Align 2-dehydro-3-deoxy-phosphogluconate aldolase (EC 4.1.2.14); 4-Hydroxy-2-oxoglutarate aldolase (EC 4.1.3.16); (4S)-4-hydroxy-2-oxoglutarate aldolase (EC 4.1.3.42) (characterized)
to candidate WP_011952721.1 SWIT_RS09510 bifunctional 4-hydroxy-2-oxoglutarate aldolase/2-dehydro-3-deoxy-phosphogluconate aldolase
Query= BRENDA::P0A955 (213 letters) >NCBI__GCF_000016765.1:WP_011952721.1 Length = 203 Score = 206 bits (525), Expect = 2e-58 Identities = 106/203 (52%), Positives = 141/203 (69%), Gaps = 4/203 (1%) Query: 7 SAESILTTGPVVPVIVVKKLEHAVPMAKALVAGGVRVLEVTLRTECAVDAIRAIAKEVPE 66 + E ++T PV+PV+VV ++HA P+A+ALV GG+ LEVTLRT A+D IR +AK V Sbjct: 2 TVEQVMTLAPVIPVLVVHDVKHARPIAEALVEGGLPALEVTLRTPVALDVIREMAK-VEG 60 Query: 67 AIVGAGTVLNPQQLAEVTEAGAQFAISPGLTEPLLKAATEGTIPLIPGISTVSELMLGMD 126 A+VGAGTVLNP + +AGA+F +SPGLT+ L AA +P +PG + ++M G+D Sbjct: 61 AVVGAGTVLNPDDVKASVDAGARFLVSPGLTDRLANAAIGCGLPFLPGTANAGDIMRGLD 120 Query: 127 YGLKEFKFFPAEANGGVKALQAIAGPFSQVRFCPTGGISPANYRDYLALKSVLCIGGSWL 186 GL FKFFPA ANGGV AL+A+A P + RFCPTGGIS AN D+LAL +VLC+GGSW+ Sbjct: 121 MGLTHFKFFPAMANGGVPALKALAAPLAAARFCPTGGISEANAPDWLALDAVLCVGGSWI 180 Query: 187 VPADALEAGDYDRITKLAREAVE 209 VP + + IT+ AR A + Sbjct: 181 VPPGKPDTAE---ITRRARAAAK 200 Lambda K H 0.317 0.135 0.387 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: 174 Number of extensions: 7 Number of successful extensions: 2 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: 213 Length of database: 203 Length adjustment: 21 Effective length of query: 192 Effective length of database: 182 Effective search space: 34944 Effective search space used: 34944 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: 45 (21.9 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