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 Bifunctional aspartokinase/homoserine dehydrogenase 2, chloroplastic; AK-HD 2; AK-HSDH 2; Beta-aspartyl phosphate homoserine 2; EC 2.7.2.4; EC 1.1.1.3 (characterized)
to candidate WP_066920368.1 ACG33_RS08530 bifunctional aspartate kinase/homoserine dehydrogenase I

Query= SwissProt::O81852
         (916 letters)



>NCBI__GCF_001579945.1:WP_066920368.1
          Length = 826

 Score =  741 bits (1912), Expect = 0.0
 Identities = 387/831 (46%), Positives = 538/831 (64%), Gaps = 14/831 (1%)

Query: 87  EMWSVHKFGGTCVGNSQRIRNVAEVIINDNSERKLVVVSAMSKVTDMMYDLIRKAQSRDD 146
           E W VHKFGG+ V ++  +  VA ++  D   R  +V+SA   VTD +  ++  A+ R+D
Sbjct: 5   ERWRVHKFGGSSVADAVCMERVARILEQDPHPRMGIVLSACRGVTDTLLGVVAAAERRED 64

Query: 147 SYLSALEAVLEKHRLTARDLLDGDDLASFLSHLHNDISNLKAMLRAIYIAGHASESFSDF 206
                +E +  +H   A  LL  +    F+S L  D  ++ ++L  I +   +S+   D 
Sbjct: 65  -VTGRIEELRRRHETIADTLLPEEARQEFMSLLTQDCRDIASILHTISLIRFSSQMVRDL 123

Query: 207 VAGHGELWSAQMLSYVVRKTGL---ECKWMDTRDVLIVNPTSSNQVDPDFGESEKRLDKW 263
           VAG+GE+WS ++ S  +R  G    + +W+D R+V++V   S       + ES++ +D+ 
Sbjct: 124 VAGYGEIWSTRLFSAYLRHRGRRPGQVQWVDAREVVVVEWGSLGP-GVRWTESQENMDRL 182

Query: 264 FSLNPSKIIIATGFIASTPQNIPTTLKRDGSDFSAAIMGALLRARQVTIWTDVDGVYSAD 323
               P+ +II TGFIA  P+ + TTL R+GSDFS +I GALL A Q+ IWTDVDGV SAD
Sbjct: 183 VPSGPATLII-TGFIARDPKGLQTTLGRNGSDFSGSIFGALLNAEQIHIWTDVDGVLSAD 241

Query: 324 PRKVNEAVILQTLSYQEAWEMSYFGANVLHPRTIIPVMRYNIPIVIRNIFNLSAPGTIIC 383
           PR V EA ++ +LSY EA E++YFGA V+HP+T+ P +R  IPI IRN F    PGT+IC
Sbjct: 242 PRLVPEAKVIDSLSYSEAMELAYFGAKVIHPQTMAPAVRKGIPIWIRNSFAPEKPGTLIC 301

Query: 384 QPPEDDYDLKLTTPVKGFATIDNLALINVEGTGMAGVPGTASDIFGCVKDVGANVIMISQ 443
             P           VKG   ID +AL+N+EG GM GVPGTA  +FG ++D G +VI+ISQ
Sbjct: 302 ANPSSQL------AVKGITCIDRVALVNLEGAGMIGVPGTAHRLFGALRDHGISVILISQ 355

Query: 444 ASSEHSVCFAVPEKEVNAVSEALRSRFSEALQAGRLSQIEVIPNCSILAAVGQKMASTPG 503
            SSEHS+CFA+PE E       +R  F   LQ G +  +EV  NCSILA VG  MA + G
Sbjct: 356 GSSEHSICFAIPEAESVRAETVVRQAFERELQDGHIQSVEVEDNCSILAVVGDGMAGSHG 415

Query: 504 VSCTLFSALAKANINVRAISQGCSEYNVTVVIKREDSVKALRAVHSRFFLSRTTLAMGIV 563
            +  +F AL  A ++VRAI+QG SE N++ VI  + S +ALR+VHS F+LS  T+++G++
Sbjct: 416 AAAKVFGALGAAAVSVRAIAQGASERNISAVIDGKHSARALRSVHSSFYLSPHTISIGLI 475

Query: 564 GPGLIGATLLDQLRDQAAVLKQEFNIDLRVLGITGSKKMLLSDIGIDLSRWRELLNEKGT 623
           GPGL+G  LLDQ   Q   L +E  +DLRV GI GS +M L+   I L RWR+       
Sbjct: 476 GPGLVGGVLLDQFASQVERLSRELKVDLRVRGIMGSSRMHLAGHEIPLGRWRDAFGAHQE 535

Query: 624 EADLDKFTQQVHGNHFIPNSVVVDCTADSAIASRYYDWLRKGIHVITPNKKANSGPLDQY 683
            AD+ +F Q V+ +H +P+++++DCT+   +A  Y  WL  GIHV+TPNKKANS  L  Y
Sbjct: 536 PADMARFVQHVNADH-LPHAIIIDCTSSLEVAQHYPAWLAGGIHVVTPNKKANSADLPFY 594

Query: 684 LKLRDLQRKSYTHYFYEATVGAGLPIISTLRGLLETGDKILRIEGICSGTLSYLFNNFVG 743
           L+L++  R+  THY YEATVGAGLPI+ TLR L  TGD+I RIEGI SGTLSYLFN + G
Sbjct: 595 LRLQEASRQGNTHYMYEATVGAGLPIVQTLRDLHGTGDRIQRIEGILSGTLSYLFNVWDG 654

Query: 744 DRSFSEVVTEAKNAGFTEPDPRDDLSGTDVARKVIILARESGLKLDLADLPIRSLVPEPL 803
            + FS+V+  A+  G+TEPDPRDDLSG D ARK+IILARE GL+L++ D+ +  LVPE L
Sbjct: 655 SQPFSQVLHTARAKGYTEPDPRDDLSGIDFARKIIILAREMGLRLEMQDVQLEGLVPEAL 714

Query: 804 KGCTSVEEFMEKLPQYDGDLAKERLDAENSGEVLRYVGVVDAVNQKGTVELRRYKKEHPF 863
             C + +EF+++LP++D  +A+    A+  G VLRYVG +DA +   +V L   ++ H F
Sbjct: 715 TSC-APQEFLDRLPEFDAPIAERLRAAQARGRVLRYVGAIDAASSSASVGLVELERSHTF 773

Query: 864 AQLAGSDNIIAFTTTRYKDHPLIVRGPGAGAQVTAGGIFSDILRLASYLGA 914
           A +  +DN++ F T RY  +PLIV+GPGAG  VTAGG+F+D+LR+ +YLGA
Sbjct: 774 ANINLTDNVVRFVTQRYNQNPLIVQGPGAGPDVTAGGVFADLLRVCAYLGA 824


Lambda     K      H
   0.319    0.135    0.394 

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: 1712
Number of extensions: 72
Number of successful extensions: 8
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: 916
Length of database: 826
Length adjustment: 42
Effective length of query: 874
Effective length of database: 784
Effective search space:   685216
Effective search space used:   685216
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_066920368.1 ACG33_RS08530 (bifunctional aspartate kinase/homoserine dehydrogenase I)
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.26911.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     5e-113  364.4   0.0   6.1e-113  364.1   0.0    1.1  1  lcl|NCBI__GCF_001579945.1:WP_066920368.1  ACG33_RS08530 bifunctional aspar


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001579945.1:WP_066920368.1  ACG33_RS08530 bifunctional aspartate kinase/homoserine dehydrogenase I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  364.1   0.0  6.1e-113  6.1e-113       5     440 ..       9     463 ..       5     465 .. 0.95

  Alignments for each domain:
  == domain 1  score: 364.1 bits;  conditional E-value: 6.1e-113
                                 TIGR00657   5 VqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee.keliekirek 72 
                                               V KFGG+Sv+++  +++va+i++++ + +  + +V+SA  gvTd L+ ++  ++++e+ +  ie++r++
  lcl|NCBI__GCF_001579945.1:WP_066920368.1   9 VHKFGGSSVADAVCMERVARILEQDPHPR--MGIVLSACRGVTDTLLGVVAAAERREDvTGRIEELRRR 75 
                                               99*********************999666..889******************9999988889******* PP

                                 TIGR00657  73 hlealeelasqalkeklkallekeleevkk............ereldlilsvGEklSaallaaaleelg 129
                                               h++++++l +++ ++++ +ll +    + +            +  +dl+  +GE  S++l++a+l+++g
  lcl|NCBI__GCF_001579945.1:WP_066920368.1  76 HETIADTLLPEEARQEFMSLLTQDCRDIASilhtislirfssQMVRDLVAGYGEIWSTRLFSAYLRHRG 144
                                               *********888888888888888888888899*******99999************************ PP

                                 TIGR00657 130 v..kavsllgaeagiltd.sefgrAkvleeikterleklleeg.iivvvaGFiGatekgeittLGRGGS 194
                                                   +v++++a+++++ + +++g  +   ++++e+++ l+  g    +++GFi+ ++kg  ttLGR+GS
  lcl|NCBI__GCF_001579945.1:WP_066920368.1 145 RrpGQVQWVDAREVVVVEwGSLGPGV-RWTESQENMDRLVPSGpATLIITGFIARDPKGLQTTLGRNGS 212
                                               98779999999998887725666666.9999999999999999999*********************** PP

                                 TIGR00657 195 DltAallAaalkAdeveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamra 263
                                               D++ ++ +a+l+A++++i+tDVdG+++aDPr+vpeA+ +d++sy Ea+ELa++Gakv+hp+t+ pa+r+
  lcl|NCBI__GCF_001579945.1:WP_066920368.1 213 DFSGSIFGALLNAEQIHIWTDVDGVLSADPRLVPEAKVIDSLSYSEAMELAYFGAKVIHPQTMAPAVRK 281
                                               ********************************************************************* PP

                                 TIGR00657 264 kipivvkstfnpeaeGTlivakskseeepavkalsldknqalvsvsgttmk..pgilaevfgalaeakv 330
                                               +ipi ++++f pe++GTli+a+  ++++ avk+++  +  alv+++g++m   pg++ ++fgal+++++
  lcl|NCBI__GCF_001579945.1:WP_066920368.1 282 GIPIWIRNSFAPEKPGTLICAN--PSSQLAVKGITCIDRVALVNLEGAGMIgvPGTAHRLFGALRDHGI 348
                                               **********************..55779**************************************** PP

                                 TIGR00657 331 nvdlilqsssetsisfvvdkedadkakellk...kkvkeekaleevevekklalvslvGagmksapgva 396
                                               +v+li+q sse+si f++++ +  +a+++ +   + ++++  +++veve++ ++ ++vG+gm++  g a
  lcl|NCBI__GCF_001579945.1:WP_066920368.1 349 SVILISQGSSEHSICFAIPEAESVRAETVVRqafERELQDGHIQSVEVEDNCSILAVVGDGMAGSHGAA 417
                                               **********************99999988767777889999*************************** PP

                                 TIGR00657 397 akifeaLaeeniniemis..sseikisvvvdekdaekavealhekl 440
                                               ak+f aL  + +++++i+  +se++is v+d+k + +a++ +h+ +
  lcl|NCBI__GCF_001579945.1:WP_066920368.1 418 AKVFGALGAAAVSVRAIAqgASERNISAVIDGKHSARALRSVHSSF 463
                                               ******************9************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (826 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 10.99
//
[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