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 AZOBR_RS29850 AZOBR_RS29850 ketohydroxyglutarate aldolase
Query= BRENDA::P0A955 (213 letters) >FitnessBrowser__azobra:AZOBR_RS29850 Length = 211 Score = 192 bits (487), Expect = 5e-54 Identities = 93/195 (47%), Positives = 138/195 (70%), Gaps = 1/195 (0%) Query: 14 TGP-VVPVIVVKKLEHAVPMAKALVAGGVRVLEVTLRTECAVDAIRAIAKEVPEAIVGAG 72 +GP +VPV+V+ + + AV +A+ALVAGG+ LEVTLRT A+ AIA VP A+VG G Sbjct: 11 SGPRIVPVLVLDEPDTAVALAEALVAGGLTTLEVTLRTPAALACAEAIAARVPGALVGLG 70 Query: 73 TVLNPQQLAEVTEAGAQFAISPGLTEPLLKAATEGTIPLIPGISTVSELMLGMDYGLKEF 132 T++ P+Q A+ +AGA+F +SPGLT+ L +AA +P +PGI+TV+E ++ M++G +E Sbjct: 71 TLIRPEQFAQARDAGARFVVSPGLTDRLAEAAKTAGLPYLPGIATVAEALIAMEHGFREL 130 Query: 133 KFFPAEANGGVKALQAIAGPFSQVRFCPTGGISPANYRDYLALKSVLCIGGSWLVPADAL 192 KFFPA NGG AL+ +A ++RFCPTGG+ + ++ L+L +V +GG+WL PADA+ Sbjct: 131 KFFPAMLNGGAPALRGMAPLMPEIRFCPTGGLKAEHVKEILSLPNVFALGGTWLTPADAV 190 Query: 193 EAGDYDRITKLAREA 207 + + I +LAREA Sbjct: 191 KERRWSEIERLAREA 205 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: 177 Number of extensions: 12 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: 213 Length of database: 211 Length adjustment: 21 Effective length of query: 192 Effective length of database: 190 Effective search space: 36480 Effective search space used: 36480 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 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