Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_081423433.1 MCA_RS12205 O-succinylhomoserine sulfhydrylase
Query= SwissProt::P55218 (403 letters) >NCBI__GCF_000008325.1:WP_081423433.1 Length = 411 Score = 516 bits (1329), Expect = e-151 Identities = 251/389 (64%), Positives = 304/389 (78%), Gaps = 1/389 (0%) Query: 11 DSDLEGAAFDTLAVRAGQRRTPEGEHGEALFTTSSYVFRTAADAAARFAGEVPGNVYSRY 70 D D A +T AVRAGQRRT E EH E +F TSSYVF +AA+AA RFAG+ GN+YSR+ Sbjct: 21 DLDWNEFAMETRAVRAGQRRTMEQEHAEPIFATSSYVFASAAEAAERFAGKAAGNIYSRF 80 Query: 71 TNPTVRTFEERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFD 130 TNPTVRTFEER+AALEG E+ VA SGM+AI + L +GDHV+ SRSVFG+T LF Sbjct: 81 TNPTVRTFEERLAALEGGERCVAVGSGMAAIASTAFGLLKAGDHVVCSRSVFGNTTLLFQ 140 Query: 131 KYFKRFGIQVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGAL 190 Y +FG+ + L+D W AA +P T+ F+E+PSNPL E+ DI LAEIAH++G L Sbjct: 141 NYLAKFGVPTTFVGLTDYDGWAAAIRPETRFLFIETPSNPLTEIADIPRLAEIAHSRGCL 200 Query: 191 LAVDNCFCTPALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQM-KEVVGFLRTA 249 L VDNCFCTPALQ+PL LGAD+VIHSATKY+DGQGR +GG + G E + E+ FLRT Sbjct: 201 LVVDNCFCTPALQRPLALGADIVIHSATKYLDGQGRCVGGAIVGGRELLDAEIYPFLRTG 260 Query: 250 GPTLSPFNAWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELA 309 GP++SPFNAW+FLKGLETL +RM+AH +AL LA WLE QP +ERV+Y GL SHPQHELA Sbjct: 261 GPSMSPFNAWVFLKGLETLNLRMKAHCENALGLARWLEAQPWVERVHYPGLASHPQHELA 320 Query: 310 RRQQSGFGAVVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRLSPED 369 RQQSGFG +VSF+VKGG++AAWR ID+TR++SIT NLGD KTTI HPATT+HGRLSPE Sbjct: 321 ARQQSGFGGIVSFEVKGGQEAAWRLIDSTRLLSITGNLGDAKTTITHPATTTHGRLSPEA 380 Query: 370 RARAGIGDSLIRVAVGLEDLDDLKADMAR 398 RA AGI D LIR+AVGLE+L D++AD+AR Sbjct: 381 RAAAGIADGLIRIAVGLENLADIQADLAR 409 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: 485 Number of extensions: 16 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: 411 Length adjustment: 31 Effective length of query: 372 Effective length of database: 380 Effective search space: 141360 Effective search space used: 141360 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