GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gatC in Burkholderia phytofirmans PsJN

Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C; Asp/Glu-ADT subunit C; EC 6.3.5.- (uncharacterized)
to candidate BPHYT_RS01550 BPHYT_RS01550 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C

Query= curated2:B4E7X5
         (99 letters)



>FitnessBrowser__BFirm:BPHYT_RS01550
          Length = 99

 Score =  166 bits (419), Expect = 8e-47
 Identities = 84/99 (84%), Positives = 92/99 (92%)

Query: 1  MALTLTDVKRIAHLARLEMADADAEHMLGQLNEFFGLVEQMQAVDTAGIAPLAHPIEQIQ 60
          MALTLTDVKRIAHLARLE+ADADAEH L QLN+FFGLVEQMQAVDT+GIAPLAHPIEQI+
Sbjct: 1  MALTLTDVKRIAHLARLELADADAEHTLVQLNDFFGLVEQMQAVDTSGIAPLAHPIEQIE 60

Query: 61 EVAQRLRDDAVTEVVDRDDNQRPAPAVQDGLYLVPKVIE 99
          +VA RLR+D VTE V+R+  QRPAPAVQDGLYLVPKVIE
Sbjct: 61 DVALRLRNDVVTETVEREAFQRPAPAVQDGLYLVPKVIE 99


Lambda     K      H
   0.319    0.135    0.371 

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: 91
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: 99
Length of database: 99
Length adjustment: 10
Effective length of query: 89
Effective length of database: 89
Effective search space:     7921
Effective search space used:     7921
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: 39 (20.9 bits)
S2: 39 (19.6 bits)

Align candidate BPHYT_RS01550 BPHYT_RS01550 (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.2957219.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
    7.3e-30   89.4   0.1    8.1e-30   89.3   0.1    1.0  1  FitnessBrowser__BFirm:BPHYT_RS01550  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__BFirm:BPHYT_RS01550  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.3   0.1   8.1e-30   8.1e-30       2      93 .]       4      99 .]       3      99 .] 0.96

  Alignments for each domain:
  == domain 1  score: 89.3 bits;  conditional E-value: 8.1e-30
                            TIGR00135  2 skeevkrlakLarlelseeeaekfaeeLkeilklveqlsevdtenvepmanplels....nklReDeveeslkrke 73
                                         +  +vkr+a+Larlel ++ ae++  +L+ +++lveq+++vdt+++ p+a+p+e+      +lR+D v+e+ +r++
  FitnessBrowser__BFirm:BPHYT_RS01550  4 TLTDVKRIAHLARLELADADAEHTLVQLNDFFGLVEQMQAVDTSGIAPLAHPIEQIedvaLRLRNDVVTETVEREA 79
                                         5689**************************************************99888889************** PP

                            TIGR00135 74 ilknapekedgfikvPkile 93
                                         ++  ap ++dg+++vPk++e
  FitnessBrowser__BFirm:BPHYT_RS01550 80 FQRPAPAVQDGLYLVPKVIE 99
                                         ******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (93 nodes)
Target sequences:                          1  (99 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: 4.87
//
[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