Align aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_012404685.1 BPHY_RS27225 aspartate/tyrosine/aromatic aminotransferase
Query= BRENDA::P04693 (397 letters) >NCBI__GCF_000020045.1:WP_012404685.1 Length = 402 Score = 444 bits (1143), Expect = e-129 Identities = 226/396 (57%), Positives = 286/396 (72%), Gaps = 1/396 (0%) Query: 1 MFQKVDAYAGDPILTLMERFKEDPRSDKVNLSIGLYYNEDGIIPQLQAVAEAEARLNAQP 60 MF+ + AY GDPIL+L E F+ DPR++KVNLSIG+Y++E+G +P + +V EAEA + AQ Sbjct: 1 MFEHIPAYPGDPILSLNEDFQRDPRTNKVNLSIGIYFDENGTLPVMSSVREAEAAIVAQG 60 Query: 61 HGASLYLPMEGLNCYRHAIAPLLFGADHPVLKQQRVATIQTLGGSGALKVGADFLKRYFP 120 S YLPM GL YR A L+FGA R+AT+QT+GGSGALKVGADFLKR+FP Sbjct: 61 MPRS-YLPMSGLPAYRDAAQALVFGAQSAARAAGRIATVQTVGGSGALKVGADFLKRHFP 119 Query: 121 ESGVWVSDPTWENHVAIFAGAGFEVSTYPWYDEATNGVRFNDLLATLKTLPARSIVLLHP 180 S +W+SDP+WENH +F AG V+TYP+YD+AT G+RF + T+ LP RSIVLLH Sbjct: 120 GSQIWLSDPSWENHRVVFEAAGHTVNTYPYYDDATGGLRFAAMRDTIDALPERSIVLLHA 179 Query: 181 CCHNPTGADLTNDQWDAVIEILKARELIPFLDIAYQGFGAGMEEDAYAIRAIASAGLPAL 240 CCHNPTG DLT DQW ++ +L+ R LI F+D+AYQGFG G+EEDA +R +A A +P + Sbjct: 180 CCHNPTGVDLTKDQWRELVPVLQRRNLIAFVDMAYQGFGDGLEEDAACVRMLADADVPMI 239 Query: 241 VSNSFSKIFSLYGERVGGLSVMCEDAEAAGRVLGQLKATVRRNYSSPPNFGAQVVAAVLN 300 V+NSFSK FSLYGER G LSV+C+DA A RVLGQL T+R NYS+PP GA++VA VL Sbjct: 240 VANSFSKNFSLYGERCGALSVVCKDAAQAQRVLGQLTFTIRANYSNPPMHGARLVAGVLG 299 Query: 301 DEALKASWLAEVEEMRTRILAMRQELVKVLSTEMPERNFDYLLNQRGMFSYTGLSAAQVD 360 D L+ASW E+ MR RI MR + + L+ + E + Q GMF+YTGLSA QV+ Sbjct: 300 DAKLRASWDDELRVMRDRIHEMRHAIHEGLAGRVDEVMRARYIAQVGMFTYTGLSAEQVE 359 Query: 361 RLREEFGVYLIASGRMCVAGLNTANVQRVAKAFAAV 396 LR E G+YL+ SGRMCVAGLN +NV VA+A AAV Sbjct: 360 TLRVEHGIYLLRSGRMCVAGLNRSNVGYVAQAIAAV 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: 492 Number of extensions: 14 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: 402 Length adjustment: 31 Effective length of query: 366 Effective length of database: 371 Effective search space: 135786 Effective search space used: 135786 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