sbjct: 241 ATVAGAIVLLTGAWMKYILITRAAFTQGFTMQHLPVRGQPSANAAVR 287 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: 233 Number of extensions: 7 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: 293 Length of database: 291 Length adjustment: 26 Effective length of query: 267 Effective length of database: 265 Effective search space: 70755 Effective search space used: 70755 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