Align aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_012401348.1 BPHY_RS09970 aspartate/tyrosine/aromatic aminotransferase
Query= BRENDA::P04693 (397 letters) >NCBI__GCF_000020045.1:WP_012401348.1 Length = 399 Score = 424 bits (1091), Expect = e-123 Identities = 222/399 (55%), Positives = 279/399 (69%), Gaps = 5/399 (1%) Query: 1 MFQKVDAYAGDPILTLMERFKEDPRSDKVNLSIGLYYNEDGIIPQLQAVAEAE-ARLNAQ 59 +F V+ DPIL L E F D R+ KVNL +G+Y NE+G IP L+AV EAE AR+ A Sbjct: 3 LFSAVELAPRDPILGLNEAFNADARTTKVNLGVGVYTNEEGKIPLLRAVREAEKARIEAA 62 Query: 60 -PHGASLYLPMEGLNCYRHAIAPLLFGADHPVLKQQRVATIQTLGGSGALKVGADFLKRY 118 P G YLP+EG+ Y A+ LL G D P++ RV T Q LGG+GALK+GADFLKR Sbjct: 63 LPRG---YLPIEGIAVYDAAVQKLLLGNDSPLIAAGRVVTAQALGGTGALKIGADFLKRV 119 Query: 119 FPESGVWVSDPTWENHVAIFAGAGFEVSTYPWYDEATNGVRFNDLLATLKTLPARSIVLL 178 P S V +SDP+WENH A+F AGFEV +YP+YD AT+GV F +L+ L + ++V+L Sbjct: 120 NPASKVAISDPSWENHRALFESAGFEVVSYPYYDAATHGVNFEGMLSALNSYAPGTVVVL 179 Query: 179 HPCCHNPTGADLTNDQWDAVIEILKARELIPFLDIAYQGFGAGMEEDAYAIRAIASAGLP 238 H CCHNPTG DLT DQW V+ ++KAREL+PFLDIAYQGFG G++ DA A+R A + L Sbjct: 180 HACCHNPTGVDLTVDQWKQVVAVVKARELVPFLDIAYQGFGDGIDADAAAVRLFAQSELN 239 Query: 239 ALVSNSFSKIFSLYGERVGGLSVMCEDAEAAGRVLGQLKATVRRNYSSPPNFGAQVVAAV 298 VS+SFSK FSLYGERVG LS++ E A RVL QLK +R NYS+PP G VVAAV Sbjct: 240 VFVSSSFSKSFSLYGERVGALSIITGSKEEAARVLSQLKRVIRTNYSNPPTHGGAVVAAV 299 Query: 299 LNDEALKASWLAEVEEMRTRILAMRQELVKVLSTEMPERNFDYLLNQRGMFSYTGLSAAQ 358 L L+A+W E+ EMR RI AMR LV+ L +R+F ++ QRGMFSY+GL+A Q Sbjct: 300 LASPELRATWETELGEMRDRIRAMRHGLVERLKAAGIDRDFSFVNAQRGMFSYSGLTAPQ 359 Query: 359 VDRLREEFGVYLIASGRMCVAGLNTANVQRVAKAFAAVM 397 VDRLREEFG+Y +++GR+CVA LNT N+ VA A AAV+ Sbjct: 360 VDRLREEFGIYAVSTGRICVAALNTRNLDVVANAVAAVL 398 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: 444 Number of extensions: 15 Number of successful extensions: 2 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: 399 Length adjustment: 31 Effective length of query: 366 Effective length of database: 368 Effective search space: 134688 Effective search space used: 134688 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