Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_011387859.1 RRU_RS00495 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
Query= SwissProt::P55218 (403 letters) >NCBI__GCF_000013085.1:WP_011387859.1 Length = 403 Score = 254 bits (648), Expect = 4e-72 Identities = 156/390 (40%), Positives = 210/390 (53%), Gaps = 9/390 (2%) Query: 21 TLAVRAGQRRTPEGEH--GEALFTTSSYVFRTAADAAARFAGEVPGNVYSRYTNPTVRTF 78 TLA+ AG +G + TS + A +A E +Y+R+ NPT Sbjct: 13 TLALHAGTTDESDGAQVLNPLVPATSFFTKPEAVGFSANDMAEDTPFLYTRWNNPTNALL 72 Query: 79 EERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDKYFKRFGI 138 EER+AALEG E AV ASGM+A+ L +S +GDH+++S + + GI Sbjct: 73 EERLAALEGGEAAVVFASGMAALSGLFLSQLKAGDHLVISSVCYAGLAEVAHDILPGLGI 132 Query: 139 QVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGALLAVDNCFC 198 S+L A AA +P T+L +E+P NP+ L DI ALA IAHA GALL+VD+ Sbjct: 133 ATTAVDTSNLEAVRAALRPETRLIHIETPGNPILRLSDIEALAAIAHAHGALLSVDSTMA 192 Query: 199 TPALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQMKEV-VGFLRTAGPTLSPFN 257 TP +PL LGAD V HS TKY G G +GG + G+ + M + L G +SPF Sbjct: 193 TPIATRPLALGADFVAHSLTKYACGHGDALGGAIIGKAQAMAALRKHALIHFGGAISPFA 252 Query: 258 AWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELARRQQSGFG 317 AWL L+GLETL +RM H A A A+A +LE P + RV + GLPSHPQH LA RQ F Sbjct: 253 AWLILRGLETLSLRMAGHQAGAAAVAAYLEGHPRLRRVLWPGLPSHPQHALACRQMKNFS 312 Query: 318 AVVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPAT----TSHGRLSPEDRA-- 371 +VSF G A + + +++S +LG T++ + + T S L +D Sbjct: 313 GMVSFSADDGPALARQLAERLQVISYAVSLGKTRSLLFYIPTEALIASSFHLDGDDARSY 372 Query: 372 RAGIGDSLIRVAVGLEDLDDLKADMARGLA 401 R GD R++VGLED DL AD+ R LA Sbjct: 373 RDWTGDGTFRLSVGLEDPADLIADLERALA 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: 411 Number of extensions: 19 Number of successful extensions: 3 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 Jul 25 2024. The underlying query database was built on Jul 25 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