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

GapMind for Amino acid biosynthesis

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

Align N-acetylglutamylphosphate reductase (EC 1.2.1.38) (characterized)
to candidate H281DRAFT_05840 H281DRAFT_05840 N-acetyl-gamma-glutamyl-phosphate reductase

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



>FitnessBrowser__Burk376:H281DRAFT_05840
          Length = 315

 Score =  246 bits (628), Expect = 5e-70
 Identities = 135/315 (42%), Positives = 189/315 (60%), Gaps = 9/315 (2%)

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

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

Query: 121 FLALVRPLVRAGLIPPDWVLTAGGASGYSGGGKSMIAEFEDG--SEPTGFRAYGLDLEHK 178
           F+  +RPLV AG++ PD+   A   +GYSGGGK MIA++E G  ++    R Y L L HK
Sbjct: 121 FVLAMRPLVDAGVVAPDFDAHAYSITGYSGGGKKMIADYEAGGNAKLKSPRPYALGLTHK 180

Query: 179 HLPEMQKHARIDHAPIFQPAVARSYRGMLIEVPLPLQMLPRKPAPAQIEQVLADAYRDSP 238
           HLPEM  H  +  APIF P V   Y+G+ +      + L RK  P Q++  LA+ Y    
Sbjct: 181 HLPEMAAHTGLTSAPIFTPIVGDFYKGLAVTTYFSPRQLARKTTPQQVQAHLAEYYAGEA 240

Query: 239 IVRVLPSD-----DVSLVRIEDDAGTDRLTIRVFGNAERGQARLVATLDNLGKGAGGAAV 293
            VRV P D     D     ++ +  T+R+ + VFG AER     VA LDNLGKGA GAA+
Sbjct: 241 FVRVAPFDAEANLDSGFFDVQANNDTNRVDLFVFGTAERFVT--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: 244
Number of extensions: 10
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 H281DRAFT_05840 H281DRAFT_05840 (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.26619.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   3.8e-134  432.8   0.0   4.3e-134  432.6   0.0    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_05840  H281DRAFT_05840 N-acetyl-gamma-g


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_05840  H281DRAFT_05840 N-acetyl-gamma-glutamyl-phosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  432.6   0.0  4.3e-134  4.3e-134       2     309 ..       3     306 ..       2     307 .. 0.99

  Alignments for each domain:
  == domain 1  score: 432.6 bits;  conditional E-value: 4.3e-134
                                    TIGR01851   2 pkvfidGeaGttGlqirerlaerddlellsidedkrkdaderakllnaadvailclpddaareavs 67 
                                                   kvf+dG++GttGl+i e+l++r d+e+l+ide krkd +er +l+na+dv++lclpd+a+re+ s
  lcl|FitnessBrowser__Burk376:H281DRAFT_05840   3 TKVFVDGQEGTTGLKIFEYLSQRADVEILRIDEAKRKDIEERRRLINASDVTFLCLPDVASRESAS 68 
                                                  69**************************************************************** PP

                                    TIGR01851  68 lvdnpntkildastayrtaedwvyGfpelaaeqrekianakrvanPGcyatgaiallrPlveaGil 133
                                                  lv+n +t+++dasta+rt+ dw+yG+pela  qre+++ akr+a+PGc+a+++++ +rPlv+aG++
  lcl|FitnessBrowser__Burk376:H281DRAFT_05840  69 LVENERTVLIDASTAFRTSADWAYGLPELARSQRERLRTAKRIAVPGCHASAFVLAMRPLVDAGVV 134
                                                  ****************************************************************** PP

                                    TIGR01851 134 PadfPvtinavsGysGGGkaliakyeeesaddskkaafiiyglalehkhlpemrkhsglaskPift 199
                                                    df  ++ +++GysGGGk++ia+ye  + +++k +++++y+l l+hkhlpem  h+gl+s Pift
  lcl|FitnessBrowser__Burk376:H281DRAFT_05840 135 APDFDAHAYSITGYSGGGKKMIADYE--AGGNAKLKSPRPYALGLTHKHLPEMAAHTGLTSAPIFT 198
                                                  **************************..7788899******************************* PP

                                    TIGR01851 200 PavGdfaqGllveiplhlaeldskvsaedihkalaeyykGekfvkvaelddaellddtildaqgln 265
                                                  P vGdf +Gl+v+  + + +l+ k++++++++ laeyy+Ge+fv+va++d +  ld++++d+q+ n
  lcl|FitnessBrowser__Burk376:H281DRAFT_05840 199 PIVGDFYKGLAVTTYFSPRQLARKTTPQQVQAHLAEYYAGEAFVRVAPFDAEANLDSGFFDVQANN 264
                                                  ****************************************************************** PP

                                    TIGR01851 266 gtnrlelfvfgsddgerallvarldnlGkGasGaavqnlnialG 309
                                                  +tnr++lfvfg++  er + varldnlGkGasGaa+q++n+a+G
  lcl|FitnessBrowser__Burk376:H281DRAFT_05840 265 DTNRVDLFVFGTA--ERFVTVARLDNLGKGASGAAIQCMNLAIG 306
                                                  ***********99..9*************************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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 6.63
//
[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