Align candidate PP_2170 PP_2170 (putative enzyme, chorismate mutase family protein)
to HMM PF01817 (CM_2)
# 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/PF01817.25.hmm # target sequence database: /tmp/gapView.11769.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CM_2 [M=79] Accession: PF01817.25 Description: Chorismate mutase type II 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.3e-24 71.4 1.7 7.5e-24 70.3 1.7 1.7 1 lcl|FitnessBrowser__Putida:PP_2170 PP_2170 putative enzyme, chorism Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_2170 PP_2170 putative enzyme, chorismate mutase family protein # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 70.3 1.7 7.5e-24 7.5e-24 1 78 [. 142 218 .. 142 219 .. 0.97 Alignments for each domain: == domain 1 score: 70.3 bits; conditional E-value: 7.5e-24 CM_2 1 RkeIdeiDrelleLlaeRmelakeiaeyKkenglpvldpeReeevlerlregaeelgldpeavekifreiisesr 75 R++IdeiDr l+ Lla+R +l+ ++a +Kk+++ +v+ p+R+e+v++++re a+e g ++e+ve+++r++is+++ lcl|FitnessBrowser__Putida:PP_2170 142 RQRIDEIDRSLVSLLAKRGRLVTQAAGFKKTTD-DVRAPARVEQVIKKAREMADETGASAEVVEQVYRAMISAFI 215 9****************************8777.9***************************************9 PP CM_2 76 alQ 78 a + lcl|FitnessBrowser__Putida:PP_2170 216 AEE 218 976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (79 nodes) Target sequences: 1 (232 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: 7.66 // [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