Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate AO353_23295 AO353_23295 cystathionine beta-lyase
Query= SwissProt::P55218 (403 letters) >FitnessBrowser__pseudo3_N2E3:AO353_23295 Length = 392 Score = 302 bits (774), Expect = 1e-86 Identities = 162/397 (40%), Positives = 248/397 (62%), Gaps = 13/397 (3%) Query: 11 DSDLEGAAFDTLAVRAGQRRTPE-GEHGEALFTTSSYVFRTAADAAARFAGEVPGNVYSR 69 D + AF T + AGQ P G ++ S+Y+ ++ G G Y R Sbjct: 5 DENATPRAFATRVIHAGQTPDPTTGALMPPIYANSTYLQQSP--------GVHKGFDYGR 56 Query: 70 YTNPTVRTFEERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLF 129 NPT E +A LEG QA A ASG++AI + V+ L +G H++ ++G T LF Sbjct: 57 SHNPTRFALERCVADLEGGTQAFAFASGLAAI-STVLELLDTGSHIVSGNDLYGGTFRLF 115 Query: 130 DKYFKRF-GIQVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKG 188 DK +R G + + L+DL A+EAA + +T++ +VE+PSNPL + D+AA+A +G Sbjct: 116 DKVRRRSAGHRFSFVDLTDLTAFEAALQDDTRMVWVETPSNPLLRITDLAAVARTCRERG 175 Query: 189 ALLAVDNCFCTPALQQPLKLGADVVIHSATKYIDGQGRGMGGV-VAGRGEQMKEVVGFLR 247 + DN F +P +Q+PL+LG D+V+HS TKY++G +GG+ V G+ +++E +GFL+ Sbjct: 176 IICVADNTFASPRIQRPLELGFDIVLHSTTKYLNGHSDVIGGIAVVGQNAELRERLGFLQ 235 Query: 248 TA-GPTLSPFNAWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQH 306 A G PF+A+L L+G++TL +RM+ H ++AL LA WL QP + RVYY GLPSHPQH Sbjct: 236 NAVGAIAGPFDAFLTLRGVKTLALRMERHCSNALELARWLSHQPQVARVYYPGLPSHPQH 295 Query: 307 ELARRQQSGFGAVVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRLS 366 ELA+RQ GFG ++S D+ A RF+++ ++ ++ +LG ++ I HPA +H + Sbjct: 296 ELAQRQMHGFGGMISLDLDTDLAGAKRFLESVQIFALAESLGGVESLIEHPAIMTHASIP 355 Query: 367 PEDRARAGIGDSLIRVAVGLEDLDDLKADMARGLAAL 403 E RA GIGD+LIR++VG+ED++DL+AD+A+ LA + Sbjct: 356 AETRAELGIGDALIRLSVGIEDVEDLRADLAQALAQI 392 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: 407 Number of extensions: 26 Number of successful extensions: 4 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: 392 Length adjustment: 31 Effective length of query: 372 Effective length of database: 361 Effective search space: 134292 Effective search space used: 134292 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