Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate H281DRAFT_00991 H281DRAFT_00991 4-hydroxy-tetrahydrodipicolinate synthase
Query= BRENDA::A9CFV4 (303 letters) >FitnessBrowser__Burk376:H281DRAFT_00991 Length = 295 Score = 243 bits (621), Expect = 3e-69 Identities = 127/291 (43%), Positives = 179/291 (61%), Gaps = 3/291 (1%) Query: 1 MKFEGIYTPAITPLGHDGEIDRDAFAAVLESLMEARVHGIIIGGSTGEYYAQTAQERFDL 60 M FEG++TP +TP DGEID +L RV G+ +GG+TGEYYA + ER Sbjct: 1 MSFEGVHTPLVTPFKADGEIDHTLLGKHAVNLA-GRVAGLGVGGTTGEYYALSFDERVQT 59 Query: 61 AAYARQVIGTRLPLVVGTGATRTEDSIEYAKAAKEIGADAILVSSPPYALPTERENAVHA 120 + G + L G AT T++ I + AK G +A+L+++P YA PT+ E H Sbjct: 60 FNTVAEAAGGKTYLTAGINATTTKEVIRLGQEAKRAGLNALLLAAPYYAQPTQDELLSHL 119 Query: 121 LAVDRAANLPIMLYNYPARMGVVMGEEYFSRVGKSKNVVAIKESSGDMGNLHLLARKF-P 179 L VD + ++P+MLYN+PAR G +G+ S++ + N +A+KES+GD+ +LH LA F Sbjct: 120 LKVDDSLDMPVMLYNFPARTGTHIGDNVLSKLLERPNFIAMKESTGDISHLHHLATHFRD 179 Query: 180 QIALSCGWDDQALEFFAWGAKSWVCAGSNFLPREHVALYEACVVEKNFDKGRAIMTAMLP 239 ++ LSCG DDQALEFF WGAKSWV SNFLP H AL +ACV +F GR +M +LP Sbjct: 180 RLVLSCGMDDQALEFFVWGAKSWVGGASNFLPEAHTALLDACVKHGDFATGRKLMAQLLP 239 Query: 240 LMDFLE-CGKFVQSIKHGCEIIGLRAGSVRAPLRPLNSDEKRTLQTVVTTL 289 +++ LE GKF+Q +++GCE+ G G RAPL L+ +E+ +V L Sbjct: 240 VLELLERSGKFIQYVRYGCELAGTPVGVARAPLGTLDENERSGFAKLVRPL 290 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: 239 Number of extensions: 7 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: 295 Length adjustment: 27 Effective length of query: 276 Effective length of database: 268 Effective search space: 73968 Effective search space used: 73968 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