Alignments for a candidate for asp-kinase in Stenotrophomonas chelatiphaga DSM 21508

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Stenotrophomonas chelatiphaga DSM 21508

Align Bifunctional aspartokinase/homoserine dehydrogenase 1, chloroplastic; AK-HD 1; AK-HSDH 1; Beta-aspartyl phosphate homoserine 1; EC 2.7.2.4; EC 1.1.1.3 (characterized)
to candidate WP_083491847.1 ABB28_RS00495 bifunctional aspartate kinase/homoserine dehydrogenase I

Query= SwissProt::Q9SA18
         (911 letters)



>NCBI__GCF_001431535.1:WP_083491847.1
          Length = 837

 Score =  648 bits (1671), Expect = 0.0
 Identities = 365/824 (44%), Positives = 514/824 (62%), Gaps = 13/824 (1%)

Query: 86  VHKFGGTCVGNSERIKDVAAVVVKDDSERKLVVVSAMSKVTDMMYDLIHRAESRDDSYLS 145
           VHKFGGT V +++  + VA ++       ++ VVSAM  VTD +  L   A + D  +  
Sbjct: 25  VHKFGGTSVADADCYRHVARLLQARPEALQVTVVSAMKGVTDALIALARLAAAGDAQWRE 84

Query: 146 ALSGVLEKHRATAVDLLDGDELSSFLARLNDDINNLKAMLRAIYIAGHATESFSDFVVGH 205
               +  +HR  A  LL G+   + +  L+   + L  +L A+ + G   E   D V G 
Sbjct: 85  DWHDLRARHRGAAASLL-GEHAGASVEWLDARFDELAELLAALAVIGGLPEEVLDRVQGL 143

Query: 206 GELWSAQMLAAVVRKSGLDCTWMDARDVLVVIPTSSNQVDPDFVESEKRLEKWFTQNSAK 265
           GE+ SA +L    + SG  C  +DAR+VLVV       V+ D+  S +RL  W   N  +
Sbjct: 144 GEVCSAHLLGQHFQASGEPCAVLDAREVLVV-EHGELGVNVDWETSAQRLHAWRQANVQQ 202

Query: 266 IIIATGFIASTPQNIPTTLKRDGSDFSAAIMSALFRSHQLTIWTDVDGVYSADPRKVSEA 325
            I+ TGFIA   ++  TTL R+GSD+S AI +ALF + +L IWTDVDGV SADPR V EA
Sbjct: 203 RIVVTGFIARDRRDRITTLGRNGSDYSGAIFAALFNADELQIWTDVDGVLSADPRLVPEA 262

Query: 326 VVLKTLSYQEAWEMSYFGANVLHPRTIIPVMKYDIPIVIRNIFNLSAPGTMICRQIDDED 385
           V L+ LSY EA E++YFGA V+HP+T+ P ++  +PI+IRN F    PGT I  +     
Sbjct: 263 VQLEALSYDEACELAYFGAKVVHPQTMSPAIQRGLPILIRNTFQPEHPGTRITAERS--- 319

Query: 386 GFKLDAPVKGFATIDNLALVNVEGTGMAGVPGTASAIFSAVKEVGANVIMISQASSEHSV 445
              +  P+KG      LA++N+EGTG+ GVPGTA  +FSA+++   +V+MISQ SSEHS+
Sbjct: 320 ---VRGPIKGLTLSAELAVLNLEGTGLIGVPGTAERVFSALRQAQVSVVMISQGSSEHSI 376

Query: 446 CFAVPEKEVKAVSEALNSRFRQALAGGRLSQIEIIPNCSILAAVGQKMASTPGVSATFFN 505
           C  V   E +   +AL   F   LA G++ ++++    S+LAAVG  MA  PGV+A  F 
Sbjct: 377 CCVVRGNESERGRDALLQAFAHELAVGQVQRVQLRGGVSVLAAVGDGMAGQPGVAARLFE 436

Query: 506 ALAKANINIRAIAQGCSEFNITVVVKREDCIRALRAVHSRFYLSRTTLAVGIIGPGLIGG 565
           +L +A +NI AIAQG SE NI+V V   D  RALRA H+ F+LS  T AVG+IGPG +G 
Sbjct: 437 SLGRAQVNILAIAQGSSERNISVAVDSGDATRALRAAHAGFWLSPQTFAVGVIGPGNVGA 496

Query: 566 TLLDQIRDQAAVLKEEFKIDLRVIGITGSSKMLMSESGIDLSRWRELMKEEGEKADMEKF 625
            LLDQ++     L  +  IDLR+  +     M ++   +    WR  + +    +D++ F
Sbjct: 497 ALLDQLQAAQPQLLGKANIDLRLRAVASRRGMHLAPRALQ-GPWRAALADAASASDLDAF 555

Query: 626 TQYVKGNHFIPNSVMVDCTADADIASCYYDWLLRGIHVVTPNKKANSGPLDQYLKIRDLQ 685
           T ++   H +P++V++DC+  A++A  Y  WL  GIHVVTPNK+A SGPL +Y  IR   
Sbjct: 556 TAHLLSAH-LPHAVVIDCSGSAEVAGRYEGWLAAGIHVVTPNKQAGSGPLARYQSIRAAA 614

Query: 686 RKSYTHYFYEATVGAGLPIISTLRGLLETGDKILRIEGIFSGTLSYLFNNFVGTRSFSEV 745
             S   + YEATVGAGLP+I+TLR L++TGD++L IEGIFSGTL++LFN F G++ FS +
Sbjct: 615 AASGARFRYEATVGAGLPVITTLRDLVDTGDEVLSIEGIFSGTLAWLFNRFDGSQPFSAL 674

Query: 746 VAEAKQAGFTEPDPRDDLSGTDVARKVTILARESGLKLDLEGLPVQNLVPKPLQACASAE 805
           V +A+  G+TEPDPRDDLSG DVARK+ ILARE+G  L LE + V++LVP+ L+A  S +
Sbjct: 675 VEQARGMGYTEPDPRDDLSGIDVARKLVILAREAGRDLSLEQVQVESLVPEALRA-GSVD 733

Query: 806 EFMEKLPQFDEELSKQREEAEAAGEVLRYVGVVDAVEKKGTVELKRYKKDHPFAQLSGAD 865
            FM++L   D+ L ++ ++A A G VLRYV  + A  +  +V L     DH FA L   D
Sbjct: 734 AFMQRLGDNDDALLQRLQQARARGAVLRYVAALSA--QGASVGLVEIPLDHAFANLKLTD 791

Query: 866 NIIAFTTKRYKEQPLIVRGPGAGAQVTAGGIFSDILRLAFYLGA 909
           N++ F T+RY + PL+V+GPGAG +VTA G+F+D+LR+A   GA
Sbjct: 792 NVVQFRTRRYCDNPLVVQGPGAGPEVTAAGVFADLLRVAAGEGA 835


Lambda     K      H
   0.319    0.134    0.385 

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: 1479
Number of extensions: 55
Number of successful extensions: 9
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: 911
Length of database: 837
Length adjustment: 42
Effective length of query: 869
Effective length of database: 795
Effective search space:   690855
Effective search space used:   690855
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_083491847.1 ABB28_RS00495 (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.29587.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.7e-108  348.0   0.0   6.3e-108  347.6   0.0    1.1  1  lcl|NCBI__GCF_001431535.1:WP_083491847.1  ABB28_RS00495 bifunctional aspar


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_083491847.1  ABB28_RS00495 bifunctional aspartate kinase/homoserine dehydrogenase I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  347.6   0.0  6.3e-108  6.3e-108       3     440 ..      23     477 ..      22     479 .. 0.91

  Alignments for each domain:
  == domain 1  score: 347.6 bits;  conditional E-value: 6.3e-108
                                 TIGR00657   3 liVqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee..kelieki 69 
                                               ++V KFGGtSv++++  ++va++++++   +   v+VvSAm+gvTdaL++la+ +  ++    e  +++
  lcl|NCBI__GCF_001431535.1:WP_083491847.1  23 VVVHKFGGTSVADADCYRHVARLLQARP--EALQVTVVSAMKGVTDALIALARLAAAGDAqwREDWHDL 89 
                                               69**********************9988..445899*******************9999888899999* PP

                                 TIGR00657  70 rekhlealeela.sqalkeklkallekeleevkk............ereldlilsvGEklSaallaaal 125
                                               r++h  a+++l  +   +  +++ l+++++e+ +            e+ ld++  +GE  Sa ll + +
  lcl|NCBI__GCF_001431535.1:WP_083491847.1  90 RARHRGAAASLLgE--HAGASVEWLDARFDELAEllaalavigglpEEVLDRVQGLGEVCSAHLLGQHF 156
                                               **998888887744..3444455555555555555667******************************* PP

                                 TIGR00657 126 eelgvkavsllgaeagiltdsefgrAkvleeikterleklleeg..iivvvaGFiGatekgeittLGRG 192
                                               ++ g +  ++l+a+++++ +   +  +v  e++++rl +  +++  +  vv+GFi+ ++  +ittLGR+
  lcl|NCBI__GCF_001431535.1:WP_083491847.1 157 QASG-EPCAVLDAREVLVVEHGELGVNVDWETSAQRLHAWRQANvqQRIVVTGFIARDRRDRITTLGRN 224
                                               ****.99999999998887655444455888999999888888877889******************** PP

                                 TIGR00657 193 GSDltAallAaalkAdeveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepam 261
                                               GSD++ a+ Aa+ +Ade++i+tDVdG+++aDPr+vpeA +l+ +sy+Ea ELa++Gakv hp+t+ pa+
  lcl|NCBI__GCF_001431535.1:WP_083491847.1 225 GSDYSGAIFAALFNADELQIWTDVDGVLSADPRLVPEAVQLEALSYDEACELAYFGAKVVHPQTMSPAI 293
                                               ********************************************************************* PP

                                 TIGR00657 262 rakipivvkstfnpeaeGTlivakskseeepavkalsldknqalvsvsgttmk..pgilaevfgalaea 328
                                               + + pi++++tf+pe +GT i+a+++++   ++k+l+l+ + a+++++gt+    pg++++vf+al++a
  lcl|NCBI__GCF_001431535.1:WP_083491847.1 294 QRGLPILIRNTFQPEHPGTRITAERSVRG--PIKGLTLSAELAVLNLEGTGLIgvPGTAERVFSALRQA 360
                                               ************************88666..9********************99*************** PP

                                 TIGR00657 329 kvnvdlilqsssetsisfvvdkedadkakellk...kkvkeekaleevevekklalvslvGagmksapg 394
                                               +v+v++i+q sse+si  vv  ++ ++   +l     ++++  ++++v++  ++++ + vG+gm+++pg
  lcl|NCBI__GCF_001431535.1:WP_083491847.1 361 QVSVVMISQGSSEHSICCVVRGNESERGRDALLqafAHELAVGQVQRVQLRGGVSVLAAVGDGMAGQPG 429
                                               *********************99999998888756656677789999********************** PP

                                 TIGR00657 395 vaakifeaLaeeniniemis..sseikisvvvdekdaekavealhekl 440
                                               vaa++fe L ++++ni +i+  sse++isv vd+ da++a++a h+ +
  lcl|NCBI__GCF_001431535.1:WP_083491847.1 430 VAARLFESLGRAQVNILAIAqgSSERNISVAVDSGDATRALRAAHAGF 477
                                               ********************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (837 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: 00:00:00.02
# Mc/sec: 15.28
//
[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