GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisA in Desulforamulus ruminis DSM 2154

Align 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase (EC 5.3.1.16) (characterized)
to candidate WP_013841339.1 DESRU_RS06610 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase

Query= reanno::azobra:AZOBR_RS01680
         (249 letters)



>NCBI__GCF_000215085.1:WP_013841339.1
          Length = 243

 Score =  242 bits (618), Expect = 4e-69
 Identities = 126/238 (52%), Positives = 166/238 (69%)

Query: 1   MIIYPAIDLKDGACVRLLRGEMSQATVFNTEPADQARLFESQGFEWLHLVDLNGAFEGKP 60
           MII+PAIDLK+G CVRLL G M  ATV++ +P   AR ++ QG  ++H+VDL+GAF GKP
Sbjct: 1   MIIFPAIDLKEGQCVRLLEGRMDSATVYSRDPGGTARNWQEQGASFIHVVDLDGAFAGKP 60

Query: 61  VNGKAVESILGAVAIPVQLGGGIRDLKTIAHWLEKGVSRVILGTVALREPELVREACREF 120
            N +A+  IL AV +PVQ+GGGIRDL+T+      GV+RVILG+ A+ +PELV EA R +
Sbjct: 61  RNREAIRQILEAVEVPVQVGGGIRDLETMEELFSMGVNRVILGSAAILKPELVAEAGRRY 120

Query: 121 PGKVAVGIDAREGYVAVAGWAETSTIKALDLALKFEDSGVAAIIYTDINRDGAMGGVNVE 180
             KV VGIDAR+G VA+ GW ET +  AL LA + ++ GV  I++TDI RDG + G N+ 
Sbjct: 121 GAKVLVGIDARDGRVAIQGWGETVSKTALQLAREVKELGVQRIVFTDIRRDGRLSGPNLG 180

Query: 181 ATSDLAFHLTTPVIASGGVSSIDDLIALKKEEDTGIEGVICGRALYDGRIDPKTALDL 238
           AT +LA      VIASGGVSS++D+ A+K  E  G+EG I G+ALY G +    AL L
Sbjct: 181 ATGELARDSGLKVIASGGVSSLEDIRAVKALEKDGVEGAIVGKALYTGAVKLPEALAL 238


Lambda     K      H
   0.318    0.138    0.401 

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: 230
Number of extensions: 7
Number of successful extensions: 2
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: 249
Length of database: 243
Length adjustment: 24
Effective length of query: 225
Effective length of database: 219
Effective search space:    49275
Effective search space used:    49275
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 bits)

Align candidate WP_013841339.1 DESRU_RS06610 (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.97254.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
      2e-86  275.4   0.5    2.3e-86  275.2   0.5    1.0  1  NCBI__GCF_000215085.1:WP_013841339.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000215085.1:WP_013841339.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  275.2   0.5   2.3e-86   2.3e-86       1     230 [.       3     234 ..       3     235 .. 0.97

  Alignments for each domain:
  == domain 1  score: 275.2 bits;  conditional E-value: 2.3e-86
                             TIGR00007   1 iiPaiDlkeGkvvrlvqGdkdkktvysddpleaakkfeeegaellHvVDLdgAkegekknlevikkiveelev 73 
                                           i+PaiDlkeG++vrl++G++d+ tvys+dp  +a++++e+ga+++HvVDLdgA++g+++n+e+i++i+e++ev
  NCBI__GCF_000215085.1:WP_013841339.1   3 IFPAIDLKEGQCVRLLEGRMDSATVYSRDPGGTARNWQEQGASFIHVVDLDGAFAGKPRNREAIRQILEAVEV 75 
                                           89*********************************************************************** PP

                             TIGR00007  74 kvqvGGGiRsleavekllelgverviigtaavenpelvkellkelgsekivvslDakegevavkGWkeksels 146
                                           +vqvGGGiR+le++e+l+++gv+rvi+g+aa+ +pelv+e+ +++g  k++v++Da++g+va++GW e+ + +
  NCBI__GCF_000215085.1:WP_013841339.1  76 PVQVGGGIRDLETMEELFSMGVNRVILGSAAILKPELVAEAGRRYG-AKVLVGIDARDGRVAIQGWGETVSKT 147
                                           **********************************************.99************************ PP

                             TIGR00007 147 lvelakkleelgleeiilTdiekdGtlsGvnveltkelvkeaeveviasGGvssiedvkalkk...lgvkgvi 216
                                           +++la++++elg+++i++Tdi +dG lsG+n+ +t el++ +  +viasGGvss ed++a+k+    gv+g+i
  NCBI__GCF_000215085.1:WP_013841339.1 148 ALQLAREVKELGVQRIVFTDIRRDGRLSGPNLGATGELARDSGLKVIASGGVSSLEDIRAVKAlekDGVEGAI 220
                                           *********************************************************98777655599***** PP

                             TIGR00007 217 vGkAlyegklklke 230
                                           vGkAly+g +kl e
  NCBI__GCF_000215085.1:WP_013841339.1 221 VGKALYTGAVKLPE 234
                                           ********999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (231 nodes)
Target sequences:                          1  (243 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: 12.33
//
[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:

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