Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_052665209.1 NITAL_RS05960 O-succinylhomoserine sulfhydrylase
Query= SwissProt::P55218 (403 letters) >NCBI__GCF_000969705.1:WP_052665209.1 Length = 399 Score = 390 bits (1001), Expect = e-113 Identities = 197/383 (51%), Positives = 265/383 (69%), Gaps = 1/383 (0%) Query: 20 DTLAVRAGQRRTPEGEHGEALFTTSSYVFRTAADAAARFAGEVPGNVYSRYTNPTVRTFE 79 DT+AVRAG R+ GE EALF TS YV+ TAA+AAA FAGE +YSR NPTV FE Sbjct: 16 DTVAVRAGTERSAFGETSEALFATSGYVYETAAEAAAAFAGESDRYIYSRLGNPTVSMFE 75 Query: 80 ERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDKYFKRFGIQ 139 ER+ LEGAE A ATASGM+A+ + + +GD V+ +R +FGS + D+ R+ ++ Sbjct: 76 ERLRRLEGAEGAWATASGMAAVFNALAATLRAGDRVVAARGLFGSCFQILDEILPRWDVR 135 Query: 140 VDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGALLAVDNCFCT 199 D+ SDL WE A + F E+PSNP+ ELVDIAA++E+AHA GA + VDN F T Sbjct: 136 TDFVDGSDLGQWERALATPAQAVFFETPSNPMQELVDIAAVSELAHAAGARVIVDNVFAT 195 Query: 200 PALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQMKEVV-GFLRTAGPTLSPFNA 258 P LQ+PL+LGADVV++S TK++DG GR MGG + G E ++E + +R GP ++PFNA Sbjct: 196 PVLQRPLELGADVVVYSTTKHLDGHGRTMGGAILGTTEFLQEELRPLMRHTGPVMAPFNA 255 Query: 259 WLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELARRQQSGFGA 318 W+ LK LETL +R++ +ASALALA WLE+ P +E V Y L SHPQHELA RQ +G G+ Sbjct: 256 WVVLKSLETLALRVERQTASALALAAWLEQHPAVEEVRYPMLASHPQHELAVRQMTGGGS 315 Query: 319 VVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRLSPEDRARAGIGDS 378 +V+F V GG + A+ ID ++ I+ NLGD K+ + HPATT+H R+ PE RA G+ D Sbjct: 316 IVTFWVPGGTERAFEVIDRLALIDISNNLGDAKSLVTHPATTTHHRIGPEVRAEMGVTDG 375 Query: 379 LIRVAVGLEDLDDLKADMARGLA 401 +IR++VGLED DL+AD+ + L+ Sbjct: 376 VIRISVGLEDPTDLQADLDQALS 398 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: 415 Number of extensions: 9 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