GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argC in Dyella japonica UNC79MFTsu3.2

Align N-acetylglutamylphosphate reductase (EC 1.2.1.38) (characterized)
to candidate N515DRAFT_3769 N515DRAFT_3769 N-acetyl-gamma-glutamyl-phosphate reductase

Query= reanno::Dyella79:N515DRAFT_3769
         (319 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3769
          Length = 319

 Score =  640 bits (1650), Expect = 0.0
 Identities = 319/319 (100%), Positives = 319/319 (100%)

Query: 1   MSIDKKTIGIVGARGHTGAELIRLIATHPALELGFVSSRELDGQRVAEHVDGYAGELRYA 60
           MSIDKKTIGIVGARGHTGAELIRLIATHPALELGFVSSRELDGQRVAEHVDGYAGELRYA
Sbjct: 1   MSIDKKTIGIVGARGHTGAELIRLIATHPALELGFVSSRELDGQRVAEHVDGYAGELRYA 60

Query: 61  NLDPAAVAAQGADVVVLALPNGKAAPYVEAIDAAKPETLILDLSADYRFNERWYYGLPEL 120
           NLDPAAVAAQGADVVVLALPNGKAAPYVEAIDAAKPETLILDLSADYRFNERWYYGLPEL
Sbjct: 61  NLDPAAVAAQGADVVVLALPNGKAAPYVEAIDAAKPETLILDLSADYRFNERWYYGLPEL 120

Query: 121 TRGKWRGERRISNPGCYATAIQLSIAPLKDVLAAPPVSFGVSGYSGAGTTPSDKNNPEKL 180
           TRGKWRGERRISNPGCYATAIQLSIAPLKDVLAAPPVSFGVSGYSGAGTTPSDKNNPEKL
Sbjct: 121 TRGKWRGERRISNPGCYATAIQLSIAPLKDVLAAPPVSFGVSGYSGAGTTPSDKNNPEKL 180

Query: 181 RDNLMPYSLTGHTHEQEASRHLGLPVEFMPHVAPHFRGLTVTTNLYLVRPMKREEILQRF 240
           RDNLMPYSLTGHTHEQEASRHLGLPVEFMPHVAPHFRGLTVTTNLYLVRPMKREEILQRF
Sbjct: 181 RDNLMPYSLTGHTHEQEASRHLGLPVEFMPHVAPHFRGLTVTTNLYLVRPMKREEILQRF 240

Query: 241 RHAYDGEKLVKVVDEAPWVSQIAHRHHAEVGGFAVSVDGKRVVIVATLDNLLKGAATQAI 300
           RHAYDGEKLVKVVDEAPWVSQIAHRHHAEVGGFAVSVDGKRVVIVATLDNLLKGAATQAI
Sbjct: 241 RHAYDGEKLVKVVDEAPWVSQIAHRHHAEVGGFAVSVDGKRVVIVATLDNLLKGAATQAI 300

Query: 301 QNINRAIGVDEYTSIPLEG 319
           QNINRAIGVDEYTSIPLEG
Sbjct: 301 QNINRAIGVDEYTSIPLEG 319


Lambda     K      H
   0.318    0.136    0.400 

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: 505
Number of extensions: 8
Number of successful extensions: 1
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: 319
Length of database: 319
Length adjustment: 28
Effective length of query: 291
Effective length of database: 291
Effective search space:    84681
Effective search space used:    84681
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: 48 (23.1 bits)

Align candidate N515DRAFT_3769 N515DRAFT_3769 (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.22801.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-96  307.3   0.0    3.7e-95  305.0   0.0    1.8  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_3769  N515DRAFT_3769 N-acetyl-gamma-gl


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_3769  N515DRAFT_3769 N-acetyl-gamma-glutamyl-phosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  305.0   0.0   3.7e-95   3.7e-95       2     340 ..       7     317 ..       6     319 .] 0.95

  Alignments for each domain:
  == domain 1  score: 305.0 bits;  conditional E-value: 3.7e-95
                                    TIGR01850   2 kvaivGasGYtGaeLlrllakHpevevtklvssre.agkklsevhphlkglvd.lkleeleeeeil 65 
                                                  +++ivGa+G+tGaeL+rl+a+Hp++e+  +vssre  g++++e+++ + g+++ ++l++ +++  +
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3769   7 TIGIVGARGHTGAELIRLIATHPALELG-FVSSRElDGQRVAEHVDGYAGELRyANLDPAAVA--A 69 
                                                  699************************9.9999999***************998899988777..6 PP

                                    TIGR01850  66 eeadvvflAlphgvsaelvpellekg..vkvidlSadfRlkdaevYekwYgkkhekeelleeavYG 129
                                                  + advv+lAlp+g +a++v+++ +++  + ++dlSad+R+++                   +++YG
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3769  70 QGADVVVLALPNGKAAPYVEAIDAAKpeTLILDLSADYRFNE-------------------RWYYG 116
                                                  79******************998855459************4...................478** PP

                                    TIGR01850 130 lpElnreeikkaklianPGCyaTaalLalaPllkekliepksiivdaksGvSgAGrkasekslfae 195
                                                  lpEl+r + ++ ++i+nPGCyaTa++L++aPl +  +     ++ +++sG+SgAG+++s+k++ ++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3769 117 LPELTRGKWRGERRISNPGCYATAIQLSIAPLKDVLAAP---PVSFGVSGYSGAGTTPSDKNNPEK 179
                                                  ********************************8655443...69********************** PP

                                    TIGR01850 196 vnenlkpYkvtkHrHtpEieqelsklaekkvkvsftphlvpmtrGilatiyaklkkelteeelrkl 261
                                                  +++nl+pY++t+H H++E +++l+        v+f+ph++p++rG++ t+++ l +++++ee+ + 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3769 180 LRDNLMPYSLTGHTHEQEASRHLG------LPVEFMPHVAPHFRGLTVTTNLYLVRPMKREEILQR 239
                                                  ************************......78********************************** PP

                                    TIGR01850 262 yeevYedepfvrvlkegelPstkavlgsnfvdig.vavdeetkrvvvvsaiDNLvKGaagqAvqnl 326
                                                  ++++Y++e++v+v++  e+P+++++++++++++g +av  + krvv+v+++DNL+KGaa+qA+qn+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3769 240 FRHAYDGEKLVKVVD--EAPWVSQIAHRHHAEVGgFAVSVDGKRVVIVATLDNLLKGAATQAIQNI 303
                                                  **************9..9***************99******************************* PP

                                    TIGR01850 327 NlmlgfdetegLek 340
                                                  N ++g de+++++ 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3769 304 NRAIGVDEYTSIPL 317
                                                  **********9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (345 nodes)
Target sequences:                          1  (319 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 2.80
//
[ok]

This GapMind analysis is from Apr 09 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:

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