Align 4-hydroxy-tetrahydrodipicolinate synthase; HTPA synthase; Protein MosA; EC 4.3.3.7 (characterized)
to candidate Ac3H11_2339 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41)
Query= SwissProt::Q07607 (292 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2339 Length = 303 Score = 117 bits (292), Expect = 4e-31 Identities = 84/269 (31%), Positives = 124/269 (46%), Gaps = 10/269 (3%) Query: 27 VEWQIEEGSFGLVPCGTTGESPTLSKSEHEQVVEITIKTANGRVPVIAGAGSNSTAEAIA 86 +EW G+ L G TGE +LS E+ +V++ + T G+VP+IAGAG T AIA Sbjct: 37 LEWLAPYGASALFAAGGTGEYFSLSGPEYSEVIKTAVDTCRGKVPIIAGAG-GPTRTAIA 95 Query: 87 FVRHAQNAGADGVLIVSPYYNKPTQEGIYQHFKAIDAASTIPIIVYNIPGRSAIEIHVET 146 + A+ GA G+L++ Y + QEG+ +H + + +IVYN R ++ E+ Sbjct: 96 HAQEAERLGAHGILLLPHYLTEAGQEGLIEHVAQVCNSVKFGVIVYN---RDRTKLTAES 152 Query: 147 LARIFEDCPNVKGVKDATGNLLRPSLERMACGEDFNLLTG---EDGTALGYMAHGGHGCI 203 LA + E CPN+ G KD GN+ S M G+ F+ L G + A Y A G Sbjct: 153 LAILAERCPNLIGFKDGVGNIETMSSIYMKMGDRFSYLGGLPTAEVYAAAYKALGTPVYS 212 Query: 204 SVTANVAPALCADFQQACLNGDFAAALKLQDRLMPLHRALFLETNPAGA---KYALQRLG 260 S N P DF +A D A KL + A+ G K + +G Sbjct: 213 SAVFNFIPKTAMDFYKAVAADDIATQHKLLKEFFMPYLAIRNRVEGYGVSIIKAGAKIVG 272 Query: 261 RMRGDLRLPLVTISPSFQEEIDDAMRHAG 289 G +R PL + P EE+ ++ G Sbjct: 273 HDGGPVRAPLTDLKPHEVEELAALIKKLG 301 Lambda K H 0.319 0.136 0.402 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: 218 Number of extensions: 17 Number of successful extensions: 3 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: 292 Length of database: 303 Length adjustment: 26 Effective length of query: 266 Effective length of database: 277 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 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