GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argC in Acidovorax sp. GW101-3H11

Align N-acetylglutamylphosphate reductase (EC 1.2.1.38) (characterized)
to candidate Ac3H11_2950 N-acetyl-gamma-glutamyl-phosphate reductase (EC 1.2.1.38)

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



>FitnessBrowser__acidovorax_3H11:Ac3H11_2950
          Length = 312

 Score =  324 bits (831), Expect = 1e-93
 Identities = 164/307 (53%), Positives = 216/307 (70%), Gaps = 5/307 (1%)

Query: 3   PKIFIDGEHGTTGLQIRVRMAGRTDLELLSIPEAERRNAAMREDLLNSADIAILCLPDDA 62
           P +FIDG+ GTTGLQI  R+ GRTDL LL++P+AER+NAA R + +N  DIAILCLPD A
Sbjct: 5   PLVFIDGDQGTTGLQIHERLRGRTDLHLLTLPDAERKNAARRAEAINHCDIAILCLPDGA 64

Query: 63  SREAVAMVAGNNRVRIIDTSTAHRVAPDWAYGFAEMDKAQPQRIRDARHVANPGCYPTGA 122
           +REAV  +  N  V++ID S+AHR  P W YGF E+D AQP RI  A+ V+NPGCYPTGA
Sbjct: 65  AREAVTAIT-NPAVQVIDASSAHRTDPQWVYGFPELDAAQPARIASAQRVSNPGCYPTGA 123

Query: 123 IALIRPLRQAGILPDGYPVTVNAVSGYTGGGKQMIAQMEDDQNPDHIGAPHF-LYGLTLK 181
           +AL+RPL QAG+L   + VTV+AVSGY+GGG+   A++E+ + P    AP F LYGL L+
Sbjct: 124 VALLRPLVQAGLLGREHAVTVHAVSGYSGGGR---ARVEEHEGPGGAQAPAFQLYGLKLE 180

Query: 182 HKHVPEMKMHGLLERAPVFSPSVGKFAQGMIVQVPLYLEDLAAGATLETIHRALVDHYAG 241
           HKH PE+  H  L + P+F P+ G F QG+++ +PL++  L AGA+ E +H  L  HYAG
Sbjct: 181 HKHTPEIAQHAGLAQRPIFVPAYGAFRQGIVLSIPLFVHQLPAGASGERLHACLQQHYAG 240

Query: 242 QSIVEVVPLDESAKLARIDATELAGSDAMKLFVFGTKGGAHVNLVALLDNLGKGASGAAV 301
            + VEV+PL ++     +D   L G++ ++L VF       V L A+ DNLGKGASGAAV
Sbjct: 241 AAHVEVMPLAQAEAAEHLDPQALNGTNQLRLGVFSNARHGQVLLTAVFDNLGKGASGAAV 300

Query: 302 QNMDLML 308
           QN+DLML
Sbjct: 301 QNLDLML 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: 334
Number of extensions: 11
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: 312
Length adjustment: 27
Effective length of query: 283
Effective length of database: 285
Effective search space:    80655
Effective search space used:    80655
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 Ac3H11_2950 (N-acetyl-gamma-glutamyl-phosphate reductase (EC 1.2.1.38))
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.26973.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   5.5e-124  399.4   0.0   6.3e-124  399.2   0.0    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2950  N-acetyl-gamma-glutamyl-phosphat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2950  N-acetyl-gamma-glutamyl-phosphate reductase (EC 1.2.1.38)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  399.2   0.0  6.3e-124  6.3e-124       2     309 ..       5     308 ..       4     309 .. 0.98

  Alignments for each domain:
  == domain 1  score: 399.2 bits;  conditional E-value: 6.3e-124
                                        TIGR01851   2 pkvfidGeaGttGlqirerlaerddlellsidedkrkdaderakllnaadvailclpddaar 63 
                                                      p vfidG++GttGlqi+erl +r+dl+ll++ +  rk+a+ ra+ +n  d+ailclpd aar
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2950   5 PLVFIDGDQGTTGLQIHERLRGRTDLHLLTLPDAERKNAARRAEAINHCDIAILCLPDGAAR 66 
                                                      679*********************************************************** PP

                                        TIGR01851  64 eavslvdnpntkildastayrtaedwvyGfpelaaeqrekianakrvanPGcyatgaiallr 125
                                                      eav+ ++np+++++das+a+rt ++wvyGfpel+a q+ +ia+a+rv+nPGcy+tga+allr
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2950  67 EAVTAITNPAVQVIDASSAHRTDPQWVYGFPELDAAQPARIASAQRVSNPGCYPTGAVALLR 128
                                                      ************************************************************** PP

                                        TIGR01851 126 PlveaGilPadfPvtinavsGysGGGkaliakyeeesaddskkaafiiyglalehkhlpemr 187
                                                      Plv+aG+l  ++ vt++avsGysGGG+a ++++e    + ++  af+ ygl+lehkh pe+ 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2950 129 PLVQAGLLGREHAVTVHAVSGYSGGGRARVEEHEG--PGGAQAPAFQLYGLKLEHKHTPEIA 188
                                                      *********************************93..33344679***************** PP

                                        TIGR01851 188 khsglaskPiftPavGdfaqGllveiplhlaeldskvsaedihkalaeyykGekfvkvaeld 249
                                                      +h+gla++Pif+Pa G f qG+++ ipl +++l + +s+e +h+ l+++y+G ++v+v++l+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2950 189 QHAGLAQRPIFVPAYGAFRQGIVLSIPLFVHQLPAGASGERLHACLQQHYAGAAHVEVMPLA 250
                                                      ************************************************************** PP

                                        TIGR01851 250 daellddtildaqglngtnrlelfvfgsddgerallvarldnlGkGasGaavqnlnialG 309
                                                      +ae+   + ld+q+lngtn+l l vf+++  +++ll+a +dnlGkGasGaavqnl+++lG
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2950 251 QAEAA--EHLDPQALNGTNQLRLGVFSNARHGQVLLTAVFDNLGKGASGAAVQNLDLMLG 308
                                                      ***66..99**************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (310 nodes)
Target sequences:                          1  (312 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 8.03
//
[ok]

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

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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:

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:

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:

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:

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