Alignments for a candidate for argC in Dechlorosoma suillum PS

GapMind for Amino acid biosynthesis

Alignments for a candidate for argC in Dechlorosoma suillum PS

Align N-acetylglutamylphosphate reductase (EC 1.2.1.38) (characterized)
to candidate Dsui_0782 Dsui_0782 N-acetyl-gamma-glutamyl-phosphate reductase, uncommon form

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



>FitnessBrowser__PS:Dsui_0782
          Length = 319

 Score =  273 bits (699), Expect = 3e-78
 Identities = 145/309 (46%), Positives = 206/309 (66%), Gaps = 7/309 (2%)

Query: 4   KIFIDGEHGTTGLQIRVRMAGRTDLELLSIPEAERRNAAMREDLLNSADIAILCLPDDAS 63
           K+FIDG HGTTGL+I  R++ R ++E+L+IPE +R++ A++ + +NSAD+  LCLPD AS
Sbjct: 4   KVFIDGRHGTTGLKIDERLSIRPEIEILTIPEDKRKDPAVKAEYINSADVVFLCLPDAAS 63

Query: 64  REAVAMVA-GNNRVRIIDTSTAHRVAPDWAYGFAEMDKAQPQRIRDARHVANPGCYPTGA 122
           RE+VA++A GN R R +D STAHR  PDW YG  E++  Q +R+  A+ VA PGC+ +G 
Sbjct: 64  RESVALLAPGNTRTRFLDASTAHRTNPDWVYGLPELNGGQRERVAKAQKVAVPGCHASGF 123

Query: 123 IALIRPLRQAGILPDGYPVTVNAVSGYTGGGKQMIAQMEDDQN-PDHIGAPHFLYGLTLK 181
           I L+ PL   GI+P  YPV+  +++GY+GGGK+MIA  E+  + PD + +P F Y L L 
Sbjct: 124 IMLMAPLVAGGIVPKDYPVSTYSITGYSGGGKEMIASYEEPASLPDAMKSPRF-YALGLT 182

Query: 182 HKHVPEMKMHGLLERAPVFSPSVGKFAQGMIVQVPLYLEDLAAGATLETIHRALVDHYAG 241
           HKH+PEM+M   L   P+F+P VG FAQGM+V VPL    L    T   +     ++YAG
Sbjct: 183 HKHLPEMQMQTGLAHQPLFTPIVGNFAQGMVVAVPLLPRMLGKKVTPADLQAFYSEYYAG 242

Query: 242 QSIVEVVPLDESAKLAR--IDATELAGSDAMKLFVFGTKGGAHVNLVALLDNLGKGASGA 299
           +  V+V+PLD +  L    + AT    ++  ++FVFG   G  + + +  DNLGKGASGA
Sbjct: 243 EVFVKVMPLDAAPVLDNGFLPATACNDTNRAEIFVFG--HGEQILVASRFDNLGKGASGA 300

Query: 300 AVQNMDLML 308
           A+Q M+LML
Sbjct: 301 AIQCMNLML 309


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: 310
Number of extensions: 19
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: 319
Length adjustment: 27
Effective length of query: 283
Effective length of database: 292
Effective search space:    82636
Effective search space used:    82636
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 Dsui_0782 Dsui_0782 (N-acetyl-gamma-glutamyl-phosphate reductase, uncommon form)
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.27547.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   9.5e-134  431.5   0.0   1.1e-133  431.3   0.0    1.0  1  lcl|FitnessBrowser__PS:Dsui_0782  Dsui_0782 N-acetyl-gamma-glutamy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_0782  Dsui_0782 N-acetyl-gamma-glutamyl-phosphate reductase, uncommon form
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  431.3   0.0  1.1e-133  1.1e-133       2     310 .]       3     311 ..       2     311 .. 0.98

  Alignments for each domain:
  == domain 1  score: 431.3 bits;  conditional E-value: 1.1e-133
                         TIGR01851   2 pkvfidGeaGttGlqirerlaerddlellsidedkrkdaderakllnaadvailclpddaareavslvd..npntki 76 
                                       +kvfidG+ GttGl+i erl+ r ++e+l+i edkrkd++ +a+ +n+adv++lclpd a+re+v+l    n++t+ 
  lcl|FitnessBrowser__PS:Dsui_0782   3 FKVFIDGRHGTTGLKIDERLSIRPEIEILTIPEDKRKDPAVKAEYINSADVVFLCLPDAASRESVALLApgNTRTRF 79 
                                       8******************************************************************974477789* PP

                         TIGR01851  77 ldastayrtaedwvyGfpelaaeqrekianakrvanPGcyatgaiallrPlveaGilPadfPvtinavsGysGGGka 153
                                       ldasta+rt++dwvyG+pel+ +qre++a+a++va+PGc+a+g+i+l++Plv+ Gi+P d+Pv++ +++GysGGGk+
  lcl|FitnessBrowser__PS:Dsui_0782  80 LDASTAHRTNPDWVYGLPELNGGQRERVAKAQKVAVPGCHASGFIMLMAPLVAGGIVPKDYPVSTYSITGYSGGGKE 156
                                       ***************************************************************************** PP

                         TIGR01851 154 liakyeeesaddskkaafiiyglalehkhlpemrkhsglaskPiftPavGdfaqGllveiplhlaeldskvsaedih 230
                                       +ia+yee ++ + + ++++ y+l l+hkhlpem+ ++gla++P+ftP vG+faqG++v +pl +  l++kv+++d++
  lcl|FitnessBrowser__PS:Dsui_0782 157 MIASYEEPASLPDAMKSPRFYALGLTHKHLPEMQMQTGLAHQPLFTPIVGNFAQGMVVAVPLLPRMLGKKVTPADLQ 233
                                       ***************************************************************************** PP

                         TIGR01851 231 kalaeyykGekfvkvaelddaellddtildaqglngtnrlelfvfgsddgerallvarldnlGkGasGaavqnlnia 307
                                       +   eyy+Ge fvkv++ld a++ld+++l a++ n+tnr+e+fvfg    e++l+++r+dnlGkGasGaa+q++n++
  lcl|FitnessBrowser__PS:Dsui_0782 234 AFYSEYYAGEVFVKVMPLDAAPVLDNGFLPATACNDTNRAEIFVFGHG--EQILVASRFDNLGKGASGAAIQCMNLM 308
                                       **********************************************76..*************************** PP

                         TIGR01851 308 lGl 310
                                       lG+
  lcl|FitnessBrowser__PS:Dsui_0782 309 LGV 311
                                       **7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (310 nodes)
Target sequences:                          1  (319 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 11.23
//
[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