Align candidate WP_050462663.1 AKL27_RS09950 (chorismate mutase AroQ, gamma subclass)
to HMM TIGR01806 (putative 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/TIGR01806.hmm # target sequence database: /tmp/gapView.6864.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01806 [M=114] Accession: TIGR01806 Description: CM_mono2: putative 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-26 78.2 0.0 3.8e-26 77.7 0.0 1.3 1 lcl|NCBI__GCF_001189915.1:WP_050462663.1 AKL27_RS09950 chorismate mutase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001189915.1:WP_050462663.1 AKL27_RS09950 chorismate mutase AroQ, gamma subclass # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 77.7 0.0 3.8e-26 3.8e-26 4 113 .. 41 156 .. 38 157 .. 0.86 Alignments for each domain: == domain 1 score: 77.7 bits; conditional E-value: 3.8e-26 TIGR01806 4 aaldqlvdlaneRleladaValyKaesnlpieDsereeqvLdslraq....aksagldedsverlfqaq 68 a++d+l+ l+++Rl +a Va K++s+ pi+D++re+q+Ld l++ +k ++ ++r+fq q lcl|NCBI__GCF_001189915.1:WP_050462663.1 41 ADVDRLLVLIEQRLDVAPMVARAKWNSGAPIDDPARERQILDGLMQTldagGKFDDAGKAFMRRFFQSQ 109 6899*************************************9988762221455566777789****** PP TIGR01806 69 inAnkaiqyrllsdWkskaepp.vevrdLe.dlRakidqlntelLea 113 +A k++q +l ++W+++ pp +v+dL+ d+R+ +d l+ +++ a lcl|NCBI__GCF_001189915.1:WP_050462663.1 110 FDAGKILQHALHAQWRQQGLPPfAQVPDLKtDIRPLLDRLTPQMIAA 156 ****************666555279*****9*************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (114 nodes) Target sequences: 1 (202 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: 6.61 // [ok]
This GapMind analysis is from Apr 10 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