Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate SMc02595 SMc02595 cystathionine gamma-synthase
Query= SwissProt::P55218 (403 letters) >FitnessBrowser__Smeli:SMc02595 Length = 408 Score = 257 bits (657), Expect = 4e-73 Identities = 140/337 (41%), Positives = 197/337 (58%), Gaps = 2/337 (0%) Query: 67 YSRYTNPTVRTFEERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTI 126 Y R NPT + +A LEG AV T SGM+A L L++ VL +G T+ Sbjct: 72 YGRSGNPTRDLLAQALAKLEGGADAVVTPSGMAA-LDLLLGRLRRNHLVLAPHDCYGGTL 130 Query: 127 SLFDKYFKRFGIQVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHA 186 L + D +EAA L +ESPSNPL + DIA L+ +A A Sbjct: 131 RLLKARADLGHLTFRLTDQRDFGGFEAALSDAPALVLIESPSNPLMRVTDIARLSTLAKA 190 Query: 187 KGALLAVDNCFCTPALQQPLKLGADVVIHSATKYIDGQGRGMGG-VVAGRGEQMKEVVGF 245 G+ +AVDN F +PALQQPL LGAD IHSATK+++G + G V+A ++ ++ + Sbjct: 191 AGSAVAVDNTFLSPALQQPLSLGADYAIHSATKFLNGHSDVIAGAVIAAEPQEAHDLKRW 250 Query: 246 LRTAGPTLSPFNAWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQ 305 G +PF+AWL L+GL TL RM + SA+ +AE+L+ P + V+YAGLP H Sbjct: 251 ANVTGAVAAPFDAWLTLRGLRTLFARMSSQERSAMTIAEYLDAHPAVRHVHYAGLPDHAD 310 Query: 306 HELARRQQSGFGAVVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRL 365 HE+ARRQQ GFGA++SF+++GG A RF+ R ++ +LG ++ +AHPAT +H + Sbjct: 311 HEVARRQQRGFGAMMSFELEGGVPAVRRFLAHIRCFTLAESLGGVESLVAHPATMTHLDM 370 Query: 366 SPEDRARAGIGDSLIRVAVGLEDLDDLKADMARGLAA 402 PE R RAGI D L+R+++GLE +DDL + GL A Sbjct: 371 GPEARERAGIRDELLRLSIGLEHIDDLMEGLELGLGA 407 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: 395 Number of extensions: 13 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: 408 Length adjustment: 31 Effective length of query: 372 Effective length of database: 377 Effective search space: 140244 Effective search space used: 140244 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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