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 200276 SO1095 O-acetylhomoserine (thiol)-lyase, putative (NCBI ptt file)
Query= SwissProt::P06106 (444 letters) >FitnessBrowser__MR1:200276 Length = 430 Score = 421 bits (1081), Expect = e-122 Identities = 217/431 (50%), Positives = 290/431 (67%), Gaps = 8/431 (1%) Query: 6 DTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNPTSN 65 +++ LH G E+ ++ AVPIY TTSY F++++HG+ LF L+V G +Y+R NPT++ Sbjct: 4 ESLALHHGYESEATT--KAAAVPIYQTTSYTFDDTQHGADLFDLKVAGNIYTRIMNPTTS 61 Query: 66 VLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFKRF 125 VLE+R+AA+EGG ALAV+SG AA T AIQ L GDNIVSTS LYGGTYN F + R Sbjct: 62 VLEQRLAAIEGGIGALAVASGMAAITYAIQALTQVGDNIVSTSQLYGGTYNLFAHTLPRQ 121 Query: 126 GIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVDNT 185 G+E R D+ EE E + D +TKA++ E+IGNP N+ D +++ IAHKHG+P++VDNT Sbjct: 122 GVEVRMAAFDDFEELEALIDAKTKALFCESIGNPAGNIVDLKRLAEIAHKHGVPLIVDNT 181 Query: 186 FGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQPAE 245 A C+P ++GADIV HS TK+IGGHGTTIGGII+DSGKF W E+F +Q Sbjct: 182 V-ATPVLCRPFEHGADIVIHSLTKYIGGHGTTIGGIIIDSGKFDWVANKERFSLLNQADP 240 Query: 246 GYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGENALK 305 YHG +Y EA+G A+I R LR+ G ++P ++FLLLQG+ETLSLR ERH NAL Sbjct: 241 SYHGVVYTEAFGPAAFIGRCRVVPLRNTGAALSPHSAFLLLQGLETLSLRMERHCANALA 300 Query: 306 LAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKETDPFKLS 365 LA++L P VSWV+Y L S EN +K G++SFG+K + K++ Sbjct: 301 LAEYLILHPSVSWVNYGALPSSPFRENCEKITGGKASGIISFGIK-----AATPEEGKIA 355 Query: 366 GAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGIEFID 425 G + +D LK+ L N+GDAK+L P TTH+QL+ E +GV++DLIR+SVGIE ID Sbjct: 356 GGKFIDALKMVLRLVNIGDAKSLACHPASTTHRQLDANELARAGVSEDLIRISVGIEHID 415 Query: 426 DIIADFQQSFE 436 DIIAD Q+ E Sbjct: 416 DIIADVSQALE 426 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: 523 Number of extensions: 13 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: 430 Length adjustment: 32 Effective length of query: 412 Effective length of database: 398 Effective search space: 163976 Effective search space used: 163976 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