Aligments for a candidate for argB in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for Amino acid biosynthesis

Aligments for a candidate for argB in Echinicola vietnamensis KMM 6221, DSM 17526

Align Acetylglutamate kinase; EC 2.7.2.8; N-acetyl-L-glutamate 5-phosphotransferase; NAG kinase; NAGK (uncharacterized)
to candidate Echvi_3850 Echvi_3850 acetylglutamate kinase

Query= curated2:Q11QI8
         (264 letters)



>FitnessBrowser__Cola:Echvi_3850
          Length = 266

 Score =  267 bits (682), Expect = 2e-76
 Identities = 139/259 (53%), Positives = 187/259 (72%), Gaps = 2/259 (0%)

Query: 3   KLYIIKVGGNIIDNPEALTSFLKDFASLKENKILVHGGGKVATEISKGLGIEAQMVDGRR 62
           K+ I+K+GGN+ID+P  L  FL  FA L+  KILVHGGG +A++  + LGIE +MVDGRR
Sbjct: 2   KISIVKIGGNVIDDPAKLQEFLMLFARLEGKKILVHGGGVMASKFGQQLGIEPKMVDGRR 61

Query: 63  ITDAETLKIVTMVYGGLINKNIVAKLQSNECNAIGLTGADANIMLSSKRPLKNGIDYGFV 122
           ITD  TL +VTMVY G+INK IVAKLQ  E NA+G TGAD N++ S+KRP+K+ IDYGFV
Sbjct: 62  ITDEATLDVVTMVYAGMINKKIVAKLQQLEQNAMGFTGADGNLIRSAKRPVKD-IDYGFV 120

Query: 123 GDVKKVHPQPLIHLLSQGITPVVAPLTHDGNGTMLNTNADTVASELAVALCGAFAVNLVY 182
           GDVK+V  + +  LL + + PV + +THD  G +LNTNADT+ASE+A A+     V L +
Sbjct: 121 GDVKEVDTELMEVLLEKDVVPVFSAITHDRKGNLLNTNADTIASEIATAMAVKHTVRLYF 180

Query: 183 CFELKGVLRDFEDKDSVISTINPDTYEELKSTGVINKGMIPKLDNSFNAINAGVSSVIIC 242
           CF   GVL D  + DS++  IN D Y+ELK   VI+ GMIPKLDN+F+A++ GVS+V + 
Sbjct: 181 CFNKAGVLIDEHNDDSLVPKINEDIYDELKRDNVIHSGMIPKLDNAFSALHKGVSNVWLG 240

Query: 243 QAESLVELINENKTVGTKL 261
           +AE+L+ L ++ K  GT +
Sbjct: 241 KAENLI-LASKGKKSGTNI 258


Lambda     K      H
   0.316    0.135    0.376 

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: 233
Number of extensions: 8
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: 264
Length of database: 266
Length adjustment: 25
Effective length of query: 239
Effective length of database: 241
Effective search space:    57599
Effective search space used:    57599
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 Echvi_3850 Echvi_3850 (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.30859.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-62  195.8   2.1    4.5e-62  195.6   2.1    1.0  1  lcl|FitnessBrowser__Cola:Echvi_3850  Echvi_3850 acetylglutamate kinas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_3850  Echvi_3850 acetylglutamate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.6   2.1   4.5e-62   4.5e-62       3     229 ..       5     237 ..       3     239 .. 0.91

  Alignments for each domain:
  == domain 1  score: 195.6 bits;  conditional E-value: 4.5e-62
                            TIGR00761   3 ViKiGGaaiselleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketlevvemvlig 76 
                                          ++KiGG++i++   +l + ++ ++  + k ++vHGGg + ++  ++lgie+++v+g R+Td++tl+vv+mv++g
  lcl|FitnessBrowser__Cola:Echvi_3850   5 IVKIGGNVIDD-PAKLQEFLMLFARLEGKKILVHGGGVMASKFGQQLGIEPKMVDGRRITDEATLDVVTMVYAG 77 
                                          8*********7.566666666666666666******************************************** PP

                            TIGR00761  77 kvnkelvallekhgikavGltgkDgqlltae..kldkedlgyvGeikkvnkelleallkagiipviaslaldee 148
                                           +nk++va+l++ + +a+G tg+Dg+l+      +++ d+g+vG++k+v++el+e ll+++++pv +++  d +
  lcl|FitnessBrowser__Cola:Echvi_3850  78 MINKKIVAKLQQLEQNAMGFTGADGNLIRSAkrPVKDIDYGFVGDVKEVDTELMEVLLEKDVVPVFSAITHDRK 151
                                          ****************************98844455559*********************************** PP

                            TIGR00761 149 gqllNvnaDtaAaelAaaleAe...kLvlLtdvaGileg..dkksliseleleeieqlikqavikgGmipKvea 217
                                          g+llN+naDt+A+e+A+a+  +   +L++  ++aG+l +  + +sl+ +++ + +++l + +vi++GmipK+++
  lcl|FitnessBrowser__Cola:Echvi_3850 152 GNLLNTNADTIASEIATAMAVKhtvRLYFCFNKAGVLIDehNDDSLVPKINEDIYDELKRDNVIHSGMIPKLDN 225
                                          *******************76633379999******988787888***************************** PP

                            TIGR00761 218 alealesgvkkv 229
                                          a +al++gv++v
  lcl|FitnessBrowser__Cola:Echvi_3850 226 AFSALHKGVSNV 237
                                          *********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (231 nodes)
Target sequences:                          1  (266 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 6.29
//
[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