Align 3-keto-5-aminohexanoate cleavage enzyme; EC 2.3.1.247 (uncharacterized)
to candidate H281DRAFT_00641 H281DRAFT_00641 Uncharacterized conserved protein, DUF849 family
Query= curated2:E3PRK0 (273 letters) >FitnessBrowser__Burk376:H281DRAFT_00641 Length = 312 Score = 165 bits (417), Expect = 1e-45 Identities = 108/299 (36%), Positives = 158/299 (52%), Gaps = 31/299 (10%) Query: 3 KLIITAAICGAEVTKEHNPNVPYTVEEIVREAKSAYDAGASVIHLHVRED-DGTPTQSKE 61 K+II+ AI GA + +P T E+I +A A AGA++IHLH R+ DG PT S E Sbjct: 7 KVIISCAITGATHVPSMSEFLPITPEQIRDQAIEAAQAGAAIIHLHARDPVDGRPTPSPE 66 Query: 62 RFKMCVDAIKEACPDAIIQPSTGGAVGMTDEERLQ-PVFLKPEMASLDCGTCNFG----- 115 FK V AI EA DA+I +TGG+ MT EERL P +PEM SL+ G+ NF Sbjct: 67 IFKAFVPAIAEAT-DAVINITTGGSTRMTLEERLAYPRLARPEMCSLNMGSMNFSIHPVA 125 Query: 116 ------------------GDEIFVNTENMIINFSKYMIKNGVKPECEVFDKSMIDMAIRL 157 D IF NT I N + ++G + E E +D + Sbjct: 126 AKISSWRYGWEKDYIEGMEDMIFRNTFRDIRNILLELGESGTRFEFECYDVGHLYNLAHF 185 Query: 158 AKKGHIQTPMHFNFVMGVNGGISATPRDLVFLIGSIP-----SESSFTVSAMGRNQFPMA 212 +G ++ P V G+ GG+ A P +++ + + F+V GR+Q P+ Sbjct: 186 VDQGLVKPPFFIQSVFGILGGLGADPENMLLMRSTADRLFGRENYHFSVLGAGRHQMPLV 245 Query: 213 AMAIITGGHVRVGFEDNVYIEKGVPAKSNGELVEKVVRLAKEFGRPVATPSEAREILGI 271 M+ I GG+VRVG ED+VY+ KGV A++N + V K+ R+ +E +ATP++AR++LG+ Sbjct: 246 TMSAIMGGNVRVGLEDSVYLAKGVKAETNAQQVRKIRRILEELSLEIATPADARKMLGL 304 Lambda K H 0.318 0.135 0.390 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: 227 Number of extensions: 9 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: 273 Length of database: 312 Length adjustment: 26 Effective length of query: 247 Effective length of database: 286 Effective search space: 70642 Effective search space used: 70642 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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