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_012536942.1 AFE_RS09520 O-succinylhomoserine sulfhydrylase
Query= SwissProt::P06106 (444 letters) >NCBI__GCF_000021485.1:WP_012536942.1 Length = 404 Score = 242 bits (618), Expect = 1e-68 Identities = 151/435 (34%), Positives = 224/435 (51%), Gaps = 48/435 (11%) Query: 6 DTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNPTSN 65 +T+ + AG + H I+ T+S+VF++++ + F VPG +Y+RF NPT Sbjct: 17 ETIAIRAGIHRTQEQEHSEA---IFPTSSFVFDSAEEAADRFAGRVPGNIYARFTNPTVR 73 Query: 66 VLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFKRF 125 EER+AALEG A +A +SG AA A G+ GD++V++ ++G T RF Sbjct: 74 TFEERLAALEGAEACVATASGMAACLTAFMGILKAGDHVVASRSIFGTTVQLLGNILSRF 133 Query: 126 GIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVDNT 185 G+E FV + + T+ ++LET NP + D + + +AH H +VVDN Sbjct: 134 GVETSFVPLADVPAWRAALRPNTRMLFLETPSNPLTEIGDMQALADLAHVHDAWLVVDNC 193 Query: 186 FGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQPAE 245 F QP+K+GAD+V HSATK++ G G T+GG + S + Sbjct: 194 FCTPA-LQQPLKFGADLVIHSATKYLDGQGRTLGGAVCGSTE------------------ 234 Query: 246 GYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGENALK 305 + N N +R GP ++PF +++ L+G+ETL LR ERH NA K Sbjct: 235 -----LLNSGPRN----------FVRTAGPSLSPFNAWVQLKGLETLGLRMERHCANAQK 279 Query: 306 LAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKETDPFKLS 365 +A+WLE P V+ V YPGL SH A + G +LSF DL K F Sbjct: 280 IAEWLEARPEVARVYYPGLDSHPQQALAARQ-QRLPGAILSF---DLHGGQKAAWAF--- 332 Query: 366 GAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGIEFID 425 VD L+L S AN+GDAKT + P TTH +++ + + A+GV L+R+SVG+E D Sbjct: 333 ----VDALRLLSLTANLGDAKTTITHPASTTHSRVSPEARAAAGVGDGLLRISVGLEHAD 388 Query: 426 DIIADFQQSFETVFA 440 D+ D ++ F + A Sbjct: 389 DLREDMERGFAALVA 403 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: 479 Number of extensions: 25 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 444 Length of database: 404 Length adjustment: 32 Effective length of query: 412 Effective length of database: 372 Effective search space: 153264 Effective search space used: 153264 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