Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_011912938.1 PST_RS09045 O-succinylhomoserine sulfhydrylase
Query= SwissProt::P55218 (403 letters) >NCBI__GCF_000013785.1:WP_011912938.1 Length = 403 Score = 681 bits (1757), Expect = 0.0 Identities = 334/403 (82%), Positives = 370/403 (91%) Query: 1 MTQDWDAGRLDSDLEGAAFDTLAVRAGQRRTPEGEHGEALFTTSSYVFRTAADAAARFAG 60 MT W+AGRLDS+L+G DTLAVRAGQRRTPE EHGE LF TSSYVFR+AADAAARFAG Sbjct: 1 MTIKWEAGRLDSELDGVGLDTLAVRAGQRRTPEAEHGEPLFFTSSYVFRSAADAAARFAG 60 Query: 61 EVPGNVYSRYTNPTVRTFEERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRS 120 +VPGNVYSRYTNPTVR FEERIAALEGAEQAVATASGM+AILA VMSLCS+GDHVLVSRS Sbjct: 61 DVPGNVYSRYTNPTVRAFEERIAALEGAEQAVATASGMAAILATVMSLCSAGDHVLVSRS 120 Query: 121 VFGSTISLFDKYFKRFGIQVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAAL 180 VFG+T+SLF+KYFKRFG+QVDY PL+D AAWE+A K NTKL FVESPSNPLAELVDIAAL Sbjct: 121 VFGATVSLFEKYFKRFGVQVDYVPLTDFAAWESAFKENTKLVFVESPSNPLAELVDIAAL 180 Query: 181 AEIAHAKGALLAVDNCFCTPALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQMK 240 A + H KGA+LAVDNCFCTP LQQPLKLGAD+VIHSATKYIDGQGR +GGVVAGR EQMK Sbjct: 181 AHLCHGKGAMLAVDNCFCTPVLQQPLKLGADIVIHSATKYIDGQGRCLGGVVAGRSEQMK 240 Query: 241 EVVGFLRTAGPTLSPFNAWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGL 300 E+VGFLRTAGPTLSPFNAW+FLKGLETLR+RMQAH ASA LAEWLE+QPG+ERV+YAGL Sbjct: 241 EIVGFLRTAGPTLSPFNAWVFLKGLETLRLRMQAHCASAQILAEWLEQQPGVERVFYAGL 300 Query: 301 PSHPQHELARRQQSGFGAVVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATT 360 PSHPQHELA+RQQ GFGAV+SF+V GG++ AWRFIDATR++SIT NLGD+KTTI HP +T Sbjct: 301 PSHPQHELAKRQQKGFGAVLSFEVVGGKEGAWRFIDATRLISITANLGDSKTTITHPGST 360 Query: 361 SHGRLSPEDRARAGIGDSLIRVAVGLEDLDDLKADMARGLAAL 403 +HGRLS E+RA AGI DSLIRVAVGLED+DDLKAD+ARGLAAL Sbjct: 361 THGRLSAENRATAGIRDSLIRVAVGLEDVDDLKADLARGLAAL 403 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: 550 Number of extensions: 9 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: 403 Length adjustment: 31 Effective length of query: 372 Effective length of database: 372 Effective search space: 138384 Effective search space used: 138384 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