Align 2-dehydro-3-deoxy-D-gluconate-6-phosphate aldolase (EC 4.1.2.55) (characterized)
to candidate GFF840 Psest_0854 Entner-Doudoroff aldolase
Query= metacyc::MONOMER-15645 (213 letters) >FitnessBrowser__psRCH2:GFF840 Length = 245 Score = 215 bits (547), Expect = 6e-61 Identities = 103/200 (51%), Positives = 145/200 (72%) Query: 9 EQILTAGPVVPVIVINKLEHAVPMAKALVAGGVRVLELTLRTECAVEAIRLIAQEVPDAI 68 +Q +A ++PVI I + +P+A AL AGG+RVLE+TLR+ + AIRL+ ++ P+ I Sbjct: 19 DQWCSAARILPVITIEREADILPLADALAAGGLRVLEITLRSALGLRAIRLLREQRPELI 78 Query: 69 VGAGTVTNPQQLAEVTAAGAQFAISPGLTEPLLKAATEGTIPLIPGISTVSELMLGMDYG 128 VGAGTV + L + AAGAQF +SPG T LL+AA +G +PL+PG+++ SE+MLG G Sbjct: 79 VGAGTVLDANMLEQAEAAGAQFIVSPGSTPALLEAALQGPLPLLPGVASASEIMLGYAMG 138 Query: 129 LREFKFFPAEANGGVKALQAIAGPFGKIRFCPTGGISLKNYRDYLALKSVLCVGGSWLVP 188 R FK FPAE GGV AL+A+ GPFG IRFCPTGG++ +N RDYL+L +V+CVGG+W+V Sbjct: 139 YRRFKLFPAEICGGVAALKALGGPFGDIRFCPTGGVNARNARDYLSLANVMCVGGTWMVD 198 Query: 189 ADALESGDYDRITALAREAV 208 A A+ +GD+ I + R+A+ Sbjct: 199 AKAVRAGDWAAIESATRQAL 218 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: 176 Number of extensions: 7 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: 245 Length adjustment: 23 Effective length of query: 190 Effective length of database: 222 Effective search space: 42180 Effective search space used: 42180 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: 46 (22.3 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