Alignments for a candidate for trpB in Synechococcus elongatus PCC 7942

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpB in Synechococcus elongatus PCC 7942

Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate Synpcc7942_2143 Synpcc7942_2143 tryptophan synthase subunit beta

Query= uniprot:P50383
         (425 letters)



>FitnessBrowser__SynE:Synpcc7942_2143
          Length = 420

 Score =  129 bits (324), Expect = 2e-34
 Identities = 116/364 (31%), Positives = 162/364 (44%), Gaps = 51/364 (14%)

Query: 72  IGRPTPLFRAKRLEEYLKTP----ARIYFKYEGATPTGSHKINTAIPQAYFAKEEGIEHV 127
           +GRP PL+ A+RL EY + P      IY K E    TG+HKIN A+ QA  AK  G + +
Sbjct: 75  VGRPNPLYFAERLTEYYRRPDGQGPNIYLKREDLNHTGAHKINNALGQALMAKRMGKKRI 134

Query: 128 VTETGAGQWGTAVALAASMYNMKSTIFMVKVSYEQKPMRRSIMQLYGANVYASPTNLTEY 187
           + ETGAGQ G A A   + + ++  I+M     E++ +    M+L GA V          
Sbjct: 135 IAETGAGQHGVATATVCARFGLECVIYMGVHDMERQALNVFRMRLMGAEVRGVAAG---- 190

Query: 188 GRKILETNPQHPGSLGIAMSEAIEYALKN--EFRYLVGSVLD------VVLLHQSVIGQE 239
                       G+L  A SEAI   + N     Y++GSV        +V    S+IG+E
Sbjct: 191 -----------SGTLKDATSEAIRDWVTNVETTHYILGSVAGPHPYPMIVREFHSMIGRE 239

Query: 240 TITQLDLL-GEDADILIGCVGGGSNFGGFTYPFIGNKKGKRYIAVSSAEIPKFSKGEYKY 298
              Q   L G   DIL+ CVGGGSN  G    F+ N+   R I V +A      +G    
Sbjct: 240 VRQQAQTLWGGLPDILLACVGGGSNAMGLFNEFV-NEPSVRLIGVEAA-----GRG---V 290

Query: 299 DFPDSAGLLPLVKMITL-----------GKDYVPPPIYAGGLRYHGVAPTLSLLTKEGIV 347
           D P+ A  L   ++  L               +     + GL Y GV P  S L   G  
Sbjct: 291 DTPEHAATLTKGRVGVLHGAMSYLLQDDDGQVIEAHSISAGLDYPGVGPEHSYLMDAGRA 350

Query: 348 EWREYNEREIFEAAKIFIENQGIVPAPESAHAIRAVVDEAIEARKNNERKVIVFNLSGHG 407
           E+    + E  EA +     +GI+PA E+AHA  A +++       N    +V N SG G
Sbjct: 351 EYYSVTDDEALEAFQRISRLEGIIPALETAHAF-AHLEKLCPTLSGNPN--LVINCSGRG 407

Query: 408 LLDL 411
             D+
Sbjct: 408 DKDV 411


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: 409
Number of extensions: 22
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: 420
Length adjustment: 32
Effective length of query: 393
Effective length of database: 388
Effective search space:   152484
Effective search space used:   152484
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 Synpcc7942_2143 Synpcc7942_2143 (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.11196.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.6e-192  624.5   0.0   4.1e-192  624.3   0.0    1.0  1  lcl|FitnessBrowser__SynE:Synpcc7942_2143  Synpcc7942_2143 tryptophan synth


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SynE:Synpcc7942_2143  Synpcc7942_2143 tryptophan synthase subunit beta
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  624.3   0.0  4.1e-192  4.1e-192       1     384 [.      29     417 ..      29     418 .. 0.98

  Alignments for each domain:
  == domain 1  score: 624.3 bits;  conditional E-value: 4.1e-192
                                 TIGR00263   1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskkl.....g 64 
                                               g+fg+fGGqyvpe+l++al+ele+a+ ++++d+ef++e+e ll++y+grp pl+fa++l++ +     +
  lcl|FitnessBrowser__SynE:Synpcc7942_2143  29 GRFGRFGGQYVPETLMPALAELEQAFARYSRDPEFQAEFEGLLRDYVGRPNPLYFAERLTEYYrrpdgQ 97 
                                               78**********************************************************976333224 PP

                                 TIGR00263  65 gakiylkredllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaed 133
                                               g +iylkredl+htGahkinnalgqal+akr+GkkriiaetGaGqhGvatat++a++glec++ymG +d
  lcl|FitnessBrowser__SynE:Synpcc7942_2143  98 GPNIYLKREDLNHTGAHKINNALGQALMAKRMGKKRIIAETGAGQHGVATATVCARFGLECVIYMGVHD 166
                                               679****************************************************************** PP

                                 TIGR00263 134 verqklnvfrmellgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsv 202
                                               +erq+lnvfrm+l+ga+v  v  Gs tlkda++ea+rdWvt+ve+thy+lGs++GphP+P ivref s+
  lcl|FitnessBrowser__SynE:Synpcc7942_2143 167 MERQALNVFRMRLMGAEVRGVAAGSGTLKDATSEAIRDWVTNVETTHYILGSVAGPHPYPMIVREFHSM 235
                                               ********************************************************************* PP

                                 TIGR00263 203 igeevkeqilekegrlPdaviacvGGGsnaiGifaafiedeeveligveagGkGidtekhaatlskGke 271
                                               ig+ev++q +   g lPd+++acvGGGsna+G+f++f+++++v+ligvea+G+G+dt +haatl+kG++
  lcl|FitnessBrowser__SynE:Synpcc7942_2143 236 IGREVRQQAQTLWGGLPDILLACVGGGSNAMGLFNEFVNEPSVRLIGVEAAGRGVDTPEHAATLTKGRV 304
                                               ********************************************************************* PP

                                 TIGR00263 272 GvlhGaktkllqdedGqieeahsvsaGldypgvgPehaalaetgraeyeaitdeealealkllskeeGi 340
                                               GvlhGa+++llqd+dGq+ eahs+saGldypgvgPeh++l++ graey ++td+ealea++++s+ eGi
  lcl|FitnessBrowser__SynE:Synpcc7942_2143 305 GVLHGAMSYLLQDDDGQVIEAHSISAGLDYPGVGPEHSYLMDAGRAEYYSVTDDEALEAFQRISRLEGI 373
                                               ********************************************************************* PP

                                 TIGR00263 341 ipalesshalaaleklapklkkdeivvvnlsGrGdkdletvaka 384
                                               ipale++ha a+lekl+p+l+ +  +v+n sGrGdkd++tva++
  lcl|FitnessBrowser__SynE:Synpcc7942_2143 374 IPALETAHAFAHLEKLCPTLSGNPNLVINCSGRGDKDVQTVAQR 417
                                               *****************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (420 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.10
//
[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