GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PPYAT in Epibacterium ulvae U95

Align phenylalanine aminotransferase (EC 2.6.1.57) (characterized)
to candidate WP_090218172.1 CV091_RS11085 aspartate/tyrosine/aromatic aminotransferase

Query= reanno::Marino:GFF879
         (395 letters)



>NCBI__GCF_002796795.1:WP_090218172.1
          Length = 401

 Score =  373 bits (958), Expect = e-108
 Identities = 191/397 (48%), Positives = 256/397 (64%), Gaps = 4/397 (1%)

Query: 1   MFEALQPLPQDPILQLMQTFLEDDRPDKVDLGIGVYKDDAGNTPIMAAVHEAERRLLEGE 60
           MFE  Q    D +L LMQ +  D R +KVDL +GVYKD  GN P+M AV  AE++L + E
Sbjct: 1   MFETTQSRGIDQLLALMQAYQADPRDNKVDLVVGVYKDAEGNIPVMRAVKAAEKQLYKTE 60

Query: 61  TTKSYVGPAGSAGFNSAMAELILGSNSPLVRDGRVSVIQTPGGCGALRMAAEFLRLCKAD 120
           TTK+YVG +G+A + + +  L+LG++S  V   RV+ +QTPGG GAL++A ++L + +A 
Sbjct: 61  TTKTYVGISGAADYRALVPALLLGADSQQVAAARVTSVQTPGGSGALKVACDYLNMLEAG 120

Query: 121 TKVWVSTPTWANHLPLLGGAGLTIREYPYLNPETLQVDFGAMLETLE-RADAGDVVLLHG 179
             +WVS+PTWANH+P+   AGL+I EYPY       +DF  M+  L+  A  GD +LLH 
Sbjct: 121 KTLWVSSPTWANHIPVAQDAGLSISEYPYFRASDRGLDFEGMVSHLKSNAKPGDAILLHA 180

Query: 180 CCHNPSGADLSLAQWQEVTSLIQRKGLLPFVDMAYQGLGEGLDADAAGLRHLASAVPEML 239
           CCHNP+G D S  QWQ +  L+    LLPF+D AYQGLGE + AD AGLRH+A  VPEML
Sbjct: 181 CCHNPTGVDPSFEQWQILADLVLDLQLLPFLDCAYQGLGESMTADVAGLRHMAGLVPEML 240

Query: 240 IAASCSKNFGLYRERTGALALVSETATVNAAATSQLLSVIRSHYSMPPAHGASIVETILG 299
           IA+S SKNFG+YRERTGAL +++        A   + +V+RS+YSMPP+HGA IV T+  
Sbjct: 241 IASSFSKNFGIYRERTGALTVIAADQDDLQKAHGGIETVVRSNYSMPPSHGARIVSTVFE 300

Query: 300 DDDLRAQWQQELNGMCKRILHLRHAF---ADALSPVGDFDFIARQRGMFSFLGISPEQVG 356
           + D +  W+QEL  M  RI  +RHA     DAL    D  F+  Q+GMFS+ G  P+ V 
Sbjct: 301 NADQKLDWEQELREMRDRIASMRHALKSRVDALGITADTSFLTAQKGMFSYTGFGPDAVA 360

Query: 357 RLRKEHGIHMLESSRVNVAGLNDHVLPQVASALREVL 393
           RL+ E G++M    R+NVAGL    +  VA A   +L
Sbjct: 361 RLKTEFGVYMAGDGRINVAGLTRENIDVVAHAFSAIL 397


Lambda     K      H
   0.320    0.136    0.402 

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: 405
Number of extensions: 14
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: 395
Length of database: 401
Length adjustment: 31
Effective length of query: 364
Effective length of database: 370
Effective search space:   134680
Effective search space used:   134680
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 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

Links

Downloads

Related tools

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