Alignments for a candidate for argC in Herbaspirillum seropedicae SmR1

GapMind for Amino acid biosynthesis

Alignments for a candidate for argC in Herbaspirillum seropedicae SmR1

Align N-acetyl-gamma-glutamyl-phosphate reductase; Short=AGPR; EC 1.2.1.38 (characterized, see rationale)
to candidate HSERO_RS19210 HSERO_RS19210 N-acetyl-gamma-glutamyl-phosphate reductase

Query= uniprot:E4PLW0
         (388 letters)



>FitnessBrowser__HerbieS:HSERO_RS19210
          Length = 345

 Score =  416 bits (1069), Expect = e-121
 Identities = 201/345 (58%), Positives = 252/345 (73%)

Query: 44  VIKVGIVGGTGYTGVELLRILAVHPEVSVSCITSRSEAGMPVAEMYPNLRGHYDLAFSEP 103
           +IKVGIVGGTGYTGVELLRI A HPE  V  +TSR E GMPVAEMYP+LRG  D+AFS P
Sbjct: 1   MIKVGIVGGTGYTGVELLRIFATHPEARVQAVTSRKEDGMPVAEMYPSLRGRVDVAFSSP 60

Query: 104 DVNVLGACDLVFFATPHGVAMRMVPELMSAGVRVVDLSADFRLKDLDVWANWYGMAHESP 163
           D   L  CD+VFFATPHGVAM   PEL++AGV+V+DL+ADFR++D+  +  WY + H   
Sbjct: 61  DKARLTDCDVVFFATPHGVAMAQAPELVAAGVKVIDLAADFRMQDVAAFEKWYKLPHSCT 120

Query: 164 EWAEKAVYGLPEVVRDEIRNAQLVANPGCYPTAVQLGFLPLLEQGLVDPKRLIADAKSGA 223
           +  ++A YGLPE+ R+ IR A++V NPGCYPT +QLG+ PLL+ G++D   LIAD KSG 
Sbjct: 121 DLLKEAAYGLPELNREAIRKARVVGNPGCYPTTMQLGYAPLLKAGVIDASHLIADCKSGV 180

Query: 224 SGAGRQGKIGMLHGEIGESFKAYGASGHRHLPEIRQGLCGAAGGDVGVTFVPHLIPMIRG 283
           SGAGR+ ++ +L  E  ++FKAYG SGHRH PE  + L       VG+ F PHL+PMIRG
Sbjct: 181 SGAGRKAELSLLFSEASDNFKAYGVSGHRHSPETIERLSHLTSDKVGLLFTPHLVPMIRG 240

Query: 284 IEATLYAELKNPADFDRLQALFEQRFDDEPFVDVMPFGSHPETRSVRGANQCRMALHRQE 343
           + +TLYA L    D   LQALFE  + DEPFVDV+PFG+HPETR+ R +N  R+A+HR  
Sbjct: 241 MHSTLYARLTKEIDNAALQALFEDAYKDEPFVDVLPFGAHPETRTTRASNMLRLAVHRPG 300

Query: 344 QSNIVIVSSVIDNLVKGAAGQAVQNMNIMFGLKETMGLEAPALLP 388
             + V+V  V DNLVKGA+GQAVQ MN+MFGL ET GL+   +LP
Sbjct: 301 DGDTVVVLVVQDNLVKGASGQAVQCMNLMFGLDETTGLQQVPVLP 345


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: 420
Number of extensions: 13
Number of successful extensions: 1
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: 345
Length adjustment: 30
Effective length of query: 358
Effective length of database: 315
Effective search space:   112770
Effective search space used:   112770
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 HSERO_RS19210 HSERO_RS19210 (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.28171.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   7.6e-131  422.3   0.0   8.5e-131  422.2   0.0    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS19210  HSERO_RS19210 N-acetyl-gamma-glu


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS19210  HSERO_RS19210 N-acetyl-gamma-glutamyl-phosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  422.2   0.0  8.5e-131  8.5e-131       1     345 []       2     345 .]       2     345 .] 0.98

  Alignments for each domain:
  == domain 1  score: 422.2 bits;  conditional E-value: 8.5e-131
                                  TIGR01850   1 ikvaivGasGYtGaeLlrllakHpevevtklvssreagkklsevhphlkglvdlkleeleeeeileea 68 
                                                ikv+ivG++GYtG+eLlr++a+Hpe++v++++s++e g +++e++p+l+g vd+ +++ ++++ l+++
  lcl|FitnessBrowser__HerbieS:HSERO_RS19210   2 IKVGIVGGTGYTGVELLRIFATHPEARVQAVTSRKEDGMPVAEMYPSLRGRVDVAFSSPDKAR-LTDC 68 
                                                69***************************7777777********************9988775.67** PP

                                  TIGR01850  69 dvvflAlphgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnre 136
                                                dvvf+A+phgv+++ +pel+++gvkvidl+adfR++d +++ekwY+ +h+ ++ll+ea+YGlpElnre
  lcl|FitnessBrowser__HerbieS:HSERO_RS19210  69 DVVFFATPHGVAMAQAPELVAAGVKVIDLAADFRMQDVAAFEKWYKLPHSCTDLLKEAAYGLPELNRE 136
                                                ******************************************************************** PP

                                  TIGR01850 137 eikkaklianPGCyaTaalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYk 204
                                                +i+ka++++nPGCy+T+++L+ aPllk+++i+ +++i d+ksGvSgAGrka+ + lf+e+++n+k+Y 
  lcl|FitnessBrowser__HerbieS:HSERO_RS19210 137 AIRKARVVGNPGCYPTTMQLGYAPLLKAGVIDASHLIADCKSGVSGAGRKAELSLLFSEASDNFKAYG 204
                                                ******************************************************************** PP

                                  TIGR01850 205 vtkHrHtpEieqelsklaekkvkvsftphlvpmtrGilatiyaklkkelteeelrklyeevYedepfv 272
                                                v++HrH pE  ++ls+l+++kv + ftphlvpm+rG+++t+ya+l+ke++++ l++l+e++Y+depfv
  lcl|FitnessBrowser__HerbieS:HSERO_RS19210 205 VSGHRHSPETIERLSHLTSDKVGLLFTPHLVPMIRGMHSTLYARLTKEIDNAALQALFEDAYKDEPFV 272
                                                ******************************************************************** PP

                                  TIGR01850 273 rvlkegelPstkavlgsnfvdigvavdeetkrvvvvsaiDNLvKGaagqAvqnlNlmlgfdetegLek 340
                                                +vl+ g  P+t+ +++sn+ +++v+   + ++vvv+ + DNLvKGa+gqAvq++Nlm+g+det+gL++
  lcl|FitnessBrowser__HerbieS:HSERO_RS19210 273 DVLPFGAHPETRTTRASNMLRLAVHRPGDGDTVVVLVVQDNLVKGASGQAVQCMNLMFGLDETTGLQQ 340
                                                ******************************************************************** PP

                                  TIGR01850 341 lpllp 345
                                                +p+lp
  lcl|FitnessBrowser__HerbieS:HSERO_RS19210 341 VPVLP 345
                                                **998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (345 nodes)
Target sequences:                          1  (345 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: 9.54
//
[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