Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_051678489.1 N746_RS0103335 O-succinylhomoserine sulfhydrylase
Query= SwissProt::P55218 (403 letters) >NCBI__GCF_000711195.1:WP_051678489.1 Length = 406 Score = 474 bits (1220), Expect = e-138 Identities = 234/394 (59%), Positives = 302/394 (76%), Gaps = 1/394 (0%) Query: 11 DSDLEGAAFDTLAVRAGQRRTPEGEHGEALFTTSSYVFRTAADAAARFAGEVPGNVYSRY 70 D L+ +TLA+R+G RT E E+ EA+F TSS+V+ +A AA RF+GEVPGNVYSR+ Sbjct: 12 DIKLDEFLLETLAIRSGYERTHEQENSEAIFPTSSFVYESAQQAADRFSGEVPGNVYSRF 71 Query: 71 TNPTVRTFEERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFD 130 TNPTVRTFE+R+AA+EG E VATASGM+AILA M L S GDH++ S S+FG+T LF Sbjct: 72 TNPTVRTFEKRLAAMEGGEACVATASGMAAILATFMGLLSHGDHIVSSSSIFGTTKVLFT 131 Query: 131 KYFKRFGIQVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGAL 190 KY +FGI+V + P +D AW +A + NTK F+E+PSNPL E+ DI LAE++ + AL Sbjct: 132 KYLAKFGIEVSFVPQTDHQAWCSAIQSNTKALFLETPSNPLTEIADIGYLAELSKSHNAL 191 Query: 191 LAVDNCFCTPALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQM-KEVVGFLRTA 249 L VDNCFCTP LQQPLKLGAD+VIHSATK+IDGQGR +GG V G + + +EV G +RTA Sbjct: 192 LIVDNCFCTPILQQPLKLGADIVIHSATKFIDGQGRCLGGAVIGSEKLVGEEVRGVIRTA 251 Query: 250 GPTLSPFNAWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELA 309 GP++SPFNAW+F+KGLETL +RM+AH A LA WL P +E+V+Y GL SHPQ+ LA Sbjct: 252 GPSMSPFNAWVFIKGLETLHVRMEAHCLRAHKLALWLSEHPAVEKVFYPGLESHPQYALA 311 Query: 310 RRQQSGFGAVVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRLSPED 369 ++QQ+ GA+VSF +KGGR+ AW IDAT+M+SIT NLGD KT+I HPATT+H R++ E+ Sbjct: 312 QQQQTAGGALVSFRIKGGREQAWSVIDATQMLSITANLGDVKTSITHPATTTHCRVAAEE 371 Query: 370 RARAGIGDSLIRVAVGLEDLDDLKADMARGLAAL 403 R GI D+L+RV+VGLE+L D++AD+ RGL L Sbjct: 372 RLATGITDNLVRVSVGLENLADIQADLQRGLDQL 405 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: 436 Number of extensions: 12 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: 406 Length adjustment: 31 Effective length of query: 372 Effective length of database: 375 Effective search space: 139500 Effective search space used: 139500 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