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 Pf1N1B4_4890 Cystathionine gamma-lyase (EC 4.4.1.1)
Query= SwissProt::P06106 (444 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4890 Length = 393 Score = 208 bits (530), Expect = 2e-58 Identities = 146/435 (33%), Positives = 226/435 (51%), Gaps = 58/435 (13%) Query: 2 PSHFDTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQN 61 P F T +HAGQ D + + PIYA ++Y+ ++ G+ G+ Y R N Sbjct: 10 PRGFATRVIHAGQTP--DPSTGALMPPIYANSTYLQQSP-------GVH-KGFDYGRSHN 59 Query: 62 PTSNVLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQF-KI 120 PT LE +A LEGG A A +SG AA ++ L G +IVS + LYGGT+ F K+ Sbjct: 60 PTRFALERCVADLEGGTRAFAFASGLAAIANVLE-LLDAGAHIVSGNDLYGGTFRLFDKV 118 Query: 121 SFKRFGIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPV 180 + G FV+ + FE ++ T+ V++ET NP ++ D + + I + GI Sbjct: 119 RRRSAGHRFSFVDLTDLAAFEAALEDDTRMVWVETPSNPLLSLTDLDAVARICRQRGIIC 178 Query: 181 VVDNTFGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQF 240 V DNTF A + +P++ G DIV HS TK++ GH IGGI V Sbjct: 179 VADNTF-ASPWIQRPLELGFDIVLHSTTKYLNGHSDVIGGIAV----------------- 220 Query: 241 SQPAEGYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHG 300 G A + L +G + PF +FL L+GV+TL+LR ERH Sbjct: 221 ---------------VGQNAELAERLGFLQNAVGAIAGPFDAFLTLRGVKTLALRMERHC 265 Query: 301 ENALKLAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKETD 360 NAL+LA+WLE+ P V+ V YPGL SH HE A++ + GFGG++S + N+D Sbjct: 266 SNALELAQWLERQPQVARVYYPGLPSHPQHELARRQM-RGFGGMISLDL----NSD---- 316 Query: 361 PFKLSGA-QVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSV 419 L+GA + ++++++ + ++G ++L+ P TH + + + G+ L+R+SV Sbjct: 317 ---LAGAKRFLESVRIFALAESLGGVESLIEHPAIMTHASIPVETRAQLGIGDALVRLSV 373 Query: 420 GIEFIDDIIADFQQS 434 G+E ++D+ AD Q+ Sbjct: 374 GVEDVEDLRADLAQA 388 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: 421 Number of extensions: 29 Number of successful extensions: 6 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: 393 Length adjustment: 32 Effective length of query: 412 Effective length of database: 361 Effective search space: 148732 Effective search space used: 148732 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