Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_013076055.1 BTUS_RS10490 PLP-dependent transferase
Query= SwissProt::P55218 (403 letters) >NCBI__GCF_000092905.1:WP_013076055.1 Length = 393 Score = 278 bits (711), Expect = 2e-79 Identities = 154/387 (39%), Positives = 225/387 (58%), Gaps = 18/387 (4%) Query: 20 DTLAVRAGQRRTPEGEHGEALFTTS--SYVFRTAADAAARFAGEVPGNVYSRYTNPTVRT 77 DT +AG RR P TT S A A G G Y+R +NPT Sbjct: 4 DTRCSQAGNRRDP---------TTGAISLPIHHATTYAHPGLGSSTGFDYTRTSNPTRLA 54 Query: 78 FEERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDKYFKRFG 137 EE IAAL G + A ASGM+AI A+ L GDH+++S ++G T LF+++F+ G Sbjct: 55 LEETIAALHGGCRGFAFASGMAAIDAIAR-LFRPGDHLVLSDDLYGGTYRLFERFFRPLG 113 Query: 138 IQVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGALLAVDNCF 197 ++ Y SDL A +P T+ FVE+P+NP ++ D+ L+++AH +G L VDN F Sbjct: 114 LETTYVDTSDLQAVAKQIRPRTRALFVETPTNPTLKIADLKGLSQVAHERGLWLIVDNTF 173 Query: 198 CTPALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQMKEVVGFLRTA-GPTLSPF 256 TP LQ+PL+LGAD+V+ SATKY+ G + G V + E + + F++ + G L P Sbjct: 174 MTPYLQRPLELGADIVVESATKYLGGHNDVLAGTVVVKSEALANSLAFIQNSIGAVLGPQ 233 Query: 257 NAWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELARRQQSGF 316 +AWL L+G++TL +RM H +A LAEWL P + RVYY GLP HP H + R Q SG+ Sbjct: 234 DAWLLLRGIKTLHVRMDRHEGNARTLAEWLRAHPRVSRVYYPGLPDHPGHAVHRAQASGW 293 Query: 317 GAVVSFDVKGGRDAAW--RFIDATRMVSITTNLGDTKTTIAHPATTSHGRLSPEDRARAG 374 G +++F+V R W + R+++ +LG T++ I +PA +H + P+ R R G Sbjct: 294 GGMIAFEVPNNR---WVPPILAHLRVITFAESLGGTESLITYPAVQTHADVPPDVRQRLG 350 Query: 375 IGDSLIRVAVGLEDLDDLKADMARGLA 401 + DSL+R++VGLE +DDL D+ + LA Sbjct: 351 VTDSLLRLSVGLEHVDDLIQDLDQALA 377 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: 408 Number of extensions: 19 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: 393 Length adjustment: 31 Effective length of query: 372 Effective length of database: 362 Effective search space: 134664 Effective search space used: 134664 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