GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpD_1 in Marivita geojedonensis DPG-138

Align Anthranilate synthase component 2; AS; ASII; Anthranilate synthase, GATase component; Anthranilate synthase, glutamine amidotransferase component; EC 4.1.3.27 (characterized)
to candidate WP_085637398.1 MGEO_RS11340 aminodeoxychorismate/anthranilate synthase component II

Query= SwissProt::P26922
         (196 letters)



>NCBI__GCF_002115805.1:WP_085637398.1
          Length = 193

 Score =  279 bits (714), Expect = 2e-80
 Identities = 130/187 (69%), Positives = 154/187 (82%)

Query: 1   MLLLIDNYDSFTYNLVHYLGELGAELDVRRNDSLTVEEAMALRPEGIVLSPGPCDPDKAG 60
           MLLLIDNYDSFTYNLVHYLGELG ++ V RND+LTV++AM L P GI+LSPGPCDPD+AG
Sbjct: 1   MLLLIDNYDSFTYNLVHYLGELGTDVKVVRNDALTVQDAMGLNPSGILLSPGPCDPDQAG 60

Query: 61  ICLPLIDAAAKAAVPLMGVCLGHQAIGQPFGGTVVRAPVPMHGKVDRMFHQGRGVLKDLP 120
           ICLPL  AAA+  +PLMGVCLGHQ +GQ FGG+VVR    +HGK+  M H G+GV   LP
Sbjct: 61  ICLPLTLAAAETGMPLMGVCLGHQTLGQAFGGSVVRHSEIVHGKMGLMHHAGKGVFAGLP 120

Query: 121 SPFRATRYHSLIVERATLPACLEVTGETEDGLIMALSHRELPIHGVQFHPESIESEHGHK 180
           SPF ATRYHSL+V++ T+P CLEVT   EDG +M LSHR+LP+HGVQFHPESI SEHGH 
Sbjct: 121 SPFEATRYHSLVVDKDTIPNCLEVTAWLEDGTVMGLSHRDLPMHGVQFHPESIASEHGHA 180

Query: 181 ILENFLN 187
           +L+NF+N
Sbjct: 181 LLKNFVN 187


Lambda     K      H
   0.321    0.140    0.420 

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: 208
Number of extensions: 12
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: 196
Length of database: 193
Length adjustment: 20
Effective length of query: 176
Effective length of database: 173
Effective search space:    30448
Effective search space used:    30448
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: 44 (21.6 bits)

Align candidate WP_085637398.1 MGEO_RS11340 (aminodeoxychorismate/anthranilate synthase component II)
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.415699.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    8.8e-75  236.7   0.0      1e-74  236.6   0.0    1.0  1  NCBI__GCF_002115805.1:WP_085637398.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002115805.1:WP_085637398.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  236.6   0.0     1e-74     1e-74       1     191 [.       1     187 [.       1     188 [. 0.98

  Alignments for each domain:
  == domain 1  score: 236.6 bits;  conditional E-value: 1e-74
                             TIGR00566   1 mvllidnydsftynlvqlleelgaevvvkrndsltlqeieallpllsivisPGPctPdeaaissleliehlaG 73 
                                           m+llidnydsftynlv++l elg++v v rnd+lt+q+   l p   i++sPGPc Pd+a+i     +  +  
  NCBI__GCF_002115805.1:WP_085637398.1   1 MLLLIDNYDSFTYNLVHYLGELGTDVKVVRNDALTVQDAMGLNPSG-ILLSPGPCDPDQAGICLPLTLAAAET 72 
                                           79*******************************************9.****************8777888888 PP

                             TIGR00566  74 klPilGvClGhqalaqafGadvvraekvkhGkvseiehngaavfaglfnPdalkatryhslvveaetldtlle 146
                                            +P++GvClGhq+l+qafG++vvr +++ hGk+  ++h g++vfagl +P  ++atryhslvv+ +t++++le
  NCBI__GCF_002115805.1:WP_085637398.1  73 GMPLMGVCLGHQTLGQAFGGSVVRHSEIVHGKMGLMHHAGKGVFAGLPSP--FEATRYHSLVVDKDTIPNCLE 143
                                           9*************************************************..********************* PP

                             TIGR00566 147 vtaleeeeieimairhrdlpleGvqfhPesilselGkellanflk 191
                                           vta+ e    +m++ hrdlp++GvqfhPesi se+G++ll+nf++
  NCBI__GCF_002115805.1:WP_085637398.1 144 VTAWLEDG-TVMGLSHRDLPMHGVQFHPESIASEHGHALLKNFVN 187
                                           ****9999.9*********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (192 nodes)
Target sequences:                          1  (193 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 14.43
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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