Align kynurenine-oxoglutarate transaminase (EC 2.6.1.7); cysteine-S-conjugate beta-lyase (EC 4.4.1.13) (characterized)
to candidate 352902 BT3375 aspartate aminotransferase (NCBI ptt file)
Query= BRENDA::Q6YP21 (454 letters) >FitnessBrowser__Btheta:352902 Length = 386 Score = 150 bits (380), Expect = 5e-41 Identities = 100/317 (31%), Positives = 162/317 (51%), Gaps = 22/317 (6%) Query: 64 SVVNLGQGFPDISPPTYVKEELSKIAAIDSLNQYTRGFGHPSLVKALSYLYEKLYQKQID 123 +V++ G PDI P +KE K A ++ +Y+ G L + +S Y+ Y + + Sbjct: 28 NVIDFTLGDPDIHPHDKIKEAGCK-AILEGRTRYSPNAGLLELREIISSRYKLQYNIEYN 86 Query: 124 SNKEILVTVGAYGSLFNTIQALIDEGDEVILIVPFYDCYEPMVRMAGATPVFIPLRSKPV 183 EI+VTVG L+ T+ A+++ GDEVI+ P++ Y MV M P+ + PV Sbjct: 87 PTNEIMVTVGGMEGLYLTLLAILNRGDEVIIPAPYWINYVQMVCMCSGEPII----TAPV 142 Query: 184 YGKRWSSSDWTLDPQELESKFNSKTKAIILNTPHNPLGKVYNREELQVIADLCIKYDTLC 243 S++D ++ + + KTKAIILNTP NP G++ + + +Q IA + I+ D + Sbjct: 143 -----STNDLSISIENIRKAITPKTKAIILNTPSNPSGRIISDDSIQQIAQIAIENDLIV 197 Query: 244 ISDEVYEWLVYSGNKHLKIATFPGMWERTITIGSAGKTFSVTGWKLGWSIGPNHLIKHLQ 303 I+DEVY+ L+Y I T M ERT+ I S K F +TGW+LG+ P+ LI + Sbjct: 198 ITDEVYKTLLYDNAHFKSIVTCDKMKERTVVINSLSKEFCMTGWRLGYIAAPSELISVMT 257 Query: 304 TVQQNTIYTCATPLQEALAQAFWIDIKRMDDPECYFNSLPKELEVKRDRMVRLLESVGLK 363 Q+N P Q A +A + + E Y + +E ++R+ V L E +K Sbjct: 258 MFQENIAACAPLPSQYAAIEA-------LRNSEKYSAGMIEEFTLRRN--VLLEEVAKIK 308 Query: 364 PI---VPDGGYFIIADV 377 I P G ++ + ++ Sbjct: 309 TITVDAPQGTFYAMLNI 325 Lambda K H 0.319 0.135 0.407 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: 335 Number of extensions: 11 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: 454 Length of database: 386 Length adjustment: 32 Effective length of query: 422 Effective length of database: 354 Effective search space: 149388 Effective search space used: 149388 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