Align cystathionine gamma-lyase (EC 4.4.1.1); cysteine-S-conjugate beta-lyase (EC 4.4.1.13) (characterized)
to candidate 200974 SO1812 methionine gamma-lyase (NCBI ptt file)
Query= BRENDA::A2RM21 (380 letters) >FitnessBrowser__MR1:200974 Length = 397 Score = 313 bits (801), Expect = 7e-90 Identities = 174/387 (44%), Positives = 239/387 (61%), Gaps = 11/387 (2%) Query: 1 MTSIKTKVIHGGISTDKTTGAVSVPIYQTSTY-----KQNG---LGQPKEYEYSRSGNPT 52 M T+ IH G + G++ P+YQT+T+ +Q G G Y Y+R GNPT Sbjct: 8 MWKAATQAIHAGHERE-AFGSLVTPLYQTATFVFDSAQQGGERFAGNEPGYIYTRLGNPT 66 Query: 53 RHALEELIADLEGGVQGFAFSSGLAGIHA-VLSLFSAGDHIILADDVYGGTFRLMDKVLT 111 LE +A LE A +SG+ + A +L+ GDH++ ++ VYG TF LM Sbjct: 67 VAELERKMAILERAEAAAATASGMGAVSAALLANLQIGDHLVASNAVYGCTFALMTNQFA 126 Query: 112 KTGIIYDLVDLSNLDDLKAAFKEETKAIYFETPSNPLLKVLDIKEISAIAKAHDALTLVD 171 + GI LVD S+++ ++ A K TK I+ ETP NP L+V D+ I+AIAK H ++VD Sbjct: 127 RFGIEVTLVDFSDVELIERAIKPNTKVIFCETPVNPHLQVFDLSAIAAIAKRHSLTSIVD 186 Query: 172 NTFATPYLQQPIALGADIVLHSATKYLGGHSDVVAGLVTTNSKELASEIGFLQNSIGAVL 231 NTF TP LQQPIALG D+V+HSATKYL GH DV+AG+V + +L + IGAV+ Sbjct: 187 NTFMTPLLQQPIALGIDVVVHSATKYLNGHGDVIAGIVCGSEAQLHRVKYEILKDIGAVM 246 Query: 232 GPQDSWLVQRGIKTLALRMEAHSANAQKIAEFLETSKAVSKVYYPGLNSHPGHEIAKKQM 291 P D+WL+ RG+KTL +R++ H +AQ++AEFLE AV++VYYPGL SH GH +QM Sbjct: 247 SPHDAWLILRGLKTLDVRLQRHCESAQRVAEFLEQHPAVTRVYYPGLKSHSGHRFIGQQM 306 Query: 292 SAFGGMISFEL-TDENAVKDFVENLSYFTLAESLGGVESLIEVPAVMTHASIPKELREEI 350 GG+I+FEL D FV NL F++A SLG ESLI+ PA MTH+ E R Sbjct: 307 RRAGGVIAFELAADFTQAMAFVGNLKLFSIAVSLGDAESLIQHPASMTHSPYSPEARAAA 366 Query: 351 GIKDGLIRLSVGVEAIEDLLTDIKEAL 377 GI D L+R+SVG+E +D++ D+ +AL Sbjct: 367 GIGDNLLRISVGLEDCDDIIADLSQAL 393 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: 385 Number of extensions: 15 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: 380 Length of database: 397 Length adjustment: 30 Effective length of query: 350 Effective length of database: 367 Effective search space: 128450 Effective search space used: 128450 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