Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate WP_068173718.1 HTA01S_RS16140 5-dehydro-4-deoxyglucarate dehydratase
Query= BRENDA::Q8UGL3 (294 letters) >NCBI__GCF_001592305.1:WP_068173718.1 Length = 305 Score = 124 bits (311), Expect = 3e-33 Identities = 85/283 (30%), Positives = 137/283 (48%), Gaps = 11/283 (3%) Query: 1 MFKGSIPALITPFTDNGSVDEKAFAAHVEWQIAEGSNGLVPVGTTGESPTLSHDEHKRVV 60 M G + +T F NG + +A+A +EW G+ L G TGE +L+ DE+ ++ Sbjct: 12 MSSGLLSFPLTDFDANGDFNARAYAERLEWLAPYGATALFAAGGTGEFFSLTADEYPGII 71 Query: 61 ELCIEVAAKRVPVIAGAGSNNTDEAIELALHAQEAGADALLVVTPYYNKPTQKGLFAHFS 120 + ++ +VP+IAGAG T AI+ A A++AGA +L++ Y + Q+GL AH Sbjct: 72 QTAVDTCRGKVPIIAGAG-GPTRFAIQCAQAAEKAGAHGILLLPHYLTEACQEGLIAHVE 130 Query: 121 AVAEAVKLPIVIYNIPPRSVVDMSPETMGALVKAHKNIIGVKDATGKLDRVSEQRISCGK 180 AV ++VK +++YN R+V ++PE++ L N+IG KD G ++ +S + G+ Sbjct: 131 AVCKSVKFGVIVYN---RNVCKLTPESLAILADRCPNLIGFKDGVGDIELMSSIHMKMGE 187 Query: 181 DFVQLSG---EDGTALGFNAHGGVGCISVTANVAPRLCSEFQAAMLAGDYAKALEYQDRL 237 F L G + A + A G S N PR +F A+ + D A Q RL Sbjct: 188 RFAYLGGLPTAEVYAAAYKALGTPVYSSAVFNFIPRTAMDFYEAVRSDDMAT----QHRL 243 Query: 238 MPLHRAIFMEPGVCGTKYALSKTRGGNRRVRSPLMSTLEPATE 280 + +++ YA+S + G V P TE Sbjct: 244 LRQFFMPYLQIRNRAQGYAVSIVKAGATLVGHTAGPVRAPLTE 286 Lambda K H 0.317 0.133 0.384 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: 220 Number of extensions: 16 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: 294 Length of database: 305 Length adjustment: 27 Effective length of query: 267 Effective length of database: 278 Effective search space: 74226 Effective search space used: 74226 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: 41 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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