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.3279116.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  lcl|FitnessBrowser__MR1:202522  SO3415 aspartokinase I/homoserin


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:202522  SO3415 aspartokinase I/homoserine dehydrogenase, threonine-sensitive (NCBI ptt file)
   #    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....keliekirekhlealee 79 
                                     V+KFGGtS++n +r++ +a+iv k+++ + +v++V+SA+a vT+aL+e+++ + ++e+     + +e+++++ ++ + +
  lcl|FitnessBrowser__MR1:202522   3 VMKFGGTSLANWQRFSMAADIVAKAATME-PVATVLSAPATVTNALLEMVNLAVKGEDyspvIQHVERVFTSLYQDAVS 80 
                                     9*************************777.************************9999866655566666655554444 PP

                       TIGR00657  80 lasqalkeklkallekeleevkk...............ereldlilsvGEklSaallaaaleelgvkavsllgaeagil 143
                                          ++++++ l +   +++ +               +   ++i+  GE+lSaal+ +++ ++g+ +++ l++++  l
  lcl|FitnessBrowser__MR1:202522  81 SG--LSSTQSELLFAGLGAQLARwqdrlhgitllqecpDGICAEIVVAGERLSAALMEQVMLAKGITSAQ-LDPRKLFL 156
                                     44..44455555555555555445669999*******999*************************66655.699***** PP

                       TIGR00657 144 tdsefgrAkvleeikterlekl.leegiivvvaGFiGatekgeittLGRGGSDltAallAaalkAdeveiytDVdGiyt 221
                                       ++ ++++v + +++ r ++l l+e+ + v+ GF++a+e+g+++tLGR+GSD++Aa+lAa+l+A+ +ei+tDVdG+y 
  lcl|FitnessBrowser__MR1:202522 157 GRGRPLESVVDIAVSKPRFKNLlLDEKRVWVMPGFTAADEDGKVVTLGRNGSDYSAAVLAACLDASSCEIWTDVDGVYN 235
                                     *********899998888887616778**************************************************** PP

                       TIGR00657 222 aDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpeaeGTlivakskseeepavkalsld 300
                                     +DPr+v +A++l ++sy+Ea+EL+++GakvLhp+t+ p++++ ip+ +k++fnp+a+GTl+ +  +  +  +vka+s+ 
  lcl|FitnessBrowser__MR1:202522 236 TDPRVVADAKLLSQLSYQEAMELSYFGAKVLHPKTIAPIAQFHIPCYIKNSFNPDAPGTLVSNLAD-ASGLQVKAISNL 313
                                     ***************************************************************988.556********* PP

                       TIGR00657 301 knqalvsvsgttmk..pgilaevfgalaeakvnvdlilqsssetsisfvvdkedadkakellk...kkvkeekaleeve 374
                                     +nq++++vsg++mk  +g++++ + a+++ +v+v li+qss e+sisf+v +++  k k +l+   + + + + le++e
  lcl|FitnessBrowser__MR1:202522 314 DNQTMFDVSGPGMKgmVGMASRTLAAISRSGVSVSLITQSSCEYSISFCVATSESAKVKLALEqefELEIKSDLLEPIE 392
                                     ******************************************************8888888886777788999****** PP

                       TIGR00657 375 vekklalvslvGagmksapgvaakifeaLaeeniniemis..sseikisvvvdekdaekavealheklv 441
                                     + ++la+vsl+G+gm++++gvaa++f+aLa++ +ni +i+  sse++is+v+++++ ++av a h+ ++
  lcl|FitnessBrowser__MR1:202522 393 MRHDLAIVSLIGDGMRTHKGVAARFFQALAQASVNIIAIAqgSSERSISTVIEQRKTKHAVAACHQGFF 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 29.92
//
[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:

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:

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:

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:

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