Align Beta-phenylalanine transaminase; Aromatic beta-amino acid aminotransferase; Beta-phenylalanine aminotransferase; VpAT; EC 2.6.1.- (characterized)
to candidate 6936652 Sama_0839 glutamate-1-semialdehyde aminotransferase (RefSeq)
Query= SwissProt::H8WR05 (434 letters) >FitnessBrowser__SB2B:6936652 Length = 427 Score = 210 bits (535), Expect = 6e-59 Identities = 136/417 (32%), Positives = 208/417 (49%), Gaps = 24/417 (5%) Query: 24 SQRQFEAQARYMPGANSRSVLFY---APFPLTIARGEGAALWDADGHRYADFIAEYTAGV 80 S+ FE + +PG + V + P I + +GA ++DADG Y D++ + + Sbjct: 4 SETLFEQAKKTIPGGVNSPVRAFNGVGGTPRFIEKADGAYIYDADGKAYIDYVGSWGPMI 63 Query: 81 YGHSAPEIRDAVIEAMQGGINLTGHNLLEGRLARLICERFPQIEQLRFTNSGTEANLMAL 140 GH+ P IR+AV++A+ G++ LE +A + E P ++Q+R +SGTEA + A+ Sbjct: 64 LGHNHPSIREAVLKAVHNGLSFGAPTELEVIMAEKVIEMVPSMDQVRMVSSGTEATMSAI 123 Query: 141 TAALHFTGRRKIVVFSGGYHG-----------GVLGFGARPSPTTVPFDF----LVLPYN 185 A +T R KI+ F G YHG G L G +PS +P DF L YN Sbjct: 124 RLARGYTKRDKILKFEGCYHGHADCLLVKAGSGALTLG-QPSSPGIPEDFAKHTLTAVYN 182 Query: 186 DAQTARAQIERHGPEIAVVLVEPMQGASGCIPGQPDFLQALRESATQVGALLVFDEVMTS 245 D ++ ++ +++ +IA +++EP+ G CIP P FL+ LR + GAL + DEVMT Sbjct: 183 DLESVQSFFDQYPEDIACIIIEPVAGNMNCIPPVPGFLEGLRALCDKYGALFIIDEVMTG 242 Query: 246 -RLAPHGLANKLGIRSDLTTLGKYIGGGMSFGAFGGRADVMALFDPRTGPLAHSGTFNNN 304 R++ G G+ DLTTLGK IGGGM GAFGG+ DVM P GP+ +GT + N Sbjct: 243 FRVSRSGAQGHYGVTPDLTTLGKVIGGGMPVGAFGGKKDVMQYLAP-AGPVYQAGTLSGN 301 Query: 305 VMTMAAGYAGLTKLFTPEAAGALAERGEALRARLNALCANEGVAMQFTGIGSLMNAHFVQ 364 + M AG A L L LA + + + A G+ M +G + F Sbjct: 302 PIAMTAGLAQLDALCADGLYEELAAKTKRIAEGFKAAADKHGIPMAINYVGGMFGFFFTD 361 Query: 365 GDVRSSEDLAAVDGRLRQLLFFH-LLNEDIYSSPRGFVV--LSLPLTDADIDRYVAA 418 + D F+H +L+E +Y +P + LS+ D +I+ +AA Sbjct: 362 EQHITRFDQVTRCNMDHFRAFYHGMLDEGVYLAPSAYEAGFLSMAHGDKEIEETLAA 418 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: 458 Number of extensions: 29 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 Apr 09 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