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_004314943.1 C665_RS13710 4-hydroxy-tetrahydrodipicolinate synthase
Query= curated2:Q9RDE8 (322 letters) >NCBI__GCF_000310185.1:WP_004314943.1 Length = 292 Score = 115 bits (287), Expect = 2e-30 Identities = 93/274 (33%), Positives = 126/274 (45%), Gaps = 12/274 (4%) Query: 34 LTSFHEDGSFDADGYRAYVAERLAAGPGALFPACGTGEFFSLDEDEYRQAVAIAVEETAG 93 +T H+DGS D R+ + +A G + TGE ++ DE+ + + +AVE AG Sbjct: 10 VTPMHDDGSLDFPRLRSLIDWHIAEGTDGIVIVGTTGESPTVTVDEHCELIRVAVEHCAG 69 Query: 94 SVPVVAGTG-YGWAQALRFARIAEDAGADALLVMPHYLTAAPQDGLVAQMERIAAGTRLP 152 VPV+AGTG A+A+ AR A AGA+A L + Y Q+GL IA LP Sbjct: 70 RVPVIAGTGANSTAEAVELARFAAQAGANAHLSVVPYYNRPTQEGLYRHFRTIAEAVELP 129 Query: 153 LIAYQ---RGQVAYTAESVRRLTRVPGVIGLKDGHSDLDRLQRAVLAAPDDFLFFNGAAT 209 LI Y R E+V RL VP ++GLKD +LDR + AP DF ++G Sbjct: 130 LILYNVPGRTVADLANETVMRLAEVPNIVGLKDATGNLDRACDLIERAPADFGLYSG--- 186 Query: 210 AEVQARAYAAVGVPAYSSAVHAFAPEIANAFLAALRGGDTGTVDKLLRDFYVPLVEL-RD 268 ++ + A+ +G S AP +A AA GD T LR+ L L RD Sbjct: 187 DDMTSAAFLMLGGHGVISVTANVAPRAMHALCAAAAAGDMRT----LRETNAGLTGLHRD 242 Query: 269 RVPGYAVSLVKAAARLRGCPVGPVRAPLTDPSPA 302 VK A G +R PLT S A Sbjct: 243 LFCEANPIPVKWAVARMGLIGDGLRLPLTPLSAA 276 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: 273 Number of extensions: 14 Number of successful extensions: 3 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: 292 Length adjustment: 27 Effective length of query: 295 Effective length of database: 265 Effective search space: 78175 Effective search space used: 78175 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