GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argC in Echinicola vietnamensis KMM 6221, DSM 17526

Align N-succinylglutamylphosphate reductase (EC 1.2.1.-) (characterized)
to candidate Echvi_3847 Echvi_3847 N-acetyl-gamma-glutamyl-phosphate reductase, common form

Query= reanno::Cola:Echvi_3847
         (322 letters)



>FitnessBrowser__Cola:Echvi_3847
          Length = 322

 Score =  645 bits (1663), Expect = 0.0
 Identities = 322/322 (100%), Positives = 322/322 (100%)

Query: 1   MTKIKTAIIGAAGYTGGELLRILVHHPSCELVYIHSNSQKGKKIDEVHPDLIGDSDLVFT 60
           MTKIKTAIIGAAGYTGGELLRILVHHPSCELVYIHSNSQKGKKIDEVHPDLIGDSDLVFT
Sbjct: 1   MTKIKTAIIGAAGYTGGELLRILVHHPSCELVYIHSNSQKGKKIDEVHPDLIGDSDLVFT 60

Query: 61  DEVKTTGLDAVFLGLPHGQAKAFLAENKFDDQTVIIDLSTDFRDESNGFLYGLPEVNASQ 120
           DEVKTTGLDAVFLGLPHGQAKAFLAENKFDDQTVIIDLSTDFRDESNGFLYGLPEVNASQ
Sbjct: 61  DEVKTTGLDAVFLGLPHGQAKAFLAENKFDDQTVIIDLSTDFRDESNGFLYGLPEVNASQ 120

Query: 121 TGQAKRIANPGCFATGIQLALAPAIAAGLAKSDIHITGITGSTGAGKKLSETTHFSQRNQ 180
           TGQAKRIANPGCFATGIQLALAPAIAAGLAKSDIHITGITGSTGAGKKLSETTHFSQRNQ
Sbjct: 121 TGQAKRIANPGCFATGIQLALAPAIAAGLAKSDIHITGITGSTGAGKKLSETTHFSQRNQ 180

Query: 181 NVSVYKLFTHQHLKEISQTFGQLQTGFDQHLLFVPYRGNFSRGIWVTAYFPFEGSLEEAY 240
           NVSVYKLFTHQHLKEISQTFGQLQTGFDQHLLFVPYRGNFSRGIWVTAYFPFEGSLEEAY
Sbjct: 181 NVSVYKLFTHQHLKEISQTFGQLQTGFDQHLLFVPYRGNFSRGIWVTAYFPFEGSLEEAY 240

Query: 241 KIYHDFYQNAAFTHVSEKDIDLKQVVSTNKCIVHLKKEAGQLVIYSAIDNLLKGASGQAV 300
           KIYHDFYQNAAFTHVSEKDIDLKQVVSTNKCIVHLKKEAGQLVIYSAIDNLLKGASGQAV
Sbjct: 241 KIYHDFYQNAAFTHVSEKDIDLKQVVSTNKCIVHLKKEAGQLVIYSAIDNLLKGASGQAV 300

Query: 301 QNYNLAFGLNEKEGLRLKSVAF 322
           QNYNLAFGLNEKEGLRLKSVAF
Sbjct: 301 QNYNLAFGLNEKEGLRLKSVAF 322


Lambda     K      H
   0.319    0.136    0.392 

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: 481
Number of extensions: 13
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: 322
Length of database: 322
Length adjustment: 28
Effective length of query: 294
Effective length of database: 294
Effective search space:    86436
Effective search space used:    86436
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 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate Echvi_3847 Echvi_3847 (N-acetyl-gamma-glutamyl-phosphate reductase, common form)
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.28041.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
    4.2e-94  301.5   0.3    4.7e-93  298.1   0.3    1.9  1  lcl|FitnessBrowser__Cola:Echvi_3847  Echvi_3847 N-acetyl-gamma-glutam


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_3847  Echvi_3847 N-acetyl-gamma-glutamyl-phosphate reductase, common form
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  298.1   0.3   4.7e-93   4.7e-93       1     342 [.       4     319 ..       4     321 .. 0.93

  Alignments for each domain:
  == domain 1  score: 298.1 bits;  conditional E-value: 4.7e-93
                            TIGR01850   1 ikvaivGasGYtGaeLlrllakHpevevtklvssreagkklsevhphlkglvdlkleeleeeeileeadvvflA 74 
                                          ik+ai+Ga GYtG+eLlr+l +Hp++e+++++s++++gkk++evhp l g  dl ++++ +   ++  d+vfl+
  lcl|FitnessBrowser__Cola:Echvi_3847   4 IKTAIIGAAGYTGGELLRILVHHPSCELVYIHSNSQKGKKIDEVHPDLIGDSDLVFTDEVK---TTGLDAVFLG 74 
                                          689***********************************************99998886433...3589****** PP

                            TIGR01850  75 lphgvsaelvpe.llekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnreeikkaklianP 147
                                          lphg+++++ +e   + ++++idlS dfR +++                   + YGlpE+n ++  +ak+ianP
  lcl|FitnessBrowser__Cola:Echvi_3847  75 LPHGQAKAFLAEnKFDDQTVIIDLSTDFRDESN------------------GFLYGLPEVNASQTGQAKRIANP 130
                                          ******998665156788***********7644..................589******************** PP

                            TIGR01850 148 GCyaTaalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvtkHrHtpEieqelskl 221
                                          GC+aT+++LalaP+++++l ++ +i +++++G++gAG+k se+++f+++n+n+++Yk+++H+H +Ei+q+ ++l
  lcl|FitnessBrowser__Cola:Echvi_3847 131 GCFATGIQLALAPAIAAGLAKS-DIHITGITGSTGAGKKLSETTHFSQRNQNVSVYKLFTHQHLKEISQTFGQL 203
                                          ******************8887.5************************************************** PP

                            TIGR01850 222 aek.kvkvsftphlvpmtrGilatiyaklkkelteeelrklyeevYedepfvrvlkegelPstkavlgsnfvdi 294
                                          ++  + ++ f+p   +++rGi+ t+y+ ++ +l  ee +k+y+++Y++  f +v + +++ ++k+v+ +n + +
  lcl|FitnessBrowser__Cola:Echvi_3847 204 QTGfDQHLLFVPYRGNFSRGIWVTAYFPFEGSL--EEAYKIYHDFYQNAAFTHVSE-KDI-DLKQVVSTNKCIV 273
                                          9998778************************66..899*****************8.555.9**********98 PP

                            TIGR01850 295 gvavdeetkrvvvvsaiDNLvKGaagqAvqnlNlmlgfdetegLeklp 342
                                           ++   e++++v+ saiDNL+KGa+gqAvqn Nl++g++e+egL+ ++
  lcl|FitnessBrowser__Cola:Echvi_3847 274 HLKK--EAGQLVIYSAIDNLLKGASGQAVQNYNLAFGLNEKEGLRLKS 319
                                          7665..559***********************************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (345 nodes)
Target sequences:                          1  (322 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: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 2.61
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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