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.9654.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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 7.43
//
[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