GapMind for Amino acid biosynthesis

 

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

Align Gamma-glutamyl phosphate reductase; GPR; EC 1.2.1.41; Glutamate-5-semialdehyde dehydrogenase; Glutamyl-gamma-semialdehyde dehydrogenase; GSA dehydrogenase (uncharacterized)
to candidate Echvi_2633 Echvi_2633 gamma-glutamyl phosphate reductase

Query= curated2:B5YEQ8
         (415 letters)



>lcl|FitnessBrowser__Cola:Echvi_2633 Echvi_2633 gamma-glutamyl
           phosphate reductase
          Length = 399

 Score =  304 bits (779), Expect = 3e-87
 Identities = 158/401 (39%), Positives = 250/401 (62%), Gaps = 5/401 (1%)

Query: 18  LSLLNTNEKNEALRAIANNIEKNIDKIIKENEKDIKRGEEKGLSKAILDRILLNEKRLKD 77
           + +L+T +KN+ L ++   I+KN +KI+  N+ D+   +     +A+ DR+++N+ ++  
Sbjct: 1   MKILSTQKKNDVLASMIKIIDKNREKILTANKADLDAFQRD--DQALYDRLVVNDAKIDG 58

Query: 78  IVKSIEDVIKLPDPVGEIVSMQKRPNGILVGQMRVPIGVIAIIYEARPNVTVDATILALK 137
           +++++++V    DPVG+ +S +   NG+ +     P G I IIYE+RP+VT++A +LA K
Sbjct: 59  MIQAVQEVKDQDDPVGKEISKRTLANGLDITNKTAPFGTIMIIYESRPDVTIEAAVLAFK 118

Query: 138 SGNAIVLRGSSDALNSNIILTNIMKEALSNTKIPQDAVQIIESPEHSVVEELLQMTDYID 197
           + + I+L+G  +A+NSN +L     EAL    + +D +++           L   ++ +D
Sbjct: 119 ANSKILLKGGKEAVNSNKVLVECWHEALEENGLSKDWIELFTLNREQTQAFLKNPSEKLD 178

Query: 198 VAIPRGSAKFIKHVMNISKVPVIETGAGNNHIYVEEDADFEMARKIIINAKVQRPSVCNA 257
           + +PRG  + I  V   ++  V+ +G GNN  YV EDAD+E+A+K+IINAK  + S CNA
Sbjct: 179 LIVPRGGERLIAFVKEHAQCAVLVSGRGNNFAYVAEDADWELAKKVIINAKTNKISGCNA 238

Query: 258 IEKLLVHKNIA--EEFLPVIVKDLREYNVEIRGCEKTLKIVKDAIPATEED-WYTEYLDY 314
           ++K+LV + +   E  L  + K L  Y VE+   ++ +  ++ A     ED WY E+L  
Sbjct: 239 LDKILVDEKLPDFESKLADLAKSLASYKVELVAEKELVPAIEGAKEVPSEDTWYEEFLAL 298

Query: 315 IIAIKVVDSIDEAIAHINKYNTKHSEAIITKDYHKALKFLRMVDAAAVYVNASTRFTDGG 374
              I  V+ +DEAIA INKY+  HS  I+T D  KA  F+  VD+AAVY NASTRFTDGG
Sbjct: 299 KALIGKVNGLDEAIAKINKYSGGHSATILTTDKDKAATFMEQVDSAAVYHNASTRFTDGG 358

Query: 375 EFGLGAEIGISTQKLHARGPMGLKELTTTKYVIFGEGQIRE 415
           + G+GAE+ IST KLH RGP+GL++L T KY +FG GQIR+
Sbjct: 359 QMGVGAELAISTDKLHHRGPLGLEQLVTNKYYVFGSGQIRD 399


Lambda     K      H
   0.316    0.135    0.364 

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: 392
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: 415
Length of database: 399
Length adjustment: 31
Effective length of query: 384
Effective length of database: 368
Effective search space:   141312
Effective search space used:   141312
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 Echvi_2633 Echvi_2633 (gamma-glutamyl phosphate reductase)
to HMM TIGR00407 (proA: glutamate-5-semialdehyde dehydrogenase (EC 1.2.1.41))

# 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/TIGR00407.hmm
# target sequence database:        /tmp/gapView.25340.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00407  [M=398]
Accession:   TIGR00407
Description: proA: glutamate-5-semialdehyde dehydrogenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   5.8e-111  357.0   3.2   6.6e-111  356.9   3.2    1.0  1  lcl|FitnessBrowser__Cola:Echvi_2633  Echvi_2633 gamma-glutamyl phosph


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_2633  Echvi_2633 gamma-glutamyl phosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  356.9   3.2  6.6e-111  6.6e-111       8     398 .]       1     388 [.       1     388 [. 0.94

  Alignments for each domain:
  == domain 1  score: 356.9 bits;  conditional E-value: 6.6e-111
                            TIGR00407   8 laqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksiaddvkdvieLadP 81 
                                          ++ lst++kn++l+ + + + ++ e il an+ d+ a +     +al+drL ++++k+ +++++v++v + +dP
  lcl|FitnessBrowser__Cola:Echvi_2633   1 MKILSTQKKNDVLASMIKIIDKNREKILTANKADLDAFQRD--DQALYDRLVVNDAKIDGMIQAVQEVKDQDDP 72 
                                          6789*******************************998887..589**************************** PP

                            TIGR00407  82 vGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgkeavrsnkalveviqdal 155
                                          vGk i++r+l +GL + + ++P G + +iye+rP+v++++a L++k+   ++LkGgkeav+snk+lve  ++al
  lcl|FitnessBrowser__Cola:Echvi_2633  73 VGKEISKRTLANGLDITNKTAPFGTIMIIYESRPDVTIEAAVLAFKANSKILLKGGKEAVNSNKVLVECWHEAL 146
                                          ************************************************************************** PP

                            TIGR00407 156 eqtglpveavqliedpdreevkellkl.deyvdlliPrGgnelvklikeestiPvlehadGvChiyldesadla 228
                                          e+ gl++  ++l +  +re+ + +lk   e +dl++PrGg++l+  +ke+++  vl+++ G+   y+ e+ad +
  lcl|FitnessBrowser__Cola:Echvi_2633 147 EENGLSKDWIELFTL-NREQTQAFLKNpSEKLDLIVPRGGERLIAFVKEHAQCAVLVSGRGNNFAYVAEDADWE 219
                                          *************98.9*****999863689******************************************* PP

                            TIGR00407 229 kakkvivdaktqrPstCnaietLLvnkaiae..efleeLekqleekgvelradalvlkllelekateaevsked 300
                                           akkvi++akt++ s+Cna++ +Lv++++ +  + l  L+k l+   vel a++     +e  +a+e+    + 
  lcl|FitnessBrowser__Cola:Echvi_2633 220 LAKKVIINAKTNKISGCNALDKILVDEKLPDfeSKLADLAKSLASYKVELVAEKELVPAIE--GAKEVPSE-DT 290
                                          ****************************983114455677788889999999877665554..55776655.55 PP

                            TIGR00407 301 fdkeflsldLsvkivedleeaiehirqygtkhsdailtedkknaekfvkevdsaavyvnastrfadGfrfGfGa 374
                                          + +efl+l+  +  v+ l+eai+ i++y+  hs +ilt dk +a  f+++vdsaavy+nastrf+dG++ G Ga
  lcl|FitnessBrowser__Cola:Echvi_2633 291 WYEEFLALKALIGKVNGLDEAIAKINKYSGGHSATILTTDKDKAATFMEQVDSAAVYHNASTRFTDGGQMGVGA 364
                                          ************************************************************************** PP

                            TIGR00407 375 evgistqklharGPvGLeaLvsyk 398
                                          e++ist+klh rGP+GLe Lv+ k
  lcl|FitnessBrowser__Cola:Echvi_2633 365 ELAISTDKLHHRGPLGLEQLVTNK 388
                                          *********************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (398 nodes)
Target sequences:                          1  (399 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: 00:00:00.02
# Mc/sec: 7.21
//
[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