Alignments for a candidate for asp-kinase in Clostridium kluyveri DSM 555

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Clostridium kluyveri DSM 555

Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_011989176.1 CKL_RS02980 aspartate kinase

Query= BRENDA::P08495
         (408 letters)



>NCBI__GCF_000016505.1:WP_011989176.1
          Length = 399

 Score =  344 bits (882), Expect = 3e-99
 Identities = 172/403 (42%), Positives = 276/403 (68%), Gaps = 6/403 (1%)

Query: 1   MGLIVQKFGGTSVGSVEKIQNAANRAIAEKQKGHQVVVVVSAMGKSTDELVSLAKAISDQ 60
           M +IVQK+GG+SVG+ EKI+N AN  + + + G+ +VVVVSAMG +TD+L++LA+ I+D 
Sbjct: 1   MAIIVQKYGGSSVGTPEKIKNVANTVVNKVKAGNSLVVVVSAMGDTTDDLIALARQITDN 60

Query: 61  PSKREMDMLLATGEQVTISLLSMALQEKGYDAVSYTGWQAGIRTEAIHGNARITDIDTSV 120
           P KRE+D LL+TGE ++ +LL+MA+++ GYDA+SYT +Q GI+T   +G + I DI+   
Sbjct: 61  PDKRELDALLSTGEMMSCALLAMAIKDLGYDAISYTAYQIGIKTSGQYGKSLIDDINADR 120

Query: 121 LADQLEKGKIVIVAGFQGMTEDCEITTLGRGGSDTTAVALAAALKADKCDIYTDVPGVFT 180
           +   L++GKI+I AGFQG+ ++ ++TTLGRGGSDTTAVA+A  L    C+IYTDV G+++
Sbjct: 121 MKKSLDEGKIIIAAGFQGINDEGDVTTLGRGGSDTTAVAIAVKLNG-VCEIYTDVDGIYS 179

Query: 181 TDPRYVKSARKLEGISYDEMLELANLGAGVLHPRAVEFAKNYQVPLEVRSSTETEAGTLI 240
            DPR  K+A+KL+ I Y+EMLEL++LGA V+H R++E A+ Y +P+ V  S     GT+I
Sbjct: 180 VDPRKYKNAKKLDEIDYEEMLELSSLGAQVMHSRSIELAQKYNIPVYVGLSNSNIRGTVI 239

Query: 241 EEESSME-QNLIVRGIAFEDQITRVTIYGLTSGLTTLSTIFTTLAKRNINVDIIIQTQAE 299
           +   +M  ++  V G+A  D+   +T+  + + +  +S +F ++A++ INVD+I QT   
Sbjct: 240 KGVDTMNLESKPVTGLATSDEDIAITVKDIKNDINIISNLFESVAEKKINVDMISQTAPI 299

Query: 300 D-KTGISFSVKTEDADQTVAVLEEYKDALEFEKIETESKLAKVSIVGSGMVSNPGVAAEM 358
           D K  +SF++  +D  + + +L+ Y D     +I+ +  + K SIVG GM +  GV A+M
Sbjct: 300 DGKVNVSFTIPKDDMKECLTILKSYFDN---NQIDIDKDITKFSIVGIGMKTTSGVVAKM 356

Query: 359 FAVLAQKNILIKMVSTSEIKVSTVVSENDMVKAVESLHDAFEL 401
           F +  + NI +KM++TSEI+++  + + D +K +  + + F L
Sbjct: 357 FKLFRENNIAVKMITTSEIRITCAIKQEDKMKTISIIAEKFNL 399


Lambda     K      H
   0.313    0.128    0.337 

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: 14
Number of successful extensions: 4
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: 408
Length of database: 399
Length adjustment: 31
Effective length of query: 377
Effective length of database: 368
Effective search space:   138736
Effective search space used:   138736
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 50 (23.9 bits)

Align candidate WP_011989176.1 CKL_RS02980 (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.23525.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.6e-121  392.4  16.7   2.4e-103  332.5   8.1    2.0  2  lcl|NCBI__GCF_000016505.1:WP_011989176.1  CKL_RS02980 aspartate kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016505.1:WP_011989176.1  CKL_RS02980 aspartate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.2   0.8   7.7e-23   7.7e-23       1      63 [.       1      63 [.       1      66 [. 0.96
   2 !  332.5   8.1  2.4e-103  2.4e-103     103     440 ..      63     397 ..      61     399 .] 0.95

  Alignments for each domain:
  == domain 1  score: 67.2 bits;  conditional E-value: 7.7e-23
                                 TIGR00657  1 maliVqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseeek 63
                                              ma+iVqK+GG+Svg+ e+ik+va+ v+++ + gn+ vVVvSAm+++Td+L++la+++ ++++k
  lcl|NCBI__GCF_000016505.1:WP_011989176.1  1 MAIIVQKYGGSSVGTPEKIKNVANTVVNKVKAGNSLVVVVSAMGDTTDDLIALARQITDNPDK 63
                                              799*******************************************************99964 PP

  == domain 2  score: 332.5 bits;  conditional E-value: 2.4e-103
                                 TIGR00657 103 ereldlilsvGEklSaallaaaleelgvkavsllgaeagiltdsefgrAkvleeikterleklleegii 171
                                               +reld++ls+GE++S+alla+a+++lg++a+s+++ + gi t++++g++  + +i+++r++k l+eg+i
  lcl|NCBI__GCF_000016505.1:WP_011989176.1  63 KRELDALLSTGEMMSCALLAMAIKDLGYDAISYTAYQIGIKTSGQYGKSL-IDDINADRMKKSLDEGKI 130
                                               699***********************************************.****************** PP

                                 TIGR00657 172 vvvaGFiGatekgeittLGRGGSDltAallAaalkAdeveiytDVdGiytaDPrivpeArrldeisyeE 240
                                                + aGF+G++++g++ttLGRGGSD+tA+++A  l+  ++eiytDVdGiy+ DPr+ ++A++ldei+yeE
  lcl|NCBI__GCF_000016505.1:WP_011989176.1 131 IIAAGFQGINDEGDVTTLGRGGSDTTAVAIAVKLNG-VCEIYTDVDGIYSVDPRKYKNAKKLDEIDYEE 198
                                               **********************************96.5******************************* PP

                                 TIGR00657 241 alELaslGakvLhprtlepamrakipivvkstfnpeaeGTlivaksk.seeepavkalsldknqalvsv 308
                                               +lEL+slGa+v+h r++e+a +++ip+ v  + ++   GT+i + ++ + e+++v++l+++++++ ++v
  lcl|NCBI__GCF_000016505.1:WP_011989176.1 199 MLELSSLGAQVMHSRSIELAQKYNIPVYVGLSNSNI-RGTVIKGVDTmNLESKPVTGLATSDEDIAITV 266
                                               *****************************9877776.9******9996556799*************** PP

                                 TIGR00657 309 sgttmkpgilaevfgalaeakvnvdlilqsss...etsisfvvdkedadkakellkkkvkeekaleeve 374
                                               +  + + +i++++f+ +ae+k+nvd+i+q++    + ++sf+++k+d+++  ++lk+ + ++++   ++
  lcl|NCBI__GCF_000016505.1:WP_011989176.1 267 KDIKNDINIISNLFESVAEKKINVDMISQTAPidgKVNVSFTIPKDDMKECLTILKS-YFDNNQ---ID 331
                                               *****************************998767778****************854.555554...68 PP

                                 TIGR00657 375 vekklalvslvGagmksapgvaakifeaLaeeniniemissseikisvvvdekdaekavealhekl 440
                                               ++k++ + s+vG gmk++ gv+ak+f+  +e+ni ++mi +sei+i++ ++++d  k++  + ek+
  lcl|NCBI__GCF_000016505.1:WP_011989176.1 332 IDKDITKFSIVGIGMKTTSGVVAKMFKLFRENNIAVKMITTSEIRITCAIKQEDKMKTISIIAEKF 397
                                               ************************************************************999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (399 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: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 4.06
//
[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