Alignments for a candidate for argG in Escherichia coli BW25113

GapMind for Amino acid biosynthesis

Alignments for a candidate for argG in Escherichia coli BW25113

Align argininosuccinate synthase (characterized)
to candidate 17244 b3172 argininosuccinate synthase (NCBI)

Query= CharProtDB::CH_024687
         (447 letters)



>FitnessBrowser__Keio:17244
          Length = 447

 Score =  902 bits (2330), Expect = 0.0
 Identities = 447/447 (100%), Positives = 447/447 (100%)

Query: 1   MTTILKHLPVGQRIGIAFSGGLDTSAALLWMRQKGAVPYAYTANLGQPDEEDYDAIPRRA 60
           MTTILKHLPVGQRIGIAFSGGLDTSAALLWMRQKGAVPYAYTANLGQPDEEDYDAIPRRA
Sbjct: 1   MTTILKHLPVGQRIGIAFSGGLDTSAALLWMRQKGAVPYAYTANLGQPDEEDYDAIPRRA 60

Query: 61  MEYGAENARLIDCRKQLVAEGIAAIQCGAFHNTTGGLTYFNTTPLGRAVTGTMLVAAMKE 120
           MEYGAENARLIDCRKQLVAEGIAAIQCGAFHNTTGGLTYFNTTPLGRAVTGTMLVAAMKE
Sbjct: 61  MEYGAENARLIDCRKQLVAEGIAAIQCGAFHNTTGGLTYFNTTPLGRAVTGTMLVAAMKE 120

Query: 121 DGVNIWGDGSTYKGNDIERFYRYGLLTNAELQIYKPWLDTDFIDELGGRHEMSEFMIACG 180
           DGVNIWGDGSTYKGNDIERFYRYGLLTNAELQIYKPWLDTDFIDELGGRHEMSEFMIACG
Sbjct: 121 DGVNIWGDGSTYKGNDIERFYRYGLLTNAELQIYKPWLDTDFIDELGGRHEMSEFMIACG 180

Query: 181 FDYKMSVEKAYSTDSNMLGATHEAKDLEYLNSSVKIVNPIMGVKFWDESVKIPAEEVTVR 240
           FDYKMSVEKAYSTDSNMLGATHEAKDLEYLNSSVKIVNPIMGVKFWDESVKIPAEEVTVR
Sbjct: 181 FDYKMSVEKAYSTDSNMLGATHEAKDLEYLNSSVKIVNPIMGVKFWDESVKIPAEEVTVR 240

Query: 241 FEQGHPVALNGKTFSDDVEMMLEANRIGGRHGLGMSDQIENRIIEAKSRGIYEAPGMALL 300
           FEQGHPVALNGKTFSDDVEMMLEANRIGGRHGLGMSDQIENRIIEAKSRGIYEAPGMALL
Sbjct: 241 FEQGHPVALNGKTFSDDVEMMLEANRIGGRHGLGMSDQIENRIIEAKSRGIYEAPGMALL 300

Query: 301 HIAYERLLTGIHNEDTIEQYHAHGRQLGRLLYQGRWFDSQALMLRDSLQRWVASQITGEV 360
           HIAYERLLTGIHNEDTIEQYHAHGRQLGRLLYQGRWFDSQALMLRDSLQRWVASQITGEV
Sbjct: 301 HIAYERLLTGIHNEDTIEQYHAHGRQLGRLLYQGRWFDSQALMLRDSLQRWVASQITGEV 360

Query: 361 TLELRRGNDYSILNTVSENLTYKPERLTMEKGDSVFSPDDRIGQLTMRNLDITDTREKLF 420
           TLELRRGNDYSILNTVSENLTYKPERLTMEKGDSVFSPDDRIGQLTMRNLDITDTREKLF
Sbjct: 361 TLELRRGNDYSILNTVSENLTYKPERLTMEKGDSVFSPDDRIGQLTMRNLDITDTREKLF 420

Query: 421 GYAKTGLLSSSAASGVPQVENLENKGQ 447
           GYAKTGLLSSSAASGVPQVENLENKGQ
Sbjct: 421 GYAKTGLLSSSAASGVPQVENLENKGQ 447


Lambda     K      H
   0.317    0.135    0.397 

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: 797
Number of extensions: 15
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: 447
Length of database: 447
Length adjustment: 33
Effective length of query: 414
Effective length of database: 414
Effective search space:   171396
Effective search space used:   171396
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: 51 (24.3 bits)

Align candidate 17244 b3172 (argininosuccinate synthase (NCBI))
to HMM TIGR00032 (argG: argininosuccinate synthase (EC 6.3.4.5))

# 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/TIGR00032.hmm
# target sequence database:        /tmp/gapView.19157.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00032  [M=394]
Accession:   TIGR00032
Description: argG: argininosuccinate synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   6.4e-174  564.8   0.0   7.3e-174  564.6   0.0    1.0  1  lcl|FitnessBrowser__Keio:17244  b3172 argininosuccinate synthase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:17244  b3172 argininosuccinate synthase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  564.6   0.0  7.3e-174  7.3e-174       1     393 [.      13     419 ..      13     420 .. 0.99

  Alignments for each domain:
  == domain 1  score: 564.6 bits;  conditional E-value: 7.3e-174
                       TIGR00032   1 kvvlaysGGlDtsvalklleekgaeviavtvdvGqp.eedldaieekalklGaekayviDareefvkdylfaaiqanav 78 
                                     ++++a+sGGlDts+al+++++kga+++a+t+++Gqp eed+dai+++a+++Gae+a++iD+r+++v++ ++aaiq++a+
  lcl|FitnessBrowser__Keio:17244  13 RIGIAFSGGLDTSAALLWMRQKGAVPYAYTANLGQPdEEDYDAIPRRAMEYGAENARLIDCRKQLVAE-GIAAIQCGAF 90 
                                     689*****************************************************************.********** PP

                       TIGR00032  79 yegk....YllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnpdlkviaPvreleli.....R 148
                                     ++++    Y+++t+L+R++++++lv+++k++g++++++G+t+KGnD++RF++++ll+n++l++++P++++++i     R
  lcl|FitnessBrowser__Keio:17244  91 HNTTggltYFNTTPLGRAVTGTMLVAAMKEDGVNIWGDGSTYKGNDIERFYRYGLLTNAELQIYKPWLDTDFIdelggR 169
                                     ***99999*********************************************************************** PP

                       TIGR00032 149 eeeieyaaekGievpvekekaysiDenllgrsiEageLEdp.steppediyelvkdpiektedepevveieFekGvPva 226
                                     +e++e+++++G+++++++ekays+D+n+lg+++Ea++LE++ s++++++++++vk+++e++++ +e+v+++Fe+G+Pva
  lcl|FitnessBrowser__Keio:17244 170 HEMSEFMIACGFDYKMSVEKAYSTDSNMLGATHEAKDLEYLnSSVKIVNPIMGVKFWDESVKIPAEEVTVRFEQGHPVA 248
                                     *****************************************999*********************************** PP

                       TIGR00032 227 lngesle.pvelilkaneiagkhGvGriDivEdRiiglKsReiYEapalllLikAhkdLetlvltkdvlefkeiveeky 304
                                     lng++++ +ve++l+an+i+g+hG+G++D++E+Rii++KsR+iYEap+++lL++A+++L t+++++d++e+++++++++
  lcl|FitnessBrowser__Keio:17244 249 LNGKTFSdDVEMMLEANRIGGRHGLGMSDQIENRIIEAKSRGIYEAPGMALLHIAYERLLTGIHNEDTIEQYHAHGRQL 327
                                     *******9*********************************************************************** PP

                       TIGR00032 305 seliYkGlwfdplaeal.dalikktqervtGtvrvklfkGnaivigrk.seyslYdeelvsfek.dkefdqkdaiGfik 380
                                     ++l+Y+G+wfd++a +l d+l++++++++tG+v+++l++Gn+++i+++ se+++Y++e++++ek d+ f+++d+iG+++
  lcl|FitnessBrowser__Keio:17244 328 GRLLYQGRWFDSQALMLrDSLQRWVASQITGEVTLELRRGNDYSILNTvSENLTYKPERLTMEKgDSVFSPDDRIGQLT 406
                                     ****************************************************************9************** PP

                       TIGR00032 381 irglqikvyrekl 393
                                     +r+l+i+++rekl
  lcl|FitnessBrowser__Keio:17244 407 MRNLDITDTREKL 419
                                     *********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (394 nodes)
Target sequences:                          1  (447 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: 13.27
//
[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:

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