Align Homocysteine/cysteine synthase; O-acetylserine/O-acetylhomoserine sulfhydrylase; OAS-OAH SHLase; OAS-OAH sulfhydrylase; EC 2.5.1.47; EC 2.5.1.49 (characterized)
to candidate WP_004322211.1 C665_RS15845 O-succinylhomoserine sulfhydrylase
Query= SwissProt::P06106 (444 letters) >NCBI__GCF_000310185.1:WP_004322211.1 Length = 394 Score = 232 bits (591), Expect = 2e-65 Identities = 143/427 (33%), Positives = 218/427 (51%), Gaps = 49/427 (11%) Query: 4 HFDTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNPT 63 H DT+ + AG E R +Y T+S+VF+++ + F E GYVY+RF NPT Sbjct: 10 HPDTLAVRAGTER---TQFREHGEAMYLTSSFVFDSAAQAAACFSGEEEGYVYARFSNPT 66 Query: 64 SNVLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFK 123 ++ R+AALEGG A +A +SG +A GD++V+++ L+G T F Sbjct: 67 VTAMQNRLAALEGGEACIATASGMSAILSLAMATMQAGDHVVASNGLFGATQQLFGGILS 126 Query: 124 RFGIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVD 183 +FGI FV + + RT+ + ET NP V D + AIA G+ VD Sbjct: 127 KFGIATSFVPATELDAWRAAVTPRTRLFFTETPSNPLTEVIDIAGVAAIARAAGVIFAVD 186 Query: 184 NTFGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQP 243 N F +P++ GAD+V HSATK++ G G +GG +V S Sbjct: 187 NCFCTPA-LQRPLELGADVVVHSATKYLDGQGRVLGGAVVGS------------------ 227 Query: 244 AEGYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGENA 303 I +E + + LR GP ++PF ++++L+G+ETL +R E +A Sbjct: 228 -----KAITDEVF-----------KFLRTAGPTLSPFNAWVILKGLETLRIRMEAQSASA 271 Query: 304 LKLAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKETDPFK 363 L+LA+WLE P V+ V YPGL SH H A + +G G ++SF VK A Sbjct: 272 LELARWLEAQPGVARVYYPGLESHPQHVLAMRQQKSG-GAIVSFDVKGGREA-------- 322 Query: 364 LSGAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGIEF 423 +VVD +L S AN+GD K+ + P TTH +++ + + +G+ L+R++VG+E Sbjct: 323 --AWKVVDATRLISITANLGDTKSTITHPATTTHGRISAEARATAGIGDGLLRIAVGLED 380 Query: 424 IDDIIAD 430 +DD+ AD Sbjct: 381 VDDLKAD 387 Lambda K H 0.317 0.136 0.402 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: 400 Number of extensions: 14 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: 2 Length of query: 444 Length of database: 394 Length adjustment: 32 Effective length of query: 412 Effective length of database: 362 Effective search space: 149144 Effective search space used: 149144 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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