GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argC in Shewanella sp. ANA-3

Align N-acetyl-gamma-glutamyl-phosphate reductase (EC 1.2.1.38) (characterized)
to candidate 7026773 Shewana3_3905 N-acetyl-gamma-glutamyl-phosphate reductase (RefSeq)

Query= BRENDA::P11446
         (334 letters)



>FitnessBrowser__ANA3:7026773
          Length = 326

 Score =  300 bits (767), Expect = 4e-86
 Identities = 166/329 (50%), Positives = 208/329 (63%), Gaps = 9/329 (2%)

Query: 1   MLNTLIVGASGYAGAELVTYVNRHPHMNITALTVSAQSNDAGKLISDLHPQLKGIVDLPL 60
           M N  I+GASGY GA+L   V+    ++I  L VS  S D G+ ++DL+P    I DL L
Sbjct: 1   MKNIAIIGASGYTGAQLTALVHAESELSIQGLYVSENSLDKGRALADLYPVYSHI-DLAL 59

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

Query: 119 GFTHQYPELLEQAAYGLAEWCGNKLKEANLIAVPGCYPTAAQLALKPLIDADLLDLNQWP 178
           GF H+YPE+L +A YGLAEW   ++    +IAVPGCYPTA+  ALKPL +   L  + +P
Sbjct: 120 GFEHEYPEVLAKAVYGLAEWNAKEVAATKMIAVPGCYPTASLTALKPLKN---LLTSAYP 176

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

Query: 239 ILETITCRLKSGVTQAQVAQVLQQAYAHKPLVRLYDKGVPALKNVVGLPFCDIG--FAVQ 296
           IL TIT +LK G T A VA      Y   PLV +     P + +VV  P C +G  F   
Sbjct: 237 ILATITVQLKPGTTTADVA-AAYSVYDQAPLVTVKQNQFPKVDDVVLTPNCHLGWKFDEN 295

Query: 297 GEHLIIVATEDNLLKGAAAQAVQCANIRF 325
             +L++ +  DNL+KGAA+QA+QC  I F
Sbjct: 296 SGYLVVASAIDNLMKGAASQALQCIKIHF 324


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: 351
Number of extensions: 14
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 7026773 Shewana3_3905 (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.2472820.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.4e-105  339.3   0.4   1.6e-105  339.1   0.4    1.0  1  lcl|FitnessBrowser__ANA3:7026773  Shewana3_3905 N-acetyl-gamma-glu


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7026773  Shewana3_3905 N-acetyl-gamma-glutamyl-phosphate reductase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  339.1   0.4  1.6e-105  1.6e-105       2     331 ..       3     325 ..       2     326 .] 0.95

  Alignments for each domain:
  == domain 1  score: 339.1 bits;  conditional E-value: 1.6e-105
                         TIGR01850   2 kvaivGasGYtGaeLlrllakHpevevtklvssre...agkklsevhphlkglvd..lkleeleeeeileeadvvfl 73 
                                       ++ai+GasGYtGa+L  l+++ +e++++ l++s++   +g+ l++++p ++++    + l+e+++++i +ead+v+l
  lcl|FitnessBrowser__ANA3:7026773   3 NIAIIGASGYTGAQLTALVHAESELSIQGLYVSENsldKGRALADLYPVYSHIDLalSPLTEEAKAKIVAEADAVVL 79 
                                       79***************************99998889***********99886544456666677999********* PP

                         TIGR01850  74 AlphgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnreeikkaklianPGCy 150
                                       A+ h vs +l++ ++++g+ v+dlS+++R++d ++Y kwYg++he++e+l++avYGl+E+n +e++ +k+ia+PGCy
  lcl|FitnessBrowser__ANA3:7026773  80 ATEHSVSLHLAAWFYNQGLAVFDLSGAYRFSDVAQYPKWYGFEHEYPEVLAKAVYGLAEWNAKEVAATKMIAVPGCY 156
                                       ***************************************************************************** PP

                         TIGR01850 151 aTaalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvtkHrHtpEieqelsklaekkvk 227
                                       +Ta+l al+Pl   +l+++  ++++a+sGv+gAGrka+ +++f+ev  +l+pY v +HrH+pEi+++l+       +
  lcl|FitnessBrowser__ANA3:7026773 157 PTASLTALKPLK--NLLTSAYPVINAVSGVTGAGRKAQLHTSFCEV--SLTPYGVLGHRHQPEIATQLG------QE 223
                                       ***********8..6677777*************************..*********************......57 PP

                         TIGR01850 228 vsftphlvpmtrGilatiyaklkkelteeelrklyeevYedepfvrvlkegelPstkavlgsnfvdigvavdeetkr 304
                                       v+ftphl +++rGilati+++lk ++t+++++++y +vY++ p+v+v + +++P++ +v+ +  +++g++ de+++ 
  lcl|FitnessBrowser__ANA3:7026773 224 VIFTPHLGNFKRGILATITVQLKPGTTTADVAAAY-SVYDQAPLVTVKQ-NQFPKVDDVVLTPNCHLGWKFDENSGY 298
                                       9*********************************8.69*********98.9************************** PP

                         TIGR01850 305 vvvvsaiDNLvKGaagqAvqnlNlmlg 331
                                       +vv saiDNL+KGaa+qA+q++ ++++
  lcl|FitnessBrowser__ANA3:7026773 299 LVVASAIDNLMKGAASQALQCIKIHFN 325
                                       **********************99987 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 16.90
//
[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