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 N515DRAFT_4297 N515DRAFT_4297 cystathionine beta-synthase (EC 4.2.1.22)
Query= BRENDA::P9WP53 (323 letters) >FitnessBrowser__Dyella79:N515DRAFT_4297 Length = 456 Score = 176 bits (445), Expect = 1e-48 Identities = 112/320 (35%), Positives = 168/320 (52%), Gaps = 29/320 (9%) Query: 1 MTRYDSLLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIE 60 MT + S+L+ +G TP+V QRL D L+ KLE NP GSIKDR + MIE Sbjct: 1 MTVHQSVLELIGRTPMVRAQRL--------DAGSCELFLKLESANPGGSIKDRIGLSMIE 52 Query: 61 QAEADGLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQI 120 AE G ++PGAT++E T+GNTG+ LA+ A+ KGYRL+ V+P+ S E+ L+ GA++ Sbjct: 53 GAERAGKIKPGATLVEGTAGNTGLGLALVAQQKGYRLVLVVPDKMSREKIFNLKAMGAEV 112 Query: 121 IFS---AAEGGSNTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLP-EI 176 + + A+G A+ +A P + Q+GNP N +H TGPE+L + + Sbjct: 113 VLTRSDVAKGHPEYYQDMAERIARETPGAYFINQFGNPDNPAAHIATTGPEILEQMDGRV 172 Query: 177 THFVAGLGTTGTLMGTGRFLREHVANVKIVAAEP-------RYGEGV-------YALRNM 222 V G G++GT+ G R+ EH + +IV A+P EGV + + + Sbjct: 173 DAIVVGCGSSGTMSGLSRYFAEHSPDTEIVLADPVGSILAQYINEGVLSTKSGSWMVEGI 232 Query: 223 DEGFVPELYDPEILTARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALA 282 E F+P + D + Y++ ++ REL+ EG+ G STG +L AAL Sbjct: 233 GEDFLPSISDFSRVRKAYAISDKESFLAARELLAKEGVLGGSSTGTLLSAALKY---CRE 289 Query: 283 AGERADIALVVADAGWKYLS 302 + + +V D G KYLS Sbjct: 290 QTQPKRVVTLVCDTGNKYLS 309 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: 360 Number of extensions: 17 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: 456 Length adjustment: 30 Effective length of query: 293 Effective length of database: 426 Effective search space: 124818 Effective search space used: 124818 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: 50 (23.9 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