GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpA in Enterococcus termitis LMG 8895

Align Tryptophan synthase alpha chain; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_069663039.1 BCR25_RS07700 tryptophan synthase subunit alpha

Query= uniprot:H0BV16
         (269 letters)



>NCBI__GCF_001730305.1:WP_069663039.1
          Length = 257

 Score =  140 bits (352), Expect = 4e-38
 Identities = 84/252 (33%), Positives = 133/252 (52%), Gaps = 7/252 (2%)

Query: 1   MSRIASTFSALQAQGRKALIPYVTAGFPFADITPALMHGMVEAGADVIELGVPFSDPMAD 60
           M  +    +  Q       +PY+ AG    D   A +  + +AGA  IELG+PFSDP+AD
Sbjct: 1   MKTLTEQLTKKQQANETIFVPYIMAGAQGLDQLEAEITLLCDAGASAIELGIPFSDPVAD 60

Query: 61  GPVIQKAGEKALSLGIGMVQVLDHVREFRKRNNTTPVVLMGYANPVERYDQKHGEGAFVR 120
           GPVIQ AG +AL   + + +++D   + +K +  TP++LM Y NP+  Y    G    V+
Sbjct: 61  GPVIQAAGLRALENDVSLEKIID---QLKKISTKTPLILMTYFNPIFHY----GLEQLVQ 113

Query: 121 DSAAAGVDGVLIVDYPPEECEAFAASLRAHGMDLIFLLAPTSTDERMAEVARVASGYVYY 180
           + A   V G++I D P E        L    + LI L+A T+  +R+AE+     G++Y 
Sbjct: 114 ELAETNVKGLIIPDLPYEHQHLLTPLLENSDIALIPLIALTTPKDRIAELVEAGEGFIYA 173

Query: 181 VSLKGVTGSGALDTAAVEQMLPRIRQHVTIPVGVGFGIRDAATAQAIGKVADAVVIGSRI 240
           V++ GVTG G    A++++ L  I++    PV  GFGI          K    V++GS+I
Sbjct: 174 VAVNGVTGVGREYQASLDEHLAYIQKISDKPVLAGFGISSKDHVARFRKNCAGVIVGSKI 233

Query: 241 IQLIEDQEHAKV 252
           + L+ + + A+V
Sbjct: 234 VDLLSEGKQAEV 245


Lambda     K      H
   0.321    0.137    0.389 

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: 184
Number of extensions: 11
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: 269
Length of database: 257
Length adjustment: 25
Effective length of query: 244
Effective length of database: 232
Effective search space:    56608
Effective search space used:    56608
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: 47 (22.7 bits)

Align candidate WP_069663039.1 BCR25_RS07700 (tryptophan synthase subunit alpha)
to HMM TIGR00262 (trpA: tryptophan synthase, alpha subunit (EC 4.2.1.20))

# 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/TIGR00262.hmm
# target sequence database:        /tmp/gapView.3089429.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00262  [M=256]
Accession:   TIGR00262
Description: trpA: tryptophan synthase, alpha subunit
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    6.1e-72  227.6   0.1    7.4e-72  227.3   0.1    1.0  1  NCBI__GCF_001730305.1:WP_069663039.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001730305.1:WP_069663039.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  227.3   0.1   7.4e-72   7.4e-72       4     241 ..      11     244 ..       8     256 .. 0.94

  Alignments for each domain:
  == domain 1  score: 227.3 bits;  conditional E-value: 7.4e-72
                             TIGR00262   4 lkkkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagvkvekale 76 
                                            ++++e+ fvp++ ag   l++    i+ l++aGa+a+ElG+pfsDP+aDGp+iqaa lRAl++ v++ek+++
  NCBI__GCF_001730305.1:WP_069663039.1  11 KQQANETIFVPYIMAGAQGLDQLEAEITLLCDAGASAIELGIPFSDPVADGPVIQAAGLRALENDVSLEKIID 83 
                                           57899*****************************************************************777 PP

                             TIGR00262  77 llkkvrekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleeaddlleaakkhgvkqiflvaP 149
                                            lkk+  k    P++l+ty+n+if++g+e+ +++++e+ v+g++++DlP+e ++ l+   ++ +++ i l+a 
  NCBI__GCF_001730305.1:WP_069663039.1  84 QLKKISTK---TPLILMTYFNPIFHYGLEQLVQELAETNVKGLIIPDLPYEHQHLLTPLLENSDIALIPLIAL 153
                                           77777666...9************************************************************* PP

                             TIGR00262 150 taeeerlkkiaekseGfvYlvsvaGvtgarerveeevkelikkvkalskkPvlvGFGiskkeqvkelkelgad 222
                                           t++++r+ ++ e +eGf+Y+v+v Gvtg+ ++ +++++e ++ ++++s+kPvl GFGis k++v + ++   +
  NCBI__GCF_001730305.1:WP_069663039.1 154 TTPKDRIAELVEAGEGFIYAVAVNGVTGVGREYQASLDEHLAYIQKISDKPVLAGFGISSKDHVARFRKN-CA 225
                                           ********************************************************************99.67 PP

                             TIGR00262 223 gvivGsAlvkiieekldde 241
                                           gvivGs +v++++e ++ e
  NCBI__GCF_001730305.1:WP_069663039.1 226 GVIVGSKIVDLLSEGKQAE 244
                                           8***********9996632 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (256 nodes)
Target sequences:                          1  (257 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: 19.38
//
[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