Align 6-phospho-5-dehydro-2-deoxy-D-gluconate aldolase; DKGP aldolase; EC 4.1.2.29 (characterized)
to candidate WP_029133836.1 A3GO_RS0113465 hypothetical protein
Query= SwissProt::P42420 (290 letters) >NCBI__GCF_000428045.1:WP_029133836.1 Length = 391 Score = 154 bits (388), Expect = 4e-42 Identities = 96/292 (32%), Positives = 162/292 (55%), Gaps = 12/292 (4%) Query: 1 MAFVSMKELLEDAKREQYAIGQFNINGLQWTKAILQAAQKEQSPVIAAASDRLVDYLGGF 60 MA V+M++++ A + YA+G F++ L + +A++ AA+ ++ ++ + ++ ++ Sbjct: 1 MALVNMRDMIYHAYKHNYAVGAFDLVSLDFLEAVIGAAESCRASIVLSIAEPHFEHYDYE 60 Query: 61 KTIAAMVGALIEDMAITVPVVLHLDHGSSAERCRQAIDAGFSSVMIDGSHQPIDENIAMT 120 + A+ A +VPV + LDHGSS AI+ G + VM+D S Q + +NI T Sbjct: 61 LLLPAVEAAA---QRASVPVAIQLDHGSSLASAISAINRGCNGVMLDASRQELPDNITTT 117 Query: 121 KEVTDYAAKHGVSVEAEVGTVGGME-DGLV---GGVRYADITECERIVKETNIDALAAAL 176 + V D A + GV V EVG V G E +G + G + E + V+ TN+D LA ++ Sbjct: 118 RAVVDMAHRCGVPVTGEVGYVAGYEGEGALLHPGEAAFTVPAEAKAYVERTNVDFLAVSI 177 Query: 177 GSVHGKYQGEPNLGFKEMEAISRMTDIPLVLHGASGIPQDQIKKAITLGHAKININTECM 236 G+V G+ +G L F+ ++ I++ D+PLV+HG SG+ ++Q +K ++G AKIN T Sbjct: 178 GTVQGRMKGRAKLDFQRLKLINQAVDVPLVIHGGSGLNEEQFRKLPSMGVAKINYYTALS 237 Query: 237 VAWTDETRRMFQENSD--LYEPRGYLTPGIEAVEETVRSKMREFGSAGKAAK 286 + RR + N D E + + EAV E V +R +GSAG+AA+ Sbjct: 238 DVAAEAMRRRTKANPDGSFIELKRDVK---EAVGEEVERCLRLWGSAGRAAE 286 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: 257 Number of extensions: 15 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 290 Length of database: 391 Length adjustment: 28 Effective length of query: 262 Effective length of database: 363 Effective search space: 95106 Effective search space used: 95106 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: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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