Align fused chorismate mutase/prephenate dehydrogenase (EC 5.4.99.5; EC 1.3.1.12) (characterized)
to candidate 6936707 Sama_0894 bifunctional chorismate mutase/prephenate dehydrogenase (RefSeq)
Query= ecocyc::CHORISMUTPREPHENDEHYDROG-MONOMER (373 letters) >FitnessBrowser__SB2B:6936707 Length = 379 Score = 427 bits (1098), Expect = e-124 Identities = 216/371 (58%), Positives = 269/371 (72%), Gaps = 1/371 (0%) Query: 3 AELTALRDQIDEVDKALLNLLAKRLELVAEVGEVKSRFGLPIYVPEREASMLASRRAEAE 62 AEL LR ID VD LL+LL KRL+LVA+VG VK GLPIY P REA+ML RRAEAE Sbjct: 7 AELENLRGLIDGVDSQLLSLLRKRLDLVAQVGTVKHAAGLPIYAPAREAAMLGKRRAEAE 66 Query: 63 ALGVPPDLIEDVLRRVMRESYSSENDKGFKTLCPSLRPVVIVGGGGQMGRLFEKMLTLSG 122 A+GV P LIED+LRR+MRESY SE D GFK + P L +VI+GG GQ+GRLF +M LSG Sbjct: 67 AMGVSPQLIEDILRRLMRESYMSEKDVGFKQVNPELGHIVIIGGQGQLGRLFAQMFALSG 126 Query: 123 YQVRILEQHDWDRAADIVADAGMVIVSVPIHVTEQVIG-KLPPLPKDCILVDLASVKNGP 181 Y+VR+L++ DWD A ++ AG+V+V+VPI T +I +L LP+ CIL DL SVK P Sbjct: 127 YEVRLLDKDDWDHADELFDGAGLVLVTVPIATTCSLIRERLDHLPEHCILADLTSVKGAP 186 Query: 182 LQAMLVAHDGPVLGLHPMFGPDSGSLAKQVVVWCDGRKPEAYQWFLEQIQVWGARLHRIS 241 L+AML H GPV+GLHPMFGPD GSLAKQVVV C GR PE YQW +EQI +WGARL Sbjct: 187 LKAMLETHKGPVVGLHPMFGPDVGSLAKQVVVVCHGRAPEKYQWLMEQIGIWGARLVEAD 246 Query: 242 AVEHDQNMAFIQALRHFATFAYGLHLAEENVQLEQLLALSSPIYRLELAMVGRLFAQDPQ 301 A HD+ M +QA+RHF++F YGL+L E ++ LL SSPIYRLELAMVGRLFAQ + Sbjct: 247 AGRHDKAMQLVQAMRHFSSFVYGLNLCREQADIDTLLEFSSPIYRLELAMVGRLFAQSGE 306 Query: 302 LYADIIMSSERNLALIKRYYKRFGEAIELLEQGDKQAFIDSFRKVEHWFGDYAQRFQSES 361 LYADII + E +L I + + +A+ELL+ GD+ FI F +V +WFG+Y+Q+F +ES Sbjct: 307 LYADIIFAQEESLTAISDFIDNYRDALELLKTGDRAGFIARFNEVSNWFGNYSQQFLTES 366 Query: 362 RVLLRQANDNR 372 R +L+ ND R Sbjct: 367 RAMLQSVNDMR 377 Lambda K H 0.322 0.138 0.404 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: 403 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: 373 Length of database: 379 Length adjustment: 30 Effective length of query: 343 Effective length of database: 349 Effective search space: 119707 Effective search space used: 119707 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 (21.9 bits) S2: 50 (23.9 bits)
Align candidate 6936707 Sama_0894 (bifunctional chorismate mutase/prephenate dehydrogenase (RefSeq))
to HMM TIGR01799 (tyrA: chorismate mutase (EC 5.4.99.5))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR01799.hmm # target sequence database: /tmp/gapView.15088.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01799 [M=83] Accession: TIGR01799 Description: CM_T: chorismate mutase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-47 146.2 0.8 2.7e-47 145.1 0.8 1.6 1 lcl|FitnessBrowser__SB2B:6936707 Sama_0894 bifunctional chorismat Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SB2B:6936707 Sama_0894 bifunctional chorismate mutase/prephenate dehydrogenase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 145.1 0.8 2.7e-47 2.7e-47 1 83 [] 9 91 .. 9 91 .. 0.99 Alignments for each domain: == domain 1 score: 145.1 bits; conditional E-value: 2.7e-47 TIGR01799 1 lkdlrdeidevdkellqllakrlelvaqvGkvkhraGlPiyaPereaamlakrreeaeklGiapdliedvlrrlmresy 79 l++lr+ id+vd +ll ll+krl+lvaqvG+vkh+aGlPiyaP reaaml krr+eae++G++p+lied+lrrlmresy lcl|FitnessBrowser__SB2B:6936707 9 LENLRGLIDGVDSQLLSLLRKRLDLVAQVGTVKHAAGLPIYAPAREAAMLGKRRAEAEAMGVSPQLIEDILRRLMRESY 87 799**************************************************************************** PP TIGR01799 80 anen 83 ++e+ lcl|FitnessBrowser__SB2B:6936707 88 MSEK 91 **97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (83 nodes) Target sequences: 1 (379 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 9.33 // [ok]
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