Align Beta-phenylalanine transaminase; Aromatic beta-amino acid aminotransferase; Beta-phenylalanine aminotransferase; VpAT; EC 2.6.1.- (characterized)
to candidate CA265_RS15950 CA265_RS15950 glutamate-1-semialdehyde-2,1-aminomutase
Query= SwissProt::H8WR05 (434 letters) >FitnessBrowser__Pedo557:CA265_RS15950 Length = 456 Score = 201 bits (511), Expect = 4e-56 Identities = 132/398 (33%), Positives = 201/398 (50%), Gaps = 20/398 (5%) Query: 24 SQRQFEAQARYMPGA-NSRSVLFYAPF--PLTIARGEGAALWDADGHRYADFIAEYTAGV 80 S +E Y PG NS F + + PL I +G+G +WDADG+++ DF + + Sbjct: 31 SAELYEKSKTYFPGGVNSPVRAFKSVYGTPLFIEKGDGCYIWDADGNQFIDFCGSWGPLI 90 Query: 81 YGHSAPEIRDAVIEAMQGGINLTGHNLLEGRLARLICERFPQIEQLRFTNSGTEANLMAL 140 GH+ P+IR+ V E MQ G++ LE LA LI + +E++RFT+SGTEA + A+ Sbjct: 91 LGHNNPKIREKVTEVMQNGMSFGAPTALENELAELIIKNNRFVEKIRFTSSGTEAVMSAI 150 Query: 141 TAALHFTGRRKIVVFSGGYHG-----------GVLGFGARPS---PTTVPFDFLVLPYND 186 A FT R KI+ F G YHG G++ FG S P + + +V+P ND Sbjct: 151 RLARGFTSRDKILKFEGCYHGHSDSLLVKAGSGLVTFGETSSAGVPKSFAEETIVVPLND 210 Query: 187 AQTARAQIERHGPEIAVVLVEPMQGASGCIPGQPDFLQALRESATQVGALLVFDEVMTS- 245 + +IA V++E + +G I +++ LR+ T G+LL+FDEV+T Sbjct: 211 KTAIEQAFAQFKDQIAAVIIEGIPANNGLIIQDEEYIHFLRKICTDNGSLLIFDEVITGF 270 Query: 246 RLAPHGLANKLGIRSDLTTLGKYIGGGMSFGAFGGRADVMALFDPRTGPLAHSGTFNNNV 305 R+ G A G+ D+ T GK IGGG+ G +G RA++MA P G + +GT + N Sbjct: 271 RVGFEGAAAHYGVTPDIVTYGKIIGGGLPVGMYGARAEIMAHISP-DGGVYQAGTLSGNP 329 Query: 306 MTMAAGYAGLTKLFTPEAAGALAERGEALRARLNALCANEGVAMQFTGIGSLMNAHFVQG 365 + MAAG A LT+L L + + A + + IGS+ F Sbjct: 330 VAMAAGIATLTELNKSSFYKDLNTKAQEFVASIQRFATARNYKFKVFTIGSIFWFAFTDK 389 Query: 366 D-VRSSEDLAAVDGRLRQLLFFHLLNEDIYSSPRGFVV 402 D ++S++D+ A +++ LLN IY P G+ V Sbjct: 390 DKIQSADDIDAGSMEKFKIMHRELLNRGIYLGPSGYEV 427 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: 431 Number of extensions: 16 Number of successful extensions: 5 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: 456 Length adjustment: 32 Effective length of query: 402 Effective length of database: 424 Effective search space: 170448 Effective search space used: 170448 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