Align Beta-phenylalanine transaminase; Aromatic beta-amino acid aminotransferase; Beta-phenylalanine aminotransferase; VpAT; EC 2.6.1.- (characterized)
to candidate WP_013553705.1 NITSA_RS03780 glutamate-1-semialdehyde-2,1-aminomutase
Query= SwissProt::H8WR05 (434 letters) >NCBI__GCF_000186245.1:WP_013553705.1 Length = 430 Score = 229 bits (583), Expect = 2e-64 Identities = 157/417 (37%), Positives = 210/417 (50%), Gaps = 28/417 (6%) Query: 24 SQRQFEAQARYMPGANSRSVLFYAPF---PLTIARGEGAALWDADGHRYADFIAEYTAGV 80 S+ FE RY+PG V + P I RGEG L+D DG+RY D++ + + Sbjct: 6 SEAAFEEAYRYIPGGVDSPVRAFGSVGGVPPFIERGEGPYLYDIDGNRYIDYVQSWGPLI 65 Query: 81 YGHSAPEIRDAVIEAMQGGINLTGHNLLEGRLARLICERFPQIEQLRFTNSGTEANLMAL 140 +GH PEI +AVIE + G++ LE LA+ I E F I+++RF NSGTEA + AL Sbjct: 66 FGHCDPEIENAVIETAKKGLSFGAPTELETALAKEIVELFDSIDKVRFVNSGTEAVMSAL 125 Query: 141 TAALHFTGRRKIVVFSGGYHG-----------GVLGFGARPSPTTVPFDF----LVLPYN 185 A +TGR V F+G YHG G FGA PS VP D L+ YN Sbjct: 126 RLARGYTGRDDFVKFTGCYHGHSDSLLVQAGSGAATFGA-PSSPGVPADLTKHTLLATYN 184 Query: 186 DAQTARAQIERHGPEIAVVLVEPMQGASGCIPGQPDFLQALRESATQVGALLVFDEVMTS 245 D ++ + E+ IA V++EP+ G G +P + FLQ LRE GALL+FDEVM+ Sbjct: 185 DLESVKRCFEQSEGGIACVIIEPIAGNMGLVPAEESFLQGLRELCDAHGALLIFDEVMSG 244 Query: 246 -RLAPHGLANKLGIRSDLTTLGKYIGGGMSFGAFGGRADVMALFDPRTGPLAHSGTFNNN 304 R + G +R DL TLGK IGGGM GAFGGRA++M P GP+ +GT + N Sbjct: 245 FRASLKGAQGLTTVRPDLVTLGKVIGGGMPVGAFGGRAEIMHKLSPE-GPVYQAGTLSGN 303 Query: 305 VMTMAAGYAGLTKL-FTPEAAGALAERGEALRARLNALCANEGVAMQFTGIGSLMNAHFV 363 + MAAG L KL P LAER L A + G+ + GS+ F Sbjct: 304 PVAMAAGLTSLRKLKANPSLYVTLAERARKLMEGFEAAARSAGLPLVTEVRGSMFGFFFT 363 Query: 364 QGDVRSSEDLAAVDGRLRQLLFFHLLNEDIY----SSPRGFVVLSLPLTDADIDRYV 416 V++ ED D + +L+ +Y S GF+ S L DA ID + Sbjct: 364 DEPVKNFEDAKRGDNEYFKKFHRAMLDRGVYLACSSYETGFI--STALDDALIDETI 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: 456 Number of extensions: 22 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: 430 Length adjustment: 32 Effective length of query: 402 Effective length of database: 398 Effective search space: 159996 Effective search space used: 159996 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 10 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