Align 2-dehydro-3-deoxy-D-gluconate/2-dehydro-3-deoxy-phosphogluconate aldolase; KD(P)G aldolase; EC 4.1.2.14; EC 4.1.2.51 (characterized)
to candidate BWI76_RS03425 BWI76_RS03425 dihydrodipicolinate synthase family protein
Query= SwissProt::Q704D1 (306 letters) >FitnessBrowser__Koxy:BWI76_RS03425 Length = 303 Score = 117 bits (292), Expect = 4e-31 Identities = 73/208 (35%), Positives = 112/208 (53%), Gaps = 7/208 (3%) Query: 50 SKGVDVVFVAGTTGLGPALSLQEKME-LTDAATSAARRV--IVQVASLNADEAIALAKYA 106 ++GV+ + G++G GP L E+ + L SA RV I V + +A+ LAK+A Sbjct: 40 ARGVEGFYCCGSSGEGPLLRFDERRQVLATLVQSAGGRVPVIAHVGTPRTRDAVELAKHA 99 Query: 107 ESRGAEAVASLPPYYFPRLSERQIAKYFRDLCSAVSIPVFLYNYPAAVGRDVDARAAKEL 166 E GA AV+ +PPYY+ + S +I Y+R + A+SIPV LYN P G ++DA++A L Sbjct: 100 EQDGASAVSLVPPYYY-KYSREEIIAYYRRVLDAISIPVILYNIPQFTGVELDAQSADAL 158 Query: 167 ---GCIRGVKDTNESLAHTLAYKRYLPQARVYNGSDSLVFASFAVRLDGVVASSANYLPE 223 + GVK T+ +L P+ +NG D + +S A V ++ N PE Sbjct: 159 LGDEQVLGVKHTSHNLYSLERMIARYPEKVFFNGFDEIFLSSLAAGATATVGTTVNLQPE 218 Query: 224 LLAGIRDAVAAGDIERARSLQFLLDEIV 251 L +R A G+I RA+ LQ ++E+V Sbjct: 219 LFLALRSAFQQGEIARAQRLQQQINEVV 246 Lambda K H 0.320 0.135 0.382 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: 231 Number of extensions: 12 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: 306 Length of database: 303 Length adjustment: 27 Effective length of query: 279 Effective length of database: 276 Effective search space: 77004 Effective search space used: 77004 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 48 (23.1 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