Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate HSERO_RS06450 HSERO_RS06450 dihydrodipicolinate synthetase
Query= metacyc::BSU16770-MONOMER (290 letters) >FitnessBrowser__HerbieS:HSERO_RS06450 Length = 305 Score = 93.6 bits (231), Expect = 5e-24 Identities = 89/283 (31%), Positives = 133/283 (46%), Gaps = 22/283 (7%) Query: 9 AMITPFDNKGNVDFQKLSTLIDYLLK-NGTDSLVVAGTTGESPTLSTEEKIALFEYTVKE 67 A +TPF G VD + L +L +G LVV G GE LS E+ A+ E VK Sbjct: 11 APVTPFTRDGAVDHAAIMRLGKWLGSFDGVKGLVVLGHAGEGTFLSQSEQAAVIESFVKS 70 Query: 68 VNGRVPVIAGTGSNNTKDSIKLTKKAEEAGVDAVMLVTPY------YNKPSQEGMYQHFK 121 +GRVPVIAG T+ + + K+A +AG A ++ + Y K + + Y + Sbjct: 71 TDGRVPVIAGITLEGTQVAAEEAKRAVKAGAAAGLVYPSHGWLRFGYQKGAPQDRY---R 127 Query: 122 AIAAETSLPVMLYNVPGRTVASLAPETTIRLAADIPNVVAIKEASGDLE----AITKIIA 177 AI E+ LP++L+ P T A+ ET + +AA +P V A+K ++ I + Sbjct: 128 AIYEESGLPLILFQYPDATKATYNLETQLDIAA-LPGVFAMKNGVRNMRRWDTEIPVVRR 186 Query: 178 ETPEDFYVYSGDDALTLPILSVGGRGVVSVASHIAGTDMQQMIKNYTNGQTANAALIHQK 237 E P+ + D+ L + V G +V S IA + +I A IH K Sbjct: 187 ERPDLQILTCHDEYLLHTMFDVDG-ALVGYGS-IAPELLIDLIAAGKAKDYRKARAIHDK 244 Query: 238 LLPIMKELF----KAPNPAPVKTALQLRG-LDVGSVRLPLVPL 275 LLP+ K ++ +K AL RG L+ +VR PL+PL Sbjct: 245 LLPVTKNVYHRGSHMEGTVALKHALVARGILEHATVRSPLLPL 287 Lambda K H 0.313 0.131 0.356 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: 211 Number of extensions: 7 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: 290 Length of database: 305 Length adjustment: 26 Effective length of query: 264 Effective length of database: 279 Effective search space: 73656 Effective search space used: 73656 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 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