GapMind for Amino acid biosynthesis

 

Aligments for a candidate for hisA in Magnetospirillum magneticum AMB-1

Align 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase; EC 5.3.1.16; Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (uncharacterized)
to candidate WP_011386876.1 AMB_RS22930 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase

Query= curated2:A7HSH1
         (243 letters)



>lcl|NCBI__GCF_000009985.1:WP_011386876.1 AMB_RS22930
           1-(5-phosphoribosyl)-5-((5-
           phosphoribosylamino)methylideneamino)imidazole-4-
           carboxamide isomerase
          Length = 239

 Score =  335 bits (858), Expect = 6e-97
 Identities = 166/240 (69%), Positives = 202/240 (84%), Gaps = 2/240 (0%)

Query: 1   MILFPAIDLKDGQCVRLVHGLMDQATVFNDDPAAQARAFEEAGFEYIHLVDLNGAFEGKP 60
           M LFPAIDLKDG CVRL  GLM+++TVFN DP AQAR F  AG E+IH+VDLNGAF GKP
Sbjct: 1   MFLFPAIDLKDGACVRLKLGLMEESTVFNTDPGAQARDFAAAGAEWIHVVDLNGAFAGKP 60

Query: 61  VNAAAVESILAAISIPAQLGGGIRDLATIEMWLEKGVRRVIIGTAAVKNPALVIEACRKF 120
           VN AAV+SIL ++S+P QLGGGIR++ATIE WL +G+RRVI+GT A+KNPALV EAC++F
Sbjct: 61  VNGAAVDSILKSVSVPVQLGGGIREMATIEDWLARGIRRVILGTVALKNPALVKEACQRF 120

Query: 121 PGRIAVGLDAKGGRVATEGWADVSDLTVLDMAGRFEDAGVAAIIYTDIDRDGALQGLNIE 180
           PGR+AVG+DAKGG+VA EGWA+ SDLTVL++A +FED GVAA+IYTDIDRDG L G N+ 
Sbjct: 121 PGRVAVGIDAKGGKVAVEGWAETSDLTVLELARKFEDCGVAALIYTDIDRDGVLAGPNVA 180

Query: 181 ATVSLADAISIPVIASGGLSSIEDLKKLIAANCSGIEGAISGRALYDGRLDPSEALKLLR 240
           AT +LADAISIPVIASGG+SS+ DLK L A     +EG ISGRA+YDGR+D ++A+ LL+
Sbjct: 181 ATAALADAISIPVIASGGVSSLVDLKALKA--YPKLEGVISGRAIYDGRIDVAQAIALLK 238


Lambda     K      H
   0.320    0.138    0.395 

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: 262
Number of extensions: 10
Number of successful extensions: 4
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: 243
Length of database: 239
Length adjustment: 23
Effective length of query: 220
Effective length of database: 216
Effective search space:    47520
Effective search space used:    47520
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 WP_011386876.1 AMB_RS22930 (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.2057.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    3.2e-81  258.4   0.1    3.6e-81  258.2   0.1    1.0  1  lcl|NCBI__GCF_000009985.1:WP_011386876.1  AMB_RS22930 1-(5-phosphoribosyl)


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_011386876.1  AMB_RS22930 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  258.2   0.1   3.6e-81   3.6e-81       2     230 ..       4     232 ..       3     233 .. 0.99

  Alignments for each domain:
  == domain 1  score: 258.2 bits;  conditional E-value: 3.6e-81
                                 TIGR00007   2 iPaiDlkeGkvvrlvqGdkdkktvysddpleaakkfeeegaellHvVDLdgAkegekknlevikkivee 70 
                                               +PaiDlk+G++vrl  G ++++tv+++dp ++a++f++ gae++HvVDL+gA++g+++n  ++ +i+++
  lcl|NCBI__GCF_000009985.1:WP_011386876.1   4 FPAIDLKDGACVRLKLGLMEESTVFNTDPGAQARDFAAAGAEWIHVVDLNGAFAGKPVNGAAVDSILKS 72 
                                               8******************************************************************** PP

                                 TIGR00007  71 levkvqvGGGiRsleavekllelgverviigtaavenpelvkellkelgsekivvslDakegevavkGW 139
                                               ++v+vq+GGGiR+++++e++l+ g++rvi+gt+a++np+lvke+ +++   +++v++Dak+g+vav+GW
  lcl|NCBI__GCF_000009985.1:WP_011386876.1  73 VSVPVQLGGGIREMATIEDWLARGIRRVILGTVALKNPALVKEACQRFP-GRVAVGIDAKGGKVAVEGW 140
                                               ************************************************9.******************* PP

                                 TIGR00007 140 kekselslvelakkleelgleeiilTdiekdGtlsGvnveltkelvkeaeveviasGGvssiedvkalk 208
                                               +e+s+l+++ela+k+e++g++++i+Tdi++dG l+G+nv +t  l+++ +++viasGGvss  d+kalk
  lcl|NCBI__GCF_000009985.1:WP_011386876.1 141 AETSDLTVLELARKFEDCGVAALIYTDIDRDGVLAGPNVAATAALADAISIPVIASGGVSSLVDLKALK 209
                                               ********************************************************************* PP

                                 TIGR00007 209 k.lgvkgvivGkAlyegklklke 230
                                               +  +++gvi G+A+y+g++++ +
  lcl|NCBI__GCF_000009985.1:WP_011386876.1 210 AyPKLEGVISGRAIYDGRIDVAQ 232
                                               97789**************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (231 nodes)
Target sequences:                          1  (239 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: 6.69
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code, or see 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