GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argC in Marivita geojedonensis DPG-138

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_085637320.1 MGEO_RS11185 N-acetyl-gamma-glutamyl-phosphate reductase

Query= SwissProt::Q93Z70
         (401 letters)



>NCBI__GCF_002115805.1:WP_085637320.1
          Length = 342

 Score =  354 bits (908), Expect = e-102
 Identities = 181/344 (52%), Positives = 240/344 (69%), Gaps = 5/344 (1%)

Query: 59  IRIGLLGASGYTGAEIVRLLANHPHFQVTLMTADRKAGQSMESVFPHLRAQKLPTLVSVK 118
           + I ++GASGYTGAE++RL+A HP  ++  + A+ KAGQ++  VFP LR   LP LV+ +
Sbjct: 3   LSIAIIGASGYTGAELLRLIATHPDMEIAALAANSKAGQTIAQVFPFLRHLDLPQLVTWE 62

Query: 119 DADFSTVDAVFCCLPHGTTQEIIKELPTALKIVDLSADFRLRNIAEYEEWYGQPHKAVEL 178
           + DFS++D  FC LPH T+QE+I +LPT LKIVDLSADFRLR+ A YE WYG PH AVE+
Sbjct: 63  EIDFSSIDLCFCALPHKTSQEVISKLPTDLKIVDLSADFRLRDPAAYETWYGNPHAAVEM 122

Query: 179 QKEVVYGLTEILREDIKKARLVANPGCYPTTIQLPLVPLLKANLIKHENIIIDAKSGVSG 238
           QKE VYGLTE  R+ I+ ARLVA  GC   T Q  L PL+   +I  ++II+D K  VSG
Sbjct: 123 QKEAVYGLTEFYRDAIRDARLVAGTGCNAATGQYILRPLIAEKVIGLKDIILDLKCAVSG 182

Query: 239 AGRGAKEANLYSEIAEGISSYGV-TRHRHVPEIEQGLSDVAQSKVTVSFTPHLMPMIRGM 297
           AGR  KE+ L++E++EG ++Y V   HRH+ E +Q  S +A  +V V FTPHL+P  RG+
Sbjct: 183 AGRSLKESLLHAELSEGYNAYSVGGTHRHLGEFDQEFSALAGEEVRVQFTPHLIPANRGI 242

Query: 298 QSTIYVEMAPGVRTEDLHQQLKTSYEDEEFVKVLDEGVVPRTHNVRGSNYCHMSVFPDRI 357
            +T YV        + ++  L ++Y DE F++VL  G  P TH+VRGSN+CH+ V  DRI
Sbjct: 243 LATCYV----SGDAQAVYGALASAYADEPFIEVLPFGETPSTHHVRGSNFCHIGVTGDRI 298

Query: 358 PGRAIIISVIDNLVKGASGQALQNLNIMLGYPETTGLLHQPLFP 401
            GRAII++ +DNL KG+SGQALQN N+MLG  ET GL+  P FP
Sbjct: 299 EGRAIIVAALDNLTKGSSGQALQNANLMLGLEETAGLMLAPCFP 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: 401
Number of extensions: 8
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 WP_085637320.1 MGEO_RS11185 (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.171229.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.2e-115  372.4   0.0   1.3e-115  372.2   0.0    1.0  1  NCBI__GCF_002115805.1:WP_085637320.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002115805.1:WP_085637320.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  372.2   0.0  1.3e-115  1.3e-115       2     345 .]       4     342 .]       3     342 .] 0.97

  Alignments for each domain:
  == domain 1  score: 372.2 bits;  conditional E-value: 1.3e-115
                             TIGR01850   2 kvaivGasGYtGaeLlrllakHpevevtklvssreagkklsevhphlkglvdlkleeleeeeileeadvvflA 74 
                                            +ai+GasGYtGaeLlrl+a+Hp++e+++l+++++ag+++++v+p l++l   +l + ee +  +++d+ f+A
  NCBI__GCF_002115805.1:WP_085637320.1   4 SIAIIGASGYTGAELLRLIATHPDMEIAALAANSKAGQTIAQVFPFLRHLDLPQLVTWEEID-FSSIDLCFCA 75 
                                           689**********************************************9886666666644.579******* PP

                             TIGR01850  75 lphgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnreeikkaklianP 147
                                           lph++s+e++++ l +++k++dlSadfRl+d+++Ye+wYg++h++ e+++eavYGl+E++r++i++a+l+a  
  NCBI__GCF_002115805.1:WP_085637320.1  76 LPHKTSQEVISK-LPTDLKIVDLSADFRLRDPAAYETWYGNPHAAVEMQKEAVYGLTEFYRDAIRDARLVAGT 147
                                           **********77.5888******************************************************** PP

                             TIGR01850 148 GCyaTaalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvt.kHrHtpEieqels 219
                                           GC+a + +  l Pl++ek+i  k+ii d k +vSgAGr+ +e+ l+ae++e  ++Y+v  +HrH  E  qe s
  NCBI__GCF_002115805.1:WP_085637320.1 148 GCNAATGQYILRPLIAEKVIGLKDIILDLKCAVSGAGRSLKESLLHAELSEGYNAYSVGgTHRHLGEFDQEFS 220
                                           **********************************************************99************* PP

                             TIGR01850 220 klaekkvkvsftphlvpmtrGilatiyaklkkelteeelrklyeevYedepfvrvlkegelPstkavlgsnfv 292
                                           +la+++v+v+ftphl+p  rGilat+y+  ++    + ++ +++++Y+depf++vl+ ge+Pst++v+gsnf+
  NCBI__GCF_002115805.1:WP_085637320.1 221 ALAGEEVRVQFTPHLIPANRGILATCYVSGDA----QAVYGALASAYADEPFIEVLPFGETPSTHHVRGSNFC 289
                                           ****************************9988....88*********************************** PP

                             TIGR01850 293 digvavdeetkrvvvvsaiDNLvKGaagqAvqnlNlmlgfdetegLeklpllp 345
                                           +igv+ d+ ++r+++v+a+DNL+KG +gqA+qn Nlmlg++et+gL   p++p
  NCBI__GCF_002115805.1:WP_085637320.1 290 HIGVTGDRIEGRAIIVAALDNLTKGSSGQALQNANLMLGLEETAGLMLAPCFP 342
                                           ***********************************************999987 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 26.91
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

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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:

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:

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:

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:

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