Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate WP_012335818.1 M446_RS29835 dihydrodipicolinate synthase family protein
Query= BRENDA::Q9I4W3 (292 letters) >NCBI__GCF_000019365.1:WP_012335818.1 Length = 294 Score = 121 bits (303), Expect = 2e-32 Identities = 84/267 (31%), Positives = 127/267 (47%), Gaps = 17/267 (6%) Query: 9 LVTPFDAQGRLDWDSLAKLVDFHLQEGTNAIVAVGTTGESATLDVEEHIQVIRRVVDQVK 68 LV+P DA+GR+ LA LV+ + G + + +G+TGE A L + + V+ VV+ Sbjct: 11 LVSPLDAEGRVMRPVLADLVEHLIAAGVHGLTPLGSTGEFAYLTPAQKLAVVETVVEAAA 70 Query: 69 GRIPVIAGTGANSTREAVALTEAAKSGGADACLLVTPYYNKPTQEGMYQHFRHIAEAVAI 128 GR+PVIAG A +T EAV+L A GAD + Y +G+ +F IA AV Sbjct: 71 GRVPVIAGVAATATAEAVSLARAVMERGADGVMATLEAYFPVPDDGIETYFTAIAAAVDG 130 Query: 129 PQILYNVPGRTSCDMLPETVERLSKVPNIIGIKEATGDLQRAKEVIERVGKDFLVYSGDD 188 P +LY P D+ + RLS+V NI IK+A+ + R ++ V++ Sbjct: 131 PVVLYTNPHFQRADLSLPLIRRLSRVGNIRYIKDASTNTGRLLSILSETEGRMRVFAASS 190 Query: 189 ATAVELMLLGGKGNISVTANVAPRAMSDLCAAAMRGDAAAARAINDRLMPLHKAL----- 243 +ML+GG G ++ A + PR L A GD A A A+ L +++A Sbjct: 191 HIPACVMLIGGVGWMAGPACLVPRQSVALYERARAGDWAGAMALQRDLWAVNQAFARYNL 250 Query: 244 ------------FIESNPIPVKWALHE 258 F +P+P + AL E Sbjct: 251 AACVKAGLALQGFAVGDPVPPQAALDE 277 Lambda K H 0.319 0.134 0.393 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: 204 Number of extensions: 9 Number of successful extensions: 2 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: 294 Length adjustment: 26 Effective length of query: 266 Effective length of database: 268 Effective search space: 71288 Effective search space used: 71288 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 (21.8 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