Alignments for a candidate for argC in Phaeobacter inhibens BS107

GapMind for Amino acid biosynthesis

Alignments for a candidate for argC in Phaeobacter inhibens BS107

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 GFF1682 PGA1_c17050 N-acetyl-gamma-glutamyl-phosphate reductase ArgC

Query= SwissProt::Q93Z70
         (401 letters)



>FitnessBrowser__Phaeo:GFF1682
          Length = 342

 Score =  361 bits (926), Expect = e-104
 Identities = 180/343 (52%), Positives = 238/343 (69%), Gaps = 5/343 (1%)

Query: 60  RIGLLGASGYTGAEIVRLLANHPHFQVTLMTADRKAGQSMESVFPHLRAQKLPTLVSVKD 119
           ++ +LGASGYTGAE+VRL++ HP  ++  ++A+RKAG +M  VFPHLR  +LP L  + +
Sbjct: 4   KVAILGASGYTGAELVRLISQHPTIEIAALSAERKAGMTMAQVFPHLRHLELPVLCKIGE 63

Query: 120 ADFSTVDAVFCCLPHGTTQEIIKELPTALKIVDLSADFRLRNIAEYEEWYGQPHKAVELQ 179
            DF+ +D  FC LPH T+QE+I  LP  LKIVDLSADFRLR+  EYE+WYG PH A+  Q
Sbjct: 64  IDFTGIDLCFCALPHKTSQEVIAALPQDLKIVDLSADFRLRDPDEYEKWYGNPHAALAQQ 123

Query: 180 KEVVYGLTEILREDIKKARLVANPGCYPTTIQLPLVPLLKANLIKHENIIIDAKSGVSGA 239
           KE VYGL+E  RE+IK ARLVA  GC   T Q  L PL+ + +I  ++II+D K  VSGA
Sbjct: 124 KEAVYGLSEFYREEIKSARLVAGTGCNAATGQFALRPLIASGVIDLDDIILDLKCAVSGA 183

Query: 240 GRGAKEANLYSEIAEGISSYGV-TRHRHVPEIEQGLSDVAQSKVTVSFTPHLMPMIRGMQ 298
           GR  KE  L++E++EG   Y V   HRH+ E +Q  S +A   V V FTPHL+P  RG+ 
Sbjct: 184 GRSLKENLLHAELSEGYHGYAVGGTHRHLGEFDQEFSKIAGRPVKVQFTPHLVPANRGIL 243

Query: 299 STIYVEMAPGVRTEDLHQQLKTSYEDEEFVKVLDEGVVPRTHNVRGSNYCHMSVFPDRIP 358
           +T+YV+       + +HQ L T+Y DE F+++L  G  P T ++RGSN+CH+ V  DRI 
Sbjct: 244 ATVYVK----GDAQTIHQTLATAYADEPFIELLPFGEAPSTRHIRGSNFCHIGVAADRIE 299

Query: 359 GRAIIISVIDNLVKGASGQALQNLNIMLGYPETTGLLHQPLFP 401
           GR I+I+ +DNL KG+SGQALQN N+MLG  ETTGL+  PLFP
Sbjct: 300 GRTIVIAALDNLTKGSSGQALQNANLMLGEEETTGLMMAPLFP 342


Lambda     K      H
   0.318    0.134    0.386 

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: 414
Number of extensions: 10
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: 401
Length of database: 342
Length adjustment: 30
Effective length of query: 371
Effective length of database: 312
Effective search space:   115752
Effective search space used:   115752
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: 49 (23.5 bits)

Align candidate GFF1682 PGA1_c17050 (N-acetyl-gamma-glutamyl-phosphate reductase ArgC)
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.27513.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   7.6e-118  379.6   0.0   8.6e-118  379.4   0.0    1.0  1  lcl|FitnessBrowser__Phaeo:GFF1682  PGA1_c17050 N-acetyl-gamma-gluta


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF1682  PGA1_c17050 N-acetyl-gamma-glutamyl-phosphate reductase ArgC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  379.4   0.0  8.6e-118  8.6e-118       2     345 .]       4     342 .]       3     342 .] 0.97

  Alignments for each domain:
  == domain 1  score: 379.4 bits;  conditional E-value: 8.6e-118
                          TIGR01850   2 kvaivGasGYtGaeLlrllakHpevevtklvssreagkklsevhphlkglvdlkleeleeeeileeadvvflAlph 77 
                                        kvai+GasGYtGaeL+rl+++Hp +e+++l ++r+ag ++++v+phl++l    l+++ e +  + +d+ f+Alph
  lcl|FitnessBrowser__Phaeo:GFF1682   4 KVAILGASGYTGAELVRLISQHPTIEIAALSAERKAGMTMAQVFPHLRHLELPVLCKIGEID-FTGIDLCFCALPH 78 
                                        8************************************************9998888887765.569********** PP

                          TIGR01850  78 gvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnreeikkaklianPGCyaTa 153
                                        ++s+e++ ++l +++k++dlSadfRl+d+++YekwYg++h++ ++++eavYGl+E++reeik+a+l+a  GC+a +
  lcl|FitnessBrowser__Phaeo:GFF1682  79 KTSQEVI-AALPQDLKIVDLSADFRLRDPDEYEKWYGNPHAALAQQKEAVYGLSEFYREEIKSARLVAGTGCNAAT 153
                                        *******.667999************************************************************** PP

                          TIGR01850 154 alLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvt.kHrHtpEieqelsklaekkvkv 228
                                         + al Pl+++++i+ ++ii d k +vSgAGr+ +e+ l+ae++e  + Y+v  +HrH  E  qe sk+a++ vkv
  lcl|FitnessBrowser__Phaeo:GFF1682 154 GQFALRPLIASGVIDLDDIILDLKCAVSGAGRSLKENLLHAELSEGYHGYAVGgTHRHLGEFDQEFSKIAGRPVKV 229
                                        ****************************************************99********************** PP

                          TIGR01850 229 sftphlvpmtrGilatiyaklkkelteeelrklyeevYedepfvrvlkegelPstkavlgsnfvdigvavdeetkr 304
                                        +ftphlvp  rGilat+y+k ++    ++++++++++Y+depf+++l+ ge+Pst++++gsnf++igva d+ ++r
  lcl|FitnessBrowser__Phaeo:GFF1682 230 QFTPHLVPANRGILATVYVKGDA----QTIHQTLATAYADEPFIELLPFGEAPSTRHIRGSNFCHIGVAADRIEGR 301
                                        *******************9988....88*********************************************** PP

                          TIGR01850 305 vvvvsaiDNLvKGaagqAvqnlNlmlgfdetegLeklpllp 345
                                         +v++a+DNL+KG +gqA+qn Nlmlg +et+gL + pl+p
  lcl|FitnessBrowser__Phaeo:GFF1682 302 TIVIAALDNLTKGSSGQALQNANLMLGEEETTGLMMAPLFP 342
                                        **************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (345 nodes)
Target sequences:                          1  (342 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: 00:00:00.01
# Mc/sec: 9.45
//
[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