GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argC in Pseudomonas putida KT2440

Align N-acetyl-gamma-glutamyl-phosphate reductase; Short=AGPR; EC 1.2.1.38 (characterized, see rationale)
to candidate PP_0432 PP_0432 N-acetyl-gamma-glutamyl-phosphate reductase 1

Query= uniprot:E4PLW0
         (388 letters)



>FitnessBrowser__Putida:PP_0432
          Length = 344

 Score =  472 bits (1214), Expect = e-138
 Identities = 238/346 (68%), Positives = 274/346 (79%), Gaps = 3/346 (0%)

Query: 44  VIKVGIVGGTGYTGVELLRILAVHPEVSVSCITSRSEAGMPVAEMYPNLRGHYD-LAFSE 102
           +IKVGIVGGTGYTGVELLR+LA HP+  V+ ITSRSEAG+ VA+MYPNLRGHYD LAFS 
Sbjct: 1   MIKVGIVGGTGYTGVELLRLLAQHPQAEVAVITSRSEAGVAVADMYPNLRGHYDGLAFSV 60

Query: 103 PDVNVLGACDLVFFATPHGVAMRMVPELMSAGVRVVDLSADFRLKDLDVWANWYGMAHES 162
           PD   LGACD+VFFATPHGVA  +  EL++AG +V+DLSADFRL+D   W  WYG  H +
Sbjct: 61  PDSKALGACDVVFFATPHGVAHALAGELLAAGTKVIDLSADFRLQDATEWGKWYGQPHGA 120

Query: 163 PEWAEKAVYGLPEVVRDEIRNAQLVANPGCYPTAVQLGFLPLLEQGLVDPKRLIADAKSG 222
           PE  + AVYGLPEV R++IR A+L+A PGCYPTA QLGFLPLLE GL DP RLIAD KSG
Sbjct: 121 PELLKDAVYGLPEVNREKIRQARLIAVPGCYPTATQLGFLPLLEAGLADPSRLIADCKSG 180

Query: 223 ASGAGRQGKIGMLHGEIGESFKAYGASGHRHLPEIRQGLCGAAGGDVGVTFVPHLIPMIR 282
            SGAGR   +G L  E GES KAY   GHRHLPEI QGL  AAG D+G+TFVPHL PMIR
Sbjct: 181 VSGAGRGAAVGSLFCEAGESMKAYAVKGHRHLPEISQGLRLAAGKDIGLTFVPHLTPMIR 240

Query: 283 GIEATLYAELKNPADFDRLQALFEQRFDDEPFVDVMPFGSHPETRSVRGANQCRMALHRQ 342
           GI ATLYA + + +    LQALFE+R+ DEPFVDVMP GSHPETRSVRGAN CR+A+HR 
Sbjct: 241 GIHATLYANVVDTS--VDLQALFEKRYADEPFVDVMPAGSHPETRSVRGANVCRIAVHRP 298

Query: 343 EQSNIVIVSSVIDNLVKGAAGQAVQNMNIMFGLKETMGLEAPALLP 388
           +  ++V+V SVIDNLVKGA+GQAVQN+NI+FGL E MGL    LLP
Sbjct: 299 QGGDLVVVLSVIDNLVKGASGQAVQNLNILFGLDERMGLSHAGLLP 344


Lambda     K      H
   0.321    0.137    0.412 

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: 453
Number of extensions: 19
Number of successful extensions: 3
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: 388
Length of database: 344
Length adjustment: 30
Effective length of query: 358
Effective length of database: 314
Effective search space:   112412
Effective search space used:   112412
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 PP_0432 PP_0432 (N-acetyl-gamma-glutamyl-phosphate reductase 1)
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.628.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-135  437.9   0.0   1.5e-135  437.8   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_0432  PP_0432 N-acetyl-gamma-glutamyl-


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_0432  PP_0432 N-acetyl-gamma-glutamyl-phosphate reductase 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  437.8   0.0  1.5e-135  1.5e-135       1     345 []       2     344 .]       2     344 .] 0.97

  Alignments for each domain:
  == domain 1  score: 437.8 bits;  conditional E-value: 1.5e-135
                           TIGR01850   1 ikvaivGasGYtGaeLlrllakHpevevtklvssreagkklsevhphlkglvd.lkleeleeeeileeadvvflA 74 
                                         ikv+ivG++GYtG+eLlrlla+Hp++ev+ ++s++eag  +++++p+l+g++d l ++   ++++l ++dvvf+A
  lcl|FitnessBrowser__Putida:PP_0432   2 IKVGIVGGTGYTGVELLRLLAQHPQAEVAVITSRSEAGVAVADMYPNLRGHYDgLAFSVP-DSKALGACDVVFFA 75 
                                         69***************************8888888*****************7777755.555778******** PP

                           TIGR01850  75 lphgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnreeikkaklianPGC 149
                                         +phgv+++l+ ell++g+kvidlSadfRl+da+++ kwYg++h ++ell++avYGlpE+nre+i++a+lia+PGC
  lcl|FitnessBrowser__Putida:PP_0432  76 TPHGVAHALAGELLAAGTKVIDLSADFRLQDATEWGKWYGQPHGAPELLKDAVYGLPEVNREKIRQARLIAVPGC 150
                                         *************************************************************************** PP

                           TIGR01850 150 yaTaalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvtkHrHtpEieqelsklaek 224
                                         y+Ta++L+  Pll+++l +p+++i d+ksGvSgAGr a   slf+e+ e++k+Y+v++HrH pEi+q l+ +a+k
  lcl|FitnessBrowser__Putida:PP_0432 151 YPTATQLGFLPLLEAGLADPSRLIADCKSGVSGAGRGAAVGSLFCEAGESMKAYAVKGHRHLPEISQGLRLAAGK 225
                                         **********************************************************************99999 PP

                           TIGR01850 225 kvkvsftphlvpmtrGilatiyaklkkelteeelrklyeevYedepfvrvlkegelPstkavlgsnfvdigvavd 299
                                         ++ ++f+phl+pm+rGi+at+ya++ +  t+ +l++l+e++Y+depfv+v+++g+ P+t++v+g n+++i+v+  
  lcl|FitnessBrowser__Putida:PP_0432 226 DIGLTFVPHLTPMIRGIHATLYANVVD--TSVDLQALFEKRYADEPFVDVMPAGSHPETRSVRGANVCRIAVHRP 298
                                         9**************************..89******************************************** PP

                           TIGR01850 300 eetkrvvvvsaiDNLvKGaagqAvqnlNlmlgfdetegLeklpllp 345
                                         +  + vvv+s+iDNLvKGa+gqAvqnlN+ +g+de+ gL++ +llp
  lcl|FitnessBrowser__Putida:PP_0432 299 QGGDLVVVLSVIDNLVKGASGQAVQNLNILFGLDERMGLSHAGLLP 344
                                         *****************************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (345 nodes)
Target sequences:                          1  (344 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 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 8.68
//
[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