Align O-phosphoserine sulfhydrylase monomer (EC 2.5.1.47; EC 2.5.1.65) (characterized)
to candidate 16513 b2414 cysteine synthase A, O-acetylserine sulfhydrolase A subunit (NCBI)
Query= metacyc::MONOMER-20568 (299 letters) >FitnessBrowser__Keio:16513 Length = 323 Score = 215 bits (547), Expect = 1e-60 Identities = 134/313 (42%), Positives = 177/313 (56%), Gaps = 27/313 (8%) Query: 4 DNILETIGNTPLVRINHLNPNPKVQMYAKLEGFNPTGSVKDRIALKMIEQAEAEGKLHPG 63 DN L TIG+TPLVR+N + ++ AK+E NP+ SVK RI MI AE G L PG Sbjct: 7 DNSL-TIGHTPLVRLNRIGNG---RILAKVESRNPSFSVKCRIGANMIWDAEKRGVLKPG 62 Query: 64 STIIEATSGNTGIGLAMIGRVKGYNVIIVMSEGVSIERRKMIKAFGAEIILTDKKLGTDG 123 ++E TSGNTGI LA + +GY + + M E +SIERRK++KA GA ++LT+ G G Sbjct: 63 VELVEPTSGNTGIALAYVAAARGYKLTLTMPETMSIERRKLLKALGANLVLTEGAKGMKG 122 Query: 124 AIRKVAELVKENPGKYFNPNQFSNEYNKIAHYKTTAEEIWAQTKGTVTHFVAAVGTSGTL 183 AI+K E+V NP KY QFSN N H KTT EIW T G V F+A VGT GTL Sbjct: 123 AIQKAEEIVASNPEKYLLLQQFSNPANPEIHEKTTGPEIWEDTDGQVDVFIAGVGTGGTL 182 Query: 184 MGVGKNLREKNPEIKIIE--AQPTKG----------------HYIQGLKSMEEAIVPAIY 225 GV + ++ + +I +PT H IQG+ + +PA Sbjct: 183 TGVSRYIKGTKGKTDLISVAVEPTDSPVIAQALAGEEIKPGPHKIQGIGA---GFIPANL 239 Query: 226 QADKIDEHILIESEEAFAKAREIVAQEGIFIGMSSGAAMLAAQKLA--EKIDSGVIVVLF 283 +D+ I I +EEA + AR ++ +EGI G+SSGAA+ AA KL E + IVV+ Sbjct: 240 DLKLVDKVIGITNEEAISTARRLMEEEGILAGISSGAAVAAALKLQEDESFTNKNIVVIL 299 Query: 284 ADRGEKYLSTKLF 296 GE+YLST LF Sbjct: 300 PSSGERYLSTALF 312 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: 322 Number of extensions: 15 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 299 Length of database: 323 Length adjustment: 27 Effective length of query: 272 Effective length of database: 296 Effective search space: 80512 Effective search space used: 80512 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