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 Dsui_2241 Dsui_2241 OAH/OAS sulfhydrylase
Query= SwissProt::P06106 (444 letters) >FitnessBrowser__PS:Dsui_2241 Length = 424 Score = 427 bits (1099), Expect = e-124 Identities = 216/433 (49%), Positives = 294/433 (67%), Gaps = 13/433 (3%) Query: 6 DTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNPTSN 65 +T+ +HAG D ++ AVPIY TTSY F+N++HG+ LF L+V G +Y+R NPT + Sbjct: 5 ETLAVHAGYSP--DPTTKAAAVPIYQTTSYAFDNTQHGADLFDLKVAGNIYTRIMNPTQD 62 Query: 66 VLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFKRF 125 VLE+R+AALEGG A LA++SGQAA T AIQ +A GDNIVST+ LYGGTYN F +F + Sbjct: 63 VLEKRVAALEGGIAGLALASGQAAITYAIQTIAEAGDNIVSTATLYGGTYNLFAHTFPQL 122 Query: 126 GIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVDNT 185 GI+ RF + +P FEK+ D +TKA+Y ETIGNP N+ D EK+ IAH++GIP++VDNT Sbjct: 123 GIQVRFADYRDPASFEKLIDGKTKAIYAETIGNPLGNITDIEKLAEIAHRNGIPLIVDNT 182 Query: 186 FGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQPAE 245 A + +PI++GADIV HS TK++GGHG +IGGIIVDSGKFPW ++ +F + ++P Sbjct: 183 V-ASPFLLRPIEFGADIVVHSLTKYLGGHGNSIGGIIVDSGKFPWAEHKTRFKRLNEPDV 241 Query: 246 GYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGENALK 305 YHG +Y EA G AYI R LR+ G ++PF +FL+LQG+ET +LR ER +N + Sbjct: 242 SYHGVVYTEALGPAAYIGRARVVPLRNTGAAISPFNAFLILQGIETAALRMERITDNTIA 301 Query: 306 LAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKETDPFKLS 365 +AK+L+ V WV+Y GL +H H AKKYL G+L+FGV+ Sbjct: 302 VAKYLQSHKKVKWVNYAGLENHPDHALAKKYLGGKPSGILTFGVEGGIE----------G 351 Query: 366 GAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGIEFID 425 G + D L+L + L N+GDAK+L P TTH+QLN +E +GVT D +R+S+GIE ID Sbjct: 352 GTRFQDALQLFTRLVNIGDAKSLACHPASTTHRQLNPEELAKAGVTVDTVRLSIGIEHID 411 Query: 426 DIIADFQQSFETV 438 D+IAD +Q+ V Sbjct: 412 DLIADLEQALAAV 424 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: 588 Number of extensions: 26 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: 444 Length of database: 424 Length adjustment: 32 Effective length of query: 412 Effective length of database: 392 Effective search space: 161504 Effective search space used: 161504 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