Alignments for a candidate for asp-kinase in Desulfovibrio vulgaris Hildenborough

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Desulfovibrio vulgaris Hildenborough

Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate 207382 DVU1913 aspartate kinase, monofunctional class

Query= SwissProt::Q88EI9
         (411 letters)



>MicrobesOnline__882:207382
          Length = 408

 Score =  435 bits (1118), Expect = e-126
 Identities = 228/405 (56%), Positives = 300/405 (74%), Gaps = 1/405 (0%)

Query: 1   MALIVQKFGGTSVGSIERIEQVAEKVKKHREAGDDLVVVLSAMSGETNRLIDLAKQITDQ 60
           M ++VQKFGGTSV ++E ++QV  KV   RE G  +VVVLSAMSGETNRL+ LA + + +
Sbjct: 1   MRILVQKFGGTSVANLECMKQVRAKVLAARERGYKVVVVLSAMSGETNRLLALADEWSSE 60

Query: 61  PVPRELDVIVSTGEQVTIALLTMALIKRGVPAVSYTGNQVRILTDSSHNKARILQIDDQK 120
           P P E D +V TGEQV+IAL +M L   G+ A S+ G Q+ I+T  +   ARIL IDD +
Sbjct: 61  PDPAETDALVVTGEQVSIALFSMLLKDSGIKARSFLGFQIPIVTSDTFGSARILSIDDSR 120

Query: 121 IRADLKEGRVVVVAGFQGVDEHGSITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180
           +RA+L+   V+VVAGFQG    G +TTLGRGGSDT+ VALAAAL + EC+IYTDVDGVYT
Sbjct: 121 LRAELETHDVLVVAGFQGCTADGRLTTLGRGGSDTSAVALAAALGSVECEIYTDVDGVYT 180

Query: 181 TDPRVVPQARRLEKITFEEMLEMASLGSKVLQIRSVEFAGKYNVPLRVLHSFKEGPGTLI 240
           TDP +   AR+L++IT++EMLEMAS+G+KVLQIRSVEFA KYNVP+ V  +F +  GTL+
Sbjct: 181 TDPNLCSTARKLDRITYDEMLEMASMGAKVLQIRSVEFAKKYNVPVHVRSTFTDTTGTLV 240

Query: 241 TIDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISASNIEVDMIVQNVAH 300
           T  E+ SME  ++SGIA+++D+A++T+R VPD PGVA  I  P+S + + VDMIVQN + 
Sbjct: 241 T-QEDSSMEAVLVSGIAYDKDQARITLRSVPDRPGVAAAIFVPLSTNGVVVDMIVQNPSR 299

Query: 301 DNTTDFTFTVHRNEYEKAQSVLENTAREIGAREVIGDTKIAKVSIVGVGMRSHAGVASCM 360
           +  TD TFTV R + +K  +++E    E  A EV+ D  +AKVS +GVGMR+H+GVA+  
Sbjct: 300 EGVTDMTFTVPRKDLKKTLTLMEGIREETEALEVLHDVSVAKVSAIGVGMRNHSGVAAKA 359

Query: 361 FEALAKESINIQMISTSEIKVSVVLEEKYLELAVRALHTAFDLDA 405
           F AL KE+INI MISTSEIK++ ++EEKY ELAVR LH AF L +
Sbjct: 360 FAALRKENINILMISTSEIKITCLIEEKYTELAVRVLHDAFGLSS 404


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: 448
Number of extensions: 19
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: 411
Length of database: 408
Length adjustment: 31
Effective length of query: 380
Effective length of database: 377
Effective search space:   143260
Effective search space used:   143260
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 207382 DVU1913 (aspartate kinase, monofunctional class)
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.15910.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   2.7e-134  434.1   8.1     3e-134  433.9   8.1    1.0  1  lcl|MicrobesOnline__882:207382  DVU1913 aspartate kinase, monofu


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:207382  DVU1913 aspartate kinase, monofunctional class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  433.9   8.1    3e-134    3e-134       1     406 [.       1     402 [.       1     403 [. 0.97

  Alignments for each domain:
  == domain 1  score: 433.9 bits;  conditional E-value: 3e-134
                       TIGR00656   1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisprerdelvsvG 79 
                                     + + VqKFGGtsv++ e +k++  +vl++ ++g+kvvVV+SAms++t++l++la      +  s+e+ p+e+d lv +G
  lcl|MicrobesOnline__882:207382   1 MRILVQKFGGTSVANLECMKQVRAKVLAARERGYKVVVVLSAMSGETNRLLALA------DEWSSEPDPAETDALVVTG 73 
                                     5799**************************************************......699**************** PP

                       TIGR00656  80 EllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvvaGFiGateeGeiTtLGRG 158
                                     E++s+al+s++l++ g ka+++ g + +i+T+d+fg+A+i +++  +rL   Le +++ vvaGF+G t +G+ TtLGRG
  lcl|MicrobesOnline__882:207382  74 EQVSIALFSMLLKDSGIKARSFLGFQIPIVTSDTFGSARILSIDD-SRLRAELETHDVLVVAGFQGCTADGRLTTLGRG 151
                                     ********************************************9.********************************* PP

                       TIGR00656 159 GSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEalelAtlGakvlhpralelaveakvpilvrs 237
                                     GSD++A++laaal   ++eiyTDV+GvyttDP++ ++a+k+d+i+y+E+le+A++Gakvl+ r++e+a++++vp+ vrs
  lcl|MicrobesOnline__882:207382 152 GSDTSAVALAAALGSVECEIYTDVDGVYTTDPNLCSTARKLDRITYDEMLEMASMGAKVLQIRSVEFAKKYNVPVHVRS 230
                                     ******************************************************************************* PP

                       TIGR00656 238 skekeegTlitn...kkensslvkaialeknvarltvegegmlgkrgilaeifkaLaeeeinvdlisqtese...tsis 310
                                     ++    gTl+t+   ++e   lv++ia++k++ar+t++  ++ +++g++a if  L+ +++ vd+i+q +s+   t+++
  lcl|MicrobesOnline__882:207382 231 TFTDTTGTLVTQedsSMEA-VLVSGIAYDKDQARITLR--SVPDRPGVAAAIFVPLSTNGVVVDMIVQNPSRegvTDMT 306
                                     ***********98644444.5*****************..9******************************9999**** PP

                       TIGR00656 311 lvvdeedvdeakkaLkeesgaaelesleveedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvd 389
                                     ++v ++d++++  +++   +++e  ++  +  +a+vs++g+g+++++Gva+++f+al+++ninilmis+se+ki+ l++
  lcl|MicrobesOnline__882:207382 307 FTVPRKDLKKTLTLMEGIREETEALEVLHDVSVAKVSAIGVGMRNHSGVAAKAFAALRKENINILMISTSEIKITCLIE 385
                                     ***************99999999888888999*********************************************** PP

                       TIGR00656 390 ekdaekavrklheklee 406
                                     ek++e avr lh+++ +
  lcl|MicrobesOnline__882:207382 386 EKYTELAVRVLHDAFGL 402
                                     *************9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (408 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: 10.39
//
[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