Alignments for a candidate for proA in Denitrovibrio acetiphilus DSM 12809

GapMind for Amino acid biosynthesis

Alignments for a candidate for proA in Denitrovibrio acetiphilus DSM 12809

Align Gamma-glutamyl phosphate reductase; GPR; Glutamate-5-semialdehyde dehydrogenase; Glutamyl-gamma-semialdehyde dehydrogenase; GSA dehydrogenase; EC 1.2.1.41 (characterized)
to candidate WP_013011161.1 DACET_RS09495 glutamate-5-semialdehyde dehydrogenase

Query= SwissProt::P07004
         (417 letters)



>NCBI__GCF_000025725.1:WP_013011161.1
          Length = 411

 Score =  358 bits (919), Expect = e-103
 Identities = 183/407 (44%), Positives = 267/407 (65%), Gaps = 5/407 (1%)

Query: 1   MLEQMGIAAKQASYKLAQLSSREKNRVLEKIADELEAQSEIILNANAQDVADARANGLSE 60
           MLE M   AK+ASY L  +++  K+  L  IA++LEA    I N N +D+  AR  GLS+
Sbjct: 1   MLENMFREAKKASYVLMNVNTDVKDSALSAIAEKLEANRVKIKNENLKDLDYARETGLSD 60

Query: 61  AMLDRLALTPARLKGIADDVRQVCNLADPVGQVIDGGVLDSGLRLERRRVPLGVIGVIYE 120
           A++DRL L   R+ G+   V+ + +  DPVG+V+DG    +GL + + +VPLGV+G+I+E
Sbjct: 61  ALIDRLTLDDKRIDGMIQAVKDIRSQVDPVGKVVDGYKRPNGLYITKVKVPLGVVGIIFE 120

Query: 121 ARPNVTVDVASLCLKTGNAVILRGGKETCRTNAATVAVIQDALKSCGLPAGAVQAIDNPD 180
           +RPNVT+D A+LCLK+GN  ILRGGKE   +N     ++++A+   GLP   V  I++ D
Sbjct: 121 SRPNVTIDAAALCLKSGNVAILRGGKEAVHSNTYLGRLMKEAVAEAGLPKACVNIIEDTD 180

Query: 181 RALVSEMLRMDKYIDMLIPRGGAGLHKLCREQSTIPVITGGIGVCHIYVDESVEIAEALK 240
           R LV EML+    ID++IPRGG  L + C E S IP++    G+CH+Y+D+  +I  A+ 
Sbjct: 181 RGLVMEMLKAKGSIDIMIPRGGKALIEFCTEHSLIPLVKHDDGICHVYIDKFADIEMAVS 240

Query: 241 VIVNAKTQRPSTCNTVETLLVNKNIADSFLPALSKQMAESGVTLHADAAALAQLQAGPAK 300
           + VNAK QR   CNT+ETLLV++ +A++ L  L K   E  V L         +    A 
Sbjct: 241 IAVNAKCQRVGVCNTMETLLVHEAVAETVLKRLEKAYGEHNVELRGCEHTAELISCKKA- 299

Query: 301 VVAVKAEEYDDEFLSLDLNVKIVSDLDDAIAHIREHGTQHSDAILTRDMRNAQRFVNEVD 360
                 E++  E+L   L+VK+VS +D+AI HI ++G+ HS++I+T +  N++ F+N VD
Sbjct: 300 ----AEEDWSTEYLDYILSVKVVSSIDEAIEHINKYGSMHSESIVTENYTNSEMFLNMVD 355

Query: 361 SSAVYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKW 407
           ++AVYVNASTR+TDGG+FG+GAE+ +STQKLH RGPMG + LTT K+
Sbjct: 356 AAAVYVNASTRWTDGGEFGMGAEIGISTQKLHCRGPMGADDLTTTKY 402


Lambda     K      H
   0.317    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: 422
Number of extensions: 14
Number of successful extensions: 2
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: 417
Length of database: 411
Length adjustment: 31
Effective length of query: 386
Effective length of database: 380
Effective search space:   146680
Effective search space used:   146680
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: 50 (23.9 bits)

Align candidate WP_013011161.1 DACET_RS09495 (glutamate-5-semialdehyde dehydrogenase)
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.11758.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.4e-158  512.6   3.8   3.9e-158  512.4   3.8    1.0  1  lcl|NCBI__GCF_000025725.1:WP_013011161.1  DACET_RS09495 glutamate-5-semial


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000025725.1:WP_013011161.1  DACET_RS09495 glutamate-5-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  512.4   3.8  3.9e-158  3.9e-158       1     398 []       9     401 ..       9     401 .. 0.99

  Alignments for each domain:
  == domain 1  score: 512.4 bits;  conditional E-value: 3.9e-158
                                 TIGR00407   1 akeaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksia 69 
                                               ak+a++ l++++t+ k++als+ia++L+a+   i ++n kd+  a+e+Gl+dal+drL+L+++++ +++
  lcl|NCBI__GCF_000025725.1:WP_013011161.1   9 AKKASYVLMNVNTDVKDSALSAIAEKLEANRVKIKNENLKDLDYARETGLSDALIDRLTLDDKRIDGMI 77 
                                               89******************************************************************* PP

                                 TIGR00407  70 ddvkdvieLadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgk 138
                                               ++vkd+ +  dPvGkv+++ ++ +GL + +v+vPlGv+g+i+e+rP+v++d+a+Lclk+Gn +iL+Ggk
  lcl|NCBI__GCF_000025725.1:WP_013011161.1  78 QAVKDIRSQVDPVGKVVDGYKRPNGLYITKVKVPLGVVGIIFESRPNVTIDAAALCLKSGNVAILRGGK 146
                                               ********************************************************************* PP

                                 TIGR00407 139 eavrsnkalveviqdaleqtglpveavqliedpdreevkellkldeyvdlliPrGgnelvklikeesti 207
                                               eav+sn  l +++++a++++glp+ +v++ied+dr  v+e+lk    +d++iPrGg++l++ + e+s i
  lcl|NCBI__GCF_000025725.1:WP_013011161.1 147 EAVHSNTYLGRLMKEAVAEAGLPKACVNIIEDTDRGLVMEMLKAKGSIDIMIPRGGKALIEFCTEHSLI 215
                                               ********************************************************************* PP

                                 TIGR00407 208 PvlehadGvChiyldesadlakakkvivdaktqrPstCnaietLLvnkaiaeefleeLekqleekgvel 276
                                               P ++h dG+Ch+y+d+ ad+++a  + v+ak qr  +Cn++etLLv++a+ae  l++Lek+  e++vel
  lcl|NCBI__GCF_000025725.1:WP_013011161.1 216 PLVKHDDGICHVYIDKFADIEMAVSIAVNAKCQRVGVCNTMETLLVHEAVAETVLKRLEKAYGEHNVEL 284
                                               ********************************************************************* PP

                                 TIGR00407 277 radalvlkllelekateaevskedfdkeflsldLsvkivedleeaiehirqygtkhsdailtedkknae 345
                                               r+ + + +l++++ka e     ed+ +e+l+ +Lsvk+v++++eaiehi++yg+ hs++i+te+ +n+e
  lcl|NCBI__GCF_000025725.1:WP_013011161.1 285 RGCEHTAELISCKKAAE-----EDWSTEYLDYILSVKVVSSIDEAIEHINKYGSMHSESIVTENYTNSE 348
                                               ************96655.....89********************************************* PP

                                 TIGR00407 346 kfvkevdsaavyvnastrfadGfrfGfGaevgistqklharGPvGLeaLvsyk 398
                                                f++ vd+aavyvnastr++dG++fG+Gae+gistqklh rGP+G + L+++k
  lcl|NCBI__GCF_000025725.1:WP_013011161.1 349 MFLNMVDAAAVYVNASTRWTDGGEFGMGAEIGISTQKLHCRGPMGADDLTTTK 401
                                               **************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (398 nodes)
Target sequences:                          1  (411 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: 7.97
//
[ok]

This GapMind analysis is from Apr 10 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