Alignments for a candidate for trpB in Thiomicrorhabdus arctica DSM 13458

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpB in Thiomicrorhabdus arctica DSM 13458

Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_019555908.1 F612_RS0101160 tryptophan synthase subunit beta

Query= uniprot:P50383
         (425 letters)



>NCBI__GCF_000381085.1:WP_019555908.1
          Length = 401

 Score =  131 bits (330), Expect = 3e-35
 Identities = 118/375 (31%), Positives = 172/375 (45%), Gaps = 54/375 (14%)

Query: 61  IPEEVRDRYLSIGRPTPLFRAKRLEEYLKTPARIYFKYEGATPTGSHKINTAIPQAYFAK 120
           + E   D    +GRPTPL+ AKR  E L   A+IY K E    TG+HK+N AI QA  AK
Sbjct: 48  LKELAEDLQNYVGRPTPLYYAKRWSESLGG-AKIYLKREDLNHTGAHKVNNAIGQALLAK 106

Query: 121 EEGIEHVVTETGAGQWGTAVALAASMYNMKSTIFMVKVSYEQKPMRRSIMQLYGANVYAS 180
             G   ++ ETGAGQ G A A  A+   ++  ++M      ++      M++ GA V A 
Sbjct: 107 RLGKTRIIAETGAGQHGVASATVAARLGLECVVYMGADDIVRQAPNVMRMKMLGATVIA- 165

Query: 181 PTNLTEYGRKILETNPQHPGSLGIAMSEAIEYALKN--EFRYLVGSVLD------VVLLH 232
                E G + L+           A++EA+   + N  +  Y++G+V        +V   
Sbjct: 166 ----VESGSRTLKD----------ALNEAMRDWVTNVDDTFYIIGTVAGPHPYPAMVRDF 211

Query: 233 QSVIGQETITQ-LDLLGEDADILIGCVGGGSNFGGFTYPFIGNKKGK------------- 278
           Q++IG+ET  Q L   G+  D+LI CVGGGSN  G  Y F+G+   K             
Sbjct: 212 QAIIGRETKQQSLTQEGKLPDVLIACVGGGSNAIGLFYEFLGDDSVKMVGVEPGGLGLET 271

Query: 279 -RYIAVSSAEIPKFSKGEYKYDFPDSAGLLPLVKMITLGKDYVPPPIYAGGLRYHGVAPT 337
            ++ A      P    G   Y   D  G +       LG   +     + GL Y GV P 
Sbjct: 272 GKHAAPLCKGSPGVLHGNRTYLMQDENGQI-------LGTHSI-----SAGLDYPGVGPE 319

Query: 338 LSLLTKEGIVEWREYNEREIFEAAKIFIENQGIVPAPESAHAIRAVVDEAIEARKNNERK 397
            + L     VE+   ++ E  +  +   + +GI+PA ES+HAI      A    K+   +
Sbjct: 320 HAWLKDIKRVEYVSIDDEEALQGFRDLTKYEGIIPALESSHAIAYATKLAPTLSKD---Q 376

Query: 398 VIVFNLSGHGLLDLS 412
           VIV NLSG G  D++
Sbjct: 377 VIVVNLSGRGDKDMN 391


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: 417
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: 401
Length adjustment: 31
Effective length of query: 394
Effective length of database: 370
Effective search space:   145780
Effective search space used:   145780
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_019555908.1 F612_RS0101160 (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.26209.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.8e-199  646.9   0.1   6.6e-199  646.7   0.1    1.0  1  lcl|NCBI__GCF_000381085.1:WP_019555908.1  F612_RS0101160 tryptophan syntha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000381085.1:WP_019555908.1  F612_RS0101160 tryptophan synthase subunit beta
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  646.7   0.1  6.6e-199  6.6e-199       1     383 [.      13     395 ..      13     397 .. 1.00

  Alignments for each domain:
  == domain 1  score: 646.7 bits;  conditional E-value: 6.6e-199
                                 TIGR00263   1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiy 69 
                                               g+fg +GG++ pe+l++ale+l ++y ++k+d++f kel e l++y+grptpl++ak+ s++lggakiy
  lcl|NCBI__GCF_000381085.1:WP_019555908.1  13 GHFGPYGGTFAPETLMAALEQLSQEYASVKNDPDFLKELAEDLQNYVGRPTPLYYAKRWSESLGGAKIY 81 
                                               68******************************************************************* PP

                                 TIGR00263  70 lkredllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqk 138
                                               lkredl+htGahk+nna+gqallakrlGk+riiaetGaGqhGva+at+aa+lglec+vymGa+d+ rq+
  lcl|NCBI__GCF_000381085.1:WP_019555908.1  82 LKREDLNHTGAHKVNNAIGQALLAKRLGKTRIIAETGAGQHGVASATVAARLGLECVVYMGADDIVRQA 150
                                               ********************************************************************* PP

                                 TIGR00263 139 lnvfrmellgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeev 207
                                               +nv+rm++lga+v++v+sGs+tlkda+nea+rdWvt+v+dt+y++G+++GphP+P++vr+fq++ig+e+
  lcl|NCBI__GCF_000381085.1:WP_019555908.1 151 PNVMRMKMLGATVIAVESGSRTLKDALNEAMRDWVTNVDDTFYIIGTVAGPHPYPAMVRDFQAIIGRET 219
                                               ********************************************************************* PP

                                 TIGR00263 208 keqilekegrlPdaviacvGGGsnaiGifaafiedeeveligveagGkGidtekhaatlskGkeGvlhG 276
                                               k+q l +eg+lPd++iacvGGGsnaiG+f++f+ d++v+++gve+gG+G++t khaa l kG++GvlhG
  lcl|NCBI__GCF_000381085.1:WP_019555908.1 220 KQQSLTQEGKLPDVLIACVGGGSNAIGLFYEFLGDDSVKMVGVEPGGLGLETGKHAAPLCKGSPGVLHG 288
                                               ********************************************************************* PP

                                 TIGR00263 277 aktkllqdedGqieeahsvsaGldypgvgPehaalaetgraeyeaitdeealealkllskeeGiipale 345
                                               ++t+l+qde+Gqi  +hs+saGldypgvgPeha+l++++r+ey++i+deeal++++ l+k eGiipale
  lcl|NCBI__GCF_000381085.1:WP_019555908.1 289 NRTYLMQDENGQILGTHSISAGLDYPGVGPEHAWLKDIKRVEYVSIDDEEALQGFRDLTKYEGIIPALE 357
                                               ********************************************************************* PP

                                 TIGR00263 346 sshalaaleklapklkkdeivvvnlsGrGdkdletvak 383
                                               ssha+a+++klap+l+kd+++vvnlsGrGdkd++t+a+
  lcl|NCBI__GCF_000381085.1:WP_019555908.1 358 SSHAIAYATKLAPTLSKDQVIVVNLSGRGDKDMNTIAQ 395
                                               ************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (401 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: 00:00:00.02
# Mc/sec: 6.15
//
[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