Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate BWI76_RS15245 BWI76_RS15245 dihydrodipicolinate synthase family protein
Query= BRENDA::Q7D3Z9 (297 letters) >FitnessBrowser__Koxy:BWI76_RS15245 Length = 294 Score = 238 bits (608), Expect = 9e-68 Identities = 120/283 (42%), Positives = 176/283 (62%), Gaps = 1/283 (0%) Query: 8 AIVTCFNDDETINYEATRAQVRRQVTAGNNIMCAGTNGDFTALTHSEKIRILEEVVDEVG 67 AIVT F + +N A + QV+RQ+ AGN I C GTNG+F L +EK+ + + V+EV Sbjct: 11 AIVTPFTAEGAVNIPALKQQVQRQLAAGNGIFCGGTNGEFFVLNEAEKVAVAKACVEEVA 70 Query: 68 GKVDVIVNAGMPATFETLQLAKEFDRIGVKGIAVITPFFIACTQDGLIRHFSTVADEVNT 127 G+ V+ + G +T ET++L K+ +++GV ++VITP+F+ QD LI H++ +AD ++ Sbjct: 71 GRAPVVAHIGEVSTRETIRLGKQIEQLGVDAVSVITPWFVPLKQDELIAHYTAIADALSV 130 Query: 128 PVYLYDIPARTQNHIEPETARKLATHGNIAGIKDSGGAQETLEAYLQVSKEVDGFEVYSG 187 PV+LY+IPART N IEP+TAR LA H NI G+KDS G+ E+L+ +L +++ F+V +G Sbjct: 131 PVFLYNIPARTGNTIEPQTARALAQHPNIIGVKDSAGSYESLKGFLDAVRDIADFDVLNG 190 Query: 188 PDHLVLWALQNGAAGCISGLGNAMPDVLAGIVNGFNSGDITYAERQQSVYTAFRTDLYAH 247 PD L+ +G + CISGL N P + I F +G++ + + Q T RTDLY Sbjct: 191 PDSLIHQGFVDGCSACISGLANVAPKEINAIWANFKAGNVEGSRQAQESVTGLRTDLYKV 250 Query: 248 GFPPAMVKRALYLQDPSVGASRQPALLPDAEQDQKIEEILRKY 290 F PA VK+AL L VG SR A Q ++I I+ KY Sbjct: 251 AFSPAAVKKALQLMGHDVGDSRYAVSFTSA-QCEEINHIIAKY 292 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: 224 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: 297 Length of database: 294 Length adjustment: 26 Effective length of query: 271 Effective length of database: 268 Effective search space: 72628 Effective search space used: 72628 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 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