Align 2-deoxy-3-keto-D-ribonate cleavage enzyme (characterized)
to candidate BPHYT_RS04760 BPHYT_RS04760 3-keto-5-aminohexanoate cleavage protein
Query= reanno::Burk376:H281DRAFT_00641 (312 letters) >FitnessBrowser__BFirm:BPHYT_RS04760 Length = 310 Score = 543 bits (1399), Expect = e-159 Identities = 260/307 (84%), Positives = 290/307 (94%) Query: 5 SRKVIISCAITGATHVPSMSEFLPITPEQIRDQAIEAAQAGAAIIHLHARDPVDGRPTPS 64 +RKVIISCA+TGATH PSMSE+LP+TP QI Q+IEAA+AGAAI+HLHAR+P DG+PTPS Sbjct: 3 NRKVIISCAVTGATHTPSMSEYLPVTPAQIAAQSIEAAEAGAAILHLHARNPADGKPTPS 62 Query: 65 PEIFKAFVPAIAEATDAVINITTGGSTRMTLEERLAYPRLARPEMCSLNMGSMNFSIHPV 124 PE+F+ FVPAI EATDAVIN+TTGGSTRMTL +RLAYPRLA+PEMCSLNMGSMNFSIHP+ Sbjct: 63 PEVFRQFVPAIVEATDAVINVTTGGSTRMTLADRLAYPRLAKPEMCSLNMGSMNFSIHPI 122 Query: 125 AAKISSWRYGWEKDYIEGMEDMIFRNTFRDIRNILLELGESGTRFEFECYDVGHLYNLAH 184 AA++ SWRY WEKDYIEGMED IFRNTF+DI++ILLELGE+GTRFEFECYDVGHLYNLAH Sbjct: 123 AARMQSWRYDWEKDYIEGMEDTIFRNTFKDIKSILLELGEAGTRFEFECYDVGHLYNLAH 182 Query: 185 FVDQGLVKPPFFIQSVFGILGGLGADPENMLLMRSTADRLFGRENYHFSVLGAGRHQMPL 244 FVDQGL+KPPFFIQSVFGILGGLGADPENM +MRSTADRLFGRENY FS+LGAGRHQM Sbjct: 183 FVDQGLIKPPFFIQSVFGILGGLGADPENMTVMRSTADRLFGRENYQFSILGAGRHQMAF 242 Query: 245 VTMSAIMGGNVRVGLEDSVYLAKGVKAETNAQQVRKIRRILEELSLEIATPADARKMLGL 304 VTM AIMGGNVRVGLEDSVYL+KGVKAE+NAQQVRKIRRILEELS EIATPA+AR+MLGL Sbjct: 243 VTMGAIMGGNVRVGLEDSVYLSKGVKAESNAQQVRKIRRILEELSFEIATPAEARQMLGL 302 Query: 305 KGADQVN 311 KGAD+V+ Sbjct: 303 KGADKVS 309 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: 412 Number of extensions: 10 Number of successful extensions: 1 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: 310 Length adjustment: 27 Effective length of query: 285 Effective length of database: 283 Effective search space: 80655 Effective search space used: 80655 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 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