GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cmutase in Streptacidiphilus oryzae TH49

Align chorismate mutase (EC 5.4.99.5) (characterized)
to candidate WP_084704279.1 BS73_RS23080 chorismate mutase

Query= BRENDA::P9WIC1
         (105 letters)



>NCBI__GCF_000744815.1:WP_084704279.1
          Length = 107

 Score = 66.2 bits (160), Expect = 1e-16
 Identities = 35/71 (49%), Positives = 49/71 (69%), Gaps = 1/71 (1%)

Query: 33  REEIDRLDAEILALVKRRAEVSKAIGKARMASGGTRLVHSREMKVIERY-SELGPDGKDL 91
           RE ID LD E+L +VK R  VS  + +AR+A+GG RL  +RE +++ R+ +ELG  G +L
Sbjct: 36  RERIDALDGELLRIVKERMAVSARVQRARIATGGPRLSLAREQQILARFHAELGRAGTEL 95

Query: 92  AILLLRLGRGR 102
            +LLL L RGR
Sbjct: 96  GMLLLELSRGR 106


Lambda     K      H
   0.317    0.136    0.375 

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: 40
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: 105
Length of database: 107
Length adjustment: 11
Effective length of query: 94
Effective length of database: 96
Effective search space:     9024
Effective search space used:     9024
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: 40 (21.2 bits)
S2: 40 (20.0 bits)

Align candidate WP_084704279.1 BS73_RS23080 (chorismate mutase)
to HMM TIGR01808 (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/TIGR01808.hmm
# target sequence database:        /tmp/gapView.1441759.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01808  [M=74]
Accession:   TIGR01808
Description: CM_M_hiGC-arch: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    1.4e-20   59.4   0.9    1.7e-20   59.2   0.9    1.1  1  NCBI__GCF_000744815.1:WP_084704279.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000744815.1:WP_084704279.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.2   0.9   1.7e-20   1.7e-20       2      74 .]      32     105 ..      31     105 .. 0.97

  Alignments for each domain:
  == domain 1  score: 59.2 bits;  conditional E-value: 1.7e-20
                             TIGR01808   2 ikklReEidrlDaeilslvKrRleisqaiGKirkesggtrlvrkREvevierf.aelGeegkelaellLrlgr 73 
                                           i + Re id lD e+l +vK R+ +s  + ++r + gg+rl   RE++++ rf aelG  g el  llL+l+r
  NCBI__GCF_000744815.1:WP_084704279.1  32 IAQARERIDALDGELLRIVKERMAVSARVQRARIATGGPRLSLAREQQILARFhAELGRAGTELGMLLLELSR 104
                                           5678********************************************************************9 PP

                             TIGR01808  74 g 74 
                                           g
  NCBI__GCF_000744815.1:WP_084704279.1 105 G 105
                                           7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (74 nodes)
Target sequences:                          1  (107 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: 4.38
//
[ok]

This GapMind analysis is from Jul 26 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