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 GFF2323 PGA1_c23540 O-succinylhomoserine sulfhydrylase MetZ
Query= SwissProt::P06106 (444 letters) >FitnessBrowser__Phaeo:GFF2323 Length = 396 Score = 209 bits (531), Expect = 2e-58 Identities = 138/407 (33%), Positives = 208/407 (51%), Gaps = 45/407 (11%) Query: 29 IYATTSYVFENSKHGSQLFGLEVPG-YVYSRFQNPTSNVLEERIAALEGGAAALAVSSGQ 87 IY T +V++ ++ F P ++Y+R+ NPT + EERIAALEG A A +SG Sbjct: 28 IYLTQGFVYDTAEQAEARFIETGPDEFIYARYGNPTVAMFEERIAALEGAEDAFATASGM 87 Query: 88 AAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFKRFGIEARFVEGDNPEEFEKVFDER 147 AA A+ + GD++VS L+G + R+G+E FV+G + + + Sbjct: 88 AAVNGALTSILKAGDHVVSAKALFGSCLYILENILTRYGVEVTFVDGTDLDAWRAALRPD 147 Query: 148 TKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVDNTFGAGGYFCQPIKYGADIVTHSA 207 TKAV+ E++ NP V D + +AH G VVVDN F F I+ GAD+V +SA Sbjct: 148 TKAVFFESMSNPTLEVIDIAAVAELAHAVGATVVVDNVFST-PVFSNAIEQGADVVIYSA 206 Query: 208 TKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQPAEGYHGTIYNEAYGNLAYIVHVRT 267 TK I G G +GG+I+ + F GT+ E Y Sbjct: 207 TKHIDGQGRVLGGVILGTRDF------------------IRGTV--EPY----------- 235 Query: 268 ELLRDLGPLMNPFASFLLLQGVETLSLRAERHGENALKLAKWLEQSPYVSWVSYPGLASH 327 ++ G ++PF ++ LL+G+ET+SLR E AL+LA+ L P +S + YPGL H Sbjct: 236 --MKHTGGSLSPFNAWTLLKGLETISLRVNAQAETALELAQALSGHPALSRLMYPGLEDH 293 Query: 328 SHHENAKKYLSNGFGGVLSFGVKDLPNADKETDPFKLSGAQVVDNLKLASNLANVGDAKT 387 + H ++ L G VLS +K +A F+ A + + SN N+GDAK+ Sbjct: 294 AQHALVQRQLGGKGGTVLSLDLKGGKDA-----AFRFLNALTI---PVISN--NLGDAKS 343 Query: 388 LVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGIEFIDDIIADFQQS 434 + P TTH++L+++ K G+T L+R SVG+E D+IAD Q+ Sbjct: 344 IATHPATTTHQRLSEELKSELGITPGLVRFSVGLEDAGDLIADLTQA 390 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: 400 Number of extensions: 15 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: 396 Length adjustment: 32 Effective length of query: 412 Effective length of database: 364 Effective search space: 149968 Effective search space used: 149968 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