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

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.22012.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: 00:00:00.01
# Mc/sec: 11.05
//
[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:

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