Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_004514090.1 GMET_RS03510 cystathionine gamma-synthase
Query= SwissProt::P55218 (403 letters) >NCBI__GCF_000012925.1:WP_004514090.1 Length = 378 Score = 266 bits (680), Expect = 7e-76 Identities = 140/333 (42%), Positives = 208/333 (62%), Gaps = 3/333 (0%) Query: 67 YSRYTNPTVRTFEERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTI 126 Y+R NPT EE IA LEG + A ASGM+AI ++++ L S GDH++V V+G T Sbjct: 44 YARSDNPTREALEETIAQLEGGTRGFAYASGMAAISSVLL-LFSPGDHLVVCEDVYGGTF 102 Query: 127 SLFDKYFKRFGIQVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHA 186 + + F R GI + +DL A AA +P TK F+ESPSNPL ++ D+ A IA Sbjct: 103 RVLTQLFSRLGITSTFVDATDLDAIAAAFRPETKGLFLESPSNPLLKITDLEGAARIARE 162 Query: 187 KGALLAVDNCFCTPALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQMKEVVGFL 246 +GA+ VDN F TP LQ+PL++G D+V+HS TK+++G + G + ++ + + F+ Sbjct: 163 RGAITLVDNTFMTPYLQRPLEVGCDIVLHSGTKFLNGHSDVICGFAVVKDPELGKRIRFI 222 Query: 247 RTA-GPTLSPFNAWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQ 305 + A G L P ++WL L+GL+TLR+RM+ SA +A WL + + RV Y GLPSHP Sbjct: 223 QNAFGAILGPQDSWLVLRGLKTLRVRMEESQRSATRIASWLAGEKRVTRVLYPGLPSHPG 282 Query: 306 HELARRQQSGFGAVVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRL 365 H + RQ SG GAV+SF + + R ++ ++ + +LG ++ I++PA SH + Sbjct: 283 HAIHARQSSGPGAVLSFAL-DSLEVTRRLLEGMKLAAFAVSLGGVESIISYPARMSHAAM 341 Query: 366 SPEDRARAGIGDSLIRVAVGLEDLDDLKADMAR 398 PE+RA GIGD+L+R++VGLE+ DDL A+M R Sbjct: 342 PPEERAARGIGDTLVRLSVGLEEADDLIAEMDR 374 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: 363 Number of extensions: 19 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: 378 Length adjustment: 31 Effective length of query: 372 Effective length of database: 347 Effective search space: 129084 Effective search space used: 129084 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