GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asp-kinase in Bacteroides thetaiotaomicron VPI-5482

Align aspartate kinase / homoserine dehydrogenase (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate 351931 BT2403 aspartokinase/homoserine dehydrogenase (NCBI ptt file)

Query= reanno::Btheta:351931
         (811 letters)



>FitnessBrowser__Btheta:351931
          Length = 811

 Score = 1577 bits (4083), Expect = 0.0
 Identities = 811/811 (100%), Positives = 811/811 (100%)

Query: 1   MKVMKFGGTSVGSVNSILSVKRIVESAGEPVIVVVSALGGITDKLINTSKMAAAGDSAYE 60
           MKVMKFGGTSVGSVNSILSVKRIVESAGEPVIVVVSALGGITDKLINTSKMAAAGDSAYE
Sbjct: 1   MKVMKFGGTSVGSVNSILSVKRIVESAGEPVIVVVSALGGITDKLINTSKMAAAGDSAYE 60

Query: 61  GEFREIVYRHVEMIKEVIPAGAGQVALQRQIGELLNELKDIFQGIYLIRDLSPKTSDTIV 120
           GEFREIVYRHVEMIKEVIPAGAGQVALQRQIGELLNELKDIFQGIYLIRDLSPKTSDTIV
Sbjct: 61  GEFREIVYRHVEMIKEVIPAGAGQVALQRQIGELLNELKDIFQGIYLIRDLSPKTSDTIV 120

Query: 121 SYGERLSSIIVAELIDEAKWFDSRTFIKTEKKHNKHTIDADLTNQLVKEAFHSIPKVSLV 180
           SYGERLSSIIVAELIDEAKWFDSRTFIKTEKKHNKHTIDADLTNQLVKEAFHSIPKVSLV
Sbjct: 121 SYGERLSSIIVAELIDEAKWFDSRTFIKTEKKHNKHTIDADLTNQLVKEAFHSIPKVSLV 180

Query: 181 PGFISSDKVSGDVTNLGRGGSDYTAAIIAAALDASSLEIWTDVDGFMTADPRVISTAYTI 240
           PGFISSDKVSGDVTNLGRGGSDYTAAIIAAALDASSLEIWTDVDGFMTADPRVISTAYTI
Sbjct: 181 PGFISSDKVSGDVTNLGRGGSDYTAAIIAAALDASSLEIWTDVDGFMTADPRVISTAYTI 240

Query: 241 SELSYVEATELCNFGAKVVYPPTIYPVCHKNIPIIIKNTFNPDGVGTVIKQETSNPQSKA 300
           SELSYVEATELCNFGAKVVYPPTIYPVCHKNIPIIIKNTFNPDGVGTVIKQETSNPQSKA
Sbjct: 241 SELSYVEATELCNFGAKVVYPPTIYPVCHKNIPIIIKNTFNPDGVGTVIKQETSNPQSKA 300

Query: 301 IKGISSINDTSLITVQGLGMVGVIGVNYRIFKALAKNGISVFLVSQASSENSTSIGVRNA 360
           IKGISSINDTSLITVQGLGMVGVIGVNYRIFKALAKNGISVFLVSQASSENSTSIGVRNA
Sbjct: 301 IKGISSINDTSLITVQGLGMVGVIGVNYRIFKALAKNGISVFLVSQASSENSTSIGVRNA 360

Query: 361 DADLACEVLNEEFAKEIEMGEISPILAERNLATVAIVGENMKHTPGIAGKLFGTLGRNGI 420
           DADLACEVLNEEFAKEIEMGEISPILAERNLATVAIVGENMKHTPGIAGKLFGTLGRNGI
Sbjct: 361 DADLACEVLNEEFAKEIEMGEISPILAERNLATVAIVGENMKHTPGIAGKLFGTLGRNGI 420

Query: 421 NVIACAQGASETNISFVVDSKSLRKSLNVIHDSFFLSEYQVLNLFICGIGTVGGSLVEQI 480
           NVIACAQGASETNISFVVDSKSLRKSLNVIHDSFFLSEYQVLNLFICGIGTVGGSLVEQI
Sbjct: 421 NVIACAQGASETNISFVVDSKSLRKSLNVIHDSFFLSEYQVLNLFICGIGTVGGSLVEQI 480

Query: 481 RCQQQKLMMENGLKLHVVGIIDAAKAMFSREGFDLANFREELQKKGKDSNLQTIRDEIVG 540
           RCQQQKLMMENGLKLHVVGIIDAAKAMFSREGFDLANFREELQKKGKDSNLQTIRDEIVG
Sbjct: 481 RCQQQKLMMENGLKLHVVGIIDAAKAMFSREGFDLANFREELQKKGKDSNLQTIRDEIVG 540

Query: 541 MNIFNSVFVDCTASPDIASLYKDLLQHNVSVVAANKIAASSAYENYRELKTIARQRGVKY 600
           MNIFNSVFVDCTASPDIASLYKDLLQHNVSVVAANKIAASSAYENYRELKTIARQRGVKY
Sbjct: 541 MNIFNSVFVDCTASPDIASLYKDLLQHNVSVVAANKIAASSAYENYRELKTIARQRGVKY 600

Query: 601 LFETNVGAGLPIINTINDLIHSGDKILKIEAVLSGTLNYIFNKISADIPFSRTIKMAQEE 660
           LFETNVGAGLPIINTINDLIHSGDKILKIEAVLSGTLNYIFNKISADIPFSRTIKMAQEE
Sbjct: 601 LFETNVGAGLPIINTINDLIHSGDKILKIEAVLSGTLNYIFNKISADIPFSRTIKMAQEE 660

Query: 661 RYSEPDPRIDLSGKDVIRKLVILAREAGYHIEQEDVEKNLFVPNDFFEGSLDDFWKRVPS 720
           RYSEPDPRIDLSGKDVIRKLVILAREAGYHIEQEDVEKNLFVPNDFFEGSLDDFWKRVPS
Sbjct: 661 RYSEPDPRIDLSGKDVIRKLVILAREAGYHIEQEDVEKNLFVPNDFFEGSLDDFWKRVPS 720

Query: 721 LDADFEARRQVLEKEHKHWRFVAKLEDGKASVGLQEVGANHPFYGLEGSNNIILLTTERY 780
           LDADFEARRQVLEKEHKHWRFVAKLEDGKASVGLQEVGANHPFYGLEGSNNIILLTTERY
Sbjct: 721 LDADFEARRQVLEKEHKHWRFVAKLEDGKASVGLQEVGANHPFYGLEGSNNIILLTTERY 780

Query: 781 KEYPMMIQGYGAGAGVTAAGVFADIMSIANV 811
           KEYPMMIQGYGAGAGVTAAGVFADIMSIANV
Sbjct: 781 KEYPMMIQGYGAGAGVTAAGVFADIMSIANV 811


Lambda     K      H
   0.317    0.135    0.377 

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: 1908
Number of extensions: 45
Number of successful extensions: 1
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: 811
Length of database: 811
Length adjustment: 41
Effective length of query: 770
Effective length of database: 770
Effective search space:   592900
Effective search space used:   592900
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (26.2 bits)

Align candidate 351931 BT2403 (aspartokinase/homoserine dehydrogenase (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.28863.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   7.7e-115  370.4   4.6   1.1e-114  369.9   4.6    1.2  1  lcl|FitnessBrowser__Btheta:351931  BT2403 aspartokinase/homoserine 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:351931  BT2403 aspartokinase/homoserine dehydrogenase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  369.9   4.6  1.1e-114  1.1e-114       5     441 ..       3     455 ..       1     456 [. 0.94

  Alignments for each domain:
  == domain 1  score: 369.9 bits;  conditional E-value: 1.1e-114
                          TIGR00657   5 VqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee..keliekirekhleale 78 
                                        V+KFGGtSvg+v++i  v +iv+++    ++v+VVvSA +g+Td+L+++++ +  +++  + + ++i ++h+e ++
  lcl|FitnessBrowser__Btheta:351931   3 VMKFGGTSVGSVNSILSVKRIVESAG---EPVIVVVSALGGITDKLINTSKMAAAGDSayEGEFREIVYRHVEMIK 75 
                                        9***************9988887765...79************************9998878899*********** PP

                          TIGR00657  79 ela.sqalkeklkallekeleevkk............ereldlilsvGEklSaallaaaleelgvkavsllgaeag 141
                                        e++   a +  l++ + + l+e+k             +++ d+i+s+GE+lS+ ++a+++ e       +++++  
  lcl|FitnessBrowser__Btheta:351931  76 EVIpAGAGQVALQRQIGELLNELKDifqgiylirdlsPKTSDTIVSYGERLSSIIVAELIDEAK-----WFDSRTF 146
                                        ***888999999999999999999999********************************98887.....******* PP

                          TIGR00657 142 iltdsefgrAkvleeikterleklleeg.iivvvaGFiGat.ekgeittLGRGGSDltAallAaalkAdeveiytD 215
                                        i t++++++ +  ++ +++ ++++ +   ++ +v GFi ++  +g++t LGRGGSD+tAa++Aaal+A+ +ei+tD
  lcl|FitnessBrowser__Btheta:351931 147 IKTEKKHNKHTIDADLTNQLVKEAFHSIpKVSLVPGFISSDkVSGDVTNLGRGGSDYTAAIIAAALDASSLEIWTD 222
                                        ***********666666666666666557***********9679******************************** PP

                          TIGR00657 216 VdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpeaeGTlivakskseee 291
                                        VdG +taDPr++++A  + e+sy Ea EL ++Gakv +p t+ p+ +++ipi++k+tfnp++ GT+i +++++ ++
  lcl|FitnessBrowser__Btheta:351931 223 VDGFMTADPRVISTAYTISELSYVEATELCNFGAKVVYPPTIYPVCHKNIPIIIKNTFNPDGVGTVIKQETSNPQS 298
                                        ************************************************************************9999 PP

                          TIGR00657 292 pavkalsldknqalvsvsgttmk..pgilaevfgalaeakvnvdlilqsssetsisfvvdkedadkakellk...k 362
                                        +a+k++s+ ++ +l++v+g +m    g+  ++f+ala+++++v+l++q sse+s s+ v + dad a e+l+    
  lcl|FitnessBrowser__Btheta:351931 299 KAIKGISSINDTSLITVQGLGMVgvIGVNYRIFKALAKNGISVFLVSQASSENSTSIGVRNADADLACEVLNeefA 374
                                        ***********************9999*******************************************995554 PP

                          TIGR00657 363 kvkeekaleevevekklalvslvGagmksapgvaakifeaLaeeniniemis..sseikisvvvdekdaekaveal 436
                                        k+ e  +++++  e++la+v++vG++mk++pg+a+k+f +L +++in+ + +  +se++is+vvd+k   k ++++
  lcl|FitnessBrowser__Btheta:351931 375 KEIEMGEISPILAERNLATVAIVGENMKHTPGIAGKLFGTLGRNGINVIACAqgASETNISFVVDSKSLRKSLNVI 450
                                        5566667788889***********************************99999*********************** PP

                          TIGR00657 437 heklv 441
                                        h+ ++
  lcl|FitnessBrowser__Btheta:351931 451 HDSFF 455
                                        **997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (811 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: 16.99
//
[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