Align L-2-keto-3-deoxyrhamnonate 4-dehydrogenase subunit (EC 1.1.1.401) (characterized)
to candidate Echvi_2930 Echvi_2930 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway)
Query= metacyc::MONOMER-16233 (285 letters) >FitnessBrowser__Cola:Echvi_2930 Length = 203 Score = 104 bits (260), Expect = 1e-27 Identities = 69/201 (34%), Positives = 105/201 (52%), Gaps = 12/201 (5%) Query: 67 KIVAIGLNYEDHAIESNLPIPTEPMMFMKALSSLNGPNDEVVLPKNSTHGDWEVELGVVI 126 KI+AIG NY H E P P++F+K +++ N LP+ S EVEL + I Sbjct: 2 KIIAIGRNYAKHIEELENERPENPVVFLKPDTAIIKNNLPFYLPEFSHDVHHEVELVLKI 61 Query: 127 GETCRFVSEDEALSKVAGYVLVNDVSERFNQ---KQRGTQWSKGKGHDTFCPVGPWLVTP 183 + +F+ ++ A + D + R Q K++G W K + P+G +L Sbjct: 62 NKEGKFIKKEFAHRYFGEIGIGIDFTARDVQQKCKEKGLPWEIAKAFNGSAPIGRFLPVS 121 Query: 184 DEVGDPQDLDMHLNVNGTRMQTGNTKTMIFNVAQLISYVSEYITLYPGDLMITGTPPGVG 243 D D +D++ HL++NG + Q GNT M+F+ +I YVS++ TL GDL+ TGTP GVG Sbjct: 122 D-FKDFKDINFHLDINGEQKQVGNTSLMLFDFGVIIEYVSQFFTLKKGDLIFTGTPAGVG 180 Query: 244 EGKKPQAIYLKAGDVMELGIE 264 + + AGD +E IE Sbjct: 181 K--------VAAGDHLEAFIE 193 Lambda K H 0.316 0.137 0.411 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: 172 Number of extensions: 6 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: 285 Length of database: 203 Length adjustment: 23 Effective length of query: 262 Effective length of database: 180 Effective search space: 47160 Effective search space used: 47160 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 46 (22.3 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