Alignments for a candidate for asp-kinase in Escherichia coli BW25113

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Escherichia coli BW25113

Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate 18052 b4024 aspartate kinase III (NCBI)

Query= BRENDA::P08660
         (449 letters)



>FitnessBrowser__Keio:18052
          Length = 449

 Score =  860 bits (2222), Expect = 0.0
 Identities = 449/449 (100%), Positives = 449/449 (100%)

Query: 1   MSEIVVSKFGGTSVADFDAMNRSADIVLSDANVRLVVLSASAGITNLLVALAEGLEPGER 60
           MSEIVVSKFGGTSVADFDAMNRSADIVLSDANVRLVVLSASAGITNLLVALAEGLEPGER
Sbjct: 1   MSEIVVSKFGGTSVADFDAMNRSADIVLSDANVRLVVLSASAGITNLLVALAEGLEPGER 60

Query: 61  FEKLDAIRNIQFAILERLRYPNVIREEIERLLENITVLAEAAALATSPALTDELVSHGEL 120
           FEKLDAIRNIQFAILERLRYPNVIREEIERLLENITVLAEAAALATSPALTDELVSHGEL
Sbjct: 61  FEKLDAIRNIQFAILERLRYPNVIREEIERLLENITVLAEAAALATSPALTDELVSHGEL 120

Query: 121 MSTLLFVEILRERDVQAQWFDVRKVMRTNDRFGRAEPDIAALAELAALQLLPRLNEGLVI 180
           MSTLLFVEILRERDVQAQWFDVRKVMRTNDRFGRAEPDIAALAELAALQLLPRLNEGLVI
Sbjct: 121 MSTLLFVEILRERDVQAQWFDVRKVMRTNDRFGRAEPDIAALAELAALQLLPRLNEGLVI 180

Query: 181 TQGFIGSENKGRTTTLGRGGSDYTAALLAEALHASRVDIWTDVPGIYTTDPRVVSAAKRI 240
           TQGFIGSENKGRTTTLGRGGSDYTAALLAEALHASRVDIWTDVPGIYTTDPRVVSAAKRI
Sbjct: 181 TQGFIGSENKGRTTTLGRGGSDYTAALLAEALHASRVDIWTDVPGIYTTDPRVVSAAKRI 240

Query: 241 DEIAFAEAAEMATFGAKVLHPATLLPAVRSDIPVFVGSSKDPRAGGTLVCNKTENPPLFR 300
           DEIAFAEAAEMATFGAKVLHPATLLPAVRSDIPVFVGSSKDPRAGGTLVCNKTENPPLFR
Sbjct: 241 DEIAFAEAAEMATFGAKVLHPATLLPAVRSDIPVFVGSSKDPRAGGTLVCNKTENPPLFR 300

Query: 301 ALALRRNQTLLTLHSLNMLHSRGFLAEVFGILARHNISVDLITTSEVSVALTLDTTGSTS 360
           ALALRRNQTLLTLHSLNMLHSRGFLAEVFGILARHNISVDLITTSEVSVALTLDTTGSTS
Sbjct: 301 ALALRRNQTLLTLHSLNMLHSRGFLAEVFGILARHNISVDLITTSEVSVALTLDTTGSTS 360

Query: 361 TGDTLLTQSLLMELSALCRVEVEEGLALVALIGNDLSKACGVGKEVFGVLEPFNIRMICY 420
           TGDTLLTQSLLMELSALCRVEVEEGLALVALIGNDLSKACGVGKEVFGVLEPFNIRMICY
Sbjct: 361 TGDTLLTQSLLMELSALCRVEVEEGLALVALIGNDLSKACGVGKEVFGVLEPFNIRMICY 420

Query: 421 GASSHNLCFLVPGEDAEQVVQKLHSNLFE 449
           GASSHNLCFLVPGEDAEQVVQKLHSNLFE
Sbjct: 421 GASSHNLCFLVPGEDAEQVVQKLHSNLFE 449


Lambda     K      H
   0.320    0.135    0.376 

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: 718
Number of extensions: 16
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: 449
Length of database: 449
Length adjustment: 33
Effective length of query: 416
Effective length of database: 416
Effective search space:   173056
Effective search space used:   173056
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate 18052 b4024 (aspartate kinase III (NCBI))
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.10405.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   8.2e-158  511.6   0.1   9.3e-158  511.4   0.1    1.0  1  lcl|FitnessBrowser__Keio:18052  b4024 aspartate kinase III (NCBI


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:18052  b4024 aspartate kinase III (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  511.4   0.1  9.3e-158  9.3e-158       2     406 ..       3     449 .]       2     449 .] 0.97

  Alignments for each domain:
  == domain 1  score: 511.4 bits;  conditional E-value: 9.3e-158
                       TIGR00656   2 eliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelae.............llkll....... 60 
                                     e++V+KFGGtsv+++++++++a+ivl++   ++ ++VV+SA++++t+ lv+lae             +++++       
  lcl|FitnessBrowser__Keio:18052   3 EIVVSKFGGTSVADFDAMNRSADIVLSD---ANVRLVVLSASAGITNLLVALAEglepgerfekldaIRNIQfailerl 78 
                                     89*************************9...9*****************************999999666666677777 PP

                       TIGR00656  61 ...eaisdei..................sprerdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAk 118
                                        ++i++ei                  sp+ +delvs+GEl+s+ l++++lre++v+a+++d ++++++T+d+fg+A+
  lcl|FitnessBrowser__Keio:18052  79 rypNVIREEIerllenitvlaeaaalatSPALTDELVSHGELMSTLLFVEILRERDVQAQWFD-VRKVMRTNDRFGRAE 156
                                     8888888888999999999999999999***********************************.9************** PP

                       TIGR00656 119 ikelate....erLlelLeegiivvvaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvv 193
                                     ++++a++     +Ll++L+eg +v+++GFiG++++G++TtLGRGGSD+tAalla+al+A+rv+i+TDV+G+yttDPrvv
  lcl|FitnessBrowser__Keio:18052 157 PDIAALAelaaLQLLPRLNEG-LVITQGFIGSENKGRTTTLGRGGSDYTAALLAEALHASRVDIWTDVPGIYTTDPRVV 234
                                     *****9989999*********.9******************************************************** PP

                       TIGR00656 194 eeakkidkisyeEalelAtlGakvlhpralelaveakvpilvrsskeke.egTlitnkkensslvkaialeknvarltv 271
                                     ++ak+id+i+++Ea+e+At+Gakvlhp++l +av++++p++v ssk+++  gTl++nk+en++l++a+al++n+++lt+
  lcl|FitnessBrowser__Keio:18052 235 SAAKRIDEIAFAEAAEMATFGAKVLHPATLLPAVRSDIPVFVGSSKDPRaGGTLVCNKTENPPLFRALALRRNQTLLTL 313
                                     *************************************************99**************************** PP

                       TIGR00656 272 egegmlgkrgilaeifkaLaeeeinvdlisqtesetsislvvdeedvdeakkaLkeesgaae...lesleveedlavvs 347
                                     ++ +ml++rg+lae+f++La+++i+vdli+++e  +s++l++d+++++++ ++L ++s+++e   l+++evee+la+v+
  lcl|FitnessBrowser__Keio:18052 314 HSLNMLHSRGFLAEVFGILARHNISVDLITTSE--VSVALTLDTTGSTSTGDTLLTQSLLMElsaLCRVEVEEGLALVA 390
                                     ******************************999..***************************999************** PP

                       TIGR00656 348 ivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklheklee 406
                                     ++g++l++a+Gv +e+f +le++ni+++++++s++++++lv+++dae++v+klh++l+e
  lcl|FitnessBrowser__Keio:18052 391 LIGNDLSKACGVGKEVFGVLEPFNIRMICYGASSHNLCFLVPGEDAEQVVQKLHSNLFE 449
                                     *******************************************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (449 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: 12.11
//
[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