GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpA in Streptacidiphilus oryzae TH49

Align tryptophan synthase subunit α (EC 4.1.2.8) (characterized)
to candidate WP_051941042.1 BS73_RS29030 tryptophan synthase subunit alpha

Query= metacyc::MONOMER-3561
         (251 letters)



>NCBI__GCF_000744815.1:WP_051941042.1
          Length = 280

 Score =  169 bits (429), Expect = 4e-47
 Identities = 102/254 (40%), Positives = 152/254 (59%), Gaps = 9/254 (3%)

Query: 4   KGSLIPYLTAGDPSVEKTLEFLLAV-EEFAGLIELGIPFSDPMADGKTIQESHYRALRNG 62
           + +L+ YL AG P+V+  +  + A+ E     +E+G+P SDP+ DG TIQ +   ALR G
Sbjct: 27  RAALVGYLPAGFPTVDGGIAAVKALLEGGCDAVEIGLPHSDPVLDGATIQTADDIALRAG 86

Query: 63  FKLDDTFRILREFRR-HSSTPVILMTYYNPVFRTGVKKFLGEAKASGADGILVVDLPVSH 121
            +  D  R +RE        PV++MTY+NPV R GV +F  +   +G  G+++ DLPV  
Sbjct: 87  VRTKDVLRTVREVASAFPQAPVLVMTYWNPVDRYGVDRFAADLAEAGGAGVILPDLPVEE 146

Query: 122 AGEFLDAAKEEGLKTVFLAAPNTPDERLREIDKASTGFVYLISLYGTTGARDRLPETAFE 181
           AG +L AA+  GL TVF+ AP++ DERLR +  A TGFVY  ++ G TG R+++ + A +
Sbjct: 147 AGPWLAAAERLGLDTVFVVAPSSRDERLRLVTAAGTGFVYAAAVMGVTGTREQVGDLAED 206

Query: 182 FVRRARKICNNKLAVGFGVSRREQVEELLKAG-ADGVVVGSALIELISRSENPVEE---- 236
            V+R R + +  + VG GVS  +Q  E+  AG ADGV+VGSA ++ I  S + +E     
Sbjct: 207 LVKRTRAVTDLPVCVGIGVSNEKQAAEV--AGFADGVIVGSAFVKRILESGDDLESGLAG 264

Query: 237 LRRKVAELSGYSRA 250
           +R   A L+   RA
Sbjct: 265 IRETAAALARGVRA 278


Lambda     K      H
   0.319    0.138    0.386 

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: 206
Number of extensions: 7
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: 251
Length of database: 280
Length adjustment: 25
Effective length of query: 226
Effective length of database: 255
Effective search space:    57630
Effective search space used:    57630
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: 47 (22.7 bits)

Align candidate WP_051941042.1 BS73_RS29030 (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.2891643.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    1.6e-74  236.1   0.0    1.8e-74  235.9   0.0    1.0  1  NCBI__GCF_000744815.1:WP_051941042.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000744815.1:WP_051941042.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  235.9   0.0   1.8e-74   1.8e-74       4     255 ..      22     272 ..      19     273 .. 0.98

  Alignments for each domain:
  == domain 1  score: 235.9 bits;  conditional E-value: 1.8e-74
                             TIGR00262   4 lkkkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagvkvekale 76 
                                            ++++  a+v ++ ag P+++  + ++k l + G da+E+G+p+sDP++DG tiq+a+  Al+agv+++++l+
  NCBI__GCF_000744815.1:WP_051941042.1  22 ARAEGRAALVGYLPAGFPTVDGGIAAVKALLEGGCDAVEIGLPHSDPVLDGATIQTADDIALRAGVRTKDVLR 94 
                                           5677889****************************************************************** PP

                             TIGR00262  77 llkkvrekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleeaddlleaakkhgvkqiflvaP 149
                                            +++v +  +++P+ ++ty n++ ++gv+ F a ++eag  gv+++DlP+eea+  l aa++ g++++f+vaP
  NCBI__GCF_000744815.1:WP_051941042.1  95 TVREVASAFPQAPVLVMTYWNPVDRYGVDRFAADLAEAGGAGVILPDLPVEEAGPWLAAAERLGLDTVFVVAP 167
                                           ************************************************************************* PP

                             TIGR00262 150 taeeerlkkiaekseGfvYlvsvaGvtgarerveeevkelikkvkalskkPvlvGFGiskkeqvkelkelgad 222
                                           ++ +erl+ ++  ++GfvY+ +v+Gvtg+re+v + +++l+k+ +a+++ Pv+vG G+s++ q+ e+  + ad
  NCBI__GCF_000744815.1:WP_051941042.1 168 SSRDERLRLVTAAGTGFVYAAAVMGVTGTREQVGDLAEDLVKRTRAVTDLPVCVGIGVSNEKQAAEVAGF-AD 239
                                           *********************************************************************9.9* PP

                             TIGR00262 223 gvivGsAlvkiieeklddeekaleeleefvkel 255
                                           gvivGsA+vk+i e+ dd e  l+ ++e + +l
  NCBI__GCF_000744815.1:WP_051941042.1 240 GVIVGSAFVKRILESGDDLESGLAGIRETAAAL 272
                                           ***************9********999987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (256 nodes)
Target sequences:                          1  (280 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: 16.96
//
[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