Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate WP_043745532.1 AMB_RS21365 O-succinylhomoserine sulfhydrylase
Query= reanno::Korea:Ga0059261_3194 (402 letters) >NCBI__GCF_000009985.1:WP_043745532.1 Length = 403 Score = 434 bits (1116), Expect = e-126 Identities = 220/397 (55%), Positives = 284/397 (71%), Gaps = 7/397 (1%) Query: 8 DRSITQNWKPATQAIRGGTARSEWGETSEALFLTSGYAYDCAGDAAARFSGDQQGMTYSR 67 D ++ W+P T+A+RGG +R+ + ETSEA+F+ SGY YD A +A A F G M YSR Sbjct: 5 DSKPSRTWRPRTRAVRGGLSRTNFCETSEAVFMNSGYVYDSAEEAEASFDGTLDRMVYSR 64 Query: 68 LQNPTVEMLEQRIALLEGAE-----ACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGS 122 +NPTV + EQR+A +EGA A RATASGMAA+ AALLCQL AGD ++ A FGS Sbjct: 65 FKNPTVAVFEQRLAEMEGAPPGMAVAARATASGMAAVHAALLCQLRAGDRVVASTALFGS 124 Query: 123 CRWLTDTQLPKFGIETTVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCAIA 182 C W+ + LP++G+E VD D + + A+ T F ETP+NPT++++DL AVC +A Sbjct: 125 CHWIINELLPRYGVERVFVDGTDLKSWEAALSRPTACVFLETPSNPTLEIIDLAAVCELA 184 Query: 183 RERGIVTVVDNAFATPALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGTEEFINNTLL 242 + G VVDN FATP LQ P++ GAD+V YSATK MDGQGR L GAV G+ EF + L Sbjct: 185 HKAGAKVVVDNVFATPILQSPLELGADIVVYSATKHMDGQGRCLGGAVLGSPEFCADILG 244 Query: 243 PFHRNTGPTLSPFNAWVVLKGLETLDLRIQRQSENALKVARFLEGR--VPRVNFPGLPSH 300 PF RNTGP LSPFNAWV+LKGLETLDLR++R NALKVARFLE R V RV +PGL SH Sbjct: 245 PFLRNTGPALSPFNAWVLLKGLETLDLRMERHCANALKVARFLEARPEVARVLYPGLESH 304 Query: 301 PQHNLAMSQMAAAGPIFSIELDGGRTQAHGLLDALGLIDISNNIGDSRSLMTHPASTTHS 360 PQH+LA QM G I ++EL GG+ A+ LL+ + LIDISNN+GD++SL+THP +TTH Sbjct: 305 PQHDLAKRQMRGWGSIVALELKGGKPAAYKLLNGVELIDISNNLGDAKSLITHPWTTTHQ 364 Query: 361 GVAEDQRLLMGVGEGMLRLNVGLEDPEDLIADLDQAL 397 ++ + +L MG+ EG+LRL+VGLED +DL+ DL +AL Sbjct: 365 RLSPEDKLSMGITEGLLRLSVGLEDGDDLVEDLGRAL 401 Lambda K H 0.319 0.134 0.396 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: 454 Number of extensions: 19 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: 402 Length of database: 403 Length adjustment: 31 Effective length of query: 371 Effective length of database: 372 Effective search space: 138012 Effective search space used: 138012 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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