Align fused chorismate mutase/prephenate dehydrogenase (EC 5.4.99.5; EC 1.3.1.12) (characterized)
to candidate 200537 SO1362 chorismate mutase/prephenate dehydrogenase (NCBI ptt file)
Query= ecocyc::CHORISMUTPREPHENDEHYDROG-MONOMER (373 letters) >FitnessBrowser__MR1:200537 Length = 379 Score = 426 bits (1096), Expect = e-124 Identities = 213/369 (57%), Positives = 273/369 (73%), Gaps = 1/369 (0%) Query: 3 AELTALRDQIDEVDKALLNLLAKRLELVAEVGEVKSRFGLPIYVPEREASMLASRRAEAE 62 +EL LR ID VD+ LL+LL KRL+LVA+VG VK GLPIY P+REA+MLA RR EA+ Sbjct: 7 SELEHLRGLIDGVDQQLLHLLRKRLDLVAQVGTVKHAAGLPIYAPQREAAMLAKRREEAQ 66 Query: 63 ALGVPPDLIEDVLRRVMRESYSSENDKGFKTLCPSLRPVVIVGGGGQMGRLFEKMLTLSG 122 +G+ P LIED+LRR+MRESY +E D GFK + L VVIVGG GQ+G LF++ML LSG Sbjct: 67 TMGIAPQLIEDILRRLMRESYLNEKDVGFKQVKNDLGSVVIVGGKGQLGGLFQQMLRLSG 126 Query: 123 YQVRILEQHDWDRAADIVADAGMVIVSVPIHVTEQVIG-KLPPLPKDCILVDLASVKNGP 181 YQV++L++ DW +A + ADAG+V+V+VPI +T +I KL LP+DCIL DL S+K P Sbjct: 127 YQVKVLDKDDWQQAECLFADAGLVLVTVPIAITCDIIREKLTQLPRDCILADLTSIKTEP 186 Query: 182 LQAMLVAHDGPVLGLHPMFGPDSGSLAKQVVVWCDGRKPEAYQWFLEQIQVWGARLHRIS 241 +QAML AH GPV+G HPMFGPD GSLAKQVVV C GR+ + YQW LEQI +WGAR+ Sbjct: 187 MQAMLAAHKGPVVGFHPMFGPDVGSLAKQVVVVCHGREADKYQWLLEQIAIWGARIVEAE 246 Query: 242 AVEHDQNMAFIQALRHFATFAYGLHLAEENVQLEQLLALSSPIYRLELAMVGRLFAQDPQ 301 HD M +QA+RHF+TF YGL+L +E +E LL SSPIYRLELAMVGRLFAQ P+ Sbjct: 247 PECHDNAMQLVQAMRHFSTFVYGLNLCKEEADIETLLKFSSPIYRLELAMVGRLFAQSPE 306 Query: 302 LYADIIMSSERNLALIKRYYKRFGEAIELLEQGDKQAFIDSFRKVEHWFGDYAQRFQSES 361 LYADII + + + I Y + EA+ELL++GD++ FI+ F+ V WFGD+A +FQ ES Sbjct: 307 LYADIIFAQQESQHAIGDYLDNYREALELLKRGDREEFINQFQMVAKWFGDFAPQFQRES 366 Query: 362 RVLLRQAND 370 R++L+ +D Sbjct: 367 RMMLQSVSD 375 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: 393 Number of extensions: 14 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 200537 SO1362 (chorismate mutase/prephenate dehydrogenase (NCBI ptt file))
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.18474.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4e-51 157.3 1.4 1.3e-50 155.7 1.2 2.0 2 lcl|FitnessBrowser__MR1:200537 SO1362 chorismate mutase/prephen Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__MR1:200537 SO1362 chorismate mutase/prephenate dehydrogenase (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 155.7 1.2 1.3e-50 1.3e-50 1 83 [] 9 91 .. 9 91 .. 0.99 2 ? -2.1 0.0 0.24 0.24 14 49 .. 331 368 .. 320 373 .. 0.60 Alignments for each domain: == domain 1 score: 155.7 bits; conditional E-value: 1.3e-50 TIGR01799 1 lkdlrdeidevdkellqllakrlelvaqvGkvkhraGlPiyaPereaamlakrreeaeklGiapdliedvlrrlmresyan 81 l++lr+ id+vd++ll+ll+krl+lvaqvG+vkh+aGlPiyaP+reaamlakrreea+++Giap+lied+lrrlmresy+n lcl|FitnessBrowser__MR1:200537 9 LEHLRGLIDGVDQQLLHLLRKRLDLVAQVGTVKHAAGLPIYAPQREAAMLAKRREEAQTMGIAPQLIEDILRRLMRESYLN 89 79******************************************************************************* PP TIGR01799 82 en 83 e+ lcl|FitnessBrowser__MR1:200537 90 EK 91 97 PP == domain 2 score: -2.1 bits; conditional E-value: 0.24 TIGR01799 14 ellqllak..rlelvaqvGkvkhraGlPiyaPereaam 49 e l+ll++ r e++ q v + +G +re m lcl|FitnessBrowser__MR1:200537 331 EALELLKRgdREEFINQFQMVAKWFGDFAPQFQRESRM 368 55566653336677777777777776544444566655 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 10.19 // [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