Align Probable 5-dehydro-4-deoxyglucarate dehydratase; EC 4.2.1.41; 5-keto-4-deoxy-glucarate dehydratase; KDGDH (uncharacterized)
to candidate 8499797 DvMF_0562 dihydrodipicolinate synthase (RefSeq)
Query= curated2:A4YNH1 (314 letters) >FitnessBrowser__Miya:8499797 Length = 292 Score = 123 bits (309), Expect = 5e-33 Identities = 95/293 (32%), Positives = 141/293 (48%), Gaps = 15/293 (5%) Query: 16 GLLSFPVTPFKADYSFDETTYRSNMDWLCGYDVAGLFAAGGTGEFFSLTAAEVPEVVKVA 75 G + VTPF+ + DE YR+ ++W + GL G TGE +LT E +V+++ Sbjct: 5 GAFTALVTPFR-NGEVDEERYRALVEWQIEQGINGLVPCGTTGESATLTHQEHKDVIRIC 63 Query: 76 VDETKGRVPVLAGTG-YGTAIAREIAMSAEKAGADGLLLLPPYLMHAEQEGLAAHVEAVC 134 V++ KGRVPVLAG G T A E+ A++AGADG LL+ PY QEGL H +A+ Sbjct: 64 VEQVKGRVPVLAGAGSNNTREAVELTRYAKQAGADGALLITPYYNKPTQEGLYQHFKAIA 123 Query: 135 KSVKIGVIVYN---RDNAILQPDTLARLCERCPNLVGYKDGIGDIELMTRVYTKMGDRLT 191 V + IVYN R L P+TLAR+ P ++G K+ G++ ++ + G Sbjct: 124 AEVPMPFIVYNVPSRTGTNLCPETLARMKRDIPEVIGVKEATGNLIQVSEIIEYCGADFQ 183 Query: 192 YIGGLPTAETFALPYLDMGVTTYSSAVFNFVPEFATNFYAAVRKRDHATIHAGLKDFILP 251 + G + LP L +G S N VP + A + D AT + Sbjct: 184 VLSG---DDFTVLPLLAVGGCGVISVSSNVVPAKMSELCRAFFEGDLATARR-----VHY 235 Query: 252 LIAIRNRKKGYAVSII--KAGMKVIGRDSGPVRLPLTDLTEAEMAELTALVKA 302 IA NR + I K + ++GR +RLP+ L A + L ++ A Sbjct: 236 EIASINRAMFLETNPIPVKTALSMMGRIELELRLPMVPLQPANQSRLRDILSA 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: 231 Number of extensions: 18 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: 314 Length of database: 292 Length adjustment: 27 Effective length of query: 287 Effective length of database: 265 Effective search space: 76055 Effective search space used: 76055 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