Alignments for a candidate for trpB in Pyrolobus fumarii 1A

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpB in Pyrolobus fumarii 1A

Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_014026630.1 PYRFU_RS05405 TrpB-like pyridoxal phosphate-dependent enzyme

Query= uniprot:P50383
         (425 letters)



>NCBI__GCF_000223395.1:WP_014026630.1
          Length = 429

 Score =  458 bits (1179), Expect = e-133
 Identities = 234/423 (55%), Positives = 299/423 (70%), Gaps = 15/423 (3%)

Query: 8   LPKYWYNIIPDLPKPLPPPRDPQGAYFSRIDLLRSILPKEVLRQQFTIERYIKIPEEVRD 67
           +P  WYNI+ DLP PLPP  DP     SRI LL  ILP  ++ +++T+ R++ IP+EVR 
Sbjct: 4   VPSRWYNIVADLPVPLPPLIDPLDDEGSRIQLLVRILPSRLIDEEYTLSRFLDIPDEVRA 63

Query: 68  RYLSIGRPTPLFRAKRLEEYLKTPAR--IYFKYEGATPTGSHKINTAIPQAYFAKEEGIE 125
            Y  +GRPTPL RA+ LE+ L    R  IY+K+EGA PTGSHKINTAIPQ Y+AK +G  
Sbjct: 64  AYRKVGRPTPLIRAEGLEKALGVHGRVRIYYKFEGALPTGSHKINTAIPQVYYAKLDGAN 123

Query: 126 HVVTETGAGQWGTAVALAASMYNMKSTIFMVKVSYEQKPMRRSIMQLYGANVYASPTNLT 185
            V TETGAGQWG AVA AA++  MK+TIFM + SY  K  RR +MQL GA V+ SP+ +T
Sbjct: 124 EVATETGAGQWGLAVATAAAILGMKATIFMTRSSYHSKRQRRLLMQLLGATVHPSPSEVT 183

Query: 186 EYGRKILETNPQHPGSLGIAMSEAIEYAL-KNEFRYLVGSVLDVVLLHQSVIGQETITQL 244
           E GR+ L  NP+HPGSLG+A++EA+EY L  N+ RY+ GSVL+ VL HQ+VIG E + QL
Sbjct: 184 EAGRRALRENPEHPGSLGLAITEAVEYVLSSNDRRYVAGSVLESVLTHQTVIGMEVLEQL 243

Query: 245 DLLGEDADILIGCVGGGSNFGGFTYPFIGNK------KGKRYIAVSSAEIPKFSKGEYKY 298
               E+ D +I CVGGGSN GGF+YP +G K      +  R+IA  +  +P+ SKGEY+Y
Sbjct: 244 P---EEPDYMIACVGGGSNMGGFSYPALGMKLRSEGFEKTRFIAAEATAVPRLSKGEYRY 300

Query: 299 DFPDSAGLLPLVKMITLGKDYVPPPIYAGGLRYHGVAPTLSLLTKEGIVEWREYNEREIF 358
           D  D+  +LPL KM TLGKDYVPPPI+A GLRYHG AP+LSLL K G +E R Y + E++
Sbjct: 301 DGLDTGLVLPLAKMYTLGKDYVPPPIHAAGLRYHGAAPSLSLLRKLGYIEARAYTQEEVY 360

Query: 359 EAAKIFIENQGIVPAPESAHAIRAVVDEAIEARKNNERKVIVFNLSGHGLLDLSNYESMM 418
           EA K+F  ++GI+PAPES HAIRAV+D A  A ++    VIVFNLSGHGLLD   +E + 
Sbjct: 361 EAGKLFARSEGIIPAPESTHAIRAVIDIAKRAPQDT---VIVFNLSGHGLLDTDAFEKIE 417

Query: 419 KRL 421
            R+
Sbjct: 418 SRI 420


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: 518
Number of extensions: 26
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: 429
Length adjustment: 32
Effective length of query: 393
Effective length of database: 397
Effective search space:   156021
Effective search space used:   156021
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: 51 (24.3 bits)

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