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 3609021 Dshi_2410 O-succinylhomoserine sulfhydrylase (RefSeq)
Query= SwissProt::P06106 (444 letters) >FitnessBrowser__Dino:3609021 Length = 392 Score = 191 bits (485), Expect = 4e-53 Identities = 133/434 (30%), Positives = 214/434 (49%), Gaps = 51/434 (11%) Query: 7 TVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPG--YVYSRFQNPTS 64 T +HAG + + A I+ T +V++ ++ F +E ++Y+R+ NPT Sbjct: 8 TKLVHAGTRR---SQYGEVAEAIFLTQGFVYDTAEAAEARF-IEAGADEFIYARYGNPTV 63 Query: 65 NVLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFKR 124 + E+RIAA+EG A A +SG AA A+ + GD++VS L+G + R Sbjct: 64 RMFEDRIAAVEGTEDAFATASGMAAVNGALASMLRAGDHVVSARALFGSCLYILEEVLTR 123 Query: 125 FGIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVDN 184 +G+E FV+G + + TKAV+ ETI NP V D E + +AH G V+VDN Sbjct: 124 YGVEVTFVDGTDLAAWRAAIRPDTKAVFFETISNPTLEVIDIEAVAKLAHAVGALVIVDN 183 Query: 185 TFGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQPA 244 F A F + GAD++ +SATK I G G +GG+I + +D+ K A Sbjct: 184 VF-ATPIFSRAKDQGADVIVYSATKHIDGQGRCLGGVICGT-----RDFVRKV------A 231 Query: 245 EGYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGENAL 304 E Y L+ G ++PF ++++L+ +ETL LR E A Sbjct: 232 EPY----------------------LKHTGGSLSPFNAWVMLKSMETLDLRVRAQAETAQ 269 Query: 305 KLAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKETDPFKL 364 LA+ LE + V +P L SH ++ A+ ++ G G VL+ +K K Sbjct: 270 ALAETLEGHAALEKVIFPHLPSHPQYDLARAQMAAG-GTVLALDIKG----------GKA 318 Query: 365 SGAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGIEFI 424 + ++ L++ + N+GDAK++ P TTH++L +++ G+T LIR+SVG+E Sbjct: 319 GAFRFLNALEIVTISNNLGDAKSIATHPATTTHQRLTPEQRAGLGITDGLIRLSVGLEDA 378 Query: 425 DDIIADFQQSFETV 438 D++ D Q + V Sbjct: 379 GDLLRDLQTALAAV 392 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: 377 Number of extensions: 17 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: 392 Length adjustment: 32 Effective length of query: 412 Effective length of database: 360 Effective search space: 148320 Effective search space used: 148320 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: 50 (23.9 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