Alignments for a candidate for asp-kinase in Steroidobacter denitrificans DSM 18526

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Steroidobacter denitrificans DSM 18526

Align aspartate kinase / diaminopimelate decarboxylase (EC 4.1.1.20; EC 2.7.2.4) (characterized)
to candidate WP_083536563.1 ACG33_RS07605 diaminopimelate decarboxylase

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



>NCBI__GCF_001579945.1:WP_083536563.1
          Length = 875

 Score =  810 bits (2092), Expect = 0.0
 Identities = 428/857 (49%), Positives = 576/857 (67%), Gaps = 11/857 (1%)

Query: 1   MKFGGTSVATLPRWQNIRELVASRRAEGARVLVVVSALTGITDALKQMCAQEDKGKRVEA 60
           +KFGGTSV++   W+NI +++  R AEG R LVV SAL+GITD L+Q+ +          
Sbjct: 25  LKFGGTSVSSAANWKNIADVLRERLAEGLRPLVVHSALSGITDRLEQLLSLAISNDWAPV 84

Query: 61  ARAIAQRHYDLLDHMQLAVPATLAERLSELAMLAEDGPGAMGELA--WAALVQAHGELMS 118
              I QRH DL   + +     L E+   L  +A  G   +GE++    A V A GELM+
Sbjct: 85  MDQIEQRHRDLARDLGVIPSPDLEEQFKRLRQIAS-GVALVGEVSERLRARVLAQGELMA 143

Query: 119 SALGAAFLSHAGLPTEWLDARDCLAAVALPNQNERTKLLSAMVEARPDPALNARLAELGE 178
           + LGAAFL+  GL  +W+DAR  L +    + + R   LSA     PD  L  R +  G 
Sbjct: 144 TRLGAAFLATQGLDVQWIDARTVLKSEPRAHASLRASYLSATCAYEPDHLLQQRWSSSGS 203

Query: 179 VFITQGFIAREAQGRTVLLGRGGSDTSASYFGALLKAQRVEIWTDVAGMFTANPRQVPGA 238
           V+I+QGFIA + +G TVLLGRGGSDTSASYF A L+A R+EIWTDV GMF+ANPR VP A
Sbjct: 204 VWISQGFIASDEKGETVLLGRGGSDTSASYFAAKLQACRLEIWTDVPGMFSANPRAVPAA 263

Query: 239 RLLQRLDYEEAQEIASTGAKVLHPRCLSPLREPRVPMLIKDTNRPELEGTVIGPEVREHA 298
           RLL+ L+Y+EAQEIAS+GAKVLHPRC+ P+++  +P+ +  T  P+LEGTVI       A
Sbjct: 264 RLLRSLEYDEAQEIASSGAKVLHPRCVMPVKQYGIPLHVFATQTPKLEGTVITAHGGNVA 323

Query: 299 PSVKAISARKGITLVSMESVGMWQQVGFLADVFAQFKQHGLSVDLIGSAETNVTVSLDPT 358
             VKA++ ++ ITLV+ME+VGMW  VGFLAD F  FK HGLS+DL+ ++ETNVTVSLDP 
Sbjct: 324 AQVKAVTMKRNITLVTMETVGMWHSVGFLADAFKVFKDHGLSIDLVSTSETNVTVSLDPA 383

Query: 359 ENLLDSDAIAALASDLAKVCRVKVIAPCAAITLVGRGMRSMLHTLSGVLAEFGQIRVHLI 418
            N +D   +  L  DL ++CRV++I PCAA++LVGR +R++LH L   L  F + +++L+
Sbjct: 384 ANSMDKATMDGLILDLGRICRVELIGPCAAVSLVGRNIRAILHRLGEALELFEEQKIYLV 443

Query: 419 SQSSNNLNLTFVVDENVVDDLLPHLHELLIAAGALRTDDSALFGPSWQALYGS-GEVAAP 477
           +Q++N+LN+TFV+DE+  D L+  LHE+ I      T D  L GP+W+ LY   G+V   
Sbjct: 444 TQAANDLNITFVIDEDQGDRLVARLHEIAIRK---MTADRVL-GPTWEELYSPIGKVRGT 499

Query: 478 AASWWRTAERERLLRLGAERTPRYVYHLPTVRQQARELKSLGAVDRLHYAVKANTHPAIL 537
              WW    RE LL LG E    +VY   T++ +A  L++L  +D + YA+KAN HP IL
Sbjct: 500 EGQWWH-QRREELLALGREHGAAFVYDRSTLQSRAEALQALPGIDAVFYALKANWHPDIL 558

Query: 538 KALAEEGFGFECVSPGELKAVLAAVP--ESAPLLFTPNFAPRADYEWALTTRATISLDAL 595
           +   ++G GFECVS  E++ VL  +P  +   +LFTPNFAPR++Y WAL     ++LD L
Sbjct: 559 RLFHDQGLGFECVSQREVEHVLNILPDIDRRRILFTPNFAPRSEYAWALQQGIVLTLDNL 618

Query: 596 YQLENWGELFRGREIVLRVDLGRGLGHHEKVRTGGSGSKFGLPVELVDSFLRLADAHGVI 655
           Y L+ W  LF GREI +R+D G G GHH+KVRT G  SKFG+P+  +D    L ++ GV 
Sbjct: 619 YPLKAWPNLFTGREIFIRIDTGHGRGHHDKVRTAGVHSKFGVPMFELDELESLVESSGVT 678

Query: 656 VRGLHAHLGSGILDEGHWGEVYGQLASLAERIGSVAFLDIGGGLGVPSHPGEARLDIAAL 715
           V GLHAH GSG+ +  +W  +   LA+LA R+ SV  +D+GGGLGVP   G+  + +A  
Sbjct: 679 VIGLHAHAGSGVFNVDNWASIGTTLATLARRLKSVRIVDLGGGLGVPERLGQPGIVLADF 738

Query: 716 DRVLRSVKAAYPHYQLWMEPGRYLVADAGVLLARVTQQKGKGSWRYLGVDTGMNSLIRPA 775
             ++ +++AAYP   LW+EPGRYLVA+AGVLLA+VTQ KGKG   Y+GV TGMNSLIRPA
Sbjct: 739 AAMIEALRAAYPGLALWIEPGRYLVAEAGVLLAQVTQLKGKGEVHYIGVATGMNSLIRPA 798

Query: 776 LYEAWHEIVNLTRLDEPATGLFQVVGPICESGDVLGTDRRLPEAQEGDVVLVAQAGAYGK 835
           LY A HEI+NL+RL+E  T +  VVGPICESGDVLG +R LP ++EGDV+L+A AGAYG+
Sbjct: 799 LYGAHHEILNLSRLEEAPTEIVNVVGPICESGDVLGAERLLPPSEEGDVLLIATAGAYGR 858

Query: 836 VMSSPYNMRDEAEEVIL 852
            MSS YN+R+ A E ++
Sbjct: 859 AMSSCYNLREPAREFMI 875


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: 1845
Number of extensions: 77
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: 853
Length of database: 875
Length adjustment: 42
Effective length of query: 811
Effective length of database: 833
Effective search space:   675563
Effective search space used:   675563
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 WP_083536563.1 ACG33_RS07605 (diaminopimelate decarboxylase)
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.14366.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-94  303.2   0.0    2.5e-94  302.8   0.0    1.1  1  lcl|NCBI__GCF_001579945.1:WP_083536563.1  ACG33_RS07605 diaminopimelate de


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001579945.1:WP_083536563.1  ACG33_RS07605 diaminopimelate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  302.8   0.0   2.5e-94   2.5e-94       2     438 ..      21     470 ..      20     473 .. 0.88

  Alignments for each domain:
  == domain 1  score: 302.8 bits;  conditional E-value: 2.5e-94
                                 TIGR00657   2 aliVqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseeekeliekir 70 
                                               +++V+KFGGtSv ++ + k++a+ + ++ ++g  ++VV SA +g+Td+L +l + + s++ + ++++i+
  lcl|NCBI__GCF_001579945.1:WP_083536563.1  21 NWVVLKFGGTSVSSAANWKNIADVLRERLAEGLRPLVVHSALSGITDRLEQLLSLAISNDWAPVMDQIE 89 
                                               79***********************************************************99****** PP

                                 TIGR00657  71 ekhlealeela...sqalkeklkallekeleevkk.....ereldlilsvGEklSaallaaaleelgvk 131
                                               ++h + +  l    s+ l+e++k+l +     v       er ++++l+ GE ++++l aa l ++g  
  lcl|NCBI__GCF_001579945.1:WP_083536563.1  90 QRHRDLARDLGvipSPDLEEQFKRLRQ-IASGVALvgevsERLRARVLAQGELMATRLGAAFLATQG-L 156
                                               ***999998765434445555555433.222222246688***************************.8 PP

                                 TIGR00657 132 avsllgaeagiltdsefgrAk.......vleeikterlekl.leegiivvvaGFiGatekgeittLGRG 192
                                               +v++++a+ ++ ++ + + +        + + +  + l++   + g + + +GFi+++ekge+++LGRG
  lcl|NCBI__GCF_001579945.1:WP_083536563.1 157 DVQWIDARTVLKSEPRAHASLrasylsaTCAYEPDHLLQQRwSSSGSVWISQGFIASDEKGETVLLGRG 225
                                               8888888888877644332222333442133333333333304455*********************** PP

                                 TIGR00657 193 GSDltAallAaalkAdeveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepam 261
                                               GSD++A+  Aa l+A ++ei+tDV+G ++a Pr vp Ar+l ++ y+Ea+E+as+GakvLhpr++ p++
  lcl|NCBI__GCF_001579945.1:WP_083536563.1 226 GSDTSASYFAAKLQACRLEIWTDVPGMFSANPRAVPAARLLRSLEYDEAQEIASSGAKVLHPRCVMPVK 294
                                               ********************************************************************* PP

                                 TIGR00657 262 rakipivvkstfnpeaeGTlivakskseeepavkalsldknqalvsvsgttmk..pgilaevfgalaea 328
                                               +++ip++v  t+ p+ eGT+i+a+   + + +vka+++++n +lv+++ ++m   +g+la+ f+  +++
  lcl|NCBI__GCF_001579945.1:WP_083536563.1 295 QYGIPLHVFATQTPKLEGTVITAHGG-NVAAQVKAVTMKRNITLVTMETVGMWhsVGFLADAFKVFKDH 362
                                               ************************87.6679*********************999************** PP

                                 TIGR00657 329 kvnvdlilqsssetsisfvvdkedadkakellkkkvkeekaleevevekklalvslvGagmksapgvaa 397
                                               + ++dl++  +set+++  +d    +  k+ ++  ++++  +++ve+    a vslvG +++     ++
  lcl|NCBI__GCF_001579945.1:WP_083536563.1 363 GLSIDLVS--TSETNVTVSLDPAANSMDKATMDGLILDLGRICRVELIGPCAAVSLVGRNIRAILHRLG 429
                                               ********..7778888888877766666667789********************************** PP

                                 TIGR00657 398 kifeaLaeeniniemissseikisvvvdekdaekavealhe 438
                                               +++e  +e++i  +  ++++ +i++v+de++++++v  lhe
  lcl|NCBI__GCF_001579945.1:WP_083536563.1 430 EALELFEEQKIYLVTQAANDLNITFVIDEDQGDRLVARLHE 470
                                               ****************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (875 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: 20.81
//
[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