Alignments for a candidate for trpB in Pseudomonas fluorescens FW300-N2E3

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpB in Pseudomonas fluorescens FW300-N2E3

Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate AO353_10710 AO353_10710 tryptophan synthase subunit beta

Query= uniprot:P50383
         (425 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_10710
          Length = 406

 Score =  129 bits (324), Expect = 2e-34
 Identities = 108/363 (29%), Positives = 163/363 (44%), Gaps = 54/363 (14%)

Query: 72  IGRPTPLFRAKRLEEYLKTPARIYFKYEGATPTGSHKINTAIPQAYFAKEEGIEHVVTET 131
           +GRP+PL+ A+RL E+    A+IY K E    TG+HKIN  I Q   A+  G + ++ ET
Sbjct: 60  VGRPSPLYFAERLTEFCGG-AKIYLKREELNHTGAHKINNCIGQILLARRMGKKRIIAET 118

Query: 132 GAGQWGTAVALAASMYNMKSTIFMVKVSYEQKPMRRSIMQLYGANVYASPTNLTEYGRKI 191
           GAG  G A A  A+ + +   I+M     E++      M+L GA V              
Sbjct: 119 GAGMHGVATATVAARFGLDCVIYMGTTDIERQQANVFRMKLLGAEVIPVVAG-------- 170

Query: 192 LETNPQHPGSLGIAMSEAIEYALKN--EFRYLVGSVLD------VVLLHQSVIGQETITQ 243
                   G+L  AM+EA+   + N     YL+G+V        +V   Q+VIG+ET  Q
Sbjct: 171 -------TGTLKDAMNEALRDWVTNVDSTFYLIGTVAGPHPYPAMVRDFQAVIGKETREQ 223

Query: 244 LDLL-GEDADILIGCVGGGSNFGGFTYPFIGNKKGK--------------RYIAVSSAEI 288
           L    G   D L+ C+GGGSN  G  +PF+ +K  +              ++ A  +  +
Sbjct: 224 LQAKEGRLPDSLVACIGGGSNAMGLFHPFLDDKSVEIIGVEAAGHGIETGKHAASLNGGV 283

Query: 289 PKFSKGEYKYDFPDSAGLLPLVKMITLGKDYVPPPIYAGGLRYHGVAPTLSLLTKEGIVE 348
           P    G   +   D  G +            +     + GL Y G+ P  + L   G V+
Sbjct: 284 PGVLHGNRTFLLQDDDGQI------------IDAHSISAGLDYPGIGPEHAWLHDIGRVQ 331

Query: 349 WREYNEREIFEAAKIFIENQGIVPAPESAHAIRAVVDEAIEARKNNERKVIVFNLSGHGL 408
           +    + E  +A       +GI+PA ESAHA+  V   A    K++   ++V NLSG G 
Sbjct: 332 YTSVTDHEALDAFHKCCRLEGIIPALESAHALAEVFKRAPTLPKDH---LMVVNLSGRGD 388

Query: 409 LDL 411
            D+
Sbjct: 389 KDM 391


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: 377
Number of extensions: 18
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: 406
Length adjustment: 31
Effective length of query: 394
Effective length of database: 375
Effective search space:   147750
Effective search space used:   147750
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 AO353_10710 AO353_10710 (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.10334.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   4.9e-198  643.8   0.0   5.7e-198  643.6   0.0    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_10710  AO353_10710 tryptophan synthase 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_10710  AO353_10710 tryptophan synthase subunit beta
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  643.6   0.0  5.7e-198  5.7e-198       1     384 [.      14     397 ..      14     398 .. 0.99

  Alignments for each domain:
  == domain 1  score: 643.6 bits;  conditional E-value: 5.7e-198
                                     TIGR00263   1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklgg 65 
                                                   g fg+fGG+yv+e+l++ + +l ++ye ak+d++fk+el ++ ++y+grp+pl+fa++l++  gg
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_10710  14 GLFGAFGGRYVAETLMPLILDLAREYEAAKDDPAFKEELAYFQRDYVGRPSPLYFAERLTEFCGG 78 
                                                   67*************************************************************** PP

                                     TIGR00263  66 akiylkredllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymG 130
                                                   akiylkre+l+htGahkinn +gq+lla+r+GkkriiaetGaG hGvatat+aa++gl+c++ymG
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_10710  79 AKIYLKREELNHTGAHKINNCIGQILLARRMGKKRIIAETGAGMHGVATATVAARFGLDCVIYMG 143
                                                   ***************************************************************** PP

                                     TIGR00263 131 aedverqklnvfrmellgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPei 195
                                                   ++d+erq+ nvfrm+llga+v+pv  G+ tlkda+nealrdWvt+v++t+y++G+++GphP+P++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_10710 144 TTDIERQQANVFRMKLLGAEVIPVVAGTGTLKDAMNEALRDWVTNVDSTFYLIGTVAGPHPYPAM 208
                                                   ***************************************************************** PP

                                     TIGR00263 196 vrefqsvigeevkeqilekegrlPdaviacvGGGsnaiGifaafiedeeveligveagGkGidte 260
                                                   vr+fq+vig+e++eq+++kegrlPd ++ac+GGGsna+G+f++f++d++ve+igvea+G+Gi+t 
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_10710 209 VRDFQAVIGKETREQLQAKEGRLPDSLVACIGGGSNAMGLFHPFLDDKSVEIIGVEAAGHGIETG 273
                                                   ***************************************************************** PP

                                     TIGR00263 261 khaatlskGkeGvlhGaktkllqdedGqieeahsvsaGldypgvgPehaalaetgraeyeaitde 325
                                                   khaa+l+ G +GvlhG++t llqd+dGqi +ahs+saGldypg+gPeha+l+++gr++y+++td+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_10710 274 KHAASLNGGVPGVLHGNRTFLLQDDDGQIIDAHSISAGLDYPGIGPEHAWLHDIGRVQYTSVTDH 338
                                                   ***************************************************************** PP

                                     TIGR00263 326 ealealkllskeeGiipalesshalaaleklapklkkdeivvvnlsGrGdkdletvaka 384
                                                   eal+a++++++ eGiipales+hala + k ap+l+kd+++vvnlsGrGdkd++tv+++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_10710 339 EALDAFHKCCRLEGIIPALESAHALAEVFKRAPTLPKDHLMVVNLSGRGDKDMQTVMHH 397
                                                   ********************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (406 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.14
//
[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