Align P-protein; EC 4.2.1.51; EC 5.4.99.5 (characterized)
to candidate 200542 SO1367 chorismate mutase/prephenate dehydratase (NCBI ptt file)
Query= CharProtDB::CH_024084 (386 letters) >FitnessBrowser__MR1:200542 Length = 671 Score = 411 bits (1056), Expect = e-119 Identities = 213/386 (55%), Positives = 277/386 (71%), Gaps = 7/386 (1%) Query: 1 MTSENPLLALREKISALDEKLLALLAERRELAVEVGKAKLLSHRPVRDIDRERDLLERLI 60 M PL RE+I+ LD LL+LLAERR L++EV ++K + RP+RD RE++LL RL+ Sbjct: 1 MQKPQPLNHTREQITQLDNDLLSLLAERRRLSLEVARSKEVDVRPIRDTQREKELLARLV 60 Query: 61 TLGKAHHLDAHYITRLFQLIIEDSVLTQQALLQQHLNKINPHSAR----IAFLGPKGSYS 116 T G+ LDAHY+ L+Q IIEDSVL QQA L + NP + + IA+LG +GSYS Sbjct: 61 TAGREKGLDAHYVISLYQSIIEDSVLNQQAYLH---GRANPETQKQQYCIAYLGARGSYS 117 Query: 117 HLAARQYAARHFEQFIESGCAKFADIFNQVETGQADYAVVPIENTSSGAINDVYDLLQHT 176 +LAA +Y R + ++ GC F +I VE+G ADY +PIENTSSG+IN+VYD+LQHT Sbjct: 118 YLAASRYCQRRQVEMLDLGCQSFDEIVQAVESGHADYGFLPIENTSSGSINEVYDVLQHT 177 Query: 177 SLSIVGEMTLTIDHCLLVSGTTDLSTINTVYSHPQPFQQCSKFLNRYPHWKIEYTESTSA 236 SLSIVGE T+ + HCLL + LS I TVY+HPQP QCS++L+++ ++EY S++ Sbjct: 178 SLSIVGETTIEVSHCLLGKPGSKLSEIKTVYAHPQPISQCSRYLSQHKALRLEYCSSSAE 237 Query: 237 AMEKVAQAKSPHVAALGSEAGGTLYGLQVLERIEANQRQNFTRFVVLARKAINVSDQVPA 296 AMEKV Q+ AA+GS GG LY L+ +E ANQ+ N +RF+V+ARKA+ V +Q+PA Sbjct: 238 AMEKVNQSPDNSAAAIGSAEGGALYQLESIESGLANQKINQSRFIVVARKAVAVPEQLPA 297 Query: 297 KTTLLMATGQQAGALVEALLVLRNHNLIMTRLESRPIHGNPWEEMFYLDIQANLESAEMQ 356 KTTL+MATGQ+AGALVEALLVL+ H L M++LESRPI G PWEEMFYLDI AN+ S MQ Sbjct: 298 KTTLIMATGQKAGALVEALLVLKAHQLNMSKLESRPIPGTPWEEMFYLDIDANISSEAMQ 357 Query: 357 KALKELGEITRSMKVLGCYPSENVVP 382 + LK+L ITR +KVLGCYP E V P Sbjct: 358 QGLKQLERITRFIKVLGCYPCETVTP 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: 545 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: 671 Length adjustment: 34 Effective length of query: 352 Effective length of database: 637 Effective search space: 224224 Effective search space used: 224224 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