GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argB in Xenophilus azovorans DSM 13620

Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate WP_038216199.1 Q392_RS27375 acetylglutamate kinase

Query= BRENDA::Q9HTN2
         (301 letters)



>NCBI__GCF_000745855.1:WP_038216199.1
          Length = 297

 Score =  331 bits (848), Expect = 1e-95
 Identities = 169/288 (58%), Positives = 216/288 (75%), Gaps = 5/288 (1%)

Query: 12  AKVLSEALPYIRRFVGKTLVIKYGGNAMESEELKAGFARDVVLMKAVGINPVVVHGGGPQ 71
           A++L++ALPYIR++ GKT+VIKYGGNAM    L+A FA DVVL+K VGINPVVVHGGGPQ
Sbjct: 14  AEILAQALPYIRKYHGKTMVIKYGGNAMTDPALQADFAEDVVLLKLVGINPVVVHGGGPQ 73

Query: 72  IGDLLKRLSIESHFIDGMRVTDAATMDVVEMVLGGQVNKDIVNLINRHGGSAIGLTGKDA 131
           I   L +L  + HFI GMRVTDA TM+VVE VL G+V +DIV LIN+ GG A+GLTG+D 
Sbjct: 74  IEAALNKLGKKGHFIQGMRVTDAETMEVVEWVLAGEVQQDIVGLINQAGGKAVGLTGRDG 133

Query: 132 ELIRAKKLTVT-RQTPEMTKPEIIDIGHVGEVTGVNVGLLNMLVKGDFIPVIAPIGVGSN 190
            LIRA+KL +  R  P +    + D+G VG++  ++ G++  L    FIPV++PIG G  
Sbjct: 134 GLIRAQKLKMADRNDPAL----MHDVGQVGDIVSIDPGVVQALQDDAFIPVVSPIGFGEE 189

Query: 191 GESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKQGQVLTGLSTEQVNELIADGTIYG 250
            ESYNINAD+VAGK+A  LKAEKL+LLTN  G++DK GQ+LT LS  ++++L ADGTI G
Sbjct: 190 NESYNINADVVAGKLATVLKAEKLVLLTNTPGVLDKNGQLLTNLSAREIDDLFADGTISG 249

Query: 251 GMLPKIRCALEAVQGGVTSAHIIDGRVPNAVLLEIFTDSGVGTLISNR 298
           GMLPKI  AL+A + GV + HIIDGRVP+++LLEI TD   GT+I  R
Sbjct: 250 GMLPKIEGALDAAKSGVNAVHIIDGRVPHSMLLEILTDQAYGTMIRAR 297


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: 321
Number of extensions: 15
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: 297
Length adjustment: 27
Effective length of query: 274
Effective length of database: 270
Effective search space:    73980
Effective search space used:    73980
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 WP_038216199.1 Q392_RS27375 (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.2606696.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    4.4e-77  244.7   4.1    5.2e-77  244.5   4.1    1.0  1  NCBI__GCF_000745855.1:WP_038216199.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000745855.1:WP_038216199.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  244.5   4.1   5.2e-77   5.2e-77       1     231 []      31     271 ..      31     271 .. 0.98

  Alignments for each domain:
  == domain 1  score: 244.5 bits;  conditional E-value: 5.2e-77
                             TIGR00761   1 tiViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketlevve 71 
                                           t+ViK+GG+a++   l+ ++a+d++ l+ +gi++v+vHGGgp+i+++l+klg + +f++g+RvTd+et+evve
  NCBI__GCF_000745855.1:WP_038216199.1  31 TMVIKYGGNAMTdpALQADFAEDVVLLKLVGINPVVVHGGGPQIEAALNKLGKKGHFIQGMRVTDAETMEVVE 103
                                           69**********9889********************************************************* PP

                             TIGR00761  72 mvligkvnkelvallekhgikavGltgkDgqlltaekldke.........dlgyvGeikkvnkelleallkag 135
                                            vl+g+v++ +v l++++g kavGltg Dg l+ a+kl+ +         d+g vG+i ++++ +++al +  
  NCBI__GCF_000745855.1:WP_038216199.1 104 WVLAGEVQQDIVGLINQAGGKAVGLTGRDGGLIRAQKLKMAdrndpalmhDVGQVGDIVSIDPGVVQALQDDA 176
                                           ************************************88777779***************************** PP

                             TIGR00761 136 iipviaslaldeegqllNvnaDtaAaelAaaleAekLvlLtdvaGilegdkksliseleleeieqlikqavik 208
                                           +ipv++++++ ee++ +N+naD++A++lA++l+AekLvlLt+++G+l+++++ l+++l+++ei++l   + i 
  NCBI__GCF_000745855.1:WP_038216199.1 177 FIPVVSPIGFGEENESYNINADVVAGKLATVLKAEKLVLLTNTPGVLDKNGQ-LLTNLSAREIDDLFADGTIS 248
                                           *************************************************666.******************** PP

                             TIGR00761 209 gGmipKveaalealesgvkkvvi 231
                                           gGm pK+e al+a++sgv++v+i
  NCBI__GCF_000745855.1:WP_038216199.1 249 GGMLPKIEGALDAAKSGVNAVHI 271
                                           *********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (231 nodes)
Target sequences:                          1  (297 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 17.51
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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