Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate WP_066328440.1 BLR17_RS00850 dihydrodipicolinate synthase family protein
Query= BRENDA::Q9I4W3 (292 letters) >NCBI__GCF_900100165.1:WP_066328440.1 Length = 309 Score = 130 bits (326), Expect = 5e-35 Identities = 88/273 (32%), Positives = 145/273 (53%), Gaps = 7/273 (2%) Query: 4 GSMVALVTPFDAQGRLDWDSLAKLVDFHLQEGTNAIVAVGTTGESATLDVEEHIQVIRRV 63 G +V +VTP A +D +++A LV+ HL +G +GTTGES+++ E + ++++ Sbjct: 9 GVVVPMVTPLRADSGIDLEAVAVLVN-HLIDGGCHPFVLGTTGESSSISFESKVALVKKT 67 Query: 64 VDQVKGRIPVIAGTGANSTREAVALTEAAKSGGADACLLVTPYYNKPTQEGMYQHFRHIA 123 V+ KG+ V AG N +E++ + G D + PYY Q + +F+ +A Sbjct: 68 VEVAKGKATVYAGISGNCFQESLDQAKIYTDLGVDVLVAHVPYYYPLNQNHILNYFQQLA 127 Query: 124 EAVAIPQILYNVPGRTSCDMLPETVERLSKVPNIIGIKEA-TGDLQRAKEV-IERVGKDF 181 AVA+P I+YN+P T+ + ET + LSK PNI+G KE+ G+ + AK + + + DF Sbjct: 128 SAVALPLIVYNMPMTTNMSIDLETADELSKHPNIVGYKESERGEERMAKAIGLWKDRADF 187 Query: 182 LVYSGDDATAVELMLLGGKGNISVTANVAPRAMSDLCAAAMRGDAAAARAI---NDRLMP 238 G A + E M LG G + T N+ P S + A + GD A+A+A +D + Sbjct: 188 SYLLGWAAKSYEGMKLGADGLVPSTGNLTPELYSTIYNAVLSGDDASAKAAQEKSDAISK 247 Query: 239 LHKALFIESNPIPV-KWALHEMGLIPEGIRLPL 270 +++ I N IP+ K L L + + LP+ Sbjct: 248 IYQENQILVNAIPILKVLLAHHKLCSKAVLLPM 280 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: 217 Number of extensions: 8 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: 309 Length adjustment: 27 Effective length of query: 265 Effective length of database: 282 Effective search space: 74730 Effective search space used: 74730 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 Jul 26 2024. The underlying query database was built on Jul 25 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