Alignments for a candidate for asp-kinase in Dechlorosoma suillum PS

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Dechlorosoma suillum PS

Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate Dsui_2134 Dsui_2134 aspartate kinase, monofunctional class

Query= SwissProt::Q88EI9
         (411 letters)



>FitnessBrowser__PS:Dsui_2134
          Length = 407

 Score =  576 bits (1485), Expect = e-169
 Identities = 297/405 (73%), Positives = 348/405 (85%), Gaps = 1/405 (0%)

Query: 1   MALIVQKFGGTSVGSIERIEQVAEKVKKHREAGDDLVVVLSAMSGETNRLIDLAKQITDQ 60
           MALIVQK+GGTSVGS ERI+ VA++V + +  G D+VVV SAMSGETNRLI LAK+I+  
Sbjct: 1   MALIVQKYGGTSVGSTERIKNVAKRVARWKAMGHDVVVVPSAMSGETNRLIGLAKEISAT 60

Query: 61  PVPRELDVIVSTGEQVTIALLTMALIKRGVPAVSYTGNQVRILTDSSHNKARILQIDDQK 120
           P PRELDVI STGEQVTI LL MA+ + G+ A SYTG+QVR+LTDS+  KARILQIDD++
Sbjct: 61  PSPRELDVIASTGEQVTIGLLAMAIQEEGLKAKSYTGSQVRVLTDSTFTKARILQIDDER 120

Query: 121 IRADLKEGRVVVVAGFQGVDEHGSITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180
           +R DL EG VVVVAGFQG DE+G+ITTLGRGGSDT+ VALAAALKADECQIYTDVDGVYT
Sbjct: 121 MRKDLAEGNVVVVAGFQGADENGNITTLGRGGSDTSAVALAAALKADECQIYTDVDGVYT 180

Query: 181 TDPRVVPQARRLEKITFEEMLEMASLGSKVLQIRSVEFAGKYNVPLRVLHSFK-EGPGTL 239
           TDPRVVP+AR+L+ ITFEEMLEMASLGSKVLQIRSVEFAGKY V LRVL SF+ EG GTL
Sbjct: 181 TDPRVVPEARKLDTITFEEMLEMASLGSKVLQIRSVEFAGKYKVKLRVLSSFQDEGEGTL 240

Query: 240 ITIDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISASNIEVDMIVQNVA 299
           IT++++++MEQPIISGIAFNRDEAKLT+ GVPD PG+A++ILGPI+ +NI+VDMI+QNV 
Sbjct: 241 ITVEDDKNMEQPIISGIAFNRDEAKLTVLGVPDRPGIAYQILGPIADANIDVDMIIQNVG 300

Query: 300 HDNTTDFTFTVHRNEYEKAQSVLENTAREIGAREVIGDTKIAKVSIVGVGMRSHAGVASC 359
            D TTDF+FTV+R+EY KA +VLE   + +GARE++GD K  KVS VGVGMRSH GVAS 
Sbjct: 301 VDGTTDFSFTVNRSEYTKAMAVLEQVKQHVGAREIVGDNKTCKVSAVGVGMRSHPGVASQ 360

Query: 360 MFEALAKESINIQMISTSEIKVSVVLEEKYLELAVRALHTAFDLD 404
           MF  LA+E INIQMISTSEIK+SVV++EKYLELAVR LH  F LD
Sbjct: 361 MFRTLAEEGINIQMISTSEIKISVVIDEKYLELAVRILHKTFGLD 405


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: 548
Number of extensions: 14
Number of successful extensions: 2
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: 407
Length adjustment: 31
Effective length of query: 380
Effective length of database: 376
Effective search space:   142880
Effective search space used:   142880
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 Dsui_2134 Dsui_2134 (aspartate kinase, monofunctional class)
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.8837.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.8e-143  464.8  10.5   2.8e-140  454.2  10.5    2.0  1  lcl|FitnessBrowser__PS:Dsui_2134  Dsui_2134 aspartate kinase, mono


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_2134  Dsui_2134 aspartate kinase, monofunctional class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  454.2  10.5  2.8e-140  2.8e-140       1     441 [.       1     403 [.       1     404 [. 0.98

  Alignments for each domain:
  == domain 1  score: 454.2 bits;  conditional E-value: 2.8e-140
                         TIGR00657   1 maliVqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseeekeliekirekhleal 77 
                                       maliVqK+GGtSvg+ erik+vak+v + k+ g++vvVV SAm+g T++L+ la+++s  +                
  lcl|FitnessBrowser__PS:Dsui_2134   1 MALIVQKYGGTSVGSTERIKNVAKRVARWKAMGHDVVVVPSAMSGETNRLIGLAKEISATP---------------- 61 
                                       89***********************************************************................ PP

                         TIGR00657  78 eelasqalkeklkallekeleevkkereldlilsvGEklSaallaaaleelgvkavsllgaeagiltdsefgrAkvl 154
                                           s                    +reld+i s+GE++++ lla+a++e+g ka s++g++  +ltds+f++A+ +
  lcl|FitnessBrowser__PS:Dsui_2134  62 ----S--------------------PRELDVIASTGEQVTIGLLAMAIQEEGLKAKSYTGSQVRVLTDSTFTKAR-I 113
                                       ....5....................8*************************************************.* PP

                         TIGR00657 155 eeikterleklleegiivvvaGFiGatekgeittLGRGGSDltAallAaalkAdeveiytDVdGiytaDPrivpeAr 231
                                        +i+ er+ k l eg +vvvaGF+Ga+e+g+ittLGRGGSD++A++lAaalkAde++iytDVdG+yt+DPr+vpeAr
  lcl|FitnessBrowser__PS:Dsui_2134 114 LQIDDERMRKDLAEGNVVVVAGFQGADENGNITTLGRGGSDTSAVALAAALKADECQIYTDVDGVYTTDPRVVPEAR 190
                                       ***************************************************************************** PP

                         TIGR00657 232 rldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpeaeGTlivaksk.seeepavkalsldknqalvs 307
                                       +ld+i++eE+lE+aslG+kvL+ r++e+a ++k++++v s+f++e+eGTli+ +++ ++e+p+++++++++++a+++
  lcl|FitnessBrowser__PS:Dsui_2134 191 KLDTITFEEMLEMASLGSKVLQIRSVEFAGKYKVKLRVLSSFQDEGEGTLITVEDDkNMEQPIISGIAFNRDEAKLT 267
                                       ***************************************************9887779999**************** PP

                         TIGR00657 308 vsgttmkpgilaevfgalaeakvnvdlilqsss...etsisfvvdkedadkakellkkkvkeekaleevevekklal 381
                                       v g++++pgi+ +++g +a+a+++vd+i+q+++   +t  sf+v+++++ ka ++l+ +vk++   +e+  ++k ++
  lcl|FitnessBrowser__PS:Dsui_2134 268 VLGVPDRPGIAYQILGPIADANIDVDMIIQNVGvdgTTDFSFTVNRSEYTKAMAVLE-QVKQHVGAREIVGDNKTCK 343
                                       ********************************9654444****************95.6****************** PP

                         TIGR00657 382 vslvGagmksapgvaakifeaLaeeniniemissseikisvvvdekdaekavealheklv 441
                                       vs vG gm+s+pgva+++f +Laee+ini+mis+seikisvv+dek+ e av+ lh+ + 
  lcl|FitnessBrowser__PS:Dsui_2134 344 VSAVGVGMRSHPGVASQMFRTLAEEGINIQMISTSEIKISVVIDEKYLELAVRILHKTFG 403
                                       *********************************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (407 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: 0.06u 0.00s 00:00:00.06 Elapsed: 00:00:00.06
# Mc/sec: 2.63
//
[ok]

This GapMind analysis is from Apr 09 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