GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argC in Caldicellulosiruptor kronotskyensis 2002

Align N-acetyl-gamma-glutamyl-phosphate reductase; AGPR; N-acetyl-glutamate semialdehyde dehydrogenase; NAGSA dehydrogenase; EC 1.2.1.38 (characterized)
to candidate WP_013430561.1 CALKRO_RS08160 N-acetyl-gamma-glutamyl-phosphate reductase

Query= SwissProt::Q07906
         (345 letters)



>NCBI__GCF_000166775.1:WP_013430561.1
          Length = 343

 Score =  279 bits (714), Expect = 7e-80
 Identities = 149/338 (44%), Positives = 210/338 (62%), Gaps = 2/338 (0%)

Query: 1   MMNVAIIGATGYSGAELFRLLYGHPHVSQCDVFSSSQDGIHLSESFPHVGAVDGAVLHKL 60
           M+  +IIGA+GY G EL RLL  HP V    + SSS + + + ++ P    V   V  + 
Sbjct: 1   MIKASIIGASGYVGVELIRLLLRHPEVEIVSIISSSSNQLSIDKTNPQFKKVSNLVFEEF 60

Query: 61  EIEALAKYDAVFFATPPGVSGEWAPALVDRGVKVIDLSGDFRLKDGAVYAQWYGREAAPS 120
           +IEA+ + D VF A P G+S E+     D G  VIDLS DFR KD   YA+ Y +   P 
Sbjct: 61  KIEAIQEADVVFCALPHGISQEYVKIGYDIGKVVIDLSADFRYKDLQRYAKDYSQHKYPE 120

Query: 121 AYLERAVYGLTEWNREAVRGAVLLSNPGCYPTATLLGLAPLVKEGLIKEDSIIVDAKSGV 180
             L ++ YGL E NRE ++ A ++ NPGCYPT+ +LG+APL+K  LI ++SII+D+KSGV
Sbjct: 121 L-LSKSAYGLCEINREEIKNAQIIGNPGCYPTSAILGIAPLLKNKLIDKNSIIIDSKSGV 179

Query: 181 SGAGRKAGLGTHFSEVNENVKIYKVNAHQHIPEIEQALQTWNEAVAPITFSTHLIPMTRG 240
           SGAG+K+     F E++EN K Y V  H+H  EIE+           ++F+ HL+P+ RG
Sbjct: 180 SGAGKKSDFAYSFCELDENFKAYSVAKHRHTSEIEEKCSLLFGENLNLSFTPHLLPVKRG 239

Query: 241 IMATIYAKAKQSISPNDLVDLYKTSYEGSPFVRIRQLGQFPATKDVYGSNYCDIGLAYDE 300
           I++TIYA   ++I+  DLV++Y   Y+   FVRI +    P  K V G+N+ DIG   D+
Sbjct: 240 ILSTIYATFVKNINKGDLVEIYNEFYKDEYFVRIFE-DDLPELKYVRGTNFVDIGFEIDK 298

Query: 301 RTERVTVVSVIDNLMKGAAGQAVQNFNLMMGWDEAEGL 338
           +T RV ++S IDNL+KGAAGQA+QN N+    +E  GL
Sbjct: 299 KTNRVIIISCIDNLIKGAAGQAIQNMNIRFSLNEKMGL 336


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: 310
Number of extensions: 15
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: 345
Length of database: 343
Length adjustment: 29
Effective length of query: 316
Effective length of database: 314
Effective search space:    99224
Effective search space used:    99224
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_013430561.1 CALKRO_RS08160 (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.1839701.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.1e-132  425.7   0.0   8.4e-132  425.5   0.0    1.0  1  NCBI__GCF_000166775.1:WP_013430561.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000166775.1:WP_013430561.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  425.5   0.0  8.4e-132  8.4e-132       1     341 [.       2     339 ..       2     342 .. 0.98

  Alignments for each domain:
  == domain 1  score: 425.5 bits;  conditional E-value: 8.4e-132
                             TIGR01850   1 ikvaivGasGYtGaeLlrllakHpevevtklvssreagkklsevhphlkglvdlkleeleeeeileeadvvfl 73 
                                           ik++i+GasGY G+eL+rll +Hpeve+++++ss+++  ++++++p++k++ +l +ee+++e+i +eadvvf+
  NCBI__GCF_000166775.1:WP_013430561.1   2 IKASIIGASGYVGVELIRLLLRHPEVEIVSIISSSSNQLSIDKTNPQFKKVSNLVFEEFKIEAI-QEADVVFC 73 
                                           5899*********************************************************976.59****** PP

                             TIGR01850  74 AlphgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnreeikkaklian 146
                                           Alphg+s+e+v+  ++ g +vidlSadfR kd + Y+k Y + h+++ell++ +YGl+E+nreeik+a++i+n
  NCBI__GCF_000166775.1:WP_013430561.1  74 ALPHGISQEYVKIGYDIGKVVIDLSADFRYKDLQRYAKDYSQ-HKYPELLSKSAYGLCEINREEIKNAQIIGN 145
                                           ****************************************98.99**************************** PP

                             TIGR01850 147 PGCyaTaalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvtkHrHtpEieqels 219
                                           PGCy+T+a+L++aPllk+kli+++sii+d+ksGvSgAG+k   + +f+e++en+k+Y+v+kHrHt Eie+++s
  NCBI__GCF_000166775.1:WP_013430561.1 146 PGCYPTSAILGIAPLLKNKLIDKNSIIIDSKSGVSGAGKKSDFAYSFCELDENFKAYSVAKHRHTSEIEEKCS 218
                                           ************************************************************************* PP

                             TIGR01850 220 klaekkvkvsftphlvpmtrGilatiyaklkkelteeelrklyeevYedepfvrvlkegelPstkavlgsnfv 292
                                            l +++ ++sftphl+p++rGil+tiya++ k++++ +l ++y+e+Y+de fvr+++ ++lP++k v+g+nfv
  NCBI__GCF_000166775.1:WP_013430561.1 219 LLFGENLNLSFTPHLLPVKRGILSTIYATFVKNINKGDLVEIYNEFYKDEYFVRIFE-DDLPELKYVRGTNFV 290
                                           ********************************************************8.9************** PP

                             TIGR01850 293 digvavdeetkrvvvvsaiDNLvKGaagqAvqnlNlmlgfdetegLekl 341
                                           dig+++d++t+rv+++s iDNL+KGaagqA+qn+N+++ ++e+ gL ++
  NCBI__GCF_000166775.1:WP_013430561.1 291 DIGFEIDKKTNRVIIISCIDNLIKGAAGQAIQNMNIRFSLNEKMGLIMV 339
                                           **********************************************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (345 nodes)
Target sequences:                          1  (343 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: 26.17
//
[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