Align Beta-phenylalanine transaminase; Aromatic beta-amino acid aminotransferase; Beta-phenylalanine aminotransferase; VpAT; EC 2.6.1.- (characterized)
to candidate Echvi_0150 Echvi_0150 glutamate-1-semialdehyde-2,1-aminomutase
Query= SwissProt::H8WR05 (434 letters) >FitnessBrowser__Cola:Echvi_0150 Length = 429 Score = 224 bits (572), Expect = 3e-63 Identities = 143/416 (34%), Positives = 211/416 (50%), Gaps = 22/416 (5%) Query: 24 SQRQFEAQARYMPGANSRSVLFYAPF---PLTIARGEGAALWDADGHRYADFIAEYTAGV 80 S+ F ++PG + V + PL I + EGA L+D D +RY + I + + Sbjct: 6 SKTLFSNAQNFIPGGVNSPVRAFKAVGGDPLFIKKAEGAYLFDEDDNRYIELINSWGPMI 65 Query: 81 YGHSAPEIRDAVIEAMQGGINLTGHNLLEGRLARLICERFPQIEQLRFTNSGTEANLMAL 140 GH+ PEI +A+++A++ G + E +A LIC+ P +E++R NSGTEA + A+ Sbjct: 66 LGHNHPEINEAIVKAVENGTSFGAPTAKEIDIAELICKMVPSVEKVRMVNSGTEATMSAV 125 Query: 141 TAALHFTGRRKIVVFSGGYHG-----------GVLGFGARPSPTT---VPFDFLVLPYND 186 A +TGR K + F G YHG G + GA SP D L+ PYND Sbjct: 126 RLARGYTGRDKFLKFEGNYHGHGDSFLIAAGSGAMTMGAPNSPGVTKGTAKDTLLAPYND 185 Query: 187 AQTARAQIERHGPEIAVVLVEPMQGASGCIPGQPDFLQALRESATQVGALLVFDEVMTS- 245 + +E + E+A +++EP+ G G + FLQ LR+ + G +L+FDEVMT Sbjct: 186 LNAVKEVLEANRDEVAAIILEPVPGNMGLVLPNEGFLQGLRKLCDEEGIVLIFDEVMTGF 245 Query: 246 RLAPHGLANKLGIRSDLTTLGKYIGGGMSFGAFGGRADVMALFDPRTGPLAHSGTFNNNV 305 RLA G G+ DLTT+GK IGGGM GA+GG+ ++M P GP+ +GT + N Sbjct: 246 RLAQGGAQEVFGVTPDLTTMGKIIGGGMPVGAYGGKKEIMDFVSP-VGPVYQAGTLSGNP 304 Query: 306 MTMAAGYAGLTKLFT-PEAAGALAERGEALRARLNALCANEGVAMQFTGIGSLMNAHFVQ 364 + MAAG+A L L+ PE L + G L A + + G+ T +GS+ + F + Sbjct: 305 IAMAAGFAMLDHLYQHPEVYQQLDQAGSKLVAGVKSSVEKLGLEYTMTHLGSMYSLFFTK 364 Query: 365 GDVRSSEDLAAVDGRLRQLLFFHLLNEDIYSSPRGF--VVLSLPLTDADIDRYVAA 418 V E D L F +L +Y P F + LS LTD ID+ + A Sbjct: 365 EKVVDFETAKTSDTVLFGKYFQAMLKRGVYLPPSQFESLFLSTALTDEHIDQIIDA 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: 419 Number of extensions: 21 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: 429 Length adjustment: 32 Effective length of query: 402 Effective length of database: 397 Effective search space: 159594 Effective search space used: 159594 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