Align 2-deoxy-3-keto-D-ribonate cleavage enzyme (characterized)
to candidate WP_011842613.1 RSPH17029_RS18915 3-keto-5-aminohexanoate cleavage protein
Query= reanno::Burk376:H281DRAFT_00641 (312 letters) >NCBI__GCF_000015985.1:WP_011842613.1 Length = 306 Score = 352 bits (904), Expect = e-102 Identities = 178/305 (58%), Positives = 221/305 (72%), Gaps = 2/305 (0%) Query: 6 RKVIISCAITGATHVPSMSEFLPITPEQIRDQAIEAAQAGAAIIHLHARDPVDGRPTPSP 65 +K IISCA+TG+ H PSMS LP+T EQI + AI AA+AGAAI+HLHAR P G P+ P Sbjct: 2 KKTIISCAVTGSIHTPSMSPHLPVTAEQIAESAIGAAEAGAAILHLHARVPDTGAPSQDP 61 Query: 66 EIFKAFVPAIAEATDAVINITTGGSTRMTLEERLAYPRLARPEMCSLNMGSMNFSIHPVA 125 + AF+ I ATDA++NITTGG M+++ R+A PE+ SLNMGS NF+I A Sbjct: 62 AHYAAFLSRIRTATDAIVNITTGGGLGMSMDARIAPALKYAPELASLNMGSFNFNIS-AA 120 Query: 126 AKISSWRYGWEKDYIEGMEDMIFRNTFRDIRNILLELGESGTRFEFECYDVGHLYNLAHF 185 K WE DY+ G D+I NTF I +L L GTRFEFECYD GHLYNLAHF Sbjct: 121 EKGCRDPQPWEVDYLRGTRDLIMSNTFSQIETVLTRLSAQGTRFEFECYDTGHLYNLAHF 180 Query: 186 VDQGLVKPPFFIQSVFGILGGLGADPENMLLMRSTADRLFGRENYHFSVLGAGRHQMPLV 245 D+GLVKPPFF+Q++FG+ G G DPEN++ MR+TA RLFG ++ SVLGAGR Q PLV Sbjct: 181 ADRGLVKPPFFVQAIFGVTGAQGTDPENLMHMRATAQRLFGSDHL-LSVLGAGRSQFPLV 239 Query: 246 TMSAIMGGNVRVGLEDSVYLAKGVKAETNAQQVRKIRRILEELSLEIATPADARKMLGLK 305 TM AI+GG+VRVGLED++Y+A+G AE+NA+ V K+RRILEEL EIATP +AR+MLG K Sbjct: 240 TMGAILGGHVRVGLEDNLYIARGQLAESNARMVAKVRRILEELGHEIATPDEARRMLGTK 299 Query: 306 GADQV 310 GA +V Sbjct: 300 GAGEV 304 Lambda K H 0.321 0.137 0.400 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: 301 Number of extensions: 11 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: 312 Length of database: 306 Length adjustment: 27 Effective length of query: 285 Effective length of database: 279 Effective search space: 79515 Effective search space used: 79515 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: 48 (23.1 bits)
This GapMind analysis is from Apr 10 2024. 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