Align 2-deoxy-3-keto-D-ribonate cleavage enzyme (characterized)
to candidate WP_041100197.1 SUTH_RS14325 3-keto-5-aminohexanoate cleavage protein
Query= reanno::Burk376:H281DRAFT_00641 (312 letters) >NCBI__GCF_000828635.1:WP_041100197.1 Length = 294 Score = 113 bits (283), Expect = 5e-30 Identities = 94/314 (29%), Positives = 145/314 (46%), Gaps = 32/314 (10%) Query: 4 TSRKVIISCAITGATHVPSMSEFLPITPEQIRDQAIEAAQAGAAIIHLHARDPVDGR--- 60 T K I++CA+TG P +P+TP Q+ A EA AGA+I+H+H R G Sbjct: 3 THDKAILTCALTGVLTDPKQHP-VPVTPSQMAAAAREAFDAGASIMHVHLRRQEPGMGHL 61 Query: 61 PTPSPEIFKAFVPAIAEATDAVINITTGGSTRMTLEERLAYPRLARPEMCSLNMGSMNFS 120 P+ P + V AI A VI T G + A R +PE+ + N G++N+ Sbjct: 62 PSWDPAVAAEIVDAIRAACPGVIINLTTGVIGADISGPAACIRRVKPEIAACNAGTLNY- 120 Query: 121 IHPVAAKISS-WRYGWEKDYIEGMEDMIFRNTFRDIRNILLELGESGTRFEFECYDVGHL 179 K+ R+ W M+F N ++ L + E+GTR EFEC+DVG + Sbjct: 121 -----LKLKDDGRWAWPP--------MVFDNPVEKVQAFLDVMAETGTRPEFECFDVGIV 167 Query: 180 YNLAHFVDQGLVKPPFFIQS----VFGILGGLGADPENM-LLMRSTADRLFGRENYHFSV 234 ++ + + + P + V G+ G+ D + + LL+R + + + Sbjct: 168 RSVGMY-RKAAMSPQLANHAEYNFVMGVASGMPVDADLLQLLLR------WIQPGSSWQA 220 Query: 235 LGAGRHQM-PLVTMSAIMGGNVRVGLEDSVYLAKGVKAETNAQQVRKIRRILEELSLEIA 293 GR ++ PL A +GG +R GLEDS YL G +A N + + E+A Sbjct: 221 TLIGRAEIWPLHQRVAELGGMLRTGLEDSFYLPDGSRAAGNGAMIEALAACARRAGREVA 280 Query: 294 TPADARKMLGLKGA 307 +PA+AR LGL A Sbjct: 281 SPAEARVALGLPAA 294 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: 209 Number of extensions: 11 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: 312 Length of database: 294 Length adjustment: 27 Effective length of query: 285 Effective length of database: 267 Effective search space: 76095 Effective search space used: 76095 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 09 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