GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gatC in Phaeobacter inhibens BS107

Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C; Asp/Glu-ADT subunit C; EC 6.3.5.- (uncharacterized)
to candidate GFF2166 PGA1_c21980 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C

Query= curated2:A8LJ24
         (95 letters)



>FitnessBrowser__Phaeo:GFF2166
          Length = 95

 Score =  150 bits (379), Expect = 3e-42
 Identities = 78/95 (82%), Positives = 83/95 (87%)

Query: 1  MSIDIETARRVAKLARIKVEDDALPALAGEFNHILGFIEQLNEVDVDDVEPMTSVTPMRL 60
          MSID  TA +VAKLARIKVE+DALPALA EFN ILGFIEQLNEVDV+ VEPMTSVTP RL
Sbjct: 1  MSIDQSTAAKVAKLARIKVEEDALPALADEFNTILGFIEQLNEVDVEGVEPMTSVTPQRL 60

Query: 61 KRREDVVTDGDQQAAVLSNAPDAREGFFAVPKVVE 95
          KRR D VTDG QQ  +L+NAPDAREGFFAVPKVVE
Sbjct: 61 KRRVDEVTDGSQQDKILANAPDAREGFFAVPKVVE 95


Lambda     K      H
   0.317    0.135    0.366 

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: 83
Number of extensions: 2
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 (20.8 bits)
S2: 39 (19.6 bits)

Align candidate GFF2166 PGA1_c21980 (aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C)
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.10959.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
    3.5e-30   90.4   0.2    3.9e-30   90.3   0.2    1.0  1  lcl|FitnessBrowser__Phaeo:GFF2166  PGA1_c21980 aspartyl/glutamyl-tR


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF2166  PGA1_c21980 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.3   0.2   3.9e-30   3.9e-30       1      93 []       3      95 .]       3      95 .] 0.97

  Alignments for each domain:
  == domain 1  score: 90.3 bits;  conditional E-value: 3.9e-30
                          TIGR00135  1 iskeevkrlakLarlelseeeaekfaeeLkeilklveqlsevdtenvepmanplelsnklReDeveeslkrkeilkna 78
                                       i++++ +++akLar++++e+   ++a e+++il+++eql+evd+e+vepm+++ ++  k R Dev+++ ++++il+na
  lcl|FitnessBrowser__Phaeo:GFF2166  3 IDQSTAAKVAKLARIKVEEDALPALADEFNTILGFIEQLNEVDVEGVEPMTSVTPQRLKRRVDEVTDGSQQDKILANA 80
                                       57778899********************************************************************** PP

                          TIGR00135 79 pekedgfikvPkile 93
                                       p++ +gf++vPk++e
  lcl|FitnessBrowser__Phaeo:GFF2166 81 PDAREGFFAVPKVVE 95
                                       *************97 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: 3.16
//
[ok]

This GapMind analysis is from Apr 09 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