Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate Dsui_3185 Dsui_3185 O-succinylhomoserine sulfhydrylase
Query= SwissProt::P55218 (403 letters) >FitnessBrowser__PS:Dsui_3185 Length = 395 Score = 497 bits (1280), Expect = e-145 Identities = 246/384 (64%), Positives = 299/384 (77%) Query: 20 DTLAVRAGQRRTPEGEHGEALFTTSSYVFRTAADAAARFAGEVPGNVYSRYTNPTVRTFE 79 +TLAVRAGQ R+ EH EAL+ TSS+VF AA AAARF+GE GNVYSR++NPT+ F+ Sbjct: 12 ETLAVRAGQERSQFNEHSEALYLTSSFVFENAAQAAARFSGEEEGNVYSRFSNPTLSLFQ 71 Query: 80 ERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDKYFKRFGIQ 139 +R+AALEGAE A+ TASGMSAI++LVM+ +GDHV+ S +FG+TI LF+ RFGI Sbjct: 72 DRLAALEGAESAICTASGMSAIMSLVMAHLKAGDHVVASAGLFGATIQLFNNILARFGIS 131 Query: 140 VDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGALLAVDNCFCT 199 Y + W AA +P TKLFF+E+PSNPL E+ DIAALAEIAHAKG L+AVDNCFCT Sbjct: 132 TTYASQTRPEEWAAAIRPETKLFFLETPSNPLTEVADIAALAEIAHAKGILVAVDNCFCT 191 Query: 200 PALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQMKEVVGFLRTAGPTLSPFNAW 259 PALQ+PL+LGAD+V+HSATKY+DGQGR +GG V G + +EV FLRTAGPTLS FNAW Sbjct: 192 PALQRPLELGADLVVHSATKYLDGQGRVLGGAVVGSKKLTEEVFKFLRTAGPTLSAFNAW 251 Query: 260 LFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELARRQQSGFGAV 319 + KGLETL+IRM A SA+AL LA WLE P + RV+Y GL SHPQH LA RQQ GA+ Sbjct: 252 VLAKGLETLKIRMAAQSANALELATWLEAHPKVARVFYPGLASHPQHALAMRQQKSGGAI 311 Query: 320 VSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRLSPEDRARAGIGDSL 379 VSF+VKGG+ AW+ +D R++SIT NLGD KTTI HPATT+HGR+S E RA AGIGD L Sbjct: 312 VSFEVKGGKPEAWKVVDNCRLLSITANLGDVKTTITHPATTTHGRISAEARATAGIGDGL 371 Query: 380 IRVAVGLEDLDDLKADMARGLAAL 403 +R+AVGLE + DL+AD+ RGLA L Sbjct: 372 LRIAVGLEAVPDLQADLERGLAQL 395 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: 460 Number of extensions: 12 Number of successful extensions: 1 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: 395 Length adjustment: 31 Effective length of query: 372 Effective length of database: 364 Effective search space: 135408 Effective search space used: 135408 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 09 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