Align 3-keto-5-aminohexanoate cleavage enzyme (EC 2.3.1.247) (characterized)
to candidate GFF242 PGA1_c02540 Uncharacterized conserved protein
Query= BRENDA::Q8RHX2 (272 letters) >FitnessBrowser__Phaeo:GFF242 Length = 278 Score = 187 bits (476), Expect = 2e-52 Identities = 111/276 (40%), Positives = 147/276 (53%), Gaps = 7/276 (2%) Query: 1 MMEKLIITAAICGAEVTKEHNPAVPYTVEEIAREAESAYKAGASIIHLHVREDDGTPTQD 60 M II AI G+ K HNPAVP ++EE AY+AGASI H HVR +D TPT D Sbjct: 1 MNNPCIICVAITGSVPRKAHNPAVPISIEEQIESTHEAYEAGASIAHCHVRLEDETPTSD 60 Query: 61 KERFRKCIEAIREKCPDVIIQPSTGGAVGMTDLERLQPTELHPEMATLDCGTCNFGGDEI 120 +RF + + IR CPD+IIQ STGG G ER L P+MA+L G+ NF + Sbjct: 61 PDRFARLMGGIRHHCPDMIIQLSTGGRSG-AGRERGGMLSLRPDMASLSVGSNNF-PTRV 118 Query: 121 FVNTENTIKNFGKILIERGVKPEIEVFDKGMIDYAIRYQKQGFIQKPMHFDFVLGVQMSA 180 + N + + ++ VKPEIE FD I A+ + G ++ P++ FVLGV+ + Sbjct: 119 YENPPDLVDWLAAQMLAYDVKPEIEAFDLSHIHQAVAMSRDGRLKAPLYVQFVLGVKNAM 178 Query: 181 SARDLVF-----MSESIPEGSTWTVAGVGRHQFQMAALAIVMGGHVRVGFEDNVYIDKGI 235 VF E + + W AG+G Q ++ AI GGH R G EDN+ +D+ Sbjct: 179 PVDRNVFDYYVKTMERLAPDAQWCAAGIGAGQLEVNEWAIAAGGHTRTGLEDNLRLDRQT 238 Query: 236 LAKSNGELVERVVRLAKELGREIATPDEARQILSLK 271 LA SN LV R L R +AT DEAR IL L+ Sbjct: 239 LAPSNAALVRRAADLCDRYDRPVATCDEARAILGLR 274 Lambda K H 0.319 0.137 0.394 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: 203 Number of extensions: 15 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: 272 Length of database: 278 Length adjustment: 25 Effective length of query: 247 Effective length of database: 253 Effective search space: 62491 Effective search space used: 62491 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 (21.8 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