Align P-protein; EC 4.2.1.51; EC 5.4.99.5 (characterized)
to candidate WP_106711779.1 CU102_RS13840 prephenate dehydratase
Query= CharProtDB::CH_024084 (386 letters) >NCBI__GCF_003010955.1:WP_106711779.1 Length = 288 Score = 145 bits (367), Expect = 1e-39 Identities = 98/279 (35%), Positives = 139/279 (49%), Gaps = 9/279 (3%) Query: 103 SARIAFLGPKGSYSHLAARQYAARHFEQFIESGCAKFADIFNQVETGQADYAVVPIENTS 162 S RI+F G G+ S A R F + C F D FN VE+G AD A++PIENT Sbjct: 5 STRISFQGEPGANSDTACRNM----FPEMEPMPCPTFEDAFNAVESGAADLAMIPIENTI 60 Query: 163 SGAINDVYDLLQHTSLSIVGEMTLTIDHCLLVSGTTDLSTINTVYSHPQPFQQCSKFLNR 222 +G + D++ LL + L IVGE L I L+V T S I +V+SH QC K++ R Sbjct: 61 AGRVADIHHLLPESRLHIVGEYFLPIHFQLMVLPGTKRSDITSVHSHIHALGQCRKYI-R 119 Query: 223 YPHWKIEYTESTSAAMEKVAQAKSPHVAALGSEAGGTLYGLQVLERIEANQRQNFTRFVV 282 WK T+ A VA + +AAL LYGL +LE + N TRFVV Sbjct: 120 KNGWKPVIAGDTAGAARLVADVRDKSMAALAPRLASDLYGLDILEEDVEDTENNVTRFVV 179 Query: 283 LARK---AINVSDQVPAKTTLLMATGQQAGALVEALLVLRNHNLIMTRLESRPIHGNPWE 339 L + A SD++ TT + AL +A+ + + MT+LES I G Sbjct: 180 LNKTKKWAPRTSDEL-MMTTFVFRVRNVPAALYKAMGGFATNGVNMTKLESYQIDGKFTA 238 Query: 340 EMFYLDIQANLESAEMQKALKELGEITRSMKVLGCYPSE 378 FY DI+ + + + AL EL ++ +++LG YP++ Sbjct: 239 TQFYADIEGHPDDKNVAHALDELEFFSKEVRILGVYPAD 277 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: 189 Number of extensions: 6 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: 288 Length adjustment: 28 Effective length of query: 358 Effective length of database: 260 Effective search space: 93080 Effective search space used: 93080 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 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