Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_057508709.1 ABB28_RS11200 O-succinylhomoserine (thiol)-lyase
Query= SwissProt::P55218 (403 letters) >NCBI__GCF_001431535.1:WP_057508709.1 Length = 412 Score = 231 bits (588), Expect = 4e-65 Identities = 130/340 (38%), Positives = 195/340 (57%), Gaps = 6/340 (1%) Query: 67 YSRYTNPTVRTFEERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTI 126 Y+R NPT E +A LEG V TA+GM AI ++ +L D ++V +G + Sbjct: 54 YTRSGNPTRDLLGEALAELEGGAGGVVTATGMGAISLVLQALLGPEDTLVVPHDAYGGSW 113 Query: 127 SLFDKYFKRFGIQVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHA 186 LF+ + ++ L+D + A + KL VE+PSNPL + D+ + + AH Sbjct: 114 RLFNALAGKGQFKLVTADLTDPRSLAQALAGSPKLVLVETPSNPLLRITDLRFVIDAAHK 173 Query: 187 KGALLAVDNCFCTPALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQM-KEVVGF 245 GAL+ VDN F +PALQQPL GAD+V+HS TKYI+G +GG V R ++ +++ + Sbjct: 174 AGALVVVDNTFLSPALQQPLAFGADLVLHSTTKYINGHSDVVGGAVVARDPELAQQLTWW 233 Query: 246 LRTAGPTLSPFNAWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQ 305 G T SPF+A+L L+GL TL R++ H + A+ L + VYY GL HP Sbjct: 234 ANALGLTGSPFDAFLTLRGLRTLDARLRVHQENTAAIVPLLAAHRAVSAVYYPGLADHPG 293 Query: 306 HELARRQQSGFGAVVSFDVK--GGRD---AAWRFIDATRMVSITTNLGDTKTTIAHPATT 360 H +A RQQSGFGA++SF++ G D A F+D + ++ +LG ++ +AHPAT Sbjct: 294 HAIAARQQSGFGAMLSFELVTCDGDDPHAAVRAFVDGLQYFTLAESLGGVESLVAHPATM 353 Query: 361 SHGRLSPEDRARAGIGDSLIRVAVGLEDLDDLKADMARGL 400 +H ++ + R AGI + L+R++VG+E DL AD+A L Sbjct: 354 THAAMTVQARQAAGISEGLLRLSVGIESERDLLADLAAAL 393 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: 394 Number of extensions: 20 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: 403 Length of database: 412 Length adjustment: 31 Effective length of query: 372 Effective length of database: 381 Effective search space: 141732 Effective search space used: 141732 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