Alignments for a candidate for trpD_1 in Pseudomonas stutzeri RCH2

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpD_1 in Pseudomonas stutzeri RCH2

Align Anthranilate synthase component 2; AS; ASII; Anthranilate synthase, GATase component; Anthranilate synthase, glutamine amidotransferase component; EC 4.1.3.27 (characterized)
to candidate GFF3582 Psest_3649 glutamine amidotransferase of anthranilate synthase or aminodeoxychorismate synthase

Query= SwissProt::P00901
         (198 letters)



>FitnessBrowser__psRCH2:GFF3582
          Length = 197

 Score =  361 bits (926), Expect = e-105
 Identities = 173/197 (87%), Positives = 186/197 (94%)

Query: 2   LLMMIDNYDSFTYNVVQYLGELGAEVKVIRNDEMTIAQIEALNPERIVVSPGPCTPSEAG 61
           +L+M+DNYDSFTYNVVQYLGELGA+VKV+RNDE+++A+IEALNPERIVVSPGPCTP+EAG
Sbjct: 1   MLLMLDNYDSFTYNVVQYLGELGADVKVVRNDELSVAEIEALNPERIVVSPGPCTPNEAG 60

Query: 62  VSIEAILHFAGKLPILGVCLGHQSIGQAFGGDVVRARQVMHGKTSPVHHRDLGVFTGLNN 121
           VS+E I HFAGKLPILGVCLGHQSIGQAFGGDVVRARQ MHGKTSPV H D GVF GLNN
Sbjct: 61  VSLELIRHFAGKLPILGVCLGHQSIGQAFGGDVVRARQAMHGKTSPVFHHDQGVFAGLNN 120

Query: 122 PLTVTRYHSLVVKRETLPDCLEVTAWTAHEDGSVDEIMGLRHKTLNIEGVQFHPESILTE 181
           PLTVTRYHSLVVKRETLP+ LE+TAWT  EDGSVDEIMGLRHKTLNIEGVQFHPESILTE
Sbjct: 121 PLTVTRYHSLVVKRETLPESLEITAWTQLEDGSVDEIMGLRHKTLNIEGVQFHPESILTE 180

Query: 182 QGHELFANFLKQTGGRR 198
           QGHELFANFLKQTGG R
Sbjct: 181 QGHELFANFLKQTGGMR 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: 232
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 GFF3582 Psest_3649 (glutamine amidotransferase of anthranilate synthase or aminodeoxychorismate synthase)
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.16604.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
    9.9e-90  285.5   0.0    1.1e-89  285.3   0.0    1.0  1  lcl|FitnessBrowser__psRCH2:GFF3582  Psest_3649 glutamine amidotransf


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF3582  Psest_3649 glutamine amidotransferase of anthranilate synthase or aminodeoxychori
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  285.3   0.0   1.1e-89   1.1e-89       1     191 [.       1     191 [.       1     192 [. 0.98

  Alignments for each domain:
  == domain 1  score: 285.3 bits;  conditional E-value: 1.1e-89
                           TIGR00566   1 mvllidnydsftynlvqlleelgaevvvkrndsltlqeieallpllsivisPGPctPdeaaissleliehlaGkl 75 
                                         m+l++dnydsftyn+vq+l elga+v v rnd+l ++eieal p+  iv+sPGPctP+ea++s leli+h+aGkl
  lcl|FitnessBrowser__psRCH2:GFF3582   1 MLLMLDNYDSFTYNVVQYLGELGADVKVVRNDELSVAEIEALNPER-IVVSPGPCTPNEAGVS-LELIRHFAGKL 73 
                                         79********************************************.****************.*********** PP

                           TIGR00566  76 PilGvClGhqalaqafGadvvraekvkhGkvseiehngaavfaglfnPdalkatryhslvveaetldtllevtal 150
                                         PilGvClGhq+++qafG+dvvra++ +hGk+s + h++++vfagl nP  l++tryhslvv+ etl++ le+ta+
  lcl|FitnessBrowser__psRCH2:GFF3582  74 PILGVCLGHQSIGQAFGGDVVRARQAMHGKTSPVFHHDQGVFAGLNNP--LTVTRYHSLVVKRETLPESLEITAW 146
                                         ************************************************..************************* PP

                           TIGR00566 151 eeee....ieimairhrdlpleGvqfhPesilselGkellanflk 191
                                         ++ e    +eim++rh+ l++eGvqfhPesil+e+G+el anflk
  lcl|FitnessBrowser__psRCH2:GFF3582 147 TQLEdgsvDEIMGLRHKTLNIEGVQFHPESILTEQGHELFANFLK 191
                                         987667889**********************************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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 6.40
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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
the source code
instructions for running GapMind on your computer
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