Align Phenylacetyl-CoA:acceptor oxidoreductase small subunit PadC (characterized, see rationale)
to candidate 3607829 Dshi_1237 4Fe-4S ferredoxin iron-sulfur binding domain protein (RefSeq)
Query= uniprot:A0A2R4BLY8 (215 letters) >FitnessBrowser__Dino:3607829 Length = 248 Score = 117 bits (292), Expect = 2e-31 Identities = 80/226 (35%), Positives = 98/226 (43%), Gaps = 44/226 (19%) Query: 3 RYAMVADLRRCVGCQTCTAACKHTN---------------ATPPGVQWRWVLDVEAGEFP 47 + +V DL CVGC C ACK N A P G V E Sbjct: 11 KLGLVIDLDTCVGCHACVVACKGWNDQAYGAPLSDQDPYGADPTGSFLNRVHSYEVTPAS 70 Query: 48 DVSR-TFVPVGCQHCDEPPCETVCPTTATKKRA-DGLVTIDYDLCIGCAYCSVACPYNAR 105 ++ P C HC++ PC TVCPT A+ KRA DG+V ++ D CIGC C+ ACPY AR Sbjct: 71 GPAQLVHFPKSCLHCEDAPCVTVCPTGASYKRAEDGIVLVNEDACIGCGLCAWACPYGAR 130 Query: 106 YKVNFAEPAYGDRLMANEKQRADPARVGVATKCTFCSDRIDYGVAHGLTPGVDPDATPAC 165 A GV KCT C DRI Y A + D PAC Sbjct: 131 EM---------------------DAAAGVMKKCTLCVDRI-YNEAL-----PEEDRQPAC 163 Query: 166 ANACIANALTFGDIDDPNSKASRLLRENEHFRMHEELGTGPGFFYL 211 C A A FGD+ DP+S+ S+L+ + E GT P YL Sbjct: 164 VRTCPAGARHFGDLGDPDSEVSQLVAARGGVDLMPEQGTKPVNKYL 209 Lambda K H 0.323 0.137 0.461 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: 279 Number of extensions: 26 Number of successful extensions: 7 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: 215 Length of database: 248 Length adjustment: 23 Effective length of query: 192 Effective length of database: 225 Effective search space: 43200 Effective search space used: 43200 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 46 (22.3 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