GapMind for Amino acid biosynthesis

 

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

Align N-acetyl-gamma-glutamyl-phosphate reductase; AGPR; EC 1.2.1.38; N-acetyl-glutamate semialdehyde dehydrogenase; NAGSA dehydrogenase (uncharacterized)
to candidate Ac3H11_1253 N-acetyl-gamma-glutamyl-phosphate reductase (EC 1.2.1.38)

Query= curated2:Q1IXY5
         (321 letters)



>lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1253
           N-acetyl-gamma-glutamyl-phosphate reductase (EC
           1.2.1.38)
          Length = 310

 Score =  327 bits (837), Expect = 3e-94
 Identities = 173/317 (54%), Positives = 220/317 (69%), Gaps = 22/317 (6%)

Query: 5   RIFIDGEAGTTGLQIRARLEGREDLELLSIDPARRKDPEARRELLNAADIAVLCLHDDVA 64
           ++FIDGEAGTTGLQIR RL+    +EL+SI P  RKDP A+R+L+   D+ VLCLHDD A
Sbjct: 3   KVFIDGEAGTTGLQIRERLQAMPQIELVSIAPELRKDPAAKRDLIAGVDLVVLCLHDDAA 62

Query: 65  REAVAMIEN------PATRVLDASSAHRTAQGWAYGFPELTKQSREEIRAARLVSNPGCY 118
           R+ VAM++          +V+DAS+AHRTA GW YGFPEL     + +R A  VSNPGCY
Sbjct: 63  RDTVAMVDEIERSSGRKVKVIDASTAHRTADGWVYGFPELAASQTQAVRDATRVSNPGCY 122

Query: 119 ATGAVALLRPLTDAGLLPPDLPLSVQGFSGYSGGGRALVEAHEGRGEHPMAGPFKSYALS 178
           ATGA+A+LRPL DAGL+P D PLS+   SGYSGGGR ++EA+E       A P+++YAL 
Sbjct: 123 ATGAIAMLRPLVDAGLIPADYPLSLPSVSGYSGGGRTMIEAYEA----GTAAPYEAYALG 178

Query: 179 LIHKHQPEMARHGGLKHAPLFTPHVGGWRQGMLVQIPLHLGLL--GVTAAQLHEALADHY 236
           L HKH PE+ R+ GL   P+F P VG +RQGMLVQ+PLHL LL     A+ LH+ALA HY
Sbjct: 179 LSHKHIPEILRYTGLTRRPVFIPAVGNFRQGMLVQLPLHLDLLPGAPKASDLHDALASHY 238

Query: 237 A----GERFVRVMPFEHGQPADPI-LDPQTLNGTNELELFVYAGPNGEHALLVSRLDNLG 291
           +     E++V V+P     P D + L   TL  TN+LEL V+A      A++++RLDNLG
Sbjct: 239 SHTNTPEQWVSVLP-----PTDDLKLAADTLTDTNKLELRVFANEQYRQAVVIARLDNLG 293

Query: 292 KGASGAAVQNLDVMLGL 308
           KGASGAAVQNL +MLG+
Sbjct: 294 KGASGAAVQNLQLMLGV 310


Lambda     K      H
   0.318    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: 330
Number of extensions: 16
Number of successful extensions: 5
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: 321
Length of database: 310
Length adjustment: 27
Effective length of query: 294
Effective length of database: 283
Effective search space:    83202
Effective search space used:    83202
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate Ac3H11_1253 (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.13475.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   1.5e-121  391.5   0.0   1.6e-121  391.3   0.0    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1253  N-acetyl-gamma-glutamyl-phosphat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1253  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 !  391.3   0.0  1.6e-121  1.6e-121       2     310 .]       2     310 .]       1     310 [] 0.94

  Alignments for each domain:
  == domain 1  score: 391.3 bits;  conditional E-value: 1.6e-121
                                        TIGR01851   2 pkvfidGeaGttGlqirerlaerddlellsidedkrkdaderakllnaadvailclpddaar 63 
                                                       kvfidGeaGttGlqirerl+    +el+si+++ rkd++++ +l+  +d ++lcl+ddaar
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1253   2 SKVFIDGEAGTTGLQIRERLQAMPQIELVSIAPELRKDPAAKRDLIAGVDLVVLCLHDDAAR 63 
                                                      59************************************************************ PP

                                        TIGR01851  64 eavslvdn......pntkildastayrtaedwvyGfpelaaeqrekianakrvanPGcyatg 119
                                                      ++v++vd+       ++k++dasta+rta++wvyGfpelaa q + +++a rv+nPGcyatg
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1253  64 DTVAMVDEierssgRKVKVIDASTAHRTADGWVYGFPELAASQTQAVRDATRVSNPGCYATG 125
                                                      ******863332224689******************************************** PP

                                        TIGR01851 120 aiallrPlveaGilPadfPvtinavsGysGGGkaliakyeeesaddskkaafiiyglalehk 181
                                                      aia+lrPlv+aG++Pad+P+++ +vsGysGGG+++i++ye     + + a++ +y+l l+hk
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1253 126 AIAMLRPLVDAGLIPADYPLSLPSVSGYSGGGRTMIEAYE-----AGTAAPYEAYALGLSHK 182
                                                      ****************************************.....3345799********** PP

                                        TIGR01851 182 hlpemrkhsglaskPiftPavGdfaqGllveiplhlaeldskvsaedihkalaeyykG.... 239
                                                      h+pe+ +++gl+++P+f+PavG+f qG+lv++plhl  l +++ a d+h+ala++y      
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1253 183 HIPEILRYTGLTRRPVFIPAVGNFRQGMLVQLPLHLDLLPGAPKASDLHDALASHYSHtntp 244
                                                      ********************************************************743333 PP

                                        TIGR01851 240 ekfvkvaelddaellddtildaqglngtnrlelfvfgsddgerallvarldnlGkGasGaav 301
                                                      e++v v +  d        l a++l +tn+lel vf++++ ++a+++arldnlGkGasGaav
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1253 245 EQWVSVLPPTDDL-----KLAADTLTDTNKLELRVFANEQYRQAVVIARLDNLGKGASGAAV 301
                                                      8999999876655.....468999************************************** PP

                                        TIGR01851 302 qnlnialGl 310
                                                      qnl+++lG+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1253 302 QNLQLMLGV 310
                                                      ********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (310 nodes)
Target sequences:                          1  (310 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: 7.20
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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:

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see 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