Align [CysO sulfur-carrier protein]-thiocarboxylate-dependent cysteine synthase (EC 2.5.1.113); O-phosphoserine sulfhydrylase (EC 2.5.1.65) (characterized)
to candidate Synpcc7942_B2664 Synpcc7942_B2664 cysteine synthase
Query= BRENDA::P9WP53 (323 letters) >FitnessBrowser__SynE:Synpcc7942_B2664 Length = 329 Score = 179 bits (454), Expect = 8e-50 Identities = 117/325 (36%), Positives = 173/325 (53%), Gaps = 25/325 (7%) Query: 9 QALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQAEADGLL 68 Q +G TPLV L R+ G + AK+E RNP S+K R MI AE GLL Sbjct: 13 QTIGKTPLVRLNRIVK-------GAPATVLAKIEGRNPAYSVKCRIGAAMIWDAEQRGLL 65 Query: 69 RPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFSAAEGG 128 PG ++EPTSGNTGI+LA A +G L MPE S+ERR+LL YGA+++ + G Sbjct: 66 GPGKELIEPTSGNTGIALAFVAAARGIPLTLTMPETMSLERRKLLAAYGAKLVLTEGVKG 125 Query: 129 SNTAVATAKELAATNPS-WVMLYQYGNPANTDSHYCGTGPELLADL-PEITHFVAGLGTT 186 AV A+++AA++P +V+L Q+ NPAN H TGPE+ D I V+G+GT Sbjct: 126 MTGAVRRAEDIAASDPDRYVLLQQFRNPANPAIHEQTTGPEIWEDTGGAIDILVSGVGTG 185 Query: 187 GTLMGTGRFLREHVAN-VKIVAAEPRYG-------------EGVYALRNMDEGFVPELYD 232 GT+ G R++++ + VA EP G + ++ + GF+PE D Sbjct: 186 GTITGVSRYIKQTQGKPILSVAVEPEASPVISQQRSGLPLKPGPHKIQGIGAGFIPENLD 245 Query: 233 PEILTARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALV 292 ++ V +A+ R L EG+ +GIS GA + AA+ + + AG+ I +V Sbjct: 246 LSLVDQVERVSNEEAIAYARRLAQEEGLISGISCGAAVAAAVRLAQQSEHAGK--TIVVV 303 Query: 293 VADAGWKYLSTGAYAGSLDDAETAL 317 + D+G +YLST + G ++ A+ Sbjct: 304 LPDSGERYLSTALFDGIFNEQGLAV 328 Lambda K H 0.317 0.134 0.398 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: 305 Number of extensions: 18 Number of successful extensions: 5 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: 323 Length of database: 329 Length adjustment: 28 Effective length of query: 295 Effective length of database: 301 Effective search space: 88795 Effective search space used: 88795 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: 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