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.30566.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 6.52
//
[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:

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:

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:

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:

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