Align Probable 5-dehydro-4-deoxyglucarate dehydratase 2; EC 4.2.1.41; 5-keto-4-deoxy-glucarate dehydratase 2; KDGDH 2 (uncharacterized)
to candidate WP_067648532.1 I596_RS12675 4-hydroxy-tetrahydrodipicolinate synthase
Query= curated2:Q9RDE8 (322 letters) >NCBI__GCF_001632775.1:WP_067648532.1 Length = 304 Score = 89.7 bits (221), Expect = 8e-23 Identities = 73/244 (29%), Positives = 109/244 (44%), Gaps = 14/244 (5%) Query: 39 EDGSF--DADGYRAYVAERLAAGPGALFPACGTGEFFSLDEDEYRQAVAIAVEETAGSVP 96 +DG D + + + ++A G AL A TGE LD+ E+ VA VE AG +P Sbjct: 17 QDGELPIDFEAFGRLIDHQVAGGTRALVAAGSTGEAAMLDDAEFSALVAFTVERAAGRIP 76 Query: 97 VVAGTGY-GWAQALRFARIAEDAGADALLVMPHYLTAAPQDGLVAQMERIAAGTRLPLIA 155 V+AGTG + + R A DAGA A LV+ Q+GL +A RLP++ Sbjct: 77 VLAGTGQASTRRTIEQTRRAADAGAGAALVVTPPYVRPTQEGLYRHFMDVAEHGRLPVVL 136 Query: 156 YQ---RGQVAYTAESVRRLTRVPGVIGLKDGHSDLDRLQRAVLAAPDD--FLFFNGAATA 210 Y R E+V RL ++ +K+ +D +R++R + A P F +G Sbjct: 137 YNVPGRTACDLLPETVERLAAQGNIVAIKEARADAERMERLLAARPTTRRFAILSGDDPT 196 Query: 211 EVQARAYAAVGVPAYSSAVHAFAPEIANAFLAALRGGD---TGTVDKLLRDFYVPLVELR 267 V+A A GV + ++ V AP A A D +D L+D Y L Sbjct: 197 CVRAMLAGADGVISVAANV---APAALQAIAEACADADRPRAEALDAALQDLYALLAAEP 253 Query: 268 DRVP 271 + +P Sbjct: 254 NPIP 257 Lambda K H 0.320 0.136 0.395 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: 279 Number of extensions: 12 Number of successful extensions: 2 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: 322 Length of database: 304 Length adjustment: 27 Effective length of query: 295 Effective length of database: 277 Effective search space: 81715 Effective search space used: 81715 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 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