Alignments for a candidate for asp-kinase in Halomonas desiderata SP1

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Halomonas desiderata SP1

Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_176342944.1 BZY95_RS20540 aspartate kinase

Query= BRENDA::Q57991
         (473 letters)



>NCBI__GCF_002151265.1:WP_176342944.1
          Length = 434

 Score =  144 bits (364), Expect = 4e-39
 Identities = 103/319 (32%), Positives = 166/319 (52%), Gaps = 18/319 (5%)

Query: 1   MTTVMKFGGTSVGSGERIRHVAKIVTKRKKEDDDVVVVVSAMSEVTNALVEISQQALDVR 60
           MTTV KFGG S+   + IRH+  ++ + +  D  +VVVVSAM + TN L  +   A    
Sbjct: 1   MTTVFKFGGASIKDADAIRHLTPLLERHR--DRPLVVVVSAMGKTTNKLEALLAAARG-- 56

Query: 61  DIAKVGD----FIKFIREKHYKAIEEAIKSEEIKEEVKKIIDSRIEELEKVLIGVAYLGE 116
           +    GD      + ++ +H +AIE      +  +  ++ +D+  +EL+       +   
Sbjct: 57  EGGTQGDEYRRCFEALQTEHREAIEALFG--DAADSPRECVDALFDELDAQ--HRRHRDS 112

Query: 117 LTPKSRDYILSFGERLSSPILSGAIRDLGEKSIALEGGEAG--IITDNNFGSARVKRLEV 174
              K  D  + +GE +S+ I++     L    IA +  +A   + TD  + +A +     
Sbjct: 113 DHAKHYDQTVCYGELISTTIVAAW---LNHNDIATDWHDARELVRTDACYQAANLDWSTT 169

Query: 175 KERLLPLLKEGIIPVVT-GFIGTTEEGYITTLGRGGSDYSAALIGYGLDADIIEIWTDVS 233
            E +   L      ++T GFIG T EG  TTLGR GSD+SAA+  + LDA  + IW DV+
Sbjct: 170 AETVRQRLAGSDRVILTQGFIGGTAEGEATTLGREGSDFSAAIFAHCLDAREVVIWKDVT 229

Query: 234 GVYTTDPRLVPTARRIPKLSYIEAMELAYFGAKVLHPRTIEPAMEKGIPILVKNTFEPES 293
           G++  DPR    A ++ ++SY EA E A+ GAKV+HP+T+ P  EK IP+ V++   P++
Sbjct: 230 GLFNADPRRFDNAVQLERISYAEATERAWHGAKVIHPKTLGPLQEKSIPLTVRSFETPDA 289

Query: 294 EGTLITNDMEMSDSIVKAI 312
           E T+I  +      +   I
Sbjct: 290 EPTVIDAERRFDSDVASCI 308


Lambda     K      H
   0.316    0.135    0.364 

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: 372
Number of extensions: 18
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: 473
Length of database: 434
Length adjustment: 33
Effective length of query: 440
Effective length of database: 401
Effective search space:   176440
Effective search space used:   176440
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: 51 (24.3 bits)

Align candidate WP_176342944.1 BZY95_RS20540 (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.1294133.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    2.5e-73  233.6   0.0    2.9e-73  233.3   0.0    1.0  1  NCBI__GCF_002151265.1:WP_176342944.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002151265.1:WP_176342944.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  233.3   0.0   2.9e-73   2.9e-73       2     331 ..       1     344 [.       1     378 [. 0.86

  Alignments for each domain:
  == domain 1  score: 233.3 bits;  conditional E-value: 2.9e-73
                             TIGR00657   2 aliVqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee......keliek 68 
                                           ++ V KFGG S+++++ i+++  ++++++  +++ vVVvSAm+++T++L +l   +  e         +  e+
  NCBI__GCF_002151265.1:WP_176342944.1   1 MTTVFKFGGASIKDADAIRHLTPLLERHR--DRPLVVVVSAMGKTTNKLEALLAAARGEGGtqgdeyRRCFEA 71 
                                           567*********************99988..789******************999988777788888777888 PP

                             TIGR00657  69 irekhlealeela...sqalkeklkallekeleevkk......ereldlilsvGEklSaallaaaleelgvka 132
                                           ++++h ea+e+l     ++ +e + al ++  ++ ++       +++d  +++GE +S++++aa+l++ +  a
  NCBI__GCF_002151265.1:WP_176342944.1  72 LQTEHREAIEALFgdaADSPRECVDALFDELDAQHRRhrdsdhAKHYDQTVCYGELISTTIVAAWLNHND-IA 143
                                           888888888887542234456666666666666655599999999*************************.99 PP

                             TIGR00657 133 vsllgaeagiltdsefgrAkvleeikterleklleeg.iivvvaGFiGatekgeittLGRGGSDltAallAaa 204
                                            ++ +a++ ++td+ ++ A+   ++++e + + l     + +++GFiG t +ge ttLGR GSD++Aa+ A++
  NCBI__GCF_002151265.1:WP_176342944.1 144 TDWHDARELVRTDACYQAANLDWSTTAETVRQRLAGSdRVILTQGFIGGTAEGEATTLGREGSDFSAAIFAHC 216
                                           ********************777888888888877767*********************************** PP

                             TIGR00657 205 lkAdeveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpea 277
                                           l+A+ev i++DV G + aDPr   +A +l+ isy+Ea E a +Gakv+hp+tl p+ +++ip+ v+s   p+a
  NCBI__GCF_002151265.1:WP_176342944.1 217 LDAREVVIWKDVTGLFNADPRRFDNAVQLERISYAEATERAWHGAKVIHPKTLGPLQEKSIPLTVRSFETPDA 289
                                           ************************************************************************* PP

                             TIGR00657 278 eGTlivakskseeepavkalsldknqalvsvsgttmk...pgilaevfgalaeakvn 331
                                           e T+i a++    ++ v +  l++ q+ v+v+             +++g+l +a+ +
  NCBI__GCF_002151265.1:WP_176342944.1 290 EPTVIDAERRF--DSDVASCILREAQVWVEVRPRDFSfmdEPRQHDILGRLVKAGLH 344
                                           ********773..35788888888888888876655544455555666666555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (434 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 19.08
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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 2024 update 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 original 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