Align 4-hydroxy-4-methyl-2-oxoglutarate aldolase/4-carboxy-4-hydroxy-2-oxoadipate aldolase; HMG/CHA aldolase; Oxaloacetate decarboxylase; OAA decarboxylase; EC 4.1.3.17; EC 4.1.1.112 (characterized)
to candidate WP_011427805.1 RHE_RS23745 4-carboxy-4-hydroxy-2-oxoadipate aldolase/oxaloacetate decarboxylase
Query= SwissProt::A5W059 (238 letters) >NCBI__GCF_000092045.1:WP_011427805.1 Length = 224 Score = 174 bits (440), Expect = 2e-48 Identities = 89/212 (41%), Positives = 132/212 (62%) Query: 16 QRAELDSIDALGRLGVATVHEAQNRKGLLSSKMRPIQQGTSLAGSAVTVLVAPGDNWMFH 75 +R + +I+A+ + AT+HEAQ R+G LSS+++P+ L G A TV AP DN M Sbjct: 9 ERPDKAAIEAVSKFSPATIHEAQGRRGALSSRLKPVDYRMKLCGPAFTVKCAPRDNIMLQ 68 Query: 76 VAVEQCRPGDVLVVSPSSPCTDGYFGDLLATSLQARGVRALIVDAGVRDTQTLRDMGFAV 135 +A+ +PGD++VVS G FGD+LA + A+G+ L+ D GVRDT LR++GF V Sbjct: 69 LAINYAKPGDIIVVSAGEYEEAGSFGDVLANACLAKGIGGLVTDTGVRDTLQLRELGFPV 128 Query: 136 WARAINAQGTVKETLGSVNLPVICGGQLINPGDIVVADDDGVVVVRRDECESTLVAAAER 195 ++ ++ +GTVKET+ +VN P+I GG+ INPGDI+V D DG+VVVRR E + + R Sbjct: 129 FSLSVCIKGTVKETIAAVNDPIIVGGETINPGDIIVGDADGLVVVRRQEAQEAARLSQAR 188 Query: 196 AGLEEEKRLRLAAGELGLDIYKMRERLEAKGL 227 E AG+ +++ + L+AKGL Sbjct: 189 EDAEAGYITAYKAGKSVIEVSNLAPVLKAKGL 220 Lambda K H 0.318 0.136 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: 145 Number of extensions: 5 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: 238 Length of database: 224 Length adjustment: 23 Effective length of query: 215 Effective length of database: 201 Effective search space: 43215 Effective search space used: 43215 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 (21.7 bits) S2: 46 (22.3 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