Align 6-phospho-5-dehydro-2-deoxy-D-gluconate aldolase; DKGP aldolase; EC 4.1.2.29 (characterized)
to candidate BWI76_RS24855 BWI76_RS24855 tagatose-bisphosphate aldolase
Query= SwissProt::P42420 (290 letters) >FitnessBrowser__Koxy:BWI76_RS24855 Length = 284 Score = 204 bits (519), Expect = 2e-57 Identities = 109/288 (37%), Positives = 166/288 (57%), Gaps = 10/288 (3%) Query: 1 MAFVSMKELLEDAKREQYAIGQFNINGLQWTKAILQAAQKEQSPVIAAASDRLVDYLGGF 60 M +S K +L A+R YA+ FNI+ L+ + +++ A + +SP+I A + Y G Sbjct: 1 MFIISSKNMLLKAQRLGYAVPAFNIHNLETMQVVVETAAELRSPLILAGTPGTYSYAG-- 58 Query: 61 KTIAAMVGALIEDMAIT--VPVVLHLDHGSSAERCRQAIDAGFSSVMIDGSHQPIDENIA 118 V A+ D+A +P+ +HLDH + + AG SVMIDGSH P +EN+A Sbjct: 59 ---TGNVVAIARDLAKIWDLPLAVHLDHHEDLADITRKVQAGIRSVMIDGSHSPFEENVA 115 Query: 119 MTKEVTDYAAKHGVSVEAEVGTVGGMEDGLVGGVR---YADITECERIVKETNIDALAAA 175 + K V + + ++ SVEAE+G +GG+ED LV + Y + + V T ID+LA A Sbjct: 116 LVKSVVELSHRYDASVEAELGRLGGVEDDLVVDAKDALYTNPEQAREFVARTGIDSLAVA 175 Query: 176 LGSVHGKYQGEPNLGFKEMEAISRMTDIPLVLHGASGIPQDQIKKAITLGHAKININTEC 235 +G+ HG Y EP L F + AI D+PLVLHGASG+P I++AI+LG K+N+ TE Sbjct: 176 IGTAHGLYAAEPKLDFDRLAAIRDRVDVPLVLHGASGLPDSDIRRAISLGVCKVNVATEL 235 Query: 236 MVAWTDETRRMFQENSDLYEPRGYLTPGIEAVEETVRSKMREFGSAGK 283 +A++D + F+EN D +PR Y+ P A+++ VR + G G+ Sbjct: 236 KIAFSDALKHYFEENPDANDPRHYMKPAKAAMKDVVRKVIHVCGCEGQ 283 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: 194 Number of extensions: 6 Number of successful extensions: 4 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