Align O-phosphoserine sulfhydrylase monomer (EC 2.5.1.47; EC 2.5.1.65) (characterized)
to candidate 202695 SO3598 cysteine synthase B (NCBI ptt file)
Query= metacyc::MONOMER-20568 (299 letters) >FitnessBrowser__MR1:202695 Length = 288 Score = 239 bits (611), Expect = 4e-68 Identities = 128/287 (44%), Positives = 183/287 (63%), Gaps = 6/287 (2%) Query: 10 IGNTPLVRINHLNPNPKVQMYAKLEGFNPTGSVKDRIALKMIEQAEAEGKLHPGSTIIEA 69 IG TPLVR+ L+ + KLEG NP GSVKDR AL MI QAE ++ PG T+IEA Sbjct: 7 IGQTPLVRLQRLDCGSSTVLL-KLEGNNPAGSVKDRAALNMINQAELRQEIAPGDTLIEA 65 Query: 70 TSGNTGIGLAMIGRVKGYNVIIVMSEGVSIERRKMIKAFGAEIILTDKKLGTDGAIRKVA 129 TSGNTGI LAM +KGY +I++M + ER+ ++A+GAE++L D + A Sbjct: 66 TSGNTGIALAMAAAIKGYKMILIMPSNSTQERKDAMQAYGAELLLVDNM---EAARDLAL 122 Query: 130 ELVKENPGKYFNPNQFSNEYNKIAHYKTTAEEIWAQTKGTVTHFVAAVGTSGTLMGVGKN 189 L E GK + QF+N+ N AH+ TT EIW Q++G +THFV+++GT+GT+MGV K Sbjct: 123 ALQAEGKGKVLD--QFNNQDNANAHFLTTGPEIWQQSQGKITHFVSSMGTTGTIMGVSKY 180 Query: 190 LREKNPEIKIIEAQPTKGHYIQGLKSMEEAIVPAIYQADKIDEHILIESEEAFAKAREIV 249 L+ +NP+I I+ QP G I G++ + +P I+ A ++D + IE ++A A AR + Sbjct: 181 LKSRNPDITIVGLQPADGSSIPGIRRWPQEYLPGIFDAARVDLMMDIEEQDAKAMARALA 240 Query: 250 AQEGIFIGMSSGAAMLAAQKLAEKIDSGVIVVLFADRGEKYLSTKLF 296 +EGI G+SSG A+ AA +LA + V+V + DRG++YLS+ LF Sbjct: 241 REEGICAGVSSGGAVYAALELARQYPGSVVVAIVCDRGDRYLSSGLF 287 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: 267 Number of extensions: 13 Number of successful extensions: 3 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: 288 Length adjustment: 26 Effective length of query: 273 Effective length of database: 262 Effective search space: 71526 Effective search space used: 71526 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