Alignments for a candidate for asp-kinase in Methylococcus capsulatus Bath

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Methylococcus capsulatus Bath

Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_010959750.1 MCA_RS01930 aspartate kinase

Query= BRENDA::O69077
         (412 letters)



>NCBI__GCF_000008325.1:WP_010959750.1
          Length = 409

 Score =  590 bits (1520), Expect = e-173
 Identities = 303/405 (74%), Positives = 348/405 (85%), Gaps = 2/405 (0%)

Query: 1   MALIVQKFGGTSVGTVERIEQVAEKVKKFREAGDDVVVVVSAMSGETNRLIGLANQIMEQ 60
           MAL V K+GGTSVG+ ERI+ VA+ V + R  GDD++VVVSAMSGETNRL+ LA+++ E+
Sbjct: 1   MALFVHKYGGTSVGSPERIKNVAKNVIRARSRGDDIIVVVSAMSGETNRLVALAHEMHER 60

Query: 61  PVPRELDVMVSTGEQVTIALLSMALIKRGVPAVSYTGNQVRILTDSAHTKARILHIDDTH 120
           P  RE+DV+++TGEQVTIALLSMAL   G PA SYTG QVRILTD AHTKARIL ID   
Sbjct: 61  PSTREMDVLLATGEQVTIALLSMALEAAGCPACSYTGGQVRILTDDAHTKARILDIDTDR 120

Query: 121 IRADLKAGRVVVVAGFQGVDGNGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180
           IR+DL AGRVVVVAGFQG+   G+ITTLGRGGSDTT VALAAALKADEC IYTDVDGVYT
Sbjct: 121 IRSDLAAGRVVVVAGFQGITEAGDITTLGRGGSDTTAVALAAALKADECLIYTDVDGVYT 180

Query: 181 TDPRVVPQARRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFQEGPGTLI 240
           TDPR+ P+ARRLD+ITFEEMLEMASLGSKVLQIR+VEFAGKYNVPLRVL SF  GPGTLI
Sbjct: 181 TDPRIEPKARRLDRITFEEMLEMASLGSKVLQIRSVEFAGKYNVPLRVLSSFAAGPGTLI 240

Query: 241 TIDDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDMIVQNVA 300
           T   EE S+E+P+ISGIAFNRDEAKLT++GVPD PGVA++ILGP++ AN+EVDMIVQNVA
Sbjct: 241 TY--EEASVEKPLISGIAFNRDEAKLTVKGVPDKPGVAYQILGPVAHANIEVDMIVQNVA 298

Query: 301 HDNTTDFTFTVHRNDYLNALEILKQTAANIGAREAIGDTNIAKVSIVGVGMRSHAGVASR 360
            D TTDFTFTVHRNDY  AL+IL+ T   +GARE  GD  I KVS+VGVGMRSHAG+A+R
Sbjct: 299 EDATTDFTFTVHRNDYRKALDILQATCTALGAREVTGDDKIVKVSLVGVGMRSHAGIAAR 358

Query: 361 MFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELD 405
           MFEALA+E INI+MISTSEIK+S+V++EKYLELAVR LH AF LD
Sbjct: 359 MFEALAREGINIRMISTSEIKISIVVDEKYLELAVRTLHEAFNLD 403


Lambda     K      H
   0.317    0.133    0.362 

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: 540
Number of extensions: 14
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: 412
Length of database: 409
Length adjustment: 31
Effective length of query: 381
Effective length of database: 378
Effective search space:   144018
Effective search space used:   144018
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: 50 (23.9 bits)

Align candidate WP_010959750.1 MCA_RS01930 (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.13862.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.5e-142  461.7   4.0   2.4e-139  451.2   4.0    2.0  1  lcl|NCBI__GCF_000008325.1:WP_010959750.1  MCA_RS01930 aspartate kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000008325.1:WP_010959750.1  MCA_RS01930 aspartate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  451.2   4.0  2.4e-139  2.4e-139       1     441 [.       1     401 [.       1     402 [. 0.97

  Alignments for each domain:
  == domain 1  score: 451.2 bits;  conditional E-value: 2.4e-139
                                 TIGR00657   1 maliVqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseeekelieki 69 
                                               mal V K+GGtSvg+ erik+vak v++++  g++ +VVvSAm+g T++Lv+la+++++++        
  lcl|NCBI__GCF_000008325.1:WP_010959750.1   1 MALFVHKYGGTSVGSPERIKNVAKNVIRARSRGDDIIVVVSAMSGETNRLVALAHEMHERP-------- 61 
                                               7899*********************************************************........ PP

                                 TIGR00657  70 rekhlealeelasqalkeklkallekeleevkkereldlilsvGEklSaallaaaleelgvkavsllga 138
                                                           s                     re+d++l++GE++++all++ale+ g+ a s++g+
  lcl|NCBI__GCF_000008325.1:WP_010959750.1  62 ------------S--------------------TREMDVLLATGEQVTIALLSMALEAAGCPACSYTGG 98 
                                               ............5....................79********************************** PP

                                 TIGR00657 139 eagiltdsefgrAkvleeikterleklleegiivvvaGFiGatekgeittLGRGGSDltAallAaalkA 207
                                               +  iltd+++++A+ + +i+t+r+ + l +g +vvvaGF+G+te g+ittLGRGGSD+tA++lAaalkA
  lcl|NCBI__GCF_000008325.1:WP_010959750.1  99 QVRILTDDAHTKAR-ILDIDTDRIRSDLAAGRVVVVAGFQGITEAGDITTLGRGGSDTTAVALAAALKA 166
                                               **************.****************************************************** PP

                                 TIGR00657 208 deveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpe 276
                                               de+ iytDVdG+yt+DPri p+Arrld i++eE+lE+aslG+kvL+ r++e+a ++++p++v s+f   
  lcl|NCBI__GCF_000008325.1:WP_010959750.1 167 DECLIYTDVDGVYTTDPRIEPKARRLDRITFEEMLEMASLGSKVLQIRSVEFAGKYNVPLRVLSSFAAG 235
                                               *******************************************************************99 PP

                                 TIGR00657 277 aeGTlivakskseeepavkalsldknqalvsvsgttmkpgilaevfgalaeakvnvdlilqsssets.. 343
                                                +GTli+ ++ s e+p ++++++++++a+++v+g+++kpg++ +++g +a+a+++vd+i+q++ e+   
  lcl|NCBI__GCF_000008325.1:WP_010959750.1 236 -PGTLITYEEASVEKPLISGIAFNRDEAKLTVKGVPDKPGVAYQILGPVAHANIEVDMIVQNVAEDAtt 303
                                               .********999999*************************************************66556 PP

                                 TIGR00657 344 .isfvvdkedadkakellkkkvkeekaleevevekklalvslvGagmksapgvaakifeaLaeeninie 411
                                                 +f+v+++d+ ka  +l+ ++ ++ a +ev+ ++k+ +vslvG gm+s+ g+aa++feaLa+e+ini+
  lcl|NCBI__GCF_000008325.1:WP_010959750.1 304 dFTFTVHRNDYRKALDILQATCTALGA-REVTGDDKIVKVSLVGVGMRSHAGIAARMFEALAREGINIR 371
                                               8****************9876666665.57*************************************** PP

                                 TIGR00657 412 missseikisvvvdekdaekavealheklv 441
                                               mis+seikis+vvdek+ e av++lhe++ 
  lcl|NCBI__GCF_000008325.1:WP_010959750.1 372 MISTSEIKISIVVDEKYLELAVRTLHEAFN 401
                                               ***************************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (409 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: 0.06u 0.01s 00:00:00.06 Elapsed: 00:00:00.06
# Mc/sec: 2.70
//
[ok]

This GapMind analysis is from Apr 10 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