GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argC in Xenophilus azovorans DSM 13620

Align N-acetylglutamylphosphate reductase (EC 1.2.1.38) (characterized)
to candidate WP_038206433.1 Q392_RS10930 N-acetyl-gamma-glutamyl-phosphate reductase

Query= reanno::Smeli:SMc01801
         (310 letters)



>NCBI__GCF_000745855.1:WP_038206433.1
          Length = 307

 Score =  276 bits (706), Expect = 4e-79
 Identities = 152/312 (48%), Positives = 199/312 (63%), Gaps = 14/312 (4%)

Query: 3   PKIFIDGEHGTTGLQIRVRMAGRTDLELLSIPEAERRNAAMREDLLNSADIAILCLPDDA 62
           PK+FIDGE GTTGLQIR R+A    +EL+SI    R++A+ + DL+   D+ ILCL DDA
Sbjct: 2   PKVFIDGEAGTTGLQIRERLALMPQIELVSIAPELRKDASAKRDLMAGVDLVILCLHDDA 61

Query: 63  SREAVAMV--AGNNRVRIIDTSTAHRVAPDWAYGFAEMDKAQPQRIRDARHVANPGCYPT 120
           +RE+VA++   G  R RIID STAHRVAP W YGF E+   Q + ++ A  VANPGCY T
Sbjct: 62  ARESVALIDGLGERRPRIIDASTAHRVAPGWVYGFPELAAGQAEAVQAADRVANPGCYAT 121

Query: 121 GAIALIRPLRQAGILPDGYPVTVNAVSGYTGGGKQMIAQMEDDQNPDHIGAPHFLYGLTL 180
           GAIA++RPL  AG+LP   P+ + +VSGY+GGG+ MI   E    P     P   Y L L
Sbjct: 122 GAIAIVRPLVDAGLLPADLPIALPSVSGYSGGGRTMIEAYEAGAAP-----PFETYALGL 176

Query: 181 KHKHVPEMKMHGLLERAPVFSPSVGKFAQGMIVQVPLYLEDLAAGATLETIHRALVDHYA 240
           KHKH+PE+  +  L   PVF PSVG F QGM+V +PL+L+ L        +H AL  HYA
Sbjct: 177 KHKHIPEIMNYTGLATRPVFIPSVGNFRQGMLVNLPLHLDALPGKPQAADLHDALAAHYA 236

Query: 241 GQS----IVEVVPLDESAKLARIDATELAGSDAMKLFVFGTKGGAHVNLVALLDNLGKGA 296
             +     V+V+P  E  KL   D   L  ++ +++ VF  +   H  ++A LDNLGKGA
Sbjct: 237 KSNTPAQYVKVLPPTEDGKL---DPLALNDTNTLEIRVFPNEDHRHAVVIARLDNLGKGA 293

Query: 297 SGAAVQNMDLML 308
           SGAAVQN++LML
Sbjct: 294 SGAAVQNLELML 305


Lambda     K      H
   0.319    0.136    0.395 

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: 301
Number of extensions: 12
Number of successful extensions: 4
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: 310
Length of database: 307
Length adjustment: 27
Effective length of query: 283
Effective length of database: 280
Effective search space:    79240
Effective search space used:    79240
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 (21.8 bits)
S2: 48 (23.1 bits)

Align candidate WP_038206433.1 Q392_RS10930 (N-acetyl-gamma-glutamyl-phosphate reductase)
to HMM TIGR01851 (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/TIGR01851.hmm
# target sequence database:        /tmp/gapView.2119451.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01851  [M=310]
Accession:   TIGR01851
Description: argC_other: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     4e-126  406.5   0.0   4.4e-126  406.3   0.0    1.0  1  NCBI__GCF_000745855.1:WP_038206433.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000745855.1:WP_038206433.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  406.3   0.0  4.4e-126  4.4e-126       2     310 .]       2     307 .]       1     307 [] 0.95

  Alignments for each domain:
  == domain 1  score: 406.3 bits;  conditional E-value: 4.4e-126
                             TIGR01851   2 pkvfidGeaGttGlqirerlaerddlellsidedkrkdaderakllnaadvailclpddaareavslvd...n 71 
                                           pkvfidGeaGttGlqirerla    +el+si+++ rkda+++ +l+  +d +ilcl+ddaare+v+l+d   +
  NCBI__GCF_000745855.1:WP_038206433.1   2 PKVFIDGEAGTTGLQIRERLALMPQIELVSIAPELRKDASAKRDLMAGVDLVILCLHDDAARESVALIDglgE 74 
                                           8*******************************************************************93334 PP

                             TIGR01851  72 pntkildastayrtaedwvyGfpelaaeqrekianakrvanPGcyatgaiallrPlveaGilPadfPvtinav 144
                                            + +i+dasta+r+a++wvyGfpelaa+q e +++a rvanPGcyatgaia++rPlv+aG+lPad+P+++ +v
  NCBI__GCF_000745855.1:WP_038206433.1  75 RRPRIIDASTAHRVAPGWVYGFPELAAGQAEAVQAADRVANPGCYATGAIAIVRPLVDAGLLPADLPIALPSV 147
                                           6789********************************************************************* PP

                             TIGR01851 145 sGysGGGkaliakyeeesaddskkaafiiyglalehkhlpemrkhsglaskPiftPavGdfaqGllveiplhl 217
                                           sGysGGG+++i++ye ++       +f +y+l l+hkh+pe+++++gla++P+f+P+vG+f qG+lv++plhl
  NCBI__GCF_000745855.1:WP_038206433.1 148 SGYSGGGRTMIEAYEAGA-----APPFETYALGLKHKHIPEIMNYTGLATRPVFIPSVGNFRQGMLVNLPLHL 215
                                           ***************332.....2589********************************************** PP

                             TIGR01851 218 aeldskvsaedihkalaeyykGe....kfvkvaelddaellddtildaqglngtnrlelfvfgsddgerallv 286
                                             l +k+ a+d+h+ala +y+      ++vkv +  +     d+ ld+ +ln+tn+le+ vf+++d ++a+++
  NCBI__GCF_000745855.1:WP_038206433.1 216 DALPGKPQAADLHDALAAHYAKSntpaQYVKVLPPTE-----DGKLDPLALNDTNTLEIRVFPNEDHRHAVVI 283
                                           ********************86423338999998665.....4578*************************** PP

                             TIGR01851 287 arldnlGkGasGaavqnlnialGl 310
                                           arldnlGkGasGaavqnl+++lGl
  NCBI__GCF_000745855.1:WP_038206433.1 284 ARLDNLGKGASGAAVQNLELMLGL 307
                                           ***********************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (310 nodes)
Target sequences:                          1  (307 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: 00:00:00.00
# Mc/sec: 13.18
//
[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:

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