Align aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate CA265_RS08140 CA265_RS08140 methionine aminotransferase
Query= BRENDA::O59096 (389 letters) >FitnessBrowser__Pedo557:CA265_RS08140 Length = 381 Score = 182 bits (462), Expect = 1e-50 Identities = 113/367 (30%), Positives = 192/367 (52%), Gaps = 15/367 (4%) Query: 23 AGMKDVISLGIGEPDFDTPQHIKEYAKEALDKGLTHYGPNIGLLELREAIAEKLKKQNGI 82 A + I+L G PD+ + E +A+ G Y P G L+E IAEK++ I Sbjct: 23 AAEHNAINLSQGFPDYACDPKLVELVNKAMQDGFNQYAPMPGSTFLKETIAEKVENLYNI 82 Query: 83 EADPKTEIMVLLGANQAFLMGLSAFLKDGEEVLIPTPAFVSYAPAVILAGGKPVEVPTYE 142 + +P+TEI V G QA L++ + G+EV+I PA+ SYAP + L GG V TYE Sbjct: 83 KYNPETEITVTAGGTQAIFTALASIINAGDEVIIFEPAYDSYAPTIKLLGGL---VKTYE 139 Query: 143 --EDEFRLNVDELKKYVTDKTRALIINSPCNPTGAVLTKKDLEEIADFVVEHDLIVISDE 200 + ++ D +KK T KTR +I+N+P NPTG++L+ D++ + + D++++SDE Sbjct: 140 LAPPNYAIDWDMVKKLFTAKTRMIILNTPQNPTGSILSSDDMKSLIKLISGTDILILSDE 199 Query: 201 VYEHFIYDDARHYSIASLDGMFERTITVNGFSKTFAMTGWRLGFVAAPSWIIERMVKFQM 260 VYEH IYD+ +H S+ + +R+ + F K TGW+LG+ AP + + K Sbjct: 200 VYEHLIYDEQKHQSVMLYPELKQRSFIIASFGKLLHATGWKLGYCLAPEKLTKEFRKVHQ 259 Query: 261 YNATCPVTFIQYAAAKALKDERSWKAVEEMRKEYDRRRKLVWKRLNEMGLPTVKPKGAFY 320 +N + +Q A A +K+ +++ E+ + ++R L E + G++ Sbjct: 260 FNVFSVNSPMQQAIAHYIKEPKNY---TEIGSFFQQKRDYFRSLLAESRFKLLPCNGSY- 315 Query: 321 IFPRIRDTGLTSKK---FSELMLKEARVAVVPGSAFGKAGEGY--VRISYATAYEKLEEA 375 F + + ++ +K FS ++KE VA +P SAF + G + +R +A L A Sbjct: 316 -FQCVSYSSISDEKDTDFSMRLIKEFGVATIPVSAFYQKGIDHKIIRFCFAKENATLALA 374 Query: 376 MDRMERV 382 ++++ V Sbjct: 375 AEKLKNV 381 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: 344 Number of extensions: 14 Number of successful extensions: 3 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: 381 Length adjustment: 30 Effective length of query: 359 Effective length of database: 351 Effective search space: 126009 Effective search space used: 126009 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 09 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