Alignments for a candidate for asp-kinase in Methylomonas methanica MC09

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Methylomonas methanica MC09

Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_013817476.1 METME_RS03820 aspartate kinase

Query= SwissProt::Q88EI9
         (411 letters)



>NCBI__GCF_000214665.1:WP_013817476.1
          Length = 408

 Score =  584 bits (1505), Expect = e-171
 Identities = 308/405 (76%), Positives = 349/405 (86%), Gaps = 2/405 (0%)

Query: 1   MALIVQKFGGTSVGSIERIEQVAEKVKKHREAGDDLVVVLSAMSGETNRLIDLAKQITDQ 60
           MAL V KFGGTSVG++ERI+ VAEKVKK  +AGD +VVV+SAMSGETNRL+ LAK++  Q
Sbjct: 1   MALYVYKFGGTSVGTVERIKAVAEKVKKSHDAGDQIVVVVSAMSGETNRLVALAKEMQVQ 60

Query: 61  PVPRELDVIVSTGEQVTIALLTMALIKRGVPAVSYTGNQVRILTDSSHNKARILQIDDQK 120
           P  RELDV++STGEQVTIALL+MAL   GV A SYTG QV+ILTDS+H KARI +ID+  
Sbjct: 61  PTDRELDVLLSTGEQVTIALLSMALHNVGVDARSYTGAQVKILTDSAHTKARIREIDEAN 120

Query: 121 IRADLKEGRVVVVAGFQGVDEHGSITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180
           +RADL  GRVVVVAGFQGVDE G+ITTLGRGGSDTTGVALAAALKADEC IYTDVDGVYT
Sbjct: 121 MRADLDAGRVVVVAGFQGVDEQGNITTLGRGGSDTTGVALAAALKADECHIYTDVDGVYT 180

Query: 181 TDPRVVPQARRLEKITFEEMLEMASLGSKVLQIRSVEFAGKYNVPLRVLHSFKEGPGTLI 240
           TDPRVVP+ARRLE+ITFEEMLEMASLGSKVLQIRSVEFAGKYNV LRVL SF EG GTLI
Sbjct: 181 TDPRVVPKARRLEQITFEEMLEMASLGSKVLQIRSVEFAGKYNVKLRVLSSFMEGNGTLI 240

Query: 241 TIDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISASNIEVDMIVQNVAH 300
           T +E E ME+ +ISGIAFNRDEAKLT+ GVPD PGVA KILGP++A NIEVDMIVQN++ 
Sbjct: 241 TYEESE-MERALISGIAFNRDEAKLTLTGVPDLPGVASKILGPVAAENIEVDMIVQNISA 299

Query: 301 DNTTDFTFTVHRNEYEKAQSVLENTAREIGAR-EVIGDTKIAKVSIVGVGMRSHAGVASC 359
             TTDFTFTV+RN++ +A+SVLE    E+G   ++IGD  I KVSIVGVGMRSHAG+AS 
Sbjct: 300 HGTTDFTFTVNRNDFARAKSVLEGLRNELGGNTQIIGDNSIVKVSIVGVGMRSHAGIAST 359

Query: 360 MFEALAKESINIQMISTSEIKVSVVLEEKYLELAVRALHTAFDLD 404
           MF+ LA E INIQMISTSEIK+SVV++EKYLELAVRALH AFDLD
Sbjct: 360 MFKTLADEGINIQMISTSEIKISVVVDEKYLELAVRALHKAFDLD 404


Lambda     K      H
   0.316    0.133    0.358 

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: 561
Number of extensions: 16
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: 411
Length of database: 408
Length adjustment: 31
Effective length of query: 380
Effective length of database: 377
Effective search space:   143260
Effective search space used:   143260
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: 50 (23.9 bits)

Align candidate WP_013817476.1 METME_RS03820 (aspartate kinase)
to HMM TIGR00656 (aspartate kinase, monofunctional class (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/TIGR00656.hmm
# target sequence database:        /tmp/gapView.17579.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00656  [M=407]
Accession:   TIGR00656
Description: asp_kin_monofn: aspartate kinase, monofunctional class
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     2e-134  434.6  15.0   2.2e-134  434.4  15.0    1.0  1  lcl|NCBI__GCF_000214665.1:WP_013817476.1  METME_RS03820 aspartate kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000214665.1:WP_013817476.1  METME_RS03820 aspartate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  434.4  15.0  2.2e-134  2.2e-134       2     406 ..       2     403 ..       1     404 [. 0.97

  Alignments for each domain:
  == domain 1  score: 434.4 bits;  conditional E-value: 2.2e-134
                                 TIGR00656   2 eliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeispr 70 
                                                l V KFGGtsvg +erik++a++v+k+   g++ vVVvSAms++t++lv+la      + ++ ++++r
  lcl|NCBI__GCF_000214665.1:WP_013817476.1   2 ALYVYKFGGTSVGTVERIKAVAEKVKKSHDAGDQIVVVVSAMSGETNRLVALA------KEMQVQPTDR 64 
                                               688**************************************************......9********* PP

                                 TIGR00656  71 erdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivv 139
                                               e d l+s+GE++++alls+al++ gv+a++++g++  ilTd+ +++A+i+e++   ++   L+ g +vv
  lcl|NCBI__GCF_000214665.1:WP_013817476.1  65 ELDVLLSTGEQVTIALLSMALHNVGVDARSYTGAQVKILTDSAHTKARIREIDE-ANMRADLDAGRVVV 132
                                               *****************************************************9.99************ PP

                                 TIGR00656 140 vaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEal 208
                                               vaGF+G +e+G+iTtLGRGGSD+t ++laaalkAd+++iyTDV+GvyttDPrvv++a+++++i++eE+l
  lcl|NCBI__GCF_000214665.1:WP_013817476.1 133 VAGFQGVDEQGNITTLGRGGSDTTGVALAAALKADECHIYTDVDGVYTTDPRVVPKARRLEQITFEEML 201
                                               ********************************************************************* PP

                                 TIGR00656 209 elAtlGakvlhpralelaveakvpilvrsskekeegTlitn.kkens.slvkaialeknvarltvegeg 275
                                               e+A+lG kvl+ r++e+a +++v+++v ss+ + +gTlit  ++e++  l+++ia++++ a+lt++  g
  lcl|NCBI__GCF_000214665.1:WP_013817476.1 202 EMASLGSKVLQIRSVEFAGKYNVKLRVLSSFMEGNGTLITYeESEMErALISGIAFNRDEAKLTLT--G 268
                                               ***************************************9864444446*****************..9 PP

                                 TIGR00656 276 mlgkrgilaeifkaLaeeeinvdlisqtese...tsislvvdeedvdeakkaLkeesgaae.lesleve 340
                                               + + +g++++i + +a e+i vd+i+q  s    t+ +++v+++d  +ak++L+   ++++  +++  +
  lcl|NCBI__GCF_000214665.1:WP_013817476.1 269 VPDLPGVASKILGPVAAENIEVDMIVQNISAhgtTDFTFTVNRNDFARAKSVLEGLRNELGgNTQIIGD 337
                                               ***************************9988888********************99888877899999* PP

                                 TIGR00656 341 edlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklheklee 406
                                               + + +vsivg+g++++ G+as +fk l++++ini mis+se+kisv+vdek++e avr+lh+++ +
  lcl|NCBI__GCF_000214665.1:WP_013817476.1 338 NSIVKVSIVGVGMRSHAGIASTMFKTLADEGINIQMISTSEIKISVVVDEKYLELAVRALHKAFDL 403
                                               **************************************************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (408 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: 00:00:00.02
# Mc/sec: 7.47
//
[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