GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asp-kinase in Lacinutrix algicola AKS293

Align candidate WP_055436038.1 ASC41_RS07585 (aspartate kinase)
to HMM TIGR00657 (aspartate kinase (EC 2.7.2.4))

# 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/TIGR00657.hmm
# target sequence database:        /tmp/gapView.372404.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00657  [M=442]
Accession:   TIGR00657
Description: asp_kinases: aspartate 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
      3e-84  269.5   0.3    3.4e-84  269.4   0.3    1.0  1  NCBI__GCF_001418085.1:WP_055436038.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001418085.1:WP_055436038.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  269.4   0.3   3.4e-84   3.4e-84       5     384 ..       3     384 ..       1     415 [. 0.88

  Alignments for each domain:
  == domain 1  score: 269.4 bits;  conditional E-value: 3.4e-84
                             TIGR00657   5 VqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee..keliekirekhle 75 
                                           V KFGG Sv++++ +k+v+k ++k  +++   ++VvSAm+++T+aL  +++k  +e++   ++++++++ h +
  NCBI__GCF_001418085.1:WP_055436038.1   3 VFKFGGASVKDANGVKNVVKVLEKVGHEN--TLIVVSAMGKTTNALEVVIDKYLNEKNtfIAELDTVKNYHRT 73 
                                           89******************999988555..999******************999998787888899999999 PP

                             TIGR00657  76 aleela.sqalkeklkallekeleevkk..........ereldlilsvGEklSaallaaaleelgvkavsllg 137
                                           ++  l  +   + ++   +++ ++e+ +          +  +d ++ +GE +S+++++ +l++l   + ++l+
  NCBI__GCF_001418085.1:WP_055436038.1  74 IMMDLFnN--QQDQVFITVQALFNELLQffksnkspnyNFIYDQVIGYGELVSTTIISHYLNSLH-INNTWLD 143
                                           88887744..4555555556666555555667999999999************************.677899* PP

                             TIGR00657 138 aeagiltdsefgrAkvleeikterleklleegiivvvaGFiGatekgeittLGRGGSDltAallAaalkAdev 210
                                            ++ i td+ ++rA+v  ei+++ + + ++e ++++++GFi++++++ +ttLGR GSD+tAa+ A +l+A+ v
  NCBI__GCF_001418085.1:WP_055436038.1 144 VRQCIKTDDYYRRANVNWEITQNSIISKVKESTLYITQGFIASDSNNFTTTLGREGSDYTAAIFAYCLNAQSV 216
                                           ************************************************************************* PP

                             TIGR00657 211 eiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpeaeGTliv 283
                                            i++DV+G++  DPr+ +++++l++isy Ea ELa +Ga v+hp+tl+p+ r++ip++vks  npe+ GT + 
  NCBI__GCF_001418085.1:WP_055436038.1 217 TIWKDVPGVLNGDPRYFNNTQLLNTISYTEAIELAFYGASVIHPKTLQPLQRKEIPLHVKSFINPENAGTTVN 289
                                           ************************************************************************9 PP

                             TIGR00657 284 akskseeepavkalsldknqalvsvsgttmk...pgilaevfgalaeakvnvdlilqsssetsisfvvdked. 352
                                           +++    ep+v    l++nq+l+s+s         + ++e+f+ la  k +vd+i  +s    isf v  e+ 
  NCBI__GCF_001418085.1:WP_055436038.1 290 KSQG--IEPKVPCFILKQNQVLLSLSTLDFSyvvEENISEIFNLLALYKMKVDVIQ-NS---AISFSVCFENt 356
                                           9955..669*******************999888888999**************98.33...48898887773 PP

                             TIGR00657 353 adkakellkkkvkeekaleevevekklalvsl 384
                                            ++ ++l    ++++ka  +ve++++++l ++
  NCBI__GCF_001418085.1:WP_055436038.1 357 FNNLEKL----LLHLKAKFKVECHENVSLFTI 384
                                           4555555....466666678999999998777 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (416 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: 00:00:00.01
# Mc/sec: 13.74
//
[ok]

This GapMind analysis is from Jul 26 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