GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gatC in Prosthecochloris aestuarii DSM 271

Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C; Asp/Glu-ADT subunit C; EC 6.3.5.- (uncharacterized)
to candidate WP_012506414.1 PAES_RS09325 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatC

Query= curated2:B3QL05
         (95 letters)



>NCBI__GCF_000020625.1:WP_012506414.1
          Length = 95

 Score =  153 bits (387), Expect = 4e-43
 Identities = 75/95 (78%), Positives = 85/95 (89%)

Query: 1  MSVTTKDVAYIAELARLKFTDAEQERMTDELNMILHYVDKLNEVDTEGVEPLNTIHDQIN 60
          MSVT KDVAYIAELA+L+FT+AEQE+MT ELN ILHYVDKLNEVDT+GVEPL++IHDQ+N
Sbjct: 1  MSVTKKDVAYIAELAKLRFTEAEQEKMTTELNAILHYVDKLNEVDTDGVEPLSSIHDQVN 60

Query: 61 VLRADVEHTPLSNEEALKNAPDRQDRFFKVPKVIG 95
          VLR D     L NEEALKNAPDRQ+RFF+VPKVIG
Sbjct: 61 VLREDCLKPSLDNEEALKNAPDRQERFFRVPKVIG 95


Lambda     K      H
   0.315    0.132    0.363 

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: 79
Number of extensions: 1
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: 95
Length of database: 95
Length adjustment: 10
Effective length of query: 85
Effective length of database: 85
Effective search space:     7225
Effective search space used:     7225
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: 39 (20.6 bits)
S2: 39 (19.6 bits)

Align candidate WP_012506414.1 PAES_RS09325 (Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatC)
to HMM TIGR00135 (gatC: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, C subunit (EC 6.3.5.-))

# 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/TIGR00135.hmm
# target sequence database:        /tmp/gapView.1213491.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00135  [M=93]
Accession:   TIGR00135
Description: gatC: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, C subunit
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    4.3e-34  103.0   0.5    4.7e-34  102.9   0.5    1.0  1  NCBI__GCF_000020625.1:WP_012506414.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000020625.1:WP_012506414.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.9   0.5   4.7e-34   4.7e-34       1      92 [.       3      94 ..       3      95 .] 0.98

  Alignments for each domain:
  == domain 1  score: 102.9 bits;  conditional E-value: 4.7e-34
                             TIGR00135  1 iskeevkrlakLarlelseeeaekfaeeLkeilklveqlsevdtenvepmanplelsnklReDeveeslkrkeil 75
                                          ++k++v+ +a+La+l ++e+e+ek+++eL+ il +v++l+evdt++vep+ ++++++n+lReD  + sl+ +e+l
  NCBI__GCF_000020625.1:WP_012506414.1  3 VTKKDVAYIAELAKLRFTEAEQEKMTTELNAILHYVDKLNEVDTDGVEPLSSIHDQVNVLREDCLKPSLDNEEAL 77
                                          689************************************************************************ PP

                             TIGR00135 76 knapekedgfikvPkil 92
                                          knap+ ++ f++vPk++
  NCBI__GCF_000020625.1:WP_012506414.1 78 KNAPDRQERFFRVPKVI 94
                                          ****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (93 nodes)
Target sequences:                          1  (95 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: 7.35
//
[ok]

This GapMind analysis is from Jul 25 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