Alignments for a candidate for argB in Cupriavidus basilensis 4G11

GapMind for Amino acid biosynthesis

Alignments for a candidate for argB in Cupriavidus basilensis 4G11

Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate RR42_RS01125 RR42_RS01125 acetylglutamate kinase

Query= BRENDA::Q9HTN2
         (301 letters)



>FitnessBrowser__Cup4G11:RR42_RS01125
          Length = 305

 Score =  336 bits (862), Expect = 3e-97
 Identities = 170/285 (59%), Positives = 218/285 (76%), Gaps = 5/285 (1%)

Query: 12  AKVLSEALPYIRRFVGKTLVIKYGGNAMESEELKAGFARDVVLMKAVGINPVVVHGGGPQ 71
           A++L+EALPYIR+F GKT+V+KYGGNAM  E+LK GFARDV+L+K VG+NPVVVHGGGPQ
Sbjct: 22  AEILAEALPYIRKFHGKTIVVKYGGNAMTEEKLKHGFARDVILLKLVGMNPVVVHGGGPQ 81

Query: 72  IGDLLKRLSIESHFIDGMRVTDAATMDVVEMVLGGQVNKDIVNLINRHGGSAIGLTGKDA 131
           I + LK++     FI GMRVTD  TM+VVE VLGG+V +DIV LIN++GG A+GLTGKD 
Sbjct: 82  IDEALKKVGKVGTFIQGMRVTDEETMEVVEWVLGGEVQQDIVMLINQYGGQAVGLTGKDG 141

Query: 132 ELIRAKKLTVTRQTPEMTKP-EIIDIGHVGEVTGVNVGLLNMLVKGDFIPVIAPIGVGSN 190
            LIRAK+L    + P+   P   IDIG VG++  +N  ++  L    FIPVI+PIG   +
Sbjct: 142 GLIRAKRL----KMPDRESPGAFIDIGFVGDIEAINPAVVKALQDDAFIPVISPIGFSDD 197

Query: 191 GESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKQGQVLTGLSTEQVNELIADGTIYG 250
           G++YNINAD+VAGK+AE LKAEKL+++TNI G+MDK G +LT LS  ++ EL ADGTI G
Sbjct: 198 GQAYNINADVVAGKMAEILKAEKLVMMTNIPGVMDKAGNLLTDLSAREIEELFADGTISG 257

Query: 251 GMLPKIRCALEAVQGGVTSAHIIDGRVPNAVLLEIFTDSGVGTLI 295
           GMLPKI  AL+A + GV S HIIDGR+ +++LLEI T+   GT+I
Sbjct: 258 GMLPKISSALDAAKSGVNSVHIIDGRIEHSLLLEILTEQAFGTMI 302


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: 336
Number of extensions: 13
Number of successful extensions: 3
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: 305
Length adjustment: 27
Effective length of query: 274
Effective length of database: 278
Effective search space:    76172
Effective search space used:    76172
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 RR42_RS01125 RR42_RS01125 (acetylglutamate kinase)
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.21899.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
      4e-78  248.1   2.9      4e-78  248.1   2.9    1.3  2  lcl|FitnessBrowser__Cup4G11:RR42_RS01125  RR42_RS01125 acetylglutamate kin


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS01125  RR42_RS01125 acetylglutamate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.7      0.47      0.47     158     171 ..      11      24 ..       2      26 .. 0.67
   2 !  248.1   2.9     4e-78     4e-78       1     231 []      39     279 ..      39     279 .. 0.98

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 0.47
                                 TIGR00761 158 taAaelAaaleAek 171
                                               ta a++A al+Ae 
  lcl|FitnessBrowser__Cup4G11:RR42_RS01125  11 TAVAAIAPALKAEI 24 
                                               55567777888874 PP

  == domain 2  score: 248.1 bits;  conditional E-value: 4e-78
                                 TIGR00761   1 tiViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketl 67 
                                               tiV+K+GG+a++  +l++ +a+d++ l+ +g+++v+vHGGgp+i+e+l+k+g    f++g+RvTd+et+
  lcl|FitnessBrowser__Cup4G11:RR42_RS01125  39 TIVVKYGGNAMTeeKLKHGFARDVILLKLVGMNPVVVHGGGPQIDEALKKVGKVGTFIQGMRVTDEETM 107
                                               69*********99899***************************************************** PP

                                 TIGR00761  68 evvemvligkvnkelvallekhgikavGltgkDgqlltaekldke.........dlgyvGeikkvnkel 127
                                               evve vl g+v++ +v l+++ g +avGltgkDg l+ a++l+           d+g+vG+i+++n+++
  lcl|FitnessBrowser__Cup4G11:RR42_RS01125 108 EVVEWVLGGEVQQDIVMLINQYGGQAVGLTGKDGGLIRAKRLKMPdrespgafiDIGFVGDIEAINPAV 176
                                               ****************************************76665569********************* PP

                                 TIGR00761 128 leallkagiipviaslaldeegqllNvnaDtaAaelAaaleAekLvlLtdvaGilegdkksliselele 196
                                               ++al +  +ipvi++++++++gq++N+naD++A+++A+ l+AekLv++t+++G++++ + +l++ l+++
  lcl|FitnessBrowser__Cup4G11:RR42_RS01125 177 VKALQDDAFIPVISPIGFSDDGQAYNINADVVAGKMAEILKAEKLVMMTNIPGVMDK-AGNLLTDLSAR 244
                                               *********************************************************.666******** PP

                                 TIGR00761 197 eieqlikqavikgGmipKveaalealesgvkkvvi 231
                                               eie+l   + i gGm pK+++al+a++sgv++v+i
  lcl|FitnessBrowser__Cup4G11:RR42_RS01125 245 EIEELFADGTISGGMLPKISSALDAAKSGVNSVHI 279
                                               *********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (231 nodes)
Target sequences:                          1  (305 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: 9.99
//
[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