Alignments for a candidate for asp-kinase in Dyella japonica UNC79MFTsu3.2

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Dyella japonica UNC79MFTsu3.2

Align aspartate kinase / diaminopimelate decarboxylase (EC 4.1.1.20; EC 2.7.2.4) (characterized)
to candidate N515DRAFT_4002 N515DRAFT_4002 aspartate kinase

Query= reanno::Dyella79:N515DRAFT_4002
         (853 letters)



>FitnessBrowser__Dyella79:N515DRAFT_4002
          Length = 853

 Score = 1678 bits (4345), Expect = 0.0
 Identities = 853/853 (100%), Positives = 853/853 (100%)

Query: 1   MKFGGTSVATLPRWQNIRELVASRRAEGARVLVVVSALTGITDALKQMCAQEDKGKRVEA 60
           MKFGGTSVATLPRWQNIRELVASRRAEGARVLVVVSALTGITDALKQMCAQEDKGKRVEA
Sbjct: 1   MKFGGTSVATLPRWQNIRELVASRRAEGARVLVVVSALTGITDALKQMCAQEDKGKRVEA 60

Query: 61  ARAIAQRHYDLLDHMQLAVPATLAERLSELAMLAEDGPGAMGELAWAALVQAHGELMSSA 120
           ARAIAQRHYDLLDHMQLAVPATLAERLSELAMLAEDGPGAMGELAWAALVQAHGELMSSA
Sbjct: 61  ARAIAQRHYDLLDHMQLAVPATLAERLSELAMLAEDGPGAMGELAWAALVQAHGELMSSA 120

Query: 121 LGAAFLSHAGLPTEWLDARDCLAAVALPNQNERTKLLSAMVEARPDPALNARLAELGEVF 180
           LGAAFLSHAGLPTEWLDARDCLAAVALPNQNERTKLLSAMVEARPDPALNARLAELGEVF
Sbjct: 121 LGAAFLSHAGLPTEWLDARDCLAAVALPNQNERTKLLSAMVEARPDPALNARLAELGEVF 180

Query: 181 ITQGFIAREAQGRTVLLGRGGSDTSASYFGALLKAQRVEIWTDVAGMFTANPRQVPGARL 240
           ITQGFIAREAQGRTVLLGRGGSDTSASYFGALLKAQRVEIWTDVAGMFTANPRQVPGARL
Sbjct: 181 ITQGFIAREAQGRTVLLGRGGSDTSASYFGALLKAQRVEIWTDVAGMFTANPRQVPGARL 240

Query: 241 LQRLDYEEAQEIASTGAKVLHPRCLSPLREPRVPMLIKDTNRPELEGTVIGPEVREHAPS 300
           LQRLDYEEAQEIASTGAKVLHPRCLSPLREPRVPMLIKDTNRPELEGTVIGPEVREHAPS
Sbjct: 241 LQRLDYEEAQEIASTGAKVLHPRCLSPLREPRVPMLIKDTNRPELEGTVIGPEVREHAPS 300

Query: 301 VKAISARKGITLVSMESVGMWQQVGFLADVFAQFKQHGLSVDLIGSAETNVTVSLDPTEN 360
           VKAISARKGITLVSMESVGMWQQVGFLADVFAQFKQHGLSVDLIGSAETNVTVSLDPTEN
Sbjct: 301 VKAISARKGITLVSMESVGMWQQVGFLADVFAQFKQHGLSVDLIGSAETNVTVSLDPTEN 360

Query: 361 LLDSDAIAALASDLAKVCRVKVIAPCAAITLVGRGMRSMLHTLSGVLAEFGQIRVHLISQ 420
           LLDSDAIAALASDLAKVCRVKVIAPCAAITLVGRGMRSMLHTLSGVLAEFGQIRVHLISQ
Sbjct: 361 LLDSDAIAALASDLAKVCRVKVIAPCAAITLVGRGMRSMLHTLSGVLAEFGQIRVHLISQ 420

Query: 421 SSNNLNLTFVVDENVVDDLLPHLHELLIAAGALRTDDSALFGPSWQALYGSGEVAAPAAS 480
           SSNNLNLTFVVDENVVDDLLPHLHELLIAAGALRTDDSALFGPSWQALYGSGEVAAPAAS
Sbjct: 421 SSNNLNLTFVVDENVVDDLLPHLHELLIAAGALRTDDSALFGPSWQALYGSGEVAAPAAS 480

Query: 481 WWRTAERERLLRLGAERTPRYVYHLPTVRQQARELKSLGAVDRLHYAVKANTHPAILKAL 540
           WWRTAERERLLRLGAERTPRYVYHLPTVRQQARELKSLGAVDRLHYAVKANTHPAILKAL
Sbjct: 481 WWRTAERERLLRLGAERTPRYVYHLPTVRQQARELKSLGAVDRLHYAVKANTHPAILKAL 540

Query: 541 AEEGFGFECVSPGELKAVLAAVPESAPLLFTPNFAPRADYEWALTTRATISLDALYQLEN 600
           AEEGFGFECVSPGELKAVLAAVPESAPLLFTPNFAPRADYEWALTTRATISLDALYQLEN
Sbjct: 541 AEEGFGFECVSPGELKAVLAAVPESAPLLFTPNFAPRADYEWALTTRATISLDALYQLEN 600

Query: 601 WGELFRGREIVLRVDLGRGLGHHEKVRTGGSGSKFGLPVELVDSFLRLADAHGVIVRGLH 660
           WGELFRGREIVLRVDLGRGLGHHEKVRTGGSGSKFGLPVELVDSFLRLADAHGVIVRGLH
Sbjct: 601 WGELFRGREIVLRVDLGRGLGHHEKVRTGGSGSKFGLPVELVDSFLRLADAHGVIVRGLH 660

Query: 661 AHLGSGILDEGHWGEVYGQLASLAERIGSVAFLDIGGGLGVPSHPGEARLDIAALDRVLR 720
           AHLGSGILDEGHWGEVYGQLASLAERIGSVAFLDIGGGLGVPSHPGEARLDIAALDRVLR
Sbjct: 661 AHLGSGILDEGHWGEVYGQLASLAERIGSVAFLDIGGGLGVPSHPGEARLDIAALDRVLR 720

Query: 721 SVKAAYPHYQLWMEPGRYLVADAGVLLARVTQQKGKGSWRYLGVDTGMNSLIRPALYEAW 780
           SVKAAYPHYQLWMEPGRYLVADAGVLLARVTQQKGKGSWRYLGVDTGMNSLIRPALYEAW
Sbjct: 721 SVKAAYPHYQLWMEPGRYLVADAGVLLARVTQQKGKGSWRYLGVDTGMNSLIRPALYEAW 780

Query: 781 HEIVNLTRLDEPATGLFQVVGPICESGDVLGTDRRLPEAQEGDVVLVAQAGAYGKVMSSP 840
           HEIVNLTRLDEPATGLFQVVGPICESGDVLGTDRRLPEAQEGDVVLVAQAGAYGKVMSSP
Sbjct: 781 HEIVNLTRLDEPATGLFQVVGPICESGDVLGTDRRLPEAQEGDVVLVAQAGAYGKVMSSP 840

Query: 841 YNMRDEAEEVILD 853
           YNMRDEAEEVILD
Sbjct: 841 YNMRDEAEEVILD 853


Lambda     K      H
   0.319    0.135    0.398 

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: 2350
Number of extensions: 90
Number of successful extensions: 1
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: 853
Length of database: 853
Length adjustment: 42
Effective length of query: 811
Effective length of database: 811
Effective search space:   657721
Effective search space used:   657721
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (26.2 bits)

Align candidate N515DRAFT_4002 N515DRAFT_4002 (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.17050.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
    1.4e-96  310.2   0.0    1.7e-96  309.9   0.0    1.1  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_4002  N515DRAFT_4002 aspartate kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_4002  N515DRAFT_4002 aspartate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  309.9   0.0   1.7e-96   1.7e-96       6     441 ..       1     448 [.       1     449 [. 0.87

  Alignments for each domain:
  == domain 1  score: 309.9 bits;  conditional E-value: 1.7e-96
                                    TIGR00657   6 qKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseeekeliekire 71 
                                                  +KFGGtSv++  r +++ ++v +++++g  v+VVvSA  g+TdaL +++ + +++++ e +++i +
  lcl|FitnessBrowser__Dyella79:N515DRAFT_4002   1 MKFGGTSVATLPRWQNIRELVASRRAEGARVLVVVSALTGITDALKQMCAQEDKGKRVEAARAIAQ 66 
                                                  7***************************************************************** PP

                                    TIGR00657  72 khlealeelasqalkeklkallekeleevkk.......ereldlilsvGEklSaallaaaleelgv 130
                                                  +h++ l++++  + ++  ++l e  +  +          +  +l+ ++GE +S+al aa l++ g 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_4002  67 RHYDLLDHMQLAVPATLAERLSELAMLAE-DgpgamgeLAWAALVQAHGELMSSALGAAFLSHAG- 130
                                                  ********996455555555555555544.3599999778889999*******************. PP

                                    TIGR00657 131 kavsllgaeagiltd...sefgrAk.....vleeikterleklleegiivvvaGFiGatekgeitt 188
                                                     ++l+a+  + +    ++ +r k     v +  + +  + l e g + +++GFi+ + +g++++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_4002 131 LPTEWLDARDCLAAValpNQNERTKllsamVEARPDPALNARLAELGEVFITQGFIAREAQGRTVL 196
                                                  56666666655444311134444444443244444445555556667******************* PP

                                    TIGR00657 189 LGRGGSDltAallAaalkAdeveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhp 254
                                                  LGRGGSD++A+  +a+lkA++vei+tDV G +ta Pr+vp Ar+l+ ++yeEa+E+as GakvLhp
  lcl|FitnessBrowser__Dyella79:N515DRAFT_4002 197 LGRGGSDTSASYFGALLKAQRVEIWTDVAGMFTANPRQVPGARLLQRLDYEEAQEIASTGAKVLHP 262
                                                  ****************************************************************** PP

                                    TIGR00657 255 rtlepamrakipivvkstfnpeaeGTlivakskseeepavkalsldknqalvsvsgttmk..pgil 318
                                                  r+l p+++  +p+++k+t  pe eGT+i+++   e++p vka+s +k  +lvs+++++m   +g+l
  lcl|FitnessBrowser__Dyella79:N515DRAFT_4002 263 RCLSPLREPRVPMLIKDTNRPELEGTVIGPEVR-EHAPSVKAISARKGITLVSMESVGMWqqVGFL 327
                                                  *******************************77.888*********************9888**** PP

                                    TIGR00657 319 aevfgalaeakvnvdlilqsssetsisfvvdked..adkakellkkkvkeekaleevevekklalv 382
                                                  a+vf + ++++ +vdli   s et+++  +d ++  +d+ +      + +++++++v+v    a +
  lcl|FitnessBrowser__Dyella79:N515DRAFT_4002 328 ADVFAQFKQHGLSVDLIG--SAETNVTVSLDPTEnlLDSDAI--AALASDLAKVCRVKVIAPCAAI 389
                                                  *****************9..6677877777766633443333..356899**************** PP

                                    TIGR00657 383 slvGagmksapgvaakifeaLaeeniniemis..sseikisvvvdekdaekavealheklv 441
                                                  +lvG gm+s    ++ ++++  +  i ++ is  s++ ++++vvde+ ++ ++  lhe l+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_4002 390 TLVGRGMRSMLHTLSGVLAEFGQ--IRVHLISqsSNNLNLTFVVDENVVDDLLPHLHELLI 448
                                                  *********99999999999999..9999999666778999****************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (853 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 20.22
//
[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