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_013553393.1 NITSA_RS02180 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= SwissProt::P06106 (444 letters) >NCBI__GCF_000186245.1:WP_013553393.1 Length = 421 Score = 320 bits (819), Expect = 7e-92 Identities = 177/433 (40%), Positives = 264/433 (60%), Gaps = 18/433 (4%) Query: 6 DTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNPTSN 65 +T+ +HAG + N + AVPIY TT+Y F +++H + LF L+ G +Y+R NPT++ Sbjct: 4 NTLAIHAGYDG---NEFGTMAVPIYQTTAYEFRDAEHAANLFELKELGNIYTRLMNPTTD 60 Query: 66 VLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFKRF 125 V E+R AALEGGAAA+A +SG +A AI +A GDNI+ +YGGT + +RF Sbjct: 61 VFEKRFAALEGGAAAVATASGMSAIFYAIANVAEAGDNIIVAKQVYGGTTTLTGHTIRRF 120 Query: 126 GIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVDNT 185 GIEAR+ + PEE E + DERTK ++ E+I NP +V D +IV IA +HG+ DNT Sbjct: 121 GIEARYFDVYEPEELEAMIDERTKLIHFESITNPSVDVADIAEIVRIADRHGVLTCTDNT 180 Query: 186 FGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVD-SGKFPWKDYPEKFPQFSQPA 244 A C+PI++G D+V HSA+K+ G G IGGI+V+ G +++ F++P Sbjct: 181 V-ATPVICKPIEHGVDVVVHSASKYTTGQGLAIGGIVVEREGLVEKLKGNQRYYHFNEPD 239 Query: 245 EGYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGENAL 304 YHG +Y + + + R LLRDLG +PF S+L +QG+ETL LR +H ++AL Sbjct: 240 PSYHGLVYTD-LPLPPFTLRTRLALLRDLGAAPSPFNSWLYIQGLETLPLRMRQHSDSAL 298 Query: 305 KLAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGF-GGVLSFGVKDLPNADKETDPFK 363 +A++LE P V V+YPGL S ++ +KY G G+LSF V+ A + Sbjct: 299 AIAEFLEAHPKVKKVNYPGLKSDPNYPLVQKYFKKGMASGLLSFEVESREEAQR------ 352 Query: 364 LSGAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGIEF 423 + D+ KL + N+GD+K+L+ P TTH+QL+ +E A+GV + LIR+SVG+E Sbjct: 353 -----IADSTKLFKLVVNIGDSKSLITHPASTTHQQLSKEELEAAGVPEGLIRLSVGLED 407 Query: 424 IDDIIADFQQSFE 436 +D+I D +Q+ + Sbjct: 408 TEDLIEDLRQALQ 420 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: 495 Number of extensions: 20 Number of successful extensions: 4 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: 444 Length of database: 421 Length adjustment: 32 Effective length of query: 412 Effective length of database: 389 Effective search space: 160268 Effective search space used: 160268 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: 51 (24.3 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