Align Beta-phenylalanine transaminase; Aromatic beta-amino acid aminotransferase; Beta-phenylalanine aminotransferase; VpAT; EC 2.6.1.- (characterized)
to candidate 14300 b0154 glutamate-1-semialdehyde aminotransferase (NCBI)
Query= SwissProt::H8WR05 (434 letters) >FitnessBrowser__Keio:14300 Length = 426 Score = 234 bits (597), Expect = 4e-66 Identities = 146/397 (36%), Positives = 207/397 (52%), Gaps = 22/397 (5%) Query: 24 SQRQFEAQARYMPGANSRSVLFYAPF---PLTIARGEGAALWDADGHRYADFIAEYTAGV 80 S+ + A +PG + V + PL I + +GA L+D DG Y D++ + V Sbjct: 4 SENLYSAARELIPGGVNSPVRAFTGVGGTPLFIEKADGAYLYDVDGKAYIDYVGSWGPMV 63 Query: 81 YGHSAPEIRDAVIEAMQGGINLTGHNLLEGRLARLICERFPQIEQLRFTNSGTEANLMAL 140 GH+ P IR+AVIEA + G++ +E ++A+L+ E P ++ +R NSGTEA + A+ Sbjct: 64 LGHNHPAIRNAVIEAAERGLSFGAPTEMEVKMAQLVTELVPTMDMVRMVNSGTEATMSAI 123 Query: 141 TAALHFTGRRKIVVFSGGYHG-----------GVLGFGARPSPTTVPFDF----LVLPYN 185 A FTGR KI+ F G YHG G L G +P+ VP DF L YN Sbjct: 124 RLARGFTGRDKIIKFEGCYHGHADCLLVKAGSGALTLG-QPNSPGVPADFAKYTLTCTYN 182 Query: 186 DAQTARAQIERHGPEIAVVLVEPMQGASGCIPGQPDFLQALRESATQVGALLVFDEVMTS 245 D + RA E++ EIA ++VEP+ G C+P P+FL LR + GALL+ DEVMT Sbjct: 183 DLASVRAAFEQYPQEIACIIVEPVAGNMNCVPPLPEFLPGLRALCDEFGALLIIDEVMTG 242 Query: 246 -RLAPHGLANKLGIRSDLTTLGKYIGGGMSFGAFGGRADVMALFDPRTGPLAHSGTFNNN 304 R+A G + G+ DLT LGK IGGGM GAFGGR DVM P TGP+ +GT + N Sbjct: 243 FRVALAGAQDYYGVVPDLTCLGKIIGGGMPVGAFGGRRDVMDALAP-TGPVYQAGTLSGN 301 Query: 305 VMTMAAGYAGLTKLFTPEAAGALAERGEALRARLNALCANEGVAMQFTGIGSLMNAHFVQ 364 + MAAG+A L ++ P L E L L G+ + +G + F Sbjct: 302 PIAMAAGFACLNEVAQPGVHETLDELTTRLAEGLLEAAEEAGIPLVVNHVGGMFGIFFTD 361 Query: 365 GD-VRSSEDLAAVDGRLRQLLFFHLLNEDIYSSPRGF 400 + V +D+ A D + F +L+E +Y +P F Sbjct: 362 AESVTCYQDVMACDVERFKRFFHMMLDEGVYLAPSAF 398 Lambda K H 0.322 0.138 0.408 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: 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: 434 Length of database: 426 Length adjustment: 32 Effective length of query: 402 Effective length of database: 394 Effective search space: 158388 Effective search space used: 158388 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 (21.9 bits) S2: 51 (24.3 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