Align 2-keto-3-deoxy-L-lyxonate dehydratase (EC 4.2.1.43) (characterized)
to candidate N515DRAFT_2411 N515DRAFT_2411 hypothetical protein
Query= metacyc::MONOMER-18708 (331 letters) >FitnessBrowser__Dyella79:N515DRAFT_2411 Length = 335 Score = 401 bits (1031), Expect = e-116 Identities = 201/318 (63%), Positives = 233/318 (73%), Gaps = 4/318 (1%) Query: 1 MRLIQFEDRAGQRRVGVVEGAGIQV--LRGVRSTRELGLAAIRAGSGLHDEVLRRGSEPG 58 MRLIQ D + RVGVV+ G+QV L GV S+ L AI G L + +G E Sbjct: 1 MRLIQLLDDSDATRVGVVDAQGLQVRVLDGVDSSYALATRAIEGGRSLQAQAELQGGEVR 60 Query: 59 PDYAGLLEEGRVLPPLDHDDPAHCLVSGTGLTHLGSAATRDRMHQ--QNQGDETALTDTM 116 DYA LL GR+L PL H DPAHC V+GTGLTHLGSAA RD MHQ + + + ALTD+M Sbjct: 61 LDYASLLASGRILTPLHHPDPAHCRVTGTGLTHLGSAAARDAMHQNLKQKAEAGALTDSM 120 Query: 117 RIFRWGLEGGKPPAGQVGAQPEWFYKGDGGIVVRPGADFPLPAFAEDAGEEPELVGLYLI 176 R+F+WG+EGG P GAQPEWFYKGDG IV+ PG P P FA D GEEPELVGLYLI Sbjct: 121 RMFQWGVEGGIPKGDAPGAQPEWFYKGDGSIVMAPGEALPSPDFALDGGEEPELVGLYLI 180 Query: 177 GDDRRPYRLGYALGNEFSDHLMERRNYLYLAHSKLRACCYGPELRVGELPRHLQGESRIL 236 G D P+RLG+A+GNEFSDH+ ER+NYLYLAHSKLRAC GPELRVGELP+ L+G SRI Sbjct: 181 GPDGTPHRLGFAIGNEFSDHVTERQNYLYLAHSKLRACAVGPELRVGELPQDLRGTSRIR 240 Query: 237 RDGEVLWQQAFLSGEDNMCHSLENLEYHHFKYAQFLRPGDVHVHYFGTATLSFADGIKAA 296 R VLW++ FL+GE NMCH+L NLEYHHFKYA RPGDVH+H+FGTATLSFAD ++ Sbjct: 241 RGDGVLWEKPFLTGEANMCHALANLEYHHFKYAAHRRPGDVHLHFFGTATLSFADEVRVQ 300 Query: 297 PGDVFEIAMAEFGAPLRN 314 PGDVFEI + GAPLRN Sbjct: 301 PGDVFEIDLPALGAPLRN 318 Lambda K H 0.321 0.141 0.435 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: 483 Number of extensions: 23 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: 331 Length of database: 335 Length adjustment: 28 Effective length of query: 303 Effective length of database: 307 Effective search space: 93021 Effective search space used: 93021 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: 49 (23.5 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