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_075386831.1 BK574_RS12860 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= SwissProt::P06106 (444 letters) >NCBI__GCF_002019605.1:WP_075386831.1 Length = 428 Score = 422 bits (1084), Expect = e-122 Identities = 216/429 (50%), Positives = 297/429 (69%), Gaps = 15/429 (3%) Query: 6 DTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNPTSN 65 +TV +H GQE D A +SRAVPIY TTSY F+N++H + LF L G +Y+R NPT + Sbjct: 9 ETVAVHGGQEV--DPATQSRAVPIYQTTSYGFKNTEHAANLFSLAESGNIYTRIMNPTQD 66 Query: 66 VLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFKRF 125 V E+R+A LEGG AALA +SG +A LAI + GD IV++S LYGGTYN F + K+ Sbjct: 67 VFEKRVAELEGGVAALATASGSSAIHLAILNICENGDEIVASSALYGGTYNLFVHTLKKM 126 Query: 126 GIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVDNT 185 GI V+G +P+ FE+ +TK ++ E IGNP+ ++ D E + A+AH++G+P++VD T Sbjct: 127 GITVHLVDGTDPQAFEQAITPKTKLLFGEMIGNPQGDILDVEAVAAVAHRNGVPLMVDAT 186 Query: 186 FGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQPAE 245 C+PI++GADIV HSATK++GGHGT+IGG+IVD G F W + KFP ++P Sbjct: 187 LVTPA-LCRPIEHGADIVVHSATKFMGGHGTSIGGVIVDGGNFDWNN--GKFPGLTEPDP 243 Query: 246 GYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGENALK 305 YHG +Y EA GNLAYI+ R +LLRDLGP + P SFLLLQG+ETL LR ERH ENA+K Sbjct: 244 SYHGLVYTEALGNLAYIIKARVQLLRDLGPAIAPLNSFLLLQGLETLHLRMERHCENAMK 303 Query: 306 LAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKETDPFKLS 365 +A++LE V WVS+ GL SH ++ A KYL NG G +L+FG+K Sbjct: 304 VAQYLENHELVEWVSFAGLPSHRSYDLANKYLPNGKGAILTFGIKGGIE----------E 353 Query: 366 GAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGIEFID 425 G ++ L+L S++ANVGDAK+LVI P TTH+QL++ ++ A+GV+ +LIR+SVGIE ++ Sbjct: 354 GKSFINALELFSHVANVGDAKSLVIHPASTTHQQLSEADQRAAGVSPELIRLSVGIENVN 413 Query: 426 DIIADFQQS 434 DII+D +Q+ Sbjct: 414 DIISDLEQA 422 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: 511 Number of extensions: 22 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: 428 Length adjustment: 32 Effective length of query: 412 Effective length of database: 396 Effective search space: 163152 Effective search space used: 163152 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 10 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