Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_011650342.1 RL_RS02910 O-succinylhomoserine sulfhydrylase
Query= SwissProt::P55218 (403 letters) >NCBI__GCF_000009265.1:WP_011650342.1 Length = 394 Score = 339 bits (869), Expect = 9e-98 Identities = 171/382 (44%), Positives = 249/382 (65%), Gaps = 1/382 (0%) Query: 21 TLAVRAGQRRTPEGEHGEALFTTSSYVFRTAADAAARFAGEVPGNVYSRYTNPTVRTFEE 80 T V G R+ GE EA++ T +V+ T+ A ARF GE G +Y+RY +PT FE+ Sbjct: 9 TQLVHGGTLRSQYGETSEAIYLTQGFVYETSEAAEARFKGETEGFIYARYGSPTNDMFEK 68 Query: 81 RIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDKYFKRFGIQV 140 R+ LEGAE A ATASGM+A+ A ++ SGDH++ +R++FGS + + ++GI Sbjct: 69 RMCLLEGAEDARATASGMAAVTAAILCQLKSGDHIVAARALFGSCRWVVETLAPKYGIDC 128 Query: 141 DYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGALLAVDNCFCTP 200 DLA WE A P TK+FF+ESP+NP E++DIA +A++A+ GA + VDN F TP Sbjct: 129 TLIDGRDLANWEKAITPKTKVFFLESPTNPTLEVIDIAGVAKLANQIGAKVVVDNVFATP 188 Query: 201 ALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQMKE-VVGFLRTAGPTLSPFNAW 259 Q+PL+LGA +V++SATK+IDGQGR +GGVV E + E + + R GP +SPFNAW Sbjct: 189 LFQKPLELGAHIVVYSATKHIDGQGRCLGGVVLSDKEWIDENLHDYFRHTGPAMSPFNAW 248 Query: 260 LFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELARRQQSGFGAV 319 LKG+ETL +R++ + +A +A++L Q + +V Y G HPQ ++ +Q +G + Sbjct: 249 TLLKGIETLPLRVRQQTENAAKIADFLAEQGKVAKVIYPGRKDHPQADIIAKQMTGGSTL 308 Query: 320 VSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRLSPEDRARAGIGDSL 379 V+F++KGG+DAA+ +A ++ I+ NLGD+K+ I HPATT+H L+ E RA GI Sbjct: 309 VAFELKGGKDAAFALQNALEIIKISNNLGDSKSLITHPATTTHKNLTDEARAELGISPGT 368 Query: 380 IRVAVGLEDLDDLKADMARGLA 401 +R++ G+ED DDL D AR LA Sbjct: 369 VRLSAGIEDTDDLIEDFARALA 390 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: 7 Number of successful extensions: 2 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: 394 Length adjustment: 31 Effective length of query: 372 Effective length of database: 363 Effective search space: 135036 Effective search space used: 135036 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