Alignments for a candidate for trpB in Clostridium kluyveri DSM 555

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpB in Clostridium kluyveri DSM 555

Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_012101666.1 CKL_RS06295 tryptophan synthase subunit beta

Query= uniprot:P50383
         (425 letters)



>NCBI__GCF_000016505.1:WP_012101666.1
          Length = 396

 Score =  137 bits (346), Expect = 4e-37
 Identities = 114/357 (31%), Positives = 174/357 (48%), Gaps = 32/357 (8%)

Query: 73  GRPTPLFRAKRLEEYLKTPARIYFKYEGATPTGSHKINTAIPQAYFAKEEGIEHVVTETG 132
           GRPTPL+ A+ L + L   A+IY K E    TG+HKIN  + Q   AK  G + V+ ETG
Sbjct: 56  GRPTPLYYAENLTKNLGG-AKIYLKREDLNHTGAHKINNVLGQILLAKRMGKKKVIAETG 114

Query: 133 AGQWGTAVALAASMYNMKSTIFMVKVSYEQKPMRRSIMQLYGANVYASPTNLTEYGRKIL 192
           AGQ G AVA  A+M+ M+  I+M +    ++ +    M++ GA V +      E G K L
Sbjct: 115 AGQHGVAVATGAAMFQMECVIYMGEEDCRRQSLNVLRMKILGAKVVS-----VESGTKTL 169

Query: 193 ETNPQHPGSLGIAMSEAIEYALKN--EFRYLVGSVL------DVVLLHQSVIGQETITQ- 243
           +           A++EA+   ++N  +  Y++GSV+       +V   Q +IG ET  Q 
Sbjct: 170 KD----------AVNEALRKWVENIEDTFYVMGSVVGPHPYPTMVRDFQRIIGDETKEQI 219

Query: 244 LDLLGEDADILIGCVGGGSNFGGFTYPFIGNKKGKRYIAVSSAEIPKFSKGEYKYDFPDS 303
           L   G+  + +I CVGGGSN  G  YPF+ +K  K  I V +A +   +          S
Sbjct: 220 LKKEGKLPNYIIACVGGGSNSMGIFYPFVEDKSVK-LIGVEAAGLGVDTDKHAASMAKGS 278

Query: 304 AGLLPLVKMITLGKD---YVPPPIYAGGLRYHGVAPTLSLLTKEGIVEWREYNEREIFEA 360
            G+L  +    +  D    +P    + GL Y GV P  + L      E+    ++E  +A
Sbjct: 279 VGVLHGMMTYLIQDDEGQILPVYSVSAGLDYPGVGPEHAYLKDTKRAEYTYVTDQEALDA 338

Query: 361 AKIFIENQGIVPAPESAHAIRAVVDEAIEARKNNERKVIVFNLSGHGLLDLSNYESM 417
                  +GI+PA ES+HA+   +  A E  K    +++V N+SG G  D+     +
Sbjct: 339 FGYLSRCEGIIPALESSHALAYTMKLAPELSK---EEIVVVNISGRGDKDVDTISEL 392


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: 395
Number of extensions: 18
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: 396
Length adjustment: 31
Effective length of query: 394
Effective length of database: 365
Effective search space:   143810
Effective search space used:   143810
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_012101666.1 CKL_RS06295 (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.16661.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.9e-204  663.6   0.7   5.6e-204  663.4   0.7    1.0  1  lcl|NCBI__GCF_000016505.1:WP_012101666.1  CKL_RS06295 tryptophan synthase 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016505.1:WP_012101666.1  CKL_RS06295 tryptophan synthase subunit beta
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  663.4   0.7  5.6e-204  5.6e-204       1     383 [.       9     391 ..       9     393 .. 1.00

  Alignments for each domain:
  == domain 1  score: 663.4 bits;  conditional E-value: 5.6e-204
                                 TIGR00263   1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiy 69 
                                               g+fg+fGGqyvpe++++al ele+ ++kak+d++f +e++++l+ey+grptpl++a+nl+k+lggakiy
  lcl|NCBI__GCF_000016505.1:WP_012101666.1   9 GRFGRFGGQYVPETVMTALMELEESFNKAKEDSKFIDEYMYYLQEYSGRPTPLYYAENLTKNLGGAKIY 77 
                                               78******************************************************************* PP

                                 TIGR00263  70 lkredllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqk 138
                                               lkredl+htGahkinn+lgq+llakr+Gkk++iaetGaGqhGva at aa++++ec++ymG+ed  rq+
  lcl|NCBI__GCF_000016505.1:WP_012101666.1  78 LKREDLNHTGAHKINNVLGQILLAKRMGKKKVIAETGAGQHGVAVATGAAMFQMECVIYMGEEDCRRQS 146
                                               ********************************************************************* PP

                                 TIGR00263 139 lnvfrmellgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeev 207
                                               lnv rm++lgakvv+v+sG+ktlkdavnealr+Wv ++edt+yv+Gs+vGphP+P++vr+fq++ig+e+
  lcl|NCBI__GCF_000016505.1:WP_012101666.1 147 LNVLRMKILGAKVVSVESGTKTLKDAVNEALRKWVENIEDTFYVMGSVVGPHPYPTMVRDFQRIIGDET 215
                                               ********************************************************************* PP

                                 TIGR00263 208 keqilekegrlPdaviacvGGGsnaiGifaafiedeeveligveagGkGidtekhaatlskGkeGvlhG 276
                                               keqil+keg+lP+++iacvGGGsn++Gif++f+ed++v+ligvea+G+G+dt+khaa+++kG++GvlhG
  lcl|NCBI__GCF_000016505.1:WP_012101666.1 216 KEQILKKEGKLPNYIIACVGGGSNSMGIFYPFVEDKSVKLIGVEAAGLGVDTDKHAASMAKGSVGVLHG 284
                                               ********************************************************************* PP

                                 TIGR00263 277 aktkllqdedGqieeahsvsaGldypgvgPehaalaetgraeyeaitdeealealkllskeeGiipale 345
                                               ++t+l+qd++Gqi +++svsaGldypgvgPeha+l++t+raey+ +td+eal+a+ +ls++eGiipale
  lcl|NCBI__GCF_000016505.1:WP_012101666.1 285 MMTYLIQDDEGQILPVYSVSAGLDYPGVGPEHAYLKDTKRAEYTYVTDQEALDAFGYLSRCEGIIPALE 353
                                               ********************************************************************* PP

                                 TIGR00263 346 sshalaaleklapklkkdeivvvnlsGrGdkdletvak 383
                                               sshala+ +klap+l+k+eivvvn+sGrGdkd++t+ +
  lcl|NCBI__GCF_000016505.1:WP_012101666.1 354 SSHALAYTMKLAPELSKEEIVVVNISGRGDKDVDTISE 391
                                               ***********************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (396 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: 9.72
//
[ok]

This GapMind analysis is from Apr 10 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