GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpD_1 in Desulfallas geothermicus DSM 3669

Align Aminodeoxychorismate/anthranilate synthase component 2; ADC synthase; ADCS; 4-amino-4-deoxychorismate synthase component 2; Aminodeoxychorismate synthase, glutamine amidotransferase component; EC 2.6.1.85; EC 4.1.3.27 (characterized)
to candidate WP_092485904.1 BM299_RS14590 aminodeoxychorismate/anthranilate synthase component II

Query= SwissProt::P28819
         (194 letters)



>NCBI__GCF_900115975.1:WP_092485904.1
          Length = 196

 Score =  262 bits (669), Expect = 3e-75
 Identities = 122/190 (64%), Positives = 150/190 (78%)

Query: 1   MILMIDNYDSFTYNLVQYLGELGEELVVKRNDSITIDEIEELSPDFLMISPGPCSPDEAG 60
           MIL+IDNYDSF +NL QYL ELG E+VV RND IT+ EI E+ P+ +++SPGPC+PDEAG
Sbjct: 1   MILLIDNYDSFVFNLYQYLSELGREVVVHRNDRITVTEITEMEPECIVLSPGPCTPDEAG 60

Query: 61  ISLEAIKHFAGKIPIFGVCLGHQSIAQVFGGDVVRAERLMHGKTSDIEHDGKTIFEGLKN 120
           ISLEA++  AG  PIFGVCLGHQ+I Q FGG VVRA+RLMHGKTS I HDGK+I+ GL N
Sbjct: 61  ISLEAVRRLAGVFPIFGVCLGHQTIGQAFGGKVVRAKRLMHGKTSRIFHDGKSIYTGLPN 120

Query: 121 PLVATRYHSLIVKPETLPSCFTVTAQTKEGEIMAIRHNDLPIEGVQFHPESIMTSFGKEM 180
           PL   RYHSLI++ E LP C  VTA+T  GEIM +RH  L +EGVQFHPESI+T  GK+M
Sbjct: 121 PLQVARYHSLILEQEALPGCLEVTARTARGEIMGVRHRHLAVEGVQFHPESILTVHGKKM 180

Query: 181 LRNFIETYRK 190
           L N+++  ++
Sbjct: 181 LTNYLQIIQR 190


Lambda     K      H
   0.320    0.139    0.404 

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: 146
Number of extensions: 4
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: 194
Length of database: 196
Length adjustment: 20
Effective length of query: 174
Effective length of database: 176
Effective search space:    30624
Effective search space used:    30624
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_092485904.1 BM299_RS14590 (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.18746.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    7.6e-83  263.0   0.0    8.7e-83  262.9   0.0    1.0  1  lcl|NCBI__GCF_900115975.1:WP_092485904.1  BM299_RS14590 aminodeoxychorisma


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900115975.1:WP_092485904.1  BM299_RS14590 aminodeoxychorismate/anthranilate synthase component II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  262.9   0.0   8.7e-83   8.7e-83       1     191 [.       1     186 [.       1     187 [. 0.99

  Alignments for each domain:
  == domain 1  score: 262.9 bits;  conditional E-value: 8.7e-83
                                 TIGR00566   1 mvllidnydsftynlvqlleelgaevvvkrndsltlqeieallpllsivisPGPctPdeaaisslelie 69 
                                               m+llidnydsf +nl+q+l+elg evvv+rnd +t++ei ++ p+  iv+sPGPctPdea+is le+++
  lcl|NCBI__GCF_900115975.1:WP_092485904.1   1 MILLIDNYDSFVFNLYQYLSELGREVVVHRNDRITVTEITEMEPEC-IVLSPGPCTPDEAGIS-LEAVR 67 
                                               79*******************************************9.****************.***** PP

                                 TIGR00566  70 hlaGklPilGvClGhqalaqafGadvvraekvkhGkvseiehngaavfaglfnPdalkatryhslvvea 138
                                               +laG +Pi+GvClGhq+++qafG++vvra++++hGk+s i h+g+++++gl nP  l+++ryhsl++e 
  lcl|NCBI__GCF_900115975.1:WP_092485904.1  68 RLAGVFPIFGVCLGHQTIGQAFGGKVVRAKRLMHGKTSRIFHDGKSIYTGLPNP--LQVARYHSLILEQ 134
                                               ******************************************************..************* PP

                                 TIGR00566 139 etldtllevtaleeeeieimairhrdlpleGvqfhPesilselGkellanflk 191
                                               e+l+ +levta + +  eim++rhr+l++eGvqfhPesil+ +Gk++l+n+l+
  lcl|NCBI__GCF_900115975.1:WP_092485904.1 135 EALPGCLEVTARTARG-EIMGVRHRHLAVEGVQFHPESILTVHGKKMLTNYLQ 186
                                               *************999.**********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (192 nodes)
Target sequences:                          1  (196 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: 8.89
//
[ok]

This GapMind analysis is from Apr 10 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