Alignments for a candidate for argC in Derxia gummosa DSM 723

GapMind for Amino acid biosynthesis

Alignments for a candidate for argC in Derxia gummosa DSM 723

Align N-acetyl-gamma-glutamyl-phosphate reductase; Short=AGPR; EC 1.2.1.38 (characterized, see rationale)
to candidate WP_028310458.1 H566_RS0104200 N-acetyl-gamma-glutamyl-phosphate reductase

Query= uniprot:E4PLW0
         (388 letters)



>NCBI__GCF_000482785.1:WP_028310458.1
          Length = 348

 Score =  424 bits (1090), Expect = e-123
 Identities = 217/348 (62%), Positives = 260/348 (74%), Gaps = 3/348 (0%)

Query: 44  VIKVGIVGGTGYTGVELLRILAVHPEVSVSCITSRSEAGMPVAEMYPNLRGHYDLAFSEP 103
           +IKVGIVGGTGYTGVELLR+LA HP+V +  ITSR EAGMPVA+M+P+LRG  D+AFS P
Sbjct: 1   MIKVGIVGGTGYTGVELLRLLAQHPQVQLQAITSRKEAGMPVADMFPSLRGRVDIAFSAP 60

Query: 104 DVNVLGACDLVFFATPHGVAMRMVPELMSAGVRVVDLSADFRLKDLDVWANWYGMAHESP 163
           D   LGACD+VFFATPHGVAM   P L+ AGV+V+DL+ADFRL+D  V+  WYGM H + 
Sbjct: 61  DAATLGACDVVFFATPHGVAMEQGPALLEAGVKVIDLAADFRLRDPVVFEKWYGMPHSAL 120

Query: 164 EWAEKAVYGLPEVVRDEIRNAQLVANPGCYPTAVQLGFLPLLEQG--LVDPKRLIADAKS 221
              +KAVYGLPEV RD IR+A+L+  PGCYPT+VQLGFLP+L  G  LVD   LIAD KS
Sbjct: 121 ALLDKAVYGLPEVNRDRIRDARLIGLPGCYPTSVQLGFLPVLRDGAKLVDGTTLIADCKS 180

Query: 222 GASGAGRQGKIGMLHGEIGESFKAYGASGHRHLPEIRQGLCGAAGGD-VGVTFVPHLIPM 280
           G SGAGR+ ++  L  E  ++FKAYG  GHRHLPEI QGL   AG D + +TFVPHL+PM
Sbjct: 181 GVSGAGRKAEVHTLLAEASDNFKAYGVKGHRHLPEIEQGLRAIAGHDAINLTFVPHLVPM 240

Query: 281 IRGIEATLYAELKNPADFDRLQALFEQRFDDEPFVDVMPFGSHPETRSVRGANQCRMALH 340
           IRGI +TLYA +   A     QALFE  + +EPFVDVMP GSHPETRSVR AN  R+A+H
Sbjct: 241 IRGIHSTLYARILPEARETDFQALFEAAYANEPFVDVMPAGSHPETRSVRSANTVRIAVH 300

Query: 341 RQEQSNIVIVSSVIDNLVKGAAGQAVQNMNIMFGLKETMGLEAPALLP 388
           R    + ++V  V DNLVKGA+GQ VQ MN+MFGL E+ GL    +LP
Sbjct: 301 RPGGGDQLVVLVVEDNLVKGASGQGVQCMNLMFGLPESTGLTMLPVLP 348


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: 444
Number of extensions: 17
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: 348
Length adjustment: 30
Effective length of query: 358
Effective length of database: 318
Effective search space:   113844
Effective search space used:   113844
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 WP_028310458.1 H566_RS0104200 (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.8404.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.6e-127  409.6   0.0   6.3e-127  409.4   0.0    1.0  1  lcl|NCBI__GCF_000482785.1:WP_028310458.1  H566_RS0104200 N-acetyl-gamma-gl


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000482785.1:WP_028310458.1  H566_RS0104200 N-acetyl-gamma-glutamyl-phosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  409.4   0.0  6.3e-127  6.3e-127       1     345 []       2     348 .]       2     348 .] 0.97

  Alignments for each domain:
  == domain 1  score: 409.4 bits;  conditional E-value: 6.3e-127
                                 TIGR01850   1 ikvaivGasGYtGaeLlrllakHpevevtklvssreagkklsevhphlkglvdlkleeleeeeileead 69 
                                               ikv+ivG++GYtG+eLlrlla+Hp+v++++++s++eag ++++++p+l+g vd  +++ ++++ l ++d
  lcl|NCBI__GCF_000482785.1:WP_028310458.1   2 IKVGIVGGTGYTGVELLRLLAQHPQVQLQAITSRKEAGMPVADMFPSLRGRVDIAFSAPDAAT-LGACD 69 
                                               69***************************8888888*********************988875.679** PP

                                 TIGR01850  70 vvflAlphgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnreei 138
                                               vvf+A+phgv++e  p+lle+gvkvidl+adfRl+d+ v+ekwYg++h++ +ll++avYGlpE+nr++i
  lcl|NCBI__GCF_000482785.1:WP_028310458.1  70 VVFFATPHGVAMEQGPALLEAGVKVIDLAADFRLRDPVVFEKWYGMPHSALALLDKAVYGLPEVNRDRI 138
                                               ********************************************************************* PP

                                 TIGR01850 139 kkaklianPGCyaTaalLalaPllk..ekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkv 205
                                               ++a+li+ PGCy+T+++L+  P+l+  +kl++ +++i d+ksGvSgAGrka+ ++l+ae+++n+k+Y v
  lcl|NCBI__GCF_000482785.1:WP_028310458.1 139 RDARLIGLPGCYPTSVQLGFLPVLRdgAKLVDGTTLIADCKSGVSGAGRKAEVHTLLAEASDNFKAYGV 207
                                               ************************83347899999********************************** PP

                                 TIGR01850 206 tkHrHtpEieqelsklaek.kvkvsftphlvpmtrGilatiyaklkkelteeelrklyeevYedepfvr 273
                                               ++HrH pEieq l+++a++  ++++f+phlvpm+rGi++t+ya++  e +e++ ++l+e++Y++epfv+
  lcl|NCBI__GCF_000482785.1:WP_028310458.1 208 KGHRHLPEIEQGLRAIAGHdAINLTFVPHLVPMIRGIHSTLYARILPEARETDFQALFEAAYANEPFVD 276
                                               *****************995666********************************************** PP

                                 TIGR01850 274 vlkegelPstkavlgsnfvdigvavdeetkrvvvvsaiDNLvKGaagqAvqnlNlmlgfdetegLeklp 342
                                               v+++g+ P+t++v+  n+v+i+v+     +++vv+ + DNLvKGa+gq vq++Nlm+g++e++gL++lp
  lcl|NCBI__GCF_000482785.1:WP_028310458.1 277 VMPAGSHPETRSVRSANTVRIAVHRPGGGDQLVVLVVEDNLVKGASGQGVQCMNLMFGLPESTGLTMLP 345
                                               ********************************************************************* PP

                                 TIGR01850 343 llp 345
                                               +lp
  lcl|NCBI__GCF_000482785.1:WP_028310458.1 346 VLP 348
                                               988 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (345 nodes)
Target sequences:                          1  (348 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: 9.81
//
[ok]

This GapMind analysis is from Apr 10 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