Align aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_012169089.1 AZC_RS02835 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::O59096 (389 letters) >NCBI__GCF_000010525.1:WP_012169089.1 Length = 394 Score = 272 bits (695), Expect = 1e-77 Identities = 148/371 (39%), Positives = 222/371 (59%), Gaps = 6/371 (1%) Query: 21 IAAGMKDVISLGIGEPDFDTPQHIKEYAKEALDKGLTHYGPNIGLLELREAIAEKLKKQN 80 +AA +D+I+LGIG+PDF TP+HI E A +AL G Y P++G+ LREA+A L K+ Sbjct: 26 LAAQGRDIINLGIGQPDFRTPEHIVEAAVKALKDGQHGYTPSVGIQPLREAVARDLHKRF 85 Query: 81 GIEADPKTEIMVLLGANQAFLMGLSAFLKDGEEVLIPTPAFVSYAPAVILAGGKPVEVPT 140 +E DP +M++ G + F + G E+L P P F Y + G P+ VP Sbjct: 86 DVEVDPGL-VMIMPGGKVTMYAAILLFGEPGAEILYPDPGFPIYRSMIEYTGATPIPVPI 144 Query: 141 YEEDEFRLNVDELKKYVTDKTRALIINSPCNPTGAVLTKKDLEEIADFVVEH-DLIVISD 199 EE+ F + +E +T KTR LIINSP NPTG V K +++++ + +H + ++SD Sbjct: 145 REENGFAFSAEETLALITPKTRLLIINSPANPTGGVTPKAEIDKLVKGLADHPHVALMSD 204 Query: 200 EVYEHFIYDDARHYSIASLDGMFERTITVNGFSKTFAMTGWRLGFVAAPSWIIERMVKFQ 259 E+Y+ F++D RH ++ + + +R I +NG+SKT+AMTGWRLG+ P + +++ K Sbjct: 205 EIYDQFLFDGERHQTLLAYPEIRDRLILLNGWSKTYAMTGWRLGYSIWPQALYDKVRKLS 264 Query: 260 MYNATCPVTFIQYAAAKALKDERSWKAVEEMRKEYDRRRKLVWKRLNEM-GLPTVKPKGA 318 + +C QYA AL E + V M E+D+RR+LV + LN + G+ KPKGA Sbjct: 265 VNAWSCVNAATQYAGIAAL--EGPQEPVAAMLAEFDKRRRLVVEGLNALPGVTCAKPKGA 322 Query: 319 FYIFPRIRDTGLTS-KKFSELMLKEARVAVVPGSAFGKAGEGYVRISYATAYEKLEEAMD 377 FY FP + TG TS K + +L++A VA + G FG GEGY+R+SYA + E + A++ Sbjct: 323 FYAFPNVSRTGWTSAKALASALLEDAGVATIGGPDFGVHGEGYIRLSYANSAENIARALE 382 Query: 378 RMERVLKERKL 388 RM L ERK+ Sbjct: 383 RMGAFLSERKV 393 Lambda K H 0.319 0.136 0.391 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: 24 Number of successful extensions: 6 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: 389 Length of database: 394 Length adjustment: 31 Effective length of query: 358 Effective length of database: 363 Effective search space: 129954 Effective search space used: 129954 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