Align 4-hydroxy-tetrahydrodipicolinate synthase; HTPA synthase; Protein MosA; EC 4.3.3.7 (characterized)
to candidate H281DRAFT_03816 H281DRAFT_03816 5-dehydro-4-deoxyglucarate dehydratase
Query= SwissProt::Q07607 (292 letters) >FitnessBrowser__Burk376:H281DRAFT_03816 Length = 305 Score = 113 bits (282), Expect = 6e-30 Identities = 89/284 (31%), Positives = 134/284 (47%), Gaps = 20/284 (7%) Query: 3 EGSITALVTPF---ADDRIDEVALHDLVEWQIEEGSFGLVPCGTTGESPTLSKSEHEQVV 59 EG ++ VT F D R D A +EW G+ L G TGE +L+KS++ V+ Sbjct: 13 EGLLSFPVTDFDAQGDFRADTYAQR--LEWLAPYGATALFAAGGTGEFFSLTKSDYTNVI 70 Query: 60 EITIKTANGRVPVIAGAGSNSTAEAIAFVRHAQNAGADGVLIVSPYYNKPTQEGIYQHFK 119 +T G+VP++AGAG T AI + R A+ GA+GVL++ Y + +QEGI H + Sbjct: 71 RTATETCKGKVPILAGAG-GPTRVAIEYAREAERLGANGVLLMPHYLTEASQEGIAAHVE 129 Query: 120 AI-DAASTIPIIVYNIPGRSAIEIHVETLARIFEDCPNVKGVKDATGNLLRPSLERMACG 178 + A I +IVYN R+ +++ + L R+ + CPN+ G KD G + R G Sbjct: 130 QVCHAVKNIGVIVYN---RANSKLNADMLERLADRCPNLIGFKDGVGEIEAMVTIRRRLG 186 Query: 179 EDFNLLTG---EDGTALGYMAHGGHGCISVTANVAPALCADFQQACLNGDFAAALKLQDR 235 + F+ L G + A Y A G S N P +F +A D A +L D Sbjct: 187 DRFSYLGGLPTAEVYAAAYKALGVPVYSSAVFNFIPKTAMEFYRAIAADDHATTSRLIDE 246 Query: 236 LMPLHRALFLETNPAG-----AKYALQRLGRMRGDLRLPLVTIS 274 + L + AG K + +GR G +R PL ++ Sbjct: 247 FFLPY--LAIRNRRAGYAVSIVKAGAKLVGRDAGPVRAPLTDLT 288 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: 214 Number of extensions: 14 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: 305 Length adjustment: 27 Effective length of query: 265 Effective length of database: 278 Effective search space: 73670 Effective search space used: 73670 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