Alignments for a candidate for asp-kinase in Shewanella oneidensis MR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Shewanella oneidensis MR-1

Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate 202522 SO3415 aspartokinase I/homoserine dehydrogenase, threonine-sensitive (NCBI ptt file)

Query= BRENDA::P00561
         (820 letters)



>FitnessBrowser__MR1:202522
          Length = 822

 Score =  906 bits (2342), Expect = 0.0
 Identities = 474/821 (57%), Positives = 590/821 (71%), Gaps = 10/821 (1%)

Query: 1   MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDA 60
           M+V+KFGGTS+AN +RF   ADI+   A    VATVLSAPA +TN L+ M+   + G+D 
Sbjct: 1   MKVMKFGGTSLANWQRFSMAADIVAKAATMEPVATVLSAPATVTNALLEMVNLAVKGEDY 60

Query: 61  LPNISDAERIFAELL-----TGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCP 115
            P I   ER+F  L      +GL++ Q     A L      + A+ +  LHGI+LL +CP
Sbjct: 61  SPVIQHVERVFTSLYQDAVSSGLSSTQSELLFAGLGA----QLARWQDRLHGITLLQECP 116

Query: 116 DSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIA 175
           D I A ++  GE++S A+M  V+ A+G     +DP +  L  G  LES VDIA S  R  
Sbjct: 117 DGICAEIVVAGERLSAALMEQVMLAKGITSAQLDPRKLFLGRGRPLESVVDIAVSKPRFK 176

Query: 176 ASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTC 235
              +    + +M GFTA +E G++V LGRNGSDYSAAVLAACL A  CEIWTDVDGVY  
Sbjct: 177 NLLLDEKRVWVMPGFTAADEDGKVVTLGRNGSDYSAAVLAACLDASSCEIWTDVDGVYNT 236

Query: 236 DPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLI 295
           DPR V DA+LL  +SYQEAMELSYFGAKVLHP+TI PIAQF IPC IKN+ NP APGTL+
Sbjct: 237 DPRVVADAKLLSQLSYQEAMELSYFGAKVLHPKTIAPIAQFHIPCYIKNSFNPDAPGTLV 296

Query: 296 GASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSE 355
               D   L VK ISNL+N  MF VSGPGMKGMVGMA+R  AA+SR+ +SV LITQSS E
Sbjct: 297 SNLADASGLQVKAISNLDNQTMFDVSGPGMKGMVGMASRTLAAISRSGVSVSLITQSSCE 356

Query: 356 YSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAK 415
           YSISFCV  S+  + + A+++EF LE+K  LLEP+ +   LAI+S++GDGMRT +G++A+
Sbjct: 357 YSISFCVATSESAKVKLALEQEFELEIKSDLLEPIEMRHDLAIVSLIGDGMRTHKGVAAR 416

Query: 416 FFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGG 475
           FF ALA+A++NI+AIAQGSSERSIS V+        V   HQ  F+  Q ++VF++G G 
Sbjct: 417 FFQALAQASVNIIAIAQGSSERSISTVIEQRKTKHAVAACHQGFFDVQQYLDVFLVGCGN 476

Query: 476 VGGALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLG 535
           VG  LLEQ+K+Q   LK +HI +RVCG+ NS  +L +  G++L NWQ  LA +++  +L 
Sbjct: 477 VGAGLLEQIKQQAIVLKEQHISIRVCGIVNSSKMLLDSAGIDLNNWQNLLADSQQSSDLP 536

Query: 536 RLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYA 595
            L+  VKE  LLNPV+VDCTSS+ V++QY + +  G HVVTPNKKANT    YY  LR  
Sbjct: 537 ALLAWVKEQQLLNPVLVDCTSSEQVSNQYLEVMNAGMHVVTPNKKANTRDYAYYQALRQT 596

Query: 596 AEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSE 655
           A   RR+FLY+TNVGAGLPVI+NL+ LL AGD+L KF+GILSGSLS+IFGKLDEGMS SE
Sbjct: 597 ALTQRRQFLYETNVGAGLPVIDNLKKLLFAGDKLHKFNGILSGSLSFIFGKLDEGMSLSE 656

Query: 656 ATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDV 715
           AT LARE  +TEPDPRDDLSGMDVARK+LILARE G +LEL+DI ++ VLP  F+  GDV
Sbjct: 657 ATKLAREKCFTEPDPRDDLSGMDVARKVLILAREVGLKLELSDIVVDSVLPESFDDSGDV 716

Query: 716 AAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGE 775
            +FMA L + D   AARVA+A+ +GKVLRYVG I E+G C V+IAEVD  DPL+ VK GE
Sbjct: 717 ESFMARLPEADAAIAARVAEAKAQGKVLRYVGQI-EEGACHVRIAEVDATDPLYSVKGGE 775

Query: 776 NALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSW 816
           NALAFYS YYQP+P VLRGYGAG +VTAAG FAD+LRTL+W
Sbjct: 776 NALAFYSRYYQPIPFVLRGYGAGTEVTAAGAFADVLRTLNW 816


Lambda     K      H
   0.319    0.135    0.384 

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: 1501
Number of extensions: 57
Number of successful extensions: 6
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: 820
Length of database: 822
Length adjustment: 42
Effective length of query: 778
Effective length of database: 780
Effective search space:   606840
Effective search space used:   606840
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 202522 SO3415 (aspartokinase I/homoserine dehydrogenase, threonine-sensitive (NCBI ptt file))
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.3727619.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-126  409.1   0.1   1.7e-126  408.8   0.1    1.1  1  FitnessBrowser__MR1:202522  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__MR1:202522  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  408.8   0.1  1.7e-126  1.7e-126       5     441 ..       3     461 ..       1     462 [. 0.91

  Alignments for each domain:
  == domain 1  score: 408.8 bits;  conditional E-value: 1.7e-126
                   TIGR00657   5 VqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee....keliekirekhlealeelasq 83 
                                 V+KFGGtS++n +r++ +a+iv k+++ + +v++V+SA+a vT+aL+e+++ + ++e+     + +e+++++ ++ + +    
  FitnessBrowser__MR1:202522   3 VMKFGGTSLANWQRFSMAADIVAKAATME-PVATVLSAPATVTNALLEMVNLAVKGEDyspvIQHVERVFTSLYQDAVSSG-- 82 
                                 9*************************777.************************999986665556666665555444444.. PP

                   TIGR00657  84 alkeklkallekeleevkk...............ereldlilsvGEklSaallaaaleelgvkavsllgaeagiltdsefgrA 151
                                  ++++++ l +   +++ +               +   ++i+  GE+lSaal+ +++ ++g+ +++ l++++  l  ++ +++
  FitnessBrowser__MR1:202522  83 LSSTQSELLFAGLGAQLARwqdrlhgitllqecpDGICAEIVVAGERLSAALMEQVMLAKGITSAQ-LDPRKLFLGRGRPLES 164
                                 44455555555555555445669999*******999*************************66655.699************* PP

                   TIGR00657 152 kvleeikterlekl.leegiivvvaGFiGatekgeittLGRGGSDltAallAaalkAdeveiytDVdGiytaDPrivpeArrl 233
                                 +v + +++ r ++l l+e+ + v+ GF++a+e+g+++tLGR+GSD++Aa+lAa+l+A+ +ei+tDVdG+y +DPr+v +A++l
  FitnessBrowser__MR1:202522 165 VVDIAVSKPRFKNLlLDEKRVWVMPGFTAADEDGKVVTLGRNGSDYSAAVLAACLDASSCEIWTDVDGVYNTDPRVVADAKLL 247
                                 *899998888887616778**************************************************************** PP

                   TIGR00657 234 deisyeEalELaslGakvLhprtlepamrakipivvkstfnpeaeGTlivakskseeepavkalsldknqalvsvsgttmk.. 314
                                  ++sy+Ea+EL+++GakvLhp+t+ p++++ ip+ +k++fnp+a+GTl+ +  +  +  +vka+s+ +nq++++vsg++mk  
  FitnessBrowser__MR1:202522 248 SQLSYQEAMELSYFGAKVLHPKTIAPIAQFHIPCYIKNSFNPDAPGTLVSNLAD-ASGLQVKAISNLDNQTMFDVSGPGMKgm 329
                                 ***************************************************988.556************************* PP

                   TIGR00657 315 pgilaevfgalaeakvnvdlilqsssetsisfvvdkedadkakellk...kkvkeekaleevevekklalvslvGagmksapg 394
                                 +g++++ + a+++ +v+v li+qss e+sisf+v +++  k k +l+   + + + + le++e+ ++la+vsl+G+gm++++g
  FitnessBrowser__MR1:202522 330 VGMASRTLAAISRSGVSVSLITQSSCEYSISFCVATSESAKVKLALEqefELEIKSDLLEPIEMRHDLAIVSLIGDGMRTHKG 412
                                 **************************************8888888886777788999************************** PP

                   TIGR00657 395 vaakifeaLaeeniniemis..sseikisvvvdekdaekavealheklv 441
                                 vaa++f+aLa++ +ni +i+  sse++is+v+++++ ++av a h+ ++
  FitnessBrowser__MR1:202522 413 VAARFFQALAQASVNIIAIAqgSSERSISTVIEQRKTKHAVAACHQGFF 461
                                 **********************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (822 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 31.01
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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