Align 4-hydroxy-tetrahydrodipicolinate synthase; HTPA synthase; Protein MosA; EC 4.3.3.7 (characterized)
to candidate HSERO_RS15785 HSERO_RS15785 5-dehydro-4-deoxyglucarate dehydratase
Query= SwissProt::Q07607 (292 letters) >FitnessBrowser__HerbieS:HSERO_RS15785 Length = 306 Score = 114 bits (286), Expect = 2e-30 Identities = 82/273 (30%), Positives = 125/273 (45%), Gaps = 18/273 (6%) Query: 27 VEWQIEEGSFGLVPCGTTGESPTLSKSEHEQVVEITIKTANGRVPVIAGAGSNSTAEAIA 86 +EW G+ L G TGE +L E+ ++ + T G+VP+IAGAG ST AIA Sbjct: 40 LEWLAPYGASALFAAGGTGEFFSLVPGEYSDIIRTAVDTCRGKVPIIAGAG-GSTRAAIA 98 Query: 87 FVRHAQNAGADGVLIVSPYYNKPTQEGIYQHFKAIDAASTIPIIVYNIPGRSAIEIHVET 146 + + A+ GA G+L++ Y + +Q+GI H +A+ + +I+YN R+ +++ +T Sbjct: 99 YAQEAERLGAHGILLMPHYLTEASQDGIAAHVEAVCKSVKFGVIIYN---RAVCKLNADT 155 Query: 147 LARIFEDCPNVKGVKDATGNLLRPSLERMACGEDFNLLTG---EDGTALGYMAHGGHGCI 203 L ++ + CPN+ G KD G + R G+ F L G + A Y A G Sbjct: 156 LQKLADRCPNLIGFKDGIGEIEPMVHIRRKLGDRFTYLGGLPTAEVYAAAYKALGVPVYS 215 Query: 204 SVTANVAPALCADFQQACLNGDFAAALKLQDRLMPLHRAL-------FLETNPAGAKYAL 256 S N P +F QA D KL D + A+ + AGA+ A Sbjct: 216 SAVFNFIPKTAVEFYQAIAKEDHDTVGKLIDEFFLPYLAIRNRKAGYAVSIVKAGARIA- 274 Query: 257 QRLGRMRGDLRLPLVTISPSFQEEIDDAMRHAG 289 G G +R PL +P EE+ M G Sbjct: 275 ---GHDAGPVRTPLTDCTPEEHEELAALMNKLG 304 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: 16 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: 292 Length of database: 306 Length adjustment: 27 Effective length of query: 265 Effective length of database: 279 Effective search space: 73935 Effective search space used: 73935 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