Align Beta-phenylalanine transaminase; Aromatic beta-amino acid aminotransferase; Beta-phenylalanine aminotransferase; VpAT; EC 2.6.1.- (characterized)
to candidate WP_012473666.1 CPHAMN1_RS01040 glutamate-1-semialdehyde 2,1-aminomutase
Query= SwissProt::H8WR05 (434 letters) >NCBI__GCF_000020545.1:WP_012473666.1 Length = 431 Score = 196 bits (498), Expect = 1e-54 Identities = 135/420 (32%), Positives = 208/420 (49%), Gaps = 30/420 (7%) Query: 24 SQRQFEAQARYMPGANSRSVLFYAPF---PLTIARGEGAALWDADGHRYADFIAEYTAGV 80 S FE +++PG + V + P+ +A+G+GA + D DG+ Y D++ + + Sbjct: 7 SAELFEKAKQFIPGGVNSPVRAFKSVGGTPIFMAKGQGAYMTDVDGNTYLDYVGSWGPFI 66 Query: 81 YGHSAPEIRDAVIEAMQG-GINLTGHNLLEGRLARLICERFPQIEQLRFTNSGTEANLMA 139 G P I A+ + G + +E +A L+ + P IE +R NSGTEA + A Sbjct: 67 LGSMHPRITAAIENTLTKIGTSFGTPIEMEIEIAELLTQIVPSIEMVRMVNSGTEATMSA 126 Query: 140 LTAALHFTGRRKIVVFSGGYHG-----------GVLGFGARPSPTTVPF---DFLVLPYN 185 + A +TGR KI+ F G YHG G L GA SP D L YN Sbjct: 127 VRLARGYTGRDKIIKFEGCYHGHGDSFLIKAGSGALTLGAPDSPGVTKGTANDTLNAKYN 186 Query: 186 DAQTARAQIERHGPEIAVVLVEPMQGASGCIPGQPDFLQALRESATQVGALLVFDEVMTS 245 D ++ R ++ + IA +++EP+ G +G IP + DFLQALR+ T+ G +L+FDEVM Sbjct: 187 DIESVRVLVKENKDSIAAIIIEPVAGNTGVIPAKTDFLQALRDLCTEEGIVLIFDEVMCG 246 Query: 246 -RLAPHGLANKLGIRSDLTTLGKYIGGGMSFGAFGGRADVMALFDPRTGPLAHSGTFNNN 304 R+A G + GI DLTT+GK IGGG+ GAFGG+ ++M P G + +GT + N Sbjct: 247 FRVALGGAQERYGITPDLTTMGKIIGGGLPVGAFGGKREIMQRVAP-IGDVYQAGTLSGN 305 Query: 305 VMTMAAGYAGLTKLFT----PEAAGALAERGEALRARLNALCANEGVAMQFTGIGSLMNA 360 + + AG L L PE A E R +N L G++ +GS+ Sbjct: 306 PLALTAGLETLKILRDDNPYPELERKAAFLEEGFRDNMNKL----GLSYVQNRVGSMACL 361 Query: 361 HFVQGDVRSSEDLAAVDGRLRQLLFFHLLNEDIYSSPRGFVVL--SLPLTDADIDRYVAA 418 F + V + + D + + +L++ IY +P F + S +TD D+++ V A Sbjct: 362 FFTETPVENYDTAITCDLKKYGKYYHSMLDQGIYLAPSQFEAMFTSAVMTDEDLEKTVKA 421 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: 412 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: 431 Length adjustment: 32 Effective length of query: 402 Effective length of database: 399 Effective search space: 160398 Effective search space used: 160398 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