Alignments for a candidate for hisA in Pseudomonas fluorescens FW300-N2C3

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisA in Pseudomonas fluorescens FW300-N2C3

Align 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase (EC 5.3.1.16) (characterized)
to candidate AO356_09800 AO356_09800 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase

Query= reanno::pseudo5_N2C3_1:AO356_09800
         (245 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_09800
          Length = 245

 Score =  486 bits (1252), Expect = e-142
 Identities = 245/245 (100%), Positives = 245/245 (100%)

Query: 1   MLIIPAIDLKDGACVRLRQGRMEDSTVFSDDPVSMAAKWVEGGCRRLHLVDLNGAFEGQP 60
           MLIIPAIDLKDGACVRLRQGRMEDSTVFSDDPVSMAAKWVEGGCRRLHLVDLNGAFEGQP
Sbjct: 1   MLIIPAIDLKDGACVRLRQGRMEDSTVFSDDPVSMAAKWVEGGCRRLHLVDLNGAFEGQP 60

Query: 61  VNGEVVTAIAKRYPNLPIQIGGGIRSLETIEHYVKAGVSYVIIGTKAVKEPEFVAEACRA 120
           VNGEVVTAIAKRYPNLPIQIGGGIRSLETIEHYVKAGVSYVIIGTKAVKEPEFVAEACRA
Sbjct: 61  VNGEVVTAIAKRYPNLPIQIGGGIRSLETIEHYVKAGVSYVIIGTKAVKEPEFVAEACRA 120

Query: 121 FPGKVIVGLDAKDGFVATDGWAEVSTVQVIDLAKRFEADGVSAIVYTDIAKDGMMQGCNV 180
           FPGKVIVGLDAKDGFVATDGWAEVSTVQVIDLAKRFEADGVSAIVYTDIAKDGMMQGCNV
Sbjct: 121 FPGKVIVGLDAKDGFVATDGWAEVSTVQVIDLAKRFEADGVSAIVYTDIAKDGMMQGCNV 180

Query: 181 PFTAALAAATKIPVIASGGIHNLGDIKALLDAKAPGIIGAITGRAIYEGTLDVAEAQAFC 240
           PFTAALAAATKIPVIASGGIHNLGDIKALLDAKAPGIIGAITGRAIYEGTLDVAEAQAFC
Sbjct: 181 PFTAALAAATKIPVIASGGIHNLGDIKALLDAKAPGIIGAITGRAIYEGTLDVAEAQAFC 240

Query: 241 DSYKG 245
           DSYKG
Sbjct: 241 DSYKG 245


Lambda     K      H
   0.320    0.138    0.407 

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: 403
Number of extensions: 9
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: 245
Length of database: 245
Length adjustment: 24
Effective length of query: 221
Effective length of database: 221
Effective search space:    48841
Effective search space used:    48841
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 46 (22.3 bits)

Align candidate AO356_09800 AO356_09800 (1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase)
to HMM TIGR00007 (hisA: 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase (EC 5.3.1.16))

# 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/TIGR00007.hmm
# target sequence database:        /tmp/gapView.4023243.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00007  [M=231]
Accession:   TIGR00007
Description: TIGR00007: 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                   -----------
    1.3e-81  259.7   0.4    1.4e-81  259.5   0.4    1.0  1  FitnessBrowser__pseudo5_N2C3_1:AO356_09800  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__pseudo5_N2C3_1:AO356_09800  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  259.5   0.4   1.4e-81   1.4e-81       1     230 [.       3     235 ..       3     236 .. 0.96

  Alignments for each domain:
  == domain 1  score: 259.5 bits;  conditional E-value: 1.4e-81
                                   TIGR00007   1 iiPaiDlkeGkvvrlvqGdkdkktvysddpleaakkfeeegaellHvVDLdgAkegekknlevikki 67 
                                                 iiPaiDlk+G++vrl qG+++ +tv+sddp+ +a+k+ e g ++lH+VDL+gA+eg+++n ev+  i
  FitnessBrowser__pseudo5_N2C3_1:AO356_09800   3 IIPAIDLKDGACVRLRQGRMEDSTVFSDDPVSMAAKWVEGGCRRLHLVDLNGAFEGQPVNGEVVTAI 69 
                                                 8****************************************************************** PP

                                   TIGR00007  68 veel.evkvqvGGGiRsleavekllelgverviigtaavenpelvkellkelgsekivvslDakege 133
                                                 +++  ++++q+GGGiRsle++e+++++gv++viigt+av++pe+v+e+ +++   k++v+lDak+g 
  FitnessBrowser__pseudo5_N2C3_1:AO356_09800  70 AKRYpNLPIQIGGGIRSLETIEHYVKAGVSYVIIGTKAVKEPEFVAEACRAFP-GKVIVGLDAKDGF 135
                                                 9876489*********************************************9.9************ PP

                                   TIGR00007 134 vavkGWkekselslvelakkleelgleeiilTdiekdGtlsGvnveltkelvkeaeveviasGGvss 200
                                                 va+ GW+e s++++++lak++e  g+++i++Tdi+kdG+++G nv  t  l+++++++viasGG+++
  FitnessBrowser__pseudo5_N2C3_1:AO356_09800 136 VATDGWAEVSTVQVIDLAKRFEADGVSAIVYTDIAKDGMMQGCNVPFTAALAAATKIPVIASGGIHN 202
                                                 ******************************************************************* PP

                                   TIGR00007 201 iedvkalkk...lgvkgvivGkAlyegklklke 230
                                                   d+kal +    g+ g+i G+A+yeg+l++ e
  FitnessBrowser__pseudo5_N2C3_1:AO356_09800 203 LGDIKALLDakaPGIIGAITGRAIYEGTLDVAE 235
                                                 *****9866333788889***********9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (231 nodes)
Target sequences:                          1  (245 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: 15.24
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis