Alignments for a candidate for argC in Desulfovibrio vulgaris Miyazaki F

GapMind for Amino acid biosynthesis

Alignments for a candidate for argC in Desulfovibrio vulgaris Miyazaki F

Align N-acetyl-gamma-glutamyl-phosphate reductase; Short=AGPR; EC 1.2.1.38 (characterized, see rationale)
to candidate 8500980 DvMF_1717 N-acetyl-gamma-glutamyl-phosphate reductase (RefSeq)

Query= uniprot:E4PLW0
         (388 letters)



>FitnessBrowser__Miya:8500980
          Length = 350

 Score =  315 bits (808), Expect = 1e-90
 Identities = 165/349 (47%), Positives = 224/349 (64%), Gaps = 5/349 (1%)

Query: 44  VIKVGIVGGTGYTGVELLRILAVHPEVSVSCITSRSEAGMPVAEMYPNLRG----HYDLA 99
           +I+ G+VG TGYTG+EL R+LA HP + +   TSR+EAG P++++YP LRG    +  + 
Sbjct: 3   IIRAGLVGVTGYTGMELTRLLAGHPNMRLVRATSRTEAGRPLSDIYPFLRGLPGGNAVMT 62

Query: 100 FSEPDVNVLGACDLVFFATPHGVAMRMVPELMSAGVRVVDLSADFRLKDLDVWANWYGMA 159
             +PD ++   CD+ F A PHG AM M   L   G+RVVDLSADFRL+D DV+  WY + 
Sbjct: 63  APDPD-DLADNCDVAFLAVPHGAAMEMGATLRQRGLRVVDLSADFRLRDPDVYEAWYKVP 121

Query: 160 HESPEWAEKAVYGLPEVVRDEIRNAQLVANPGCYPTAVQLGFLPLLEQGLVDPKRLIADA 219
           H       +AVYGLPE+  D ++ A LVANPGCYPTA  LG    L+ GLV+   ++ DA
Sbjct: 122 HTRRAELPQAVYGLPELYGDAVKKAGLVANPGCYPTATILGLYAALKHGLVETDGIVVDA 181

Query: 220 KSGASGAGRQGKIGMLHGEIGESFKAYGASGHRHLPEIRQGLCGAAGGDVGVTFVPHLIP 279
           KSGA+GAGR+  +G L  E+ ++F+AY    HRH PEI Q L   AG  + V+F PHL+P
Sbjct: 182 KSGATGAGRKAAVGTLFCEVSDTFRAYNIGKHRHTPEIEQELSAIAGTSMVVSFNPHLLP 241

Query: 280 MIRGIEATLYAELKNPADFDRLQALFEQRFDDEPFVDVMPFGSHPETRSVRGANQCRMAL 339
           + RGI AT+YA+L  P     +QA FEQ +    +V V+P G  PETR VRG   C + +
Sbjct: 242 INRGILATIYAKLAKPVSPQDVQAAFEQTWQGSRWVRVLPAGQLPETRHVRGTMFCDVGV 301

Query: 340 HRQEQSNIVIVSSVIDNLVKGAAGQAVQNMNIMFGLKETMGLEAPALLP 388
              +++N +++ S IDNL +GA+GQAV N N+MFGL    GL    L+P
Sbjct: 302 VTDQRTNRLVILSAIDNLCRGASGQAVANANLMFGLPVETGLMLAPLMP 350


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: 388
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: 388
Length of database: 350
Length adjustment: 30
Effective length of query: 358
Effective length of database: 320
Effective search space:   114560
Effective search space used:   114560
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 8500980 DvMF_1717 (N-acetyl-gamma-glutamyl-phosphate reductase (RefSeq))
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.8424.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.3e-128  415.0   0.0   1.5e-128  414.8   0.0    1.0  1  lcl|FitnessBrowser__Miya:8500980  DvMF_1717 N-acetyl-gamma-glutamy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8500980  DvMF_1717 N-acetyl-gamma-glutamyl-phosphate reductase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  414.8   0.0  1.5e-128  1.5e-128       1     345 []       4     350 .]       4     350 .] 0.98

  Alignments for each domain:
  == domain 1  score: 414.8 bits;  conditional E-value: 1.5e-128
                         TIGR01850   1 ikvaivGasGYtGaeLlrllakHpevevtklvssreagkklsevhphlkglvd..lkleeleeeeileeadvvflAl 75 
                                       i++++vG +GYtG+eL rlla Hp++++++++s++eag++ls+++p l+gl    + +++ + +++++++dv flA+
  lcl|FitnessBrowser__Miya:8500980   4 IRAGLVGVTGYTGMELTRLLAGHPNMRLVRATSRTEAGRPLSDIYPFLRGLPGgnAVMTAPDPDDLADNCDVAFLAV 80 
                                       5789*************************9999999**************988645566666699************ PP

                         TIGR01850  76 phgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnreeikkaklianPGCyaT 152
                                       phg+++e+ ++l ++g++v+dlSadfRl+d++vYe+wY+ +h++++ l +avYGlpEl+ +++kka l+anPGCy+T
  lcl|FitnessBrowser__Miya:8500980  81 PHGAAMEMGATLRQRGLRVVDLSADFRLRDPDVYEAWYKVPHTRRAELPQAVYGLPELYGDAVKKAGLVANPGCYPT 157
                                       ***************************************************************************** PP

                         TIGR01850 153 aalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvtkHrHtpEieqelsklaekkvkvs 229
                                       a++L+l+ +lk++l+e++ i+vdaksG +gAGrka   +lf+ev++ +++Y++ kHrHtpEieqels++a+++++vs
  lcl|FitnessBrowser__Miya:8500980 158 ATILGLYAALKHGLVETDGIVVDAKSGATGAGRKAAVGTLFCEVSDTFRAYNIGKHRHTPEIEQELSAIAGTSMVVS 234
                                       *****************99********************************************************** PP

                         TIGR01850 230 ftphlvpmtrGilatiyaklkkelteeelrklyeevYedepfvrvlkegelPstkavlgsnfvdigvavdeetkrvv 306
                                       f phl+p+ rGilatiyakl+k+++ +++++++e++++++++vrvl++g+lP+t++v+g+ f+d+gv +d++t+r+v
  lcl|FitnessBrowser__Miya:8500980 235 FNPHLLPINRGILATIYAKLAKPVSPQDVQAAFEQTWQGSRWVRVLPAGQLPETRHVRGTMFCDVGVVTDQRTNRLV 311
                                       ***************************************************************************** PP

                         TIGR01850 307 vvsaiDNLvKGaagqAvqnlNlmlgfdetegLeklpllp 345
                                       ++saiDNL +Ga+gqAv n Nlm+g++ ++gL   pl+p
  lcl|FitnessBrowser__Miya:8500980 312 ILSAIDNLCRGASGQAVANANLMFGLPVETGLMLAPLMP 350
                                       **********************************99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (345 nodes)
Target sequences:                          1  (350 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: 6.74
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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