Align arogenate dehydratase (EC 4.2.1.91) (characterized)
to candidate WP_012473995.1 CPHAMN1_RS02740 prephenate dehydratase
Query= BRENDA::Q9SSE7 (381 letters) >NCBI__GCF_000020545.1:WP_012473995.1 Length = 279 Score = 227 bits (578), Expect = 3e-64 Identities = 141/285 (49%), Positives = 173/285 (60%), Gaps = 22/285 (7%) Query: 101 VAYQGVRGAYSESAAEKAYPNCEAVPCEEFDTAFEAVERWLVDRAVLPIENSLGGSIHRN 160 VAYQG GAYSE AA + + P E FD AF AVE V AV+PIENSLGGSIH N Sbjct: 6 VAYQGEPGAYSEIAALRFG---DPAPFESFDEAFYAVEHRSVSCAVIPIENSLGGSIHHN 62 Query: 161 YDLLLRHNLHIVGEVKLAVRHCLLANHGVNIEDLRRVLSHPQALAQCENTL-TKLGLVRE 219 YDLLL+H + IV E ++V HCLL G + E +VLSHPQAL+QC + L E Sbjct: 63 YDLLLQHPVRIVAETFVSVEHCLLGLPGASEEKKGKVLSHPQALSQCRKFFASHNNLKPE 122 Query: 220 AVDDTAGAAKQIAFENLNDAAAVASEKAAKIYGLNIVAKDIQDDCDNVTRFLMLAREP-- 277 DTAG+AK IA E A+AS++A ++YGL I +++ D+ N+TRF + E Sbjct: 123 VAYDTAGSAKVIAEERNPAHFAIASKRAGELYGLKIFRENLADEEWNITRFFCITHEDHT 182 Query: 278 ------IIPGTNRLFKTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRKHPLRAS 331 P T R KTSIVF+L PG LF+A+A ALR I+LTKIESRP + Sbjct: 183 TELELRTAPDTARQ-KTSIVFTLPNEPGSLFRAMATLALRDIDLTKIESRPSK------- 234 Query: 332 GGLKYFDYLFYVDFEASMADEVAQNALRHLEEFATFLRVLGSYPV 376 LK F+Y FYVDF S +D NAL HL EFAT ++VLGSY V Sbjct: 235 --LKAFEYFFYVDFIGSQSDATIHNALTHLREFATMVKVLGSYGV 277 Lambda K H 0.319 0.134 0.384 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: 272 Number of extensions: 15 Number of successful extensions: 5 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: 381 Length of database: 279 Length adjustment: 28 Effective length of query: 353 Effective length of database: 251 Effective search space: 88603 Effective search space used: 88603 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 10 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