Alignments for a candidate for trpB in Dechlorosoma suillum PS

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpB in Dechlorosoma suillum PS

Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate Dsui_3192 Dsui_3192 tryptophan synthase, beta subunit

Query= uniprot:P50383
         (425 letters)



>FitnessBrowser__PS:Dsui_3192
          Length = 398

 Score =  132 bits (333), Expect = 1e-35
 Identities = 111/361 (30%), Positives = 165/361 (45%), Gaps = 50/361 (13%)

Query: 72  IGRPTPLFRAKRLEEYLKTPARIYFKYEGATPTGSHKINTAIPQAYFAKEEGIEHVVTET 131
           +GRP+P++ AKR  E L   A+IY K E    TG+HK+N  I QA  AK  G   V+ ET
Sbjct: 56  VGRPSPIYHAKRWSELLGG-AQIYLKREDLNHTGAHKVNNCIGQALLAKRMGKPRVIAET 114

Query: 132 GAGQWGTAVALAASMYNMKSTIFMVKVSYEQKPMRRSIMQLYGANVYASPTNLTEYGRKI 191
           GAGQ G A A  A+ Y  +  ++M     +++      M+L GA V        E G K 
Sbjct: 115 GAGQHGVATATVAARYGFECVVYMGSEDVKRQAANVYRMKLLGATVVP-----VESGSKT 169

Query: 192 LETNPQHPGSLGIAMSEAIEYALKNEFRYLVGSVLD------VVLLHQSVIGQETITQL- 244
           L+       +L  AM + +   ++N F Y++G+V        +V   Q+VIG+E + Q+ 
Sbjct: 170 LK------DALNEAMRDWVT-NIENTF-YIIGTVAGPHPYPMMVRDFQTVIGKEALVQMP 221

Query: 245 DLLGEDADILIGCVGGGSNFGGFTYPFIGNKKGK--------------RYIAVSSAEIPK 290
           ++ G   D +I  VGGGSN  G  +P+I ++  K              R+ A      P 
Sbjct: 222 EMAGRQPDAVIAAVGGGSNAMGIFHPYIPHESVKLIGVEAAGEGMDTNRHSASLQKGRPG 281

Query: 291 FSKGEYKYDFPDSAGLLPLVKMITLGKDYVPPPIYAGGLRYHGVAPTLSLLTKEGIVEWR 350
              G   Y   D  G +     I+ G D            Y GV P  + L   G  E+ 
Sbjct: 282 VLHGNRTYLLQDENGQITETHSISAGLD------------YPGVGPEHAWLKDSGRAEYV 329

Query: 351 EYNEREIFEAAKIFIENQGIVPAPESAHAIRAVVDEAIEARKNNERKVIVFNLSGHGLLD 410
             ++ E  +A       +GI+PA ES+HA+      A    K+   K+++ NLSG G  D
Sbjct: 330 GISDSEALQAFHDLCRFEGIIPALESSHALAYAAKLAPSLAKD---KILLVNLSGRGDKD 386

Query: 411 L 411
           +
Sbjct: 387 M 387


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: 376
Number of extensions: 15
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: 398
Length adjustment: 31
Effective length of query: 394
Effective length of database: 367
Effective search space:   144598
Effective search space used:   144598
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 Dsui_3192 Dsui_3192 (tryptophan synthase, beta subunit)
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.16064.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.4e-196  639.0   0.1   1.6e-196  638.8   0.1    1.0  1  lcl|FitnessBrowser__PS:Dsui_3192  Dsui_3192 tryptophan synthase, b


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_3192  Dsui_3192 tryptophan synthase, beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  638.8   0.1  1.6e-196  1.6e-196       1     384 [.      10     393 ..      10     394 .. 1.00

  Alignments for each domain:
  == domain 1  score: 638.8 bits;  conditional E-value: 1.6e-196
                         TIGR00263   1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiylkredllh 77 
                                       g+fg +GG +v+e+l++aleel++ay +a +d++f++e+++ lk+y+grp+p+++ak+ s+ lgga+iylkredl+h
  lcl|FitnessBrowser__PS:Dsui_3192  10 GHFGPYGGIFVSETLIAALEELKAAYAHACTDPAFQAEFDYELKHYVGRPSPIYHAKRWSELLGGAQIYLKREDLNH 86 
                                       68*************************************************************************** PP

                         TIGR00263  78 tGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqklnvfrmellgakvvpv 154
                                       tGahk+nn +gqallakr+Gk r+iaetGaGqhGvatat+aa+ g+ec+vymG+edv+rq+ nv+rm+llga+vvpv
  lcl|FitnessBrowser__PS:Dsui_3192  87 TGAHKVNNCIGQALLAKRMGKPRVIAETGAGQHGVATATVAARYGFECVVYMGSEDVKRQAANVYRMKLLGATVVPV 163
                                       ***************************************************************************** PP

                         TIGR00263 155 tsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeevkeqilekegrlPdaviacvGGGsn 231
                                       +sGsktlkda+nea+rdWvt++e+t+y++G+++GphP+P +vr+fq+vig+e+  q+ e++gr Pdavia+vGGGsn
  lcl|FitnessBrowser__PS:Dsui_3192 164 ESGSKTLKDALNEAMRDWVTNIENTFYIIGTVAGPHPYPMMVRDFQTVIGKEALVQMPEMAGRQPDAVIAAVGGGSN 240
                                       ***************************************************************************** PP

                         TIGR00263 232 aiGifaafiedeeveligveagGkGidtekhaatlskGkeGvlhGaktkllqdedGqieeahsvsaGldypgvgPeh 308
                                       a+Gif+++i +e+v+ligvea+G+G+dt++h+a+l+kG++GvlhG++t+llqde+Gqi+e+hs+saGldypgvgPeh
  lcl|FitnessBrowser__PS:Dsui_3192 241 AMGIFHPYIPHESVKLIGVEAAGEGMDTNRHSASLQKGRPGVLHGNRTYLLQDENGQITETHSISAGLDYPGVGPEH 317
                                       ***************************************************************************** PP

                         TIGR00263 309 aalaetgraeyeaitdeealealkllskeeGiipalesshalaaleklapklkkdeivvvnlsGrGdkdletvaka 384
                                       a+l+++graey+ i+d+eal+a++ l++ eGiipalesshala++ klap+l+kd+i++vnlsGrGdkd++tva++
  lcl|FitnessBrowser__PS:Dsui_3192 318 AWLKDSGRAEYVGISDSEALQAFHDLCRFEGIIPALESSHALAYAAKLAPSLAKDKILLVNLSGRGDKDMHTVAEK 393
                                       *************************************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (398 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 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 9.10
//
[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