Align aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_011654119.1 RL_RS27700 aspartate/tyrosine/aromatic aminotransferase
Query= BRENDA::P04693 (397 letters) >NCBI__GCF_000009265.1:WP_011654119.1 Length = 395 Score = 254 bits (649), Expect = 3e-72 Identities = 148/395 (37%), Positives = 213/395 (53%), Gaps = 10/395 (2%) Query: 1 MFQKVDAYAGDPILTLMERFKEDPRSDKVNLSIGLYYNEDGIIPQLQAVAEAEARLNAQP 60 MF+K+ A D +L L++ F+ DPR KV+L +G+Y +E G P ++AV AE +L + Sbjct: 1 MFEKLTAQPADSLLALIKAFQADPRGYKVDLGVGVYRDEQGRTPVMRAVKLAEKQL-LET 59 Query: 61 HGASLYLPMEGLNCYRHAIAPLLFGADHPVLKQQRVATIQTLGGSGALKVGADFLKRYFP 120 + YL EG + + + P++FGA H V IQT GGSGAL++GA+ + P Sbjct: 60 QDSKRYLGPEGDLNFVNLLKPIIFGATH---NAGNVVGIQTPGGSGALRLGAELIASATP 116 Query: 121 ESGVWVSDPTWENHVAIFAGAGFEVSTYPWYDEATNGVRFNDLLATLKTLPARSIVLLHP 180 + VW+ P+W NH IF A V Y + D A + F+ +L L A ++LLH Sbjct: 117 GAKVWLGTPSWPNHAPIFESARLTVKDYRFVDLAKQQIDFDRVLEALDAAQAGDVILLHG 176 Query: 181 CCHNPTGADLTNDQWDAVIEILKARELIPFLDIAYQGFGAGMEEDAYAIRAIASAGLPAL 240 CCHNPTG D QW + L R+L+PF+D+AYQG G G+E DA R I A AL Sbjct: 177 CCHNPTGIDFDIQQWKQIAAKLVERKLLPFIDLAYQGLGDGLEADAEPTRLILEAVDEAL 236 Query: 241 VSNSFSKIFSLYGERVGGLSVMCEDAEAAGRVLGQLKATVRRNYSSPPNFGAQVVAAVLN 300 V+ S K F LY ERVG L ++ +A+ G + + R N+S PP+ GA +V +L Sbjct: 237 VAYSCDKNFGLYRERVGALYLVSRNADQLKIADGNMASLARVNWSMPPDHGAAIVRVILE 296 Query: 301 DEALKASWLAEVEEMRTRILAMRQELVKVLSTEMPERNFDYLLNQRGMFSYTGLSAAQVD 360 L W E+ EM R+ R L+ PE F + NQRG+FS +S Sbjct: 297 SAELTQIWKQELVEMCARVNGNR----AALAASHPELGF--IANQRGLFSNLAMSKETAV 350 Query: 361 RLREEFGVYLIASGRMCVAGLNTANVQRVAKAFAA 395 L + G+Y+ SGRM +AG+ ++ + KA +A Sbjct: 351 ALCHKHGIYMADSGRMNLAGMQPSDAAAIVKALSA 385 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: 351 Number of extensions: 14 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: 395 Length adjustment: 31 Effective length of query: 366 Effective length of database: 364 Effective search space: 133224 Effective search space used: 133224 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