Align O-phosphoserine sulfhydrylase monomer (EC 2.5.1.47; EC 2.5.1.65) (characterized)
to candidate Echvi_0220 Echvi_0220 cysteine synthase B
Query= metacyc::MONOMER-20568 (299 letters) >FitnessBrowser__Cola:Echvi_0220 Length = 292 Score = 258 bits (659), Expect = 1e-73 Identities = 136/291 (46%), Positives = 190/291 (65%), Gaps = 2/291 (0%) Query: 6 ILETIGNTPLVRINHLNPNPKVQMYAKLEGFNPTGSVKDRIALKMIEQAEAEGKLHPGST 65 + E IGNTPLV + H+ NP V++Y KLEG NP GSVKDR A MI++A G L G Sbjct: 3 LFELIGNTPLVELEHIPTNPNVKIYCKLEGQNPGGSVKDRAAYSMIKRAMDRGDLKQGDR 62 Query: 66 IIEATSGNTGIGLAMIGRVKGYNVIIVMSEGVSIERRKMIKAFGAEIILTDKKLGTDGAI 125 ++EATSGNTGI LAMI +V G + ++M + + ER ++A+GA++ILT + + Sbjct: 63 VVEATSGNTGIALAMIAKVLGVEMTLIMPDNSTRERVVSMEAYGAKVILTPAAKTIEYS- 121 Query: 126 RKVAELVKENPGKYFNPNQFSNEYNKIAHYKTTAEEIWAQTKGTVTHFVAAVGTSGTLMG 185 R +AE + +N G Y+ NQF+N N AHY+ T EI T G +THFV+A+GT+GT+MG Sbjct: 122 RTLAEEMAKNEG-YYILNQFANPDNYQAHYEGTGPEIMRDTNGEITHFVSAMGTTGTIMG 180 Query: 186 VGKNLREKNPEIKIIEAQPTKGHYIQGLKSMEEAIVPAIYQADKIDEHILIESEEAFAKA 245 V + L+E+ P ++I+ QPT G I G++ +P IY A ++D+ I + EEA Sbjct: 181 VSRYLKEQKPAVQIVGTQPTDGSSIPGIRRWSPEFLPKIYDASRVDQIIDVSQEEATEMT 240 Query: 246 REIVAQEGIFIGMSSGAAMLAAQKLAEKIDSGVIVVLFADRGEKYLSTKLF 296 R + +EGI GMSSG A+ AA KLAE +DSGVIV + DRG++YLS+ LF Sbjct: 241 RRMAKEEGILAGMSSGGALHAAVKLAESLDSGVIVCITCDRGDRYLSSDLF 291 Lambda K H 0.315 0.133 0.367 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: 287 Number of extensions: 12 Number of successful extensions: 2 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: 299 Length of database: 292 Length adjustment: 26 Effective length of query: 273 Effective length of database: 266 Effective search space: 72618 Effective search space used: 72618 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: 42 (22.0 bits) S2: 48 (23.1 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