Align aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_028312920.1 H566_RS0120605 aspartate/tyrosine/aromatic aminotransferase
Query= BRENDA::P04693 (397 letters) >NCBI__GCF_000482785.1:WP_028312920.1 Length = 396 Score = 402 bits (1034), Expect = e-117 Identities = 209/397 (52%), Positives = 266/397 (67%), Gaps = 6/397 (1%) Query: 1 MFQKVDAYAGDPILTLMERFKEDPRSDKVNLSIGLYYNEDGIIPQLQAVAEAEARLNAQP 60 +F +D DPIL L E F D R KVNL +G+YY++ G IP L AV EAE +L + Sbjct: 5 LFAAIDLAPRDPILGLNEAFAADKRDTKVNLGVGVYYDDAGKIPLLAAVREAE-KLRFEQ 63 Query: 61 HGASLYLPMEGLNCYRHAIAPLLFGADHPVLKQQRVATIQTLGGSGALKVGADFLKRYFP 120 A YLP+EG+ Y A+ LLFGA+ P++ + R+ T Q LGG+GALK+GADFLKRYFP Sbjct: 64 AAARGYLPIEGIAAYDAAVGKLLFGAESPIVTEGRLVTAQALGGTGALKIGADFLKRYFP 123 Query: 121 ESGVWVSDPTWENHVAIFAGAGFEVSTYPWYDEATNGVRFNDLLATLKTLPARSIVLLHP 180 S V +S+P+WENH A+F AGFEV TY +Y T+G +LA LK ++IV+LH Sbjct: 124 ASKVLISNPSWENHRALFESAGFEVGTYAYYVSPTDGANVAGMLADLKAAAPQTIVVLHA 183 Query: 181 CCHNPTGADLTNDQWDAVIEILKARELIPFLDIAYQGFGAGMEEDAYAIRAIASAGLPAL 240 CCHNPTG DLT D W V+E++K R LI FLDIAYQGFG G++ DA A+R A AG+ L Sbjct: 184 CCHNPTGVDLTADDWKQVVEVVKERNLIAFLDIAYQGFGDGIDADAVAVRLFADAGISFL 243 Query: 241 VSNSFSKIFSLYGERVGGLSVMCEDAEAAGRVLGQLKATVRRNYSSPPNFGAQVVAAVLN 300 VS+SFSK FSLYGERVG L+V+ + + RVL QLK +R NYS+PP G VVA+VLN Sbjct: 244 VSSSFSKSFSLYGERVGALTVVDGSKDESARVLSQLKRVIRTNYSNPPTHGGTVVASVLN 303 Query: 301 DEALKASWLAEVEEMRTRILAMRQELVKVLSTEMPERNFDYLLNQRGMFSYTGLSAAQVD 360 L+ W E+ MR RI MR L + L F ++ QRGMFSYTGLSAAQV+ Sbjct: 304 TPELRKLWEDELAGMRDRIKTMRAGLAEGLG-----EKFAFVTRQRGMFSYTGLSAAQVE 358 Query: 361 RLREEFGVYLIASGRMCVAGLNTANVQRVAKAFAAVM 397 RL+EEFG+Y ++SGR+CVA LN+ N+ V A V+ Sbjct: 359 RLKEEFGIYAVSSGRICVAALNSKNLGYVVDAIGKVV 395 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: 426 Number of extensions: 20 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: 396 Length adjustment: 31 Effective length of query: 366 Effective length of database: 365 Effective search space: 133590 Effective search space used: 133590 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