Align 6-phospho-5-dehydro-2-deoxy-D-gluconate aldolase; DKGP aldolase; EC 4.1.2.29 (characterized)
to candidate 16203 b2096 tagatose-bisphosphate aldolase 1 (VIMSS)
Query= SwissProt::P42420 (290 letters) >FitnessBrowser__Keio:16203 Length = 284 Score = 175 bits (444), Expect = 9e-49 Identities = 99/287 (34%), Positives = 156/287 (54%), Gaps = 6/287 (2%) Query: 1 MAFVSMKELLEDAKREQYAIGQFNINGLQWTKAILQAAQKEQSPVIAAASDRLVDYLGGF 60 M VS K++L +A+R YA+ FNI+ L+ + +++ A +PVI A + + G Sbjct: 1 MYVVSTKQMLNNAQRGGYAVPAFNIHNLETMQVVVETAANLHAPVIIAGTPGTFTH-AGT 59 Query: 61 KTIAAMVGALIEDMAITVPVVLHLDHGSSAERCRQAIDAGFSSVMIDGSHQPIDENIAMT 120 + + A+V A+ + P+ +HLDH + + Q + +G SVMID SH P +NI+ Sbjct: 60 ENLLALVSAMAKQYHH--PLAIHLDHHTKFDDIAQKVRSGVRSVMIDASHLPFAQNISRV 117 Query: 121 KEVTDYAAKHGVSVEAEVGTVGGMEDGLV---GGVRYADITECERIVKETNIDALAAALG 177 KEV D+ + VSVEAE+G +GG ED + Y + + + T ID+LA A+G Sbjct: 118 KEVVDFCHRFDVSVEAELGQLGGQEDDVQVNEADALYTNPAQAREFAEATGIDSLAVAIG 177 Query: 178 SVHGKYQGEPNLGFKEMEAISRMTDIPLVLHGASGIPQDQIKKAITLGHAKININTECMV 237 + HG Y P L F +E I + ++PLVLHGASG+ I++ I LG KIN+ TE Sbjct: 178 TAHGMYASAPALDFSRLENIRQWVNLPLVLHGASGLSTKDIQQTIKLGICKINVATELKN 237 Query: 238 AWTDETRRMFQENSDLYEPRGYLTPGIEAVEETVRSKMREFGSAGKA 284 A++ + E+ + +PR YL A+ + V + + G G+A Sbjct: 238 AFSQALKNYLTEHPEATDPRDYLQSAKSAMRDVVSKVIADCGCEGRA 284 Lambda K H 0.316 0.132 0.372 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: 183 Number of extensions: 4 Number of successful extensions: 3 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: 290 Length of database: 284 Length adjustment: 26 Effective length of query: 264 Effective length of database: 258 Effective search space: 68112 Effective search space used: 68112 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 (21.6 bits) S2: 47 (22.7 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