Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate WP_090442034.1 BLS63_RS07455 O-succinylhomoserine sulfhydrylase
Query= BRENDA::Q5H4T8 (397 letters) >NCBI__GCF_900100495.1:WP_090442034.1 Length = 403 Score = 310 bits (793), Expect = 6e-89 Identities = 173/384 (45%), Positives = 244/384 (63%), Gaps = 13/384 (3%) Query: 19 TLAIHGGQSPDPSTGAVMPPIYATSTY--------AQSSPGEHQGFEYSRTHNPTRFAYE 70 TLA+ GQ P G I+ TS+Y A GE G YSR NPT A+E Sbjct: 21 TLAVRAGQRRTPE-GEHSEAIFPTSSYVFRTAADAAARFAGEVPGNVYSRYTNPTVRAFE 79 Query: 71 RCVAALEGGTRAFAFASGMAAT-STVMELLDAGSHVVAMDDLYGGTFRLFERVRRRTAGL 129 +AALEG +A A +SGMAA + VM L G HV+ ++G T LFE+ +R G+ Sbjct: 80 ERLAALEGAEQAVATSSGMAAILAIVMSLCSGGDHVLVSRSVFGSTISLFEKYLKRF-GV 138 Query: 130 DFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTFA 189 +V L+D AA++AA + +TK++++E+P+NP+ +LVDIAA+A IA G L VDN F Sbjct: 139 QVDYVALSDLAAWEAAFKPNTKLLFVESPSNPLAELVDIAALAEIAHGKGALLAVDNCFC 198 Query: 190 SPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAVVGDNAELAEQMAFLQNSIGGVQGPF 249 +P LQ+PL L AD+V+HSATKY++G +GG+ V G ++ E + FL+ + G PF Sbjct: 199 TPALQQPLKLRADIVMHSATKYIDGQGRSMGGV-VAGRAEQMKEVVGFLRTA-GPTLSPF 256 Query: 250 DSFLALRGLKTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLASHPQHVLAKRQMSGF 309 ++++ L+GL+TL +RM+AHC +AL LA WLE P +E+V Y GL SHPQH LAKRQ SGF Sbjct: 257 NAWIFLKGLETLRVRMQAHCASALELALWLEQQPGVERVYYAGLPSHPQHALAKRQQSGF 316 Query: 310 GGIVSIVLKGGFDAAKRFCEKTELFTLAESLGGVESLVNHPAVMTHASIPVARREQLGIS 369 G +VS +KGG +AA RF + T + ++ +LG ++ + HPA +H + A R GI Sbjct: 317 GAVVSFEVKGGKEAAWRFIDATRVISITTNLGDTKTTIAHPASTSHGRLSPAERANAGIR 376 Query: 370 DALVRLSVGIEDLGDLRGDLERAL 393 D L+R++VG+EDL DL+ DL R L Sbjct: 377 DNLIRVAVGLEDLVDLKADLARGL 400 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: 439 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: 397 Length of database: 403 Length adjustment: 31 Effective length of query: 366 Effective length of database: 372 Effective search space: 136152 Effective search space used: 136152 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