Align cystathionine gamma-lyase (EC 4.4.1.1); cysteine-S-conjugate beta-lyase (EC 4.4.1.13) (characterized)
to candidate Ac3H11_2452 O-acetylhomoserine sulfhydrylase (EC 2.5.1.49) / O-succinylhomoserine sulfhydrylase (EC 2.5.1.48)
Query= BRENDA::A2RM21 (380 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2452 Length = 415 Score = 204 bits (518), Expect = 5e-57 Identities = 138/406 (33%), Positives = 207/406 (50%), Gaps = 32/406 (7%) Query: 3 SIKTKVIHGGISTDKTTGAVSVPIYQTSTYKQNGL--------GQPKE-YEYSRSGNPTR 53 S T+++H GA+ PI+ + Y + + G K + Y+R G PT Sbjct: 8 SFTTQIVHADRLGGAEQGAIHQPIHTSVQYGYDKVEDLIAVFQGTAKGGFNYARQGTPTT 67 Query: 54 HALEELIADLEGGVQGFAFSSGLAGIHAV-LSLFSAGDHIILADDVYGGTFRLMDKVLTK 112 ALE I +E G FSSG+AGI AV L+L AGDH++ + V+G T ++ L Sbjct: 68 AALEAKITKMERGHGTIVFSSGMAGICAVFLTLLKAGDHLVASQFVFGNTNSVLG-TLAD 126 Query: 113 TGIIYDLVDLSNLDDLKAAFKEETKAIYFETPSNPLLKVLDIKEISAIAKAHDALTLVDN 172 G+ VD+++ ++ AA + T+ ++ ET +NP ++ D++ I A+ KAH AL +VDN Sbjct: 127 LGVEVTTVDVTDAANVAAALRPNTRMVFVETIANPGTQIPDLEGIGALCKAHGALYVVDN 186 Query: 173 TFATPYLQQPIALGADIVLHSATKYLGGHSDVVAGLVTTNS---------------KELA 217 T A+PYL + +GA +V++S TK +GG D + G +T K A Sbjct: 187 TVASPYLFRAATVGAGLVVNSLTKSIGGLGDALGGAITDTGLYDWSRYPNIFAAYRKGDA 246 Query: 218 SEIGFLQ------NSIGAVLGPQDSWLVQRGIKTLALRMEAHSANAQKIAEFLETSKAVS 271 G Q +G L + + G +TLALRM+ SA A +A++LE A++ Sbjct: 247 KGWGLQQLRKKGLRDMGGTLSSHAAHQLALGAETLALRMDRTSATALALAQWLEAHPAIA 306 Query: 272 KVYYPGLNSHPGHEIAKKQMSAFGGMISFELTDENAVKDFVENLSYFTLAESLGGVESLI 331 +V+YP L SHP H AKK + A ++SFEL D + L A L +LI Sbjct: 307 RVHYPLLPSHPQHAFAKKHLKAGSWLLSFELRDPDQCLPVCNRLQLPIKATGLADTRTLI 366 Query: 332 EVPAVMTHASIPKELREEIGIKDGLIRLSVGVEAIEDLLTDIKEAL 377 A +R +GI D +IRLSVG+E +EDLL D ++AL Sbjct: 367 IPVAHTIFWEAGPAVRASMGIADSMIRLSVGLEEVEDLLADFEQAL 412 Lambda K H 0.315 0.133 0.366 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: 406 Number of extensions: 22 Number of successful extensions: 4 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: 380 Length of database: 415 Length adjustment: 31 Effective length of query: 349 Effective length of database: 384 Effective search space: 134016 Effective search space used: 134016 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 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