Align 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41) (characterized)
to candidate WP_043744492.1 AMB_RS12805 4-hydroxy-tetrahydrodipicolinate synthase
Query= reanno::BFirm:BPHYT_RS24155 (305 letters) >NCBI__GCF_000009985.1:WP_043744492.1 Length = 290 Score = 114 bits (285), Expect = 3e-30 Identities = 89/295 (30%), Positives = 140/295 (47%), Gaps = 13/295 (4%) Query: 13 EGLLSFPVTDFDEQGDFRADTYAERLEWLAPYGASALFVAGGTGEFFSLTHNDYSNVVKT 72 +G ++ +T F G + + + W G A+ G TGE +L+H+++ VV+ Sbjct: 3 KGSITALITPF-RNGKVDEKAFQDLVAWQIAEGTHAVVPCGTTGESPTLSHDEHHRVVEL 61 Query: 73 ATEVCKGKVPILAGAG-GPTRVAIAYAQEAERHGANGILLMPHYLTEACQEGIAAHAEEV 131 EV +GKVP++AG G T A+A Q A + GA+ L++ Y + QEG+ H E + Sbjct: 62 CLEVARGKVPVIAGTGSNSTDEAVALTQHARKAGADAALVVAPYYNKPSQEGLFRHFEAI 121 Query: 132 CKSVPNMGVIIYN---RANSKLNADMLEGLAERCPNLIGFKDGVGEIENMVSIRRRLGDR 188 KSV ++ +I+YN R+ ++ + L+ PN+ G KD ++ + IR L +R Sbjct: 122 AKSV-DIPIIVYNIPGRSVIDISVETFVRLS-ALPNIAGIKDATADLARPLRIRAALDER 179 Query: 189 FSYLGGLPTAEVYAAAYKALGVPVYSSAVFNFIPKTAMDFYRAIAADDHATVGKLIDEFF 248 L G + A A+ A G S N PK A AA D AT +L ++ Sbjct: 180 LCQLSG---EDATAIAFNAQGGVGCISVTSNIAPKLCARMQNAWAAGDLATCNEL-NKIL 235 Query: 249 LPYLAIRNRRAGYAVSIVKAGAKLVGHSAGPVRAPLTDLTEEEMGKLDALIKTLG 303 +P A VK A L+G SA VR PL +E +++A +K G Sbjct: 236 MPLHDALFCETSPAP--VKYAASLLGKSAPDVRLPLVPASENARHRVEAAMKAAG 288 Lambda K H 0.319 0.136 0.398 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: 197 Number of extensions: 8 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: 305 Length of database: 290 Length adjustment: 26 Effective length of query: 279 Effective length of database: 264 Effective search space: 73656 Effective search space used: 73656 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 (21.7 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