GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisA in Denitrovibrio acetiphilus DSM 12809

Align 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase (EC 5.3.1.16) (characterized)
to candidate WP_013012037.1 DACET_RS14095 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase

Query= reanno::psRCH2:GFF155
         (247 letters)



>NCBI__GCF_000025725.1:WP_013012037.1
          Length = 238

 Score =  223 bits (568), Expect = 3e-63
 Identities = 112/239 (46%), Positives = 162/239 (67%), Gaps = 3/239 (1%)

Query: 1   MLIIPAIDLKDGACVRLRQGLMDDATVFSDDPVAMAAKWVEAGCRRLHLVDLNGAFEGQP 60
           MLIIPAIDL  G  VRLRQG MDD TV+ D+P+  A K+ + G +RLH+VDL+GA +G+ 
Sbjct: 1   MLIIPAIDLLGGKAVRLRQGDMDDYTVYYDNPLDAAKKFADMGVKRLHIVDLDGARDGET 60

Query: 61  VNGEVVTAIAKRYPDLPIQIGGGIRTLETIEHYVRAGVSYVIIGTKAVKEPGFVTEACRA 120
            N +++  I  +   + +++GGG+R L  +E Y   GV Y I+GT  VK+P FV  A + 
Sbjct: 61  TNFDLIEQIVSK-AGMDVEVGGGLRKLVRVEGYFNIGVKYCILGTAVVKDPDFVMAAMKK 119

Query: 121 FPGKVIVGLDAKDGFVATDGWAEVSSVQAVDLARRFEADGVSAIVYTDIAKDGMMQGCNV 180
           +P ++I+G+DAKDG VAT+GW E S + A ++ + +E     +++YTDI +DGM+ G N+
Sbjct: 120 YPHQIILGIDAKDGCVATEGWYEKSELTAAEVIKSYEGYCAESVIYTDIMRDGMLSGINI 179

Query: 181 EATVALANASRIPVIASGGIHNIGDIQKLLDTNTPGIVGAITGRAIYEGTLDVAEAQAL 239
           EAT++LA   + PVIASGG+  I DI+ L  +    I+GAITG+A YEG +D+ EA  L
Sbjct: 180 EATLSLAEEIQYPVIASGGLKGIEDIEAL--SGKKNILGAITGKAFYEGRIDLEEALRL 236


Lambda     K      H
   0.320    0.138    0.405 

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: 207
Number of extensions: 7
Number of successful extensions: 3
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: 247
Length of database: 238
Length adjustment: 23
Effective length of query: 224
Effective length of database: 215
Effective search space:    48160
Effective search space used:    48160
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_013012037.1 DACET_RS14095 (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.17588.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    6.6e-82  260.6   1.1    7.5e-82  260.4   1.1    1.0  1  lcl|NCBI__GCF_000025725.1:WP_013012037.1  DACET_RS14095 1-(5-phosphoribosy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000025725.1:WP_013012037.1  DACET_RS14095 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneami
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  260.4   1.1   7.5e-82   7.5e-82       1     231 []       3     233 ..       3     233 .. 0.99

  Alignments for each domain:
  == domain 1  score: 260.4 bits;  conditional E-value: 7.5e-82
                                 TIGR00007   1 iiPaiDlkeGkvvrlvqGdkdkktvysddpleaakkfeeegaellHvVDLdgAkegekknlevikkive 69 
                                               iiPaiDl  Gk+vrl qGd+d  tvy+d+pl+aakkf+++g+++lH+VDLdgA++ge++n+++i++iv+
  lcl|NCBI__GCF_000025725.1:WP_013012037.1   3 IIPAIDLLGGKAVRLRQGDMDDYTVYYDNPLDAAKKFADMGVKRLHIVDLDGARDGETTNFDLIEQIVS 71 
                                               8******************************************************************** PP

                                 TIGR00007  70 elevkvqvGGGiRsleavekllelgverviigtaavenpelvkellkelgsekivvslDakegevavkG 138
                                               ++ ++v+vGGG+R+l +ve ++++gv+++i+gta+v++p++v  ++k++  ++i++++Dak+g va++G
  lcl|NCBI__GCF_000025725.1:WP_013012037.1  72 KAGMDVEVGGGLRKLVRVEGYFNIGVKYCILGTAVVKDPDFVMAAMKKYP-HQIILGIDAKDGCVATEG 139
                                               *************************************************9.9***************** PP

                                 TIGR00007 139 WkekselslvelakkleelgleeiilTdiekdGtlsGvnveltkelvkeaeveviasGGvssiedvkal 207
                                               W eksel+++e++k +e + +e++i+Tdi +dG+lsG+n+e+t +l++e + +viasGG + ied++al
  lcl|NCBI__GCF_000025725.1:WP_013012037.1 140 WYEKSELTAAEVIKSYEGYCAESVIYTDIMRDGMLSGINIEATLSLAEEIQYPVIASGGLKGIEDIEAL 208
                                               ********************************************************************* PP

                                 TIGR00007 208 kk.lgvkgvivGkAlyegklklkea 231
                                                   ++ g+i GkA+yeg+++l+ea
  lcl|NCBI__GCF_000025725.1:WP_013012037.1 209 SGkKNILGAITGKAFYEGRIDLEEA 233
                                               97589****************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (231 nodes)
Target sequences:                          1  (238 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: 6.86
//
[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