Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate SM_b20140 SM_b20140 dihydrodipicolinate synthase
Query= BRENDA::Q7D3Z9 (297 letters) >FitnessBrowser__Smeli:SM_b20140 Length = 293 Score = 504 bits (1299), Expect = e-148 Identities = 247/293 (84%), Positives = 273/293 (93%) Query: 1 MTKKAFVAIVTCFNDDETINYEATRAQVRRQVTAGNNIMCAGTNGDFTALTHSEKIRILE 60 M+KKAFVA+VTCFN+DETINY+ATRAQVRRQV AGNNIMCAGTNGDFTALTH EKIR+ E Sbjct: 1 MSKKAFVALVTCFNEDETINYDATRAQVRRQVAAGNNIMCAGTNGDFTALTHEEKIRLTE 60 Query: 61 EVVDEVGGKVDVIVNAGMPATFETLQLAKEFDRIGVKGIAVITPFFIACTQDGLIRHFST 120 EVVDEVGG+VDVIVNAGMPATFETLQLA+ FDRIGV GIAVITPFFIACTQDGLIRHFST Sbjct: 61 EVVDEVGGRVDVIVNAGMPATFETLQLARAFDRIGVSGIAVITPFFIACTQDGLIRHFST 120 Query: 121 VADEVNTPVYLYDIPARTQNHIEPETARKLATHGNIAGIKDSGGAQETLEAYLQVSKEVD 180 VAD V TPVYLYDIP+RTQNHIEPETA KL+ HGNIAGIKDSGGAQ+TLEAYLQV+++V Sbjct: 121 VADAVETPVYLYDIPSRTQNHIEPETALKLSAHGNIAGIKDSGGAQDTLEAYLQVARDVP 180 Query: 181 GFEVYSGPDHLVLWALQNGAAGCISGLGNAMPDVLAGIVNGFNSGDITYAERQQSVYTAF 240 GFEVYSGPDHLVLW+LQNGAAGCISGLGNAMP+VLAGI++ FNSG+I AER+Q++YTAF Sbjct: 181 GFEVYSGPDHLVLWSLQNGAAGCISGLGNAMPEVLAGILSAFNSGNIAEAERRQAIYTAF 240 Query: 241 RTDLYAHGFPPAMVKRALYLQDPSVGASRQPALLPDAEQDQKIEEILRKYGLL 293 RT+LYA GFPPA+VKR+LYLQDPSVGASRQPALLP EQD KI EIL ++ LL Sbjct: 241 RTELYALGFPPALVKRSLYLQDPSVGASRQPALLPSEEQDAKIREILVRHRLL 293 Lambda K H 0.318 0.135 0.391 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: 376 Number of extensions: 5 Number of successful extensions: 1 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: 297 Length of database: 293 Length adjustment: 26 Effective length of query: 271 Effective length of database: 267 Effective search space: 72357 Effective search space used: 72357 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 09 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