Align aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_090447114.1 BLS63_RS17730 aspartate/tyrosine/aromatic aminotransferase
Query= BRENDA::P04693 (397 letters) >NCBI__GCF_900100495.1:WP_090447114.1 Length = 398 Score = 321 bits (823), Expect = 2e-92 Identities = 176/395 (44%), Positives = 235/395 (59%), Gaps = 2/395 (0%) Query: 2 FQKVDAYAGDPILTLMERFKEDPRSDKVNLSIGLYYNEDGIIPQLQAVAEAEARLNAQPH 61 F +V GDPIL L+E ++ DP K++L +G+Y + G+ P QAV AE RL + Sbjct: 4 FAQVVRVPGDPILGLIEAYRADPNPAKLDLGVGVYKDARGLTPIPQAVKRAEQRL-VETE 62 Query: 62 GASLYLPMEGLNCYRHAIAPLLFGADHPVLKQQRVATIQTLGGSGALKVGADFLKRYFPE 121 + Y+ G + +A L+ GAD P+L QR QT GG+GAL++ ADF+ P Sbjct: 63 TSKSYIGGHGDPLFGARLAELVLGADSPLLAAQRAGASQTPGGTGALRLAADFIAHCLPG 122 Query: 122 SGVWVSDPTWENHVAIFAGAGFEVSTYPWYDEATNGVRFNDLLATLKTLPARSIVLLHPC 181 G+W+S+PTW H +FA AG + YP Y A N + +LA L LP +VLLH C Sbjct: 123 RGIWLSEPTWPIHETLFAAAGLRIGHYP-YVGADNRLDVEAMLAALNQLPKGDVVLLHAC 181 Query: 182 CHNPTGADLTNDQWDAVIEILKARELIPFLDIAYQGFGAGMEEDAYAIRAIASAGLPALV 241 CHNPTG DL W V+E++KAREL+P +D AYQGFG G+E+DA+A+R AS LV Sbjct: 182 CHNPTGFDLAPRDWKRVLEVVKARELLPLIDFAYQGFGDGLEDDAWAVRLFASELPELLV 241 Query: 242 SNSFSKIFSLYGERVGGLSVMCEDAEAAGRVLGQLKATVRRNYSSPPNFGAQVVAAVLND 301 ++S SK F LY ER G L V + V QL + R +S+PP GA VVA +L+D Sbjct: 242 TSSCSKNFGLYRERTGALLVCAATPDKLQDVRSQLASLARNLWSTPPAHGAAVVATILDD 301 Query: 302 EALKASWLAEVEEMRTRILAMRQELVKVLSTEMPERNFDYLLNQRGMFSYTGLSAAQVDR 361 LKA W+ E+E MR R+ ++R LV+ L F ++ QRGMFSYTGL+ AQV R Sbjct: 302 AELKALWIDELEAMRQRVASLRLGLVEALRPYGLAERFAHIAEQRGMFSYTGLTPAQVQR 361 Query: 362 LREEFGVYLIASGRMCVAGLNTANVQRVAKAFAAV 396 LR E VYL+ SGR VAGL+ + +A A A V Sbjct: 362 LRAEDSVYLVGSGRANVAGLDANRLDDLASAIARV 396 Lambda K H 0.320 0.135 0.401 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: 413 Number of extensions: 21 Number of successful extensions: 3 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: 397 Length of database: 398 Length adjustment: 31 Effective length of query: 366 Effective length of database: 367 Effective search space: 134322 Effective search space used: 134322 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 (21.8 bits) S2: 50 (23.9 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