Align dihydrodipicolinate synthase; EC 4.2.1.52 (characterized)
to candidate WP_012333617.1 M446_RS18420 dihydrodipicolinate synthase family protein
Query= CharProtDB::CH_021853 (292 letters) >NCBI__GCF_000019365.1:WP_012333617.1 Length = 299 Score = 150 bits (380), Expect = 3e-41 Identities = 88/287 (30%), Positives = 151/287 (52%), Gaps = 3/287 (1%) Query: 2 IDFGTIATAMVTPFDINGNIDFAKTTKLVNYLIDNGTTAIVVGGTTGESPTLTSEEKVAL 61 ID+G I +VTPF +G+I+ + +L++ I NG IV G+TGE LT E+ L Sbjct: 4 IDWGGIFPVLVTPFGPDGSINELRYKELIDEAIRNGARGIVAAGSTGEFYALTISERARL 63 Query: 62 YRHVVSVVDKRVPVIAGTGSNNTHASIDLTKKATEVGVDAVMLVAPYYNKPSQEGMYQHF 121 Y+ V V R+PV+AG +D + A G M++ P Y PS + F Sbjct: 64 YKLTVDHVAGRIPVLAGVADLRVEDVVDACQAAVAAGCVGGMILPPIYAMPSPREIVAFF 123 Query: 122 KAIAESTPLPVMLYNVPGRSIVQISVDTVVRLSEIENIVAIKDAGGDVLTMTEIIEKTAD 181 + ++ S+ LP+MLYN P R+ + I+ V +LS++ +VAIKD+ G + +TE++++ Sbjct: 124 EHVSRSSSLPLMLYNSPRRAGIDINPALVEQLSKLPTVVAIKDSSGLINQVTELVQRVGG 183 Query: 182 DFAVYSGDDGLTLPAMAVGAKGIVSVASHVIGNEMQE-MIAAFQAGEFKKAQKLHQLLVR 240 V+ G + + +PA AVGA G++++A + G +++ A + GE + + + Sbjct: 184 SLRVFVGYETMIVPARAVGAHGVIAMAHQIAGPLIRDYWDQALKGGE--SVDDMGRDVFA 241 Query: 241 VTDSLFMAPSPTPVKTALQMVGLDVGSVRLPLLPLTEEERVTLQSVM 287 +K + +G D G RLPLLPLT +++ + ++ Sbjct: 242 FYRCFQSGAYYAAIKETMTQLGRDAGGPRLPLLPLTGDQKAAIAKII 288 Lambda K H 0.316 0.132 0.362 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: 180 Number of extensions: 6 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: 292 Length of database: 299 Length adjustment: 26 Effective length of query: 266 Effective length of database: 273 Effective search space: 72618 Effective search space used: 72618 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 (21.6 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