Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_081442714.1 ALVIN_RS05095 O-succinylhomoserine sulfhydrylase
Query= SwissProt::P55218 (403 letters) >NCBI__GCF_000025485.1:WP_081442714.1 Length = 431 Score = 512 bits (1318), Expect = e-150 Identities = 254/402 (63%), Positives = 309/402 (76%), Gaps = 10/402 (2%) Query: 4 DWDAGRLDSDLEGAAFDTLAVRAGQRRTPEGEHGEALFTTSSYVFRTAADAAARFAGEVP 63 DWD + F T A+R G RRT E EH E +F TSS+VF +AA+AAARFAGE Sbjct: 27 DWDGAE-----DAPGFATRAIRVGHRRTGESEHSEPIFATSSFVFASAAEAAARFAGEQA 81 Query: 64 GNVYSRYTNPTVRTFEERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFG 123 GN+YSR+TNPTVR FEER+AALEG E VATASGM+AIL++ + L +GD +L +RS+FG Sbjct: 82 GNIYSRFTNPTVRAFEERLAALEGGESCVATASGMAAILSVCLGLLKTGDRILAARSLFG 141 Query: 124 STISLFDKYFKRFGIQVDYPPLSDLAAWEAACKPN----TKLFFVESPSNPLAELVDIAA 179 ST LFDKY RFGI+ DY PLSDL+AWE A + + T+L F E+PSNPL E+VD+ Sbjct: 142 STTMLFDKYLARFGIRTDYVPLSDLSAWETALERDGERRTRLLFCETPSNPLTEMVDLRQ 201 Query: 180 LAEIAHAKGALLAVDNCFCTPALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQM 239 LA +AH GALL VDNCFCTPALQ+PL LGAD+V+HSATKY+DGQGR +GG V G +++ Sbjct: 202 LAALAHRHGALLVVDNCFCTPALQRPLALGADIVVHSATKYLDGQGRCVGGAVVGDRKRV 261 Query: 240 -KEVVGFLRTAGPTLSPFNAWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYA 298 +EV G LRTAGPTLSPFNAW+FLKGLETL +RM A S +A LAEWL+RQP +ERV+Y Sbjct: 262 GEEVYGVLRTAGPTLSPFNAWIFLKGLETLELRMLAQSRAAAELAEWLQRQPAVERVHYP 321 Query: 299 GLPSHPQHELARRQQSGFGAVVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPA 358 GL +HPQH L QQ GA+V+F V+GGR+AAWR IDATR++SIT NLGD KTTI HPA Sbjct: 322 GLANHPQHHLVGSQQRTGGAIVAFAVRGGREAAWRVIDATRLLSITANLGDVKTTITHPA 381 Query: 359 TTSHGRLSPEDRARAGIGDSLIRVAVGLEDLDDLKADMARGL 400 TT+HGRL+PE RA GIG+ LIR+AVGLED D++AD+ GL Sbjct: 382 TTTHGRLTPEQRAETGIGEGLIRLAVGLEDPADIRADLEYGL 423 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: 518 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: 431 Length adjustment: 31 Effective length of query: 372 Effective length of database: 400 Effective search space: 148800 Effective search space used: 148800 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