Alignments for a candidate for argC in Thermodesulforhabdus norvegica DSM 9990

GapMind for Amino acid biosynthesis

Alignments for a candidate for argC in Thermodesulforhabdus norvegica DSM 9990

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_093392448.1 BM091_RS00090 N-acetyl-gamma-glutamyl-phosphate reductase

Query= SwissProt::Q93Z70
         (401 letters)



>NCBI__GCF_900114975.1:WP_093392448.1
          Length = 346

 Score =  310 bits (793), Expect = 5e-89
 Identities = 161/346 (46%), Positives = 227/346 (65%), Gaps = 4/346 (1%)

Query: 59  IRIGLLGASGYTGAEIVRLLANHPHFQVTLMTADRKAGQSMESVFPHLRAQKLPTLVSVK 118
           +++G+LG SGYTG E++RLLA HP  ++  +++  +   ++   +P  R       V   
Sbjct: 2   LKVGVLGGSGYTGFELIRLLATHPEVKIVAVSSRAQEESAVSEHYPAFRKFVDLRYVLPD 61

Query: 119 DADFST-VDAVFCCLPHGTTQEIIKEL-PTALKIVDLSADFRLRNIAEYEEWYGQPHKAV 176
           D  F   VD VF  LPHG + + +  L    ++++DLSADFR+R+ A YE+WY +PH + 
Sbjct: 62  DPVFEKGVDVVFSALPHGASMKAVSGLVEKGVRVIDLSADFRIRDAAVYEQWY-EPHTSP 120

Query: 177 ELQKEVVYGLTEILREDIKKARLVANPGCYPTTIQLPLVPLLKANLIKHENIIIDAKSGV 236
           +L K+ VYGL E+ R +I  ARLVANPGCYPT+I L L PLLK  LI+ ++IIID+KSGV
Sbjct: 121 DLLKDAVYGLPELYRREIASARLVANPGCYPTSIILALAPLLKNRLIEEDSIIIDSKSGV 180

Query: 237 SGAGRGAKEANLYSEIAEGISSYGVTR-HRHVPEIEQGLSDVAQSKVTVSFTPHLMPMIR 295
           +GAGRG      + E+ EG  +Y V   HRH+PEIEQ LS ++  ++ V+FTPHL+PM R
Sbjct: 181 TGAGRGLSLTTHFCEVNEGFKAYKVGGVHRHIPEIEQELSLISGKEIRVTFTPHLVPMSR 240

Query: 296 GMQSTIYVEMAPGVRTEDLHQQLKTSYEDEEFVKVLDEGVVPRTHNVRGSNYCHMSVFPD 355
           G+ ST+YV    GV+  ++ +  +T Y DE FV+++  G +P T  VRGSN+C +    D
Sbjct: 241 GILSTLYVVPREGVKAGEIDEAYRTMYADEPFVRLVGSGEMPSTLQVRGSNFCDIGWKLD 300

Query: 356 RIPGRAIIISVIDNLVKGASGQALQNLNIMLGYPETTGLLHQPLFP 401
              GR I++S IDNL +GASGQA+ N+NIM G PETTGL + P  P
Sbjct: 301 GRSGRLIVVSAIDNLTRGASGQAVCNMNIMFGIPETTGLFYVPWQP 346


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: 404
Number of extensions: 16
Number of successful extensions: 5
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: 346
Length adjustment: 30
Effective length of query: 371
Effective length of database: 316
Effective search space:   117236
Effective search space used:   117236
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 WP_093392448.1 BM091_RS00090 (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.7059.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-138  445.4   0.0   8.5e-138  445.2   0.0    1.0  1  lcl|NCBI__GCF_900114975.1:WP_093392448.1  BM091_RS00090 N-acetyl-gamma-glu


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900114975.1:WP_093392448.1  BM091_RS00090 N-acetyl-gamma-glutamyl-phosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  445.2   0.0  8.5e-138  8.5e-138       2     345 .]       3     346 .]       2     346 .] 0.98

  Alignments for each domain:
  == domain 1  score: 445.2 bits;  conditional E-value: 8.5e-138
                                 TIGR01850   2 kvaivGasGYtGaeLlrllakHpevevtklvssreagkklsevhphlkglvdlkleeleeeeileeadv 70 
                                               kv+++G+sGYtG eL+rlla+Hpev+++++ s+ ++++ +se++p ++++vdl++   ++  +++ +dv
  lcl|NCBI__GCF_900114975.1:WP_093392448.1   3 KVGVLGGSGYTGFELIRLLATHPEVKIVAVSSRAQEESAVSEHYPAFRKFVDLRYVLPDDPVFEKGVDV 71 
                                               8***************************6666666*****************999999998899***** PP

                                 TIGR01850  71 vflAlphgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnreeik 139
                                               vf Alphg+s++ v+ l+ekgv+vidlSadfR++da+vYe+wY+  h++++ll++avYGlpEl+r+ei+
  lcl|NCBI__GCF_900114975.1:WP_093392448.1  72 VFSALPHGASMKAVSGLVEKGVRVIDLSADFRIRDAAVYEQWYEP-HTSPDLLKDAVYGLPELYRREIA 139
                                               *******************************************87.9999******************* PP

                                 TIGR01850 140 kaklianPGCyaTaalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvt.k 207
                                               +a+l+anPGCy+T+++LalaPllk++lie++sii+d+ksGv+gAGr  s +++f+evne +k+Ykv   
  lcl|NCBI__GCF_900114975.1:WP_093392448.1 140 SARLVANPGCYPTSIILALAPLLKNRLIEEDSIIIDSKSGVTGAGRGLSLTTHFCEVNEGFKAYKVGgV 208
                                               ******************************************************************989 PP

                                 TIGR01850 208 HrHtpEieqelsklaekkvkvsftphlvpmtrGilatiyaklkkelteeelrklyeevYedepfvrvlk 276
                                               HrH+pEieqels +++k+++v+ftphlvpm+rGil+t+y+  ++++++ e+ ++y+++Y+depfvr++ 
  lcl|NCBI__GCF_900114975.1:WP_093392448.1 209 HRHIPEIEQELSLISGKEIRVTFTPHLVPMSRGILSTLYVVPREGVKAGEIDEAYRTMYADEPFVRLVG 277
                                               ********************************************************************* PP

                                 TIGR01850 277 egelPstkavlgsnfvdigvavdeetkrvvvvsaiDNLvKGaagqAvqnlNlmlgfdetegLeklpllp 345
                                               +ge+Pst +v+gsnf+dig+++d +++r++vvsaiDNL++Ga+gqAv n+N+m+g +et+gL ++p  p
  lcl|NCBI__GCF_900114975.1:WP_093392448.1 278 SGEMPSTLQVRGSNFCDIGWKLDGRSGRLIVVSAIDNLTRGASGQAVCNMNIMFGIPETTGLFYVPWQP 346
                                               **************************************************************9999876 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 9.15
//
[ok]

This GapMind analysis is from Apr 10 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