Alignments for a candidate for argC in Acidimicrobium ferrooxidans DSM 10331

GapMind for Amino acid biosynthesis

Alignments for a candidate for argC in Acidimicrobium ferrooxidans DSM 10331

Align N-acetyl-gamma-glutamyl-phosphate reductase (EC 1.2.1.38) (characterized)
to candidate WP_015799060.1 AFER_RS08625 N-acetyl-gamma-glutamyl-phosphate reductase

Query= BRENDA::P9WPZ9
         (352 letters)



>NCBI__GCF_000023265.1:WP_015799060.1
          Length = 337

 Score =  190 bits (483), Expect = 4e-53
 Identities = 141/352 (40%), Positives = 178/352 (50%), Gaps = 28/352 (7%)

Query: 12  VAVAGASGYAGGEILRLLLGHPAYADGRLRIGALTAATSAGSTLGEHHPHLT-PLAHRVV 70
           V V GASG+ G E++R+L  HP +        A  A   AG  LGE  P L+  LA R +
Sbjct: 3   VVVVGASGFVGQELVRVLARHPVFEPV-----AFQAHQRAGRRLGELVPGLSVDLAERPI 57

Query: 71  EPTEAAVLGGHDAVFLALPHGHSAVLAQQLSPETL-IIDCGADFRLTDAAVWERFYGSSH 129
           EP +   +   +  F ALPHGHS  + ++L    + ++D GAD RL D A W R+YG  H
Sbjct: 58  EPIDPRAVAA-ELAFCALPHGHSGGIIRELRARGVRVVDLGADLRLADEATWRRWYGDDH 116

Query: 130 A-----GSWPYGLPELPGARDQLRGTRRIAVPGCYPTAALLALFPALAADLIEPAVTVV- 183
                 GS   G+ E    R +L   +  AVPGCY TA +LA  P + A L    + VV 
Sbjct: 117 PAPELLGSAVVGVAE--HVRTELASAQVWAVPGCYVTATVLAAKPLIDAGLARRDLVVVD 174

Query: 184 AVSGTSGAGRAATTDLLGAEVIGSARAYNIAGVHRHTPEIAQGLRAVTDRDVSVSFTPVL 243
           A+SG +GAG AAT       V    RAY + G HRHTPE+   L       V V FTP L
Sbjct: 175 AISGVTGAGSAATETTHFVNVAEGVRAYALGG-HRHTPEMRSLL------GVPVRFTPHL 227

Query: 244 IPASRGILATCT---ARTRSPLSQLRAAYEKAYHAEPFIYLMPEGQLPRTGAVIGSNAAH 300
            P SRGI AT T   A        +R    +AY   PF+ +      P T  V GSN A 
Sbjct: 228 GPYSRGIAATITLPVADATVDADSVRDVLARAYGTSPFVEVRETP--PSTREVRGSNRAV 285

Query: 301 IAVAVDEDAQTFVAIAAIDNLVKGTAGAAVQSMNLALGWPETDGLSVVGVAP 352
           +A  VD++    VA + IDNL KG A  AVQ  NL +G  E  GL  +GV P
Sbjct: 286 LAATVDDEVGVIVATSVIDNLGKGAAQHAVQGANLMVGVDEVLGLEGLGVWP 337


Lambda     K      H
   0.318    0.133    0.393 

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: 343
Number of extensions: 24
Number of successful extensions: 7
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: 352
Length of database: 337
Length adjustment: 29
Effective length of query: 323
Effective length of database: 308
Effective search space:    99484
Effective search space used:    99484
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate WP_015799060.1 AFER_RS08625 (N-acetyl-gamma-glutamyl-phosphate reductase)
to HMM TIGR01850 (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/TIGR01850.hmm
# target sequence database:        /tmp/gapView.1042771.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01850  [M=345]
Accession:   TIGR01850
Description: argC: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.3e-102  327.2   0.0   7.1e-102  327.1   0.0    1.0  1  NCBI__GCF_000023265.1:WP_015799060.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000023265.1:WP_015799060.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  327.1   0.0  7.1e-102  7.1e-102       2     345 .]       2     337 .]       1     337 [] 0.97

  Alignments for each domain:
  == domain 1  score: 327.1 bits;  conditional E-value: 7.1e-102
                             TIGR01850   2 kvaivGasGYtGaeLlrllakHpevevtklvssreagkklsevhphlkglvd.lkleeleeeeileeadvvfl 73 
                                            v++vGasG+ G+eL+r+la+Hp +e +++ ++++ag++l e++p l+  +    +e+++ ++   +a++ f+
  NCBI__GCF_000023265.1:WP_015799060.1   2 DVVVVGASGFVGQELVRVLARHPVFEPVAFQAHQRAGRRLGELVPGLSVDLAeRPIEPIDPRA--VAAELAFC 72 
                                           799*************************9999999************9877768899988884..479***** PP

                             TIGR01850  74 AlphgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnreeikkaklian 146
                                           Alphg+s  +++el ++gv+v+dl+ad Rl d++++++wYg +h+++ell +av G++E  r e+++a++ a+
  NCBI__GCF_000023265.1:WP_015799060.1  73 ALPHGHSGGIIRELRARGVRVVDLGADLRLADEATWRRWYGDDHPAPELLGSAVVGVAEHVRTELASAQVWAV 145
                                           ************************************************************************* PP

                             TIGR01850 147 PGCyaTaalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvtkHrHtpEieqels 219
                                           PGCy Ta++La +Pl++++l +++ ++vda+sGv+gAG++a+e+++f +v+e +++Y++ +HrHtpE+++ l+
  NCBI__GCF_000023265.1:WP_015799060.1 146 PGCYVTATVLAAKPLIDAGLARRDLVVVDAISGVTGAGSAATETTHFVNVAEGVRAYALGGHRHTPEMRSLLG 218
                                           **********************999************************************************ PP

                             TIGR01850 220 klaekkvkvsftphlvpmtrGilatiyaklkke.lteeelrklyeevYedepfvrvlkegelPstkavlgsnf 291
                                                 v v+ftphl p +rGi ati++ +++  ++++++r++++++Y ++pfv+v +  + Pst++v+gsn 
  NCBI__GCF_000023265.1:WP_015799060.1 219 ------VPVRFTPHLGPYSRGIAATITLPVADAtVDADSVRDVLARAYGTSPFVEVRE--TPPSTREVRGSNR 283
                                           ......88*********************999879999*******************8..89*********** PP

                             TIGR01850 292 vdigvavdeetkrvvvvsaiDNLvKGaagqAvqnlNlmlgfdetegLeklpllp 345
                                           + ++ +vd+e + +v +s+iDNL KGaa +Avq  Nlm+g de  gLe l+++p
  NCBI__GCF_000023265.1:WP_015799060.1 284 AVLAATVDDEVGVIVATSVIDNLGKGAAQHAVQGANLMVGVDEVLGLEGLGVWP 337
                                           ************************************************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (345 nodes)
Target sequences:                          1  (337 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: 00:00:00.00
# Mc/sec: 14.98
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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