Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_057508383.1 ABB28_RS09425 cystathionine gamma-synthase
Query= SwissProt::P55218 (403 letters) >NCBI__GCF_001431535.1:WP_057508383.1 Length = 392 Score = 308 bits (789), Expect = 2e-88 Identities = 168/384 (43%), Positives = 245/384 (63%), Gaps = 13/384 (3%) Query: 21 TLAVRAGQRRTPE-GEHGEALFTTSSYVFRTAADAAARFAGEVPGNVYSRYTNPTVRTFE 79 TLA+ GQ P G ++ TS+Y A GE G YSR NPT +E Sbjct: 17 TLAIHGGQSPDPSTGAVMPPIYATSTY--------AQSSPGEHQGFEYSRTHNPTRFAYE 68 Query: 80 ERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDKYFKRF-GI 138 +A+LEG + A ASGM+A + VM L +G HV+ ++G T LF++ +R G+ Sbjct: 69 RCVASLEGGSRGFAFASGMAAT-STVMELLDAGSHVVAMDDIYGGTFRLFERVRRRTAGL 127 Query: 139 QVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGALLAVDNCFC 198 + L+DLAA+EAA P TK+ ++E+P+NP+ ++VDIAA+A IA G ++ VDN F Sbjct: 128 DFSFVDLTDLAAFEAAITPATKMVWIETPTNPMLKIVDIAAVAAIAKQHGLIIVVDNTFA 187 Query: 199 TPALQQPLKLGADVVIHSATKYIDGQGRGMGG-VVAGRGEQMKEVVGFLRTA-GPTLSPF 256 +P LQ+PL+LGAD+V+HSATKY++G +GG VV G + E + FL+ + G PF Sbjct: 188 SPMLQRPLELGADLVLHSATKYLNGHSDMVGGMVVVGDNTGLAEQMAFLQNSIGAVQGPF 247 Query: 257 NAWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELARRQQSGF 316 +++L L+GL+TL +RM+AH A+ALALA+WLE QP +E+V Y GL SHPQHELA RQ +G+ Sbjct: 248 DSFLALRGLKTLPLRMKAHCANALALAQWLETQPSVEKVIYPGLTSHPQHELATRQMNGY 307 Query: 317 GAVVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRLSPEDRARAGIG 376 G +VS +KGG +AA RF + T + ++ +LG ++ + HPA +H + E R GI Sbjct: 308 GGIVSIVLKGGFEAAKRFCERTELFTLAESLGGVESLVNHPAVMTHASIPVERRENLGIS 367 Query: 377 DSLIRVAVGLEDLDDLKADMARGL 400 + L+R++VG+E+L DL D+ R L Sbjct: 368 EGLVRLSVGVEELGDLMVDLERAL 391 Lambda K H 0.319 0.133 0.392 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: 378 Number of extensions: 16 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: 403 Length of database: 392 Length adjustment: 31 Effective length of query: 372 Effective length of database: 361 Effective search space: 134292 Effective search space used: 134292 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