Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_044407443.1 NA59_RS02555 O-succinylhomoserine sulfhydrylase
Query= SwissProt::P55218 (403 letters) >NCBI__GCF_000934765.1:WP_044407443.1 Length = 399 Score = 478 bits (1230), Expect = e-139 Identities = 233/391 (59%), Positives = 298/391 (76%), Gaps = 1/391 (0%) Query: 14 LEGAAFDTLAVRAGQRRTPEGEHGEALFTTSSYVFRTAADAAARFAGEVPGNVYSRYTNP 73 +E TLA+RAG RT E E+ EA+F TSS+V+ +A AA RF+GE PGNVYSR+TNP Sbjct: 1 MEAYTLATLAIRAGYDRTHEQENSEAIFPTSSFVYESAQQAADRFSGEEPGNVYSRFTNP 60 Query: 74 TVRTFEERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDKYF 133 TVRTFE ++A +EG E VATASGM+AILA M S+GDH++ S S+FG+T LF+ Y Sbjct: 61 TVRTFENKLALMEGGEACVATASGMAAILACFMGTLSAGDHIVSSASIFGTTKVLFNNYL 120 Query: 134 KRFGIQVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGALLAV 193 K+FGI V + P +D AW A +PNTK F+E+PSNPL E+ DIA L+++A ALL V Sbjct: 121 KKFGIDVCFVPQTDYQAWSEAIQPNTKALFLETPSNPLTEVADIARLSQLASQAKALLIV 180 Query: 194 DNCFCTPALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQM-KEVVGFLRTAGPT 252 DNCFCTP LQQPLK GAD+VIHSATK++DGQGR +GG + G + ++V G +RTAGPT Sbjct: 181 DNCFCTPILQQPLKQGADIVIHSATKFLDGQGRCLGGAIVGSQSIVGEDVRGVIRTAGPT 240 Query: 253 LSPFNAWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELARRQ 312 +SPFNAW+F+KGLETL IRM+AH+ A LAEWL + P +ERV+Y GL SHPQ+ LA+RQ Sbjct: 241 MSPFNAWVFIKGLETLAIRMEAHTLRAQLLAEWLSQHPAVERVFYPGLGSHPQYALAQRQ 300 Query: 313 QSGFGAVVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRLSPEDRAR 372 Q G GA++SF VKGGRD AW IDAT+M+SIT NLGD KT+I HPA+T+H R+ P +R Sbjct: 301 QKGAGALLSFRVKGGRDQAWSVIDATKMLSITANLGDVKTSITHPASTTHSRVEPNEREA 360 Query: 373 AGIGDSLIRVAVGLEDLDDLKADMARGLAAL 403 AGI ++LIR++VGLED++D+K D+ GL AL Sbjct: 361 AGITENLIRISVGLEDVEDIKNDLVAGLNAL 391 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: 441 Number of extensions: 11 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: 399 Length adjustment: 31 Effective length of query: 372 Effective length of database: 368 Effective search space: 136896 Effective search space used: 136896 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