Align aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_012044279.1 BBTA_RS19770 aspartate/tyrosine/aromatic aminotransferase
Query= BRENDA::P04693 (397 letters) >NCBI__GCF_000015165.1:WP_012044279.1 Length = 388 Score = 261 bits (666), Expect = 3e-74 Identities = 150/396 (37%), Positives = 217/396 (54%), Gaps = 8/396 (2%) Query: 1 MFQKVDAYAGDPILTLMERFKEDPRSDKVNLSIGLYYNEDGIIPQLQAVAEAEARLNAQP 60 MF+++ DP+L L+ FK DPR+DKV+L +G+Y +E G P +AV AE RL + Sbjct: 1 MFERLSRQPDDPLLALIGIFKADPRADKVDLGVGVYRDEAGHSPIFRAVKAAE-RLIWES 59 Query: 61 HGASLYLPMEGLNCYRHAIAPLLFGADHPVLKQQRVATIQTLGGSGALKVGADFLKRYFP 120 + Y+ EG Y + ++ G PV A +QT GGSGAL++ AD + R Sbjct: 60 QSSKAYVAPEGDQTYLDLLWTMVGGTASPV----HAAGVQTPGGSGALRLAADLI-RQAG 114 Query: 121 ESGVWVSDPTWENHVAIFAGAGFEVSTYPWYDEATNGVRFNDLLATLKTLPARSIVLLHP 180 +W+ P+W NH IFA AG ++ TYP++D + ++ + ++ L+ VLLH Sbjct: 115 TGKIWLGLPSWPNHAGIFAAAGLKIETYPYFDVPSQSLQLDSMIEALQRAEPGDAVLLHA 174 Query: 181 CCHNPTGADLTNDQWDAVIEILKARELIPFLDIAYQGFGAGMEEDAYAIRAIASAGLPAL 240 CHNPTGA L + W V ++ AR L+P +D AYQGFGAG + D +RA+ +A AL Sbjct: 175 SCHNPTGAPLGAEDWARVTAVIAARGLVPLIDSAYQGFGAGFDGDVAGLRAMIAAIPEAL 234 Query: 241 VSNSFSKIFSLYGERVGGLSVMCEDAEAAGRVLGQLKATVRRNYSSPPNFGAQVVAAVLN 300 ++ S SK F LY ER G L + AA L A R +YS PP+ G+ +V +L Sbjct: 235 IAVSCSKSFGLYRERTGALYAVAAAQAAADTARSNLVAIARTSYSMPPDHGSAIVKTILG 294 Query: 301 DEALKASWLAEVEEMRTRILAMRQELVKVLSTEMPERNFDYLLNQRGMFSYTGLSAAQVD 360 L W +E++ MR R+ +R+ L N + Q GMFS ++ A V Sbjct: 295 TPDLYDDWRSELDSMRQRLATLRRAFADALGDRW--SNSLAIGRQEGMFSLLPVTPADVM 352 Query: 361 RLREEFGVYLIASGRMCVAGLNTANVQRVAKAFAAV 396 LRE+ GVY+ SGR+ +AGL A+V RVA F A+ Sbjct: 353 ALREKHGVYMPTSGRINIAGLKLADVARVAGLFKAL 388 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: 399 Number of extensions: 16 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: 397 Length of database: 388 Length adjustment: 31 Effective length of query: 366 Effective length of database: 357 Effective search space: 130662 Effective search space used: 130662 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