Alignments for a candidate for argC in Desulfovibrio vulgaris Hildenborough

GapMind for Amino acid biosynthesis

Alignments for a candidate for argC in Desulfovibrio vulgaris Hildenborough

Align N-acetyl-gamma-glutamyl-phosphate reductase; Short=AGPR; EC 1.2.1.38 (characterized, see rationale)
to candidate 209429 DVU0492 N-acetyl-gamma-glutamyl-phosphate reductase

Query= uniprot:E4PLW0
         (388 letters)



>MicrobesOnline__882:209429
          Length = 354

 Score =  290 bits (741), Expect = 6e-83
 Identities = 160/351 (45%), Positives = 214/351 (60%), Gaps = 7/351 (1%)

Query: 45  IKVGIVGGTGYTGVELLRILAVHPEVSVSCITSRSEAGMPVAEMYPNLRG--HYDLAFSE 102
           I+ G+VG TGYTG+EL R+LA HP + +   TSR+EAG  + ++YP L G    D+    
Sbjct: 4   IRAGLVGVTGYTGMELARLLAGHPAMRLVLATSRAEAGRRLDDIYPFLIGLPGGDITIVA 63

Query: 103 PDVNVLGA-CDLVFFATPHGVAMRMVPELMSAGVRVVDLSADFRLKDLDVWANWYGMAHE 161
           PD +V+ A CD+ F A PHG AM M   L   G+RVVDLSADFRL+D+ V+ +WY   H 
Sbjct: 64  PDPDVIAASCDIAFLAVPHGAAMEMAASLRERGLRVVDLSADFRLRDVTVYESWYRTDHT 123

Query: 162 SPEWAEKAVYGLPEVVRDEIRNAQLVANPGCYPTAVQLGFLPLLEQGLVDPKRLIADAKS 221
                 +AVYGLPE+   ++  A LVANPGCYPT+V LG    L+  +V    ++ DAKS
Sbjct: 124 RKGLLPEAVYGLPELYGKDVAQAGLVANPGCYPTSVILGLAAALDTDIVHRDDIVIDAKS 183

Query: 222 GASGAGRQGKIGMLHGEIGESFKAYGASGHRHLPEIRQGLCGAAGGDVGVTFVPHLIPMI 281
           GASGAGR+  +G L  E+ +SFKAY    HRH PEI Q L   AG  + V+F  HL+P+ 
Sbjct: 184 GASGAGRKAAVGSLFCEVHDSFKAYNLGKHRHTPEIEQELSVIAGEALTVSFNTHLLPID 243

Query: 282 RGIEATLYAELKNPADFDRLQALFEQRFDDEP----FVDVMPFGSHPETRSVRGANQCRM 337
           RGI +T+Y  +K P D D + A++   +        +V ++P G  PETR V+G   C +
Sbjct: 244 RGILSTMYLRMKKPLDLDTVHAMYADYWAAHQTRGGWVRLLPKGRLPETRHVKGTMFCDI 303

Query: 338 ALHRQEQSNIVIVSSVIDNLVKGAAGQAVQNMNIMFGLKETMGLEAPALLP 388
            L    ++  +IV S IDNL +GA+GQAV N NIM GL    GL    L+P
Sbjct: 304 GLVVDPRTGRLIVVSAIDNLCRGASGQAVANANIMLGLPVDAGLRLAPLMP 354


Lambda     K      H
   0.321    0.137    0.412 

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: 425
Number of extensions: 15
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: 388
Length of database: 354
Length adjustment: 30
Effective length of query: 358
Effective length of database: 324
Effective search space:   115992
Effective search space used:   115992
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate 209429 DVU0492 (N-acetyl-gamma-glutamyl-phosphate reductase)
to HMM TIGR01850 (argC: N-acetyl-gamma-glutamyl-phosphate reductase (EC 1.2.1.38))

# 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/TIGR01850.hmm
# target sequence database:        /tmp/gapView.25608.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01850  [M=345]
Accession:   TIGR01850
Description: argC: N-acetyl-gamma-glutamyl-phosphate reductase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   2.7e-121  390.9   0.0     3e-121  390.8   0.0    1.0  1  lcl|MicrobesOnline__882:209429  DVU0492 N-acetyl-gamma-glutamyl-


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:209429  DVU0492 N-acetyl-gamma-glutamyl-phosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  390.8   0.0    3e-121    3e-121       1     345 []       4     354 .]       4     354 .] 0.96

  Alignments for each domain:
  == domain 1  score: 390.8 bits;  conditional E-value: 3e-121
                       TIGR01850   1 ikvaivGasGYtGaeLlrllakHpevevtklvssre.agkklsevhphlkglvd..lkleeleeeeileeadvvflAlp 76 
                                     i++++vG +GYtG+eL rlla Hp+++++ l++sr+ ag++l++++p l gl     ++ + + + i++++d+ flA+p
  lcl|MicrobesOnline__882:209429   4 IRAGLVGVTGYTGMELARLLAGHPAMRLV-LATSRAeAGRRLDDIYPFLIGLPGgdITIVAPDPDVIAASCDIAFLAVP 81 
                                     5789*************************.5555555*************9987446666777799************* PP

                       TIGR01850  77 hgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnreeikkaklianPGCyaTaal 155
                                     hg+++e++++l e+g++v+dlSadfRl+d +vYe+wY+++h+++ ll eavYGlpEl+ +++++a l+anPGCy+T+++
  lcl|MicrobesOnline__882:209429  82 HGAAMEMAASLRERGLRVVDLSADFRLRDVTVYESWYRTDHTRKGLLPEAVYGLPELYGKDVAQAGLVANPGCYPTSVI 160
                                     ******************************************************************************* PP

                       TIGR01850 156 LalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvtkHrHtpEieqelsklaekkvkvsftphl 234
                                     L+la +l+++++++++i++daksG SgAGrka   slf+ev++++k+Y++ kHrHtpEieqels +a++  +vsf +hl
  lcl|MicrobesOnline__882:209429 161 LGLAAALDTDIVHRDDIVIDAKSGASGAGRKAAVGSLFCEVHDSFKAYNLGKHRHTPEIEQELSVIAGEALTVSFNTHL 239
                                     *******************************************************************99********** PP

                       TIGR01850 235 vpmtrGilatiyaklkkelteeelrklyeevYedep....fvrvlkegelPstkavlgsnfvdigvavdeetkrvvvvs 309
                                     +p+ rGil+t+y+++kk+l+ ++++++y+++++ ++    +vr+l++g+lP+t++v g+ f+dig+ vd +t+r++vvs
  lcl|MicrobesOnline__882:209429 240 LPIDRGILSTMYLRMKKPLDLDTVHAMYADYWAAHQtrggWVRLLPKGRLPETRHVKGTMFCDIGLVVDPRTGRLIVVS 318
                                     *******************************9977545559************************************** PP

                       TIGR01850 310 aiDNLvKGaagqAvqnlNlmlgfdetegLeklpllp 345
                                     aiDNL +Ga+gqAv n N+mlg++ ++gL+  pl+p
  lcl|MicrobesOnline__882:209429 319 AIDNLCRGASGQAVANANIMLGLPVDAGLRLAPLMP 354
                                     ********************************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (345 nodes)
Target sequences:                          1  (354 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 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 8.11
//
[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