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_092056754.1 BQ4888_RS09545 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= SwissProt::P06106 (444 letters) >NCBI__GCF_900111775.1:WP_092056754.1 Length = 425 Score = 372 bits (954), Expect = e-107 Identities = 194/428 (45%), Positives = 276/428 (64%), Gaps = 14/428 (3%) Query: 8 VQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNPTSNVL 67 ++ A Q A +R I +T++ +++++H ++LF L++P Y+R NPT++ Sbjct: 7 IETQAVQGTYAPKATEARIPTICQSTTFKYDSAEHVAKLFDLDLPDPFYTRLGNPTTDAF 66 Query: 68 EERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFKRFGI 127 E +IA +EGG ALA SSGQAA L+I + G +IV+ LYGGTY+ F + + GI Sbjct: 67 EGKIALMEGGVGALATSSGQAATALSIMNICRAGQHIVTAGTLYGGTYSLFANTLPKLGI 126 Query: 128 EARFVEGDNP-EEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVDNTF 186 E FV D+ EE +K F TKA++ ETIGNP NV DFEK A+A G+P+++DNTF Sbjct: 127 EVSFVNPDSSAEEIKKHFRPETKALFAETIGNPGLNVLDFEKFSAVARATGVPLLIDNTF 186 Query: 187 GAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQPAEG 246 Y C+P+ +GADIV HSATK+I GH +++GG+IVD GKF W KFP+ ++P Sbjct: 187 PTP-YLCRPLDHGADIVIHSATKYIDGHASSLGGVIVDGGKFDWTS--GKFPELTEPDSS 243 Query: 247 YHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGENALKL 306 YHG Y E +G AYIV R + +RDLG +PF SFL QG+ TL LR ERH NAL L Sbjct: 244 YHGLRYVEKFGPSAYIVKARAQYMRDLGVTPSPFNSFLFHQGLTTLPLRMERHSANALAL 303 Query: 307 AKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKETDPFKLSG 366 A +L+ P VSWV+YPGL SH + A++Y+ G GVL+FG+K A G Sbjct: 304 AHFLQGHPKVSWVNYPGLESHPSYPLAQRYMPKGASGVLTFGIKGAREA----------G 353 Query: 367 AQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGIEFIDD 426 + ++ ++ + + +VGDA++ V+ P TTH+QL++ +++ASGVT DLIR+SVGIE IDD Sbjct: 354 IRFMEATRIIALVVHVGDARSCVLHPASTTHRQLSEAQQIASGVTPDLIRLSVGIEHIDD 413 Query: 427 IIADFQQS 434 +IAD +Q+ Sbjct: 414 LIADVEQA 421 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: 484 Number of extensions: 21 Number of successful extensions: 5 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: 425 Length adjustment: 32 Effective length of query: 412 Effective length of database: 393 Effective search space: 161916 Effective search space used: 161916 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