GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PPYAT in Pseudomonas simiae WCS417

Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate GFF1598 PS417_08130 aspartate aminotransferase

Query= reanno::BFirm:BPHYT_RS14905
         (370 letters)



>FitnessBrowser__WCS417:GFF1598
          Length = 370

 Score =  371 bits (952), Expect = e-107
 Identities = 191/359 (53%), Positives = 250/359 (69%), Gaps = 3/359 (0%)

Query: 10  VRAIAPYIAGKPISEVAREFGLDEATIVKLASNENPLGMPESAQRAMAQAASELGRYPDA 69
           V+ ++PY+ GKP+ E+ARE  LD A IVKLASNENPLG       A+ +  +EL RYPD 
Sbjct: 13  VQQLSPYVPGKPVDELARELNLDPANIVKLASNENPLGPSPKVLAAIREELAELTRYPDG 72

Query: 70  NAFELKAALSERYGVPADWVTLGNGSNDILEIAAHAFVEKGQSIVYAQYSFAVYALATQG 129
           N F LK+ L+++ GV  + VTLGNGSNDILE+   A++  G + V+++++FAVY + TQ 
Sbjct: 73  NGFALKSLLAQKCGVELNQVTLGNGSNDILELVGRAYLAPGLNAVFSEHAFAVYPIVTQA 132

Query: 130 LGARAIVVPAVKYGHDLDAMLAAVSDDTRLIFVANPNNPTGTFIEGPKLEAFLDKVPRHV 189
           +GA A VVPA ++GHDL AMLAA+   TR++F+ANPNNPTGT+ +   L  FL  VP HV
Sbjct: 133 VGADAKVVPAKEWGHDLPAMLAAIDAQTRVVFIANPNNPTGTWFDAQALSDFLQDVPEHV 192

Query: 190 VVVLDEAYTEYLPQEKRYDSIAWVRRYPNLLVSRTFSKAFGLAGLRVGFAIAQPELTDLL 249
           +VVLDEAY EY       + + ++  YPNLLVSRTFSKA+GLA LRVG+ ++   + D+L
Sbjct: 193 LVVLDEAYIEYAKGSDLPNGLDFLAAYPNLLVSRTFSKAYGLASLRVGYGLSTAVVADVL 252

Query: 250 NRVRQPFNVNTLAQAAAIAALNDKAFLEKSAALNAQGYRRLTEAFDKLGLEYVPSDGNFV 309
           NRVRQPFNVN+LA AAA AA+ D  +LE+   LN  G  +L E F +LGL ++PS GNF+
Sbjct: 253 NRVRQPFNVNSLALAAACAAVKDAEYLEEGRRLNESGMLQLQEGFRELGLGWIPSKGNFI 312

Query: 310 LVRVGNDDAAGNRVNLELLKQGVIVRPVGNYGLPQWLRITIGLPEENEAFIAALERTLA 368
            V +G   A    V   LL++GVIVRP  NYG+P  LRITIGLP EN  F+ AL + LA
Sbjct: 313 CVDLGQVAAP---VFQGLLREGVIVRPTANYGMPNHLRITIGLPAENARFLEALAKVLA 368


Lambda     K      H
   0.318    0.135    0.385 

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: 437
Number of extensions: 16
Number of successful extensions: 2
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: 370
Length of database: 370
Length adjustment: 30
Effective length of query: 340
Effective length of database: 340
Effective search space:   115600
Effective search space used:   115600
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)

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:

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