Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate WP_081423433.1 MCA_RS12205 O-succinylhomoserine sulfhydrylase
Query= BRENDA::Q5H4T8 (397 letters) >NCBI__GCF_000008325.1:WP_081423433.1 Length = 411 Score = 318 bits (814), Expect = 2e-91 Identities = 176/363 (48%), Positives = 232/363 (63%), Gaps = 11/363 (3%) Query: 38 PIYATSTY--------AQSSPGEHQGFEYSRTHNPTRFAYERCVAALEGGTRAFAFASGM 89 PI+ATS+Y A+ G+ G YSR NPT +E +AALEGG R A SGM Sbjct: 49 PIFATSSYVFASAAEAAERFAGKAAGNIYSRFTNPTVRTFEERLAALEGGERCVAVGSGM 108 Query: 90 AA-TSTVMELLDAGSHVVAMDDLYGGTFRLFERVRRRTAGLDFSFVDLTDPAAFKAAIRA 148 AA ST LL AG HVV ++G T LF+ + G+ +FV LTD + AAIR Sbjct: 109 AAIASTAFGLLKAGDHVVCSRSVFGNTTLLFQNYLAKF-GVPTTFVGLTDYDGWAAAIRP 167 Query: 149 DTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTFASPMLQRPLSLGADLVVHSA 208 +T+ ++IETP+NP+ ++ DI +A IA G L VVDN F +P LQRPL+LGAD+V+HSA Sbjct: 168 ETRFLFIETPSNPLTEIADIPRLAEIAHSRGCLLVVDNCFCTPALQRPLALGADIVIHSA 227 Query: 209 TKYLNGHSDMVGGIAVVGDNAELAEQMAFLQNSIGGVQGPFDSFLALRGLKTLPLRMRAH 268 TKYL+G VGG V G AE FL+ G PF++++ L+GL+TL LRM+AH Sbjct: 228 TKYLDGQGRCVGGAIVGGRELLDAEIYPFLRTG-GPSMSPFNAWVFLKGLETLNLRMKAH 286 Query: 269 CENALALAQWLETHPAIEKVIYPGLASHPQHVLAKRQMSGFGGIVSIVLKGGFDAAKRFC 328 CENAL LA+WLE P +E+V YPGLASHPQH LA RQ SGFGGIVS +KGG +AA R Sbjct: 287 CENALGLARWLEAQPWVERVHYPGLASHPQHELAARQQSGFGGIVSFEVKGGQEAAWRLI 346 Query: 329 EKTELFTLAESLGGVESLVNHPAVMTHASIPVARREQLGISDALVRLSVGIEDLGDLRGD 388 + T L ++ +LG ++ + HPA TH + R GI+D L+R++VG+E+L D++ D Sbjct: 347 DSTRLLSITGNLGDAKTTITHPATTTHGRLSPEARAAAGIADGLIRIAVGLENLADIQAD 406 Query: 389 LER 391 L R Sbjct: 407 LAR 409 Lambda K H 0.320 0.134 0.391 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: 477 Number of extensions: 21 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: 397 Length of database: 411 Length adjustment: 31 Effective length of query: 366 Effective length of database: 380 Effective search space: 139080 Effective search space used: 139080 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 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