Align Probable 5-dehydro-4-deoxyglucarate dehydratase; EC 4.2.1.41; 5-keto-4-deoxy-glucarate dehydratase; KDGDH (uncharacterized)
to candidate WP_043768161.1 U743_RS10725 4-hydroxy-tetrahydrodipicolinate synthase
Query= curated2:A4YNH1 (314 letters) >NCBI__GCF_000733765.1:WP_043768161.1 Length = 293 Score = 90.5 bits (223), Expect = 4e-23 Identities = 93/294 (31%), Positives = 123/294 (41%), Gaps = 28/294 (9%) Query: 22 VTPFKADYSFDETTYRSNMDWLCGYDVAGLFAAGGTGEFFSLTAAEVPEVVKVAVDETKG 81 VTP AD + D + W A + A G TGE +L E V++ V Sbjct: 10 VTPMDADGAVDYEALDRLVAWHIEAGTAAIVAVGTTGESATLDNDEHIAVIRRVVAAADR 69 Query: 82 RVPVLAGTGYG-TAIAREIAMSAEKAGADGLLLLPPYLMHAEQEGLAAHVEAVCKSVKIG 140 R+PV+AGTG T+ A + +A GAD LL+ PY QEGL H AV ++V I Sbjct: 70 RIPVIAGTGANATSEAIALTRAAADCGADAALLVTPYYNKPPQEGLYRHFRAVAEAVDIP 129 Query: 141 VIVYN---RDNAILQPDTLARLCERCPNLVGYKDGIGDIELMTRVY--TKMGDRLTYIGG 195 I+YN R L P T+ RL E PN++G K+ + D + + GD Y G Sbjct: 130 QILYNVPGRTGCDLLPVTVKRLAE-VPNIIGLKEALADEARIKELVGCGLPGDFALYSGD 188 Query: 196 LPTAETFALPYLDMGVTTYSSAVFNFVPEFATNFYAAVRKRDHATIH------AGL-KDF 248 TA L G S V N P AA D A AGL +D Sbjct: 189 DGTACGAML----AGFHGDVSVVANVAPAMMARMCAAATAGDRAAAEAADAELAGLHRDL 244 Query: 249 ILPLIAIRNRKKGYAVSIIKAGMKVIGRDSGPVRLPLTDLTEAEMAELTALVKA 302 L I + +A+ +I AG +RLPL L E L A ++A Sbjct: 245 FLQANPIPVKWALHAMGLIGAG----------IRLPLVPLAEEHHDTLRATLRA 288 Lambda K H 0.320 0.136 0.392 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: 220 Number of extensions: 16 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: 314 Length of database: 293 Length adjustment: 27 Effective length of query: 287 Effective length of database: 266 Effective search space: 76342 Effective search space used: 76342 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