Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_013518386.1 ALIDE2_RS16910 O-succinylhomoserine sulfhydrylase
Query= SwissProt::P55218 (403 letters) >NCBI__GCF_000204645.1:WP_013518386.1 Length = 404 Score = 431 bits (1109), Expect = e-125 Identities = 225/391 (57%), Positives = 282/391 (72%), Gaps = 7/391 (1%) Query: 20 DTLAVRAGQRRTPEGEHGEALFTTSSYVFRTAADAAARFAGEVPGNVYSRYTNPTVRTFE 79 DTLAVR R+ GEH EAL+ TSS+V A AA RFA E G YSR +NPTV +FE Sbjct: 13 DTLAVREAVERSQWGEHSEALYLTSSFVQSDCASAARRFANEEAGYTYSRTSNPTVTSFE 72 Query: 80 ERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDKYFKRFGIQ 139 R+AA+EG E AVATA+GMSAIL + ++ +GDHV+ S+S+FGSTI L RFG++ Sbjct: 73 RRLAAMEGTECAVATATGMSAILLVALTALKAGDHVICSQSMFGSTIKLLGTEMARFGVE 132 Query: 140 VDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGALLAVDNCFCT 199 + +D+ AW+AA +PNT+L F E+P+NPL +L DIAALAE+AHA GALLAVDN F + Sbjct: 133 TSFVSQTDVQAWKAAMRPNTRLLFAETPTNPLTDLCDIAALAELAHAHGALLAVDNSFAS 192 Query: 200 PALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQMKEVVG-FLRTAGPTLSPFNA 258 P LQQP++ GAD+V+HS TK +DGQGR M G V G + +V+G FLR+ G L+PFNA Sbjct: 193 PVLQQPVRFGADLVVHSGTKLLDGQGRVMAGAVCGTVALVDKVMGTFLRSGGLNLAPFNA 252 Query: 259 WLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELARRQQSGF-G 317 W+ LKGLETL +R++A SA+AL LA WLE P + RVYY GL SHPQHELA RQQ+G G Sbjct: 253 WVVLKGLETLGLRVKAESAAALELATWLEAHPKVARVYYPGLKSHPQHELAMRQQNGMGG 312 Query: 318 AVVSFDVKGG-----RDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRLSPEDRAR 372 V++FDV G R A+ +D+TR+ SIT NLGD KTTI HPA+TSHGRL+ E R Sbjct: 313 TVLAFDVAGQGAQQLRANAFHVVDSTRVCSITANLGDVKTTITHPASTSHGRLTEEQRQA 372 Query: 373 AGIGDSLIRVAVGLEDLDDLKADMARGLAAL 403 AGIG LIR++VGLE L DL+ D+ARGL L Sbjct: 373 AGIGQGLIRISVGLEHLGDLQNDLARGLDTL 403 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: 434 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: 404 Length adjustment: 31 Effective length of query: 372 Effective length of database: 373 Effective search space: 138756 Effective search space used: 138756 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