Align phenylalanine aminotransferase (EC 2.6.1.57) (characterized)
to candidate SMc00387 SMc00387 aromatic amino acid aminotransferase
Query= reanno::Marino:GFF879 (395 letters) >FitnessBrowser__Smeli:SMc00387 Length = 389 Score = 342 bits (876), Expect = 1e-98 Identities = 182/388 (46%), Positives = 242/388 (62%), Gaps = 7/388 (1%) Query: 1 MFEALQPLPQDPILQLMQTFLEDDRPDKVDLGIGVYKDDAGNTPIMAAVHEAERRLLEGE 60 MF+AL DP+L L+ F +D+RP KVDLG+GVY+D+ G TPI AV AE+RLLE + Sbjct: 1 MFDALARQADDPLLALIGLFRKDERPGKVDLGVGVYRDETGRTPIFRAVKAAEKRLLETQ 60 Query: 61 TTKSYVGPAGSAGFNSAMAELILGSNSPLVRDGRVSVIQTPGGCGALRMAAEFLRLCKAD 120 +K+Y+GP G F + EL+ G + V+ +QTPGG GALR+AA+ + Sbjct: 61 DSKAYIGPEGDLVFLDRLWELVGGDT---IERSHVAGVQTPGGSGALRLAADLIARM-GG 116 Query: 121 TKVWVSTPTWANHLPLLGGAGLTIREYPYLNPETLQVDFGAMLETLERADAGDVVLLHGC 180 +W+ P+W NH P+ AGL I Y + + + V F ++ LE A +GD VLLH Sbjct: 117 RGIWLGLPSWPNHAPIFKAAGLDIATYDFFDIPSQSVIFDNLVSALEGAASGDAVLLHAS 176 Query: 181 CHNPSGADLSLAQWQEVTSLIQRKGLLPFVDMAYQGLGEGLDADAAGLRHLASAVPEMLI 240 CHNP+G LS AQW E+ +L+ +GLLP VD+AYQG G GLD D AGLRHL VPE L+ Sbjct: 177 CHNPTGGVLSEAQWMEIAALVAERGLLPLVDLAYQGFGRGLDQDVAGLRHLLGVVPEALV 236 Query: 241 AASCSKNFGLYRERTGAL-ALVSETATVNAAATSQLLSVIRSHYSMPPAHGASIVETILG 299 A SCSK+FGLYRER GA+ A S TA+ + S L + R+ YSMPP HGA++V TIL Sbjct: 237 AVSCSKSFGLYRERAGAIFARTSSTASAD-RVRSNLAGLARTSYSMPPDHGAAVVRTILD 295 Query: 300 DDDLRAQWQQELNGMCKRILHLRHAFADAL-SPVGDFDFIARQRGMFSFLGISPEQVGRL 358 D +LR W +EL M R+ LR + A+ L + +A Q GMFS L +S +V RL Sbjct: 296 DPELRRDWTEELETMRLRMTGLRRSLAEGLRTRWQSLGAVADQEGMFSMLPLSEAEVMRL 355 Query: 359 RKEHGIHMLESSRVNVAGLNDHVLPQVA 386 R EHGI+M S R+N+AGL ++A Sbjct: 356 RTEHGIYMPASGRINIAGLKTAEAAEIA 383 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: 448 Number of extensions: 18 Number of successful extensions: 4 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: 389 Length adjustment: 31 Effective length of query: 364 Effective length of database: 358 Effective search space: 130312 Effective search space used: 130312 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 09 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