Align Chorismate mutase; CM; Monofunctional chorismate mutase AroQ(f); EC 5.4.99.5 (characterized)
to candidate WP_004511889.1 GMET_RS09875 chorismate mutase
Query= SwissProt::Q57696 (99 letters) >NCBI__GCF_000012925.1:WP_004511889.1 Length = 98 Score = 60.8 bits (146), Expect = 4e-15 Identities = 30/94 (31%), Positives = 62/94 (65%), Gaps = 3/94 (3%) Query: 7 EIRKKIDEIDNKILKLIAERNSLAKDVAEIKNQLGIPINDPEREKYIYDRIRKLCKEHNV 66 E+R++ID +D+++L++ R SLA ++ IK + G+P+ DP+REK I++R+ K + Sbjct: 5 ELRQEIDRMDSELLRIFNRRASLALEIGLIKKERGLPVYDPKREKLIFERM-KADNPGPL 63 Query: 67 DENIGIKIFQILIEHNKALQK--QYLEETQNKNK 98 D+ +++F+ +I+ ++ L++ + EET K + Sbjct: 64 DDGAIVRLFERVIDESRRLERIMTHPEETTGKEE 97 Lambda K H 0.315 0.136 0.363 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: 36 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: 99 Length of database: 98 Length adjustment: 10 Effective length of query: 89 Effective length of database: 88 Effective search space: 7832 Effective search space used: 7832 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: 39 (20.6 bits) S2: 39 (19.6 bits)
Align candidate WP_004511889.1 GMET_RS09875 (chorismate mutase)
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.16566.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6e-27 80.2 0.9 7e-27 80.0 0.9 1.1 1 lcl|NCBI__GCF_000012925.1:WP_004511889.1 GMET_RS09875 chorismate mutase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000012925.1:WP_004511889.1 GMET_RS09875 chorismate mutase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 80.0 0.9 7e-27 7e-27 1 78 [. 7 83 .. 7 84 .. 0.97 Alignments for each domain: == domain 1 score: 80.0 bits; conditional E-value: 7e-27 CM_2 1 RkeIdeiDrelleLlaeRmelakeiaeyKkenglpvldpeReeevlerlre...gaeelgldpeavekifr 68 R+eId++D+ell+++++R++la ei+ +Kke+glpv+dp+Re+ ++er+++ g+ ld+ a+ ++f+ lcl|NCBI__GCF_000012925.1:WP_004511889.1 7 RQEIDRMDSELLRIFNRRASLALEIGLIKKERGLPVYDPKREKLIFERMKAdnpGP----LDDGAIVRLFE 73 9**************************************************97777....*********** PP CM_2 69 eiisesralQ 78 ++i+esr+l+ lcl|NCBI__GCF_000012925.1:WP_004511889.1 74 RVIDESRRLE 83 ********99 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (79 nodes) Target sequences: 1 (98 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: 4.07 // [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