Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_029133561.1 A3GO_RS0111730 cystathionine gamma-synthase
Query= SwissProt::P55218 (403 letters) >NCBI__GCF_000428045.1:WP_029133561.1 Length = 390 Score = 253 bits (646), Expect = 7e-72 Identities = 142/383 (37%), Positives = 219/383 (57%), Gaps = 6/383 (1%) Query: 22 LAVRAGQRRTPEGEHGEA---LFTTSSYVFRTAADAAARFAGEVPGNVYSRY-TNPTVRT 77 LA RA T + HG ++ T+++ F + AD G PG +Y+RY NP++ Sbjct: 9 LATRAIHGSTQQDAHGSPHTPIYNTTTFAFPSTADLLYVVDGMKPGALYTRYGLNPSIFA 68 Query: 78 FEERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDKYFKRFG 137 EE +A LEGAE + A SGM+A AL ++ G ++ +G T+ L + G Sbjct: 69 LEETLAGLEGAELSWAFCSGMAAETALFLAYGQDG--IVCIGDAYGGTLELLAAQLPQLG 126 Query: 138 IQVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGALLAVDNCF 197 I+ + S+L+ + KL F E+P+NP EL DI A+A AH GA +AVD+ F Sbjct: 127 IKTHFILGSELSRLDHLLAEGPKLVFFETPTNPALELFDIRAIAAKAHIYGARVAVDSTF 186 Query: 198 CTPALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQMKEVVGFLRTAGPTLSPFN 257 +P Q+PL+LGAD V+HSATKY+ G G + G E + + + + G ++P Sbjct: 187 ASPVNQRPLELGADFVVHSATKYLGGHSDLTAGAIMGSKELLLPIWNWRKNLGSMIAPET 246 Query: 258 AWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELARRQQSGFG 317 A L + L TL +R++ +ASA A+A+ + R P +ERV Y GLP H LA+ Q GFG Sbjct: 247 ASLLARSLRTLVVRVRQQNASAQAVAQAMARHPKVERVLYPGLPDFAGHALAKAQMHGFG 306 Query: 318 AVVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRLSPEDRARAGIGD 377 +++ +V GG + A R D ++ ++ +LG ++ + P TT+H L+PE+RAR GI D Sbjct: 307 GMLTIEVAGGGEEATRVADRLQLFALAPSLGGAESLVTQPCTTTHHGLTPEERARRGISD 366 Query: 378 SLIRVAVGLEDLDDLKADMARGL 400 +++R+++GLED DL AD+ + L Sbjct: 367 AMLRLSIGLEDAADLIADLEQAL 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: 357 Number of extensions: 17 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 403 Length of database: 390 Length adjustment: 31 Effective length of query: 372 Effective length of database: 359 Effective search space: 133548 Effective search space used: 133548 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 10 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