GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpB in Sulfurihydrogenibium azorense Az-Fu1

Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_012674347.1 SULAZ_RS04145 tryptophan synthase subunit beta

Query= uniprot:P50383
         (425 letters)



>NCBI__GCF_000021545.1:WP_012674347.1
          Length = 415

 Score =  143 bits (360), Expect = 1e-38
 Identities = 112/359 (31%), Positives = 181/359 (50%), Gaps = 34/359 (9%)

Query: 73  GRPTPLFRAKRLEEYLKTPARIYFKYEGATPTGSHKINTAIPQAYFAKEEGIEHVVTETG 132
           GRPTPL+ A RL + +   A+IY K E    TG+HKIN  + Q    K  G + ++ ETG
Sbjct: 58  GRPTPLYFASRLTQVVGG-AKIYLKREDLLHTGAHKINNTLGQVLLTKRLGKKRIIAETG 116

Query: 133 AGQWGTAVALAASMYNMKSTIFMVKVSYEQKPMRRSIMQLYGANVYASPTNLTEYGRKIL 192
           AGQ G + A AA+++ ++ TI+M +   E++ +    M+L GA V      + + G + L
Sbjct: 117 AGQHGVSTATAAALFGLECTIYMGEEDAERQALNVFRMKLLGAKV-----EIVKSGSRTL 171

Query: 193 ETNPQHPGSLGIAMSEAIEYALKN--EFRYLVGSVLD------VVLLHQSVIGQETITQ- 243
           +           A++EA+   + N     Y++GS L       +V   QSVIG+E   Q 
Sbjct: 172 KD----------AVNEALRDWVTNVRTTHYIIGSALGPHPFPMIVRDFQSVIGEEVKNQI 221

Query: 244 LDLLGEDADILIGCVGGGSNFGGFTYPFIGNKKGKRYIAVSSAEIPKFSKGEYKYDFPDS 303
           L++ G+  D+++ CVGGGSN  G  YPFI +++ K  + V +      +          S
Sbjct: 222 LEIEGKLPDVIVACVGGGSNAIGIFYPFIEDEEVK-LVGVEAGGYGLETGMHAASIVGGS 280

Query: 304 AGLLPLVKMITLGKDY---VPPPIYAGGLRYHGVAPTLSLLTKEGIVEWREYNEREIFEA 360
            G+L  +K   L   +         + GL Y GV P  + L + G   +    + E  E 
Sbjct: 281 VGVLHGMKSYFLQDQWGQIETTHSISAGLDYPGVGPEHAYLKESGRATYITATDEEALEG 340

Query: 361 AKIFIENQGIVPAPESAHAIRAVVDEAIEARKN-NERKVIVFNLSGHGLLDLSNYESMM 418
             +    +GI+PA ES+HA    V +A+E  KN ++ + +V NLSG G  D+ + ++++
Sbjct: 341 FLLLSRTEGIIPALESSHA----VIKAVEIAKNLDKHQSVVINLSGRGDKDVQSVKNLL 395


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: 450
Number of extensions: 28
Number of successful extensions: 5
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: 415
Length adjustment: 32
Effective length of query: 393
Effective length of database: 383
Effective search space:   150519
Effective search space used:   150519
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 WP_012674347.1 SULAZ_RS04145 (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.1230204.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.5e-197  640.4   0.3   6.3e-197  640.2   0.3    1.0  1  NCBI__GCF_000021545.1:WP_012674347.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000021545.1:WP_012674347.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  640.2   0.3  6.3e-197  6.3e-197       1     383 [.      11     393 ..      11     395 .. 0.99

  Alignments for each domain:
  == domain 1  score: 640.2 bits;  conditional E-value: 6.3e-197
                             TIGR00263   1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiylkre 73 
                                           g++g+fGG+y+pe+l++aleele++y k+k+d +fk++l ++l eyagrptpl+fa++l++ +ggakiylkre
  NCBI__GCF_000021545.1:WP_012674347.1  11 GYYGQFGGKYLPETLIPALEELEQQYLKIKNDGDFKRQLLYYLTEYAGRPTPLYFASRLTQVVGGAKIYLKRE 83 
                                           79*********************************************************************** PP

                             TIGR00263  74 dllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqklnvfrmel 146
                                           dllhtGahkinn+lgq+ll+krlGkkriiaetGaGqhGv+tataaal+glec++ymG+ed erq+lnvfrm+l
  NCBI__GCF_000021545.1:WP_012674347.1  84 DLLHTGAHKINNTLGQVLLTKRLGKKRIIAETGAGQHGVSTATAAALFGLECTIYMGEEDAERQALNVFRMKL 156
                                           ************************************************************************* PP

                             TIGR00263 147 lgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeevkeqilekegrlP 219
                                           lgakv  v+sGs+tlkdavnealrdWvt+v++thy++Gsa+GphPfP ivr+fqsvigeevk+qile eg+lP
  NCBI__GCF_000021545.1:WP_012674347.1 157 LGAKVEIVKSGSRTLKDAVNEALRDWVTNVRTTHYIIGSALGPHPFPMIVRDFQSVIGEEVKNQILEIEGKLP 229
                                           ************************************************************************* PP

                             TIGR00263 220 daviacvGGGsnaiGifaafiedeeveligveagGkGidtekhaatlskGkeGvlhGaktkllqdedGqieea 292
                                           d+++acvGGGsnaiGif++fiedeev+l+gveagG G++t +haa++  G++GvlhG+k+++lqd+ Gqie++
  NCBI__GCF_000021545.1:WP_012674347.1 230 DVIVACVGGGSNAIGIFYPFIEDEEVKLVGVEAGGYGLETGMHAASIVGGSVGVLHGMKSYFLQDQWGQIETT 302
                                           ************************************************************************* PP

                             TIGR00263 293 hsvsaGldypgvgPehaalaetgraeyeaitdeealealkllskeeGiipalesshalaaleklapklkkdei 365
                                           hs+saGldypgvgPeha+l+e+gra+y ++tdeeale++ lls++eGiipalessha+  ++++a++l+k++ 
  NCBI__GCF_000021545.1:WP_012674347.1 303 HSISAGLDYPGVGPEHAYLKESGRATYITATDEEALEGFLLLSRTEGIIPALESSHAVIKAVEIAKNLDKHQS 375
                                           ************************************************************************* PP

                             TIGR00263 366 vvvnlsGrGdkdletvak 383
                                           vv+nlsGrGdkd+++v++
  NCBI__GCF_000021545.1:WP_012674347.1 376 VVINLSGRGDKDVQSVKN 393
                                           **************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (415 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: 00:00:00.00
# Mc/sec: 27.68
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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:

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:

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:

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:

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