Alignments for a candidate for proA in Desulfovibrio vulgaris Hildenborough

GapMind for Amino acid biosynthesis

Alignments for a candidate for proA in Desulfovibrio vulgaris Hildenborough

Align Gamma-glutamyl phosphate reductase; GPR; Glutamate-5-semialdehyde dehydrogenase; Glutamyl-gamma-semialdehyde dehydrogenase; GSA dehydrogenase; EC 1.2.1.41 (characterized)
to candidate 207423 DVU1953 gamma-glutamyl phosphate reductase

Query= SwissProt::P07004
         (417 letters)



>MicrobesOnline__882:207423
          Length = 419

 Score =  354 bits (909), Expect = e-102
 Identities = 189/415 (45%), Positives = 268/415 (64%), Gaps = 3/415 (0%)

Query: 2   LEQMGIAAKQASYKLAQLSSREKNRVLEKIADELEAQSEIILNANAQDVADARANGLSEA 61
           +E MG  A+ A  +LA  S   K   L+ +A  LE + + IL ANA D+A A   G+   
Sbjct: 7   IEDMGRRARAAGRRLAAASPAAKAGALDHLATLLEQRQDAILAANAADLAAAAEAGMDAP 66

Query: 62  MLDRLALTPARLKGIADDVRQVCNLADPVGQVIDGGVLDSGLRLERRRVPLGVIGVIYEA 121
            +DRL LTPA +  +A   R V  L DPVG +       +GL + + R+PLGVI +IYE+
Sbjct: 67  RMDRLRLTPATIAEMAAACRHVAALPDPVGAIETQWQRPNGLLVGKMRIPLGVIAMIYES 126

Query: 122 RPNVTVDVASLCLKTGNAVILRGGKETCRTNAATVAVIQDALKSCGLPAGAVQAIDNPDR 181
           RPNVT+D A LCLK GNAVILRGG E   +N A  A+I +AL S GLPA AVQ +   DR
Sbjct: 127 RPNVTIDSAILCLKAGNAVILRGGSEAIHSNLALAALITEALSSVGLPAEAVQVVSTTDR 186

Query: 182 ALVSEMLRMDKYIDMLIPRGGAGLHKLCREQSTIPVITGGIGVCHIYVDESVEIAEALKV 241
           A+++E+ +++++ID++IPRGG  L +   + + +PV+    GVCH Y+D   ++A+A+++
Sbjct: 187 AVIAELCKLEEHIDVIIPRGGETLIRAVVDMARMPVLKHYKGVCHAYIDSGADLAQAVEI 246

Query: 242 IVNAKTQRPSTCNTVETLLVNKNIADSFLPALSKQMAESGVTLHADAAALAQLQAGPAKV 301
           I NAK QRP  CN +E LLV+++ A +FLPA+++++   GV   A  A+L  L       
Sbjct: 247 IHNAKVQRPGVCNALEGLLVHRDEAAAFLPAIAERLGNDGVEFRACPASLPLL---GDSA 303

Query: 302 VAVKAEEYDDEFLSLDLNVKIVSDLDDAIAHIREHGTQHSDAILTRDMRNAQRFVNEVDS 361
           + +K E+   EF  L L V+IV D+D+A+AHI  +G+ H++ I TRD  NA RF+ E D+
Sbjct: 304 IPMKDEDNGQEFHDLILLVRIVDDMDEALAHIAAYGSNHTEIICTRDHGNAMRFLREADA 363

Query: 362 SAVYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKWIGIGDYTIR 416
           S V VNAS+RF DGGQ GLGAE+ +ST KLH+ GPMG++ LTT K++  G   IR
Sbjct: 364 SMVAVNASSRFNDGGQLGLGAEIGISTSKLHSYGPMGVQELTTTKFVVFGAGQIR 418


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: 440
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: 419
Length adjustment: 32
Effective length of query: 385
Effective length of database: 387
Effective search space:   148995
Effective search space used:   148995
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 207423 DVU1953 (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.28331.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-137  442.6   0.4   6.6e-137  442.5   0.4    1.0  1  lcl|MicrobesOnline__882:207423  DVU1953 gamma-glutamyl phosphate


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:207423  DVU1953 gamma-glutamyl phosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  442.5   0.4  6.6e-137  6.6e-137       1     398 []      14     408 ..      14     408 .. 0.99

  Alignments for each domain:
  == domain 1  score: 442.5 bits;  conditional E-value: 6.6e-137
                       TIGR00407   1 akeaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksiaddvkdvieLa 79 
                                     a+ a+ +la  s a k  al  +a  L+++ ++ilaana d+aaa e G+  + +drL Lt + + ++a++ ++v+ L+
  lcl|MicrobesOnline__882:207423  14 ARAAGRRLAAASPAAKAGALDHLATLLEQRQDAILAANAADLAAAAEAGMDAPRMDRLRLTPATIAEMAAACRHVAALP 92 
                                     899**************************************************************************** PP

                       TIGR00407  80 dPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgkeavrsnkalveviqdaleqt 158
                                     dPvG + ++ ++ +GL + ++r+PlGv+ +iye+rP+v++d a Lclk+GnaviL+Gg+ea++sn al+++i +al + 
  lcl|MicrobesOnline__882:207423  93 DPVGAIETQWQRPNGLLVGKMRIPLGVIAMIYESRPNVTIDSAILCLKAGNAVILRGGSEAIHSNLALAALITEALSSV 171
                                     ******************************************************************************* PP

                       TIGR00407 159 glpveavqliedpdreevkellkldeyvdlliPrGgnelvklikeestiPvlehadGvChiyldesadlakakkvivda 237
                                     glp+eavq++ ++dr+ + el kl+e +d++iPrGg+ l++ + + +++Pvl+h +GvCh y+d  adla+a ++i +a
  lcl|MicrobesOnline__882:207423 172 GLPAEAVQVVSTTDRAVIAELCKLEEHIDVIIPRGGETLIRAVVDMARMPVLKHYKGVCHAYIDSGADLAQAVEIIHNA 250
                                     ******************************************************************************* PP

                       TIGR00407 238 ktqrPstCnaietLLvnkaiaeefleeLekqleekgvelradalvlkllelekateaevskedfdkeflsldLsvkive 316
                                     k qrP +Cna+e LLv+++ a+ fl++++++l + gve+ra  + l ll  +    + +++ed  +ef +l+L v+iv+
  lcl|MicrobesOnline__882:207423 251 KVQRPGVCNALEGLLVHRDEAAAFLPAIAERLGNDGVEFRACPASLPLLGDS---AIPMKDEDNGQEFHDLILLVRIVD 326
                                     *****************************************99999988877...456788999*************** PP

                       TIGR00407 317 dleeaiehirqygtkhsdailtedkknaekfvkevdsaavyvnastrfadGfrfGfGaevgistqklharGPvGLeaLv 395
                                     d++ea++hi  yg++h++ i t+d+ na +f++e d++ v vnas rf dG++ G+Gae+gist+klh+ GP+G++ L+
  lcl|MicrobesOnline__882:207423 327 DMDEALAHIAAYGSNHTEIICTRDHGNAMRFLREADASMVAVNASSRFNDGGQLGLGAEIGISTSKLHSYGPMGVQELT 405
                                     ******************************************************************************* PP

                       TIGR00407 396 syk 398
                                     ++k
  lcl|MicrobesOnline__882:207423 406 TTK 408
                                     997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (398 nodes)
Target sequences:                          1  (419 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.08
//
[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