Alignments for a candidate for argC in Shewanella amazonensis SB2B

GapMind for Amino acid biosynthesis

Alignments for a candidate for argC in Shewanella amazonensis SB2B

Align N-acetyl-gamma-glutamyl-phosphate reductase (EC 1.2.1.38) (characterized)
to candidate 6936059 Sama_0256 N-acetyl-gamma-glutamyl-phosphate reductase (RefSeq)

Query= BRENDA::P11446
         (334 letters)



>FitnessBrowser__SB2B:6936059
          Length = 331

 Score =  293 bits (751), Expect = 3e-84
 Identities = 163/330 (49%), Positives = 208/330 (63%), Gaps = 9/330 (2%)

Query: 1   MLNTLIVGASGYAGAELVTYVNRHPHMNITALTVSAQSNDAGKLISDLHPQLKGIVDLPL 60
           M    I+GASGY GA+L   ++  PH+ +  L VS  S D GK +S L+P    +    L
Sbjct: 6   MKKIAIIGASGYTGAQLTALIDAEPHLQVQGLYVSEGSADKGKPLSSLYPVYSHL-KYCL 64

Query: 61  QPMSDISEFS--PGVDVVFLATAHEVSHDLAPQFLEAGCVVFDLSGAFRVNDATFYEKYY 118
            P++D ++ +     D V LAT H VS +LA  F E G  VFDLSGA+R  D   Y K+Y
Sbjct: 65  SPLTDEAKDAIVAEADAVALATEHSVSLELAAYFYEKGLAVFDLSGAYRFADTAQYPKWY 124

Query: 119 GFTHQYPELLEQAAYGLAEWCGNKLKEANLIAVPGCYPTAAQLALKPLIDADLLDLNQWP 178
           GF H +PE+L +A YGLAEW  + +    +IAVPGCYPTA+  ALKPL  A L +    P
Sbjct: 125 GFEHSHPEVLAKAVYGLAEWNADAVAATRMIAVPGCYPTASLTALKPL-KAMLTEAR--P 181

Query: 179 VINATSGVSGAGRKAAISNSFCEVSLQPYGVFTHRHQPEIATHLGADVIFTPHLGNFPRG 238
           VINA SGV+GAGRKA +  SFCEVSL PYGV  HRHQPEIAT LG +VIFTPHLGNF RG
Sbjct: 182 VINAVSGVTGAGRKAQLHTSFCEVSLTPYGVLGHRHQPEIATQLGQEVIFTPHLGNFKRG 241

Query: 239 ILETITCRLKSGVTQAQVAQVLQQAYAHKPLVRLYDKGVPALKNVVGLPFCDIG--FAVQ 296
           IL TIT +LK G ++  VA+     Y   P+V + +   P + +VV  P C +G  F   
Sbjct: 242 ILATITVQLKPGTSREDVAKA-YSVYDQSPIVTVKEGQFPKVDDVVFTPNCHLGWKFDED 300

Query: 297 GEHLIIVATEDNLLKGAAAQAVQCANIRFG 326
             +L++ +  DNL+KGAA+QA+QC  I FG
Sbjct: 301 SGYLVVASAIDNLMKGAASQALQCIKIHFG 330


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: 359
Number of extensions: 15
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: 331
Length adjustment: 28
Effective length of query: 306
Effective length of database: 303
Effective search space:    92718
Effective search space used:    92718
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 6936059 Sama_0256 (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.28788.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.1e-107  346.2   0.1   1.3e-107  346.0   0.1    1.0  1  lcl|FitnessBrowser__SB2B:6936059  Sama_0256 N-acetyl-gamma-glutamy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6936059  Sama_0256 N-acetyl-gamma-glutamyl-phosphate reductase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  346.0   0.1  1.3e-107  1.3e-107       2     331 ..       8     330 ..       7     331 .] 0.96

  Alignments for each domain:
  == domain 1  score: 346.0 bits;  conditional E-value: 1.3e-107
                         TIGR01850   2 kvaivGasGYtGaeLlrllakHpevevtklvssre...agkklsevhphlkglvd..lkleeleeeeileeadvvfl 73 
                                       k+ai+GasGYtGa+L  l+++ p+++v+ l++s+    +gk+ls+++p +++l    + l+++++++i +ead+v l
  lcl|FitnessBrowser__SB2B:6936059   8 KIAIIGASGYTGAQLTALIDAEPHLQVQGLYVSEGsadKGKPLSSLYPVYSHLKYclSPLTDEAKDAIVAEADAVAL 84 
                                       89***************************998887789**********9988776556777777799********** PP

                         TIGR01850  74 AlphgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnreeikkaklianPGCy 150
                                       A+ h vs el++ ++ekg+ v+dlS+++R+ d+++Y kwYg++h+++e+l++avYGl+E+n ++++ +++ia+PGCy
  lcl|FitnessBrowser__SB2B:6936059  85 ATEHSVSLELAAYFYEKGLAVFDLSGAYRFADTAQYPKWYGFEHSHPEVLAKAVYGLAEWNADAVAATRMIAVPGCY 161
                                       ***************************************************************************** PP

                         TIGR01850 151 aTaalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvtkHrHtpEieqelsklaekkvk 227
                                       +Ta+l al+Pl +  ++++ +++++a+sGv+gAGrka+ +++f+ev  +l+pY v +HrH+pEi+++l+       +
  lcl|FitnessBrowser__SB2B:6936059 162 PTASLTALKPLKA--MLTEARPVINAVSGVTGAGRKAQLHTSFCEV--SLTPYGVLGHRHQPEIATQLG------QE 228
                                       ***********84..556667*************************..*********************......57 PP

                         TIGR01850 228 vsftphlvpmtrGilatiyaklkkelteeelrklyeevYedepfvrvlkegelPstkavlgsnfvdigvavdeetkr 304
                                       v+ftphl +++rGilati+++lk ++++e+++k+y +vY+++p+v+v + g++P++ +v+ +  +++g++ de+++ 
  lcl|FitnessBrowser__SB2B:6936059 229 VIFTPHLGNFKRGILATITVQLKPGTSREDVAKAY-SVYDQSPIVTVKE-GQFPKVDDVVFTPNCHLGWKFDEDSGY 303
                                       9*********************************9.69********997.9************************** PP

                         TIGR01850 305 vvvvsaiDNLvKGaagqAvqnlNlmlg 331
                                       +vv saiDNL+KGaa+qA+q++ +++g
  lcl|FitnessBrowser__SB2B:6936059 304 LVVASAIDNLMKGAASQALQCIKIHFG 330
                                       ************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (345 nodes)
Target sequences:                          1  (331 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: 8.68
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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