Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate 351915 BT2387 O-acetylhomoserine (thiol)-lyase (NCBI ptt file)
Query= SwissProt::P55218 (403 letters) >FitnessBrowser__Btheta:351915 Length = 428 Score = 285 bits (730), Expect = 1e-81 Identities = 154/421 (36%), Positives = 246/421 (58%), Gaps = 36/421 (8%) Query: 19 FDTLAVRAGQRRTPEGEHGEA--LFTTSSYVFRTAADAAARFAGEVPGNVYSRYTNPTVR 76 F+TL V GQ + A ++ T+SYVF +A AAARF + PGN+Y R TN T Sbjct: 8 FETLQVHVGQEQADPATDARAVPIYQTTSYVFHNSAHAAARFGLQDPGNIYGRLTNSTQG 67 Query: 77 TFEERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDKYFKRF 136 FEER+A LEG +A ASG +AI ++ +GDH++ +++++G + +L + Sbjct: 68 VFEERVAVLEGGVAGLAVASGAAAITYAFENITRAGDHIVAAKTIYGGSYNLLAHTLPNY 127 Query: 137 GIQVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGALLAVDNC 196 G+ + SDL+ +E A + NTK F+E+ NP + ++DI A++EIAH L +DN Sbjct: 128 GVTTTFVDPSDLSNFEKAIQENTKAVFIETLGNPNSNIIDIEAVSEIAHRHKIPLIIDNT 187 Query: 197 FCTPALQQPLKLGADVVIHSATKYIDGQGRGMGGVV----------AGRGEQMKEV---- 242 F TP L +P++ GAD+V+HSATK+I G G +GGV+ +G+ Q+ E Sbjct: 188 FGTPYLIRPIEHGADIVVHSATKFIGGHGSSLGGVIVDSGKFDWVASGKFPQLTEPDPSY 247 Query: 243 --VGFLRTAGP-----------------TLSPFNAWLFLKGLETLRIRMQAHSASALALA 283 V F+ AGP T+SPFNA++ L+GLETL +R++ H +AL + Sbjct: 248 HGVRFVDAAGPAAYVTRIRATLLRDTGATISPFNAFILLQGLETLSLRVERHVENALKVV 307 Query: 284 EWLERQPGIERVYYAGLPSHPQHELARRQ-QSGFGAVVSFDVKGGRDAAWRFIDATRMVS 342 +L P +++V + L HP H L +R +G G++ +F+VKGG++ A RFID+ + S Sbjct: 308 NFLNNHPKVKKVNHPSLSDHPDHALYQRYFPNGAGSIFTFEVKGGQEEAHRFIDSLEIFS 367 Query: 343 ITTNLGDTKTTIAHPATTSHGRLSPEDRARAGIGDSLIRVAVGLEDLDDLKADMARGLAA 402 + N+ D K+ + HPA+T+H +L+ ++ A I +R+++G E ++DL AD+ + LA Sbjct: 368 LLANVADVKSLVIHPASTTHSQLNAQELAEQEIYPGTVRLSIGTEHINDLIADLEQALAK 427 Query: 403 L 403 + Sbjct: 428 I 428 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: 377 Number of extensions: 17 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: 428 Length adjustment: 31 Effective length of query: 372 Effective length of database: 397 Effective search space: 147684 Effective search space used: 147684 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