Alignments for a candidate for asnA in Escherichia coli BW25113

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnA in Escherichia coli BW25113

Align Aspartate--ammonia ligase; Asparagine synthetase A; EC 6.3.1.1 (characterized)
to candidate 17804 b3744 asparagine synthetase AsnA (NCBI)

Query= SwissProt::P00963
         (330 letters)



>FitnessBrowser__Keio:17804
          Length = 330

 Score =  667 bits (1722), Expect = 0.0
 Identities = 330/330 (100%), Positives = 330/330 (100%)

Query: 1   MKTAYIAKQRQISFVKSHFSRQLEERLGLIEVQAPILSRVGDGTQDNLSGCEKAVQVKVK 60
           MKTAYIAKQRQISFVKSHFSRQLEERLGLIEVQAPILSRVGDGTQDNLSGCEKAVQVKVK
Sbjct: 1   MKTAYIAKQRQISFVKSHFSRQLEERLGLIEVQAPILSRVGDGTQDNLSGCEKAVQVKVK 60

Query: 61  ALPDAQFEVVHSLAKWKRQTLGQHDFSAGEGLYTHMKALRPDEDRLSPLHSVYVDQWDWE 120
           ALPDAQFEVVHSLAKWKRQTLGQHDFSAGEGLYTHMKALRPDEDRLSPLHSVYVDQWDWE
Sbjct: 61  ALPDAQFEVVHSLAKWKRQTLGQHDFSAGEGLYTHMKALRPDEDRLSPLHSVYVDQWDWE 120

Query: 121 RVMGDGERQFSTLKSTVEAIWAGIKATEAAVSEEFGLAPFLPDQIHFVHSQELLSRYPDL 180
           RVMGDGERQFSTLKSTVEAIWAGIKATEAAVSEEFGLAPFLPDQIHFVHSQELLSRYPDL
Sbjct: 121 RVMGDGERQFSTLKSTVEAIWAGIKATEAAVSEEFGLAPFLPDQIHFVHSQELLSRYPDL 180

Query: 181 DAKGRERAIAKDLGAVFLVGIGGKLSDGHRHDVRAPDYDDWSTPSELGHAGLNGDILVWN 240
           DAKGRERAIAKDLGAVFLVGIGGKLSDGHRHDVRAPDYDDWSTPSELGHAGLNGDILVWN
Sbjct: 181 DAKGRERAIAKDLGAVFLVGIGGKLSDGHRHDVRAPDYDDWSTPSELGHAGLNGDILVWN 240

Query: 241 PVLEDAFELSSMGIRVDADTLKHQLALTGDEDRLELEWHQALLRGEMPQTIGGGIGQSRL 300
           PVLEDAFELSSMGIRVDADTLKHQLALTGDEDRLELEWHQALLRGEMPQTIGGGIGQSRL
Sbjct: 241 PVLEDAFELSSMGIRVDADTLKHQLALTGDEDRLELEWHQALLRGEMPQTIGGGIGQSRL 300

Query: 301 TMLLLQLPHIGQVQCGVWPAAVRESVPSLL 330
           TMLLLQLPHIGQVQCGVWPAAVRESVPSLL
Sbjct: 301 TMLLLQLPHIGQVQCGVWPAAVRESVPSLL 330


Lambda     K      H
   0.318    0.136    0.410 

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: 604
Number of extensions: 5
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: 330
Length of database: 330
Length adjustment: 28
Effective length of query: 302
Effective length of database: 302
Effective search space:    91204
Effective search space used:    91204
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate 17804 b3744 (asparagine synthetase AsnA (NCBI))
to HMM TIGR00669 (asnA: aspartate--ammonia ligase (EC 6.3.1.1))

# 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/TIGR00669.hmm
# target sequence database:        /tmp/gapView.3579.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00669  [M=330]
Accession:   TIGR00669
Description: asnA: aspartate--ammonia ligase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   9.7e-205  665.1   0.1   1.1e-204  665.0   0.1    1.0  1  lcl|FitnessBrowser__Keio:17804  b3744 asparagine synthetase AsnA


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:17804  b3744 asparagine synthetase AsnA (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  665.0   0.1  1.1e-204  1.1e-204       1     330 []       1     330 []       1     330 [] 1.00

  Alignments for each domain:
  == domain 1  score: 665.0 bits;  conditional E-value: 1.1e-204
                       TIGR00669   1 mkkafilkqqeisfvkstftqklierlglievqgpilsqvgdgiqdnlsgiekavqvkvkaipdaafevvhslakwkrh 79 
                                     mk+a+i+kq++isfvks+f+++l+erlglievq+pils+vgdg+qdnlsg+ekavqvkvka+pda+fevvhslakwkr+
  lcl|FitnessBrowser__Keio:17804   1 MKTAYIAKQRQISFVKSHFSRQLEERLGLIEVQAPILSRVGDGTQDNLSGCEKAVQVKVKALPDAQFEVVHSLAKWKRQ 79 
                                     9****************************************************************************** PP

                       TIGR00669  80 tlarydfkedeglfvhmkalrpdedsldpvrsvyvdqwdwekvvpegernlaylketveaiyaairatevavserfgla 158
                                     tl+++df+++egl++hmkalrpded+l+p++svyvdqwdwe+v+++ger++++lk+tveai+a+i+ate+avse+fgla
  lcl|FitnessBrowser__Keio:17804  80 TLGQHDFSAGEGLYTHMKALRPDEDRLSPLHSVYVDQWDWERVMGDGERQFSTLKSTVEAIWAGIKATEAAVSEEFGLA 158
                                     ******************************************************************************* PP

                       TIGR00669 159 allpkqivfvhseelvkrypdldskgredaiakelgavfligiggklsdgkphdvrapdyddwtteselgykglngdil 237
                                     ++lp+qi+fvhs+el++rypdld+kgre+aiak+lgavfl+giggklsdg++hdvrapdyddw+t+selg++glngdil
  lcl|FitnessBrowser__Keio:17804 159 PFLPDQIHFVHSQELLSRYPDLDAKGRERAIAKDLGAVFLVGIGGKLSDGHRHDVRAPDYDDWSTPSELGHAGLNGDIL 237
                                     ******************************************************************************* PP

                       TIGR00669 238 vwnpvlgkafelssmgirvdedalrlqlaltgdedrlelewhqdllngklpqtigggigqsrlamlllqkkhigevqas 316
                                     vwnpvl++afelssmgirvd+d+l++qlaltgdedrlelewhq+ll+g++pqtigggigqsrl+mlllq +hig+vq++
  lcl|FitnessBrowser__Keio:17804 238 VWNPVLEDAFELSSMGIRVDADTLKHQLALTGDEDRLELEWHQALLRGEMPQTIGGGIGQSRLTMLLLQLPHIGQVQCG 316
                                     ******************************************************************************* PP

                       TIGR00669 317 vwpkevreevenil 330
                                     vwp++vre+v+++l
  lcl|FitnessBrowser__Keio:17804 317 VWPAAVRESVPSLL 330
                                     ***********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (330 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 7.77
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis