Alignments for a candidate for trpB in Thiomicrospira cyclica ALM1

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpB in Thiomicrospira cyclica ALM1

Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_013835176.1 THICY_RS03185 tryptophan synthase subunit beta

Query= uniprot:P50383
         (425 letters)



>NCBI__GCF_000214825.1:WP_013835176.1
          Length = 407

 Score =  127 bits (318), Expect = 8e-34
 Identities = 121/409 (29%), Positives = 179/409 (43%), Gaps = 59/409 (14%)

Query: 29  PQGAYFSRIDLLRSILPKEVLRQQFTIERYIKI--PEEVRDRYLSIGRPTPLFRAKRLEE 86
           P G  F+   L+    P E LR Q+   +   +   E + D    IGRPTPL+ AKR  E
Sbjct: 23  PYGGIFAPETLMA---PLEALRDQYAAVKDDPVFRAELLNDYQNYIGRPTPLYHAKRWSE 79

Query: 87  YLKTPARIYFKYEGATPTGSHKINTAIPQAYFAKEEGIEHVVTETGAGQWGTAVALAASM 146
           +L   A+IY K E    TG+HKIN  I QA  AK  G   ++ ETGAGQ G A A  A+ 
Sbjct: 80  HLGG-AQIYLKREDLNHTGAHKINNTIGQALLAKRLGKTRIIAETGAGQHGVASATVAAR 138

Query: 147 YNMKSTIFMVKVSYEQKPMRRSIMQLYGANVYASPTNLTEYGRKILETNPQHPGSLGIAM 206
             ++  ++M      ++    + M++ GA V        E G + L+           A+
Sbjct: 139 LGLECVVYMGADDVVRQAPNVARMKMLGATVVP-----VESGTRTLKD----------AL 183

Query: 207 SEAIEYALKN--EFRYLVGSVLD------VVLLHQSVIGQETITQ-LDLLGEDADILIGC 257
           +EA+   + N  +  Y++G+V        +V   Q++IGQE   Q LD  G   DI++ C
Sbjct: 184 NEAMRDWVTNVDDTFYIIGTVAGPHPYPMMVRDFQAIIGQEARQQMLDQEGVLPDIVMAC 243

Query: 258 VGGGSNFGGFTYPFIGNKKGK--------------RYIAVSSAEIPKFSKGEYKYDFPDS 303
           VGGGSN  G  + F+ ++  +              R+ A      P    G   Y   D 
Sbjct: 244 VGGGSNAMGLFHAFLPDESVRIIGVEAGGDGLETGRHAAPLCKGTPGVLHGNRTYLMQDE 303

Query: 304 AGLLPLVKMITLGKDYVPPPIYAGGLRYHGVAPTLSLLTKEGIVEWREYNEREIFEAAKI 363
           AG +     I+ G D            Y GV P L+ L   G  E+    + E     + 
Sbjct: 304 AGQIMGTHSISAGLD------------YPGVGPELAWLKDIGRAEFFAVTDDEAMAGWRD 351

Query: 364 FIENQGIVPAPESAHAIRAVVDEAIEARKNNERKVIVFNLSGHGLLDLS 412
               +GI+ A E++HA+   +  A    K      I+ NLSG G  D++
Sbjct: 352 VTRMEGIISALETSHALAYAIKLAPTLPKTQR---IIINLSGRGDKDMN 397


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: 378
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: 407
Length adjustment: 31
Effective length of query: 394
Effective length of database: 376
Effective search space:   148144
Effective search space used:   148144
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_013835176.1 THICY_RS03185 (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.1934770.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.2e-191  620.7   0.0   5.9e-191  620.5   0.0    1.0  1  NCBI__GCF_000214825.1:WP_013835176.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000214825.1:WP_013835176.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  620.5   0.0  5.9e-191  5.9e-191       1     383 [.      19     401 ..      19     403 .. 1.00

  Alignments for each domain:
  == domain 1  score: 620.5 bits;  conditional E-value: 5.9e-191
                             TIGR00263   1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiylkre 73 
                                           g+fg +GG + pe+l++ le l+++y  +k+d+ f++el +  ++y grptpl++ak+ s++lgga+iylkre
  NCBI__GCF_000214825.1:WP_013835176.1  19 GHFGPYGGIFAPETLMAPLEALRDQYAAVKDDPVFRAELLNDYQNYIGRPTPLYHAKRWSEHLGGAQIYLKRE 91 
                                           68*********************************************************************** PP

                             TIGR00263  74 dllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqklnvfrmel 146
                                           dl+htGahkinn++gqallakrlGk+riiaetGaGqhGva+at+aa+lglec+vymGa+dv rq++nv rm++
  NCBI__GCF_000214825.1:WP_013835176.1  92 DLNHTGAHKINNTIGQALLAKRLGKTRIIAETGAGQHGVASATVAARLGLECVVYMGADDVVRQAPNVARMKM 164
                                           ************************************************************************* PP

                             TIGR00263 147 lgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeevkeqilekegrlP 219
                                           lga+vvpv+sG++tlkda+nea+rdWvt+v+dt+y++G+++GphP+P +vr+fq++ig+e+++q+l++eg lP
  NCBI__GCF_000214825.1:WP_013835176.1 165 LGATVVPVESGTRTLKDALNEAMRDWVTNVDDTFYIIGTVAGPHPYPMMVRDFQAIIGQEARQQMLDQEGVLP 237
                                           ************************************************************************* PP

                             TIGR00263 220 daviacvGGGsnaiGifaafiedeeveligveagGkGidtekhaatlskGkeGvlhGaktkllqdedGqieea 292
                                           d+v+acvGGGsna+G+f+af+ de+v++igveagG G++t +haa l kG++GvlhG++t+l+qde Gqi  +
  NCBI__GCF_000214825.1:WP_013835176.1 238 DIVMACVGGGSNAMGLFHAFLPDESVRIIGVEAGGDGLETGRHAAPLCKGTPGVLHGNRTYLMQDEAGQIMGT 310
                                           ************************************************************************* PP

                             TIGR00263 293 hsvsaGldypgvgPehaalaetgraeyeaitdeealealkllskeeGiipalesshalaaleklapklkkdei 365
                                           hs+saGldypgvgPe+a+l+++grae+ a+td+ea+++++ +++ eGii+ale+shala+++klap+l+k + 
  NCBI__GCF_000214825.1:WP_013835176.1 311 HSISAGLDYPGVGPELAWLKDIGRAEFFAVTDDEAMAGWRDVTRMEGIISALETSHALAYAIKLAPTLPKTQR 383
                                           ************************************************************************* PP

                             TIGR00263 366 vvvnlsGrGdkdletvak 383
                                           +++nlsGrGdkd++t+ak
  NCBI__GCF_000214825.1:WP_013835176.1 384 IIINLSGRGDKDMNTIAK 401
                                           ****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (407 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: 12.94
//
[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:

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