Align Phenylacetyl-CoA:acceptor oxidoreductase-like protein subunit C, PadD; EC 1.8.5.3 (characterized, see rationale)
to candidate WP_052473452.1 SUTH_RS08070 DmsC/YnfH family molybdoenzyme membrane anchor subunit
Query= uniprot:A0A2R4BLZ0 (293 letters) >NCBI__GCF_000828635.1:WP_052473452.1 Length = 306 Score = 257 bits (657), Expect = 2e-73 Identities = 139/287 (48%), Positives = 169/287 (58%), Gaps = 3/287 (1%) Query: 6 PELQPFWDARAAGNFIGGGTGTGLLLWAVLAATAHDTALLPPLLLALACIGGGLFCVWLE 65 P+ Q WD RAA NFI GG G GLL WA A AL +LL LA I GGL CVW E Sbjct: 14 PKQQRNWDWRAAANFICGGAGGGLLFWAAFAGL-DPVALRVAVLLGLALIAGGLTCVWFE 72 Query: 66 IGKPWRALNVFFHARTSWMTREAIVAMPLFAAGALAVLTGALAAAWLAALVGLGFLYCQA 125 IG+PWRALNV+ H TSWMTREA+VA+ +FAAG LA+LT A A ++GLGFLY QA Sbjct: 73 IGRPWRALNVYRHIATSWMTREAVVALLVFAAGGLALLTANALPALFAGVLGLGFLYSQA 132 Query: 126 RILQAARGIPAWREAALLPLVITTGLAEGAGLFALVAALLPQGPGTAFALPMLILVVLRG 185 RIL A +GIPAWR +PL++ TGLAEGAG A V +L G G + +++L+ R Sbjct: 133 RILAANKGIPAWRNRRSIPLMVATGLAEGAGFLACVLSLTSAGAGLPMLVGLIVLIGARA 192 Query: 186 WLWRRYRARLAAPDSAPLKAVRALDAEGRLFVPLGHYLPAVLLALALVLQGGAATALMAL 245 W RY L A D AP ++ L GH LPA+ + A+ G L+ + Sbjct: 193 LFWHRYLGALVA-DGAPDATLKVLGGIAARLAVFGHILPALFVMAAVAGMPGRG-GLVFV 250 Query: 246 AGVAMAAAGWHFKLALITRIAYTQGFALTHVPARTPGHARPGVKPGW 292 AG+ A GW K L+ R AYTQG AL H+P R G A KPGW Sbjct: 251 AGIMAVAGGWFLKFTLVRRAAYTQGLALQHMPMRGQGAAGAAAKPGW 297 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: 215 Number of extensions: 8 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: 293 Length of database: 306 Length adjustment: 27 Effective length of query: 266 Effective length of database: 279 Effective search space: 74214 Effective search space used: 74214 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 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