Alignments for a candidate for proA in Desulfitobacterium hafniense DCB-2

GapMind for Amino acid biosynthesis

Alignments for a candidate for proA in Desulfitobacterium hafniense DCB-2

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_015944065.1 DHAF_RS12410 gamma-glutamyl-phosphate reductase

Query= SwissProt::P07004
         (417 letters)



>NCBI__GCF_000021925.1:WP_015944065.1
          Length = 417

 Score =  370 bits (950), Expect = e-107
 Identities = 188/408 (46%), Positives = 276/408 (67%), Gaps = 5/408 (1%)

Query: 5   MGIAAKQASYKLAQLSSREKNRVLEKIADELEAQSEIILNANAQDVADARANGLSEAMLD 64
           +G  AK A+ KLA   +  KN+ L  +A+ L    + IL AN +DV  A   G  +++++
Sbjct: 10  IGQKAKDAARKLAYAGTAAKNKALLAMAEALLNHEQKILEANRKDVEAAIQKGTKKSLVN 69

Query: 65  RLALTPARLKGIADDVRQVCNLADPVGQVIDGGVLDSGLRLERRRVPLGVIGVIYEARPN 124
           RLALT   ++ ++D +++V NL DPVG+  +     +GLR++R RVPLGV+ +IYEARPN
Sbjct: 70  RLALTSEGIRQMSDALKEVVNLGDPVGEG-EFWTRPNGLRIQRTRVPLGVVAMIYEARPN 128

Query: 125 VTVDVASLCLKTGNAVILRGGKETCRTNAATVAVIQDALKSCGLPAGAVQAIDNPDRALV 184
           VTVD A+LCLK+GNAVILRGG E   +N     VI  A +S G+P   +Q ++N +R  V
Sbjct: 129 VTVDAAALCLKSGNAVILRGGSEAIESNKILSKVIAGAAESQGMPTACIQLLENTNRQWV 188

Query: 185 SEMLRMDKYIDMLIPRGGAGLHKLCREQSTIPVITGGIGVCHIYVDESVEIAEALKVIVN 244
            ++++M+ Y+D++IPRGGAGL +   +++T+PVI  G GVCH YVD   ++A+ + ++ N
Sbjct: 189 QQLMKMNGYVDVIIPRGGAGLIETVVKEATVPVIETGTGVCHAYVDGEADLAKGVSIVFN 248

Query: 245 AKTQRPSTCNTVETLLVNKNIADSFLPALSKQMAESGVTLHADAAALAQLQAGPAKVVAV 304
           AKTQ+P  CN +E +LVN+ +A  FLP L ++  + GV +       A L          
Sbjct: 249 AKTQKPGVCNALEAVLVNEAVAQEFLPLLGEKFRDYGVEIRGCEKTCAIL----PYAAKA 304

Query: 305 KAEEYDDEFLSLDLNVKIVSDLDDAIAHIREHGTQHSDAILTRDMRNAQRFVNEVDSSAV 364
           K E++  E L L ++ K+V  +D+A+ HI ++GT+HS+ I+T +   AQRF+NEVD++AV
Sbjct: 305 KEEDWGIEHLDLIISAKVVQGVDEAMDHIYQYGTKHSETIITENYTTAQRFLNEVDAAAV 364

Query: 365 YVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKWIGIGD 412
           YVNASTRFTDGG+FG GAE+ +STQKLHARGPMGL+ALTT K++  G+
Sbjct: 365 YVNASTRFTDGGRFGFGAEIGISTQKLHARGPMGLQALTTMKYMVYGE 412


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: 402
Number of extensions: 14
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: 417
Length of database: 417
Length adjustment: 31
Effective length of query: 386
Effective length of database: 386
Effective search space:   148996
Effective search space used:   148996
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_015944065.1 DHAF_RS12410 (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.6868.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.6e-158  512.5   1.7   4.1e-158  512.3   1.7    1.0  1  lcl|NCBI__GCF_000021925.1:WP_015944065.1  DHAF_RS12410 gamma-glutamyl-phos


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000021925.1:WP_015944065.1  DHAF_RS12410 gamma-glutamyl-phosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  512.3   1.7  4.1e-158  4.1e-158       1     398 []      14     406 ..      14     406 .. 0.99

  Alignments for each domain:
  == domain 1  score: 512.3 bits;  conditional E-value: 4.1e-158
                                 TIGR00407   1 akeaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksia 69 
                                               ak+aa kla   ta kn+al ++a++L ++ + il+an+kd++aa ++G  ++l++rL+Lt e ++++ 
  lcl|NCBI__GCF_000021925.1:WP_015944065.1  14 AKDAARKLAYAGTAAKNKALLAMAEALLNHEQKILEANRKDVEAAIQKGTKKSLVNRLALTSEGIRQMS 82 
                                               89******************************************************************* PP

                                 TIGR00407  70 ddvkdvieLadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgk 138
                                               d++k+v++L dPvG+  e  ++ +GL+++r rvPlGv+ +iyearP+v+vd+a+Lclk+GnaviL+Gg+
  lcl|NCBI__GCF_000021925.1:WP_015944065.1  83 DALKEVVNLGDPVGEG-EFWTRPNGLRIQRTRVPLGVVAMIYEARPNVTVDAAALCLKSGNAVILRGGS 150
                                               **************97.567889********************************************** PP

                                 TIGR00407 139 eavrsnkalveviqdaleqtglpveavqliedpdreevkellkldeyvdlliPrGgnelvklikeesti 207
                                               ea++snk+l +vi  a e+ g+p+ ++ql+e+++r+ v++l+k++ yvd++iPrGg++l++ + +e+t+
  lcl|NCBI__GCF_000021925.1:WP_015944065.1 151 EAIESNKILSKVIAGAAESQGMPTACIQLLENTNRQWVQQLMKMNGYVDVIIPRGGAGLIETVVKEATV 219
                                               ********************************************************************* PP

                                 TIGR00407 208 PvlehadGvChiyldesadlakakkvivdaktqrPstCnaietLLvnkaiaeefleeLekqleekgvel 276
                                               Pv+e+++GvCh y+d +adlak   ++ +aktq+P +Cna+e++Lvn+a+a+efl+ L ++  + gve+
  lcl|NCBI__GCF_000021925.1:WP_015944065.1 220 PVIETGTGVCHAYVDGEADLAKGVSIVFNAKTQKPGVCNALEAVLVNEAVAQEFLPLLGEKFRDYGVEI 288
                                               ********************************************************************* PP

                                 TIGR00407 277 radalvlkllelekateaevskedfdkeflsldLsvkivedleeaiehirqygtkhsdailtedkknae 345
                                               r+ ++++++l+ +    a++++ed+  e+l+l++s+k+v+ ++ea++hi qygtkhs++i+te+ ++a+
  lcl|NCBI__GCF_000021925.1:WP_015944065.1 289 RGCEKTCAILPYA----AKAKEEDWGIEHLDLIISAKVVQGVDEAMDHIYQYGTKHSETIITENYTTAQ 353
                                               ***********99....677899********************************************** PP

                                 TIGR00407 346 kfvkevdsaavyvnastrfadGfrfGfGaevgistqklharGPvGLeaLvsyk 398
                                               +f++evd+aavyvnastrf+dG+rfGfGae+gistqklharGP+GL+aL+++k
  lcl|NCBI__GCF_000021925.1:WP_015944065.1 354 RFLNEVDAAAVYVNASTRFTDGGRFGFGAEIGISTQKLHARGPMGLQALTTMK 406
                                               **************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (398 nodes)
Target sequences:                          1  (417 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.84
//
[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