Alignments for a candidate for trpB in Pseudomonas fluorescens FW300-N2C3

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpB in Pseudomonas fluorescens FW300-N2C3

Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate AO356_10915 AO356_10915 tryptophan synthase subunit beta

Query= uniprot:P50383
         (425 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_10915
          Length = 410

 Score =  132 bits (332), Expect = 2e-35
 Identities = 111/372 (29%), Positives = 166/372 (44%), Gaps = 54/372 (14%)

Query: 72  IGRPTPLFRAKRLEEYLKTPARIYFKYEGATPTGSHKINTAIPQAYFAKEEGIEHVVTET 131
           +GRP+PL+ A+RL EY    A+IY K E    TG+HKIN  I Q   A+  G + ++ ET
Sbjct: 64  VGRPSPLYFAERLTEYCGG-AKIYLKREELNHTGAHKINNCIGQILLARRMGKKRIIAET 122

Query: 132 GAGQWGTAVALAASMYNMKSTIFMVKVSYEQKPMRRSIMQLYGANVYASPTNLTEYGRKI 191
           GAG  G A A  A+ + +   I+M     E++      M+L GA V              
Sbjct: 123 GAGMHGVATATVAARFGLDCVIYMGTTDIERQQANVFRMKLLGAEVIPVVAG-------- 174

Query: 192 LETNPQHPGSLGIAMSEAIEYALKN--EFRYLVGSVLD------VVLLHQSVIGQETITQ 243
                   G+L  AM+EA+   + N     YL+G+V        +V   Q+VIG+ET  Q
Sbjct: 175 -------TGTLKDAMNEALRDWVTNVDSTFYLIGTVAGPHPYPAMVRDFQAVIGKETRDQ 227

Query: 244 LDLL-GEDADILIGCVGGGSNFGGFTYPFIGNKKGK--------------RYIAVSSAEI 288
           L    G   D L+ C+GGGSN  G  +PF+ +K  +              ++ A  +  +
Sbjct: 228 LQAQEGRLPDSLVACIGGGSNAMGLFHPFLDDKSVEIIGVEAAGYGIETGKHAASLNGGV 287

Query: 289 PKFSKGEYKYDFPDSAGLLPLVKMITLGKDYVPPPIYAGGLRYHGVAPTLSLLTKEGIVE 348
           P    G   +   D  G +            +     + GL Y G+ P  + L   G V+
Sbjct: 288 PGVLHGNRTFLLQDDDGQI------------IDAHSISAGLDYPGIGPEHAWLHDIGRVQ 335

Query: 349 WREYNEREIFEAAKIFIENQGIVPAPESAHAIRAVVDEAIEARKNNERKVIVFNLSGHGL 408
           +    + E  EA       +GI+PA ESAHA+  V   A    K++   ++V NLSG G 
Sbjct: 336 YTSVTDAEALEAFHKCCRLEGIIPALESAHALAEVFKRAPNLPKDH---LMVVNLSGRGD 392

Query: 409 LDLSNYESMMKR 420
            D+      M++
Sbjct: 393 KDMQTVMHHMEQ 404


Lambda     K      H
   0.318    0.138    0.403 

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: 387
Number of extensions: 20
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: 425
Length of database: 410
Length adjustment: 32
Effective length of query: 393
Effective length of database: 378
Effective search space:   148554
Effective search space used:   148554
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate AO356_10915 AO356_10915 (tryptophan synthase subunit beta)
to HMM TIGR00263 (trpB: tryptophan synthase, beta 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/TIGR00263.hmm
# target sequence database:        /tmp/gapView.10634.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00263  [M=385]
Accession:   TIGR00263
Description: trpB: tryptophan synthase, beta 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   2.8e-197  641.3   0.0   3.3e-197  641.1   0.0    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_10915  AO356_10915 tryptophan synthase 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_10915  AO356_10915 tryptophan synthase subunit beta
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  641.1   0.0  3.3e-197  3.3e-197       1     384 [.      18     401 ..      18     402 .. 0.99

  Alignments for each domain:
  == domain 1  score: 641.1 bits;  conditional E-value: 3.3e-197
                                       TIGR00263   1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskkl 63 
                                                     g fg+fGG+yv+e+l++ + +l ++ye ak+d++f +el ++ ++y+grp+pl+fa++l++  
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_10915  18 GLFGAFGGRYVAETLMPLILDLAREYEVAKEDPAFIEELAYFQRDYVGRPSPLYFAERLTEYC 80 
                                                     67************************************************************* PP

                                       TIGR00263  64 ggakiylkredllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglece 126
                                                     ggakiylkre+l+htGahkinn +gq+lla+r+GkkriiaetGaG hGvatat+aa++gl+c+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_10915  81 GGAKIYLKREELNHTGAHKINNCIGQILLARRMGKKRIIAETGAGMHGVATATVAARFGLDCV 143
                                                     *************************************************************** PP

                                       TIGR00263 127 vymGaedverqklnvfrmellgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGp 189
                                                     +ymG++d+erq+ nvfrm+llga+v+pv  G+ tlkda+nealrdWvt+v++t+y++G+++Gp
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_10915 144 IYMGTTDIERQQANVFRMKLLGAEVIPVVAGTGTLKDAMNEALRDWVTNVDSTFYLIGTVAGP 206
                                                     *************************************************************** PP

                                       TIGR00263 190 hPfPeivrefqsvigeevkeqilekegrlPdaviacvGGGsnaiGifaafiedeeveligvea 252
                                                     hP+P++vr+fq+vig+e++ q++++egrlPd ++ac+GGGsna+G+f++f++d++ve+igvea
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_10915 207 HPYPAMVRDFQAVIGKETRDQLQAQEGRLPDSLVACIGGGSNAMGLFHPFLDDKSVEIIGVEA 269
                                                     *************************************************************** PP

                                       TIGR00263 253 gGkGidtekhaatlskGkeGvlhGaktkllqdedGqieeahsvsaGldypgvgPehaalaetg 315
                                                     +G Gi+t khaa+l+ G +GvlhG++t llqd+dGqi +ahs+saGldypg+gPeha+l+++g
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_10915 270 AGYGIETGKHAASLNGGVPGVLHGNRTFLLQDDDGQIIDAHSISAGLDYPGIGPEHAWLHDIG 332
                                                     *************************************************************** PP

                                       TIGR00263 316 raeyeaitdeealealkllskeeGiipalesshalaaleklapklkkdeivvvnlsGrGdkdl 378
                                                     r++y+++td+ealea++++++ eGiipales+hala + k ap+l+kd+++vvnlsGrGdkd+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_10915 333 RVQYTSVTDAEALEAFHKCCRLEGIIPALESAHALAEVFKRAPNLPKDHLMVVNLSGRGDKDM 395
                                                     *************************************************************** PP

                                       TIGR00263 379 etvaka 384
                                                     +tv+++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_10915 396 QTVMHH 401
                                                     ***986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (410 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 9.54
//
[ok]

This GapMind analysis is from Apr 09 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis