Align O-phosphoserine sulfhydrylase monomer (EC 2.5.1.47; EC 2.5.1.65) (characterized)
to candidate 3608924 Dshi_2314 Pyridoxal-5'-phosphate-dependent protein beta subunit (RefSeq)
Query= metacyc::MONOMER-20568 (299 letters) >FitnessBrowser__Dino:3608924 Length = 345 Score = 158 bits (400), Expect = 1e-43 Identities = 109/315 (34%), Positives = 160/315 (50%), Gaps = 19/315 (6%) Query: 3 YDNILETIGNTPLVRINHLNPNPKVQMYAKLEGFNPTGSVKDRIALKMIEQAEAEGKLHP 62 Y ++ E IG+TPL+R+N + ++ K E NP SVKDR AL +I A A G L P Sbjct: 4 YRDLAEAIGHTPLIRLNAASEATGCEILGKAEFLNPGQSVKDRAALYIIRDAVARGTLKP 63 Query: 63 GSTIIEATSGNTGIGLAMIGRVKGYNVIIVMSEGVSIERRKMIKAFGAEIILTDKK--LG 120 G TI+E T+GNTGIGLA++G G+ +IV+ E S E++ M++ GA+++ Sbjct: 64 GGTIVEGTAGNTGIGLALVGASMGFKTVIVIPETQSEEKKDMLRLAGADLVQVPAAPYRN 123 Query: 121 TDGAIRKVAELVKE----NPGKYFNPNQFSNEYNKIAHYKTTAEEIWAQTKGTVTHFVAA 176 + +R L K P NQF N N+ AH +TT EIW QT G V F+ A Sbjct: 124 PNNYVRYSERLAKRLAETEPHGAIWANQFDNVANRQAHVETTGPEIWDQTGGKVDGFICA 183 Query: 177 VGTSGTLMGVGKNLREKNPEIKIIEAQPTK--GHYIQG-LKSMEEAI--------VPAIY 225 G+ GT+ GVG L+ K ++ + + Y QG LKS +I + A Sbjct: 184 AGSGGTVAGVGLALQPKGVKVGLADPDGAALYNFYTQGELKSEGSSISEGIGQGRITANL 243 Query: 226 QADKIDEHILIESEEAFAKAREIVAQEGIFIGMSSGAAMLAAQKLAEKIDSG-VIVVLFA 284 + D + EA +++ EGI +G SSG + A ++A + G IV + Sbjct: 244 EGFTPDFACNVPDSEALPIVFDLLRHEGICLGGSSGINIAGAIRMARHMGPGHTIVTILC 303 Query: 285 DRGEKYLSTKLFDTE 299 D G +Y S KLF+ + Sbjct: 304 DYGTRYQS-KLFNPD 317 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: 300 Number of extensions: 19 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: 345 Length adjustment: 28 Effective length of query: 271 Effective length of database: 317 Effective search space: 85907 Effective search space used: 85907 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