Align Chorismate mutase AroH; CM; EC 5.4.99.5 (characterized)
to candidate Synpcc7942_1915 Synpcc7942_1915 chorismate mutase
Query= SwissProt::P19080 (127 letters) >FitnessBrowser__SynE:Synpcc7942_1915 Length = 130 Score = 100 bits (250), Expect = 6e-27 Identities = 49/122 (40%), Positives = 74/122 (60%) Query: 3 IRGIRGATTVERDTEEEILQKTKQLLEKIIEENHTKPEDVVQMLLSATPDLHAVFPAKAV 62 ++ IRGATTV +T E + + +LL+++ N P+D+V + S T DL A+FPA Sbjct: 5 VKAIRGATTVRENTAEAMREAVSELLDELERRNPLNPDDIVSLTFSVTRDLDAMFPAAVA 64 Query: 63 RELSGWQYVPVTCMQEMDVTGGLKKCIRVMMTVQTDVPQDQIRHVYLEKVVVLRPDLSLT 122 R+ +GWQ VP+ +Q+M V G L++CIR+++ Q I H YL VLRPD LT Sbjct: 65 RQRAGWQNVPLLDVQQMYVEGSLERCIRLLLHFNCPEDQPPIEHPYLRGAQVLRPDWVLT 124 Query: 123 KN 124 ++ Sbjct: 125 ES 126 Lambda K H 0.318 0.133 0.376 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: 66 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: 127 Length of database: 130 Length adjustment: 14 Effective length of query: 113 Effective length of database: 116 Effective search space: 13108 Effective search space used: 13108 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 (21.7 bits) S2: 41 (20.4 bits)
Align candidate Synpcc7942_1915 Synpcc7942_1915 (chorismate mutase)
to HMM TIGR01796 (aroH: 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/TIGR01796.hmm # target sequence database: /tmp/gapView.3886.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01796 [M=117] Accession: TIGR01796 Description: CM_mono_aroH: 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.6e-51 158.7 0.0 4e-51 158.6 0.0 1.0 1 lcl|FitnessBrowser__SynE:Synpcc7942_1915 Synpcc7942_1915 chorismate mutas Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SynE:Synpcc7942_1915 Synpcc7942_1915 chorismate mutase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 158.6 0.0 4e-51 4e-51 1 117 [] 5 121 .. 5 121 .. 0.99 Alignments for each domain: == domain 1 score: 158.6 bits; conditional E-value: 4e-51 TIGR01796 1 lravrGattveaneaeeileaveeLleellerneltaedlisviltvteDlsaafPakavrelaGiedv 69 ++a+rGattv++n+ae+++eav+eLl+el++rn l+++d++s++++vt+Dl+a+fPa+++r++aG+++v lcl|FitnessBrowser__SynE:Synpcc7942_1915 5 VKAIRGATTVRENTAEAMREAVSELLDELERRNPLNPDDIVSLTFSVTRDLDAMFPAAVARQRAGWQNV 73 79******************************************************************* PP TIGR01796 70 pvlcaqeldvegslercirvlihiesekarseiahvyLreakkLrpDl 117 p+l++q++ vegslercir+l+h + + + +i+h yLr+a++LrpD+ lcl|FitnessBrowser__SynE:Synpcc7942_1915 74 PLLDVQQMYVEGSLERCIRLLLHFNCPEDQPPIEHPYLRGAQVLRPDW 121 ***********************************************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (117 nodes) Target sequences: 1 (130 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: 5.92 // [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