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-acetylglutamylphosphate reductase (EC 1.2.1.38) (characterized)
to candidate HSERO_RS14025 HSERO_RS14025 N-acetyl-gamma-glutamyl-phosphate reductase

Query= reanno::Smeli:SMc01801
         (310 letters)



>FitnessBrowser__HerbieS:HSERO_RS14025
          Length = 309

 Score =  310 bits (793), Expect = 4e-89
 Identities = 160/307 (52%), Positives = 208/307 (67%), Gaps = 3/307 (0%)

Query: 3   PKIFIDGEHGTTGLQIRVRMAGRTDLELLSIPEAERRNAAMREDLLNSADIAILCLPDDA 62
           P IFIDG+ GTTGLQI  R+  R DL +L++P AER++A  R + +NSADIA+LCLPD A
Sbjct: 5   PLIFIDGDQGTTGLQIHERLRARQDLRVLTLPAAERKDAQRRAEAINSADIALLCLPDAA 64

Query: 63  SREAVAMVAGNNRVRIIDTSTAHRVAPDWAYGFAEMDKAQPQRIRDARHVANPGCYPTGA 122
           +REAVAM++ N RVR+ID S+AHR +PDW YGF EM   Q + I  A  V+NPGCYPTGA
Sbjct: 65  AREAVAMIS-NPRVRVIDASSAHRTSPDWVYGFPEMAAGQAEAIATALRVSNPGCYPTGA 123

Query: 123 IALIRPLRQAGILPDGYPVTVNAVSGYTGGGKQMIAQMEDDQNPDHIGAPHFLYGLTLKH 182
           IAL+RPL QAG++P  YP+ ++AVSGY+GGG+  + Q E  +      AP   YGL L+H
Sbjct: 124 IALLRPLVQAGLVPADYPLNIHAVSGYSGGGRAQVEQYEGAEAAH--AAPFVTYGLGLQH 181

Query: 183 KHVPEMKMHGLLERAPVFSPSVGKFAQGMIVQVPLYLEDLAAGATLETIHRALVDHYAGQ 242
           KH PEM++H  L + P+F PS G F QG+++ + L    L A A+LE +   L  HY G 
Sbjct: 182 KHPPEMQLHAGLSQRPLFVPSYGAFRQGIVLTIALQSRLLPAQASLERLRATLQAHYDGA 241

Query: 243 SIVEVVPLDESAKLARIDATELAGSDAMKLFVFGTKGGAHVNLVALLDNLGKGASGAAVQ 302
             V V+   +S    ++D T    S+ M L VFG  G  H+ L A+ DNLGKGASGAAVQ
Sbjct: 242 HYVTVLDAAQSESTTQLDPTRHNHSNQMSLGVFGHAGHGHILLCAVFDNLGKGASGAAVQ 301

Query: 303 NMDLMLS 309
           N+DLML+
Sbjct: 302 NLDLMLT 308


Lambda     K      H
   0.319    0.136    0.395 

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: 316
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: 310
Length of database: 309
Length adjustment: 27
Effective length of query: 283
Effective length of database: 282
Effective search space:    79806
Effective search space used:    79806
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: 48 (23.1 bits)

Align candidate HSERO_RS14025 HSERO_RS14025 (N-acetyl-gamma-glutamyl-phosphate reductase)
to HMM TIGR01851 (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/TIGR01851.hmm
# target sequence database:        /tmp/gapView.3620535.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01851  [M=310]
Accession:   TIGR01851
Description: argC_other: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                              -----------
   2.6e-123  397.2   0.0     3e-123  397.0   0.0    1.0  1  FitnessBrowser__HerbieS:HSERO_RS14025  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__HerbieS:HSERO_RS14025  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  397.0   0.0    3e-123    3e-123       2     308 ..       5     307 ..       4     309 .] 0.98

  Alignments for each domain:
  == domain 1  score: 397.0 bits;  conditional E-value: 3e-123
                              TIGR01851   2 pkvfidGeaGttGlqirerlaerddlellsidedkrkdaderakllnaadvailclpddaareavslvdnpn 73 
                                            p +fidG++GttGlqi+erl  r+dl++l++ +  rkda+ ra+ +n+ad+a+lclpd aareav++++np+
  FitnessBrowser__HerbieS:HSERO_RS14025   5 PLIFIDGDQGTTGLQIHERLRARQDLRVLTLPAAERKDAQRRAEAINSADIALLCLPDAAAREAVAMISNPR 76 
                                            569********************************************************************* PP

                              TIGR01851  74 tkildastayrtaedwvyGfpelaaeqrekianakrvanPGcyatgaiallrPlveaGilPadfPvtinavs 145
                                            ++++das+a+rt++dwvyGfpe+aa+q e ia a rv+nPGcy+tgaiallrPlv+aG++Pad+P++i+avs
  FitnessBrowser__HerbieS:HSERO_RS14025  77 VRVIDASSAHRTSPDWVYGFPEMAAGQAEAIATALRVSNPGCYPTGAIALLRPLVQAGLVPADYPLNIHAVS 148
                                            ************************************************************************ PP

                              TIGR01851 146 GysGGGkaliakyeeesaddskkaafiiyglalehkhlpemrkhsglaskPiftPavGdfaqGllveiplhl 217
                                            GysGGG+a +++ye   a++++ a+f++ygl l+hkh pem+ h+gl ++P+f+P+ G f qG++++i+l+ 
  FitnessBrowser__HerbieS:HSERO_RS14025 149 GYSGGGRAQVEQYE--GAEAAHAAPFVTYGLGLQHKHPPEMQLHAGLSQRPLFVPSYGAFRQGIVLTIALQS 218
                                            **************..45555579************************************************ PP

                              TIGR01851 218 aeldskvsaedihkalaeyykGekfvkvaelddaellddtildaqglngtnrlelfvfgsddgerallvarl 289
                                              l +++s e + ++l+ +y+G ++v v +++++e  + t ld++  n +n+++l vfg +  +++ll+a +
  FitnessBrowser__HerbieS:HSERO_RS14025 219 RLLPAQASLERLRATLQAHYDGAHYVTVLDAAQSE--STTQLDPTRHNHSNQMSLGVFGHAGHGHILLCAVF 288
                                            *******************************9999..459******************************** PP

                              TIGR01851 290 dnlGkGasGaavqnlnial 308
                                            dnlGkGasGaavqnl+++l
  FitnessBrowser__HerbieS:HSERO_RS14025 289 DNLGKGASGAAVQNLDLML 307
                                            ******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (310 nodes)
Target sequences:                          1  (309 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: 00:00:00.00
# Mc/sec: 18.46
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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