GapMind for Amino acid biosynthesis

 

Aligments for a candidate for PPYAT in Pseudomonas fluorescens FW300-N2C3

Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate AO356_03460 AO356_03460 aspartate aminotransferase

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



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_03460 AO356_03460
           aspartate aminotransferase
          Length = 370

 Score =  380 bits (976), Expect = e-110
 Identities = 197/358 (55%), Positives = 255/358 (71%), Gaps = 3/358 (0%)

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

Query: 70  NAFELKAALSERYGVPADWVTLGNGSNDILEIAAHAFVEKGQSIVYAQYSFAVYALATQG 129
           N F LK+ L+ER GV  + VTLGNGSNDILE+ A A++  G + V+++++FAVY +ATQ 
Sbjct: 73  NGFALKSLLAERCGVELNQVTLGNGSNDILELVARAYLAPGLNAVFSEHAFAVYPIATQA 132

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

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

Query: 250 NRVRQPFNVNTLAQAAAIAALNDKAFLEKSAALNAQGYRRLTEAFDKLGLEYVPSDGNFV 309
           NRVRQPFNVN+ A AAA AAL D+A+L +S  LNA G ++L     +LGL ++PS GNF+
Sbjct: 253 NRVRQPFNVNSFALAAACAALQDEAYLAESRRLNAAGMQQLEAGLRELGLGWIPSKGNFI 312

Query: 310 LVRVGNDDAAGNRVNLELLKQGVIVRPVGNYGLPQWLRITIGLPEENEAFIAALERTL 367
            V +G   A    V   LL++GVIVRPV NYG+P  LRITIGLP EN  F+ AL + L
Sbjct: 313 CVDLGRVAAP---VYQGLLREGVIVRPVANYGMPNHLRITIGLPTENSRFLEALSKVL 367


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: 452
Number of extensions: 18
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 Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code, or see 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