Alignments for a candidate for proA in Desulfovibrio vulgaris Miyazaki F

GapMind for Amino acid biosynthesis

Alignments for a candidate for proA in Desulfovibrio vulgaris Miyazaki F

Align Gamma-glutamyl phosphate reductase; GPR; Glutamate-5-semialdehyde dehydrogenase; Glutamyl-gamma-semialdehyde dehydrogenase; GSA dehydrogenase; EC 1.2.1.41 (characterized)
to candidate 8499847 DvMF_0612 gamma-glutamyl phosphate reductase (RefSeq)

Query= SwissProt::P07004
         (417 letters)



>FitnessBrowser__Miya:8499847
          Length = 436

 Score =  356 bits (914), Expect = e-103
 Identities = 194/416 (46%), Positives = 265/416 (63%), Gaps = 3/416 (0%)

Query: 1   MLEQMGIAAKQASYKLAQLSSREKNRVLEKIADELEAQSEIILNANAQDVADARANGLSE 60
           ++E MG  AK A+ KLA  S   K   L ++A  LE++   IL ANA+D+A A A G+  
Sbjct: 23  LVESMGKRAKAAARKLAAASPAAKIDALVRLAGLLESREADILAANARDLAAAEAAGMDT 82

Query: 61  AMLDRLALTPARLKGIADDVRQVCNLADPVGQVIDGGVLDSGLRLERRRVPLGVIGVIYE 120
             +DRL LTP  +  +A   R V  L DPVG V       +GL + R R+PLGVI +IYE
Sbjct: 83  PRMDRLRLTPRIMAEMAAACRHVAGLPDPVGAVETQWQRPNGLLVGRMRIPLGVIAIIYE 142

Query: 121 ARPNVTVDVASLCLKTGNAVILRGGKETCRTNAATVAVIQDALKSCGLPAGAVQAIDNPD 180
           +RPNVT+D A LCLK GNAVILRGG E   +N A   +I +A+ + GLP  AVQ +   D
Sbjct: 143 SRPNVTIDSAILCLKAGNAVILRGGSEAIHSNLALAGLIAEAMSASGLPDDAVQVVSRTD 202

Query: 181 RALVSEMLRMDKYIDMLIPRGGAGLHKLCREQSTIPVITGGIGVCHIYVDESVEIAEALK 240
           RA V  +  +++YID++IPRGG  L +   +Q+T+PV+    GVCH YVD   ++ +A++
Sbjct: 203 RAAVGALCALEQYIDVIIPRGGETLIRAVVQQATMPVLKHYKGVCHAYVDAGADLDQAVE 262

Query: 241 VIVNAKTQRPSTCNTVETLLVNKNIADSFLPALSKQMAESGVTLHADAAALAQLQAGPAK 300
           ++ N K QRP  CN +E LLV+K+ A + LPA++ ++A +GVT  A   AL  L  G A 
Sbjct: 263 IVFNGKVQRPGVCNALECLLVHKDEAAALLPAVAARLAPAGVTFRACPTALPLL--GDA- 319

Query: 301 VVAVKAEEYDDEFLSLDLNVKIVSDLDDAIAHIREHGTQHSDAILTRDMRNAQRFVNEVD 360
             A   E+Y  EF  L L V++V D+D+A+AHI  HG+ H++ I TRD   A RF+ E D
Sbjct: 320 ATAAAPEDYGMEFHDLILAVRVVDDMDEALAHIAAHGSNHTEIICTRDHGRAMRFLREAD 379

Query: 361 SSAVYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKWIGIGDYTIR 416
           +S V VNASTRF DGGQ GLGAE+ +ST KLH+ GPMG++ LTT K++  G   +R
Sbjct: 380 ASMVAVNASTRFNDGGQLGLGAEIGISTSKLHSYGPMGVQELTTTKFVVFGAGQVR 435


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: 439
Number of extensions: 12
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: 436
Length adjustment: 32
Effective length of query: 385
Effective length of database: 404
Effective search space:   155540
Effective search space used:   155540
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: 51 (24.3 bits)

Align candidate 8499847 DvMF_0612 (gamma-glutamyl phosphate reductase (RefSeq))
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.12376.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   8.7e-135  435.5   0.3     1e-134  435.3   0.3    1.0  1  lcl|FitnessBrowser__Miya:8499847  DvMF_0612 gamma-glutamyl phospha


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8499847  DvMF_0612 gamma-glutamyl phosphate reductase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  435.3   0.3    1e-134    1e-134       1     398 []      31     425 ..      31     425 .. 0.98

  Alignments for each domain:
  == domain 1  score: 435.3 bits;  conditional E-value: 1e-134
                         TIGR00407   1 akeaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksiaddvkdvie 77 
                                       ak aa kla  s a k +al  +a  L+ +   ilaana+d+aaa++ G+  + +drL Lt + + ++a++ ++v+ 
  lcl|FitnessBrowser__Miya:8499847  31 AKAAARKLAAASPAAKIDALVRLAGLLESREADILAANARDLAAAEAAGMDTPRMDRLRLTPRIMAEMAAACRHVAG 107
                                       899************************************************************************** PP

                         TIGR00407  78 LadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgkeavrsnkalveviqda 154
                                       L+dPvG v ++ ++ +GL + r+r+PlGv+ +iye+rP+v++d a Lclk+GnaviL+Gg+ea++sn al+ +i +a
  lcl|FitnessBrowser__Miya:8499847 108 LPDPVGAVETQWQRPNGLLVGRMRIPLGVIAIIYESRPNVTIDSAILCLKAGNAVILRGGSEAIHSNLALAGLIAEA 184
                                       ***************************************************************************** PP

                         TIGR00407 155 leqtglpveavqliedpdreevkellkldeyvdlliPrGgnelvklikeestiPvlehadGvChiyldesadlakak 231
                                       +  +glp  avq++  +dr+ v  l  l++y+d++iPrGg+ l++ + +++t+Pvl+h +GvCh y+d+ adl +a 
  lcl|FitnessBrowser__Miya:8499847 185 MSASGLPDDAVQVVSRTDRAAVGALCALEQYIDVIIPRGGETLIRAVVQQATMPVLKHYKGVCHAYVDAGADLDQAV 261
                                       ***************************************************************************** PP

                         TIGR00407 232 kvivdaktqrPstCnaietLLvnkaiaeefleeLekqleekgvelradalvlkllelekateaevskedfdkeflsl 308
                                       +++ + k qrP +Cna+e LLv+k+ a+  l++++ +l+ +gv++ra  ++l ll  +     +++ ed+  ef +l
  lcl|FitnessBrowser__Miya:8499847 262 EIVFNGKVQRPGVCNALECLLVHKDEAAALLPAVAARLAPAGVTFRACPTALPLLGDA--AT-AAAPEDYGMEFHDL 335
                                       ***********************************************99999998766..33.345689******** PP

                         TIGR00407 309 dLsvkivedleeaiehirqygtkhsdailtedkknaekfvkevdsaavyvnastrfadGfrfGfGaevgistqklha 385
                                       +L+v++v+d++ea++hi  +g++h++ i t+d+  a +f++e d++ v vnastrf dG++ G+Gae+gist+klh+
  lcl|FitnessBrowser__Miya:8499847 336 ILAVRVVDDMDEALAHIAAHGSNHTEIICTRDHGRAMRFLREADASMVAVNASTRFNDGGQLGLGAEIGISTSKLHS 412
                                       ***************************************************************************** PP

                         TIGR00407 386 rGPvGLeaLvsyk 398
                                        GP+G++ L+++k
  lcl|FitnessBrowser__Miya:8499847 413 YGPMGVQELTTTK 425
                                       **********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (398 nodes)
Target sequences:                          1  (436 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: 12.05
//
[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