Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate WP_027178454.1 G496_RS0105825 dihydrodipicolinate synthase family protein
Query= BRENDA::Q6G468 (294 letters) >NCBI__GCF_000429985.1:WP_027178454.1 Length = 300 Score = 145 bits (367), Expect = 8e-40 Identities = 96/294 (32%), Positives = 149/294 (50%), Gaps = 5/294 (1%) Query: 2 LKGAVTALITPFDDNGAIDEKAFCNFVEWQITQGINGVSPVGTTGESPTLTHEEHKRIIE 61 LKG + + T +NG D+ F+E + +NG+ +G+ GE L++ K I E Sbjct: 6 LKGIIPPVSTILKENGEFDKTGMGVFIERLVASDVNGLLFLGSAGEFSQLSNPVRKEIAE 65 Query: 62 LCVEQVAKRVPVVAGAGSNSTSEAVELAKHAEKAGADAVLVVTPYYNRPNQRGLYTHFSS 121 CV+ VA R PV+ G G+ T+E ++L+ HA GADAV+VV PYY + LY H+ + Sbjct: 66 FCVKSVAGRKPVIIGTGACGTAEVIDLSLHAASIGADAVIVVNPYYQPMDDERLYNHYRT 125 Query: 122 IAKAISIPIIIYNIPSRSVIDMAVETMRDLCRDFKNIIGVKDATGKIERASE---QREKC 178 IA+A ++P+IIYN P+ + D++ + ++ L D NI+G+KD I + + Sbjct: 126 IAEASTLPVIIYNFPALTGQDLSPQLIKRLALDCPNIVGIKDTVDCISHIRDLIIHVKGA 185 Query: 179 GKDFVQLSGDDCTALGFNAHGGVGCISVSSNVAPKLCAQLHAACLCSDYKTALKLNDLLM 238 DF + G D A GG G I +SN AP++ ++ A +D +T +L L Sbjct: 186 RPDFKVICGYDEYLFMTLAMGGDGAIPGTSNFAPEITCGIYKAFQENDLETIKELAPRLA 245 Query: 239 PLNRAVFIE-PSPAGIKYAAAKLGL-CGTIVRSPIVPLSDTTKKIIDEALYHAG 290 L + ++ P +K A G T V +P S+ KK E L AG Sbjct: 246 TLAQLYSLDVPFSWLLKEAIRSTGSDIPTGVAAPATAPSEDVKKRFHEILKQAG 299 Lambda K H 0.318 0.134 0.394 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: 207 Number of extensions: 10 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: 294 Length of database: 300 Length adjustment: 26 Effective length of query: 268 Effective length of database: 274 Effective search space: 73432 Effective search space used: 73432 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