Align 4-hydroxy-tetrahydrodipicolinate synthase; HTPA synthase; EC 4.3.3.7 (characterized)
to candidate 18322 b4298 putative lyase/synthase (VIMSS)
Query= SwissProt::Q9X1K9 (294 letters) >FitnessBrowser__Keio:18322 Length = 301 Score = 162 bits (410), Expect = 9e-45 Identities = 89/296 (30%), Positives = 159/296 (53%), Gaps = 3/296 (1%) Query: 2 FRGVGTAIVTPF-KNGELDLESYERLVRYQLENGVNALIVLGTTGESPTVNEDEREKLVS 60 F G+ + + F ++G LD ++ + + + GV+ L LGT GE +N +R L Sbjct: 4 FSGIIPPVSSTFHRDGTLDKKAMREVADFLINKGVDGLFYLGTGGEFSQMNTAQRMALAE 63 Query: 61 RTLEIVDGKIPVIVGAGTNSTEKTLKLVKQAEKLGANGVLVVTPYYNKPTQEGLYQHYKY 120 + IVDG++PV++G G+ ST++ +KL + A+ GA+G++ + PYY K L +Y+ Sbjct: 64 EAVTIVDGRVPVLIGVGSPSTDEAVKLAQHAQAYGADGIVAINPYYWKVAPRNLDDYYQQ 123 Query: 121 ISERTDLGIVVYNVPGRTGVNVLPETAARIAADLKNVVGIKEANPDIDQIDRTVSLTKQA 180 I+ L +++YN P TG ++ PET R+A +N+VGIK+ + + ++ K Sbjct: 124 IARSVTLPVILYNFPDLTGQDLTPETVTRLALQNENIVGIKDTIDSVGHLRTMINTVKSV 183 Query: 181 RSDFMVWSGNDDRTFYLLCAGGDGVISVVSNVAPKQMVELCAEYFSGNLEKSREVHRKLR 240 R F V+ G DD + GGDG I+ +N AP+ V + + G+L + +++KL Sbjct: 184 RPSFSVFCGYDDHLLNTMLLGGDGAITASANFAPELSVGIYRAWREGDLATAATLNKKLL 243 Query: 241 PLMKALFVETNPIP-VKAALNLMGF-IENELRLPLVPASEKTVELLRNVLKESGLL 294 L +ET + +K ++ +G +E P++ ASE+ + + +L G+L Sbjct: 244 QLPAIYALETPFVSLIKYSMQCVGLPVETYCLPPILEASEEAKDKVHVLLTAQGIL 299 Lambda K H 0.316 0.135 0.378 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: 189 Number of extensions: 8 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: 294 Length of database: 301 Length adjustment: 26 Effective length of query: 268 Effective length of database: 275 Effective search space: 73700 Effective search space used: 73700 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.5 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