Align 3-keto-5-aminohexanoate cleavage enzyme (EC 2.3.1.247) (characterized)
to candidate 3610094 Dshi_3475 protein of unknown function DUF849 (RefSeq)
Query= BRENDA::Q8RHX2 (272 letters) >FitnessBrowser__Dino:3610094 Length = 279 Score = 169 bits (429), Expect = 5e-47 Identities = 104/271 (38%), Positives = 140/271 (51%), Gaps = 7/271 (2%) Query: 6 IITAAICGAEVTKEHNPAVPYTVEEIAREAESAYKAGASIIHLHVREDDGTPTQDKERFR 65 II AI G+ TK NPAVP TV E A++AGASI H HVR DD TP+ D E+F Sbjct: 7 IICVAITGSVATKSANPAVPITVAEQVESTHEAFEAGASICHAHVRNDDETPSSDPEKFA 66 Query: 66 KCIEAIREKCPDVIIQPSTGGAVGMTDLERLQPTELHPEMATLDCGTCNFGGDEIFVNTE 125 + E +++ CP +IIQ STGG G ER L P+MA+L G+ NF ++ N Sbjct: 67 RLQEGLQKHCPGMIIQFSTGGRSG-AGRERGGMLPLRPDMASLTVGSNNF-PTRVYENPP 124 Query: 126 NTIKNFGKILIERGVKPEIEVFDKGMIDYAIRYQKQGFIQKPMHFDFVLGVQMSASARDL 185 + + + V PEIE FD I +A + G + + FV+GV+ + Sbjct: 125 DLVDWLASEMRAHEVIPEIEAFDLSHIHHAALMHRDGRLATRPYIQFVMGVKNAMPVDRE 184 Query: 186 VF-----MSESIPEGSTWTVAGVGRHQFQMAALAIVMGGHVRVGFEDNVYIDKGILAKSN 240 F E + G+ W A +G Q M + GGH R G EDNV +D+ LA SN Sbjct: 185 TFDFYRATVERLLPGAEWCGAAIGASQIVMNEWCVAEGGHARTGLEDNVRLDRETLAPSN 244 Query: 241 GELVERVVRLAKELGREIATPDEARQILSLK 271 LV RVV L + R +A P +AR+IL L+ Sbjct: 245 AALVRRVVELCNQYERPVADPAQAREILGLR 275 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: 200 Number of extensions: 11 Number of successful extensions: 4 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: 279 Length adjustment: 25 Effective length of query: 247 Effective length of database: 254 Effective search space: 62738 Effective search space used: 62738 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: 47 (22.7 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