Alignments for a candidate for trpB in Bacteroides thetaiotaomicron VPI-5482

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpB in Bacteroides thetaiotaomicron VPI-5482

Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate 350061 BT0533 tryptophan synthase beta chain (NCBI ptt file)

Query= uniprot:P50383
         (425 letters)



>FitnessBrowser__Btheta:350061
          Length = 394

 Score =  127 bits (320), Expect = 5e-34
 Identities = 116/371 (31%), Positives = 173/371 (46%), Gaps = 54/371 (14%)

Query: 72  IGRPTPLFRAKRLEEYLKTPARIYFKYEGATPTGSHKINTAIPQAYFAKEEGIEHVVTET 131
           +GRP+PL+ A+RL E  K   ++Y K E    TG+HKIN  I Q   A+  G + ++ ET
Sbjct: 56  VGRPSPLYLARRLSE--KYGCKMYLKREDLNHTGAHKINNTIGQILLARRMGKKRIIAET 113

Query: 132 GAGQWGTAVALAASMYNMKSTIFMVKVSYEQKPMRRSIMQLYGANVY-ASPTNLTEYGRK 190
           GAGQ G A A   ++ +M+  ++M K   E++ +    M++ GA V   +  N+T     
Sbjct: 114 GAGQHGVATATVCALMDMECIVYMGKTDVERQHINVEKMKMLGATVIPVTSGNMT----- 168

Query: 191 ILETNPQHPGSLGIAMSEAIE--YALKNEFRYLVGSVL------DVVLLHQSVIGQETIT 242
                      L  A +EAI        +  Y++GS +      D+V   QSVI +E   
Sbjct: 169 -----------LKDATNEAIRDWCCHPADTYYIIGSTVGPHPYPDMVARLQSVISEEIKK 217

Query: 243 QL-DLLGED-ADILIGCVGGGSNFGGFTYPFIGNKKGKRYIAVSSAEIPKFSKGEYKYDF 300
           QL +  G D  D LI CVGGGSN  G  Y +I +  G+  I ++ A       G    + 
Sbjct: 218 QLMEKEGRDHPDYLIACVGGGSNAAGTIYHYIND--GRVGIILAEA-------GGKGIET 268

Query: 301 PDSAGLLPLVKM--ITLGKDYV---------PPPIYAGGLRYHGVAPTLSLLTKEGIVEW 349
             +A  + L KM  I   + YV          P   + GL Y G+ P  + L  +     
Sbjct: 269 GMTAATIQLGKMGIIHGARTYVIQNEDGQIEEPYSISAGLDYPGIGPIHANLAAQRRATV 328

Query: 350 REYNEREIFEAAKIFIENQGIVPAPESAHAIRAVVDEAIEARKNNERKVIVFNLSGHGLL 409
              N+ E  EAA    + +GI+PA ESAHA+      A++  K     V+V  +SG G  
Sbjct: 329 LAVNDDEAIEAAYELTKLEGIIPALESAHAL-----GALKKLKFKPEDVVVLTVSGRGDK 383

Query: 410 DLSNYESMMKR 420
           D+  Y S  ++
Sbjct: 384 DIETYLSFNEK 394


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: 364
Number of extensions: 16
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: 394
Length adjustment: 31
Effective length of query: 394
Effective length of database: 363
Effective search space:   143022
Effective search space used:   143022
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 350061 BT0533 (tryptophan synthase beta chain (NCBI ptt file))
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.5484.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   1.8e-178  579.4   0.5     2e-178  579.3   0.5    1.0  1  lcl|FitnessBrowser__Btheta:350061  BT0533 tryptophan synthase beta 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:350061  BT0533 tryptophan synthase beta chain (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  579.3   0.5    2e-178    2e-178       1     380 [.      10     387 ..      10     392 .. 0.98

  Alignments for each domain:
  == domain 1  score: 579.3 bits;  conditional E-value: 2e-178
                          TIGR00263   1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiylkredll 76 
                                        g++gefGG+yvpe+l++ +eel+++y  + + e+fkke+++ll++y+grp+pl+ a++ls+k+g +k+ylkredl+
  lcl|FitnessBrowser__Btheta:350061  10 GYYGEFGGAYVPEILHKCVEELKNTYLGVLESEDFKKEFDQLLRDYVGRPSPLYLARRLSEKYG-CKMYLKREDLN 84 
                                        79*************************************************************8.*********** PP

                          TIGR00263  77 htGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqklnvfrmellgakvv 152
                                        htGahkinn++gq+lla+r+GkkriiaetGaGqhGvatat++al+++ec vymG++dverq++nv +m++lga+v+
  lcl|FitnessBrowser__Btheta:350061  85 HTGAHKINNTIGQILLARRMGKKRIIAETGAGQHGVATATVCALMDMECIVYMGKTDVERQHINVEKMKMLGATVI 160
                                        **************************************************************************** PP

                          TIGR00263 153 pvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeevkeqilekegr.lPdaviacvG 227
                                        pvtsG++tlkda+nea+rdW  + +dt+y++Gs+vGphP+P++v ++qsvi+ee+k+q++ekegr  Pd++iacvG
  lcl|FitnessBrowser__Btheta:350061 161 PVTSGNMTLKDATNEAIRDWCCHPADTYYIIGSTVGPHPYPDMVARLQSVISEEIKKQLMEKEGRdHPDYLIACVG 236
                                        ***************************************************************6637********* PP

                          TIGR00263 228 GGsnaiGifaafiedeeveligveagGkGidtekhaatlskGkeGvlhGaktkllqdedGqieeahsvsaGldypg 303
                                        GGsna G+ +++i+d +v +i  eagGkGi+t ++aat++ Gk G++hGa+t+++q+edGqiee +s+saGldypg
  lcl|FitnessBrowser__Btheta:350061 237 GGSNAAGTIYHYINDGRVGIILAEAGGKGIETGMTAATIQLGKMGIIHGARTYVIQNEDGQIEEPYSISAGLDYPG 312
                                        **************************************************************************** PP

                          TIGR00263 304 vgPehaalaetgraeyeaitdeealealkllskeeGiipalesshalaaleklapklkkdeivvvnlsGrGdkdle 379
                                        +gP ha+la + ra+  a++d+ea+ea   l+k eGiipales+hal al+kl+   k +++vv+++sGrGdkd+e
  lcl|FitnessBrowser__Btheta:350061 313 IGPIHANLAAQRRATVLAVNDDEAIEAAYELTKLEGIIPALESAHALGALKKLKF--KPEDVVVLTVSGRGDKDIE 386
                                        ****************************************************987..7899**************9 PP

                          TIGR00263 380 t 380
                                        t
  lcl|FitnessBrowser__Btheta:350061 387 T 387
                                        8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (394 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: 8.57
//
[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