Align P-protein; EC 4.2.1.51; EC 5.4.99.5 (characterized)
to candidate WP_011386516.1 AMB_RS21090 prephenate dehydratase
Query= CharProtDB::CH_024084 (386 letters) >NCBI__GCF_000009985.1:WP_011386516.1 Length = 289 Score = 150 bits (379), Expect = 4e-41 Identities = 99/277 (35%), Positives = 140/277 (50%), Gaps = 6/277 (2%) Query: 100 NPHSARIAFLGPKGSYSHLAARQYAARHFEQFIESGCAKFADIFNQVETGQADYAVVPIE 159 NP A IAF G G+YSHLA R + CA F D F V G+A YA++PI+ Sbjct: 6 NPDQA-IAFQGEPGAYSHLACRNA----YPGMQPLPCATFEDTFAAVREGRARYAMIPID 60 Query: 160 NTSSGAINDVYDLLQHTSLSIVGEMTLTIDHCLLVSGTTDLSTINTVYSHPQPFQQCSKF 219 N+ +G + DV+ L+ + L I+ E I H LLV L TI TV SH QC Sbjct: 61 NSVAGRVADVHHLMPYAGLHIIAEHFERISHHLLVVPGATLDTIKTVKSHVHALGQCRNL 120 Query: 220 LNRYPHWKIEYTESTSAAMEKVAQAKSPHVAALGSEAGGTLYGLQVLERIEANQRQNFTR 279 + I T++ AA E +A+ + P +AA+ SE YGL L+ + N TR Sbjct: 121 IRELGLKVIVGTDTAGAAAE-LAERQDPTMAAIASELAAEAYGLVSLKAGIEDAEHNTTR 179 Query: 280 FVVLARKAINVSDQVPAKTTLLMATGQQAGALVEALLVLRNHNLIMTRLESRPIHGNPWE 339 FVVLAR+A+ + P TT + A AL +AL + + MTRLES + G Sbjct: 180 FVVLAREALEPNPNQPCVTTFVFRVRNVAAALYKALGGFATNGINMTRLESYMVGGEFAA 239 Query: 340 EMFYLDIQANLESAEMQKALKELGEITRSMKVLGCYP 376 FY D++ + ++ AL+EL + +++LG YP Sbjct: 240 TQFYADVEGHPTQRNLRLALEELDFFSHEVRILGVYP 276 Lambda K H 0.318 0.132 0.374 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: 238 Number of extensions: 13 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: 386 Length of database: 289 Length adjustment: 28 Effective length of query: 358 Effective length of database: 261 Effective search space: 93438 Effective search space used: 93438 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 (21.8 bits) S2: 49 (23.5 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