Align cystathionine gamma-lyase (EC 4.4.1.1); cysteine-S-conjugate beta-lyase (EC 4.4.1.13) (characterized)
to candidate WP_011307957.1 MBAR_RS16035 aminotransferase class V-fold PLP-dependent enzyme
Query= BRENDA::A2RM21 (380 letters) >NCBI__GCF_000195895.1:WP_011307957.1 Length = 394 Score = 329 bits (844), Expect = 7e-95 Identities = 176/385 (45%), Positives = 247/385 (64%), Gaps = 13/385 (3%) Query: 6 TKVIHGGISTDKTTGAVSVPIYQTSTY-----KQNGL---GQPKEYEYSR--SGNPTRHA 55 TK +H D GA + PI+QTST+ +Q G+ Y Y+R PT Sbjct: 9 TKCVHAAEKPDPIFGAHTTPIFQTSTFIFENARQGAARFAGEESGYVYARIPPNTPTHAV 68 Query: 56 LEELIADLEGGVQGFAFSSGLAGIHAV-LSLFSAGDHIILADDVYGGTFRLMDKVLTKTG 114 L E A LEGG G F+SG+A + A+ L+ GDH+I D VYG T+ L +VL G Sbjct: 69 LAEKFAALEGGEAGQTFASGMAAVTAIALTALKQGDHLISTDVVYGCTYSLFSQVLPGLG 128 Query: 115 IIYDLVDLSNLDDLKAAFKEETKAIYFETPSNPLLKVLDIKEISAIAKAHDALTLVDNTF 174 I VD S +++K AFK ETK ++ E+P+NP L V DI EI+ IA+ ++AL +VDNTF Sbjct: 129 IEVSFVDTSKTENVKRAFKPETKMVFLESPANPTLNVCDIPEIARIARENEALCVVDNTF 188 Query: 175 ATPYLQQPIALGADIVLHSATKYLGGHSDVVAGLVTTNSKELASEIGFLQNSIGAVLGPQ 234 ATPY Q+P+ LGAD+ L S TKY+GGH+D++ G+V N+ + + + G ++GP Sbjct: 189 ATPYFQRPLELGADLSLSSCTKYIGGHADLLGGIVAGNN-DFIDRMSEVVGYTGGIMGPH 247 Query: 235 DSWLVQRGIKTLALRMEAHSANAQKIAEFLETSKAVSKVYYPGLNSHPGHEIAKKQMSAF 294 ++WL RG+KTL +RME H+ NA K+AEFLE+ V V YPGL HP +E+A+KQMS F Sbjct: 248 EAWLCIRGLKTLHIRMERHAENAMKVAEFLESRPEVEWVRYPGLPGHPQYELARKQMSGF 307 Query: 295 GGMISFELTDE-NAVKDFVENLSYFTLAESLGGVESLIEVPAVMTHASIPKELREEIGIK 353 GM+SFE+ A + ++N+ +LA SLG ++LI+ PA MTHA +P E+R+ +GI Sbjct: 308 SGMLSFEVKGGIEAGRKLMDNVKLCSLAVSLGATDTLIQHPASMTHACVPHEVRKSVGIT 367 Query: 354 DGLIRLSVGVEAIEDLLTDIKEALE 378 DGL+RLSVG+E ED++ D+K+ALE Sbjct: 368 DGLVRLSVGIEDPEDIIADLKQALE 392 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: 431 Number of extensions: 24 Number of successful extensions: 5 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: 394 Length adjustment: 30 Effective length of query: 350 Effective length of database: 364 Effective search space: 127400 Effective search space used: 127400 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 10 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