Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate PfGW456L13_3142 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7)
Query= BRENDA::A9CFV4 (303 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3142 Length = 301 Score = 468 bits (1203), Expect = e-136 Identities = 228/300 (76%), Positives = 259/300 (86%) Query: 1 MKFEGIYTPAITPLGHDGEIDRDAFAAVLESLMEARVHGIIIGGSTGEYYAQTAQERFDL 60 MKFEGIYTPAITPL GEID+ AFA VLE L+E++VHGIIIGGSTGEYYA T+QER +L Sbjct: 1 MKFEGIYTPAITPLTASGEIDKAAFADVLEYLIESKVHGIIIGGSTGEYYAHTSQERIEL 60 Query: 61 AAYARQVIGTRLPLVVGTGATRTEDSIEYAKAAKEIGADAILVSSPPYALPTERENAVHA 120 A A+ VIG RLPLV+GTGA RTEDS+EYAKAA+EI ADAILV SPPYALPTE+ENA+HA Sbjct: 61 ATQAKDVIGGRLPLVIGTGAIRTEDSVEYAKAAREIKADAILVGSPPYALPTEKENAIHA 120 Query: 121 LAVDRAANLPIMLYNYPARMGVVMGEEYFSRVGKSKNVVAIKESSGDMGNLHLLARKFPQ 180 L VDRAA LPIMLYNYPARMGV MG EYF+ V +SKN+VAIKESSGDM +H LAR++P Sbjct: 121 LTVDRAAGLPIMLYNYPARMGVSMGPEYFAAVAESKNIVAIKESSGDMAQVHRLAREYPN 180 Query: 181 IALSCGWDDQALEFFAWGAKSWVCAGSNFLPREHVALYEACVVEKNFDKGRAIMTAMLPL 240 I+LSCGWDDQALEFFAWGA+SWVCAGSNF+PREHVALYEACVVEK+FDKGR IM+A +PL Sbjct: 181 ISLSCGWDDQALEFFAWGARSWVCAGSNFIPREHVALYEACVVEKDFDKGRKIMSAFMPL 240 Query: 241 MDFLECGKFVQSIKHGCEIIGLRAGSVRAPLRPLNSDEKRTLQTVVTTLKRTVAQIASGA 300 MDFLE GKFVQSIK GCE+ GLR G VR+PL+PL EK+ LQ ++TTLKR VAQ+ A Sbjct: 241 MDFLESGKFVQSIKVGCELNGLRTGGVRSPLQPLYEHEKQALQDIITTLKRDVAQVTGSA 300 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: 342 Number of extensions: 5 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: 303 Length of database: 301 Length adjustment: 27 Effective length of query: 276 Effective length of database: 274 Effective search space: 75624 Effective search space used: 75624 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 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