GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisI in Methylosarcina fibrata AML-C10

Align phosphoribosyl-ATP pyrophosphatase (EC 3.6.1.31) (characterized)
to candidate WP_020561659.1 A3OW_RS0101480 phosphoribosyl-ATP diphosphatase

Query= reanno::pseudo5_N2C3_1:AO356_09525
         (110 letters)



>NCBI__GCF_000372865.1:WP_020561659.1
          Length = 105

 Score =  122 bits (307), Expect = 9e-34
 Identities = 65/109 (59%), Positives = 80/109 (73%), Gaps = 4/109 (3%)

Query: 1   MSDTLTRLAQVLEERKGAAADSSYVASLYHKGLNKILEKVGEESVETIIAAKDAAISGDC 60
           M+D L +LA +LE+RK   A+ SYVASLY KGL+ IL+KVGEE+ E +IA K     GD 
Sbjct: 1   MNDVLQQLANILEQRKQEPAEKSYVASLYSKGLDTILKKVGEEATELVIAGK----GGDQ 56

Query: 61  SDVIYETADLWFHSLVMLAQLGQHPQAVLDELDRRFGLSGHVEKASRPS 109
           + +IYETADLWFH+LV+LAQ    P  VL+EL+RRFGLSG  EKA R S
Sbjct: 57  AQIIYETADLWFHTLVLLAQQNLSPDDVLNELERRFGLSGLEEKARRKS 105


Lambda     K      H
   0.314    0.129    0.357 

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: 63
Number of extensions: 2
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: 110
Length of database: 105
Length adjustment: 12
Effective length of query: 98
Effective length of database: 93
Effective search space:     9114
Effective search space used:     9114
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 (21.1 bits)
S2: 40 (20.0 bits)

Align candidate WP_020561659.1 A3OW_RS0101480 (phosphoribosyl-ATP diphosphatase)
to HMM TIGR03188 (hisE: phosphoribosyl-ATP diphosphatase (EC 3.6.1.31))

# 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/TIGR03188.hmm
# target sequence database:        /tmp/gapView.17947.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03188  [M=84]
Accession:   TIGR03188
Description: histidine_hisI: phosphoribosyl-ATP diphosphatase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    2.5e-37  113.2   0.1    2.9e-37  113.0   0.1    1.1  1  lcl|NCBI__GCF_000372865.1:WP_020561659.1  A3OW_RS0101480 phosphoribosyl-AT


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000372865.1:WP_020561659.1  A3OW_RS0101480 phosphoribosyl-ATP diphosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.0   0.1   2.9e-37   2.9e-37       1      84 []       5      88 ..       5      88 .. 0.99

  Alignments for each domain:
  == domain 1  score: 113.0 bits;  conditional E-value: 2.9e-37
                                 TIGR03188  1 leeLeevieerkeedpeeSytakllekgedkilkKvgEEavEviiaaknedkeelveEaaDllYhllVlla 71
                                              l++L++++e+rk+e+ e+Sy+a+l++kg d+ilkKvgEEa+E++ia k +d+ ++++E+aDl++h+lVlla
  lcl|NCBI__GCF_000372865.1:WP_020561659.1  5 LQQLANILEQRKQEPAEKSYVASLYSKGLDTILKKVGEEATELVIAGKGGDQAQIIYETADLWFHTLVLLA 75
                                              799******************************************************************** PP

                                 TIGR03188 72 ekgvsledvlaeL 84
                                              ++++s++dvl+eL
  lcl|NCBI__GCF_000372865.1:WP_020561659.1 76 QQNLSPDDVLNEL 88
                                              ***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (84 nodes)
Target sequences:                          1  (105 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: 2.95
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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