Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate WP_012976848.1 AZL_RS23055 dihydrodipicolinate synthase family protein
Query= BRENDA::Q7D3Z9 (297 letters) >NCBI__GCF_000010725.1:WP_012976848.1 Length = 300 Score = 283 bits (725), Expect = 3e-81 Identities = 146/285 (51%), Positives = 192/285 (67%), Gaps = 1/285 (0%) Query: 6 FVAIVTCFNDDETINYEATRAQVRRQVTAGNNIMCAGTNGDFTALTHSEKIRILEEVVDE 65 FVAIVT F+ DE + A R QV+RQ +AGN + CAGTNG+F AL+ EK+ + E V+ Sbjct: 13 FVAIVTPFDGDERVEIAALRRQVKRQASAGNGVFCAGTNGEFYALSFDEKLAVAEICVEA 72 Query: 66 VGGKVDVIVNAGMPATFETLQLAKEFDRIGVKGIAVITPFFIACTQDGLIRHFSTVADEV 125 G+V V+ + G +T +T+ L + +GVK ++ ITP FIAC+Q LI H+ VAD + Sbjct: 73 AAGQVPVLAHIGEISTHQTIALGRAIQALGVKAVSAITPSFIACSQAELIAHYLRVADAL 132 Query: 126 NTPVYLYDIPARTQNHIEPETARKLATHGNIAGIKDSGGAQETLEAYLQVSKEVDGFEVY 185 P+YLY+IPART N +EPETAR LA H NI GIKDS G+QE+L+ +L +++E F+V Sbjct: 133 TVPLYLYNIPARTGNTLEPETARVLADHPNIIGIKDSAGSQESLDGFLAIARERGDFDVL 192 Query: 186 SGPDHLVLWALQNGAAGCISGLGNAMPDVLAGIVNGFNSGDITYAERQQSVYTAFRTDLY 245 GPD LVL L+NGAAGCISGLGN P L GI F +GD AE Q+ ++ R +LY Sbjct: 193 VGPDSLVLHGLRNGAAGCISGLGNIAPVTLNGIHAAFVAGDAAAAEAHQTHFSTLRKELY 252 Query: 246 AHGFPPAMVKRALYLQDPSVGASRQPALLPDAEQDQKIEEILRKY 290 A GFPPAMVKRALY P VG SR P L+ + E D +I+E+ +Y Sbjct: 253 ALGFPPAMVKRALYRAMPEVGLSRAPVLIAN-EADNRIKELAARY 296 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: 264 Number of extensions: 7 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: 300 Length adjustment: 27 Effective length of query: 270 Effective length of database: 273 Effective search space: 73710 Effective search space used: 73710 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