GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpB in Archaeoglobus veneficus SNP6

Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_013684029.1 ARCVE_RS06800 TrpB-like pyridoxal phosphate-dependent enzyme

Query= uniprot:P50383
         (425 letters)



>NCBI__GCF_000194625.1:WP_013684029.1
          Length = 434

 Score =  469 bits (1207), Expect = e-137
 Identities = 232/421 (55%), Positives = 305/421 (72%), Gaps = 4/421 (0%)

Query: 1   MVKEDEILPKYWYNIIPDLPKPLPPPRDPQGAYFSRIDLLRSILPKEVLRQQFTIERYIK 60
           ++ + E +P+ WYNI+PDLPKPLPPP  P      +   L  I PKE+++Q+ + ER+I+
Sbjct: 8   VILDPEEMPREWYNILPDLPKPLPPPLHPVTKEPIKPSDLEPIFPKELIKQEMSDERWIR 67

Query: 61  IPEEVRDRYLSIGRPTPLFRAKRLEEYLKTPARIYFKYEGATPTGSHKINTAIPQAYFAK 120
           IPEEV + Y  + RPTPL RAKRLEE LKTPA+IY+KYEG +P GSHK NTA+ QAY+  
Sbjct: 68  IPEEVLEVY-RLWRPTPLIRAKRLEEALKTPAKIYYKYEGVSPPGSHKPNTAVAQAYYNM 126

Query: 121 EEGIEHVVTETGAGQWGTAVALAASMYNMKSTIFMVKVSYEQKPMRRSIMQLYGANVYAS 180
           +EG+E + TETGAGQWG+A++ A  +++MK T++MVKVSY QKP RR +M+ +G  V  S
Sbjct: 127 KEGVERLTTETGAGQWGSALSFATRLFDMKCTVYMVKVSYHQKPYRRILMETWGGEVIPS 186

Query: 181 PTNLTEYGRKILETNPQHPGSLGIAMSEAIEYALKNE-FRYLVGSVLDVVLLHQSVIGQE 239
           P++ TE GR+ILE +P + GSLGIA+SEA+E A K+E   Y +GSVL+ VLLHQ++IG E
Sbjct: 187 PSDRTESGRRILEKDPDNTGSLGIAISEAVEDAAKHENTNYSLGSVLNHVLLHQTIIGLE 246

Query: 240 TITQLDLLGEDADILIGCVGGGSNFGGFTYPFI--GNKKGKRYIAVSSAEIPKFSKGEYK 297
              Q +L+ E  D+LIGCVGGGSNF GF YPFI    K+G R +AV  A  P  + GEY+
Sbjct: 247 AKKQFELIDEKPDVLIGCVGGGSNFAGFCYPFIKDAEKEGIRIVAVEPAACPTLTAGEYR 306

Query: 298 YDFPDSAGLLPLVKMITLGKDYVPPPIYAGGLRYHGVAPTLSLLTKEGIVEWREYNEREI 357
           YD+ D+ GL PL+ M TLG D++PPPI+AGGLRYHG APTLSLL  EG++E     +   
Sbjct: 307 YDYGDTVGLTPLLMMYTLGHDFMPPPIHAGGLRYHGDAPTLSLLVAEGVIEAVAVKQIPT 366

Query: 358 FEAAKIFIENQGIVPAPESAHAIRAVVDEAIEARKNNERKVIVFNLSGHGLLDLSNYESM 417
           FEA  +F   +GIVPAPES HAIR  +DEA++A++  E KVI FNLSGHG  DL+ Y+  
Sbjct: 367 FEAGLLFARTEGIVPAPESNHAIRVAIDEALKAKEEGEEKVIAFNLSGHGYFDLAAYDDY 426

Query: 418 M 418
           +
Sbjct: 427 L 427


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: 551
Number of extensions: 32
Number of successful extensions: 6
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: 434
Length adjustment: 32
Effective length of query: 393
Effective length of database: 402
Effective search space:   157986
Effective search space used:   157986
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:

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:

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:

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:

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