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 Synpcc7942_0370 Synpcc7942_0370 O-acetylhomoserine/O-acetylserine sulfhydrylase
Query= SwissProt::P06106 (444 letters) >FitnessBrowser__SynE:Synpcc7942_0370 Length = 434 Score = 425 bits (1093), Expect = e-123 Identities = 222/444 (50%), Positives = 297/444 (66%), Gaps = 23/444 (5%) Query: 1 MPSHFDTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQ 60 M H +T+ LHAGQ+ D SRAVPIY TTSYVFE+++H + LF L+ G +Y+R Sbjct: 1 MSQHLETLALHAGQKP--DPTTGSRAVPIYQTTSYVFEDAEHAANLFALKAFGNIYTRLM 58 Query: 61 NPTSNVLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKI 120 NPT++VLE+R+AAL GG A+A SSGQAA AI + G NI+ST+ LYGGT N F+ Sbjct: 59 NPTTDVLEQRLAALHGGTGAVATSSGQAAIFYAIAAITSAGQNIISTTNLYGGTINLFRH 118 Query: 121 SFKRFGIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPV 180 + KRFGIE RFV+ + DE T+ VY E+IGNPK NV DFE I AIAH GIP Sbjct: 119 TLKRFGIEVRFVDSSDASSVAAAIDENTRLVYTESIGNPKGNVDDFEAIAAIAHDSGIPF 178 Query: 181 VVDNTFGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQF 240 +VDNT F P+++GAD+V S TK GGHGT++GGI+++ G FPW + KFP+ Sbjct: 179 IVDNTVSPPPLF-NPLEHGADVVVLSLTKLAGGHGTSLGGIVIEKGDFPWNN--GKFPEI 235 Query: 241 SQPAEGYHGTIYNEAYGN--------LAYIVHVRTELLRDLGPLMNPFASFLLLQGVETL 292 + P YHG + +A+GN LAY++ +RT LLRD+G ++PF + +L GVETL Sbjct: 236 AGPDPSYHGVNFWDAFGNHPEAVAPGLAYVLKIRTGLLRDIGATLSPFNAQQVLLGVETL 295 Query: 293 SLRAERHGENALKLAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDL 352 LRAERH NA +A+WLE+ P V+WV+YPGL SH ++ A++YL NG G +L FGV+ Sbjct: 296 PLRAERHVRNAQAVAEWLERHPLVTWVNYPGLPSHPDYDRAQRYLPNGAGAILGFGVQGG 355 Query: 353 PNADKETDPFKLSGAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTK 412 A G + + +KLASNLANV DAKTLVI P TTH+QL+ +E+ A+GV+ Sbjct: 356 LEA----------GKRFISAVKLASNLANVLDAKTLVIHPASTTHQQLSPEEQAAAGVSP 405 Query: 413 DLIRVSVGIEFIDDIIADFQQSFE 436 D +R+SVG+E +DDI+AD Q+ + Sbjct: 406 DFVRLSVGLEHLDDILADLDQALQ 429 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: 564 Number of extensions: 30 Number of successful extensions: 6 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: 434 Length adjustment: 32 Effective length of query: 412 Effective length of database: 402 Effective search space: 165624 Effective search space used: 165624 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: 51 (24.3 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