Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_041773934.1 LFE_RS02030 PLP-dependent transferase
Query= SwissProt::P55218 (403 letters) >NCBI__GCF_000284315.1:WP_041773934.1 Length = 402 Score = 255 bits (651), Expect = 2e-72 Identities = 146/368 (39%), Positives = 209/368 (56%), Gaps = 7/368 (1%) Query: 40 LFTTSSYVFRTAADAAARFAGEVPGNVYSRYTNPTVRTFEERIAALEGAEQAVATASGMS 99 L+ TS++ F GE G VY R NPT FE ++ LEG E+ A ASGM Sbjct: 37 LYQTSTFTFPDFDQVDRVLKGEEEGFVYGRMGNPTTERFETLVSELEGGEKTRAFASGMG 96 Query: 100 AILALVMSLCSSGDHVLVSRSVFGSTISLFDKYFKRFGIQVD-YPPLSDLAAWEAACK-- 156 AI A+++ L S + + ++G T + +KY G + + P + E + + Sbjct: 97 AISAILIHLTKSRPEMAFPKVLYGGTRAFIEKYLIPQGCLIHWFDPREEGWGEELSRRLS 156 Query: 157 PNTKLFFVESPSNPLAELVDIAALAEIAHAKGALLAVDNCFCTPALQQPLKLGADVVIHS 216 P T F E+PSNP+ ++D+ L+ IA + G L VDN F TP LQ+PL LGAD+V+HS Sbjct: 157 PKTAAVFAETPSNPVMTVIDLGRLSGIAKSAGVPLVVDNTFATPILQKPLALGADIVVHS 216 Query: 217 ATKYIDGQGRGMGGVVAGRGEQMKEVVGFLRTA--GPTLSPFNAWLFLKGLETLRIRMQA 274 ATKY+ G G +GG V G M E + F + G TLSPF++WL L+G++TL +RM+A Sbjct: 217 ATKYLGGHGDLLGGTVTGNASLM-ERLSFEEGSYLGATLSPFHSWLLLRGMKTLPLRMEA 275 Query: 275 HSASALALAEWLERQPGIERVYYAGLPSHPQHELARRQQSGFGAVVSFDVKGGRDAAWRF 334 H A+ +AE+L P ++ V+Y GLP P H++A Q GFG ++SF + G A + Sbjct: 276 HCRGAMNIAEFLSHHPMVKSVHYPGLPGDPGHKVAALQMKGFGGMLSFSL-GDDQKARKV 334 Query: 335 IDATRMVSITTNLGDTKTTIAHPATTSHGRLSPEDRARAGIGDSLIRVAVGLEDLDDLKA 394 I +LGD ++ I HPA+ SH ++SPE R GI +RV+VGLED +DL Sbjct: 335 ASRLEFFKIAVSLGDPESLIEHPASLSHRQMSPEGRMALGIDPGFLRVSVGLEDPEDLIL 394 Query: 395 DMARGLAA 402 D+ R L A Sbjct: 395 DLKRALEA 402 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: 398 Number of extensions: 13 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: 402 Length adjustment: 31 Effective length of query: 372 Effective length of database: 371 Effective search space: 138012 Effective search space used: 138012 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