Alignments for a candidate for proB in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for Amino acid biosynthesis

Alignments for a candidate for proB in Echinicola vietnamensis KMM 6221, DSM 17526

Align glutamate 5-kinase (EC 2.7.2.11) (characterized)
to candidate Echvi_4033 Echvi_4033 glutamate 5-kinase

Query= reanno::Cola:Echvi_4033
         (362 letters)



>FitnessBrowser__Cola:Echvi_4033
          Length = 362

 Score =  710 bits (1832), Expect = 0.0
 Identities = 362/362 (100%), Positives = 362/362 (100%)

Query: 1   MIHRKANTIVIKIGSNVLTQADGTPDTMRMKALVRQMVYLREQGQEIVLITSGAVAYGRT 60
           MIHRKANTIVIKIGSNVLTQADGTPDTMRMKALVRQMVYLREQGQEIVLITSGAVAYGRT
Sbjct: 1   MIHRKANTIVIKIGSNVLTQADGTPDTMRMKALVRQMVYLREQGQEIVLITSGAVAYGRT 60

Query: 61  STVFEEKTDPVIQKQILAAVGQIELIRQYKQLFGDHNTPIAQIMVTKSDFRDRKHFLNMK 120
           STVFEEKTDPVIQKQILAAVGQIELIRQYKQLFGDHNTPIAQIMVTKSDFRDRKHFLNMK
Sbjct: 61  STVFEEKTDPVIQKQILAAVGQIELIRQYKQLFGDHNTPIAQIMVTKSDFRDRKHFLNMK 120

Query: 121 NCLEGLLKNNIIPVINENDTVSVTELMFTDNDELAGLVAAMLDAKDLIILSNVEGIFKGH 180
           NCLEGLLKNNIIPVINENDTVSVTELMFTDNDELAGLVAAMLDAKDLIILSNVEGIFKGH
Sbjct: 121 NCLEGLLKNNIIPVINENDTVSVTELMFTDNDELAGLVAAMLDAKDLIILSNVEGIFKGH 180

Query: 181 PSDPEAVLIEKVDADTPSMANFISSSKSSFGRGGMLTKMNMAKKSADLGIGVTIANGKRE 240
           PSDPEAVLIEKVDADTPSMANFISSSKSSFGRGGMLTKMNMAKKSADLGIGVTIANGKRE
Sbjct: 181 PSDPEAVLIEKVDADTPSMANFISSSKSSFGRGGMLTKMNMAKKSADLGIGVTIANGKRE 240

Query: 241 DVLVDYFHNRLRCTYFEPSKAKQSPKKWIAHSEHYSTGEVIINSGAENALRSDKITSLLP 300
           DVLVDYFHNRLRCTYFEPSKAKQSPKKWIAHSEHYSTGEVIINSGAENALRSDKITSLLP
Sbjct: 241 DVLVDYFHNRLRCTYFEPSKAKQSPKKWIAHSEHYSTGEVIINSGAENALRSDKITSLLP 300

Query: 301 IGVLEIRGDFSKGDIIRILSEDGRKIGLGKSAYGAKVAAEKKGLSNQKPLIHYDYLYLHQ 360
           IGVLEIRGDFSKGDIIRILSEDGRKIGLGKSAYGAKVAAEKKGLSNQKPLIHYDYLYLHQ
Sbjct: 301 IGVLEIRGDFSKGDIIRILSEDGRKIGLGKSAYGAKVAAEKKGLSNQKPLIHYDYLYLHQ 360

Query: 361 DS 362
           DS
Sbjct: 361 DS 362


Lambda     K      H
   0.317    0.134    0.374 

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: 564
Number of extensions: 7
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: 362
Length of database: 362
Length adjustment: 29
Effective length of query: 333
Effective length of database: 333
Effective search space:   110889
Effective search space used:   110889
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate Echvi_4033 Echvi_4033 (glutamate 5-kinase)
to HMM TIGR01027 (proB: glutamate 5-kinase (EC 2.7.2.11))

# 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/TIGR01027.hmm
# target sequence database:        /tmp/gapView.1543.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01027  [M=363]
Accession:   TIGR01027
Description: proB: glutamate 5-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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
     2e-104  335.6   0.3   2.4e-104  335.3   0.3    1.0  1  lcl|FitnessBrowser__Cola:Echvi_4033  Echvi_4033 glutamate 5-kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_4033  Echvi_4033 glutamate 5-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  335.3   0.3  2.4e-104  2.4e-104       2     342 ..       8     348 ..       7     360 .. 0.96

  Alignments for each domain:
  == domain 1  score: 335.3 bits;  conditional E-value: 2.4e-104
                            TIGR01027   2 riVvKlGsssLteesgklkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglperpkklaekQalaaVG 75 
                                          +iV+K+Gs++Lt+ +g++++ ++++lv+q+  l+++G+e+v+++SGava G ++  ++e++  + +kQ+laaVG
  lcl|FitnessBrowser__Cola:Echvi_4033   8 TIVIKIGSNVLTQADGTPDTMRMKALVRQMVYLREQGQEIVLITSGAVAYGRTSTVFEEKTDPVIQKQILAAVG 81 
                                          8************************************************************************* PP

                            TIGR01027  76 QgrLmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvaveeikfGDNDtLs 149
                                          Q +L+++y++lf  +++ +aQi+ t++d+++r+++lN +n le ll+++++p++NENDtv+v+e+ f DND+L+
  lcl|FitnessBrowser__Cola:Echvi_4033  82 QIELIRQYKQLFGDHNTPIAQIMVTKSDFRDRKHFLNMKNCLEGLLKNNIIPVINENDTVSVTELMFTDNDELA 155
                                          ************************************************************************** PP

                            TIGR01027 150 alvaalveAdlLvlltdvdgLydadprtnpdAklieeveeieeelkavagssgssvGTGGmrtKleaaelAsra 223
                                           lvaa+++A  L++l++v+g+++  p ++p+A lie+v++ + ++ ++ +ss ss+G GGm tK++ a+  +++
  lcl|FitnessBrowser__Cola:Echvi_4033 156 GLVAAMLDAKDLIILSNVEGIFKGHP-SDPEAVLIEKVDADTPSMANFISSSKSSFGRGGMLTKMNMAKKSADL 228
                                          **************************.*********************************************** PP

                            TIGR01027 224 gveviiasgekpekiadlledaavgtlfeakkkklknrkqwilaase.akGkiivdegaeeallekg.ksLlpa 295
                                          g+ v+ia+g++++ ++d+ +++   t+fe++k+k ++ k+wi++ ++ ++G++i+++gae+al++ + +sLlp 
  lcl|FitnessBrowser__Cola:Echvi_4033 229 GIGVTIANGKREDVLVDYFHNRLRCTYFEPSKAK-QSPKKWIAHSEHySTGEVIINSGAENALRSDKiTSLLPI 301
                                          ******************************9885.566789998765278*************9865268**** PP

                            TIGR01027 296 gvvevegnFsrgevveilaeegqeigkglvnysseelekikglksee 342
                                          gv+e++g+Fs+g++++il+e+g++ig g+++y ++  ++ kgl++++
  lcl|FitnessBrowser__Cola:Echvi_4033 302 GVLEIRGDFSKGDIIRILSEDGRKIGLGKSAYGAKVAAEKKGLSNQK 348
                                          ***********************************999999988764 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (363 nodes)
Target sequences:                          1  (362 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: 7.84
//
[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