Align 3-keto-5-aminohexanoate cleavage enzyme (EC 2.3.1.247) (characterized)
to candidate HSERO_RS17240 HSERO_RS17240 hypothetical protein
Query= BRENDA::Q8RHX2 (272 letters) >FitnessBrowser__HerbieS:HSERO_RS17240 Length = 310 Score = 158 bits (399), Expect = 2e-43 Identities = 106/299 (35%), Positives = 159/299 (53%), Gaps = 32/299 (10%) Query: 4 KLIITAAICGAEVTKEHNPAVPYTVEEIAREAESAYKAGASIIHLHVRED-DGTPTQDKE 62 K+IIT A+ GA T +P +P T E+I EA +A +AGA+I+HLH R+ +G PTQD + Sbjct: 6 KVIITCAVTGAIHTPSMSPYLPVTPEQIRDEALAAAEAGAAIVHLHARDPGNGKPTQDPD 65 Query: 63 RFRKCIEAIREKCPDVIIQPSTGGAVGMTDLERLQPT-ELHPEMATLDCGTCNFG----- 116 FRK + I+ + +V+I +TGGA M ERLQP +L PE+A+L+ G+ NFG Sbjct: 66 AFRKFLPQIKARS-NVVINLTTGGAPTMGVEERLQPALQLKPEVASLNMGSMNFGLYEML 124 Query: 117 ------------------GDEIFVNTENTIKNFGKILIERGVKPEIEVFDKGMIDYAIRY 158 D IF NT I + + EIE +D G + A + Sbjct: 125 NRFKDFKYDWEQPYLAGSDDRIFRNTFKDIAYILESCSANQTRFEIECYDIGHLYTAAHF 184 Query: 159 QKQGFIQKPMHFDFVLGVQ--MSASARDLVFMSESIP----EGSTWTVAGVGRHQFQMAA 212 +G I+ P V G++ + D++ M + + W+V G GR Q +A Sbjct: 185 IDRGLIKPPFLIQSVFGLRGGIGNDVEDVMHMKRTADRLFGQDYFWSVLGAGRGQIPIAT 244 Query: 213 LAIVMGGHVRVGFEDNVYIDKGILAKSNGELVERVVRLAKELGREIATPDEARQILSLK 271 +A MGGH RVG ED+++ G LA+SN + V R+ + + L E+A+P++AR +L LK Sbjct: 245 MAAAMGGHTRVGLEDSLWDGPGKLARSNADQVRRIRTVIEALSLEVASPEDARAMLKLK 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: 226 Number of extensions: 12 Number of successful extensions: 5 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 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