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_106715050.1 CU100_RS02980 hypothetical protein
Query= SwissProt::P06106 (444 letters) >NCBI__GCF_003010935.1:WP_106715050.1 Length = 394 Score = 159 bits (402), Expect = 1e-43 Identities = 116/410 (28%), Positives = 188/410 (45%), Gaps = 51/410 (12%) Query: 28 PIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNPTSNVLEERIAALEGGAAALAVSSGQ 87 PI+ T+ + +++ + +F Y+YSR NPT E A LEG S+G Sbjct: 33 PIFQTSLFTYDSYEAMEDVFAGRSRNYIYSRGDNPTVREFELLTARLEGAEDGRGFSNGT 92 Query: 88 AAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFKRFGIEARFVEGDNPEEFEKVFDER 147 AA T I L GD +V+ +LY Y F RFG+ FV+ N +E Sbjct: 93 AAITATILSLVEAGDRVVAVRHLYNDIYRLFVKLLARFGVAVDFVDPSNHDEVRAAL-PG 151 Query: 148 TKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVDNTFGAGGYFCQPIKYGADIVTHSA 207 K +YLE + + + D E + A+A ++G+ V+DN++ A F +PI++G D+V H+A Sbjct: 152 AKLLYLENPTSMVFELQDIEALAAMAKEYGVVSVIDNSW-ATPLFQKPIQHGVDLVIHAA 210 Query: 208 TKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQPAEGYHGTIYNEAYGNLAYIVHVRT 267 +K++GGH T+ G++V G I + + Sbjct: 211 SKYLGGHSDTVAGVVV---------------------------------GPRDLIAKINS 237 Query: 268 ELLRDLGPLMNPFASFLLLQGVETLSLRAERHGENALKLAKWLEQSPYVSWVSYPGLASH 327 +G ++PF ++LLL+G+ TL +R + H N L LA+ L+Q P +S V +P + H Sbjct: 238 TTYPYIGAKLSPFEAWLLLRGMRTLKVRLKEHMHNGLVLARHLQQHPDISLVRHPAFSDH 297 Query: 328 SHHENAKKYLSNGFGGVLSFGVKDLPNADKETDPFKLSGAQVVDNLKLASNLANVGDAKT 387 KK L+ GF G+ +F + P+ D A+ V+ L+ + G +T Sbjct: 298 ----QGKKTLT-GFSGLFAFDLS--PDVDV---------ARFVNALRHIRLGVSWGGPET 341 Query: 388 LVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGIEFIDDIIADFQQSFET 437 LV+ + GV IR +VG+E + I D QQ+ + Sbjct: 342 LVVPAKAALQIPDRMTSFVRFGVNPQTIRFAVGLEEPEIIWNDLQQALHS 391 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: 430 Number of extensions: 21 Number of successful extensions: 5 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: 394 Length adjustment: 32 Effective length of query: 412 Effective length of database: 362 Effective search space: 149144 Effective search space used: 149144 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 Jul 26 2024. The underlying query database was built on Jul 25 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