Align Beta-phenylalanine transaminase; Aromatic beta-amino acid aminotransferase; Beta-phenylalanine aminotransferase; VpAT; EC 2.6.1.- (characterized)
to candidate WP_017549034.1 C792_RS0108435 glutamate-1-semialdehyde 2,1-aminomutase
Query= SwissProt::H8WR05 (434 letters) >NCBI__GCF_000330705.1:WP_017549034.1 Length = 428 Score = 207 bits (527), Expect = 5e-58 Identities = 137/418 (32%), Positives = 203/418 (48%), Gaps = 22/418 (5%) Query: 24 SQRQFEAQARYMPGANSRSVLFYAPF---PLTIARGEGAALWDADGHRYADFIAEYTAGV 80 S+ ++ MPG + V + P+ I + A +D DG+ Y D++ + + Sbjct: 5 SKALYKKATELMPGGVNSPVRAFNSVGMDPVFIDHAKDARTYDVDGNEYIDYVLSFGPLI 64 Query: 81 YGHSAPEIRDAVIEAMQGGINLTGHNLLEGRLARLICERFPQIEQLRFTNSGTEANLMAL 140 GHS + DAV EA Q G + LE LA L+ +R P +E +R +SGTEA L AL Sbjct: 65 LGHSDDRVVDAVSEAAQKGTSFGAPTSLENELAELVIDRVPSVEMIRMVSSGTEATLAAL 124 Query: 141 TAALHFTGRRKIVVFSGGYHG-----------GVLGFGARPSPTT---VPFDFLVLPYND 186 A FTGR KI+ F G YHG GV G SP + + +PYND Sbjct: 125 RLARGFTGRSKILKFEGCYHGHSDSLLIKAGSGVATLGLPDSPGVPEGTAANTITVPYND 184 Query: 187 AQTARAQIERHGPEIAVVLVEPMQGASGCIPGQPDFLQALRESATQVGALLVFDEVMTS- 245 ++ + ++ G +IA V++EP+ G G +P +L +R + G LL+FDEVMT Sbjct: 185 EESLKEAFDQFGEDIAAVIMEPVAGNMGVVPPVEGYLDFVRRITEENGTLLIFDEVMTGF 244 Query: 246 RLAPHGLANKLGIRSDLTTLGKYIGGGMSFGAFGGRADVMALFDPRTGPLAHSGTFNNNV 305 R+ + GI DLT LGK IGGG+ GA+GGR D+M P TG + +GT + N Sbjct: 245 RVGYNCAQGHYGITPDLTCLGKVIGGGLPVGAYGGRRDIMEHIAP-TGDIYQAGTLSGNP 303 Query: 306 MTMAAGYAGLTKLFTPEAAGALAERGEALRARLNALCANEGVAMQFTGIGSLMNAHFVQG 365 + M AG L +L TPE+ G+ L L + + +G + GS++ +G Sbjct: 304 LAMTAGLETLKQL-TPESYEYFNRLGDMLENGLKEIFSEKGYPITVNRAGSMIGFFLTEG 362 Query: 366 DVRSSEDLAAVDGRLRQLLFFHLLNEDIYSSPRGF--VVLSLPLTDADIDRYVAAIGS 421 V + D L ++ LL E +Y P F + LS T+ DI + + A + Sbjct: 363 PVTDFDSANTSDLDLFAQMYRSLLEEGVYLPPSQFEGMFLSTKHTEEDISKTLTAFSN 420 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: 415 Number of extensions: 17 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: 428 Length adjustment: 32 Effective length of query: 402 Effective length of database: 396 Effective search space: 159192 Effective search space used: 159192 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 26 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