GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argC in Lentibacillus jeotgali Grbi

Align N-acetyl-gamma-glutamyl-phosphate reductase; AGPR; N-acetyl-glutamate semialdehyde dehydrogenase; NAGSA dehydrogenase; EC 1.2.1.38 (characterized)
to candidate WP_010530240.1 ON01_RS06665 N-acetyl-gamma-glutamyl-phosphate reductase

Query= SwissProt::Q07906
         (345 letters)



>NCBI__GCF_000224785.1:WP_010530240.1
          Length = 345

 Score =  388 bits (996), Expect = e-112
 Identities = 194/345 (56%), Positives = 239/345 (69%), Gaps = 1/345 (0%)

Query: 2   MNVAIIGATGYSGAELFRLLYGHPHVSQCDVFSSSQDGIHLSESFPHVGAVDGAVLHKLE 61
           M  AI+GATGY GAEL R+L  HP V+     SSS  G  ++E +PH  AV    L  ++
Sbjct: 1   MKAAIVGATGYGGAELIRILQQHPDVTLQSYHSSSHQGESMAEKYPHFKAVSEMDLEGID 60

Query: 62  IEALAK-YDAVFFATPPGVSGEWAPALVDRGVKVIDLSGDFRLKDGAVYAQWYGREAAPS 120
            E +A+  D VF ATP GVS E  P  +  G +VIDLSGDFRLKD   Y +WY ++A   
Sbjct: 61  PEYIAQDADVVFVATPSGVSAELVPEFIKAGARVIDLSGDFRLKDTLQYEKWYKKKAPDE 120

Query: 121 AYLERAVYGLTEWNREAVRGAVLLSNPGCYPTATLLGLAPLVKEGLIKEDSIIVDAKSGV 180
             LE AVYGLTEW         L++NPGCYPTA LLGLAPLVK  LI  +SII+DAK+GV
Sbjct: 121 TILENAVYGLTEWLDTEATETQLMTNPGCYPTAALLGLAPLVKNQLIHPNSIIIDAKTGV 180

Query: 181 SGAGRKAGLGTHFSEVNENVKIYKVNAHQHIPEIEQALQTWNEAVAPITFSTHLIPMTRG 240
           SGAG+     THF+E+N+N+K+YKV  HQH PEIEQ L  WN    P+TF THL+PMTRG
Sbjct: 181 SGAGKNPTAVTHFTEMNDNLKVYKVLEHQHTPEIEQVLAGWNPNTGPVTFGTHLVPMTRG 240

Query: 241 IMATIYAKAKQSISPNDLVDLYKTSYEGSPFVRIRQLGQFPATKDVYGSNYCDIGLAYDE 300
           IM TIYA A + ++   L DLYK +Y+ S FVRIR+ G +P+TK+VYGSN+CD+ +AYDE
Sbjct: 241 IMTTIYADAAEDMTAAKLSDLYKETYKDSYFVRIREQGTYPSTKEVYGSNFCDVSVAYDE 300

Query: 301 RTERVTVVSVIDNLMKGAAGQAVQNFNLMMGWDEAEGLRSLPIYP 345
           RT R+ +VSVIDNL+KGA+GQAVQN N M G DE  GL   P+YP
Sbjct: 301 RTNRIMIVSVIDNLVKGASGQAVQNMNRMFGIDEKAGLAFAPVYP 345


Lambda     K      H
   0.318    0.135    0.404 

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: 371
Number of extensions: 11
Number of successful extensions: 2
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: 345
Length of database: 345
Length adjustment: 29
Effective length of query: 316
Effective length of database: 316
Effective search space:    99856
Effective search space used:    99856
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_010530240.1 ON01_RS06665 (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.3706868.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.6e-142  459.2   0.1   5.1e-142  459.1   0.1    1.0  1  NCBI__GCF_000224785.1:WP_010530240.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000224785.1:WP_010530240.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  459.1   0.1  5.1e-142  5.1e-142       1     345 []       1     345 []       1     345 [] 0.99

  Alignments for each domain:
  == domain 1  score: 459.1 bits;  conditional E-value: 5.1e-142
                             TIGR01850   1 ikvaivGasGYtGaeLlrllakHpevevtklvssreagkklsevhphlkglvdlkleeleeeeileeadvvfl 73 
                                           +k+aivGa+GY+GaeL+r+l++Hp+v++++++ss+++g++++e +ph+k + ++ le ++ e i+++advvf+
  NCBI__GCF_000224785.1:WP_010530240.1   1 MKAAIVGATGYGGAELIRILQQHPDVTLQSYHSSSHQGESMAEKYPHFKAVSEMDLEGIDPEYIAQDADVVFV 73 
                                           689********************************************************************** PP

                             TIGR01850  74 AlphgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnreeikkaklian 146
                                           A+p+gvsaelvpe++++g++vidlS+dfRlkd+ +YekwY+kk+++e++le+avYGl+E+   e ++++l+ n
  NCBI__GCF_000224785.1:WP_010530240.1  74 ATPSGVSAELVPEFIKAGARVIDLSGDFRLKDTLQYEKWYKKKAPDETILENAVYGLTEWLDTEATETQLMTN 146
                                           ************************************************************************* PP

                             TIGR01850 147 PGCyaTaalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvtkHrHtpEieqels 219
                                           PGCy+TaalL+laPl+k++li+p+sii+dak+GvSgAG+++++ ++f+e+n+nlk+Ykv +H+HtpEieq l 
  NCBI__GCF_000224785.1:WP_010530240.1 147 PGCYPTAALLGLAPLVKNQLIHPNSIIIDAKTGVSGAGKNPTAVTHFTEMNDNLKVYKVLEHQHTPEIEQVLA 219
                                           ************************************************************************* PP

                             TIGR01850 220 klaekkvkvsftphlvpmtrGilatiyaklkkelteeelrklyeevYedepfvrvlkegelPstkavlgsnfv 292
                                            ++ ++  v+f +hlvpmtrGi++tiya +++++t+++l +ly+e+Y+d+ fvr+ ++g++Pstk+v+gsnf+
  NCBI__GCF_000224785.1:WP_010530240.1 220 GWNPNTGPVTFGTHLVPMTRGIMTTIYADAAEDMTAAKLSDLYKETYKDSYFVRIREQGTYPSTKEVYGSNFC 292
                                           ***99999***************************************************************** PP

                             TIGR01850 293 digvavdeetkrvvvvsaiDNLvKGaagqAvqnlNlmlgfdetegLeklpllp 345
                                           d++va+de+t+r+++vs+iDNLvKGa+gqAvqn+N m+g de++gL + p++p
  NCBI__GCF_000224785.1:WP_010530240.1 293 DVSVAYDERTNRIMIVSVIDNLVKGASGQAVQNMNRMFGIDEKAGLAFAPVYP 345
                                           ***************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (345 nodes)
Target sequences:                          1  (345 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: 26.80
//
[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