GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisA in Lacinutrix algicola AKS293

Align 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase (EC 5.3.1.16) (characterized)
to candidate WP_055437260.1 ASC41_RS13930 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase

Query= reanno::Btheta:350907
         (239 letters)



>NCBI__GCF_001418085.1:WP_055437260.1
          Length = 241

 Score =  303 bits (775), Expect = 3e-87
 Identities = 142/238 (59%), Positives = 189/238 (79%)

Query: 2   IEIIPAIDIIDGKCVRLSQGDYDSKKVYNENPVEVAKEFEANGVRRLHVVDLDGAASHHV 61
           + IIPAIDIIDGKCVRLS+GDY++KK+YNE+P+EVAK FE  G++ LHVVDLDGA + H+
Sbjct: 1   MRIIPAIDIIDGKCVRLSKGDYNTKKIYNESPLEVAKSFEGAGIQYLHVVDLDGAKAKHI 60

Query: 62  VNHRVLEQIATRTSLIVDFGGGVKSDEDLKIAFESGAQMVTGGSVAVKDPELFCHWLEVY 121
           +NH+VLEQIAT+T+L +DFGGG+K++EDLKIAF SGA  +TGGS+AVK+P++F  WL  +
Sbjct: 61  INHKVLEQIATKTNLKIDFGGGLKTNEDLKIAFNSGASQITGGSIAVKNPKIFQEWLTKF 120

Query: 122 GSEKIILGADVKEHKIAVNGWKDESACELFPFLEDYINKGIQKVICTDISCDGMLKGPSI 181
           GS+KIILGAD     IA++GW +ES  ++ PF++DY  KG   VICTDIS DGML+GPS 
Sbjct: 121 GSDKIILGADCNNENIAISGWLEESDLKVIPFIQDYQTKGASYVICTDISKDGMLEGPSF 180

Query: 182 DLYKEMLEKFPNLYLMASGGVSNVDDIIALNEAGVPGVIFGKALYEGHITLKDLRIFL 239
           +LY+ +L++  NL L+ASGG+S  D++  L E G  GVI GKA+YE  I+LK L  ++
Sbjct: 181 ELYERILKETKNLNLIASGGISTFDELPKLAELGCEGVIIGKAIYENRISLKQLENYI 238


Lambda     K      H
   0.320    0.140    0.413 

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: 229
Number of extensions: 4
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: 239
Length of database: 241
Length adjustment: 23
Effective length of query: 216
Effective length of database: 218
Effective search space:    47088
Effective search space used:    47088
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 (21.7 bits)
S2: 46 (22.3 bits)

Align candidate WP_055437260.1 ASC41_RS13930 (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.3741163.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    7.4e-81  257.2   0.1    8.4e-81  257.0   0.1    1.0  1  NCBI__GCF_001418085.1:WP_055437260.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001418085.1:WP_055437260.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  257.0   0.1   8.4e-81   8.4e-81       1     230 [.       3     233 ..       3     234 .. 0.99

  Alignments for each domain:
  == domain 1  score: 257.0 bits;  conditional E-value: 8.4e-81
                             TIGR00007   1 iiPaiDlkeGkvvrlvqGdkdkktvysddpleaakkfeeegaellHvVDLdgAkegekknlevikkiveelev 73 
                                           iiPaiD+++Gk+vrl +Gd+++k++y+++ple+ak+fe  g+++lHvVDLdgAk+++  n +v+++i++++++
  NCBI__GCF_001418085.1:WP_055437260.1   3 IIPAIDIIDGKCVRLSKGDYNTKKIYNESPLEVAKSFEGAGIQYLHVVDLDGAKAKHIINHKVLEQIATKTNL 75 
                                           8************************************************************************ PP

                             TIGR00007  74 kvqvGGGiRsleavekllelgverviigtaavenpelvkellkelgsekivvslDakegevavkGWkeksels 146
                                           k++ GGG+++ e+++ +++ g++++  g++av+np++++e+l+++gs+ki+++ D +++++a++GW e+s+l+
  NCBI__GCF_001418085.1:WP_055437260.1  76 KIDFGGGLKTNEDLKIAFNSGASQITGGSIAVKNPKIFQEWLTKFGSDKIILGADCNNENIAISGWLEESDLK 148
                                           ************************************************************************* PP

                             TIGR00007 147 lvelakkleelgleeiilTdiekdGtlsGvnveltkelvke.aeveviasGGvssiedvkalkklgvkgvivG 218
                                           ++ +++ +++ g++ +i+Tdi+kdG+l+G+ +el+++++ke ++ ++iasGG+s+ +++ +l++lg++gvi+G
  NCBI__GCF_001418085.1:WP_055437260.1 149 VIPFIQDYQTKGASYVICTDISKDGMLEGPSFELYERILKEtKNLNLIASGGISTFDELPKLAELGCEGVIIG 221
                                           *****************************************99****************************** PP

                             TIGR00007 219 kAlyegklklke 230
                                           kA+ye++++lk+
  NCBI__GCF_001418085.1:WP_055437260.1 222 KAIYENRISLKQ 233
                                           ********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (231 nodes)
Target sequences:                          1  (241 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: 20.40
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

Links

Downloads

Related tools

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