Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_012592297.1 MSIL_RS16900 PLP-dependent transferase
Query= SwissProt::P55218 (403 letters) >NCBI__GCF_000021745.1:WP_012592297.1 Length = 392 Score = 216 bits (550), Expect = 9e-61 Identities = 133/363 (36%), Positives = 195/363 (53%), Gaps = 8/363 (2%) Query: 40 LFTTSSYVFRTAADAAARFAGEVPGNVYSRYTNPTVRTFEERIAALEGAEQAVATASGMS 99 +F TSS+ F D A +AG +YSR NPTV FE +A L+GAE A A +SGM Sbjct: 33 IFQTSSFFFDNFDDMADVYAGRSRRLIYSRGDNPTVMEFERVMAELDGAEAARAFSSGMG 92 Query: 100 AILALVMSLCSSGDHVLVSRSVFGSTISLFDKYFKRFGIQVDYPPLSDLAAWEAACKPNT 159 AI A +++ S+GD ++ R+V+ LF+ +FG+ VDY +D A AA P Sbjct: 93 AIAATIIAFVSAGDRIVTVRNVYSDAYRLFELVLAKFGVTVDYLDGADAGA-IAAALPGA 151 Query: 160 KLFFVESPSNPLAELVDIAALAEIAHAKGALLAVDNCFCTPALQQPLKLGADVVIHSATK 219 KL ++E+P++ EL DIA LA +A A+G + +DN + TP Q+P+ G D+VIH+A+K Sbjct: 152 KLLYLETPTSLTFELQDIATLAALARAQGVVSVIDNSWATPQFQKPIAHGVDLVIHAASK 211 Query: 220 YIDGQGRGMGGVVAGRGEQMKEV-VGFLRTAGPTLSPFNAWLFLKGLETLRIRMQAHSAS 278 Y+ G + GVV+G E + + G G LSPF AWL L+GL TL +R+ H S Sbjct: 212 YLGGHSDTVAGVVSGSAEHVARINAGAYAYLGAKLSPFEAWLLLRGLATLELRLPRHMQS 271 Query: 279 ALALAEWLERQPGIERVYYAGLPSHPQHELARRQQSGFGAVVSFDVKGGRDAAWRFIDAT 338 L +A L+ P + V + HP + SGF + S +V D F +A Sbjct: 272 GLLIAGRLKAHPNVSLVRHPAYSDHP----GKATLSGFSGLFSIEVGENIDVR-TFANAL 326 Query: 339 RMVSITTNLGDTKTTIAHPATTSHGRLSPEDRARAGIGDSLIRVAVGLEDLDDLKADMAR 398 ++ + + G ++ + PA + AR G+ LIR+ VGLED + L D+ R Sbjct: 327 KLFRLGVSWGGPESLVV-PALAPLQLRTANCFARFGVSPRLIRLHVGLEDAEALWDDLER 385 Query: 399 GLA 401 LA Sbjct: 386 ALA 388 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: 384 Number of extensions: 16 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: 392 Length adjustment: 31 Effective length of query: 372 Effective length of database: 361 Effective search space: 134292 Effective search space used: 134292 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 Jul 25 2024. The underlying query database was built on Jul 25 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