Alignments for a candidate for argA in Burkholderia phytofirmans PsJN

GapMind for Amino acid biosynthesis

Alignments for a candidate for argA in Burkholderia phytofirmans PsJN

Align amino-acid acetyltransferase (characterized)
to candidate BPHYT_RS12985 BPHYT_RS12985 amino acid acetyltransferase

Query= CharProtDB::CH_024150
         (443 letters)



>FitnessBrowser__BFirm:BPHYT_RS12985
          Length = 462

 Score =  399 bits (1026), Expect = e-116
 Identities = 201/438 (45%), Positives = 296/438 (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--TNDDGDI-VSELFPNEAQARVEAQEEKGDYN 244
             E++A+  AI L+A+K++    + G+    ++G + V EL  ++A    E+ E  GD  
Sbjct: 209 AMEDVASAAAIALRADKIVFLTETPGLMEAGEEGPVLVRELSLDDAYKLHESGEVTGDAG 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: 498
Number of extensions: 18
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 BPHYT_RS12985 BPHYT_RS12985 (amino acid acetyltransferase)
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.24043.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   2.1e-197  642.2   0.1   2.4e-197  642.0   0.1    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS12985  BPHYT_RS12985 amino acid acetylt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS12985  BPHYT_RS12985 amino acid acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  642.0   0.1  2.4e-197  2.4e-197       1     429 []      30     462 .]      30     462 .] 0.97

  Alignments for each domain:
  == domain 1  score: 642.0 bits;  conditional E-value: 2.4e-197
                                TIGR01890   1 fvkwlreaaPyinahrdktlvvglggelvedknlgklvadiallhslGvrlvlvhGarpqieerlakrgr 70 
                                              fv+w+r++aPyi+a+r+kt+vvg+gge+v+++ l++lv+diall+++G+++vlvhG+rpq+ee++  +g+
  lcl|FitnessBrowser__BFirm:BPHYT_RS12985  30 FVDWMRSVAPYIHAFRNKTFVVGFGGEVVHQGLLNALVSDIALLQAMGIQIVLVHGSRPQVEEQMSLHGV 99 
                                              8********************************************************************* PP

                                TIGR01890  71 tthyvrGlrvtdeaslelvkeaaGelrlaiearlsmslantpmagsrlsvvsGnfvtarPiGvveGvdye 140
                                              ++++ +G+r+td+ +le++keaaGe+rl+iea++s+ l+ntpma +++svvsGnfvtarP+G+++Gvd+ 
  lcl|FitnessBrowser__BFirm:BPHYT_RS12985 100 ESEFSHGMRITDARALESAKEAAGEVRLDIEAAISQGLPNTPMAHAHISVVSGNFVTARPVGILDGVDFA 169
                                              ********************************************************************** PP

                                TIGR01890 141 htGevrkidaegirrlldersivllsPlgfsvtGeifnlamedvatsvaiklkadklillteedGilda. 209
                                              htG+vrkida++ir++l +r++vllsPlgfs+tGe+fnlamedva+ +ai+l+adk+++lte++G+++a 
  lcl|FitnessBrowser__BFirm:BPHYT_RS12985 170 HTGVVRKIDADSIRHSLASRKLVLLSPLGFSPTGEAFNLAMEDVASAAAIALRADKIVFLTETPGLMEAg 239
                                              *******************************************************************973 PP

                                TIGR01890 210 .dG.klvaelsaqeveslverleeet.tarllsaavkalrgGvarshlvsyaedGallqelftrdGiGtl 276
                                               +G  lv+els +++ +l e+ e       +l++ ++a+rgGvar+h+++ya dG+ll+elf++dG+Gt+
  lcl|FitnessBrowser__BFirm:BPHYT_RS12985 240 eEGpVLVRELSLDDAYKLHESGEVTGdAGFYLKHSIRACRGGVARAHIIPYALDGSLLLELFLHDGVGTM 309
                                              24534899***9999998887554333689**************************************** PP

                                TIGR01890 277 vskealesireatiddvggilelirPleeqGilvrrsrellereieefsviekdGliigcaalypyaeee 346
                                              +s e+les+reat ddvggil+li+Ple +G+lvrr r+++er+i++fsvie+dG+++gcaalypy++e+
  lcl|FitnessBrowser__BFirm:BPHYT_RS12985 310 ISYENLESLREATPDDVGGILALIEPLESDGTLVRRGRHQIERDIDHFSVIEHDGVLFGCAALYPYTQER 379
                                              ********************************************************************** PP

                                TIGR01890 347 vgelaclavsPeardggrGerllkhiedrarqvGlkrlfvlttrtehWfrerGfaeasvdelPearrkly 416
                                              +ge+acl+v+Pea+++g+Gerllk+ie+rar+ Gl r+fvlttrtehWf++rGf++++vd+lPe+rr+ly
  lcl|FitnessBrowser__BFirm:BPHYT_RS12985 380 IGEMACLTVAPEAQGTGDGERLLKRIEQRARARGLTRIFVLTTRTEHWFLKRGFVKVTVDDLPEDRRRLY 449
                                              ********************************************************************** PP

                                TIGR01890 417 nyqrrskilvkkl 429
                                              n+qr+s +l+k+l
  lcl|FitnessBrowser__BFirm:BPHYT_RS12985 450 NWQRKSLVLMKQL 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 11.41
//
[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