Align Beta-phenylalanine transaminase; Aromatic beta-amino acid aminotransferase; Beta-phenylalanine aminotransferase; VpAT; EC 2.6.1.- (characterized)
to candidate WP_057509163.1 ABB28_RS13760 glutamate-1-semialdehyde-2,1-aminomutase
Query= SwissProt::H8WR05 (434 letters) >NCBI__GCF_001431535.1:WP_057509163.1 Length = 426 Score = 213 bits (541), Expect = 1e-59 Identities = 138/389 (35%), Positives = 191/389 (49%), Gaps = 20/389 (5%) Query: 30 AQARYMPGANS--RSVLFYAPFPLTIARGEGAALWDADGHRYADFIAEYTAGVYGHSAPE 87 AQA G NS R+ P + R +GA L D DG+RY D++ + + GH+ P Sbjct: 13 AQALLPGGVNSPVRAFKSVGGEPFFVERADGAYLHDVDGNRYIDYVGSWGPMIVGHNHPA 72 Query: 88 IRDAVIEAMQGGINLTGHNLLEGRLARLICERFPQIEQLRFTNSGTEANLMALTAALHFT 147 +R AV +A G++ E +A + P E +R NSGTEA L A+ A T Sbjct: 73 VRQAVKKAADSGLSFGAPCAAEVTMAETLTRLVPSCEMVRMVNSGTEATLSAIRLARGAT 132 Query: 148 GRRKIVVFSGGYHG-----------GVLGFGARPSPTTVPFDF----LVLPYNDAQTARA 192 GR +IV F G YHG G+L G SP VP L LPYND A A Sbjct: 133 GRSRIVKFEGCYHGHGDSFLVKAGSGMLTLGVPTSP-GVPAGLSELTLTLPYNDFDAATA 191 Query: 193 QIERHGPEIAVVLVEPMQGASGCIPGQPDFLQALRESATQVGALLVFDEVMTS-RLAPHG 251 E G +IA +++EP+ G + CIP + +LQ LR T+ G +L+FDEVMT R+A G Sbjct: 192 LFEAQGEQIAGLIIEPVVGNANCIPPREGYLQHLRALCTRFGTVLIFDEVMTGFRVALGG 251 Query: 252 LANKLGIRSDLTTLGKYIGGGMSFGAFGGRADVMALFDPRTGPLAHSGTFNNNVMTMAAG 311 G+ DLTT GK IGGGM GA+GG+ ++M P GP+ +GT + N + MAAG Sbjct: 252 AQAHYGVTPDLTTFGKIIGGGMPVGAYGGKRELMQQISP-AGPIYQAGTLSGNPVAMAAG 310 Query: 312 YAGLTKLFTPEAAGALAERGEALRARLNALCANEGVAMQFTGIGSLMNAHFVQGDVRSSE 371 A L + P L+ R L A L A GV++ T +G + F V + Sbjct: 311 LAMLELVQQPGFHAQLSARAARLCAGLEQAAAEAGVSVTTTQVGGMFGLFFTDQKVETYA 370 Query: 372 DLAAVDGRLRQLLFFHLLNEDIYSSPRGF 400 A D F +L + ++ +P + Sbjct: 371 QATACDIPAFNRFFHAMLEQGVFLAPSAY 399 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: 425 Number of extensions: 19 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 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