Align P-protein; EC 4.2.1.51; EC 5.4.99.5 (characterized)
to candidate 5208561 Shew_1072 chorismate mutase (RefSeq)
Query= CharProtDB::CH_024084 (386 letters) >FitnessBrowser__PV4:5208561 Length = 654 Score = 416 bits (1070), Expect = e-121 Identities = 213/383 (55%), Positives = 280/383 (73%), Gaps = 1/383 (0%) Query: 1 MTSENPLLALREKISALDEKLLALLAERRELAVEVGKAKLLSHRPVRDIDRERDLLERLI 60 MT +PL RE+I+ALD +LLALLA+RR L+++V ++K + RP+RD RE++LL RL+ Sbjct: 1 MTKPHPLSHTREQITALDNELLALLAKRRALSLDVARSKEVDIRPIRDTQREKELLARLV 60 Query: 61 TLGKAHHLDAHYITRLFQLIIEDSVLTQQALLQQHLNK-INPHSARIAFLGPKGSYSHLA 119 G+ LDAHY+ L+Q IIEDSVL QQA LQ N + IA+LG +GSYS+LA Sbjct: 61 KQGREQGLDAHYVLSLYQSIIEDSVLNQQAYLQGRANPDLQKQQYNIAYLGARGSYSYLA 120 Query: 120 ARQYAARHFEQFIESGCAKFADIFNQVETGQADYAVVPIENTSSGAINDVYDLLQHTSLS 179 A +Y R + GC F +I VE+G ADY +PIENTSSG+IN+VYD+LQHTSL+ Sbjct: 121 ATRYCERRQVGMQDLGCKSFDEIVQAVESGHADYGFLPIENTSSGSINEVYDVLQHTSLA 180 Query: 180 IVGEMTLTIDHCLLVSGTTDLSTINTVYSHPQPFQQCSKFLNRYPHWKIEYTESTSAAME 239 IVGE T+ + HCLL T++ I T+Y+HPQP QCS++L+++ +K+EY S++ AME Sbjct: 181 IVGETTIEVGHCLLAKPGTNVKQIKTIYAHPQPISQCSRYLSQHGEFKLEYCSSSAEAME 240 Query: 240 KVAQAKSPHVAALGSEAGGTLYGLQVLERIEANQRQNFTRFVVLARKAINVSDQVPAKTT 299 +V +A VAA+GS GG LY L+ +E ANQ+ N +RF+V+ARKAI V +Q+PAKTT Sbjct: 241 RVLEADDNSVAAIGSVEGGALYQLEAVEHELANQKINQSRFIVVARKAIAVPEQLPAKTT 300 Query: 300 LLMATGQQAGALVEALLVLRNHNLIMTRLESRPIHGNPWEEMFYLDIQANLESAEMQKAL 359 L+MATGQ+ GALVEALL+L+ H+L M++LESRPI G PWEEMFYLD+ ANL S EMQ+AL Sbjct: 301 LIMATGQKPGALVEALLILKAHDLNMSKLESRPIPGTPWEEMFYLDLDANLASDEMQQAL 360 Query: 360 KELGEITRSMKVLGCYPSENVVP 382 KEL ITR +KVLGCYP E V P Sbjct: 361 KELERITRFIKVLGCYPCETVNP 383 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: 534 Number of extensions: 17 Number of successful extensions: 2 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: 654 Length adjustment: 34 Effective length of query: 352 Effective length of database: 620 Effective search space: 218240 Effective search space used: 218240 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: 52 (24.6 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