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.2590710.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  NCBI__GCF_000016505.1:WP_011989176.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000016505.1:WP_011989176.1  
   #    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
  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 ereldlilsvGEklSaallaaaleelgvkavsllgaeagiltdsefgrAkvleeikterleklleegiivvva 175
                                           +reld++ls+GE++S+alla+a+++lg++a+s+++ + gi t++++g++  + +i+++r++k l+eg+i + a
  NCBI__GCF_000016505.1:WP_011989176.1  63 KRELDALLSTGEMMSCALLAMAIKDLGYDAISYTAYQIGIKTSGQYGKSL-IDDINADRMKKSLDEGKIIIAA 134
                                           699***********************************************.********************** PP

                             TIGR00657 176 GFiGatekgeittLGRGGSDltAallAaalkAdeveiytDVdGiytaDPrivpeArrldeisyeEalELaslG 248
                                           GF+G++++g++ttLGRGGSD+tA+++A  l+  ++eiytDVdGiy+ DPr+ ++A++ldei+yeE+lEL+slG
  NCBI__GCF_000016505.1:WP_011989176.1 135 GFQGINDEGDVTTLGRGGSDTTAVAIAVKLNG-VCEIYTDVDGIYSVDPRKYKNAKKLDEIDYEEMLELSSLG 206
                                           ******************************96.5*************************************** PP

                             TIGR00657 249 akvLhprtlepamrakipivvkstfnpeaeGTlivaksk.seeepavkalsldknqalvsvsgttmkpgilae 320
                                           a+v+h r++e+a +++ip+ v  + ++   GT+i + ++ + e+++v++l+++++++ ++v+  + + +i+++
  NCBI__GCF_000016505.1:WP_011989176.1 207 AQVMHSRSIELAQKYNIPVYVGLSNSNI-RGTVIKGVDTmNLESKPVTGLATSDEDIAITVKDIKNDINIISN 278
                                           *********************9877776.9******9996556799*************************** PP

                             TIGR00657 321 vfgalaeakvnvdlilqsss...etsisfvvdkedadkakellkkkvkeekaleevevekklalvslvGagmk 390
                                           +f+ +ae+k+nvd+i+q++    + ++sf+++k+d+++  ++lk+ + ++++   ++++k++ + s+vG gmk
  NCBI__GCF_000016505.1:WP_011989176.1 279 LFESVAEKKINVDMISQTAPidgKVNVSFTIPKDDMKECLTILKS-YFDNNQ---IDIDKDITKFSIVGIGMK 347
                                           *****************998767778****************854.555554...68**************** PP

                             TIGR00657 391 sapgvaakifeaLaeeniniemissseikisvvvdekdaekavealhekl 440
                                           ++ gv+ak+f+  +e+ni ++mi +sei+i++ ++++d  k++  + ek+
  NCBI__GCF_000016505.1:WP_011989176.1 348 TTSGVVAKMFKLFRENNIAVKMITTSEIRITCAIKQEDKMKTISIIAEKF 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 8.91
//
[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