Align chorismate mutase (EC 5.4.99.5) (characterized)
to candidate WP_086511287.1 BZY95_RS18095 gamma subclass chorismate mutase AroQ
Query= BRENDA::Q2SY64 (202 letters) >NCBI__GCF_002151265.1:WP_086511287.1 Length = 197 Score = 95.9 bits (237), Expect = 4e-25 Identities = 61/141 (43%), Positives = 73/141 (51%), Gaps = 4/141 (2%) Query: 10 LRASLVAALLGCAALSAPRIAAADGDDTALTNLVALASQRLALAEPVAHWKWINRKPISD 69 L +LV L GC D D A+ ++ L +RL +A VA KW + PI Sbjct: 15 LAIALVLLLAGCQTQPPE---PPDEDKAAIDRMLVLIDERLDVAPLVAQSKWNSGAPIEA 71 Query: 70 PPREAALLTDVEKRATANGVDPAYARTFFDDQIAASKQLQNALFATW-RATHGPEGPAPD 128 P REA +L V + A A GVD A+AR FFD Q ASKQ+Q L W + P PD Sbjct: 72 PEREAQILDQVAEDAEAAGVDDAFARRFFDKQFEASKQIQRRLHHQWLQEGRSPFADPPD 131 Query: 129 LATSTRPQLDRLTQSLIAALA 149 LA RP LDRLT LI ALA Sbjct: 132 LAEEVRPVLDRLTPQLIEALA 152 Lambda K H 0.318 0.128 0.380 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: 122 Number of extensions: 9 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: 202 Length of database: 197 Length adjustment: 21 Effective length of query: 181 Effective length of database: 176 Effective search space: 31856 Effective search space used: 31856 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: 45 (21.9 bits)
Align candidate WP_086511287.1 BZY95_RS18095 (gamma subclass chorismate mutase AroQ)
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.12569.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.2e-32 96.6 0.3 6.7e-32 96.2 0.3 1.1 1 lcl|NCBI__GCF_002151265.1:WP_086511287.1 BZY95_RS18095 gamma subclass cho Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002151265.1:WP_086511287.1 BZY95_RS18095 gamma subclass chorismate mutase AroQ # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 96.2 0.3 6.7e-32 6.7e-32 3 114 .] 38 151 .. 36 151 .. 0.96 Alignments for each domain: == domain 1 score: 96.2 bits; conditional E-value: 6.7e-32 TIGR01806 3 saaldqlvdlaneRleladaValyKaesnlpieDsereeqvLdslraqaksagldedsverlfqaqinA 71 +aa+d+++ l++eRl +a Va++K++s+ pie +ere+q+Ld+++++a++ag+d+ ++r+f+ q +A lcl|NCBI__GCF_002151265.1:WP_086511287.1 38 KAAIDRMLVLIDERLDVAPLVAQSKWNSGAPIEAPEREAQILDQVAEDAEAAGVDDAFARRFFDKQFEA 106 56899**************************************************************** PP TIGR01806 72 nkaiqyrllsdWk.skaeppvevrdLe.dlRakidqlntelLeal 114 +k iq rl +W+ + ++p +++dL ++R+ +d l+ +l+eal lcl|NCBI__GCF_002151265.1:WP_086511287.1 107 SKQIQRRLHHQWLqEGRSPFADPPDLAeEVRPVLDRLTPQLIEAL 151 *************777788889****99**************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (114 nodes) Target sequences: 1 (197 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: 8.27 // [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