Alignments for a candidate for trpB in Acidovorax sp. GW101-3H11

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpB in Acidovorax sp. GW101-3H11

Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate Ac3H11_1534 Tryptophan synthase beta chain (EC 4.2.1.20)

Query= uniprot:P50383
         (425 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1534
          Length = 425

 Score =  123 bits (308), Expect = 1e-32
 Identities = 112/357 (31%), Positives = 165/357 (46%), Gaps = 36/357 (10%)

Query: 72  IGRPTPLFRAKRLEEYLKTPARIYFKYEGATPTGSHKINTAIPQAYFAKEEGIEHVVTET 131
           +GRP+P++ A R    L   A+IY K E    TG+HKIN  I QA  A+  G   V+ ET
Sbjct: 57  VGRPSPVYHAARTSRELGG-AQIYLKREDLNHTGAHKINNVIGQAMLARRMGKPRVIAET 115

Query: 132 GAGQWGTAVALAASMYNMKSTIFMVKVSYEQKPMRRSIMQLYGANVYASPTNLTEYGRKI 191
           GAGQ G A A   + Y ++  ++M     +++      M+L GA V        E G K 
Sbjct: 116 GAGQHGVATATICARYGLECVVYMGSEDVKRQSPNVFRMKLLGATVVP-----VESGSKT 170

Query: 192 LETNPQHPGSLGIAMSEAIEYALKNEFRYLVGSVLD------VVLLHQSVIGQETITQL- 244
           L+       +L  AM + +   + N F Y++G+V        +V   QSVIG+E+I Q+ 
Sbjct: 171 LK------DALNEAMRDWVA-NVDNTF-YIIGTVAGPHPYPMMVRDFQSVIGKESIEQMP 222

Query: 245 ------DLLGEDADILIGCVGGGSNFGGFTYPFIGNKKGKRYIAVSSAEIPKFSKGEYKY 298
                  +  E  D +I CVGGGSN  G  +P+I   K  R I V +A       G++  
Sbjct: 223 AMLAEQKIAAEQPDAVIACVGGGSNAMGIFHPYIPFAK-TRLIGVEAAG-EGLDSGKHSA 280

Query: 299 DFP-DSAGLLPLVKMITL---GKDYVPPPIYAGGLRYHGVAPTLSLLTKEGIVEWREYNE 354
                S+G+L   +   L             + GL Y GV P  + L + G  E+    +
Sbjct: 281 SLQRGSSGVLHGNRTFILQDANGQITETHSISAGLDYPGVGPEHAWLQEIGRAEYVGITD 340

Query: 355 REIFEAAKIFIENQGIVPAPESAHAIRAVVDEAIEARKNNERKVIVFNLSGHGLLDL 411
           +E   A       +GI+PA ES+HA    +  A   R +   + I+ NLSG G  D+
Sbjct: 341 QEALSAFHHLCRTEGIIPALESSHAFAYALKLAPTMRPD---QAILVNLSGRGDKDI 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: 369
Number of extensions: 19
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: 425
Length adjustment: 32
Effective length of query: 393
Effective length of database: 393
Effective search space:   154449
Effective search space used:   154449
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: 51 (24.3 bits)

Align candidate Ac3H11_1534 (Tryptophan synthase beta chain (EC 4.2.1.20))
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.27630.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   1.3e-190  619.4   0.1   1.5e-190  619.2   0.1    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1534  Tryptophan synthase beta chain (


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1534  Tryptophan synthase beta chain (EC 4.2.1.20)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  619.2   0.1  1.5e-190  1.5e-190       1     383 [.      11     399 ..      11     401 .. 0.97

  Alignments for each domain:
  == domain 1  score: 619.2 bits;  conditional E-value: 1.5e-190
                                        TIGR00263   1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskk 62 
                                                      g+fg +GG +v+e+l +a++el++ay ++++d++f++e+ + lk+++grp+p+++a++ s++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1534  11 GHFGPYGGSFVSETLTHAIQELRDAYARYQNDPDFVAEFAYELKHFVGRPSPVYHAARTSRE 72 
                                                      68************************************************************ PP

                                        TIGR00263  63 lggakiylkredllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallgle 124
                                                      lgga+iylkredl+htGahkinn++gqa+la+r+Gk r+iaetGaGqhGvatat++a+ gle
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1534  73 LGGAQIYLKREDLNHTGAHKINNVIGQAMLARRMGKPRVIAETGAGQHGVATATICARYGLE 134
                                                      ************************************************************** PP

                                        TIGR00263 125 cevymGaedverqklnvfrmellgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsa 186
                                                      c+vymG+edv+rq++nvfrm+llga+vvpv+sGsktlkda+nea+rdWv++v++t+y++G++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1534 135 CVVYMGSEDVKRQSPNVFRMKLLGATVVPVESGSKTLKDALNEAMRDWVANVDNTFYIIGTV 196
                                                      ************************************************************** PP

                                        TIGR00263 187 vGphPfPeivrefqsvigeevkeqi......lekegrlPdaviacvGGGsnaiGifaafied 242
                                                      +GphP+P +vr+fqsvig+e  eq+      ++ +++ PdaviacvGGGsna+Gif+++i  
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1534 197 AGPHPYPMMVRDFQSVIGKESIEQMpamlaeQKIAAEQPDAVIACVGGGSNAMGIFHPYIPF 258
                                                      *********************99974333223334889************************ PP

                                        TIGR00263 243 eeveligveagGkGidtekhaatlskGkeGvlhGaktkllqdedGqieeahsvsaGldypgv 304
                                                       + +ligvea+G+G+d+ kh+a+l++G++GvlhG++t +lqd +Gqi+e+hs+saGldypgv
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1534 259 AKTRLIGVEAAGEGLDSGKHSASLQRGSSGVLHGNRTFILQDANGQITETHSISAGLDYPGV 320
                                                      ************************************************************** PP

                                        TIGR00263 305 gPehaalaetgraeyeaitdeealealkllskeeGiipalesshalaaleklapklkkdeiv 366
                                                      gPeha+l+e+graey+ itd+eal+a+++l+++eGiipalessha a++ klap+++ d+ +
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1534 321 GPEHAWLQEIGRAEYVGITDQEALSAFHHLCRTEGIIPALESSHAFAYALKLAPTMRPDQAI 382
                                                      ************************************************************** PP

                                        TIGR00263 367 vvnlsGrGdkdletvak 383
                                                      +vnlsGrGdkd+ tva+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1534 383 LVNLSGRGDKDIGTVAD 399
                                                      **************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (425 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: 11.00
//
[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