GapMind for Amino acid biosynthesis

 

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

Align Glutamate 5-kinase; EC 2.7.2.11; Gamma-glutamyl kinase; GK (uncharacterized)
to candidate Echvi_4033 Echvi_4033 glutamate 5-kinase

Query= curated2:Q8A1E7
         (360 letters)



>lcl|FitnessBrowser__Cola:Echvi_4033 Echvi_4033 glutamate 5-kinase
          Length = 362

 Score =  357 bits (916), Expect = e-103
 Identities = 178/353 (50%), Positives = 254/353 (71%), Gaps = 4/353 (1%)

Query: 8   IAVKVGSNVLARRDGTLDVTRMSALVDQIAELNKSGVEIILISSGAVASGRSEIHPQKKL 67
           I +K+GSNVL + DGT D  RM ALV Q+  L + G EI+LI+SGAVA GR+    ++K 
Sbjct: 9   IVIKIGSNVLTQADGTPDTMRMKALVRQMVYLREQGQEIVLITSGAVAYGRTSTVFEEKT 68

Query: 68  DSVDQRQLFSAVGQAKLINRYYELFREHGIAVGQVLTTKENFSTRRHYLNQKNCMTVMLE 127
           D V Q+Q+ +AVGQ +LI +Y +LF +H   + Q++ TK +F  R+H+LN KNC+  +L+
Sbjct: 69  DPVIQKQILAAVGQIELIRQYKQLFGDHNTPIAQIMVTKSDFRDRKHFLNMKNCLEGLLK 128

Query: 128 NGVIPIVNENDTISVSELMFTDNDELSGLIASMMDAQALIILSNIDGIYNGSPSDPASAV 187
           N +IP++NENDT+SV+ELMFTDNDEL+GL+A+M+DA+ LIILSN++GI+ G PSDP + +
Sbjct: 129 NNIIPVINENDTVSVTELMFTDNDELAGLVAAMLDAKDLIILSNVEGIFKGHPSDPEAVL 188

Query: 188 IREIE-HGKDLSNYIQATKSSFGRGGMLTKTNIARKVADEGITVIIANGKRDNILVDLLQ 246
           I +++     ++N+I ++KSSFGRGGMLTK N+A+K AD GI V IANGKR+++LVD   
Sbjct: 189 IEKVDADTPSMANFISSSKSSFGRGGMLTKMNMAKKSADLGIGVTIANGKREDVLVDYFH 248

Query: 247 QPDDTVCTRFIPSTEAVSSVKKWIAHSEGFAKGEIHINECATDILSSEKAASILPVGITH 306
             +   CT F PS +A  S KKWIAHSE ++ GE+ IN  A + L S+K  S+LP+G+  
Sbjct: 249 --NRLRCTYFEPS-KAKQSPKKWIAHSEHYSTGEVIINSGAENALRSDKITSLLPIGVLE 305

Query: 307 IEGEFEKDDIVRIMDFLGNQVGVGKANCDSAQAREAMGKHGKKPVVHYDYLYI 359
           I G+F K DI+RI+   G ++G+GK+   +  A E  G   +KP++HYDYLY+
Sbjct: 306 IRGDFSKGDIIRILSEDGRKIGLGKSAYGAKVAAEKKGLSNQKPLIHYDYLYL 358


Lambda     K      H
   0.316    0.133    0.369 

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: 342
Number of extensions: 21
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: 360
Length of database: 362
Length adjustment: 29
Effective length of query: 331
Effective length of database: 333
Effective search space:   110223
Effective search space used:   110223
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: 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.30919.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 6.90
//
[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