Alignments for a candidate for asp-kinase in Desulfovibrio vulgaris Miyazaki F

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Desulfovibrio vulgaris Miyazaki F

Align Aspartate kinase Ask_LysC; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate 8499506 DvMF_0276 aspartate kinase (RefSeq)

Query= SwissProt::A4VJB4
         (412 letters)



>FitnessBrowser__Miya:8499506
          Length = 409

 Score =  440 bits (1131), Expect = e-128
 Identities = 226/409 (55%), Positives = 305/409 (74%), Gaps = 1/409 (0%)

Query: 1   MALIVQKFGGTSVGTVERIEQVAEKVKKFRDGGDDIVVVVSAMSGETNRLIDLAKQISEQ 60
           M ++VQKFGGTSV  +E ++QV EKV++    G   VVV+SA SGETNRL+ LA++ S  
Sbjct: 1   MRILVQKFGGTSVANLECMKQVREKVRRALRDGYKPVVVLSARSGETNRLLALAEEWSTD 60

Query: 61  PVPRELDVMVSTGEQVTIALLAMALIKRGVPAVSYTGNQVRILTDSAHTKARILQIDAQR 120
           P P E+D +++TGEQV++AL +M L   G+ A S TG QV I T  A  +ARI+ IDA R
Sbjct: 61  PDPAEVDALIATGEQVSVALFSMLLKDSGIKARSMTGFQVPITTSDAFGRARIMDIDASR 120

Query: 121 IQRDIKAGRVVVVAGFQGVDEKGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180
           ++++++   V+VVAGFQGV  +G +TTLGRGGSDT+ VALAAAL + EC+IYTDVDGVYT
Sbjct: 121 LRKELETHDVIVVAGFQGVTSEGRVTTLGRGGSDTSAVALAAALGSVECEIYTDVDGVYT 180

Query: 181 TDPRVVAKAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYSVPLRVLHSFQEGPGTLI 240
           TDP + + A++LD+++++EMLEMAS+G+KVLQIR+VEFA KY VP+ V  +F + PGT++
Sbjct: 181 TDPNLCSTARKLDRVSYDEMLEMASMGAKVLQIRSVEFAKKYKVPVHVRSTFTDTPGTMV 240

Query: 241 TLDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDMIVQNVAH 300
           T  E+  ME  ++SGIA+++D+A++T+R VPD PGV+  I GP+S   + VDMIVQN + 
Sbjct: 241 T-QEDCEMEAVLVSGIAYDKDQARVTLRSVPDKPGVSAAIFGPLSQQGILVDMIVQNPSR 299

Query: 301 DNTTDFTFTVHRNDYNNALQVLQGIAAEMGAREAIGDTNIAKVSIVGVGMRSHAGVASRM 360
           D  TD TFTV R D    L +++ I A  GA+E + DT +AKVS +GVGMR+H+GVA++ 
Sbjct: 300 DGVTDMTFTVPRKDLKKTLALMEEIRARTGAQEVLHDTQVAKVSAIGVGMRNHSGVAAKA 359

Query: 361 FEALAKENINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELDAPAGN 409
           F AL  ENINI MISTSEIK++ +IEEKY ELAVR LH AF L+   GN
Sbjct: 360 FAALHAENINILMISTSEIKITCLIEEKYTELAVRTLHDAFGLNHDLGN 408


Lambda     K      H
   0.317    0.133    0.357 

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: 451
Number of extensions: 9
Number of successful extensions: 2
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: 412
Length of database: 409
Length adjustment: 31
Effective length of query: 381
Effective length of database: 378
Effective search space:   144018
Effective search space used:   144018
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 8499506 DvMF_0276 (aspartate kinase (RefSeq))
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.13341.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   8.4e-136  439.1   5.8   9.5e-136  438.9   5.8    1.0  1  lcl|FitnessBrowser__Miya:8499506  DvMF_0276 aspartate kinase (RefS


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8499506  DvMF_0276 aspartate kinase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  438.9   5.8  9.5e-136  9.5e-136       1     405 [.       1     401 [.       1     403 [. 0.98

  Alignments for each domain:
  == domain 1  score: 438.9 bits;  conditional E-value: 9.5e-136
                         TIGR00656   1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisprerdelvs 77 
                                       + + VqKFGGtsv++ e +k++ ++v ++l++g+k+vVV+SA s++t++l++la      e  s ++ p+e d l++
  lcl|FitnessBrowser__Miya:8499506   1 MRILVQKFGGTSVANLECMKQVREKVRRALRDGYKPVVVLSARSGETNRLLALA------EEWSTDPDPAEVDALIA 71 
                                       5799**************************************************......799************** PP

                         TIGR00656  78 vGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvvaGFiGateeGeiTt 154
                                       +GE++s+al+s++l++ g ka++++g + +i T+d fg+A+i +++  +rL + Le ++++vvaGF+G t+eG++Tt
  lcl|FitnessBrowser__Miya:8499506  72 TGEQVSVALFSMLLKDSGIKARSMTGFQVPITTSDAFGRARIMDIDA-SRLRKELETHDVIVVAGFQGVTSEGRVTT 147
                                       ***********************************************.***************************** PP

                         TIGR00656 155 LGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEalelAtlGakvlhpralelaveakv 231
                                       LGRGGSD++A++laaal   ++eiyTDV+GvyttDP++ ++a+k+d++sy+E+le+A++Gakvl+ r++e+a+++kv
  lcl|FitnessBrowser__Miya:8499506 148 LGRGGSDTSAVALAAALGSVECEIYTDVDGVYTTDPNLCSTARKLDRVSYDEMLEMASMGAKVLQIRSVEFAKKYKV 224
                                       ***************************************************************************** PP

                         TIGR00656 232 pilvrsskekeegTlitn...kkensslvkaialeknvarltvegegmlgkrgilaeifkaLaeeeinvdlisqtes 305
                                       p+ vrs++    gT +t+   ++e   lv++ia++k++ar+t++  ++ +k+g+ a if+ L++++i vd+i+q +s
  lcl|FitnessBrowser__Miya:8499506 225 PVHVRSTFTDTPGTMVTQedcEMEA-VLVSGIAYDKDQARVTLR--SVPDKPGVSAAIFGPLSQQGILVDMIVQNPS 298
                                       *****************98544444.5*****************..9****************************** PP

                         TIGR00656 306 e...tsislvvdeedvdeakkaLkeesgaaelesleveedlavvsivgaglveapGvaseifkaleekninilmiss 379
                                       +   t+++++v ++d++++ ++++e    ++ +++  + ++a+vs++g+g+++++Gva+++f+al+ +ninilmis+
  lcl|FitnessBrowser__Miya:8499506 299 RdgvTDMTFTVPRKDLKKTLALMEEIRARTGAQEVLHDTQVAKVSAIGVGMRNHSGVAAKAFAALHAENINILMIST 375
                                       9999***********************999*********************************************** PP

                         TIGR00656 380 setkisvlvdekdaekavrklhekle 405
                                       se+ki+ l++ek++e avr+lh+++ 
  lcl|FitnessBrowser__Miya:8499506 376 SEIKITCLIEEKYTELAVRTLHDAFG 401
                                       ***********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (409 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: 11.96
//
[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