Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate AZOBR_RS02140 AZOBR_RS02140 O-succinylhomoserine sulfhydrylase
Query= SwissProt::P55218 (403 letters) >FitnessBrowser__azobra:AZOBR_RS02140 Length = 402 Score = 344 bits (883), Expect = 2e-99 Identities = 178/382 (46%), Positives = 255/382 (66%), Gaps = 2/382 (0%) Query: 24 VRAGQRRTPEGEHGEALFTTSSYVFRTAADAAARFAGEVPGNVYSRYTNPTVRTFEERIA 83 V G RR+ E EAL+ TS +V+ +A +A + F + +VYSR+ NPT FE+R+ Sbjct: 21 VHGGVRRSSFDETCEALYQTSGFVYGSAEEAESAFVNDGSRHVYSRFRNPTTAMFEDRLC 80 Query: 84 ALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDKYFKRFGIQVDYP 143 EGA A AT SGM+A+ + S +GD ++ RS+F S + + RFG++ + Sbjct: 81 EYEGAAWAYATTSGMAAVHGALWSNLRTGDRIVAPRSLFISCYWVIKELSARFGVEAVFV 140 Query: 144 PLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGALLAVDNCFCTPALQ 203 +DL+ WE A TK+ F+E+PSNP E+VD+ A++ +AH GA + VDN F TP LQ Sbjct: 141 DGTDLSQWEEALAKPTKVVFLETPSNPGLEVVDLRAVSALAHKAGAKVVVDNAFATPVLQ 200 Query: 204 QPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQMKEVV--GFLRTAGPTLSPFNAWLF 261 +P ++GADVVI+SATK+IDGQGR +GG++ +Q V +LR GPT+SPFNAWL Sbjct: 201 RPFEMGADVVIYSATKHIDGQGRCLGGIILTNDKQYGSDVIHPYLRHTGPTISPFNAWLL 260 Query: 262 LKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELARRQQSGFGAVVS 321 LKGLETL +R+ A SA+AL +AE+LE +ERV Y GL SHPQH+L R Q +G G ++S Sbjct: 261 LKGLETLELRVSAQSAAALTVAEFLEGHAKVERVLYPGLASHPQHDLVRSQMTGGGTMLS 320 Query: 322 FDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRLSPEDRARAGIGDSLIR 381 +KGG++ A+R ++ RMV I+ NLGD+K+ I HP TT+H +L+ E++A A I +L+R Sbjct: 321 IFLKGGKEEAFRALNDLRMVMISNNLGDSKSLITHPDTTTHSKLTVEEKAAANIRPNLLR 380 Query: 382 VAVGLEDLDDLKADMARGLAAL 403 ++VGLED D+ D+ R LA+L Sbjct: 381 LSVGLEDAQDIVEDLDRALASL 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: 403 Number of extensions: 8 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: 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 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