Alignments for a candidate for argC in Burkholderia phytofirmans PsJN

GapMind for Amino acid biosynthesis

Alignments for a candidate for argC in Burkholderia phytofirmans PsJN

Align N-acetylglutamylphosphate reductase (EC 1.2.1.38) (characterized)
to candidate BPHYT_RS18340 BPHYT_RS18340 n-acetyl-gamma-glutamyl-phosphate reductase

Query= reanno::Korea:Ga0059261_0351
         (310 letters)



>FitnessBrowser__BFirm:BPHYT_RS18340
          Length = 315

 Score =  243 bits (620), Expect = 4e-69
 Identities = 131/315 (41%), Positives = 185/315 (58%), Gaps = 9/315 (2%)

Query: 1   MSVSVFIDGAAGTTGLEIRERLATRSDISLIGLDDAHRKDAGKRAEAINSADFVILCLPD 60
           MS  VF+DG  GTTGL+I E L+ R+D+ ++ +++A RKD  +R   IN++D   LCLPD
Sbjct: 1   MSTKVFVDGQEGTTGLKIFEYLSQRADVEILRIEEAKRKDLEERRRLINASDVTFLCLPD 60

Query: 61  DAAREAVALIANDTTRVIDASTAHRVADGWTYGFAELEPAQAAAIAEARYVSNPGCWPTG 120
            A+RE+ +L+AND T +IDASTA R +  W YG  EL  +Q   +  A+ ++ PGC  + 
Sbjct: 61  VASRESASLVANDRTVLIDASTAFRTSADWAYGLPELARSQRERLRTAKRIAVPGCHASA 120

Query: 121 FLALVRPLVRAGLIPPDWVLTAGGASGYSGGGKSMIAEFEDGSEP--TGFRAYGLDLEHK 178
           F+  +RPLV AG++ P++   A   +GYSGGGK MIA++E G        R Y L L HK
Sbjct: 121 FVLAMRPLVEAGVVTPEFAAHAYSITGYSGGGKKMIADYEAGGNDKLKSPRPYALGLTHK 180

Query: 179 HLPEMQKHARIDHAPIFQPAVARSYRGMLIEVPLPLQMLPRKPAPAQIEQVLADAYRDSP 238
           HLPEM  H  +  APIF P V   Y+G+ +        L +K  P  ++ + A+ Y    
Sbjct: 181 HLPEMAAHTGLKSAPIFTPIVGDFYKGLAVTTFFSPNQLAKKATPQDVQALFAEYYAGEA 240

Query: 239 IVRVLPSD-----DVSLVRIEDDAGTDRLTIRVFGNAERGQARLVATLDNLGKGAGGAAV 293
            V V P D     D     ++ +  T+R+ + VFGN ER     VA LDNLGKGA GAA+
Sbjct: 241 FVNVAPFDAEANLDSGFFDVQANNDTNRVDLFVFGNEERFVT--VARLDNLGKGASGAAI 298

Query: 294 QNLNIMAGFDQTAGL 308
           Q +N+  G  + +GL
Sbjct: 299 QCMNLAIGAAEESGL 313


Lambda     K      H
   0.319    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: 234
Number of extensions: 12
Number of successful extensions: 4
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: 310
Length of database: 315
Length adjustment: 27
Effective length of query: 283
Effective length of database: 288
Effective search space:    81504
Effective search space used:    81504
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 BPHYT_RS18340 BPHYT_RS18340 (n-acetyl-gamma-glutamyl-phosphate reductase)
to HMM TIGR01851 (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/TIGR01851.hmm
# target sequence database:        /tmp/gapView.15617.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01851  [M=310]
Accession:   TIGR01851
Description: argC_other: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   1.1e-133  431.3   0.0   1.3e-133  431.1   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS18340  BPHYT_RS18340 n-acetyl-gamma-glu


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS18340  BPHYT_RS18340 n-acetyl-gamma-glutamyl-phosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  431.1   0.0  1.3e-133  1.3e-133       2     309 ..       3     306 ..       2     307 .. 0.99

  Alignments for each domain:
  == domain 1  score: 431.1 bits;  conditional E-value: 1.3e-133
                                TIGR01851   2 pkvfidGeaGttGlqirerlaerddlellsidedkrkdaderakllnaadvailclpddaareavslvdn 71 
                                               kvf+dG++GttGl+i e+l++r d+e+l+i+e krkd +er +l+na+dv++lclpd+a+re+ slv n
  lcl|FitnessBrowser__BFirm:BPHYT_RS18340   3 TKVFVDGQEGTTGLKIFEYLSQRADVEILRIEEAKRKDLEERRRLINASDVTFLCLPDVASRESASLVAN 72 
                                              69******************************************************************** PP

                                TIGR01851  72 pntkildastayrtaedwvyGfpelaaeqrekianakrvanPGcyatgaiallrPlveaGilPadfPvti 141
                                               +t+++dasta+rt+ dw+yG+pela  qre+++ akr+a+PGc+a+++++ +rPlveaG++  +f  ++
  lcl|FitnessBrowser__BFirm:BPHYT_RS18340  73 DRTVLIDASTAFRTSADWAYGLPELARSQRERLRTAKRIAVPGCHASAFVLAMRPLVEAGVVTPEFAAHA 142
                                              ********************************************************************** PP

                                TIGR01851 142 navsGysGGGkaliakyeeesaddskkaafiiyglalehkhlpemrkhsglaskPiftPavGdfaqGllv 211
                                               +++GysGGGk++ia+ye  + ++ k +++++y+l l+hkhlpem  h+gl s PiftP vGdf +Gl+v
  lcl|FitnessBrowser__BFirm:BPHYT_RS18340 143 YSITGYSGGGKKMIADYE--AGGNDKLKSPRPYALGLTHKHLPEMAAHTGLKSAPIFTPIVGDFYKGLAV 210
                                              ******************..7778889******************************************* PP

                                TIGR01851 212 eiplhlaeldskvsaedihkalaeyykGekfvkvaelddaellddtildaqglngtnrlelfvfgsddge 281
                                              +  + +++l++k++++d+++ +aeyy+Ge+fv+va++d +  ld++++d+q+ n+tnr++lfvfg++  e
  lcl|FitnessBrowser__BFirm:BPHYT_RS18340 211 TTFFSPNQLAKKATPQDVQALFAEYYAGEAFVNVAPFDAEANLDSGFFDVQANNDTNRVDLFVFGNE--E 278
                                              ******************************************************************9..9 PP

                                TIGR01851 282 rallvarldnlGkGasGaavqnlnialG 309
                                              r + varldnlGkGasGaa+q++n+a+G
  lcl|FitnessBrowser__BFirm:BPHYT_RS18340 279 RFVTVARLDNLGKGASGAAIQCMNLAIG 306
                                              *************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (310 nodes)
Target sequences:                          1  (315 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 10.31
//
[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