Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_015819756.1 TERTU_RS11015 O-succinylhomoserine sulfhydrylase
Query= SwissProt::P55218 (403 letters) >NCBI__GCF_000023025.1:WP_015819756.1 Length = 402 Score = 535 bits (1377), Expect = e-156 Identities = 259/391 (66%), Positives = 317/391 (81%), Gaps = 1/391 (0%) Query: 14 LEGAAFDTLAVRAGQRRTPEGEHGEALFTTSSYVFRTAADAAARFAGEVPGNVYSRYTNP 73 L GA DTLAVRAGQ R PEGEH E ++TTSS+VF +A AAARF G+ PGNVYSRYTNP Sbjct: 12 LAGAELDTLAVRAGQVRGPEGEHSEPIYTTSSFVFASAGQAAARFRGDDPGNVYSRYTNP 71 Query: 74 TVRTFEERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDKYF 133 TVRTFE+RIAALEG E VATASGM+AIL+ M+L S+GDHV+ SRSVFG+T LF KY Sbjct: 72 TVRTFEDRIAALEGGEAGVATASGMAAILSTCMALLSAGDHVVCSRSVFGTTTVLFTKYL 131 Query: 134 KRFGIQVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGALLAV 193 ++FG+QVD L+DLAAWE + KPNT+L F+E+PSNP+ ++ D+ LA++AH+ G LL V Sbjct: 132 QKFGVQVDLVGLTDLAAWEQSLKPNTRLLFLETPSNPICDVADVRKLADLAHSNGCLLVV 191 Query: 194 DNCFCTPALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQMKEVVGFLRTAGPTL 253 DNCFCTPALQ+PL LGAD+V+HSATK++DGQGR MGG V GR +QM EV FLRT GPT+ Sbjct: 192 DNCFCTPALQKPLALGADIVVHSATKFLDGQGRCMGGAVVGRADQMAEVTAFLRTCGPTM 251 Query: 254 SPFNAWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELARRQQ 313 SPFNAW+F+KGLETLR+RM+AHSASALALA+WL+ P + +V YAGLP HP H LA +QQ Sbjct: 252 SPFNAWVFVKGLETLRLRMEAHSASALALAQWLDEHPKVGKVNYAGLPEHPGHSLAVQQQ 311 Query: 314 SGFGAVVSFDV-KGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRLSPEDRAR 372 S FG V+SF+V R+AAW +DA R++S+T NLGD KTTI HPATT+HGRLS E+R+ Sbjct: 312 SAFGGVLSFEVLPNTREAAWTVVDAARIMSLTANLGDAKTTIVHPATTTHGRLSDEERSA 371 Query: 373 AGIGDSLIRVAVGLEDLDDLKADMARGLAAL 403 AGI + LIRVAVGLE ++DLK D+ RGL+ L Sbjct: 372 AGISEGLIRVAVGLESINDLKKDLDRGLSLL 402 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: 486 Number of extensions: 11 Number of successful extensions: 2 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: 402 Length adjustment: 31 Effective length of query: 372 Effective length of database: 371 Effective search space: 138012 Effective search space used: 138012 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