Aligments for a candidate for argB in Phaeobacter inhibens BS107

GapMind for Amino acid biosynthesis

Aligments for a candidate for argB in Phaeobacter inhibens BS107

Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate GFF201 PGA1_c02050 acetylglutamate kinase ArgB

Query= BRENDA::Q9HTN2
         (301 letters)



>FitnessBrowser__Phaeo:GFF201
          Length = 286

 Score =  288 bits (737), Expect = 1e-82
 Identities = 149/289 (51%), Positives = 202/289 (69%), Gaps = 13/289 (4%)

Query: 7   DAAQVAKVLSEALPYIRRFVGKTLVIKYGGNAMESEELKAGFARDVVLMKAVGINPVVVH 66
           D    A+ LS ALPY++R+ G  +V+K GG+AM S+E    FARD+VL++ VG+NPV+VH
Sbjct: 9   DWIATAETLSSALPYLQRYDGAIVVVKLGGHAMGSDEAMETFARDIVLLRQVGVNPVIVH 68

Query: 67  GGGPQIGDLLKRLSIESHFIDGMRVTDAATMDVVEMVLGGQVNKDIVNLINRHGGSAIGL 126
           GGGP I  +L++L I+S F++G RVTDAATM+VVEMVL G VNK IV  INR GG+ +GL
Sbjct: 69  GGGPMINAMLEKLQIKSDFVNGKRVTDAATMEVVEMVLSGVVNKRIVQAINRQGGAGVGL 128

Query: 127 TGKDAELIRAKKLTVTRQTPEMTKPEIIDIGHVGEVTGVNVGLLNMLVKGDFIPVIAPIG 186
           +GKDA LI     T T+  P        D+G VG  + ++  +L+ L + D IPVIAPIG
Sbjct: 129 SGKDANLI-----TCTQADP--------DLGFVGTPSQMDPSVLHHLFEQDMIPVIAPIG 175

Query: 187 VGSNGESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKQGQVLTGLSTEQVNELIADG 246
            G +GE++NIN D  AG +A ALKA++L+LLT+++G+ +  G+V+T L    V  +  DG
Sbjct: 176 AGPDGETFNINGDTAAGAIASALKADRLLLLTDVSGVKNGAGEVVTELKAADVEAMTRDG 235

Query: 247 TIYGGMLPKIRCALEAVQGGVTSAHIIDGRVPNAVLLEIFTDSGVGTLI 295
            I GGM+PK   AL AV+ GV +  I+DGRVPNAVLLE+FTD G G++I
Sbjct: 236 VIIGGMIPKTETALAAVRSGVRACTIVDGRVPNAVLLELFTDHGAGSMI 284


Lambda     K      H
   0.318    0.138    0.381 

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: 283
Number of extensions: 10
Number of successful extensions: 2
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: 301
Length of database: 286
Length adjustment: 26
Effective length of query: 275
Effective length of database: 260
Effective search space:    71500
Effective search space used:    71500
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: 48 (23.1 bits)

Align candidate GFF201 PGA1_c02050 (acetylglutamate kinase ArgB)
to HMM TIGR00761 (argB: acetylglutamate kinase (EC 2.7.2.8))

# 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/TIGR00761.hmm
# target sequence database:        /tmp/gapView.18451.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00761  [M=231]
Accession:   TIGR00761
Description: argB: acetylglutamate kinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    6.6e-81  257.2   4.3      8e-81  256.9   4.3    1.1  1  lcl|FitnessBrowser__Phaeo:GFF201  PGA1_c02050 acetylglutamate kina


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF201  PGA1_c02050 acetylglutamate kinase ArgB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  256.9   4.3     8e-81     8e-81       2     231 .]      32     261 ..      31     261 .. 0.98

  Alignments for each domain:
  == domain 1  score: 256.9 bits;  conditional E-value: 8e-81
                         TIGR00761   2 iViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketlevvemvlig 76 
                                       +V+K+GG+a+   e++e++a+di+ lr++g+++vivHGGgp+in++lekl+i+ +fvng RvTd++t+evvemvl g
  lcl|FitnessBrowser__Phaeo:GFF201  32 VVVKLGGHAMGsdEAMETFARDIVLLRQVGVNPVIVHGGGPMINAMLEKLQIKSDFVNGKRVTDAATMEVVEMVLSG 108
                                       8*********8889*************************************************************** PP

                         TIGR00761  77 kvnkelvallekhgikavGltgkDgqlltaekldkedlgyvGeikkvnkelleallkagiipviaslaldeegqllN 153
                                        vnk++v++++++g + vGl+gkD++l+t ++ d + lg+vG+ +++++++l++l ++++ipvia++++  +g+++N
  lcl|FitnessBrowser__Phaeo:GFF201 109 VVNKRIVQAINRQGGAGVGLSGKDANLITCTQADPD-LGFVGTPSQMDPSVLHHLFEQDMIPVIAPIGAGPDGETFN 184
                                       ***********************************9.**************************************** PP

                         TIGR00761 154 vnaDtaAaelAaaleAekLvlLtdvaGilegdkksliseleleeieqlikqavikgGmipKveaalealesgvkkvv 230
                                       +n+DtaA+++A+al+A++L+lLtdv+G+ +g + ++++el+++++e + + +vi gGmipK e al+a++sgv++  
  lcl|FitnessBrowser__Phaeo:GFF201 185 INGDTAAGAIASALKADRLLLLTDVSGVKNG-AGEVVTELKAADVEAMTRDGVIIGGMIPKTETALAAVRSGVRACT 260
                                       *******************************.777**************************************9877 PP

                         TIGR00761 231 i 231
                                       i
  lcl|FitnessBrowser__Phaeo:GFF201 261 I 261
                                       6 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (231 nodes)
Target sequences:                          1  (286 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: 00:00:00.00
# Mc/sec: 8.49
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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