Align L-2-keto-3-deoxyrhamnonate 4-dehydrogenase subunit (EC 1.1.1.401) (characterized)
to candidate GFF2606 HP15_2550 fumarylacetoacetate hydrolase family protein
Query= metacyc::MONOMER-16233 (285 letters) >FitnessBrowser__Marino:GFF2606 Length = 220 Score = 128 bits (322), Expect = 1e-34 Identities = 76/205 (37%), Positives = 115/205 (56%), Gaps = 6/205 (2%) Query: 59 GVPVK-GIGKIVAIGLNYEDHAIESNLPIPTEPMMFMKALSSLNGPNDEVVLPKNSTHGD 117 G PV +GKIV IG NY +HA E N P+P EP++F+K +S + P++ Sbjct: 11 GTPVHLPLGKIVCIGRNYAEHARELNNPVPDEPLLFIKPATSAVHITRPLDFPRDQGAVH 70 Query: 118 WEVELGVVIGETCRFVSEDEALSKVAGYVLVNDVSERFNQ---KQRGTQWSKGKGHDTFC 174 +E EL V+IG S EA S + GY L D++ R Q K++G W + KG D C Sbjct: 71 FETELAVLIGRPLTRASASEAKSAILGYGLALDLTLRDLQGKLKEKGQPWERAKGFDGAC 130 Query: 175 PVGPWLVTPDEVGDPQDLDMHLNVNGTRMQTGNTKTMIFNVAQLISYVSEYITLYPGDLM 234 P+ P+ V D+ D + ++++G R QTG+T M+ + LI+++S TL PGD++ Sbjct: 131 PLSPF-VAADKFPD-APIHFTMDIDGNRQQTGDTGDMLNPIIPLIAHISSQFTLLPGDVV 188 Query: 235 ITGTPPGVGEGKKPQAIYLKAGDVM 259 +TGTP GVG Q + L+ D++ Sbjct: 189 LTGTPKGVGPLVSGQTLSLELEDLL 213 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: 192 Number of extensions: 8 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: 285 Length of database: 220 Length adjustment: 24 Effective length of query: 261 Effective length of database: 196 Effective search space: 51156 Effective search space used: 51156 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 Apr 09 2024. 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