Align Bifunctional chorismate mutase/prephenate dehydratase; Chorismate mutase-prephenate dehydratase; P-protein; EC 5.4.99.5; EC 4.2.1.51 (characterized)
to candidate WP_010531115.1 ON01_RS11090 prephenate dehydratase
Query= SwissProt::P27603 (365 letters) >NCBI__GCF_000224785.1:WP_010531115.1 Length = 286 Score = 135 bits (339), Expect = 2e-36 Identities = 92/282 (32%), Positives = 150/282 (53%), Gaps = 21/282 (7%) Query: 95 LRVAYLGPEGTFSQAAALKHFG----HSVISKPMAAIDEVFREVVAGAVNFGVVPVENST 150 +++ YLGP GTF++ A F S + P ID VF E ++ GVVP+EN+ Sbjct: 2 VKIGYLGPRGTFTKLAVDTAFNGENKQSFTTVP-ECIDAVFHE----EIDIGVVPLENAI 56 Query: 151 EGAVNHTLDSFLEHDI--VICGEVELRIHHHLLV--GETTKTDRITRIYSHAQSLAQCRK 206 EG V T+D +L H + + E+ + I +LLV G T + + ++SH+ ++AQC + Sbjct: 57 EGTVQITVD-YLVHQVRLPVVAEIVVPIQQNLLVKPGFTGEISEVLEVFSHSHAIAQCHQ 115 Query: 207 WLDAHYPNVERVAVSSNADAAKRVK-SEWNSAAIAGDMAAQLYGLSKLAEKIEDRPVNST 265 +L H P+ + SS AA+ V S+ N AAI +AA YGL E I D P N T Sbjct: 116 FLHMHMPDAKLNFTSSTGKAAEVVSGSDRNIAAIGNRLAASEYGLDIFHENIHDYPNNHT 175 Query: 266 RFLIIGSQEV-----PPTGDDKTSIIVSMRNK-PGALHELLMPFHSNGIDLTRIETRPSR 319 RF ++ + G +KTS+++++ + GAL+++L F ++L++IE+RP + Sbjct: 176 RFAVLAKDKEIVNVKHEAGAEKTSLLITLPSDYAGALYQVLAAFAWRRMNLSKIESRPMK 235 Query: 320 SGKWTYVFFIDCMGHHQDPLIKNVLEKIGHEAVALKVLGSYP 361 +G Y F +D + D L V ++ + +LG+YP Sbjct: 236 TGLGNYFFIVDVNQPYDDVLFPGVKAELEALGCNVTILGTYP 277 Lambda K H 0.319 0.133 0.390 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: 213 Number of extensions: 11 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: 365 Length of database: 286 Length adjustment: 28 Effective length of query: 337 Effective length of database: 258 Effective search space: 86946 Effective search space used: 86946 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 Jul 26 2024. The underlying query database was built on Jul 25 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