Align 3-keto-5-aminohexanoate cleavage enzyme (EC 2.3.1.247) (characterized)
to candidate WP_038069183.1 DL1_RS18540 3-keto-5-aminohexanoate cleavage protein
Query= BRENDA::Q8RHX2 (272 letters) >NCBI__GCF_000715505.1:WP_038069183.1 Length = 310 Score = 148 bits (374), Expect = 1e-40 Identities = 100/300 (33%), Positives = 158/300 (52%), Gaps = 34/300 (11%) Query: 4 KLIITAAICGAEVTKEHNPAVPYTVEEIAREAESAYKAGASIIHLHVRE-DDGTPTQDKE 62 K II+ AI GA T + A+PYT ++IA ++ +A +AGASI+HLH R +DG + D + Sbjct: 6 KTIISCAITGAIHTPTMSDALPYTADDIASQSIAAAEAGASILHLHARRPEDGGVSVDPD 65 Query: 63 RFRKCIEAIREKCPDVIIQPSTGGAVGMTDLERLQPT-ELHPEMATLDCGTCNFG----- 116 F + I++ D ++ STGG++ + ER++P PEM +++ G+ NF Sbjct: 66 HFAAFLPRIKQ-ATDAVVNISTGGSLHLPISERIKPALTFSPEMCSMNMGSMNFSFHPLA 124 Query: 117 ------------------GDEIFVNTENTIKNFGKILIERGVKPEIEVFDKGMIDYAIRY 158 IF NT I+ L +K E E +D G + Y +++ Sbjct: 125 KRYDDWKFDWEKDYVESSEGNIFRNTFADIREAATSLAPHDIKFEHECYDVGHL-YNLKF 183 Query: 159 QKQ-GFIQKPMHFDFVLGVQ--MSASARDLVFMSESIP----EGSTWTVAGVGRHQFQMA 211 G + P+ F+ G+ + +L+FM + + W+V G G Q +A Sbjct: 184 CMDIGLFKAPIFIQFIFGILGGIGPEVDNLIFMKRTADRLFGDDYRWSVLGAGGAQMGLA 243 Query: 212 ALAIVMGGHVRVGFEDNVYIDKGILAKSNGELVERVVRLAKELGREIATPDEARQILSLK 271 + A MGG++RVG ED++ I +G LA+SN + V ++ R+ ++LG EIATPDEAR IL LK Sbjct: 244 STAAQMGGNLRVGLEDSLLIRRGQLAESNAQQVAKIRRIVEDLGSEIATPDEARDILGLK 303 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: 205 Number of extensions: 9 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: 272 Length of database: 310 Length adjustment: 26 Effective length of query: 246 Effective length of database: 284 Effective search space: 69864 Effective search space used: 69864 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: 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