Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_058930869.1 AU252_RS11760 O-succinylhomoserine sulfhydrylase
Query= SwissProt::P55218 (403 letters) >NCBI__GCF_001484605.1:WP_058930869.1 Length = 402 Score = 350 bits (897), Expect = e-101 Identities = 184/394 (46%), Positives = 255/394 (64%), Gaps = 6/394 (1%) Query: 13 DLEGAAFDTLAVRAGQRRTPEGEHGEALFTTSSYVFRTAADAAARFAGEVPGNVYSRYTN 72 D G + +T AVR G RT E E +F S +V+ +AA A F GE VYSRY N Sbjct: 6 DAAGWSAETQAVRGGLDRTNFQETTEPVFLNSGFVYESAAAAERAFTGEDERFVYSRYGN 65 Query: 73 PTVRTFEERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDKY 132 P+V TF+ER+ LEG E ATASGMSA+ + +L ++GD V+ +RS+FGS + ++ Sbjct: 66 PSVATFQERLRLLEGTEACFATASGMSAVFTALGALLAAGDRVVAARSLFGSCFVILNEI 125 Query: 133 FKRFGIQVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGALLA 192 R+G++ + DL W AA T F ESPSNP+ E+VDIAA++E+AHA GA + Sbjct: 126 LPRWGVETVFVDGPDLEQWAAALSEPTTAVFFESPSNPMQEIVDIAAVSELAHAAGATVV 185 Query: 193 VDNCFCTPALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQMK-EVVGFLRTAGP 251 VDN F TP LQ+ +LGADV+++S TK+IDGQGR +GG + G E + V +R GP Sbjct: 186 VDNVFATPLLQRCGQLGADVIVYSGTKHIDGQGRVLGGAILGTKEFIDGPVKQLMRHTGP 245 Query: 252 TLSPFNAWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELARR 311 LS FNAW+ KGLET+ +R+ SASAL LAEWLE+QP + V Y L SHPQ+ELA + Sbjct: 246 ALSAFNAWVLTKGLETMALRVNHSSASALRLAEWLEQQPAVSWVRYPLLKSHPQYELAAK 305 Query: 312 QQSGFGAVVSFDV-----KGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRLS 366 Q G V++ ++ + G++AA+ +DA R++ I+ NLGD K+ I HPATT+H + Sbjct: 306 QMKAGGTVLTLELATTGGRSGKEAAFALLDALRIIDISNNLGDAKSLITHPATTTHRAMG 365 Query: 367 PEDRARAGIGDSLIRVAVGLEDLDDLKADMARGL 400 PE RA G+ D ++R++VGLED+DDL D+ + L Sbjct: 366 PEGRAAIGLSDGVVRLSVGLEDVDDLIGDLEQAL 399 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: 400 Number of extensions: 12 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: 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