GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpD_1 in Pseudomonas putida KT2440

Align Anthranilate synthase component 2; AS; ASII; Anthranilate synthase, GATase component; Anthranilate synthase, glutamine amidotransferase component; EC 4.1.3.27 (characterized)
to candidate PP_0420 PP_0420 aminodeoxychorismate synthase / para-aminobenzoate synthase multi-enzyme complex

Query= SwissProt::P00901
         (198 letters)



>FitnessBrowser__Putida:PP_0420
          Length = 197

 Score =  389 bits (999), Expect = e-113
 Identities = 190/197 (96%), Positives = 194/197 (98%)

Query: 2   LLMMIDNYDSFTYNVVQYLGELGAEVKVIRNDEMTIAQIEALNPERIVVSPGPCTPSEAG 61
           +L+MIDNYDSFTYNVVQYLGELGAEVKVIRNDEMTIAQIEALNPERIVVSPGPCTPSEAG
Sbjct: 1   MLLMIDNYDSFTYNVVQYLGELGAEVKVIRNDEMTIAQIEALNPERIVVSPGPCTPSEAG 60

Query: 62  VSIEAILHFAGKLPILGVCLGHQSIGQAFGGDVVRARQVMHGKTSPVHHRDLGVFTGLNN 121
           VSIEAILHFAGKLPILGVCLGHQSIGQAFGGDVVRARQVMHGKTSPV+HRDLGVF  LNN
Sbjct: 61  VSIEAILHFAGKLPILGVCLGHQSIGQAFGGDVVRARQVMHGKTSPVYHRDLGVFASLNN 120

Query: 122 PLTVTRYHSLVVKRETLPDCLEVTAWTAHEDGSVDEIMGLRHKTLNIEGVQFHPESILTE 181
           PLTVTRYHSLVVKRETLPDCLEVTAWT+H DGSVDEIMGLRHKTLNIEGVQFHPESILTE
Sbjct: 121 PLTVTRYHSLVVKRETLPDCLEVTAWTSHADGSVDEIMGLRHKTLNIEGVQFHPESILTE 180

Query: 182 QGHELFANFLKQTGGRR 198
           QGHELFANFLKQTGGRR
Sbjct: 181 QGHELFANFLKQTGGRR 197


Lambda     K      H
   0.320    0.138    0.411 

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: 247
Number of extensions: 1
Number of successful extensions: 1
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: 198
Length of database: 197
Length adjustment: 20
Effective length of query: 178
Effective length of database: 177
Effective search space:    31506
Effective search space used:    31506
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: 45 (21.9 bits)

Align candidate PP_0420 PP_0420 (aminodeoxychorismate synthase / para-aminobenzoate synthase multi-enzyme complex)
to HMM TIGR00566 (glutamine amidotransferase of anthranilate synthase or aminodeoxychorismate synthase)

# 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/TIGR00566.hmm
# target sequence database:        /tmp/gapView.4541.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00566  [M=192]
Accession:   TIGR00566
Description: trpG_papA: glutamine amidotransferase of anthranilate synthase or aminodeoxychorismate synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
    3.1e-90  287.1   0.1    3.5e-90  287.0   0.1    1.0  1  lcl|FitnessBrowser__Putida:PP_0420  PP_0420 aminodeoxychorismate syn


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_0420  PP_0420 aminodeoxychorismate synthase / para-aminobenzoate synthase multi-enzyme 
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  287.0   0.1   3.5e-90   3.5e-90       1     191 [.       1     191 [.       1     192 [. 0.98

  Alignments for each domain:
  == domain 1  score: 287.0 bits;  conditional E-value: 3.5e-90
                           TIGR00566   1 mvllidnydsftynlvqlleelgaevvvkrndsltlqeieallpllsivisPGPctPdeaaissleliehlaGkl 75 
                                         m+l+idnydsftyn+vq+l elgaev v rnd++t+++ieal p+  iv+sPGPctP ea++s +e+i h+aGkl
  lcl|FitnessBrowser__Putida:PP_0420   1 MLLMIDNYDSFTYNVVQYLGELGAEVKVIRNDEMTIAQIEALNPER-IVVSPGPCTPSEAGVS-IEAILHFAGKL 73 
                                         79********************************************.****************.*********** PP

                           TIGR00566  76 PilGvClGhqalaqafGadvvraekvkhGkvseiehngaavfaglfnPdalkatryhslvveaetldtllevtal 150
                                         PilGvClGhq+++qafG+dvvra++v+hGk+s + h + +vfa+l nP  l++tryhslvv+ etl+++levta+
  lcl|FitnessBrowser__Putida:PP_0420  74 PILGVCLGHQSIGQAFGGDVVRARQVMHGKTSPVYHRDLGVFASLNNP--LTVTRYHSLVVKRETLPDCLEVTAW 146
                                         ************************************************..************************* PP

                           TIGR00566 151 eeee....ieimairhrdlpleGvqfhPesilselGkellanflk 191
                                         +++     +eim++rh+ l++eGvqfhPesil+e+G+el anflk
  lcl|FitnessBrowser__Putida:PP_0420 147 TSHAdgsvDEIMGLRHKTLNIEGVQFHPESILTEQGHELFANFLK 191
                                         988768889**********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (192 nodes)
Target sequences:                          1  (197 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: 7.20
//
[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