Alignments for a candidate for trpD_1 in Shewanella oneidensis MR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpD_1 in Shewanella oneidensis MR-1

Align anthranilate synthase (subunit 2/2) (EC 4.1.3.27) (characterized)
to candidate 199801 SO0613 para-aminobenzoate synthase glutamine amidotransferase, component II (NCBI ptt file)

Query= BRENDA::P20576
         (201 letters)



>FitnessBrowser__MR1:199801
          Length = 191

 Score =  238 bits (607), Expect = 5e-68
 Identities = 122/192 (63%), Positives = 147/192 (76%), Gaps = 3/192 (1%)

Query: 1   MLLMIDNYDSFTYNLVQYFGELKAEVKVVRNDELSVEQIEALAPERIVLSPGPCTPNEAG 60
           MLLMIDNYDSFT+NLVQYF +L  E+ V RNDE+S+E IEALAP  +V+SPGPC+PNEAG
Sbjct: 1   MLLMIDNYDSFTFNLVQYFQQLGQEIVVKRNDEISLEGIEALAPSHLVISPGPCSPNEAG 60

Query: 61  VSLAVIERFAGKLPLLGVCLGHQSIGQAFGGEVVRARQVMHGKTSPIHHKDLGVFAGLAN 120
           +SLA IE FA +LP+LGVCLGHQ++ Q FG +VVRA++VMHGK S I H    +F GL  
Sbjct: 61  ISLAAIEHFATRLPILGVCLGHQAMAQVFGAKVVRAQRVMHGKVSAIAHTGERLFKGLNQ 120

Query: 121 PLTVTRYHSLVVKRESLPECLEVTAWTQHADGSLDEIMGVRHKTLNVEGVQFHPESILTE 180
           PLTVTRYHSL+V  +++P+   + AW         EIM + HK L + GVQFHPESILTE
Sbjct: 121 PLTVTRYHSLLV--DTVPKDFVLDAWFDDPTHG-REIMAMSHKELPLFGVQFHPESILTE 177

Query: 181 QGHELLANFLRQ 192
           QGHELLANFL Q
Sbjct: 178 QGHELLANFLSQ 189


Lambda     K      H
   0.319    0.137    0.403 

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: 166
Number of extensions: 4
Number of successful extensions: 2
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: 201
Length of database: 191
Length adjustment: 20
Effective length of query: 181
Effective length of database: 171
Effective search space:    30951
Effective search space used:    30951
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 (21.7 bits)
S2: 45 (21.9 bits)

Align candidate 199801 SO0613 (para-aminobenzoate synthase glutamine amidotransferase, component II (NCBI ptt file))
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.31613.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
    1.2e-85  272.2   0.0    1.4e-85  272.0   0.0    1.0  1  lcl|FitnessBrowser__MR1:199801  SO0613 para-aminobenzoate syntha


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:199801  SO0613 para-aminobenzoate synthase glutamine amidotransferase, component II (NCBI ptt
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  272.0   0.0   1.4e-85   1.4e-85       1     191 [.       1     188 [.       1     189 [. 0.96

  Alignments for each domain:
  == domain 1  score: 272.0 bits;  conditional E-value: 1.4e-85
                       TIGR00566   1 mvllidnydsftynlvqlleelgaevvvkrndsltlqeieallpllsivisPGPctPdeaaissleliehlaGklPilG 79 
                                     m+l+idnydsft+nlvq++++lg+e+vvkrnd++ l+ ieal+p + +visPGPc+P+ea+is l++ieh+a +lPilG
  lcl|FitnessBrowser__MR1:199801   1 MLLMIDNYDSFTFNLVQYFQQLGQEIVVKRNDEISLEGIEALAPSH-LVISPGPCSPNEAGIS-LAAIEHFATRLPILG 77 
                                     79********************************************.****************.*************** PP

                       TIGR00566  80 vClGhqalaqafGadvvraekvkhGkvseiehngaavfaglfnPdalkatryhslvveaetldtllevtaleeee...i 155
                                     vClGhqa+aq+fGa+vvra++v+hGkvs+i h g+ +f+gl +P  l++tryhsl v+  t+++ + + a+ + +    
  lcl|FitnessBrowser__MR1:199801  78 VCLGHQAMAQVFGAKVVRAQRVMHGKVSAIAHTGERLFKGLNQP--LTVTRYHSLLVD--TVPKDFVLDAWFDDPthgR 152
                                     ********************************************..**********96..6777777777766655589 PP

                       TIGR00566 156 eimairhrdlpleGvqfhPesilselGkellanflk 191
                                     eima+ h++lpl+GvqfhPesil+e+G+ellanfl 
  lcl|FitnessBrowser__MR1:199801 153 EIMAMSHKELPLFGVQFHPESILTEQGHELLANFLS 188
                                     **********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (192 nodes)
Target sequences:                          1  (191 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: 6.56
//
[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:

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