GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisA in Pseudomonas fluorescens FW300-N2E2

Align 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase (EC 5.3.1.16) (characterized)
to candidate Pf6N2E2_3839 Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (EC 5.3.1.16)

Query= reanno::pseudo6_N2E2:Pf6N2E2_3839
         (245 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3839
          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 PFTAALAAATRIPVIASGGIHNLGDIKALLDAKAPGIIGAITGRAIYEGTLDVAEAQAFC 240
           PFTAALAAATRIPVIASGGIHNLGDIKALLDAKAPGIIGAITGRAIYEGTLDVAEAQAFC
Sbjct: 181 PFTAALAAATRIPVIASGGIHNLGDIKALLDAKAPGIIGAITGRAIYEGTLDVAEAQAFC 240

Query: 241 DSYKG 245
           DSYKG
Sbjct: 241 DSYKG 245


Lambda     K      H
   0.320    0.138    0.408 

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 Pf6N2E2_3839 (Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (EC 5.3.1.16))
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.14266.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
    1.5e-81  259.4   0.3    1.7e-81  259.2   0.3    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3839  Phosphoribosylformimino-5-aminoi


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3839  Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomeras
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  259.2   0.3   1.7e-81   1.7e-81       1     230 [.       3     235 ..       3     236 .. 0.96

  Alignments for each domain:
  == domain 1  score: 259.2 bits;  conditional E-value: 1.7e-81
                                      TIGR00007   1 iiPaiDlkeGkvvrlvqGdkdkktvysddpleaakkfeeegaellHvVDLdgAkegekknlevi 64 
                                                    iiPaiDlk+G++vrl qG+++ +tv+sddp+ +a+k+ e g ++lH+VDL+gA+eg+++n ev+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3839   3 IIPAIDLKDGACVRLRQGRMEDSTVFSDDPVSMAAKWVEGGCRRLHLVDLNGAFEGQPVNGEVV 66 
                                                    8*************************************************************** PP

                                      TIGR00007  65 kkiveel.evkvqvGGGiRsleavekllelgverviigtaavenpelvkellkelgsekivvsl 127
                                                      i+++  ++++q+GGGiRsle++e+++++gv++viigt+av++pe+v+e+ +++   k++v+l
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3839  67 TAIAKRYpNLPIQIGGGIRSLETIEHYVKAGVSYVIIGTKAVKEPEFVAEACRAFP-GKVIVGL 129
                                                    ***9876489*********************************************9.9****** PP

                                      TIGR00007 128 DakegevavkGWkekselslvelakkleelgleeiilTdiekdGtlsGvnveltkelvkeaeve 191
                                                    Dak+g va+ GW+e s++++++lak++e  g+++i++Tdi+kdG+++G nv  t  l+++++++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3839 130 DAKDGFVATDGWAEVSTVQVIDLAKRFEADGVSAIVYTDIAKDGMMQGCNVPFTAALAAATRIP 193
                                                    **************************************************************** PP

                                      TIGR00007 192 viasGGvssiedvkalkk...lgvkgvivGkAlyegklklke 230
                                                    viasGG+++  d+kal +    g+ g+i G+A+yeg+l++ e
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3839 194 VIASGGIHNLGDIKALLDakaPGIIGAITGRAIYEGTLDVAE 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 6.90
//
[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