Align 5-aminopentanamidase (EC 3.5.1.30) (characterized)
to candidate WP_086509072.1 BZY95_RS05890 acyltransferase
Query= BRENDA::B3IVI7 (264 letters) >NCBI__GCF_002151265.1:WP_086509072.1 Length = 288 Score = 108 bits (269), Expect = 2e-28 Identities = 79/247 (31%), Positives = 119/247 (48%), Gaps = 11/247 (4%) Query: 27 QLAAERGAQLLVCPEMFLTGYNIGLAQVERLAEAA---DGPAAMTVVEIAQAHRIAIVYG 83 Q AA+ G Q+L E+F Y + A A DGP + ++A HR+ ++ Sbjct: 37 QQAAQAGVQVLCFQEVFNQPYFCPSQDPKWYAAAERVPDGPTCRMMQKLAAEHRMVMIVP 96 Query: 84 YPERGDDGAIYNSVQLIDAHGRSLSNYRKTHL---FGELDRSMFSPGADHFPVVELEGWK 140 E G YNS + DA G L Y KTH+ G ++ F PG +PV + K Sbjct: 97 IYEETVTGVYYNSAAVFDADGSYLGKYHKTHIPQVAGFWEKFFFKPGRSGWPVFDTAYGK 156 Query: 141 VGLLICYDIEFPENARRLALDGAELILVPTANMTPY-DFTCQVTVRARAQENQCYLVYAN 199 +G+ ICYD FPE R LAL+GAE+I P+A + + ++ A A N C++ N Sbjct: 157 IGVYICYDRHFPEGWRALALNGAEVIFNPSATVAGLSQYLWELEQPASAAANGCFIAAIN 216 Query: 200 YCGAE---DEIEYCGQSSIIGPDGSLLAMAG-RDECQLLAELEHERVVQGRTAFPYLTDL 255 G+E + E+ G S I+ P G + A A R + L+ E++ V + R + + D Sbjct: 217 RVGSEAPWNIGEFYGSSYIVNPRGQIEAQASDRADELLVHEIDLAMVREIRNNWQFFRDR 276 Query: 256 RQELHLR 262 R E + R Sbjct: 277 RPEAYGR 283 Lambda K H 0.322 0.139 0.416 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: 209 Number of extensions: 14 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: 264 Length of database: 288 Length adjustment: 25 Effective length of query: 239 Effective length of database: 263 Effective search space: 62857 Effective search space used: 62857 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: 47 (22.7 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