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_084276347.1 B8779_RS08955 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= SwissProt::P06106 (444 letters) >NCBI__GCF_900176045.1:WP_084276347.1 Length = 396 Score = 177 bits (450), Expect = 4e-49 Identities = 126/411 (30%), Positives = 194/411 (47%), Gaps = 40/411 (9%) Query: 28 PIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNPTSNVLEERIAALEGGAAALAVSSGQ 87 PI + ++ + + K +F E +Y+R NPT+ LE +A ++ G A+ SSG Sbjct: 25 PIIGSAAFSYGDPKSAEAVFAGESRKPLYARMGNPTNAKLETLLAGIDQGDGAVVTSSGM 84 Query: 88 AAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFKRFGIEARFVEGDNPEEFEKVFDER 147 A + +GD IV L+GGTY F + RFGI+ RF + D E V + Sbjct: 85 GAIAAVVSAFLQSGDEIVCVGGLFGGTYAFFTQNLPRFGIKVRFFKADE----EVVLSPQ 140 Query: 148 TKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVDNTFGAGGYFCQPIKYGADIVTHSA 207 TK ++ E++GNP V +F K+ +A KHGI VVDNT +P +GADI+ +S Sbjct: 141 TKMIFCESVGNPSLTVVNFVKLGKLAQKHGILFVVDNTITP--LLFEPFSWGADIIVYST 198 Query: 208 TKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQPAEGYHGTIYNEAYGNLAYIVHVRT 267 TK I G +GG I+ K P KD FP + E G A + ++ Sbjct: 199 TKVISGQSQALGGAII--YKEPRKDLFIHFPFLQN---------FYENLGKDAIMGVIKK 247 Query: 268 ELLRDLGPLMNPFASFLLLQGVETLSLRAERHGENALKLAKWLEQSPYVSWVSYPGLASH 327 LRD G M A++L + G+ETL LR ++ +NA KL L+ V + Sbjct: 248 RALRDFGMSMQAHAAYLTILGLETLPLRIQKATDNAQKLFLALKDKVKVLYA-------- 299 Query: 328 SHHENAKKYLSNGFGGVLSFGVKDLPNADKETDPFKLSGAQVVDNLKLASNLANVGDAKT 387 ++Y G G ++ K + D F +++ K+ AN+GD++T Sbjct: 300 ----KNEQYFPFGTGQMMGIDFK------SKEDAFTF-----LEHAKIPFITANIGDSRT 344 Query: 388 LVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGIEFIDDIIADFQQSFETV 438 L + T ++ E GV++ L+R+SVG+E II DF+ + V Sbjct: 345 LALHMRSTIYRDFKANELEYLGVSEGLVRISVGLENCAMIIEDFENALRKV 395 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: 427 Number of extensions: 18 Number of successful extensions: 5 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: 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 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