GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisE in Pseudomonas fluorescens GW456-L13

Align Phosphoribosyl-AMP cyclohydrolase; PRA-CH; EC 3.5.4.19 (characterized)
to candidate PfGW456L13_302 Phosphoribosyl-AMP cyclohydrolase (EC 3.5.4.19)

Query= SwissProt::O26347
         (138 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_302
          Length = 133

 Score =  124 bits (312), Expect = 4e-34
 Identities = 62/121 (51%), Positives = 80/121 (66%), Gaps = 3/121 (2%)

Query: 19  NGEDLIIAVAQDHETGEVLMVAYMNREALRRTLETGTAHYWSTSRGKLWLKGESSGHVQR 78
           + + L+ A+AQDH+TG VLM+A+MNREAL  T     A YWS SRGKLW KGE SGHVQ 
Sbjct: 11  DADGLVPAIAQDHKTGRVLMMAWMNREALELTAAENRAIYWSRSRGKLWRKGEESGHVQT 70

Query: 79  VKDVLVDCDGDAVVLKVEQEGG-ACHTGYRSCFYRSIDGDELKVREDAVKVFDPEEIYGD 137
           + ++ +DCD D ++L VEQ G  ACHTG +SCFYR  +  +    +  +K  DP  IY  
Sbjct: 71  LHEMRLDCDADVIILMVEQIGDIACHTGRQSCFYRVYENGDWTTVDPVLK--DPHAIYSA 128

Query: 138 G 138
           G
Sbjct: 129 G 129


Lambda     K      H
   0.318    0.137    0.410 

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: 101
Number of extensions: 5
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: 138
Length of database: 133
Length adjustment: 15
Effective length of query: 123
Effective length of database: 118
Effective search space:    14514
Effective search space used:    14514
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: 42 (20.8 bits)

Align candidate PfGW456L13_302 (Phosphoribosyl-AMP cyclohydrolase (EC 3.5.4.19))
to HMM PF01502 (PRA-CH)

# 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/PF01502.22.hmm
# target sequence database:        /tmp/gapView.3956.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       PRA-CH  [M=74]
Accession:   PF01502.22
Description: Phosphoribosyl-AMP cyclohydrolase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                              -----------
    1.2e-38  117.1   0.2      2e-38  116.5   0.2    1.3  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_302  Phosphoribosyl-AMP cyclohydrolas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_302  Phosphoribosyl-AMP cyclohydrolase (EC 3.5.4.19)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.5   0.2     2e-38     2e-38       1      74 []      30     104 ..      30     104 .. 0.98

  Alignments for each domain:
  == domain 1  score: 116.5 bits;  conditional E-value: 2e-38
                                                 PRA-CH   1 mlaymneealektletgkavyySrsrqklwkkGetsgnvqkvkeirldcDeDalll 56 
                                                            m+a+mn+eale t ++++a+y+Srsr klw+kGe+sg+vq+++e+rldcD+D+++l
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_302  30 MMAWMNREALELTAAENRAIYWSRSRGKLWRKGEESGHVQTLHEMRLDCDADVIIL 85 
                                                            9******************************************************* PP

                                                 PRA-CH  57 kveqkg.aaCHtgersCFy 74 
                                                            +veq g  aCHtg++sCFy
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_302  86 MVEQIGdIACHTGRQSCFY 104
                                                            *****868**********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (74 nodes)
Target sequences:                          1  (133 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: 3.26
//
[ok]

This GapMind analysis is from Apr 09 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