GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cmutase in Clostridium tyrobutyricum FAM22553

Align Chorismate mutase AroH; CM; EC 5.4.99.5 (characterized)
to candidate WP_039653205.1 PN53_RS10915 chorismate mutase

Query= SwissProt::P19080
         (127 letters)



>NCBI__GCF_000816635.1:WP_039653205.1
          Length = 122

 Score = 60.8 bits (146), Expect = 6e-15
 Identities = 36/118 (30%), Positives = 63/118 (53%), Gaps = 6/118 (5%)

Query: 6   IRGATTVERDTEEEILQKTKQLLEKIIEENHTKPEDVVQMLLSATPDLHAVFPAKAVREL 65
           +RGATT+E ++  +I   + +L  +I+++N+ K + ++ + +S T D+   +P K +RE 
Sbjct: 4   LRGATTIENNSITDIKDASIELFSQILKKNNIKLQKIISIEISCTKDITKAYPGKFIREY 63

Query: 66  SGWQYVPVTCMQEMDVTGGLK----KCIRVMMTVQTDVPQDQIRHVYLEKVVVLRPDL 119
                V +    EM+V   LK     CIR ++ V  D+ + +   VYL     LR DL
Sbjct: 64  FKLDKVAIMHFNEMEVEKNLKGFIPLCIRFLLLVDEDIYKKEF--VYLNNAKKLRIDL 119


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: 46
Number of extensions: 2
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: 122
Length adjustment: 14
Effective length of query: 113
Effective length of database: 108
Effective search space:    12204
Effective search space used:    12204
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 WP_039653205.1 PN53_RS10915 (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.2410435.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    4.7e-30   90.6   0.0    5.4e-30   90.4   0.0    1.0  1  NCBI__GCF_000816635.1:WP_039653205.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000816635.1:WP_039653205.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.4   0.0   5.4e-30   5.4e-30       3     117 .]       3     119 ..       1     119 [. 0.92

  Alignments for each domain:
  == domain 1  score: 90.4 bits;  conditional E-value: 5.4e-30
                             TIGR01796   3 avrGattveaneaeeileaveeLleellerneltaedlisviltvteDlsaafPakavrelaGiedvpvlcaq 75 
                                           a+rGatt+e+n+  +i++a  eL++++l++n+++ +++is+ ++ t+D++ a+P k +re   +++v+++   
  NCBI__GCF_000816635.1:WP_039653205.1   3 ALRGATTIENNSITDIKDASIELFSQILKKNNIKLQKIISIEISCTKDITKAYPGKFIREYFKLDKVAIMHFN 75 
                                           89*********************************************************************** PP

                             TIGR01796  76 eldvegsl....ercirvlihiesekarseiahvyLreakkLrpDl 117
                                           e++ve  l    + cir+l+ ++      + + vyL++akkLr Dl
  NCBI__GCF_000816635.1:WP_039653205.1  76 EMEVEKNLkgfiPLCIRFLLLVDE--DIYKKEFVYLNNAKKLRIDL 119
                                           ****9876333368********94..4555679**********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (117 nodes)
Target sequences:                          1  (122 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: 7.68
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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