Alignments for a candidate for trpB in Burkholderia phytofirmans PsJN

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpB in Burkholderia phytofirmans PsJN

Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate BPHYT_RS33875 BPHYT_RS33875 tryptophan synthase subunit alpha

Query= uniprot:P50383
         (425 letters)



>FitnessBrowser__BFirm:BPHYT_RS33875
          Length = 397

 Score =  124 bits (312), Expect = 4e-33
 Identities = 111/372 (29%), Positives = 164/372 (44%), Gaps = 50/372 (13%)

Query: 61  IPEEVRDRYLSIGRPTPLFRAKRLEEYLKTPARIYFKYEGATPTGSHKINTAIPQAYFAK 120
           + E  R+    +GRP+P++ A+R  E L   A+I+ K E    TG+HK+N  I QA  AK
Sbjct: 44  VAEYERELKYFVGRPSPIYHAQRWSEMLGG-AQIFLKREDLNHTGAHKVNNVIGQALLAK 102

Query: 121 EEGIEHVVTETGAGQWGTAVALAASMYNMKSTIFMVKVSYEQKPMRRSIMQLYGANVYAS 180
             G   V+ ETGAGQ G A A  A+ + M+  ++M      ++      M+L GA V   
Sbjct: 103 RMGKPRVIAETGAGQHGVATATIAARFGMECVVYMGSEDVRRQAANVYRMKLLGATVVP- 161

Query: 181 PTNLTEYGRKILETNPQHPGSLGIAMSEAIEYALKNEFRYLVGSVLD------VVLLHQS 234
                E G + L+       +L  AM + +   ++N F Y++G+V        +V   Q 
Sbjct: 162 ----VESGSRTLK------DALNEAMRDWVT-NVENTF-YIIGTVAGPHPYPMMVRDFQR 209

Query: 235 VIGQETITQL-DLLGEDADILIGCVGGGSNFGGFTYPFIGNKKGK--------------R 279
           VIG E   Q+ +L+G   D +I CVGGGSN  G  YP+I +   K              R
Sbjct: 210 VIGDECKVQMPELVGRQPDAVIACVGGGSNAMGIFYPYIDDTSVKLIGVEAAGDGIESGR 269

Query: 280 YIAVSSAEIPKFSKGEYKYDFPDSAGLLPLVKMITLGKDYVPPPIYAGGLRYHGVAPTLS 339
           + A      P    G   Y   D  G +            +     + GL Y GV P  +
Sbjct: 270 HAASLIGGSPGVLHGNRTYLLQDENGQI------------IETHSVSAGLDYPGVGPEHA 317

Query: 340 LLTKEGIVEWREYNEREIFEAAKIFIENQGIVPAPESAHAIRAVVDEAIEARKNNERKVI 399
            L      E+    + E  +A       +GI+PA ES+HA+      A    K+   K +
Sbjct: 318 WLKDSKRAEYVGITDEEALKAFHDCCRIEGIIPALESSHALAYAAKLAPTLPKD---KYL 374

Query: 400 VFNLSGHGLLDL 411
           + NLSG G  D+
Sbjct: 375 LVNLSGRGDKDM 386


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: 386
Number of extensions: 18
Number of successful extensions: 4
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: 397
Length adjustment: 31
Effective length of query: 394
Effective length of database: 366
Effective search space:   144204
Effective search space used:   144204
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 BPHYT_RS33875 BPHYT_RS33875 (tryptophan synthase subunit alpha)
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.20766.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   1.9e-197  641.9   0.1   2.1e-197  641.7   0.1    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS33875  BPHYT_RS33875 tryptophan synthas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS33875  BPHYT_RS33875 tryptophan synthase subunit alpha
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  641.7   0.1  2.1e-197  2.1e-197       1     384 [.       9     392 ..       9     393 .. 1.00

  Alignments for each domain:
  == domain 1  score: 641.7 bits;  conditional E-value: 2.1e-197
                                TIGR00263   1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiyl 70 
                                              g+fg+fGG +v+e+l++al+el++ay+k+k+d++f++e+e+ lk ++grp+p+++a++ s+ lgga+i+l
  lcl|FitnessBrowser__BFirm:BPHYT_RS33875   9 GHFGQFGGVFVAETLVHALDELRAAYDKYKQDPAFVAEYERELKYFVGRPSPIYHAQRWSEMLGGAQIFL 78 
                                              68******************************************************************** PP

                                TIGR00263  71 kredllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqkln 140
                                              kredl+htGahk+nn++gqallakr+Gk r+iaetGaGqhGvatat+aa++g+ec+vymG+edv rq+ n
  lcl|FitnessBrowser__BFirm:BPHYT_RS33875  79 KREDLNHTGAHKVNNVIGQALLAKRMGKPRVIAETGAGQHGVATATIAARFGMECVVYMGSEDVRRQAAN 148
                                              ********************************************************************** PP

                                TIGR00263 141 vfrmellgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeevkeq 210
                                              v+rm+llga+vvpv+sGs+tlkda+nea+rdWvt+ve+t+y++G+++GphP+P +vr+fq+vig+e+k q
  lcl|FitnessBrowser__BFirm:BPHYT_RS33875 149 VYRMKLLGATVVPVESGSRTLKDALNEAMRDWVTNVENTFYIIGTVAGPHPYPMMVRDFQRVIGDECKVQ 218
                                              ********************************************************************** PP

                                TIGR00263 211 ilekegrlPdaviacvGGGsnaiGifaafiedeeveligveagGkGidtekhaatlskGkeGvlhGaktk 280
                                              + e  gr PdaviacvGGGsna+Gif+++i+d +v+ligvea+G Gi++ +haa+l  G++GvlhG++t+
  lcl|FitnessBrowser__BFirm:BPHYT_RS33875 219 MPELVGRQPDAVIACVGGGSNAMGIFYPYIDDTSVKLIGVEAAGDGIESGRHAASLIGGSPGVLHGNRTY 288
                                              ********************************************************************** PP

                                TIGR00263 281 llqdedGqieeahsvsaGldypgvgPehaalaetgraeyeaitdeealealkllskeeGiipalesshal 350
                                              llqde+Gqi e+hsvsaGldypgvgPeha+l++++raey+ itdeeal+a++ +++ eGiipalesshal
  lcl|FitnessBrowser__BFirm:BPHYT_RS33875 289 LLQDENGQIIETHSVSAGLDYPGVGPEHAWLKDSKRAEYVGITDEEALKAFHDCCRIEGIIPALESSHAL 358
                                              ********************************************************************** PP

                                TIGR00263 351 aaleklapklkkdeivvvnlsGrGdkdletvaka 384
                                              a++ klap+l+kd+ ++vnlsGrGdkd++tva++
  lcl|FitnessBrowser__BFirm:BPHYT_RS33875 359 AYAAKLAPTLPKDKYLLVNLSGRGDKDMHTVAER 392
                                              *******************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (397 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: 00:00:00.01
# Mc/sec: 12.27
//
[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