Align P-protein; EC 4.2.1.51; EC 5.4.99.5 (characterized)
to candidate 16694 b2599 fused chorismate mutase P/prephenate dehydratase (NCBI)
Query= CharProtDB::CH_024084 (386 letters) >FitnessBrowser__Keio:16694 Length = 386 Score = 758 bits (1956), Expect = 0.0 Identities = 386/386 (100%), Positives = 386/386 (100%) Query: 1 MTSENPLLALREKISALDEKLLALLAERRELAVEVGKAKLLSHRPVRDIDRERDLLERLI 60 MTSENPLLALREKISALDEKLLALLAERRELAVEVGKAKLLSHRPVRDIDRERDLLERLI Sbjct: 1 MTSENPLLALREKISALDEKLLALLAERRELAVEVGKAKLLSHRPVRDIDRERDLLERLI 60 Query: 61 TLGKAHHLDAHYITRLFQLIIEDSVLTQQALLQQHLNKINPHSARIAFLGPKGSYSHLAA 120 TLGKAHHLDAHYITRLFQLIIEDSVLTQQALLQQHLNKINPHSARIAFLGPKGSYSHLAA Sbjct: 61 TLGKAHHLDAHYITRLFQLIIEDSVLTQQALLQQHLNKINPHSARIAFLGPKGSYSHLAA 120 Query: 121 RQYAARHFEQFIESGCAKFADIFNQVETGQADYAVVPIENTSSGAINDVYDLLQHTSLSI 180 RQYAARHFEQFIESGCAKFADIFNQVETGQADYAVVPIENTSSGAINDVYDLLQHTSLSI Sbjct: 121 RQYAARHFEQFIESGCAKFADIFNQVETGQADYAVVPIENTSSGAINDVYDLLQHTSLSI 180 Query: 181 VGEMTLTIDHCLLVSGTTDLSTINTVYSHPQPFQQCSKFLNRYPHWKIEYTESTSAAMEK 240 VGEMTLTIDHCLLVSGTTDLSTINTVYSHPQPFQQCSKFLNRYPHWKIEYTESTSAAMEK Sbjct: 181 VGEMTLTIDHCLLVSGTTDLSTINTVYSHPQPFQQCSKFLNRYPHWKIEYTESTSAAMEK 240 Query: 241 VAQAKSPHVAALGSEAGGTLYGLQVLERIEANQRQNFTRFVVLARKAINVSDQVPAKTTL 300 VAQAKSPHVAALGSEAGGTLYGLQVLERIEANQRQNFTRFVVLARKAINVSDQVPAKTTL Sbjct: 241 VAQAKSPHVAALGSEAGGTLYGLQVLERIEANQRQNFTRFVVLARKAINVSDQVPAKTTL 300 Query: 301 LMATGQQAGALVEALLVLRNHNLIMTRLESRPIHGNPWEEMFYLDIQANLESAEMQKALK 360 LMATGQQAGALVEALLVLRNHNLIMTRLESRPIHGNPWEEMFYLDIQANLESAEMQKALK Sbjct: 301 LMATGQQAGALVEALLVLRNHNLIMTRLESRPIHGNPWEEMFYLDIQANLESAEMQKALK 360 Query: 361 ELGEITRSMKVLGCYPSENVVPVDPT 386 ELGEITRSMKVLGCYPSENVVPVDPT Sbjct: 361 ELGEITRSMKVLGCYPSENVVPVDPT 386 Lambda K H 0.318 0.132 0.374 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: 554 Number of extensions: 6 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: 386 Length of database: 386 Length adjustment: 30 Effective length of query: 356 Effective length of database: 356 Effective search space: 126736 Effective search space used: 126736 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
Align candidate 16694 b2599 (fused chorismate mutase P/prephenate dehydratase (NCBI))
to HMM TIGR01797 (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/TIGR01797.hmm # target sequence database: /tmp/gapView.18393.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01797 [M=83] Accession: TIGR01797 Description: CM_P_1: 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.5e-46 140.7 2.9 2e-45 139.2 3.2 1.7 2 lcl|FitnessBrowser__Keio:16694 b2599 fused chorismate mutase P/ Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Keio:16694 b2599 fused chorismate mutase P/prephenate dehydratase (NCBI) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 139.2 3.2 2e-45 2e-45 1 83 [] 7 89 .. 7 89 .. 0.99 2 ? -3.8 0.0 0.8 0.8 64 77 .. 121 134 .. 111 136 .. 0.74 Alignments for each domain: == domain 1 score: 139.2 bits; conditional E-value: 2e-45 TIGR01797 1 llalrekisaidkkllkllaerkelafevakskllsqkavrdierekkllqklitlgkkyqleaeyitrlfqliiedsvlt 81 llalrekisa+d+kll+llaer+ela+ev+k+klls+++vrdi+re++ll++litlgk+++l+a+yitrlfqliiedsvlt lcl|FitnessBrowser__Keio:16694 7 LLALREKISALDEKLLALLAERRELAVEVGKAKLLSHRPVRDIDRERDLLERLITLGKAHHLDAHYITRLFQLIIEDSVLT 87 799****************************************************************************** PP TIGR01797 82 qq 83 qq lcl|FitnessBrowser__Keio:16694 88 QQ 89 *8 PP == domain 2 score: -3.8 bits; conditional E-value: 0.8 TIGR01797 64 aeyitrlfqliied 77 +y +r f + ie lcl|FitnessBrowser__Keio:16694 121 RQYAARHFEQFIES 134 47999999999985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (83 nodes) Target sequences: 1 (386 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: 9.44 // [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