Alignments for a candidate for argC in Klebsiella michiganensis M5al

GapMind for Amino acid biosynthesis

Alignments for a candidate for argC in Klebsiella michiganensis M5al

Align N-acetyl-gamma-glutamyl-phosphate reductase (EC 1.2.1.38) (characterized)
to candidate BWI76_RS00845 BWI76_RS00845 N-acetyl-gamma-glutamyl-phosphate reductase

Query= BRENDA::P11446
         (334 letters)



>FitnessBrowser__Koxy:BWI76_RS00845
          Length = 334

 Score =  610 bits (1572), Expect = e-179
 Identities = 302/334 (90%), Positives = 312/334 (93%)

Query: 1   MLNTLIVGASGYAGAELVTYVNRHPHMNITALTVSAQSNDAGKLISDLHPQLKGIVDLPL 60
           MLNTLIVGASGYAGAELV YVNRHPHM ITALTVSAQSNDAGKL+SDLHPQLKGIVDLPL
Sbjct: 1   MLNTLIVGASGYAGAELVAYVNRHPHMTITALTVSAQSNDAGKLVSDLHPQLKGIVDLPL 60

Query: 61  QPMSDISEFSPGVDVVFLATAHEVSHDLAPQFLEAGCVVFDLSGAFRVNDATFYEKYYGF 120
           QPMSDISEFS GVDVVFLATAHEVSHDLAPQFL AGCVVFDLSGAFRVND  FYEKYYGF
Sbjct: 61  QPMSDISEFSAGVDVVFLATAHEVSHDLAPQFLAAGCVVFDLSGAFRVNDGAFYEKYYGF 120

Query: 121 THQYPELLEQAAYGLAEWCGNKLKEANLIAVPGCYPTAAQLALKPLIDADLLDLNQWPVI 180
           THQ+PELLEQA YGLAEW   KLKEANLIAVPGCYPTAAQL+LKPLIDA LLDLNQWPVI
Sbjct: 121 THQHPELLEQAVYGLAEWSVEKLKEANLIAVPGCYPTAAQLSLKPLIDAGLLDLNQWPVI 180

Query: 181 NATSGVSGAGRKAAISNSFCEVSLQPYGVFTHRHQPEIATHLGADVIFTPHLGNFPRGIL 240
           NATSGVSGAGRKA+I NSFCEVSLQPYGVF HRH PEI+THLGADVIFTPHLGNF RGIL
Sbjct: 181 NATSGVSGAGRKASIGNSFCEVSLQPYGVFNHRHHPEISTHLGADVIFTPHLGNFKRGIL 240

Query: 241 ETITCRLKSGVTQAQVAQVLQQAYAHKPLVRLYDKGVPALKNVVGLPFCDIGFAVQGEHL 300
           ETITCRLK GV++ QVA V QQAYA KPLVRLYDKGVPALKNVVGLPFCDIGFAVQ EH+
Sbjct: 241 ETITCRLKPGVSKEQVAAVFQQAYADKPLVRLYDKGVPALKNVVGLPFCDIGFAVQDEHI 300

Query: 301 IIVATEDNLLKGAAAQAVQCANIRFGYAETQSLI 334
           I+VA EDNLLKGAAAQAVQCANIRFG+AETQSLI
Sbjct: 301 IVVAAEDNLLKGAAAQAVQCANIRFGFAETQSLI 334


Lambda     K      H
   0.321    0.136    0.409 

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: 560
Number of extensions: 10
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: 334
Length of database: 334
Length adjustment: 28
Effective length of query: 306
Effective length of database: 306
Effective search space:    93636
Effective search space used:    93636
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: 49 (23.5 bits)

Align candidate BWI76_RS00845 BWI76_RS00845 (N-acetyl-gamma-glutamyl-phosphate reductase)
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.29134.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   2.1e-130  420.9   0.0   2.3e-130  420.7   0.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS00845  BWI76_RS00845 N-acetyl-gamma-glu


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS00845  BWI76_RS00845 N-acetyl-gamma-glutamyl-phosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  420.7   0.0  2.3e-130  2.3e-130       2     338 ..       3     333 ..       2     334 .] 0.98

  Alignments for each domain:
  == domain 1  score: 420.7 bits;  conditional E-value: 2.3e-130
                               TIGR01850   2 kvaivGasGYtGaeLlrllakHpevevtklvssre...agkklsevhphlkglvdlkleelee.eeileea 68 
                                             ++ ivGasGY+GaeL+ ++++Hp++++t+l++s +   agk +s++hp+lkg+vdl l+++++ +e+++ +
  lcl|FitnessBrowser__Koxy:BWI76_RS00845   3 NTLIVGASGYAGAELVAYVNRHPHMTITALTVSAQsndAGKLVSDLHPQLKGIVDLPLQPMSDiSEFSAGV 73 
                                             578*************************9888877789**********************999999***** PP

                               TIGR01850  69 dvvflAlphgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnreeik 139
                                             dvvflA++h+vs++l+p++l++g++v+dlS++fR++d ++Yek+Yg++h+++elle+avYGl+E+  e++k
  lcl|FitnessBrowser__Koxy:BWI76_RS00845  74 DVVFLATAHEVSHDLAPQFLAAGCVVFDLSGAFRVNDGAFYEKYYGFTHQHPELLEQAVYGLAEWSVEKLK 144
                                             *********************************************************************** PP

                               TIGR01850 140 kaklianPGCyaTaalLalaPllkekliepks.iivdaksGvSgAGrkasekslfaevnenlkpYkvtkHr 209
                                             +a+lia+PGCy+Taa+L+l+Pl++++l++ ++ ++++a sGvSgAGrkas  ++f+ev  +l+pY v++Hr
  lcl|FitnessBrowser__Koxy:BWI76_RS00845 145 EANLIAVPGCYPTAAQLSLKPLIDAGLLDLNQwPVINATSGVSGAGRKASIGNSFCEV--SLQPYGVFNHR 213
                                             **********************************************************..*********** PP

                               TIGR01850 210 HtpEieqelsklaekkvkvsftphlvpmtrGilatiyaklkkelteeelrklyeevYedepfvrvlkegel 280
                                             H pEi+++l+      + v+ftphl +++rGil ti+++lk ++++e+++++++++Y+d+p+vr+++ + +
  lcl|FitnessBrowser__Koxy:BWI76_RS00845 214 HHPEISTHLG------ADVIFTPHLGNFKRGILETITCRLKPGVSKEQVAAVFQQAYADKPLVRLYD-KGV 277
                                             **********......78************************************************9.89* PP

                               TIGR01850 281 PstkavlgsnfvdigvavdeetkrvvvvsaiDNLvKGaagqAvqnlNlmlgfdetegL 338
                                             P++k+v+g  f+dig+av++  ++++vv+a DNL+KGaa+qAvq+ N+++gf+et++L
  lcl|FitnessBrowser__Koxy:BWI76_RS00845 278 PALKNVVGLPFCDIGFAVQD--EHIIVVAAEDNLLKGAAAQAVQCANIRFGFAETQSL 333
                                             *******************9..8********************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (345 nodes)
Target sequences:                          1  (334 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: 8.63
//
[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