Align aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_011868286.1 MMARC5_RS02615 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::O59096 (389 letters) >NCBI__GCF_000016125.1:WP_011868286.1 Length = 375 Score = 292 bits (748), Expect = 9e-84 Identities = 163/387 (42%), Positives = 242/387 (62%), Gaps = 20/387 (5%) Query: 3 LSDRLELVSASEIRKLFDIAAGMKDVISLGIGEPDFDTPQHIKEYAKEALDKGLTHYGPN 62 +++R SEIRK+F++A ++ I+LGIGEPDFDTP+HI E AK ALD G THY PN Sbjct: 2 IAERCLGTEQSEIRKIFNMAT--ENSINLGIGEPDFDTPKHIVEAAKSALDAGKTHYVPN 59 Query: 63 IGLLELREAIAEKLKKQNGIEADPKTEIMVLLGANQAFLMGLSAFLKDGEEVLIPTPAFV 122 G+ EL AI+EKLKK N ++ K I+ GA++A ++ L + GEEVL+P P FV Sbjct: 60 AGIPELTSAISEKLKKDNKLDISQK-NIVTTCGASEALMLSLFTLVNRGEEVLVPDPGFV 118 Query: 123 SYAPAVILAGGKPVEVPTYEEDEFRLNVDELKKYVTDKTRALIINSPCNPTGAVLTKKDL 182 SY L GK VP +D+FR++++ +K +++KT+ +++NSP NPTG+V+TK+++ Sbjct: 119 SYKGLTELCEGK--MVPIDLDDKFRIDLESVKNSISEKTKCIVLNSPSNPTGSVMTKEEI 176 Query: 183 EEIADFVVEHDLIVISDEVYEHFIYDDARHYSIASLDGMFERTITVNGFSKTFAMTGWRL 242 + I + E ++ VISDE+YE IY +HYS + I +NGFSK +AMTGWR+ Sbjct: 177 KGICEIADEKNICVISDEIYEKIIY-GKKHYSAMEFT---DNCILINGFSKAYAMTGWRV 232 Query: 243 GFVAAPS------WIIERMVKFQMYNATCPVTFIQYAAAKALKDERSWKAVEEMRKEYDR 296 G++A I+E M+K Y C +F Q+ A +AL +++ V +M E++R Sbjct: 233 GYLAVNENFDNKYEILENMMKIHQYGFACATSFAQFGAVEALTGDQN--CVSDMVSEFER 290 Query: 297 RRKLVWKRLNEMGLPTVKPKGAFYIFPRIRDTGLTSKKFSELMLKEARVAVVPGSAFGKA 356 RR L++ + E+ KP+GAFYIFP + + G ++L+ + + VPGSAFGK Sbjct: 291 RRNLIYSGMKEI-FSVQKPEGAFYIFPDVIEYGNGMDVATKLI--QNGILCVPGSAFGKN 347 Query: 357 GEGYVRISYATAYEKLEEAMDRMERVL 383 GE VR SYAT Y+ +E A+ M+ VL Sbjct: 348 GENSVRFSYATKYDDIERALSIMKNVL 374 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: 367 Number of extensions: 21 Number of successful extensions: 7 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: 375 Length adjustment: 30 Effective length of query: 359 Effective length of database: 345 Effective search space: 123855 Effective search space used: 123855 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