Align chorismate mutase (EC 5.4.99.5) (characterized)
to candidate AO353_12165 AO353_12165 chorismate mutase
Query= BRENDA::B2JYH9 (182 letters) >FitnessBrowser__pseudo3_N2E3:AO353_12165 Length = 192 Score = 125 bits (315), Expect = 3e-34 Identities = 74/157 (47%), Positives = 95/157 (60%), Gaps = 4/157 (2%) Query: 23 AFVPLVRSMADRLNTADQVALSKWDTGQPVYDGQREAQVIANAATMASEYGLTAEDAINI 82 A PL+ ++ +RL AD+VALSKWD+G+PV D QRE +VIA+A A Y L+ E Sbjct: 36 ALAPLLSTIQERLVIADKVALSKWDSGKPVEDRQREREVIADAIAEAPYYKLSNEAVEQF 95 Query: 83 FSDQVEANKEVQYALLNNWRRQGDAPATPRQSLAGVIRPILDKLQASIMQNLQSVAPLRS 142 FS Q+EANK VQYA L++W QG AP PR L G+IRP LD LQ ++Q L P R+ Sbjct: 96 FSAQIEANKLVQYAHLSDWHAQGKAPNDPRPDLVGLIRPQLDLLQTRLLQQLADFTPYRN 155 Query: 143 IADCHALVASAVGQVAEQASLDVLHRAALDRAVARIC 179 C + +A A + A Q L L AL RA A +C Sbjct: 156 DPHCPSWLAKA-NKAATQVPLREL---ALVRATAELC 188 Lambda K H 0.318 0.129 0.369 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: 96 Number of extensions: 4 Number of successful extensions: 1 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: 182 Length of database: 192 Length adjustment: 20 Effective length of query: 162 Effective length of database: 172 Effective search space: 27864 Effective search space used: 27864 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 (21.8 bits) S2: 44 (21.6 bits)
Align candidate AO353_12165 AO353_12165 (chorismate mutase)
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.29483.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4e-37 113.1 0.2 6.3e-37 112.4 0.2 1.3 1 lcl|FitnessBrowser__pseudo3_N2E3:AO353_12165 AO353_12165 chorismate mutase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo3_N2E3:AO353_12165 AO353_12165 chorismate mutase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 112.4 0.2 6.3e-37 6.3e-37 4 114 .] 35 147 .. 32 147 .. 0.97 Alignments for each domain: == domain 1 score: 112.4 bits; conditional E-value: 6.3e-37 TIGR01806 4 aaldqlvdlaneRleladaValyKaesnlpieDsereeqvLdslraqaksagldedsverlfqaq 68 aal+ l++ ++eRl +ad+Val+K++s++p+eD++re++v++++ a+a+ l+++ ve++f aq lcl|FitnessBrowser__pseudo3_N2E3:AO353_12165 35 AALAPLLSTIQERLVIADKVALSKWDSGKPVEDRQREREVIADAIAEAPYYKLSNEAVEQFFSAQ 99 68899************************************************************ PP TIGR01806 69 inAnkaiqyrllsdWk.skaeppvevrdLe.dlRakidqlntelLeal 114 i+Ank++qy+ lsdW+ + ++p+ +++dL +R+++d l+t+lL++l lcl|FitnessBrowser__pseudo3_N2E3:AO353_12165 100 IEANKLVQYAHLSDWHaQGKAPNDPRPDLVgLIRPQLDLLQTRLLQQL 147 ****************9999999*******99**************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (114 nodes) Target sequences: 1 (192 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: 8.01 // [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