GapMind for Amino acid biosynthesis

 

Aligments for a candidate for asp-kinase in Shewanella sp. ANA-3

Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate 7023909 Shewana3_1129 aspartate kinase (RefSeq)

Query= SwissProt::Q88EI9
         (411 letters)



>lcl|FitnessBrowser__ANA3:7023909 Shewana3_1129 aspartate kinase
           (RefSeq)
          Length = 418

 Score =  338 bits (867), Expect = 2e-97
 Identities = 195/405 (48%), Positives = 273/405 (67%), Gaps = 3/405 (0%)

Query: 3   LIVQKFGGTSVGSIERIEQVAEKVKKHREAGDDLVVVLSAMSGETNRLIDLAKQITDQPV 62
           L V+KFGGTSVGSIERIE VAE++ K    G+  V+VLSAM+GETNRL  LA QI  +  
Sbjct: 12  LFVKKFGGTSVGSIERIEVVAEQIAKSAHNGELQVLVLSAMAGETNRLFALAAQIDPRAS 71

Query: 63  PRELDVIVSTGEQVTIALLTMALIKRGVPAVSYTGNQVRILTDSSHNKARILQIDDQKIR 122
            RELD++VSTGEQ++IAL+ MAL +RG+ A S TG+QV+I T+S   +A I ++D   + 
Sbjct: 72  ARELDMLVSTGEQISIALMAMALQRRGINARSLTGDQVQIHTNSQFGRASIERVDTAYLT 131

Query: 123 ADLKEGRVVVVAGFQGVDEHGSITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYTTD 182
           + L +G V +VAGFQG+D +G +TTLGRGGSDTT VALAAALKADECQI+TDV GV+TTD
Sbjct: 132 SLLNDGIVPIVAGFQGIDPNGDVTTLGRGGSDTTAVALAAALKADECQIFTDVPGVFTTD 191

Query: 183 PRVVPQARRLEKITFEEMLEMASLGSKVLQIRSVEFAGKYNVPLRVLHSFKEGPGTLITI 242
           P +   ARRL+ I F+ MLEMA LG+KVL   SVE+A ++ VPLRVL SF+ G GTLI  
Sbjct: 192 PNIDSSARRLDVIGFDVMLEMAKLGAKVLHPDSVEYAQRFKVPLRVLSSFEAGHGTLIQF 251

Query: 243 -DEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISASNIEVDMIVQNVAHD 301
            DE E      + GIA N+  A LTI+G+  +      +L  ++   I+V+ I     ++
Sbjct: 252 GDESELAMAASVQGIAINKALATLTIKGLFTSSEHYQALLACLARLEIDVEFITPLKLNE 311

Query: 302 NTTD--FTFTVHRNEYEKAQSVLENTAREIGAREVIGDTKIAKVSIVGVGMRSHAGVASC 359
            +     +F +   + +     LE  +  +   ++I + + AKVS+VG G+++  G+ + 
Sbjct: 312 TSAAECVSFMLAEAKVDILLHELELLSESLDLGQLIVERQRAKVSLVGKGLQAKVGLLTK 371

Query: 360 MFEALAKESINIQMISTSEIKVSVVLEEKYLELAVRALHTAFDLD 404
           M + L  E+I+ +++STSE K+S V++E+ L  AVRALH AF+L+
Sbjct: 372 MLDVLGNETIHAKLLSTSESKLSTVIDERDLHKAVRALHHAFELN 416


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: 421
Number of extensions: 10
Number of successful extensions: 3
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: 418
Length adjustment: 31
Effective length of query: 380
Effective length of database: 387
Effective search space:   147060
Effective search space used:   147060
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 7023909 Shewana3_1129 (aspartate kinase (RefSeq))
to HMM TIGR00657 (aspartate kinase (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/TIGR00657.hmm
# target sequence database:        /tmp/gapView.29096.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00657  [M=442]
Accession:   TIGR00657
Description: asp_kinases: aspartate kinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   2.4e-121  391.8   3.8   6.2e-106  341.0   0.8    2.0  2  lcl|FitnessBrowser__ANA3:7023909  Shewana3_1129 aspartate kinase (


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7023909  Shewana3_1129 aspartate kinase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.7   0.1   1.9e-18   1.9e-18       2      61 ..      11      70 ..      10      74 .. 0.94
   2 !  341.0   0.8  6.2e-106  6.2e-106     103     441 ..      72     414 ..      69     415 .. 0.96

  Alignments for each domain:
  == domain 1  score: 52.7 bits;  conditional E-value: 1.9e-18
                         TIGR00657  2 aliVqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvssee 61
                                      +l V KFGGtSvg++eri+ va+ + k++++g+  v V+SAmag T++L +la ++++++
  lcl|FitnessBrowser__ANA3:7023909 11 KLFVKKFGGTSVGSIERIEVVAEQIAKSAHNGELQVLVLSAMAGETNRLFALAAQIDPRA 70
                                      6789***************************************************99876 PP

  == domain 2  score: 341.0 bits;  conditional E-value: 6.2e-106
                         TIGR00657 103 ereldlilsvGEklSaallaaaleelgvkavsllgaeagiltdsefgrAkvleeikterleklleegiivvvaGFiG 179
                                        reld+++s+GE++S+al+a+al+++g++a+sl+g++ +i t+s+fgrA+ +e ++t+ l++ll+ gi+++vaGF+G
  lcl|FitnessBrowser__ANA3:7023909  72 ARELDMLVSTGEQISIALMAMALQRRGINARSLTGDQVQIHTNSQFGRAS-IERVDTAYLTSLLNDGIVPIVAGFQG 147
                                       689***********************************************.************************** PP

                         TIGR00657 180 atekgeittLGRGGSDltAallAaalkAdeveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprt 256
                                       ++++g++ttLGRGGSD+tA++lAaalkAde++i+tDV+G++t+DP+i ++Arrld i ++ +lE+a+lGakvLhp++
  lcl|FitnessBrowser__ANA3:7023909 148 IDPNGDVTTLGRGGSDTTAVALAAALKADECQIFTDVPGVFTTDPNIDSSARRLDVIGFDVMLEMAKLGAKVLHPDS 224
                                       ***************************************************************************** PP

                         TIGR00657 257 lepamrakipivvkstfnpeaeGTlivaksk..seeepavkalsldknqalvsvsgttmkpgilaevfgalaeakvn 331
                                       +e+a r+k+p++v s+f+    GTli   ++     +  v++++ +k  a ++++g    ++  + ++ +la+ +++
  lcl|FitnessBrowser__ANA3:7023909 225 VEYAQRFKVPLRVLSSFEAG-HGTLIQFGDEseLAMAASVQGIAINKALATLTIKGLFTSSEHYQALLACLARLEID 300
                                       ******************99.*****9888877444589************************************** PP

                         TIGR00657 332 vdlil.qsssets....isfvvdkedadkakellkkkvkeekaleevevekklalvslvGagmksapgvaakifeaL 403
                                       v+ i+ ++ +ets    +sf++ + ++d   ++l + + e  +l+++ ve++ a+vslvG+g++ + g+++k++++L
  lcl|FitnessBrowser__ANA3:7023909 301 VEFITpLKLNETSaaecVSFMLAEAKVDILLHEL-ELLSESLDLGQLIVERQRAKVSLVGKGLQAKVGLLTKMLDVL 376
                                       *****966666666678**************998.67999999********************************** PP

                         TIGR00657 404 aeeniniemissseikisvvvdekdaekavealheklv 441
                                        +e i  + +s+se k+s+v+de+d +kav+alh++++
  lcl|FitnessBrowser__ANA3:7023909 377 GNETIHAKLLSTSESKLSTVIDERDLHKAVRALHHAFE 414
                                       ***********************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (418 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: 0.06u 0.01s 00:00:00.06 Elapsed: 00:00:00.06
# Mc/sec: 2.95
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see 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