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

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_1253 N-acetyl-gamma-glutamyl-phosphate reductase (EC 1.2.1.38)

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



>FitnessBrowser__acidovorax_3H11:Ac3H11_1253
          Length = 310

 Score =  269 bits (688), Expect = 5e-77
 Identities = 146/314 (46%), Positives = 198/314 (63%), Gaps = 17/314 (5%)

Query: 4   KIFIDGEHGTTGLQIRVRMAGRTDLELLSIPEAERRNAAMREDLLNSADIAILCLPDDAS 63
           K+FIDGE GTTGLQIR R+     +EL+SI    R++ A + DL+   D+ +LCL DDA+
Sbjct: 3   KVFIDGEAGTTGLQIRERLQAMPQIELVSIAPELRKDPAAKRDLIAGVDLVVLCLHDDAA 62

Query: 64  REAVAMV-----AGNNRVRIIDTSTAHRVAPDWAYGFAEMDKAQPQRIRDARHVANPGCY 118
           R+ VAMV     +   +V++ID STAHR A  W YGF E+  +Q Q +RDA  V+NPGCY
Sbjct: 63  RDTVAMVDEIERSSGRKVKVIDASTAHRTADGWVYGFPELAASQTQAVRDATRVSNPGCY 122

Query: 119 PTGAIALIRPLRQAGILPDGYPVTVNAVSGYTGGGKQMIAQMEDDQNPDHIGAPHFLYGL 178
            TGAIA++RPL  AG++P  YP+++ +VSGY+GGG+ MI   E         AP+  Y L
Sbjct: 123 ATGAIAMLRPLVDAGLIPADYPLSLPSVSGYSGGGRTMIEAYEAG-----TAAPYEAYAL 177

Query: 179 TLKHKHVPEMKMHGLLERAPVFSPSVGKFAQGMIVQVPLYLEDLAAGATLETIHRALVDH 238
            L HKH+PE+  +  L R PVF P+VG F QGM+VQ+PL+L+ L        +H AL  H
Sbjct: 178 GLSHKHIPEILRYTGLTRRPVFIPAVGNFRQGMLVQLPLHLDLLPGAPKASDLHDALASH 237

Query: 239 YA----GQSIVEVVPLDESAKLARIDATELAGSDAMKLFVFGTKGGAHVNLVALLDNLGK 294
           Y+     +  V V+P  +  KLA   A  L  ++ ++L VF  +      ++A LDNLGK
Sbjct: 238 YSHTNTPEQWVSVLPPTDDLKLA---ADTLTDTNKLELRVFANEQYRQAVVIARLDNLGK 294

Query: 295 GASGAAVQNMDLML 308
           GASGAAVQN+ LML
Sbjct: 295 GASGAAVQNLQLML 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: 275
Number of extensions: 11
Number of successful extensions: 4
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: 310
Length adjustment: 27
Effective length of query: 283
Effective length of database: 283
Effective search space:    80089
Effective search space used:    80089
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_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.20324.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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 10.31
//
[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