Align cystathionine gamma-lyase (EC 4.4.1.1); cysteine-S-conjugate beta-lyase (EC 4.4.1.13) (characterized)
to candidate 6937071 Sama_1242 methionine gamma-lyase (RefSeq)
Query= BRENDA::A2RM21 (380 letters) >FitnessBrowser__SB2B:6937071 Length = 392 Score = 317 bits (812), Expect = 4e-91 Identities = 177/389 (45%), Positives = 246/389 (63%), Gaps = 13/389 (3%) Query: 2 TSIKTKVIHGGISTDKTTGAVSVPIYQTSTY-----KQNGL---GQPKEYEYSRSGNPTR 53 + + T V+HGG D GA+ P+YQ++T+ +Q G G Y Y+R GNPT Sbjct: 5 SKLATLVVHGGHERD-AMGALVSPLYQSATFVFDNARQGGARFAGDEAGYIYTRLGNPTT 63 Query: 54 HALEELIADLEGGVQGFAFSSGLAGIHA-VLSLFSAGDHIILADDVYGGTFRLMDKVLTK 112 LE +A LEG + A +SG+ + A +L+ S GDH++ + VYG TF LM ++ + Sbjct: 64 AELERKLAILEGAEEAAATASGMGAVSAALLANLSQGDHLVASRAVYGCTFALMTDLMAR 123 Query: 113 TGIIYDLVDLSNLDDLKAAFKEETKAIYFETPSNPLLKVLDIKEISAIAKAHDALTLVDN 172 GI LVD ++AA ++ T+AI+ ETP NP L V D+ I+AI K H LT+VDN Sbjct: 124 FGIEVTLVDFKEPAAIEAAIRDNTRAIFCETPVNPHLDVFDLDAIAAIGKRHGLLTIVDN 183 Query: 173 TFATPYLQQPIALGADIVLHSATKYLGGHSDVVAGLVTTNSKELASEIGF-LQNSIGAVL 231 TF TP LQ+P+ G D+V+HSATKYL GH DV+AG+V SKE ++ + + IGAV+ Sbjct: 184 TFMTPLLQRPLDHGIDMVIHSATKYLNGHGDVIAGMV-AGSKEQIDKVKYQIIKDIGAVM 242 Query: 232 GPQDSWLVQRGIKTLALRMEAHSANAQKIAEFLETSKAVSKVYYPGLNSHPGHEIAKKQM 291 P D+WL+ RG+KTL +R++ H NA+KIA+FLE V +VYYP L SH GH QM Sbjct: 243 SPHDAWLILRGMKTLDVRVQRHCDNAEKIADFLEAHPRVGRVYYPALKSHQGHRFLGTQM 302 Query: 292 SAFGGMISFEL-TDENAVKDFVENLSYFTLAESLGGVESLIEVPAVMTHASIPKELREEI 350 GG+I+FEL +D +FV++L FT+A SLG ESLI+ PA MTH+ E R E Sbjct: 303 RRAGGVIAFELKSDIEGSINFVDSLKVFTIAVSLGDAESLIQHPASMTHSPYTPEARLEA 362 Query: 351 GIKDGLIRLSVGVEAIEDLLTDIKEALEK 379 GI D L+R+SVG+E ++DL+ D+ +AL K Sbjct: 363 GITDTLLRISVGLEDVDDLIADLSQALAK 391 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: 420 Number of extensions: 17 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: 392 Length adjustment: 30 Effective length of query: 350 Effective length of database: 362 Effective search space: 126700 Effective search space used: 126700 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