Alignments for a candidate for proA in Acidovorax sp. GW101-3H11

GapMind for Amino acid biosynthesis

Alignments for a candidate for proA in Acidovorax sp. GW101-3H11

Align Gamma-glutamyl phosphate reductase; GPR; Glutamate-5-semialdehyde dehydrogenase; Glutamyl-gamma-semialdehyde dehydrogenase; GSA dehydrogenase; EC 1.2.1.41 (characterized)
to candidate Ac3H11_704 Gamma-glutamyl phosphate reductase (EC 1.2.1.41)

Query= SwissProt::P07004
         (417 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_704
          Length = 426

 Score =  338 bits (866), Expect = 2e-97
 Identities = 177/413 (42%), Positives = 268/413 (64%), Gaps = 1/413 (0%)

Query: 5   MGIAAKQASYKLAQLSSREKNRVLEKIADELEAQSEIILNANAQDVADARANGLSEAMLD 64
           +G+ AK AS  +A+  +  KN+ L+ +A  L    + +   NA+D+  ARA GL+E M+D
Sbjct: 13  LGLQAKTASALMAKAPAAIKNKALKALARLLRENVDALQIDNARDLERARAAGLAEPMVD 72

Query: 65  RLALTPARLKGIADDVRQVCNLADPVGQVIDGGVLDSGLRLERRRVPLGVIGVIYEARPN 124
           RL L+P  L+  A+   Q+  + D +G+++      SG+R+ + RVP+GV G+IYE+RPN
Sbjct: 73  RLKLSPKVLETCAEGCEQLAAMPDIIGEILGMKQQPSGIRVGQMRVPIGVFGMIYESRPN 132

Query: 125 VTVDVASLCLKTGNAVILRGGKETCRTNAATVAVIQDALKSCGLPAGAVQAIDNPDRALV 184
           VT++ ASL +K+GNA ILRGG E   +N A   ++Q AL   GLP  AVQ +   DR  V
Sbjct: 133 VTIEAASLSIKSGNACILRGGSEAIDSNKALAKLVQQALAEAGLPQDAVQLVQTTDREAV 192

Query: 185 SEMLRMDKYIDMLIPRGGAGLHKLCREQSTIPVITGGIGVCHIYVDESVEIAEALKVIVN 244
            +++ M +++D++IPRGG GL +     + +PVI    G CH YVD+  ++  A+KV  N
Sbjct: 193 GQLIAMPQFVDVIIPRGGKGLIERISRDAKVPVIKHLDGNCHTYVDDPCDVPMAVKVADN 252

Query: 245 AKTQRPSTCNTVETLLVNKNIADSFLPALSKQMAESGVTLHADAAALAQLQA-GPAKVVA 303
           AKT + S CN  E LLV + +A  FLP +    A  GV +     +LA LQ+   A++V 
Sbjct: 253 AKTNKYSPCNASEGLLVARGVAAEFLPKIGAVYAAKGVEMRGCPESLAILQSVAGAQLVP 312

Query: 304 VKAEEYDDEFLSLDLNVKIVSDLDDAIAHIREHGTQHSDAILTRDMRNAQRFVNEVDSSA 363
              +++ +E+L+  ++VKIV+ LD+AIAHI  + + H+DAILT +  +AQRF+ EVDS++
Sbjct: 313 ATEQDWSEEYLAPIISVKIVAGLDEAIAHINHYSSHHTDAILTTNHVHAQRFLREVDSAS 372

Query: 364 VYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKWIGIGDYTIR 416
           V VNASTRF DG ++GLGAE+ +ST K HARGP+G+E LT+ K++ +G+  +R
Sbjct: 373 VMVNASTRFADGFEYGLGAEIGISTDKFHARGPVGIEGLTSLKYVVLGEGEVR 425


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: 436
Number of extensions: 16
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: 426
Length adjustment: 32
Effective length of query: 385
Effective length of database: 394
Effective search space:   151690
Effective search space used:   151690
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 Ac3H11_704 (Gamma-glutamyl phosphate reductase (EC 1.2.1.41))
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.3852.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   2.9e-147  476.6   0.3   3.3e-147  476.4   0.3    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_704  Gamma-glutamyl phosphate reducta


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_704  Gamma-glutamyl phosphate reductase (EC 1.2.1.41)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  476.4   0.3  3.3e-147  3.3e-147       1     398 []      17     415 ..      17     415 .. 0.98

  Alignments for each domain:
  == domain 1  score: 476.4 bits;  conditional E-value: 3.3e-147
                                       TIGR00407   1 akeaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLtee 63 
                                                     ak a++ +a+  +a kn+al+++a  L+++++++  +na+d++ a++ Gla++++drL+L+ +
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_704  17 AKTASALMAKAPAAIKNKALKALARLLRENVDALQIDNARDLERARAAGLAEPMVDRLKLSPK 79 
                                                     899************************************************************ PP

                                       TIGR00407  64 klksiaddvkdvieLadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLcl 126
                                                      l++ a++ ++++ ++d +G+++  ++  +G+++ ++rvP+Gv g+iye+rP+v++++asL++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_704  80 VLETCAEGCEQLAAMPDIIGEILGMKQQPSGIRVGQMRVPIGVFGMIYESRPNVTIEAASLSI 142
                                                     *************************************************************** PP

                                       TIGR00407 127 ktGnaviLkGgkeavrsnkalveviqdaleqtglpveavqliedpdreevkellkldeyvdll 189
                                                     k+Gna iL+Gg+ea+ snkal++++q+al+++glp+ avql++++dre v +l+ + ++vd++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_704 143 KSGNACILRGGSEAIDSNKALAKLVQQALAEAGLPQDAVQLVQTTDREAVGQLIAMPQFVDVI 205
                                                     *************************************************************** PP

                                       TIGR00407 190 iPrGgnelvklikeestiPvlehadGvChiyldesadlakakkvivdaktqrPstCnaietLL 252
                                                     iPrGg++l++ i +++++Pv++h dG+Ch+y+d+  d+ +a kv ++akt++ s Cna e LL
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_704 206 IPRGGKGLIERISRDAKVPVIKHLDGNCHTYVDDPCDVPMAVKVADNAKTNKYSPCNASEGLL 268
                                                     *************************************************************** PP

                                       TIGR00407 253 vnkaiaeefleeLekqleekgvelra.dalvlkllelekateaevskedfdkeflsldLsvki 314
                                                     v + +a+efl+++    ++kgve+r+  +    l+++++a+ + ++++d+ +e+l++++svki
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_704 269 VARGVAAEFLPKIGAVYAAKGVEMRGcPESLAILQSVAGAQLVPATEQDWSEEYLAPIISVKI 331
                                                     **************************4344455566788999********************* PP

                                       TIGR00407 315 vedleeaiehirqygtkhsdailtedkknaekfvkevdsaavyvnastrfadGfrfGfGaevg 377
                                                     v  l+eai+hi++y+++h+dailt ++  a++f++evdsa+v vnastrfadGf++G+Gae+g
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_704 332 VAGLDEAIAHINHYSSHHTDAILTTNHVHAQRFLREVDSASVMVNASTRFADGFEYGLGAEIG 394
                                                     *************************************************************** PP

                                       TIGR00407 378 istqklharGPvGLeaLvsyk 398
                                                     ist+k+harGPvG+e+L+s k
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_704 395 ISTDKFHARGPVGIEGLTSLK 415
                                                     ******************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (398 nodes)
Target sequences:                          1  (426 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: 9.65
//
[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