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.
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:
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