Alignments for a candidate for argC in Magnetospirillum magneticum AMB-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for argC in Magnetospirillum magneticum AMB-1

Align Probable N-acetyl-gamma-glutamyl-phosphate reductase, chloroplastic; AGPR; N-acetyl-glutamate semialdehyde dehydrogenase; NAGSA dehydrogenase; EC 1.2.1.38 (characterized)
to candidate WP_043743989.1 AMB_RS09075 N-acetyl-gamma-glutamyl-phosphate reductase

Query= SwissProt::Q6AV34
         (415 letters)



>NCBI__GCF_000009985.1:WP_043743989.1
          Length = 346

 Score =  481 bits (1237), Expect = e-140
 Identities = 231/345 (66%), Positives = 278/345 (80%)

Query: 71  EEVRIAVLGASGYTGAEIVRLLANHPQFRIKVMTADRKAGEQFGSVFPHLITQDLPNLVA 130
           ++V IA+LGASGYTGAE+VRLLA HP F+IKVMT DRKAG+   SVFPHL   +LP LVA
Sbjct: 2   KDVSIAILGASGYTGAELVRLLALHPTFKIKVMTGDRKAGQSMESVFPHLGGLELPTLVA 61

Query: 131 VKDADFSNVDAVFCCLPHGTTQEIIKGLPQELKIVDLSADFRLRDINEYAEWYGHSHRAP 190
           +   DF+ VDAVFCCLPHGTTQE+I  LP  +K+VDLSADFRL D++ YA+WYGH HRAP
Sbjct: 62  IDQVDFTTVDAVFCCLPHGTTQEVIAALPASVKVVDLSADFRLFDVDTYAQWYGHEHRAP 121

Query: 191 ELQQEAVYGLTEVLRNEIRNARLVANPGCYPTSIQLPLVPLIKAKLIKVSNIIIDAKSGV 250
           ELQ++AVYGLTE+ R+ +  ARLVANPGCYPTS+QLPL+PL+KA LI+ ++I+IDAKSGV
Sbjct: 122 ELQKQAVYGLTELARDAVAKARLVANPGCYPTSVQLPLIPLLKAGLIEAADIVIDAKSGV 181

Query: 251 SGAGRGAKEANLYTEIAEGIHAYGIKGHRHVPEIEQGLSEAAESKVTISFTPNLICMKRG 310
           SGAGR AKEANLYTE+ EG+HAYG+  HRH PEIEQGLS AA   V +SFTP+LI M RG
Sbjct: 182 SGAGRAAKEANLYTEVTEGMHAYGVASHRHAPEIEQGLSAAAGVPVLVSFTPHLIPMSRG 241

Query: 311 MQSTMFVEMAPGVTANDLYQHLKSTYEGEEFVKLLNGSSVPHTRHVVGSNYCFMNVFEDR 370
           M ST++V+   G  A DL   L  T+ GE FV+++    VPHTRHV GSN+C +NVF+DR
Sbjct: 242 MLSTIYVKTKGGAKAADLRAQLSKTFGGEPFVRVVPEGVVPHTRHVRGSNHCLINVFDDR 301

Query: 371 IPGRAIIISVIDNLVKGASGQAVQNLNLMMGLPENTGLQYQPLFP 415
           +PG+ II SVIDNLVKGASGQA+QN+NLM GLPE T L  QP+FP
Sbjct: 302 VPGKVIITSVIDNLVKGASGQALQNMNLMFGLPETTALAQQPMFP 346


Lambda     K      H
   0.317    0.135    0.391 

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: 502
Number of extensions: 10
Number of successful extensions: 1
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: 415
Length of database: 346
Length adjustment: 30
Effective length of query: 385
Effective length of database: 316
Effective search space:   121660
Effective search space used:   121660
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: 50 (23.9 bits)

Align candidate WP_043743989.1 AMB_RS09075 (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.27886.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.2e-134  434.0   0.0   2.5e-134  433.8   0.0    1.0  1  lcl|NCBI__GCF_000009985.1:WP_043743989.1  AMB_RS09075 N-acetyl-gamma-gluta


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_043743989.1  AMB_RS09075 N-acetyl-gamma-glutamyl-phosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  433.8   0.0  2.5e-134  2.5e-134       2     345 .]       5     346 .]       4     346 .] 0.98

  Alignments for each domain:
  == domain 1  score: 433.8 bits;  conditional E-value: 2.5e-134
                                 TIGR01850   2 kvaivGasGYtGaeLlrllakHpevevtklvssreagkklsevhphlkglvdlkleeleeeeileeadv 70 
                                                +ai+GasGYtGaeL+rlla Hp ++++ ++++r+ag+++++v+phl gl   +l ++++ ++ +++d+
  lcl|NCBI__GCF_000009985.1:WP_043743989.1   5 SIAILGASGYTGAELVRLLALHPTFKIKVMTGDRKAGQSMESVFPHLGGLELPTLVAIDQVDF-TTVDA 72 
                                               699**********************************************99989998988765.69*** PP

                                 TIGR01850  71 vflAlphgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnreeik 139
                                               vf++lphg+++e++ ++l ++vkv+dlSadfRl d ++Y++wYg++h+++el+++avYGl+El r++++
  lcl|NCBI__GCF_000009985.1:WP_043743989.1  73 VFCCLPHGTTQEVI-AALPASVKVVDLSADFRLFDVDTYAQWYGHEHRAPELQKQAVYGLTELARDAVA 140
                                               **************.567888************************************************ PP

                                 TIGR01850 140 kaklianPGCyaTaalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvtkH 208
                                               ka+l+anPGCy+T+++L l+Pllk++lie  +i++daksGvSgAGr+a+e++l++ev+e +++Y v++H
  lcl|NCBI__GCF_000009985.1:WP_043743989.1 141 KARLVANPGCYPTSVQLPLIPLLKAGLIEAADIVIDAKSGVSGAGRAAKEANLYTEVTEGMHAYGVASH 209
                                               ********************************************************************* PP

                                 TIGR01850 209 rHtpEieqelsklaekkvkvsftphlvpmtrGilatiyaklkkelteeelrklyeevYedepfvrvlke 277
                                               rH+pEieq ls++a+  v vsftphl+pm+rG+l+tiy+k+k + ++++lr+++++++ +epfvrv++e
  lcl|NCBI__GCF_000009985.1:WP_043743989.1 210 RHAPEIEQGLSAAAGVPVLVSFTPHLIPMSRGMLSTIYVKTKGGAKAADLRAQLSKTFGGEPFVRVVPE 278
                                               ***********88888999************************************************** PP

                                 TIGR01850 278 gelPstkavlgsnfvdigvavdeetkrvvvvsaiDNLvKGaagqAvqnlNlmlgfdetegLeklpllp 345
                                               g +P+t++v+gsn++ i+v  d+  ++v+++s+iDNLvKGa+gqA+qn+Nlm+g++et++L ++p++p
  lcl|NCBI__GCF_000009985.1:WP_043743989.1 279 GVVPHTRHVRGSNHCLINVFDDRVPGKVIITSVIDNLVKGASGQALQNMNLMFGLPETTALAQQPMFP 346
                                               *****************************************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (345 nodes)
Target sequences:                          1  (346 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: 10.21
//
[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