Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_041100571.1 SUTH_RS15735 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase family protein
Query= SwissProt::P55218 (403 letters) >NCBI__GCF_000828635.1:WP_041100571.1 Length = 435 Score = 295 bits (756), Expect = 1e-84 Identities = 168/423 (39%), Positives = 244/423 (57%), Gaps = 42/423 (9%) Query: 20 DTLAVRAG-QRRTPEGEHGEALFTTSSYVFRTAADAAARFAGEVPGNVYSRYTNPTVRTF 78 +TL + AG Q G + T+S+VF +A AA+ F + GNVYSR NPTV F Sbjct: 9 ETLCLHAGAQPDAATGARALPIHQTTSFVFDSAEHAASLFNLQTFGNVYSRIGNPTVAAF 68 Query: 79 EERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDKYFKRFGI 138 EER+AALEG AVA A+G++A + +++LC +GD ++ +RS++G + S D ++ GI Sbjct: 69 EERMAALEGGRAAVAAATGLAAQMVALLTLCEAGDRIVAARSLYGGSFSQLDVSLRKLGI 128 Query: 139 QVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGALLAVDNCFC 198 + + D + AA NTK F E+ +NP ++DIAA+AEIAH G L +DN Sbjct: 129 ETVFVDSDDPENFRAALSDNTKCLFAETVANPRLNVLDIAAVAEIAHGHGVPLIIDNTVP 188 Query: 199 TPALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGE--------------------- 237 +P L +P + GAD+++HSATK++ G G +GGVV G+ Sbjct: 189 SPCLCRPFEHGADIIVHSATKFLGGHGTTLGGVVIESGKFDWGNGKFPGMTEPSAGYHGV 248 Query: 238 -----------QMKEVVGFLRTAGPTLSPFNAWLFLKGLETLRIRMQAHSASALALAEWL 286 MK + LRT GP LSPF+AWL ++G+ETL +RM+ H +ALA+A L Sbjct: 249 KFFETFGNFGFTMKARMETLRTFGPALSPFSAWLLMQGIETLPLRMKRHCENALAVARHL 308 Query: 287 ERQPGIERVYYAGLPSHPQHELARRQ-QSGFGAVVSFDVK--------GGRDAAWRFIDA 337 E+ P + V Y GLP+ P H LA+R G GA++SF V GG+ A RFIDA Sbjct: 309 EKHPRVAWVNYPGLPASPGHALAQRYLHGGAGAILSFGVDGGNPGAKGGGQAAGERFIDA 368 Query: 338 TRMVSITTNLGDTKTTIAHPATTSHGRLSPEDRARAGIGDSLIRVAVGLEDLDDLKADMA 397 + S N+GD KT + HPA+T+H +LS D+ +G+ ++R++VGLE LDD+ D+ Sbjct: 369 LQFCSHLANIGDAKTLVIHPASTTHRQLSEADQRASGVTPDMVRLSVGLETLDDILWDID 428 Query: 398 RGL 400 + L Sbjct: 429 QAL 431 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: 455 Number of extensions: 17 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 403 Length of database: 435 Length adjustment: 32 Effective length of query: 371 Effective length of database: 403 Effective search space: 149513 Effective search space used: 149513 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