GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisE in Desulforamulus ruminis DSM 2154

Align putative bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase (EC 3.5.4.19; EC 3.6.1.31) (characterized)
to candidate WP_013841341.1 DESRU_RS06620 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP diphosphatase HisIE

Query= metacyc::HISTCYCLOPRATPPHOS
         (203 letters)



>NCBI__GCF_000215085.1:WP_013841341.1
          Length = 229

 Score =  147 bits (370), Expect = 2e-40
 Identities = 86/216 (39%), Positives = 120/216 (55%), Gaps = 29/216 (13%)

Query: 17  GLMPVIVQHAVSGEVLMLGYMNPEALDKTLESGKVTFFSRTKQRLWTKGETSGNFLNVVS 76
           GL+P IVQ   S EVLM+ +MN EA++KTL +G+  F+SR++Q +W KGETSG+   V  
Sbjct: 14  GLIPAIVQEVRSREVLMMAWMNQEAVEKTLATGETWFYSRSRQAMWKKGETSGHVQRVKG 73

Query: 77  IAPDCDNDTLLVLANPI-GPTCHKGTSSCFGD---------------------------- 107
           +  DCD DTLLVLA    G  CH+G +SCF +                            
Sbjct: 74  LYYDCDADTLLVLAEQEGGAACHEGYTSCFHNRVNPDRSVSIEGEKKFEPAQVYGGQEAR 133

Query: 108 TAHQWLFLYQLEQLLAERKSADPETSYTAKLYASGTKRIAQKVGEEGVETALAATVHDRF 167
           T+     +  L +++  RK+  PE +YT  L+  G  +I +KVGEE  E  + A  + + 
Sbjct: 134 TSADPEIINDLFRVILSRKAERPEGAYTTYLFDQGVDKICKKVGEECAEVIIGAKNNSKE 193

Query: 168 ELTNEASDLMYHLLVLLQDQGLDLTTVIENLRKRHQ 203
           ELT EA+DLMYHLLVLL +QG+    +   L KR +
Sbjct: 194 ELTYEAADLMYHLLVLLANQGISPEEIYRELAKRRK 229


Lambda     K      H
   0.317    0.132    0.384 

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: 138
Number of extensions: 6
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: 203
Length of database: 229
Length adjustment: 22
Effective length of query: 181
Effective length of database: 207
Effective search space:    37467
Effective search space used:    37467
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 (21.6 bits)
S2: 45 (21.9 bits)

Align candidate WP_013841341.1 DESRU_RS06620 (bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP diphosphatase HisIE)
to HMM PF01502 (PRA-CH)

# 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/PF01502.22.hmm
# target sequence database:        /tmp/gapView.3129053.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       PRA-CH  [M=74]
Accession:   PF01502.22
Description: Phosphoribosyl-AMP cyclohydrolase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    1.4e-38  116.9   1.2    2.2e-38  116.3   1.2    1.3  1  NCBI__GCF_000215085.1:WP_013841341.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000215085.1:WP_013841341.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.3   1.2   2.2e-38   2.2e-38       1      74 []      30     104 ..      30     104 .. 0.98

  Alignments for each domain:
  == domain 1  score: 116.3 bits;  conditional E-value: 2.2e-38
                                PRA-CH   1 mlaymneealektletgkavyySrsrqklwkkGetsgnvqkvkeirldcDeDalllkveqkg.aaCHtgersC 72 
                                           m+a+mn+ea+ektl+tg++++ySrsrq +wkkGetsg+vq+vk +++dcD+D+ll+ +eq+g aaCH+g++sC
  NCBI__GCF_000215085.1:WP_013841341.1  30 MMAWMNQEAVEKTLATGETWFYSRSRQAMWKKGETSGHVQRVKGLYYDCDADTLLVLAEQEGgAACHEGYTSC 102
                                           9************************************************************649********* PP

                                PRA-CH  73 Fy 74 
                                           F+
  NCBI__GCF_000215085.1:WP_013841341.1 103 FH 104
                                           *6 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (74 nodes)
Target sequences:                          1  (229 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: 16.04
//
[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