Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_011383705.1 AMB_RS06585 cystathionine beta-lyase
Query= SwissProt::P55218 (403 letters) >NCBI__GCF_000009985.1:WP_011383705.1 Length = 390 Score = 172 bits (435), Expect = 2e-47 Identities = 128/384 (33%), Positives = 188/384 (48%), Gaps = 20/384 (5%) Query: 30 RTPEGEHGEA---LFTTSSYVFRTAADAAARFAGEVP--GNVYSRYTNPTVRTFEERIAA 84 R PE HG ++ S+ + + A A +G+ P G Y R+ PT EE +A Sbjct: 12 RKPEAFHGAVNPPVYHASTILHPSVA--AMEKSGKTPFEGVRYGRFGTPTTFALEEAVAE 69 Query: 85 LEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDKYFKRFGIQVDYPP 144 LEG + VAT+SG++AI +++ +GDH+L+ + + T D GI+ Y Sbjct: 70 LEGGHRTVATSSGLAAITGALLAFLKAGDHLLMVDTTYFPTRKFCDSVLGGLGIETTYYD 129 Query: 145 LSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGALLAVDNCFCTPALQQ 204 A A +PNT++ F ESP + E+ DI A+AE AHA GA++ +DN + Q Sbjct: 130 PLVGAGITALMRPNTRVVFTESPGSLTFEVQDIPAIAEAAHAGGAVVMMDNTWGVLHFQ- 188 Query: 205 PLKLGADVVIHSATKYIDGQGRGM-GGVVAGRGEQMKEVVGFLRTAGPTLSPFNAWLFLK 263 P G D+ I +ATKYI G M G + A E +V L G + +L L+ Sbjct: 189 PFTKGIDISIQAATKYIVGHADAMLGTITAATPELWLQVKTSLAAFGASPGTEEMYLGLR 248 Query: 264 GLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELARRQQSG----FGAV 319 GL TL +R++ H+ SAL L WLE +P ++RV Y L S P HEL +R +G FG + Sbjct: 249 GLRTLPVRLRQHAESALRLTRWLEARPEVDRVLYPPLASDPGHELWKRDFTGGCGLFGVI 308 Query: 320 VSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRLSPEDRARAGIGDSL 379 + K DA +D + + G ++ + TS + +G SL Sbjct: 309 LKPASKAAVDA---MLDGYSHFKLGFSWGGFESLV---IPTSGHSIIRTATPWTPVGPSL 362 Query: 380 IRVAVGLEDLDDLKADMARGLAAL 403 R GLED DDL+ D+ RG L Sbjct: 363 -RFHAGLEDADDLEEDLERGFERL 385 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: 366 Number of extensions: 17 Number of successful extensions: 5 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: 390 Length adjustment: 31 Effective length of query: 372 Effective length of database: 359 Effective search space: 133548 Effective search space used: 133548 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 09 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