Align Beta-phenylalanine transaminase; Aromatic beta-amino acid aminotransferase; Beta-phenylalanine aminotransferase; VpAT; EC 2.6.1.- (characterized)
to candidate WP_093428845.1 BM272_RS11010 glutamate-1-semialdehyde 2,1-aminomutase
Query= SwissProt::H8WR05 (434 letters) >NCBI__GCF_900112605.1:WP_093428845.1 Length = 427 Score = 224 bits (572), Expect = 3e-63 Identities = 143/411 (34%), Positives = 202/411 (49%), Gaps = 20/411 (4%) Query: 22 PASQRQFEAQARYMPGANSRSVLFYAPF---PLTIARGEGAALWDADGHRYADFIAEYTA 78 P + FEA +R++PG + V + P+ RGEGA + Y D++ + Sbjct: 2 PHTHELFEAASRHIPGGVNSPVRAFKGVGGEPMFFKRGEGARMISESDRSYIDYVGSWGP 61 Query: 79 GVYGHSAPEIRDAVIEAMQGGINLTGHNLLEGRLARLICERFPQIEQLRFTNSGTEANLM 138 + GH+ P++ AV E G++ +LE R+A +C+ P +E +R NSGTEA + Sbjct: 62 LILGHANPKVVRAVQETAAQGLSFGTPTVLETRMADKVCDLVPSMEMIRMVNSGTEATMS 121 Query: 139 ALTAALHFTGRRKIVVFSGGYHG-----------GVLGFGARPS---PTTVPFDFLVLPY 184 A+ A +TGR KIV F G +HG G L FG+ S P ++ L L Y Sbjct: 122 AIRLARGYTGRDKIVKFEGNFHGHVDSLLVKAGSGALTFGSPSSPGVPASLAEHTLTLTY 181 Query: 185 NDAQTARAQIERHGPEIAVVLVEPMQGASGCIPGQPDFLQALRESATQVGALLVFDEVMT 244 NDA R E G +IA ++VEP+ G C+P +P FL+ LRE G++L+FDEVMT Sbjct: 182 NDADGVRELFEHMGGQIAGIIVEPVAGNMNCVPPEPGFLETLREVCDAHGSVLIFDEVMT 241 Query: 245 S-RLAPHGLANKLGIRSDLTTLGKYIGGGMSFGAFGGRADVMALFDPRTGPLAHSGTFNN 303 R+A G + G DLT LGK +GGGM GAFGGR +M P GP+ +GT Sbjct: 242 GFRVALGGAQQRYGTTPDLTCLGKVVGGGMPVGAFGGRRAIMEQLSP-LGPVYQAGTLAG 300 Query: 304 NVMTMAAGYAGLTKLFTPEAAGALAERGEALRARLNALCANEGVAMQFTGIGSLMNAHFV 363 N +TMAAG A L ++ P L R L L G+AM +G ++ F Sbjct: 301 NPVTMAAGLATLEQIEEPGFHERLENRARELAEGLEERARAHGIAMTTNVVGGMLGIFFT 360 Query: 364 QGDVRSSEDLAAVDGRLRQLLFFH-LLNEDIYSSPRGFVVLSLPLTDADID 413 + + + R LFFH +LN IY +P F L D + Sbjct: 361 EDEQVTRYHQVVNSNLDRFRLFFHGMLNRGIYLAPAPFEACFLSSAHGDAE 411 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: 454 Number of extensions: 23 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: 427 Length adjustment: 32 Effective length of query: 402 Effective length of database: 395 Effective search space: 158790 Effective search space used: 158790 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 Jul 25 2024. The underlying query database was built on Jul 25 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