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.7744.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 8.72
//
[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