Alignments for a candidate for asp-kinase in Derxia gummosa DSM 723

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Derxia gummosa DSM 723

Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_028312931.1 H566_RS0120680 aspartate kinase

Query= SwissProt::Q88EI9
         (411 letters)



>NCBI__GCF_000482785.1:WP_028312931.1
          Length = 418

 Score =  518 bits (1333), Expect = e-151
 Identities = 274/417 (65%), Positives = 326/417 (78%), Gaps = 10/417 (2%)

Query: 1   MALIVQKFGGTSVGSIERIEQVAEKVKKHREAGDDLVVVLSAMSGETNRLIDLAKQITDQ 60
           MALIV K+GGTS+GS ERI  VA +V K   AG  +VVV SAMSGETNRL+ LAK++T  
Sbjct: 1   MALIVHKYGGTSMGSTERIRNVARRVAKWVRAGHQIVVVPSAMSGETNRLLGLAKELTSN 60

Query: 61  PVPRELDVIVSTGEQVTIALLTMALIKRGVPAVSYTGNQVRILTDSSHNKARILQIDDQK 120
           P PRELD+I STGEQV++ LL +AL   GVPAVSY G QV + TDS++ KARI  IDD +
Sbjct: 61  PDPRELDMIASTGEQVSVGLLALALQAEGVPAVSYAGWQVPVRTDSAYTKARISSIDDTR 120

Query: 121 IRADLKEGRVVVVAGFQGVDEHGSITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180
           +RADL  G+VVV+ GFQG+DE GSITTLGRGGSDT+ VA+AAALKA+EC IYTDVDGVYT
Sbjct: 121 VRADLDAGKVVVITGFQGIDELGSITTLGRGGSDTSAVAVAAALKAEECLIYTDVDGVYT 180

Query: 181 TDPRVVPQARRLEKITFEEMLEMASLGSKVLQIRSVEFAGKYNVPLRVLHSFKEG----- 235
           TDPRVVP+ARRL+ I+FEEMLEMASLGSKVLQIRSVEFAGKY V  RVL S  +      
Sbjct: 181 TDPRVVPEARRLKVISFEEMLEMASLGSKVLQIRSVEFAGKYRVRTRVLSSLTDPLMPLE 240

Query: 236 ----PGTLITIDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISASNIEV 291
                GTLIT +E+E ME  +ISGIAF+RDEAK+T+ GVPD PGVAFKILGPI+ +NI+V
Sbjct: 241 DEMISGTLITFEEDEKMETAVISGIAFSRDEAKVTVLGVPDKPGVAFKILGPIAEANIDV 300

Query: 292 DMIVQNVAHDNTTDFTFTVHRNEYEKAQSVLENTAR-EIGAREVIGDTKIAKVSIVGVGM 350
           D+I+QN + +  TDF+FTV R E  KA  VL    + EIGA+E++GD  + KVS VG+GM
Sbjct: 301 DVIIQNQSVEGFTDFSFTVARGELAKALDVLNTKVKPEIGAKEIVGDPAVCKVSAVGIGM 360

Query: 351 RSHAGVASCMFEALAKESINIQMISTSEIKVSVVLEEKYLELAVRALHTAFDLDAPA 407
           RSH G+AS MFE L  E INIQMISTSEIK+SVV+ +KY+ELAVRALH AF L+  A
Sbjct: 361 RSHVGIASKMFETLFNEGINIQMISTSEIKISVVIADKYMELAVRALHKAFGLETTA 417


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: 547
Number of extensions: 20
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: 418
Length adjustment: 31
Effective length of query: 380
Effective length of database: 387
Effective search space:   147060
Effective search space used:   147060
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_028312931.1 H566_RS0120680 (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.18154.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.5e-132  426.9   5.0   7.3e-114  367.2   2.5    2.0  2  lcl|NCBI__GCF_000482785.1:WP_028312931.1  H566_RS0120680 aspartate kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000482785.1:WP_028312931.1  H566_RS0120680 aspartate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.7   0.0     7e-21     7e-21       1      61 [.       1      61 [.       1      63 [. 0.97
   2 !  367.2   2.5  7.3e-114  7.3e-114     103     441 ..      63     412 ..      61     413 .. 0.95

  Alignments for each domain:
  == domain 1  score: 60.7 bits;  conditional E-value: 7e-21
                                 TIGR00657  1 maliVqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvssee 61
                                              maliV K+GGtS+g+ eri++va++v k  + g+q vVV SAm+g T++L+ la+++ s++
  lcl|NCBI__GCF_000482785.1:WP_028312931.1  1 MALIVHKYGGTSMGSTERIRNVARRVAKWVRAGHQIVVVPSAMSGETNRLLGLAKELTSNP 61
                                              899*****************************************************99987 PP

  == domain 2  score: 367.2 bits;  conditional E-value: 7.3e-114
                                 TIGR00657 103 ereldlilsvGEklSaallaaaleelgvkavsllgaeagiltdsefgrAkvleeikterleklleegii 171
                                               +reld+i s+GE++S+ lla+al+++gv avs+ g++ +++tds++++A+ + +i+  r+ + l++g++
  lcl|NCBI__GCF_000482785.1:WP_028312931.1  63 PRELDMIASTGEQVSVGLLALALQAEGVPAVSYAGWQVPVRTDSAYTKAR-ISSIDDTRVRADLDAGKV 130
                                               699***********************************************.****************** PP

                                 TIGR00657 172 vvvaGFiGatekgeittLGRGGSDltAallAaalkAdeveiytDVdGiytaDPrivpeArrldeisyeE 240
                                               vv++GF+G++e g+ittLGRGGSD++A+++AaalkA+e+ iytDVdG+yt+DPr+vpeArrl+ is+eE
  lcl|NCBI__GCF_000482785.1:WP_028312931.1 131 VVITGFQGIDELGSITTLGRGGSDTSAVAVAAALKAEECLIYTDVDGVYTTDPRVVPEARRLKVISFEE 199
                                               ********************************************************************* PP

                                 TIGR00657 241 alELaslGakvLhprtlepamrakipivvkst........fnpeaeGTlivaksk.seeepavkalsld 300
                                               +lE+aslG+kvL+ r++e+a ++ ++ +v s+         ++   GTli+ +++ ++e+  +++++++
  lcl|NCBI__GCF_000482785.1:WP_028312931.1 200 MLEMASLGSKVLQIRSVEFAGKYRVRTRVLSSltdplmplEDEMISGTLITFEEDeKMETAVISGIAFS 268
                                               *****************************98732222222345568****9887779999********* PP

                                 TIGR00657 301 knqalvsvsgttmkpgilaevfgalaeakvnvdlilqsssets...isfvvdkedadkakellkkkvke 366
                                               +++a+v+v g+++kpg++ +++g +aea+++vd+i+q++s ++    sf+v + ++ ka  +l++kvk 
  lcl|NCBI__GCF_000482785.1:WP_028312931.1 269 RDEAKVTVLGVPDKPGVAFKILGPIAEANIDVDVIIQNQSVEGftdFSFTVARGELAKALDVLNTKVKP 337
                                               ************************************99995556779********************** PP

                                 TIGR00657 367 ekaleevevekklalvslvGagmksapgvaakifeaLaeeniniemissseikisvvvdekdaekavea 435
                                               e   +e+  +  +++vs vG gm+s+ g+a+k+fe+L +e+ini+mis+seikisvv+ +k++e av+a
  lcl|NCBI__GCF_000482785.1:WP_028312931.1 338 EIGAKEIVGDPAVCKVSAVGIGMRSHVGIASKMFETLFNEGINIQMISTSEIKISVVIADKYMELAVRA 406
                                               ********************************************************************* PP

                                 TIGR00657 436 lheklv 441
                                               lh+++ 
  lcl|NCBI__GCF_000482785.1:WP_028312931.1 407 LHKAFG 412
                                               ***996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (418 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: 4.24
//
[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