Alignments for a candidate for argA in Paraburkholderia bryophila 376MFSha3.1

GapMind for Amino acid biosynthesis

Alignments for a candidate for argA in Paraburkholderia bryophila 376MFSha3.1

Align amino-acid acetyltransferase (characterized)
to candidate H281DRAFT_00444 H281DRAFT_00444 N-acetylglutamate synthase

Query= CharProtDB::CH_024150
         (443 letters)



>FitnessBrowser__Burk376:H281DRAFT_00444
          Length = 462

 Score =  401 bits (1031), Expect = e-116
 Identities = 201/438 (45%), Positives = 297/438 (67%), Gaps = 7/438 (1%)

Query: 8   ELVEGFRHSVPYINTHRGKTFVIMLGGEAIEHENFSSIVNDIGLLHSLGIRLVVVYGARP 67
           + V+  R   PYI+  R KTFV+  GGE +     +++V+DI LL ++GI++V+V+G+RP
Sbjct: 29  QFVDWMRSVAPYIHAFRNKTFVVGFGGEVVHQGLLNALVSDIALLQAMGIQIVLVHGSRP 88

Query: 68  QIDANLAAHHHEPLYHKNIRVTDAKTLELVKQAAGTLQLDITARLSMSLNNTPLQGAHIN 127
           Q++  ++ H  E  +   +R+TDA+ LE  K+AAG ++LDI A +S  L NTP+  AHI+
Sbjct: 89  QVEEQMSLHGVESEFSHGMRITDARALESAKEAAGEVRLDIEAAISQGLPNTPMAHAHIS 148

Query: 128 VVSGNFIIAQPLGVDDGVDYCHSGRIRRIDEDAIHRQLDSGAIVLMGPVAVSVTGESFNL 187
           VVSGNF+ A+P+G+ DGVD+ H+G +R+ID D+I   L S  +VL+ P+  S TGE+FNL
Sbjct: 149 VVSGNFVTARPVGILDGVDFAHTGVVRKIDADSIRHSLASRKLVLLSPLGFSPTGEAFNL 208

Query: 188 TSEEIATQLAIKLKAEKMIGFCSSQGV--TNDDG-DIVSELFPNEAQARVEAQEEKGDYN 244
             E++A+  AI L+A+K++    + G+    +DG +++ EL  ++A    E+ E  GD  
Sbjct: 209 AMEDVASAAAIALRADKIVFLTETPGLMQAGEDGTELIRELSLDDAYKLHESGEVTGDAG 268

Query: 245 SGTVRFLRGAVKACRSGVRRCHLISYQEDGALLQELFSRDGIGTQIVMESAEQIRRATIN 304
                +L+ +++ACR GV R H+I Y  DG+LL ELF  DG+GT I  E+ E +R AT +
Sbjct: 269 F----YLKHSIRACRGGVARAHIIPYALDGSLLLELFLHDGVGTMISYENLESLREATPD 324

Query: 305 DIGGILELIRPLEQQGILVRRSREQLEMEIDKFTIIQRDNTTIACAALYPFPEEKIGEMA 364
           D+GGIL LI PLE  G LVRR R Q+E +ID F++I+ D     CAALYP+ +E+IGEMA
Sbjct: 325 DVGGILALIEPLESDGTLVRRGRHQIERDIDHFSVIEHDGVLFGCAALYPYTQERIGEMA 384

Query: 365 CVAVHPDYRSSSRGEVLLERIAAQAKQSGLSKLFVLTTRSIHWFQERGFTPVDIDLLPES 424
           C+ V P+ + +  GE LL+RI  +A+  GL+++FVLTTR+ HWF +RGF  V +D LPE 
Sbjct: 385 CLTVAPEAQGTGDGERLLKRIEQRARARGLTRIFVLTTRTEHWFLKRGFVKVTVDDLPED 444

Query: 425 KKQLYNYQRKSKVLMADL 442
           +++LYN+QRKS VLM  L
Sbjct: 445 RRRLYNWQRKSLVLMKQL 462


Lambda     K      H
   0.319    0.136    0.384 

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: 508
Number of extensions: 19
Number of successful extensions: 3
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: 443
Length of database: 462
Length adjustment: 33
Effective length of query: 410
Effective length of database: 429
Effective search space:   175890
Effective search space used:   175890
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 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate H281DRAFT_00444 H281DRAFT_00444 (N-acetylglutamate synthase)
to HMM TIGR01890 (argA: amino-acid N-acetyltransferase (EC 2.3.1.1))

# 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/TIGR01890.hmm
# target sequence database:        /tmp/gapView.4404.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01890  [M=429]
Accession:   TIGR01890
Description: N-Ac-Glu-synth: amino-acid N-acetyltransferase
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-198  643.7   0.2     8e-198  643.6   0.2    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_00444  H281DRAFT_00444 N-acetylglutamat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_00444  H281DRAFT_00444 N-acetylglutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  643.6   0.2    8e-198    8e-198       1     429 []      30     462 .]      30     462 .] 0.97

  Alignments for each domain:
  == domain 1  score: 643.6 bits;  conditional E-value: 8e-198
                                    TIGR01890   1 fvkwlreaaPyinahrdktlvvglggelvedknlgklvadiallhslGvrlvlvhGarpqieerla 66 
                                                  fv+w+r++aPyi+a+r+kt+vvg+gge+v+++ l++lv+diall+++G+++vlvhG+rpq+ee++ 
  lcl|FitnessBrowser__Burk376:H281DRAFT_00444  30 FVDWMRSVAPYIHAFRNKTFVVGFGGEVVHQGLLNALVSDIALLQAMGIQIVLVHGSRPQVEEQMS 95 
                                                  8***************************************************************** PP

                                    TIGR01890  67 krgrtthyvrGlrvtdeaslelvkeaaGelrlaiearlsmslantpmagsrlsvvsGnfvtarPiG 132
                                                   +g+++++ +G+r+td+ +le++keaaGe+rl+iea++s+ l+ntpma +++svvsGnfvtarP+G
  lcl|FitnessBrowser__Burk376:H281DRAFT_00444  96 LHGVESEFSHGMRITDARALESAKEAAGEVRLDIEAAISQGLPNTPMAHAHISVVSGNFVTARPVG 161
                                                  ****************************************************************** PP

                                    TIGR01890 133 vveGvdyehtGevrkidaegirrlldersivllsPlgfsvtGeifnlamedvatsvaiklkadkli 198
                                                  +++Gvd+ htG+vrkida++ir++l +r++vllsPlgfs+tGe+fnlamedva+ +ai+l+adk++
  lcl|FitnessBrowser__Burk376:H281DRAFT_00444 162 ILDGVDFAHTGVVRKIDADSIRHSLASRKLVLLSPLGFSPTGEAFNLAMEDVASAAAIALRADKIV 227
                                                  ****************************************************************** PP

                                    TIGR01890 199 llteedGilda..dG.klvaelsaqeveslverleeet.tarllsaavkalrgGvarshlvsyaed 260
                                                  +lte++G+++a  dG +l++els +++ +l e+ e       +l++ ++a+rgGvar+h+++ya d
  lcl|FitnessBrowser__Burk376:H281DRAFT_00444 228 FLTETPGLMQAgeDGtELIRELSLDDAYKLHESGEVTGdAGFYLKHSIRACRGGVARAHIIPYALD 293
                                                  *********8633663599****9999998887554333689************************ PP

                                    TIGR01890 261 GallqelftrdGiGtlvskealesireatiddvggilelirPleeqGilvrrsrellereieefsv 326
                                                  G+ll+elf++dG+Gt++s e+les+reat ddvggil+li+Ple +G+lvrr r+++er+i++fsv
  lcl|FitnessBrowser__Burk376:H281DRAFT_00444 294 GSLLLELFLHDGVGTMISYENLESLREATPDDVGGILALIEPLESDGTLVRRGRHQIERDIDHFSV 359
                                                  ****************************************************************** PP

                                    TIGR01890 327 iekdGliigcaalypyaeeevgelaclavsPeardggrGerllkhiedrarqvGlkrlfvlttrte 392
                                                  ie+dG+++gcaalypy++e++ge+acl+v+Pea+++g+Gerllk+ie+rar+ Gl r+fvlttrte
  lcl|FitnessBrowser__Burk376:H281DRAFT_00444 360 IEHDGVLFGCAALYPYTQERIGEMACLTVAPEAQGTGDGERLLKRIEQRARARGLTRIFVLTTRTE 425
                                                  ****************************************************************** PP

                                    TIGR01890 393 hWfrerGfaeasvdelPearrklynyqrrskilvkkl 429
                                                  hWf++rGf++++vd+lPe+rr+lyn+qr+s +l+k+l
  lcl|FitnessBrowser__Burk376:H281DRAFT_00444 426 HWFLKRGFVKVTVDDLPEDRRRLYNWQRKSLVLMKQL 462
                                                  ***********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (429 nodes)
Target sequences:                          1  (462 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.25
//
[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