Align phenylalanine aminotransferase (EC 2.6.1.57) (characterized)
to candidate WP_042120054.1 RHE_RS27850 aspartate/tyrosine/aromatic aminotransferase
Query= reanno::Marino:GFF879 (395 letters) >NCBI__GCF_000092045.1:WP_042120054.1 Length = 392 Score = 340 bits (871), Expect = 5e-98 Identities = 180/390 (46%), Positives = 247/390 (63%), Gaps = 5/390 (1%) Query: 1 MFEALQPLPQDPILQLMQTFLEDDRPDKVDLGIGVYKDDAGNTPIMAAVHEAERRLLEGE 60 MF+ L P D +L L++ F DDRP K+DLG+GVY+D G TP+M AV AE+ LLE + Sbjct: 1 MFDQLNSRPADSLLALIKAFQADDRPGKIDLGVGVYRDAMGRTPVMRAVKAAEQFLLETQ 60 Query: 61 TTKSYVGPAGSAGFNSAMAELILGSNSPLVRDGRVSVIQTPGGCGALRMAAEFLRLCKAD 120 +K Y+GP G F + +I G NSP R++ IQTPGG GALR+ AE ++ Sbjct: 61 DSKKYLGPEGDLQFVRLLEPIIFG-NSPKFAQ-RLAGIQTPGGSGALRLGAELIQTANPS 118 Query: 121 TKVWVSTPTWANHLPLLGGAGLTIREYPYLNPETLQVDFGAMLETLERADAGDVVLLHGC 180 KV + TP+W NH P+ A L ++EY +++ + QV F +++ L A GDVVLLH C Sbjct: 119 AKVLLGTPSWPNHKPIFASARLDVKEYAFVDLTSQQVTFESVVSALSSAREGDVVLLHCC 178 Query: 181 CHNPSGADLSLAQWQEVTSLIQRKGLLPFVDMAYQGLGEGLDADAAGLRHLASAVPEMLI 240 CHNP+G D ++ QW+E+ L+ L+PF+D+AYQGLG+GL+ DAA R + AV E LI Sbjct: 179 CHNPTGIDFTMEQWREIADLLVAHRLVPFIDLAYQGLGDGLEQDAAPTRMILDAVEEALI 238 Query: 241 AASCSKNFGLYRERTGALALVSETATVNAAATSQLLSVIRSHYSMPPAHGASIVETILGD 300 A SC KNFGLYRER GAL +V+ A A S + + R ++SMPP HGA+IV+TIL Sbjct: 239 AYSCDKNFGLYRERVGALYVVARNADDVRKAESNMAGLARVNWSMPPDHGAAIVKTILES 298 Query: 301 DDLRAQWQQELNGMCKRILHLRHAFADALSPVGDFDFIARQRGMFSFLGISPEQVGRLRK 360 ++ A W+ EL MC+RI R A A A SP + F++RQRG+FS L + E LR Sbjct: 299 PEMTAIWRTELEEMCRRINGNRAALA-AASP--ELAFVSRQRGLFSNLSMRKETAVALRA 355 Query: 361 EHGIHMLESSRVNVAGLNDHVLPQVASALR 390 HGI+M +S R+N+AG+ + +ALR Sbjct: 356 NHGIYMADSGRMNLAGMQPADAGAIVAALR 385 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: 420 Number of extensions: 15 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: 392 Length adjustment: 31 Effective length of query: 364 Effective length of database: 361 Effective search space: 131404 Effective search space used: 131404 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 Apr 10 2024. The underlying query database was built on Apr 09 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