Alignments for a candidate for argC in Pseudomonas fluorescens FW300-N2C3

GapMind for Amino acid biosynthesis

Alignments for a candidate for argC in Pseudomonas fluorescens FW300-N2C3

Align N-acetylglutamylphosphate reductase (EC 1.2.1.38) (characterized)
to candidate AO356_24070 AO356_24070 N-acetyl-gamma-glutamyl-phosphate reductase

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



>FitnessBrowser__pseudo5_N2C3_1:AO356_24070
          Length = 309

 Score =  281 bits (719), Expect = 1e-80
 Identities = 146/308 (47%), Positives = 201/308 (65%), Gaps = 5/308 (1%)

Query: 3   PKIFIDGEHGTTGLQIRVRMAGRTDLELLSIPEAERRNAAMREDLLNSADIAILCLPDDA 62
           P +FIDG+ GTTGLQI  R+  R+DL LL++    R++   R + +N  DIA+LCLPD A
Sbjct: 4   PLVFIDGDQGTTGLQIHQRLRDRSDLRLLTLSADYRKDPQRRAEAINDCDIAMLCLPDPA 63

Query: 63  SREAVAMVAGNNRVRIIDTSTAHRVAPDWAYGFAEMDKAQPQRIRDARHVANPGCYPTGA 122
           +R+AVA +  N  VR+ID S+AHR  PDW YGFA+M+  Q +RI  AR V+NPGCYPTGA
Sbjct: 64  ARDAVASIK-NPAVRVIDASSAHRTHPDWVYGFAQMNSQQARRIATARRVSNPGCYPTGA 122

Query: 123 IALIRPLRQAGILPDGYPVTVNAVSGYTGGGKQMIAQMEDDQNPDHIGAPHF-LYGLTLK 181
           I L+RPL +AG+LP  YP+ + AVSGY+G G+   A +++ +    + AP F +YGL L 
Sbjct: 123 IGLLRPLLEAGLLPTDYPMNIYAVSGYSGKGR---AGVQEYEGEGALPAPAFQVYGLGLA 179

Query: 182 HKHVPEMKMHGLLERAPVFSPSVGKFAQGMIVQVPLYLEDLAAGATLETIHRALVDHYAG 241
           HKHVPE++    L   P+F P+ G F QG+ + +P+    LA G +   +H  L  HYA 
Sbjct: 180 HKHVPEIQQQSGLTERPMFVPAYGAFRQGIALTIPVQTRLLAPGVSAVQLHACLARHYAD 239

Query: 242 QSIVEVVPLDESAKLARIDATELAGSDAMKLFVFGTKGGAHVNLVALLDNLGKGASGAAV 301
              V V+ + E+ +L  +D   L G+D ++L VF       V L A+ DNLGKGA+GAAV
Sbjct: 240 AGHVHVMSMQEAKELTFLDPQALNGTDDLRLSVFENDETGQVLLAAVFDNLGKGAAGAAV 299

Query: 302 QNMDLMLS 309
           QN+DLML+
Sbjct: 300 QNLDLMLA 307


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: 270
Number of extensions: 8
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 AO356_24070 AO356_24070 (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.20242.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   5.2e-123  396.2   0.0     6e-123  396.0   0.0    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24070  AO356_24070 N-acetyl-gamma-gluta


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24070  AO356_24070 N-acetyl-gamma-glutamyl-phosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  396.0   0.0    6e-123    6e-123       2     308 ..       4     306 ..       3     308 .. 0.98

  Alignments for each domain:
  == domain 1  score: 396.0 bits;  conditional E-value: 6e-123
                                       TIGR01851   2 pkvfidGeaGttGlqirerlaerddlellsidedkrkdaderakllnaadvailclpddaare 64 
                                                     p vfidG++GttGlqi++rl +r+dl+ll++++d rkd++ ra+ +n  d+a+lclpd aar+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24070   4 PLVFIDGDQGTTGLQIHQRLRDRSDLRLLTLSADYRKDPQRRAEAINDCDIAMLCLPDPAARD 66 
                                                     679************************************************************ PP

                                       TIGR01851  65 avslvdnpntkildastayrtaedwvyGfpelaaeqrekianakrvanPGcyatgaiallrPl 127
                                                     av+ ++np+++++das+a+rt++dwvyGf++++++q  +ia a+rv+nPGcy+tgai llrPl
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24070  67 AVASIKNPAVRVIDASSAHRTHPDWVYGFAQMNSQQARRIATARRVSNPGCYPTGAIGLLRPL 129
                                                     *************************************************************** PP

                                       TIGR01851 128 veaGilPadfPvtinavsGysGGGkaliakyeeesaddskkaafiiyglalehkhlpemrkhs 190
                                                     +eaG+lP+d+P++i avsGysG G+a +++ye e a ++   af++ygl l hkh+pe++++s
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24070 130 LEAGLLPTDYPMNIYAVSGYSGKGRAGVQEYEGEGALPA--PAFQVYGLGLAHKHVPEIQQQS 190
                                                     ********************************7776665..89******************** PP

                                       TIGR01851 191 glaskPiftPavGdfaqGllveiplhlaeldskvsaedihkalaeyykGekfvkvaelddael 253
                                                     gl+++P+f+Pa G f qG++++ip++   l+  vsa ++h+ la +y+   +v+v+++++a+ 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24070 191 GLTERPMFVPAYGAFRQGIALTIPVQTRLLAPGVSAVQLHACLARHYADAGHVHVMSMQEAKE 253
                                                     **************************************************************9 PP

                                       TIGR01851 254 lddtildaqglngtnrlelfvfgsddgerallvarldnlGkGasGaavqnlnial 308
                                                     l  t+ld+q+lngt+ l l vf +d+++++ll+a +dnlGkGa+Gaavqnl+++l
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24070 254 L--TFLDPQALNGTDDLRLSVFENDETGQVLLAAVFDNLGKGAAGAAVQNLDLML 306
                                                     9..***************************************************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: 00:00:00.01
# Mc/sec: 7.10
//
[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