GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpD_1 in Pontibacter ramchanderi LP43

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_101447279.1 BD749_RS18475 aminodeoxychorismate/anthranilate synthase component II

Query= SwissProt::P28819
         (194 letters)



>NCBI__GCF_002846395.1:WP_101447279.1
          Length = 190

 Score =  175 bits (443), Expect = 5e-49
 Identities = 81/186 (43%), Positives = 126/186 (67%), Gaps = 3/186 (1%)

Query: 1   MILMIDNYDSFTYNLVQYLGELGEELVVKRNDSITIDEIEELSPDFLMISPGPCSPDEAG 60
           M+L++DN+DSFTYNLV Y G+LG E+ V RND + +DEI+ L    +++SPGP  P +AG
Sbjct: 1   MLLLLDNFDSFTYNLVDYFGQLGVEMHVLRND-VGLDEIKALPIQGIVLSPGPGEPQKAG 59

Query: 61  ISLEAIKHFAGKIPIFGVCLGHQSIAQVFGGDVVRAERLMHGKTSDIEHDGKTIFEGLKN 120
           + +E I+H+  K+P+ G+CLGHQ++ + FG  + +  + MHGK S+I  +   +F GL  
Sbjct: 60  VMMEVIRHYHDKVPMLGICLGHQALGEFFGATLAKGMKPMHGKISEIICEPDPLFNGLPA 119

Query: 121 PLVATRYHSLIVKPETLPSCFTVTAQTKEGEIMAIRHNDLPIEGVQFHPESIMTSFGKEM 180
            +   RYHSL++     P+     A T EGE+MA RH+ LP+  +QFHPE+ +T++G  M
Sbjct: 120 RMPVVRYHSLVL--TQWPASILPLAYTAEGELMAFRHSTLPLHALQFHPEAALTTYGLGM 177

Query: 181 LRNFIE 186
           L+N+++
Sbjct: 178 LKNWLD 183


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: 137
Number of extensions: 8
Number of successful extensions: 3
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: 190
Length adjustment: 20
Effective length of query: 174
Effective length of database: 170
Effective search space:    29580
Effective search space used:    29580
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_101447279.1 BD749_RS18475 (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.2283182.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    3.8e-54  169.4   0.0    4.4e-54  169.2   0.0    1.0  1  NCBI__GCF_002846395.1:WP_101447279.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002846395.1:WP_101447279.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.2   0.0   4.4e-54   4.4e-54       1     191 [.       1     183 [.       1     184 [. 0.92

  Alignments for each domain:
  == domain 1  score: 169.2 bits;  conditional E-value: 4.4e-54
                             TIGR00566   1 mvllidnydsftynlvqlleelgaevvvkrndsltlqeieallpllsivisPGPctPdeaaissleliehlaG 73 
                                           m+ll+dn+dsftynlv+++ +lg e++v rnd + l+ei+al  +  iv+sPGP++P++a++  +e+i+h+  
  NCBI__GCF_002846395.1:WP_101447279.1   1 MLLLLDNFDSFTYNLVDYFGQLGVEMHVLRND-VGLDEIKALPIQG-IVLSPGPGEPQKAGVM-MEVIRHYHD 70 
                                           79****************************98.6799***997777.***************8.9******** PP

                             TIGR00566  74 klPilGvClGhqalaqafGadvvraekvkhGkvseiehngaavfaglfnPdalkatryhslvveaetldtlle 146
                                           k+P+lG+ClGhqal+  fGa + +  k +hGk+sei  +   +f+gl     +++ ryhslv+      ++l+
  NCBI__GCF_002846395.1:WP_101447279.1  71 KVPMLGICLGHQALGEFFGATLAKGMKPMHGKISEIICEPDPLFNGLPA--RMPVVRYHSLVLTQW-PASILP 140
                                           ****************************************999999955..59********99743.345666 PP

                             TIGR00566 147 vtaleeeeieimairhrdlpleGvqfhPesilselGkellanflk 191
                                           ++ +  e  e+ma rh  lpl+ +qfhPe+ l+  G  +l+n+l+
  NCBI__GCF_002846395.1:WP_101447279.1 141 LAYTA-EG-ELMAFRHSTLPLHALQFHPEAALTTYGLGMLKNWLD 183
                                           66555.44.7********************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (192 nodes)
Target sequences:                          1  (190 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: 12.89
//
[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