GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gatC in Caulobacter crescentus NA1000

Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C; Asp/Glu-ADT subunit C; EC 6.3.5.- (uncharacterized)
to candidate CCNA_02520 CCNA_02520 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C

Query= curated2:B0T192
         (95 letters)



>FitnessBrowser__Caulo:CCNA_02520
          Length = 95

 Score =  162 bits (411), Expect = 7e-46
 Identities = 83/95 (87%), Positives = 87/95 (91%)

Query: 1  MAIDAATVRKVARLARIATPEDRLEPLAQELNGIMTWIEQLAQVDTDGVEPLTSVVHAGL 60
          MAIDAATVRKVARLARIATPE+RLEPLAQELNGIMTWIEQLA+VDTDG EPLTSVV AGL
Sbjct: 1  MAIDAATVRKVARLARIATPEERLEPLAQELNGIMTWIEQLAEVDTDGCEPLTSVVAAGL 60

Query: 61 PLREDVVTMGGDADLITANAPKSTGGFFVVPKVVE 95
          PLREDVVTMGGD   +T+NAPKS   FFVVPKVVE
Sbjct: 61 PLREDVVTMGGDPARVTSNAPKSINNFFVVPKVVE 95


Lambda     K      H
   0.317    0.134    0.378 

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: 95
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 (20.7 bits)
S2: 39 (19.6 bits)

Align candidate CCNA_02520 CCNA_02520 (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.2201496.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    1.9e-25   75.3   0.0    2.1e-25   75.2   0.0    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_02520  CCNA_02520 aspartyl/glutamyl-tRN


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_02520  CCNA_02520 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 !   75.2   0.0   2.1e-25   2.1e-25       1      93 []       3      95 .]       3      95 .] 0.99

  Alignments for each domain:
  == domain 1  score: 75.2 bits;  conditional E-value: 2.1e-25
                             TIGR00135  1 iskeevkrlakLarlelseeeaekfaeeLkeilklveqlsevdtenvepmanplelsnklReDeveeslkrkeil 75
                                          i++++v+++a+Lar++  ee  e +a+eL+ i++ +eql evdt++ ep+++++ +   lReD v+ + + + + 
  lcl|FitnessBrowser__Caulo:CCNA_02520  3 IDAATVRKVARLARIATPEERLEPLAQELNGIMTWIEQLAEVDTDGCEPLTSVVAAGLPLREDVVTMGGDPARVT 77
                                          78899********************************************************************** PP

                             TIGR00135 76 knapekedgfikvPkile 93
                                          +nap++ ++f++vPk++e
  lcl|FitnessBrowser__Caulo:CCNA_02520 78 SNAPKSINNFFVVPKVVE 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: 6.48
//
[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