Alignments for a candidate for argB in Klebsiella michiganensis M5al

GapMind for Amino acid biosynthesis

Alignments for a candidate for argB in Klebsiella michiganensis M5al

Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate BWI76_RS00850 BWI76_RS00850 acetylglutamate kinase

Query= BRENDA::A0A140NEG9
         (258 letters)



>FitnessBrowser__Koxy:BWI76_RS00850
          Length = 257

 Score =  470 bits (1209), Expect = e-137
 Identities = 241/257 (93%), Positives = 248/257 (96%)

Query: 2   MNPLIIKLGGVLLDSEEALERLFSALVNYRESHQRPLVIVHGGGCVVDELMKGLNLPVKK 61
           MNPLIIKLGGVLLDSEEALERLF+ALVNYRESHQRPL+IVHGGGCVVDELMK LNLPV K
Sbjct: 1   MNPLIIKLGGVLLDSEEALERLFTALVNYRESHQRPLIIVHGGGCVVDELMKQLNLPVNK 60

Query: 62  KNGLRVTPADQIDIITGALAGTANKTLLAWAKKHQIAAVGLFLGDGDSVKVTQLDEELGH 121
           KNGLRVTPADQIDIITGALAGTANKTLLAWAKKH +AAVGLFLGDGDSVKVTQLDEELGH
Sbjct: 61  KNGLRVTPADQIDIITGALAGTANKTLLAWAKKHGLAAVGLFLGDGDSVKVTQLDEELGH 120

Query: 122 VGLAQPGSPKLINSLLENGYLPVVSSIGVTDEGQLMNVNADQAATALAATLGADLILLSD 181
           VG AQPGSP LIN+LL  GY+PVVSSIGVTDEG+LMNVNADQAATALAATLGADLILLSD
Sbjct: 121 VGFAQPGSPALINTLLAGGYMPVVSSIGVTDEGELMNVNADQAATALAATLGADLILLSD 180

Query: 182 VSGILDGKGQRIAEMTAAKAEQLIEQGIITDGMIVKVNAALDAARTLGRPVDIASWRHAE 241
           VSGILDGKGQRIAEMTA KAEQLIEQGIITDGMIVKVNAALDAARTLGRPVDIASWRHAE
Sbjct: 181 VSGILDGKGQRIAEMTAEKAEQLIEQGIITDGMIVKVNAALDAARTLGRPVDIASWRHAE 240

Query: 242 QLPALFNGMPMGTRILA 258
           QLPALFNG P+GTRILA
Sbjct: 241 QLPALFNGTPIGTRILA 257


Lambda     K      H
   0.317    0.136    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: 355
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: 258
Length of database: 257
Length adjustment: 24
Effective length of query: 234
Effective length of database: 233
Effective search space:    54522
Effective search space used:    54522
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 (21.6 bits)
S2: 47 (22.7 bits)

Align candidate BWI76_RS00850 BWI76_RS00850 (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.17091.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
    9.5e-81  256.7   1.6    1.1e-80  256.5   1.6    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS00850  BWI76_RS00850 acetylglutamate ki


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS00850  BWI76_RS00850 acetylglutamate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  256.5   1.6   1.1e-80   1.1e-80       2     231 .]       4     233 ..       3     233 .. 0.98

  Alignments for each domain:
  == domain 1  score: 256.5 bits;  conditional E-value: 1.1e-80
                               TIGR00761   2 iViKiGGaais..elleelakdiaklrkegik.lvivHGGgpeinelleklgievefvnglRvTdketlev 69 
                                             ++iK+GG++++  e+le+l+ +++++r+++++ l+ivHGGg+ ++el+++l+++v+++nglRvT ++++++
  lcl|FitnessBrowser__Koxy:BWI76_RS00850   4 LIIKLGGVLLDseEALERLFTALVNYRESHQRpLIIVHGGGCVVDELMKQLNLPVNKKNGLRVTPADQIDI 74 
                                             69********9999******************7899*********************************** PP

                               TIGR00761  70 vemvligkvnkelvallekhgikavGltgkDgqlltaekldkedlgyvGeikkvnkelleallkagiipvi 140
                                             ++ +l+g++nk+l+a+ +khg++avGl+ +Dg+ +++++ld+e lg+vG ++  +++l+++ll+ g++pv+
  lcl|FitnessBrowser__Koxy:BWI76_RS00850  75 ITGALAGTANKTLLAWAKKHGLAAVGLFLGDGDSVKVTQLDEE-LGHVGFAQPGSPALINTLLAGGYMPVV 144
                                             ******************************************9.*************************** PP

                               TIGR00761 141 aslaldeegqllNvnaDtaAaelAaaleAekLvlLtdvaGilegdkksliseleleeieqlikqavikgGm 211
                                             +s+++++eg+l+NvnaD+aA++lAa+l+A+ L+lL+dv+Gil+g+++ +i+e+++e++eqli+q++i++Gm
  lcl|FitnessBrowser__Koxy:BWI76_RS00850 145 SSIGVTDEGELMNVNADQAATALAATLGAD-LILLSDVSGILDGKGQ-RIAEMTAEKAEQLIEQGIITDGM 213
                                             ******************************.*************555.*********************** PP

                               TIGR00761 212 ipKveaalealesgvkkvvi 231
                                             i Kv+aal+a++++ + v i
  lcl|FitnessBrowser__Koxy:BWI76_RS00850 214 IVKVNAALDAARTLGRPVDI 233
                                             **************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (231 nodes)
Target sequences:                          1  (257 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: 6.78
//
[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