Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate 7026472 Shewana3_3614 cystathionine gamma-synthase (RefSeq)
Query= SwissProt::P55218 (403 letters) >FitnessBrowser__ANA3:7026472 Length = 393 Score = 258 bits (659), Expect = 2e-73 Identities = 154/399 (38%), Positives = 231/399 (57%), Gaps = 14/399 (3%) Query: 7 AGRLDSDLEGAAFDTLAVRAG-QRRTPEGEHGEALFTTSSYVFRTAADAAARFAGEVPGN 65 AG+L ++ + A TLAVR G + T G ++ +++Y F + Sbjct: 3 AGKLVTERQLA---TLAVRQGIESDTQYGAVVPPIYLSTNYAFDGHKNPREFD------- 52 Query: 66 VYSRYTNPTVRTFEERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGST 125 YSR NPT + +A LE V T +GM+AI LV +L D ++V +G + Sbjct: 53 -YSRSGNPTRSILGDALAKLEKGATGVVTCTGMAAI-TLVTTLLGPDDLLVVPHDCYGGS 110 Query: 126 ISLFDKYFKRFGIQVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAH 185 LF K+ ++ +D A E A K+ ++E+PSNPL +VDI A+A+ +H Sbjct: 111 YRLFTNLAKKGQFKLLVVDQTDAQALEQAIAQQPKMVWIETPSNPLLRVVDIEAIAKASH 170 Query: 186 AKGALLAVDNCFCTPALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQMKEVVGF 245 A GAL+ VDN F +P LQQPL LGAD+VIHS TKYI+G +GG V + Q+ E + + Sbjct: 171 AVGALVVVDNTFLSPILQQPLLLGADIVIHSTTKYINGHSDVVGGAVIAKDPQLGETLHW 230 Query: 246 L-RTAGPTLSPFNAWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHP 304 T G T S F+++ L+GL TL +R++ H ++A + + L P + +VYY GL HP Sbjct: 231 WSNTLGLTGSAFDSYQTLRGLRTLAVRIREHQSNAQRIVDVLTSSPVVSKVYYPGLADHP 290 Query: 305 QHELARRQQSGFGAVVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGR 364 H +A +QQ GFGA++SF++KGG F+DA + S+ +LG ++ +A PAT +H Sbjct: 291 GHAIAAKQQKGFGAMLSFELKGGEAEVVAFLDALSLFSVAESLGGVESLVAVPATMTHRA 350 Query: 365 LSPEDRARAGIGDSLIRVAVGLEDLDDLKADMARGLAAL 403 + P+ R AGI D+L+R++VG+ED DDL AD+ GLAA+ Sbjct: 351 MEPQARFEAGIKDTLLRLSVGIEDADDLVADIQAGLAAV 389 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: 349 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: 393 Length adjustment: 31 Effective length of query: 372 Effective length of database: 362 Effective search space: 134664 Effective search space used: 134664 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