Align cysteine synthase (EC 2.5.1.47); L-3-cyanoalanine synthase (EC 4.4.1.9) (characterized)
to candidate N515DRAFT_4297 N515DRAFT_4297 cystathionine beta-synthase (EC 4.2.1.22)
Query= BRENDA::Q84IF9 (308 letters) >FitnessBrowser__Dyella79:N515DRAFT_4297 Length = 456 Score = 229 bits (585), Expect = 7e-65 Identities = 135/311 (43%), Positives = 186/311 (59%), Gaps = 24/311 (7%) Query: 7 SITELIGDTPAVKLNRIVDEDSADVYLKLEFMNPGSSVKDRIALAMIEAAEKAGKLKPGD 66 S+ ELIG TP V+ R+ D S +++LKLE NPG S+KDRI L+MIE AE+AGK+KPG Sbjct: 6 SVLELIGRTPMVRAQRL-DAGSCELFLKLESANPGGSIKDRIGLSMIEGAERAGKIKPGA 64 Query: 67 TIVEPTSGNTGIGLAMVAAAKGYKAVLVMPDTMSLERRNLLRAYGAELVLTPGAQGMRGP 126 T+VE T+GNTG+GLA+VA KGY+ VLV+PD MS E+ L+A GAE+VLT R Sbjct: 65 TLVEGTAGNTGLGLALVAQQKGYRLVLVVPDKMSREKIFNLKAMGAEVVLT------RSD 118 Query: 127 IAK---------AEELVRE-HGYFMPQQFKNEANPEIHRLTTGKEIVEQMGDQLDAFVAG 176 +AK AE + RE G + QF N NP H TTG EI+EQM ++DA V G Sbjct: 119 VAKGHPEYYQDMAERIARETPGAYFINQFGNPDNPAAHIATTGPEILEQMDGRVDAIVVG 178 Query: 177 VGTGGTTTGAGKVLREAYPNIKIYAVEPADSPV-------LSGGKPGPHKIQGIGAGFVP 229 G+ GT +G + E P+ +I +P S + + K G ++GIG F+P Sbjct: 179 CGSSGTMSGLSRYFAEHSPDTEIVLADPVGSILAQYINEGVLSTKSGSWMVEGIGEDFLP 238 Query: 230 DILDTSIYDGVITVTTEEAFAAARRAAREEGILGGISSGAAIHAALKVAKELGKGKKVLA 289 I D S ++ +E+F AAR +EG+LGG S+G + AALK +E + K+V+ Sbjct: 239 SISDFSRVRKAYAISDKESFLAARELLAKEGVLGGSSTGTLLSAALKYCREQTQPKRVVT 298 Query: 290 IIPSNGERYLS 300 ++ G +YLS Sbjct: 299 LVCDTGNKYLS 309 Lambda K H 0.314 0.134 0.374 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: 339 Number of extensions: 15 Number of successful extensions: 4 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: 308 Length of database: 456 Length adjustment: 30 Effective length of query: 278 Effective length of database: 426 Effective search space: 118428 Effective search space used: 118428 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 (21.9 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