Align L-2-keto-3-deoxyrhamnonate 4-dehydrogenase subunit (EC 1.1.1.401) (characterized)
to candidate WP_092054671.1 BQ4888_RS05425 FAA hydrolase family protein
Query= metacyc::MONOMER-16233 (285 letters) >NCBI__GCF_900111775.1:WP_092054671.1 Length = 218 Score = 140 bits (352), Expect = 3e-38 Identities = 83/206 (40%), Positives = 120/206 (58%), Gaps = 12/206 (5%) Query: 65 IGKIVAIGLNYEDHAIESNLPIPTEPMMFMKALSSLNGPNDEVVLPKNSTHGDWEVELGV 124 +GK++ + NY +H E +P +P++F+K SS+ G ++ VV+P S EVEL V Sbjct: 15 VGKVICLARNYSEHIKELGNAVPEKPVLFIKPASSIIGRHEAVVIPAFSQDCQHEVELAV 74 Query: 125 VIGETCRFVSEDEALSKVAGYVLVNDVSERFNQ---KQRGTQWSKGKGHDTFCPVGPWLV 181 +IG+ + +S EAL+ VAGY + D++ R Q KQ+G W KG DT CP+ + V Sbjct: 75 LIGKWGKNISAKEALNHVAGYGVALDMTLRDVQNELKQKGLPWEIAKGFDTACPLSDF-V 133 Query: 182 TPDEVGDPQDLDMHLNVNGTRMQTGNTKTMIFNVAQLISYVSEYITLYPGDLMITGTPPG 241 EVGDP +L + L VN Q GNT M+ + ++I VSE TL GD+++TGTP G Sbjct: 134 PAAEVGDPHNLRITLKVNEQLRQDGNTAQMMRRIPEIIQAVSEIFTLEEGDVILTGTPSG 193 Query: 242 VGEGKKPQAIYLKAGDVMELGIEKLG 267 VG +K+GD M IEK+G Sbjct: 194 VGA--------VKSGDRMLAEIEKVG 211 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: 169 Number of extensions: 12 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: 218 Length adjustment: 24 Effective length of query: 261 Effective length of database: 194 Effective search space: 50634 Effective search space used: 50634 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 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