Align Beta-phenylalanine transaminase; Aromatic beta-amino acid aminotransferase; Beta-phenylalanine aminotransferase; VpAT; EC 2.6.1.- (characterized)
to candidate WP_086510216.1 BZY95_RS12260 glutamate-1-semialdehyde-2,1-aminomutase
Query= SwissProt::H8WR05 (434 letters) >NCBI__GCF_002151265.1:WP_086510216.1 Length = 754 Score = 233 bits (595), Expect = 1e-65 Identities = 149/397 (37%), Positives = 201/397 (50%), Gaps = 22/397 (5%) Query: 24 SQRQFEAQARYMPGANSRSVLFYAPF---PLTIARGEGAALWDADGHRYADFIAEYTAGV 80 S+ FE R++PG + V + P+ + R +GA L+D +G RY D++ + + Sbjct: 331 SETLFEQARRHIPGGVNSPVRAFKGLHRPPVFMERAQGAYLFDVEGKRYVDYVGSWGPMI 390 Query: 81 YGHSAPEIRDAVIEAMQGGINLTGHNLLEGRLARLICERFPQIEQLRFTNSGTEANLMAL 140 GH+ P++ AV + G++ +E +A LICE P IE +R NSGTEA + A+ Sbjct: 391 TGHADPDVLGAVRSRLDHGLSFGTPTAIETTMAELICEMIPSIELVRMVNSGTEATMSAI 450 Query: 141 TAALHFTGRRKIVVFSGGYHG-----------GVLGFGARPSPTTVPFDF----LVLPYN 185 A +TGR KIV F G YHG G L G PS VP + L YN Sbjct: 451 RLARGYTGRDKIVKFEGNYHGHSDSLLVKAGSGALTHG-EPSSPGVPASLAEHTITLSYN 509 Query: 186 DAQTARAQIERHGPEIAVVLVEPMQGASGCIPGQPDFLQALRESATQVGALLVFDEVMTS 245 D A E G EIA ++VEP+ G CIP QP FL+ LR T+ G++L+FDEVMT Sbjct: 510 DLDEVEACFEEIGSEIACIIVEPVAGNMNCIPPQPGFLETLRRVCTEYGSVLIFDEVMTG 569 Query: 246 -RLAPHGLANKLGIRSDLTTLGKYIGGGMSFGAFGGRADVMALFDPRTGPLAHSGTFNNN 304 R+A G GI DLT LGK +GGGM GAFGG+ +M P GP+ +GT + N Sbjct: 570 FRVALGGAQAHFGIEPDLTCLGKIVGGGMPVGAFGGKRAIMEQISP-LGPVYQAGTLSGN 628 Query: 305 VMTMAAGYAGLTKLFTPEAAGALAERGEALRARLNALCANEGVAMQFTGIGSLMNAHFV- 363 + MAAG A LTKL P ALA+R E L L GV M +G + F Sbjct: 629 PLAMAAGIALLTKLREPGFHDALAQRVETLCHGLQERADAAGVDMITQRVGGMFGLFFTG 688 Query: 364 QGDVRSSEDLAAVDGRLRQLLFFHLLNEDIYSSPRGF 400 Q V + A D + F +L E +Y +P + Sbjct: 689 QTRVDNFAQATACDAEAFRRFFAAMLEEGVYLAPSAY 725 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: 726 Number of extensions: 31 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: 754 Length adjustment: 36 Effective length of query: 398 Effective length of database: 718 Effective search space: 285764 Effective search space used: 285764 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: 53 (25.0 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