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

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.31403.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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.03
# Mc/sec: 3.68
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis