Align 6-phospho-5-dehydro-2-deoxy-D-gluconate aldolase; DKGP aldolase; EC 4.1.2.29 (characterized)
to candidate WP_009140764.1 HMPREF9452_RS03670 class II fructose-bisphosphate aldolase
Query= SwissProt::P42420 (290 letters) >NCBI__GCF_000225705.1:WP_009140764.1 Length = 282 Score = 204 bits (519), Expect = 2e-57 Identities = 111/283 (39%), Positives = 164/283 (57%), Gaps = 5/283 (1%) Query: 4 VSMKELLEDAKREQYAIGQFNINGLQWTKAILQAAQKEQSPVIAAASDRLVDYLGGFKTI 63 V+ KE+L DA++ YA+G FN+ L++ A+L AA++ +SPVI + + G Sbjct: 3 VTTKEMLLDAQKNHYAVGAFNVENLEFVMAVLAAAEETKSPVIMQTTSGTIKKTG-LDYF 61 Query: 64 AAMVGALIEDMAITVPVVLHLDHGSSAERCRQAIDAGFSSVMIDGSHQPIDENIAMTKEV 123 MV A E +VPV LHLDHG +RC +A+ G++SVMIDGSH+ ++NIA+TK V Sbjct: 62 YGMVKAAAE--RASVPVALHLDHGDGYDRCMKALRTGYTSVMIDGSHETFEDNIALTKLV 119 Query: 124 TDYAAKHGVSVEAEVGTVGGMEDGLV--GGVRYADITECERIVKETNIDALAAALGSVHG 181 D A G+ VEAE+G VGG ED + G Y D E + V+ T +LA +G+ HG Sbjct: 120 ADAGAAMGIPVEAELGKVGGKEDDVEVEGESPYTDPVEAKEFVERTGCTSLAIGVGTAHG 179 Query: 182 KYQGEPNLGFKEMEAISRMTDIPLVLHGASGIPQDQIKKAITLGHAKININTECMVAWTD 241 Y EP++ ++AI D+PLVLHG SG+P +Q+ +A+ G K+N TE A+T Sbjct: 180 VYTEEPHIDQDVVKAIRAAVDVPLVLHGTSGVPDEQVAEAVKNGICKVNYATELRQAYTK 239 Query: 242 ETRRMFQENSDLYEPRGYLTPGIEAVEETVRSKMREFGSAGKA 284 EN + ++P+ G E + + V+ +M GS G+A Sbjct: 240 GYMAYMAENPNNFDPKNPGKAGAEEITKIVKIRMENLGSVGRA 282 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: 226 Number of extensions: 5 Number of successful extensions: 5 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: 282 Length adjustment: 26 Effective length of query: 264 Effective length of database: 256 Effective search space: 67584 Effective search space used: 67584 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 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