Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate AO353_24330 AO353_24330 cystathionine beta-lyase
Query= SwissProt::P55218 (403 letters) >FitnessBrowser__pseudo3_N2E3:AO353_24330 Length = 389 Score = 177 bits (448), Expect = 6e-49 Identities = 111/338 (32%), Positives = 172/338 (50%), Gaps = 10/338 (2%) Query: 67 YSRYTNPTVRTFEERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTI 126 Y R+ NP+ + + LEGAE V SG+SA ++S+ +GDH+L++ +V+ Sbjct: 52 YGRWNNPSTEALTQALQQLEGAEGTVLCPSGLSACTTAILSVVGAGDHLLIADNVYSPIR 111 Query: 127 SLFDKYFKRFGIQVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHA 186 + ++ +R GI+V + + A KPNTK + ESP + E+ DI A+A++AH Sbjct: 112 AFCEQVGQRLGIEVTFYDPTIGAGIVDFLKPNTKAIYTESPGSLTLEIQDIPAIAKVAHE 171 Query: 187 KGALLAVDNCFCTPALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQMKEVVGFL 246 L+ DN + TP L+LG D+ I +ATKYI G + G V+ + F Sbjct: 172 HDILVITDNTWGTPLYFPSLELGVDLSIMAATKYIVGHSDAVLGTVSASKRAWDSLKRFH 231 Query: 247 RTAGPTLSPFNAWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQH 306 G SP + L L+G+ TL +R++ H +A +A+WLE + +E VYY L SHPQH Sbjct: 232 FNMGLFASPDDVTLALRGMRTLDVRLERHYKNATTVAKWLETREEVEAVYYPALESHPQH 291 Query: 307 ELARRQQSGFGAVVSFDVKGGRDAAW-RFIDATRMVSITTNLG--DTKTTIAHPATTSHG 363 +L +R G ++SF K AA +D+ + SI + G ++ IA P Sbjct: 292 QLWKRDFKGASGLLSFVTKPSTQAAADALLDSLSLFSIGYSWGGFESLAMIADPKPV--- 348 Query: 364 RLSPEDRARAGIGDSLIRVAVGLEDLDDLKADMARGLA 401 I L+R+ +GLED DL D+ +G A Sbjct: 349 ----RSATSWEIDGHLVRLHIGLEDPSDLIEDLEQGFA 382 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: 340 Number of extensions: 19 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: 389 Length adjustment: 31 Effective length of query: 372 Effective length of database: 358 Effective search space: 133176 Effective search space used: 133176 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