Alignments for a candidate for argC in Shewanella loihica PV-4

GapMind for Amino acid biosynthesis

Alignments for a candidate for argC in Shewanella loihica PV-4

Align N-acetyl-gamma-glutamyl-phosphate reductase (EC 1.2.1.38) (characterized)
to candidate 5207680 Shew_0202 N-acetyl-gamma-glutamyl-phosphate reductase (RefSeq)

Query= BRENDA::P11446
         (334 letters)



>FitnessBrowser__PV4:5207680
          Length = 326

 Score =  296 bits (759), Expect = 4e-85
 Identities = 164/331 (49%), Positives = 211/331 (63%), Gaps = 9/331 (2%)

Query: 1   MLNTLIVGASGYAGAELVTYVNRHPHMNITALTVSAQSNDAGKLISDLHPQLKGIVDLPL 60
           M +  I+GASGY GA++ + +     + I  L VS  S D GK ++ L+P    I DL L
Sbjct: 1   MKSIAIIGASGYTGAQVTSLIQADDQLKIQGLYVSENSLDKGKTLASLYPVYSHI-DLSL 59

Query: 61  QPMSDISEFS--PGVDVVFLATAHEVSHDLAPQFLEAGCVVFDLSGAFRVNDATFYEKYY 118
            P+++ ++ +     D V LAT H VS  LA  F +AG  VFDLSGA+R  D+  Y K+Y
Sbjct: 60  APLTEQAKQAIVNEADAVVLATDHGVSLHLAAWFYQAGLAVFDLSGAYRFADSEQYPKWY 119

Query: 119 GFTHQYPELLEQAAYGLAEWCGNKLKEANLIAVPGCYPTAAQLALKPLIDADLLDLNQWP 178
           GF H YPE+L +A YGLAEW    +  + +IAVPGCYPTA+  ALKPL D   L  +  P
Sbjct: 120 GFEHIYPEVLAEAVYGLAEWNTEAIAASKMIAVPGCYPTASLTALKPLKD---LMTDSLP 176

Query: 179 VINATSGVSGAGRKAAISNSFCEVSLQPYGVFTHRHQPEIATHLGADVIFTPHLGNFPRG 238
           VINA SGV+GAGRKA +  SFCEVSL PYGV  HRHQPEIAT LG  VIFTPHLGNF RG
Sbjct: 177 VINAVSGVTGAGRKAQLHTSFCEVSLTPYGVLGHRHQPEIATQLGQQVIFTPHLGNFKRG 236

Query: 239 ILETITCRLKSGVTQAQVAQVLQQAYAHKPLVRLYDKGVPALKNVVGLPFCDIGFAVQ-- 296
           IL TIT ++K GV++A +A+   + Y   PLV +Y    P + +VV  P C +G+     
Sbjct: 237 ILATITVQMKPGVSEADIAKA-YEVYESAPLVNVYHNQFPKVDDVVHTPNCLLGWKYDPL 295

Query: 297 GEHLIIVATEDNLLKGAAAQAVQCANIRFGY 327
             +L++ +  DNL+KGAA+QA QC  I F Y
Sbjct: 296 NGYLVVASAIDNLMKGAASQAHQCIKIHFNY 326


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: 343
Number of extensions: 16
Number of successful extensions: 5
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: 326
Length adjustment: 28
Effective length of query: 306
Effective length of database: 298
Effective search space:    91188
Effective search space used:    91188
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 5207680 Shew_0202 (N-acetyl-gamma-glutamyl-phosphate reductase (RefSeq))
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.12570.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   1.6e-105  339.0   0.4   1.8e-105  338.9   0.4    1.0  1  lcl|FitnessBrowser__PV4:5207680  Shew_0202 N-acetyl-gamma-glutamy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5207680  Shew_0202 N-acetyl-gamma-glutamyl-phosphate reductase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  338.9   0.4  1.8e-105  1.8e-105       2     332 ..       3     326 .]       2     326 .] 0.95

  Alignments for each domain:
  == domain 1  score: 338.9 bits;  conditional E-value: 1.8e-105
                        TIGR01850   2 kvaivGasGYtGaeLlrllakHpevevtklvssre...agkklsevhphlkglvd..lkleeleeeeileeadvvflA 74 
                                       +ai+GasGYtGa++  l+++  +++++ l++s++   +gk+l++++p ++++    + l+e+++++i +ead+v+lA
  lcl|FitnessBrowser__PV4:5207680   3 SIAIIGASGYTGAQVTSLIQADDQLKIQGLYVSENsldKGKTLASLYPVYSHIDLslAPLTEQAKQAIVNEADAVVLA 80 
                                      589**************************9999888************998865444566777779999********* PP

                        TIGR01850  75 lphgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnreeikkaklianPGCyaT 152
                                      ++hgvs +l++ ++++g+ v+dlS+++R+ d+e+Y kwYg++h ++e+l+eavYGl+E+n e+i+ +k+ia+PGCy+T
  lcl|FitnessBrowser__PV4:5207680  81 TDHGVSLHLAAWFYQAGLAVFDLSGAYRFADSEQYPKWYGFEHIYPEVLAEAVYGLAEWNTEAIAASKMIAVPGCYPT 158
                                      ****************************************************************************** PP

                        TIGR01850 153 aalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvtkHrHtpEieqelsklaekkvkvsf 230
                                      a+l al+Pl   +l++++ ++++a+sGv+gAGrka+ +++f+ev  +l+pY v +HrH+pEi+++l+       +v+f
  lcl|FitnessBrowser__PV4:5207680 159 ASLTALKPLK--DLMTDSLPVINAVSGVTGAGRKAQLHTSFCEV--SLTPYGVLGHRHQPEIATQLG------QQVIF 226
                                      *********8..4556666*************************..*********************......579** PP

                        TIGR01850 231 tphlvpmtrGilatiyaklkkelteeelrklyeevYedepfvrvlkegelPstkavlgsnfvdigvavdeetkrvvvv 308
                                      tphl +++rGilati++++k +++e++++k+y evYe+ p+v+v++ +++P++ +v+++  + +g+++d  ++ +vv 
  lcl|FitnessBrowser__PV4:5207680 227 TPHLGNFKRGILATITVQMKPGVSEADIAKAY-EVYESAPLVNVYH-NQFPKVDDVVHTPNCLLGWKYDPLNGYLVVA 302
                                      *******************************9.59**********8.9****************************** PP

                        TIGR01850 309 saiDNLvKGaagqAvqnlNlmlgf 332
                                      saiDNL+KGaa+qA q++ +++++
  lcl|FitnessBrowser__PV4:5207680 303 SAIDNLMKGAASQAHQCIKIHFNY 326
                                      ********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (345 nodes)
Target sequences:                          1  (326 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 7.03
//
[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