GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asp-kinase in Pseudomonas putida KT2440

Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate PP_4473 PP_4473 aspartokinase

Query= SwissProt::Q88EI9
         (411 letters)



>FitnessBrowser__Putida:PP_4473
          Length = 411

 Score =  785 bits (2028), Expect = 0.0
 Identities = 411/411 (100%), Positives = 411/411 (100%)

Query: 1   MALIVQKFGGTSVGSIERIEQVAEKVKKHREAGDDLVVVLSAMSGETNRLIDLAKQITDQ 60
           MALIVQKFGGTSVGSIERIEQVAEKVKKHREAGDDLVVVLSAMSGETNRLIDLAKQITDQ
Sbjct: 1   MALIVQKFGGTSVGSIERIEQVAEKVKKHREAGDDLVVVLSAMSGETNRLIDLAKQITDQ 60

Query: 61  PVPRELDVIVSTGEQVTIALLTMALIKRGVPAVSYTGNQVRILTDSSHNKARILQIDDQK 120
           PVPRELDVIVSTGEQVTIALLTMALIKRGVPAVSYTGNQVRILTDSSHNKARILQIDDQK
Sbjct: 61  PVPRELDVIVSTGEQVTIALLTMALIKRGVPAVSYTGNQVRILTDSSHNKARILQIDDQK 120

Query: 121 IRADLKEGRVVVVAGFQGVDEHGSITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180
           IRADLKEGRVVVVAGFQGVDEHGSITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT
Sbjct: 121 IRADLKEGRVVVVAGFQGVDEHGSITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180

Query: 181 TDPRVVPQARRLEKITFEEMLEMASLGSKVLQIRSVEFAGKYNVPLRVLHSFKEGPGTLI 240
           TDPRVVPQARRLEKITFEEMLEMASLGSKVLQIRSVEFAGKYNVPLRVLHSFKEGPGTLI
Sbjct: 181 TDPRVVPQARRLEKITFEEMLEMASLGSKVLQIRSVEFAGKYNVPLRVLHSFKEGPGTLI 240

Query: 241 TIDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISASNIEVDMIVQNVAH 300
           TIDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISASNIEVDMIVQNVAH
Sbjct: 241 TIDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISASNIEVDMIVQNVAH 300

Query: 301 DNTTDFTFTVHRNEYEKAQSVLENTAREIGAREVIGDTKIAKVSIVGVGMRSHAGVASCM 360
           DNTTDFTFTVHRNEYEKAQSVLENTAREIGAREVIGDTKIAKVSIVGVGMRSHAGVASCM
Sbjct: 301 DNTTDFTFTVHRNEYEKAQSVLENTAREIGAREVIGDTKIAKVSIVGVGMRSHAGVASCM 360

Query: 361 FEALAKESINIQMISTSEIKVSVVLEEKYLELAVRALHTAFDLDAPARQGE 411
           FEALAKESINIQMISTSEIKVSVVLEEKYLELAVRALHTAFDLDAPARQGE
Sbjct: 361 FEALAKESINIQMISTSEIKVSVVLEEKYLELAVRALHTAFDLDAPARQGE 411


Lambda     K      H
   0.316    0.133    0.358 

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: 705
Number of extensions: 17
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: 411
Length of database: 411
Length adjustment: 31
Effective length of query: 380
Effective length of database: 380
Effective search space:   144400
Effective search space used:   144400
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 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate PP_4473 PP_4473 (aspartokinase)
to HMM TIGR00656 (aspartate kinase, monofunctional class (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/TIGR00656.hmm
# target sequence database:        /tmp/gapView.25473.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00656  [M=407]
Accession:   TIGR00656
Description: asp_kin_monofn: aspartate kinase, monofunctional class
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.5e-136  441.6  11.8   1.7e-136  441.4  11.8    1.0  1  lcl|FitnessBrowser__Putida:PP_4473  PP_4473 aspartokinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_4473  PP_4473 aspartokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  441.4  11.8  1.7e-136  1.7e-136       1     406 [.       1     403 [.       1     404 [. 0.98

  Alignments for each domain:
  == domain 1  score: 441.4 bits;  conditional E-value: 1.7e-136
                           TIGR00656   1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisprerdel 75 
                                         + liVqKFGGtsvgs+eri+++a++v+k+ + g++ vVV+SAms++t++l++la      ++i d++ pre d +
  lcl|FitnessBrowser__Putida:PP_4473   1 MALIVQKFGGTSVGSIERIEQVAEKVKKHREAGDDLVVVLSAMSGETNRLIDLA------KQITDQPVPRELDVI 69 
                                         579***************************************************......9************** PP

                           TIGR00656  76 vsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvvaGFiGateeG 150
                                         vs+GE++++all++al ++gv a++++g++  ilTd+++++A+i +++  +++   L+eg +vvvaGF+G +e+G
  lcl|FitnessBrowser__Putida:PP_4473  70 VSTGEQVTIALLTMALIKRGVPAVSYTGNQVRILTDSSHNKARILQIDD-QKIRADLKEGRVVVVAGFQGVDEHG 143
                                         ************************************************9.9************************ PP

                           TIGR00656 151 eiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEalelAtlGakvlhpralel 225
                                          iTtLGRGGSD+t ++laaalkAd+++iyTDV+GvyttDPrvv++a++++ki++eE+le+A+lG kvl+ r++e+
  lcl|FitnessBrowser__Putida:PP_4473 144 SITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYTTDPRVVPQARRLEKITFEEMLEMASLGSKVLQIRSVEF 218
                                         *************************************************************************** PP

                           TIGR00656 226 aveakvpilvrsskekeegTlitn....kkensslvkaialeknvarltvegegmlgkrgilaeifkaLaeeein 296
                                         a +++vp++v +s+++  gTlit     ++e++ ++++ia++++ a+lt++  g+ + +g++ +i + ++ ++i 
  lcl|FitnessBrowser__Putida:PP_4473 219 AGKYNVPLRVLHSFKEGPGTLITIdeeeSMEQP-IISGIAFNRDEAKLTIR--GVPDTPGVAFKILGPISASNIE 290
                                         **********************98555566666.*****************..9********************* PP

                           TIGR00656 297 vdlisqtese...tsislvvdeedvdeakkaLkeesgaaelesleveedlavvsivgaglveapGvaseifkale 368
                                         vd+i+q  ++   t+ +++v++++ ++a+++L+++  +++ +++  + ++a+vsivg+g++++ Gvas +f+al+
  lcl|FitnessBrowser__Putida:PP_4473 291 VDMIVQNVAHdntTDFTFTVHRNEYEKAQSVLENTAREIGAREVIGDTKIAKVSIVGVGMRSHAGVASCMFEALA 365
                                         ******99988889************************************************************* PP

                           TIGR00656 369 ekninilmisssetkisvlvdekdaekavrklheklee 406
                                         ++ ini mis+se+k+sv+ +ek++e avr+lh ++ +
  lcl|FitnessBrowser__Putida:PP_4473 366 KESINIQMISTSEIKVSVVLEEKYLELAVRALHTAFDL 403
                                         **********************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (411 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: 7.91
//
[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