Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate WP_010530050.1 ON01_RS05690 dihydrodipicolinate synthase family protein
Query= BRENDA::A9CFV4 (303 letters) >NCBI__GCF_000224785.1:WP_010530050.1 Length = 292 Score = 139 bits (350), Expect = 8e-38 Identities = 85/282 (30%), Positives = 141/282 (50%), Gaps = 3/282 (1%) Query: 2 KFEGIYTPAITPLGHDGEIDRDAFAAVLESLMEARVHGIIIGGSTGEYYAQTAQERFDLA 61 KFEG+Y +TP+ D ++D + + E L+ V G+I G GEY + +ER + Sbjct: 3 KFEGVYISLVTPMTKDYKVDYKRLSEICEWLIGKGVDGLIPAGPLGEYATLSNEERRKVV 62 Query: 62 AYARQVIGTRLPLVVGTGATRTEDSIEYAKAAKEIGADAILVSSPPYALPTERENAVHAL 121 + R+ ++VGTGA+ T D I++AK AK AD IL P P E E H Sbjct: 63 ETVIKASKRRVSVIVGTGASATRDVIDWAKHAKSNEADGILALPPVNYKPLENEVITHFE 122 Query: 122 AVDRAANLPIMLYNYPARMGVVMGEEYFSRVGKSKNVVAIKESSGDMGNLHLLARKFPQI 181 A+ +PI+ +N P GV + + +++ +S+N+V +KE SGD+ + + K + Sbjct: 123 AISE-VGIPIIAFNNPRDFGVDLSPDLLAKISESENIVGVKEFSGDIRRVQEILEK-TNL 180 Query: 182 ALSCGWDDQALEFFAWGAKSWVCAGSNFLPREHVALYEACVVEKNFDKGRAIMTAMLPLM 241 + G DD A+E GA W SN LP E + L++ E+ F++ + ++ L Sbjct: 181 EVFVGVDDLAMEGALCGASGWTSGVSNALPEEGIKLFQ-LAKERRFEEASILYRDLVKLF 239 Query: 242 DFLECGKFVQSIKHGCEIIGLRAGSVRAPLRPLNSDEKRTLQ 283 + + +QSIK+ E+ G G R P L + + ++ Sbjct: 240 HYDANPQLIQSIKYMMELAGQPVGPTRPPRLALTNKAYKEIE 281 Lambda K H 0.320 0.135 0.397 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: 176 Number of extensions: 11 Number of successful extensions: 4 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: 303 Length of database: 292 Length adjustment: 26 Effective length of query: 277 Effective length of database: 266 Effective search space: 73682 Effective search space used: 73682 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